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6695f0a4c9c6a5c07a65a0b2 | 10.26434/chemrxiv-2024-k1r4f | Native Carboxylate Assisted Palladium/Norbornene Mediated Distal C-H functionalization of Ferrocene | The traditional directing group approach for transition metal catalyzed C-H functionalization requires an exogenous auxiliary with strong coordinating ability for the selective C-H activation and therefore involves extra steps for its installation and removal after the reaction. Herein, we disclose a ligand enabled auxiliary-free, native carboxylate assisted Pd/norbornene(NBE) mediated highly regioselective C(3)-arylation of commercially available ferrocene carboxylic acids. This unique DG-free approach utilizes the Catellani-type reaction for the distal C-H activation in ferrocene where the weak chelation-assisted palladacycle formed by proximal C-H activation could relay palladium to the distal C(3)-position mediated by NBE resulting into C-C bond formation with aryl iodides. Both the norbornene derivative and the monoprotected 3-amino-2-hydroxypyridine ligand used are crucial for the successful formation of FNP intermediate, thus resulting into C(3)-arylated ferrocene carboxylic acid formation. | Princi Gupta; Shivam Waske; Suchithra Madhavan; Manmohan Kapur | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6695f0a4c9c6a5c07a65a0b2/original/native-carboxylate-assisted-palladium-norbornene-mediated-distal-c-h-functionalization-of-ferrocene.pdf |
616ead2bf718df60a2e3d2a1 | 10.26434/chemrxiv-2021-w1gg5 | Polyclonal aptamer libraries as binding entities on a graphene FET based biosensor for the discrimination of apo- and holo- retinol binding protein 4 | Oligonucleotide DNA aptamers represent an emergently important class of binding entities towards as different analytes as small molecules or even whole cells. Without the canonical isolation of individual aptamers following the SELEX process already the focused polyclonal libraries prepared by this in vitro evolution and selection can directly be used to label their dedicated analytes and to serve as binding molecules on surfaces. Here we report the first instance of a sensor able to discriminate between loaded and unloaded retinol binding protein 4 (RBP4), an important biomarker for the prediction of diabetes and kidney disease. The sensor relies purely on two aptamer libraries tuned such, that they discriminate between the protein isoforms, requiring no further sample labelling to detect RBP4 in both state. The evolution, binding properties of the libraries and the functionalization of graphene FET sensor chips are presented as well as the functionality of the resulting biosensor. | Ann-Kathrin Kissmann; Jakob Andersson; Heinz Fabian Raber; Markus Krämer; Hu Xing; Dennis Horst Kubiczek; Anil Bozdogan; Patrik Aspermair; Wolfgang Knoll; Frank Rosenau | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616ead2bf718df60a2e3d2a1/original/polyclonal-aptamer-libraries-as-binding-entities-on-a-graphene-fet-based-biosensor-for-the-discrimination-of-apo-and-holo-retinol-binding-protein-4.pdf |
60c75533702a9be06918c672 | 10.26434/chemrxiv.14054153.v1 | Spherical Neutralizing Aptamer Inhibits SARS-CoV-2 Infection | <p>New neutralizing agents against SARS-CoV-2 and the associated
mutant strains are urgently needed for the treatment and prophylaxis of COVID-19.
Herein, we develop a <u>s</u>pherical cocktail <u>n</u>eutralizing <u>a</u>ptamer-gold
nano<u>p</u>article (SNAP) to synergistically block the interaction of SARS-CoV-2
receptor-binding domain (RBD) and angiotensin-converting enzyme-2 (ACE2). Taking
advantage of the simultaneous recognition of multi-homologous and multi-heterogenous
neutralizing aptamers and dimensionally matched nano-scaffolds, the SNAP
exhibits increased affinity to the RBD with a dissociation constant value of 5.46
pM and potent neutralization against authentic SARS-CoV-2 with a half-maximal
inhibitory concentration of 142.80 aM. Additional benefits include the multi-epitope
blocking capability of the aptamer cocktail and the steric hindrance of the
nano-scaffold, which further covers the ACE2 binding interfaces and affects the
conformational transition of the spike protein. As a result, the SNAP strategy exhibits
broad neutralizing activity, almost completely blocking the infection of<a> N501Y</a> and D614G mutant strains. Overall, the SNAP
strategy provides a new direction for development of anti-virus infection
mechanisms, both to fight the COVID-19 pandemic and serve as a powerful
technical reserve for future unknown pandemics.</p> | Miao Sun; Siwen Liu; Ting Song; Fude Chen; Jialu Zhang; Jiaao Huang; Shuang Wan; Yao Lu; Honglin Chen; Weihong Tan; Yanling Song; Chaoyong Yang | Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75533702a9be06918c672/original/spherical-neutralizing-aptamer-inhibits-sars-co-v-2-infection.pdf |
6223cfa7011b58d7e1beb0de | 10.26434/chemrxiv-2022-1blx8 | The electrochemical measurement of salt diffusion coefficient, apparent cation transference number and ionic conductivity for a thin-film electrolyte. | A manuscript submitted to Electrochimica Acta._________
Further development of the electrochemical measurement procedure, namely the Symmetric Polarization Procedure (SPP), is described. The SPP allows for additional verification of measurement assumptions through a quick and simple inspection of a symmetry between the procedure outcomes. It also improves the precision of estimated transport properties. A considerable emphasis was also put on detailed outcomes analysis. In particular, a newly developed approach to the analysis of restricted diffusion data is proposed. This approach is based on a power law which is a common form for the rate equation, therefore it allows for a precise estimation of the salt diffusion coefficient and, innovatively, the diffusion domain. Importantly, as a result of this approach, the subdiffusive motion of species is recognized in every electrolyte examined herein. Additionally, four approaches that lead to a quantification of the apparent cation transference number are also extensively discussed. It has been demonstrated, how a knowledge about the salt diffusion coefficient, the apparent cation transference number and the ionic conductivity can be used to evaluate the electrochemical performance of an electrolyte. It is also shown, how these properties can be utilized to approximate the limiting-current density and the deviation from Nernst-Einstein equation. | Karol Pożyczka | Materials Science; Polymer Science; Energy; Thin Films; Conducting polymers; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6223cfa7011b58d7e1beb0de/original/the-electrochemical-measurement-of-salt-diffusion-coefficient-apparent-cation-transference-number-and-ionic-conductivity-for-a-thin-film-electrolyte.pdf |
63730a170821294c67f70a37 | 10.26434/chemrxiv-2022-1w19t-v4 | Localized surface plasmon resonance inducing cooperative Jahn–Teller effect for ultrafast crystal phase change in a nanocrystal | The Jahn–Teller effect, a phase transition phenomenon involving spontaneous breakdown of symmetry in molecules and crystals, causes important physical and chemical changes that impact various fields of science, from the natural photosystem II to superconductors. In this study, we discovered that localised surface plasmon resonance (LSPR) induced the cooperative Jahn–Teller effect in covellite CuS nanocrystals (NCs), causing metastable displacive ion movements. Although light–matter interaction of plasmonic metal NCs has been widely investigated, the scope has been limited to collective mode stimulation. Electron diffraction measurements under photo illumination, ultrafast time-resolved electron diffraction analyses, and theoretical calculations of semiconductive plasmonic CuS NCs showed that metastable displacive ion movements due to the LSPR-induced cooperative Jahn–Teller effect caused a delay in the relaxation of LSPR in the microsecond region. Furthermore, the displacive ion movements caused photo-switching of conductivity in CuS NCs films used in room temperature ranges such as in transparent variable resistance infrared sensors. This study pushes the limits of plasmonics from the increase in tentative collective oscillation to metastable crystal structure manipulation, thereby expanding on Faraday's discovery. | Masanori Sakamoto; Masaki Hada; Fumihiko Uesugi; Wataru Ota; Thoru Sato | Physical Chemistry; Materials Science; Nanoscience; Plasmonic and Photonic Structures and Devices; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63730a170821294c67f70a37/original/localized-surface-plasmon-resonance-inducing-cooperative-jahn-teller-effect-for-ultrafast-crystal-phase-change-in-a-nanocrystal.pdf |
60c751d84c89192162ad402a | 10.26434/chemrxiv.13218155.v1 | Unlocking Synergy in Bimetallic Catalysts by Core-Shell Design | <div>Extending the toolbox from mono- to bimetallic catalysts is key in realizing efficient chemical processes. Traditionally, the performance of bimetallic catalysts featuring one active and one selective metal is optimized by varying the metal composition, often resulting in a compromise between the catalytic properties of the two metals. Here we show that by designing the atomic distribution of bimetallic Au-Pd nanocatalysts, we obtain a synergistic catalytic performance in the industrially relevant selective hydrogenation of butadiene. Our single crystalline Au-core Pd-shell nanorods were up to 50 times more active than their alloyed and monometallic counterparts, while retaining high selectivity. We find a shell thickness dependent catalytic activity, indicating that not only the nature of the surface but also several sub-surface layers play a crucial role in the catalytic performance, and rationalize this finding using density-functional-theory calculations. Our results open up a novel avenue for the structural design of bimetallic catalysts.</div><div><br /></div> | Jessi van der Hoeven; Jelena Jelic; Liselotte Olthof; Giorgio Totarella; Relinde
J. A. van Dijk-Moes; Felix Studt; Alfons Van Blaaderen; Petra E. de Jongh | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751d84c89192162ad402a/original/unlocking-synergy-in-bimetallic-catalysts-by-core-shell-design.pdf |
67b8515bfa469535b947c508 | 10.26434/chemrxiv-2025-xj2lf | Insight into the carbon monoxide reduction reaction on Cu(111) from operando electrochemical X-ray photoelectron spectroscopy | In this work, we introduce a modified dip-and-pull ECXPS approach that offers new mechanistic insight into the alkaline CORR over a Cu(111) single crystal surface. We tackle two major unresolved questions in the CORR mechanism that persist in the literature. Firstly, we address the mechanism for methane formation on Cu(111) and show that the mechanism likely proceeds via atomic carbon, which subsequently couples, leading to the accumulation of amorphous carbon on the surface. Secondly, we provide insight into whether the mechanism for acetate formation occurs entirely on the surface or partially within the solution phase, showing that acetate is present on the surface, indicating a surface-based reaction. These insights into surface-based mechanisms provide a handle for designing future catalysts that can efficiently target the binding of specific intermediates. Furthermore, we expect that our modified approach to dip-and-pull ECXPS - in which we have changed the electrode geometry, the method of introducing the reactant gas, and used hard x-rays - will significantly expand the technique’s applicability, enabling studies of the CO(2)RR and beyond. | Bernadette Davies; Fernando Garcia-Martinez; Christopher Goodwin; David Degerman; Markus Soldemo; Patrick Lömker; Vladimir Grigorev; Sara Boscolo Bibi; Harri Ali-Löytty; Robin Engel; Tony Hansson; Christoph Schlueter; Xiaodong Zou; Anders Nilsson; Sergey Koroidov | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b8515bfa469535b947c508/original/insight-into-the-carbon-monoxide-reduction-reaction-on-cu-111-from-operando-electrochemical-x-ray-photoelectron-spectroscopy.pdf |
60c7529d9abda2bffff8de4e | 10.26434/chemrxiv.13311602.v1 | Three-Dimensional Triptycene-Based Covalent Organic Frameworks with ceq or acs Topology | <a>The growth of three-dimensional covalent organic
frameworks (3D COFs) with new topologies is still considered as a great
challenge due to limited availability of high-connectivity building units. Here we report the design and synthesis of novel 3D triptycene-based COFs, </a><a></a><a>termed</a> JUC-568 and JUC-569, following the deliberate symmetry-guided design principle. By combining a triangular prism (6-connected) node with a planar
triangle (3-connected) or another triangular prism node, the targeted COFs adopt
unreported <b>ceq </b>or non-interpenetrated <b>acs</b> topology, respectively.
<a>Both materials</a> show permanent porosity and impressive performance <a>in the adsorption
of CO<sub>2</sub></a> (~ 98 cm<sup>3</sup>/g at 273 K and 1 bar), CH<sub>4</sub> (~ 48 cm<sup>3</sup>/g at 273
K and 1 bar), and especially H<sub>2</sub>
(up to 274 cm<sup>3</sup>/g or
2.45 wt% at 77 K and 1 bar), which is <a>highest </a>among <a>porous organic materials</a> reported to date. This research
thus provides a promising strategy for diversifying 3D COFs based on complex
building blocks and promotes their <a></a><a>potential applications</a> <a>in</a><a></a><a> energy
storage and environment-related field</a>s. | Hui Li; Fengqian Chen; Xinyu Guan; JIali Li; Cuiyan Li; Bin Tang; Valentin Valtchev; Yushan Yan; Shilun Qiu; Qianrong Fang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7529d9abda2bffff8de4e/original/three-dimensional-triptycene-based-covalent-organic-frameworks-with-ceq-or-acs-topology.pdf |
65121f0cb927619fe7d1622c | 10.26434/chemrxiv-2023-sv1wf | Computational Examination of Transition Metal-Salen Complexes for the Reduction of CO2 | In this comprehensive study, we investigated the catalytic potential of seven transition metal-salen (TM-salen) complexes for the reduction of CO2 using ab initio methods. Our findings revealed distinct catalytic behavior among the TM-salen complexes, driven by their electronic and geometric properties. The reduction of hydrogen to H2 was most favorable on Mn-salen and Cu-salen complexes, indicating potential competition with CO2 reduction. Notably, later TM-salen complexes (Co, Ni, Cu, Zn) exhibited higher energy requirements for the initial CO2 reduction, whereas Mn- and Fe-salen complexes demonstrated potential-controlled selectivity, favoring CO2 reduction beyond HCOOH at specific thresholds. Our results highlight Cr-salen and Fe-salen complexes as promising candidates for CO2RR catalysts due to their reduced competition with hydrogen reduction and low overpotentials for CO2 reduction. Furthermore, the distinct reaction profiles of TM-salen complexes offer valuable insights for the design and development of efficient catalysts for sustainable CO2 conversion and other chemical transformations. These findings provide a foundation for further exploration and optimization of TM-salen complexes as viable catalysts in environmental and energy-related applications. | Gavin McCarver; Taner Yildirim; Wei Zhou | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65121f0cb927619fe7d1622c/original/computational-examination-of-transition-metal-salen-complexes-for-the-reduction-of-co2.pdf |
67c4f57e81d2151a02ca876f | 10.26434/chemrxiv-2025-bxmvx-v5 | Theoretical Insights into the Racemization Kinetics of Helical Foldamers: Extended Chain Inhibits Propagation of Helical Reversal from One End to Another | Helical foldamers have garnered significant attention recently with their unique chiral structures and diverse functionalities. However, their kinetic stability and racemization dynamics remain poorly understood. In this work, we introduced a novel model to describe the racemization of helical foldamers, deriving both general and approximated solutions to the kinetic equations. The general solution was in the double exponential form, while the approximated solution was in a single exponential form. The approximated solution clarified that the kinetic constant is in inverse proportion to the number of helical units (n). Analysis of the previously reported helical foldamers (o-phenylene oligomers and aromatic oligoamide) revealed that the two ends of the helical units are capped by the loose-end domains. The theory suggests that the larger n stabilizes the helical structure because the fraction of the helical domain relative to the loose domain increases, and the multiple inversion barriers in the helical domain prevent the helical reversal from traveling from one end to the other. | Nozomu Suzuki; Toyoko Suzuki; Hideto Minami | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Supramolecular Chemistry (Org.); Analytical Chemistry - General; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c4f57e81d2151a02ca876f/original/theoretical-insights-into-the-racemization-kinetics-of-helical-foldamers-extended-chain-inhibits-propagation-of-helical-reversal-from-one-end-to-another.pdf |
60c74febbdbb89e6e4a39e47 | 10.26434/chemrxiv.12959927.v1 | Quantum Mechanics / Extremely Localized Molecular Orbital Embedding Strategy for Excited-States. 1. Coupling to Time-Dependent Density Functional Theory | The QM/ELMO (quantum mechanics / extremely localized molecular orbital) method is a recently developed embedding technique in which the most important region of the system under exam is treated at fully quantum mechanical level, while the rest is described by means of transferred and frozen extremely localized molecular orbitals. In this paper, we propose the first application of the QM/ELMO approach to the investigation of excited-states and, in particular, we present the coupling of the QM/ELMO philosophy with Time-Dependent Density Functional Theory (TDDFT). The proposed TDDFT/ELMO strategy has been subjected to a series of preliminary tests that were already considered for the validations of other embedding TDDFT methods. The obtained results show that the novel technique allows the accurate description of local excitations in large systems by only including a relatively small group of atoms in the region treated at fully quantum chemical level. Furthermore, it was observed that, even using functionals that do not take into account long-range corrections, the method enables to avoid the presence of artificial low-lying charge-transfer states that may affect traditional TDDFT calculations. Finally, through the application to a reduced model of the Green Fluorescent Protein, it was proved that the TDDFT/ELMO approach can be also successfully exploited to investigate local electronic transitions in large systems and that the accuracy of the results can be improved by including a sufficient number of fragments/residues that are chemically crucial in the quantum mechanical region. This work paves the way to further extensions of the QM/ELMO philosophy for the study of local excitations in extended systems, suggesting the coupling of the QM/ELMO approach with other quantum chemical methods for excited-states, from the simplest ΔSCF techniques to the most advanced and computationally expensive multi-references methods. | Giovanni Macetti; Alessandro Genoni | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74febbdbb89e6e4a39e47/original/quantum-mechanics-extremely-localized-molecular-orbital-embedding-strategy-for-excited-states-1-coupling-to-time-dependent-density-functional-theory.pdf |
60c75074842e650b30db3a01 | 10.26434/chemrxiv.13046393.v1 | A β-Hairpin Epitope as Novel Structural Requirement for Protein Arginine Rhamnosylation | <p>Protein <i>N</i>-glycosylation is ubiquitously present in all domains of life, and confers a plethora of functions to the protein including increased solubility, protection from degradation, interaction with receptors, and activation for function. For canonical asparagine glycosylation, the recognition sequence that directs glycosylation at specific asparagine residues is well-established. It generally holds for protein glycosylation that the primary amino acid sequence is most important for substrate recognition. Here we reveal that a recently discovered bacterial enzyme called EarP, that transfers rhamnose to a specific arginine residue in its acceptor protein EF-P, specifically recognizes a β-hairpin loop. Notably, while the rhamnosyltransferase activity of EarP is abolished when presented with linear substrate peptide sequences derived from EF-P <i>in vitro</i>, the enzyme readily glycosylates the same sequence when presented in a cyclized β-hairpin mimic containing an l-Pro-d-Pro motif. Additional studies with other substrate-mimicking cyclic peptides revealed that EarP activity is sensitive to the method used to induce cyclization and in some cases is tolerant to amino acid sequence variation. Using detailed NMR approaches, we established that the active peptide substrates all share some degree of β-hairpin formation, and therefore conclude that the β-hairpin epitope is the major determinant of arginine-rhamnosylation by EarP. Our findings add a novel recognition motif to the existing knowledge on substrate specificity of protein glycosylation, and are expected to inform future identifications of rhamnosylation sites in other protein substrates.</p> | Nathaniel Martin; Marthe Walvoort; Liubov Yakovlieva; Thomas Wood; Johan Kemmink; Franziska Koller; Jürgen Lassak; Ioli Kotsogianni | Organic Synthesis and Reactions; Spectroscopy (Anal. Chem.); Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75074842e650b30db3a01/original/a-hairpin-epitope-as-novel-structural-requirement-for-protein-arginine-rhamnosylation.pdf |
66cf39e120ac769e5f1db6b5 | 10.26434/chemrxiv-2024-j5q6g | Temperature-Dependent Water Oxidation Kinetics: Implications and Insights | As a vital process for solar fuel synthesis, water oxidation remains a challenging reaction to perform using durable and cost-effective systems. Despite decades of intense research, the understanding of the detailed processes involved is still limited, particularly under photochemical conditions. Recent research has shown that the overall kinetics of water oxidation by a molecular dyad depends on the coordination between the photocharge generation and the subsequent chemical steps. This work explores similar effects by heterogeneous solar water oxidation systems. By varying a key variable, the reaction temperature, we discovered distinctly different behaviors on two model systems, TiO2 and Fe2O3. TiO2 exhibited a monotonically increasing water oxidation performance with rising temperatures across the entire applied potential range, between 0.1 V and 1.5 V vs. the reversible hydrogen electrode (RHE). In contrast, Fe2O3 showed increased performance with temperature at high applied potentials (>1.2 V vs. RHE) but decreased performance at low applied potentials (<1.2 V vs. RHE). This decrease in performance with temperature on Fe2O3 was attributed to increased electron-hole recombination, as confirmed by intensity modulated photocurrent spectroscopy (IMPS). The origin of the differing temperature dependences on TiO2 and Fe2O3 was further ascribed to their different surface chemical kinetics. These results highlight the chemical nature of charge recombination in photoelectrochemical (PEC) systems, where surface electrons recombine with holes stored in surface chemical species. It also indicates that PEC kinetics are not constrained by a single rate determining chemical step, highlighting the importance of an integrated approach to studying the system. Moreover, the results suggest that for practical solar water splitting devices, higher temperatures are not always beneficial for reaction rates, especially under low driving force conditions. | Tianying Liu; Pan Wang; Wei Li; David Wang; Damith Lekamlage; Boqiang Chen; Frances Houle; Matthias Waegele; Dunwei Wang | Physical Chemistry; Catalysis; Energy; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cf39e120ac769e5f1db6b5/original/temperature-dependent-water-oxidation-kinetics-implications-and-insights.pdf |
60c73e584c891959bcad1d99 | 10.26434/chemrxiv.6936653.v1 | Melanogenesis Using Tyrosinate (Not Tyrosinase) | <p>We present our initial observations regarding the
effect of the presence of L-tyrosinate (= L-tyrosine disodium salt) on the
auto- or Fe<sup>2+</sup>/H<sub>2</sub>O<sub>2</sub>-mediated oxidation of
various catecholic substances into melanin-like pigments. We observed that L-tyrosinate
inhibited the Fe<sup>2+</sup>/H<sub>2</sub>O<sub>2</sub>-mediated oxidation. In
contrast, L-tyrosinate promoted the auto-oxidation of ortho-diphenols like L-DOPA,
dopamine, epinephrine, norepinephrine, catechol or pyrogallol, but not a meta-diphenol
like resorcinol. In addition, we briefly demonstrated the melanogenic
properties of cell culture media containing L-tyrosinate. The reactions were
monitored using UV-Vis spectroscopy and size exclusion chromatography. For a
reaction between L-tyrosinate and L-DOPA, a large scale experiment was set up
allowing us to isolate, purify and characterize using FT-IR spectroscopy the
melanin-like material obtained. We discuss our observations in the context of
the <i>in vitro</i> and <i>in vivo</i> study of melanogenesis and provide some directions for
future research efforts.<i></i></p> | Koen Vercruysse; Nahfisa Richardson | Biochemistry; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e584c891959bcad1d99/original/melanogenesis-using-tyrosinate-not-tyrosinase.pdf |
62c88e41244ce0240f4094d7 | 10.26434/chemrxiv-2022-88802-v3 | 3-Selective Halogenation of Pyridines via Zincke Imine Intermediates | Pyridine halogenation reactions are crucial for obtaining the vast array of derivatives required for drug and agrochemical development. Yet, despite more than a century of synthetic endeavors, there are no broadly applicable 3-selective halogenation processes that function directly from pyridine C–H precursors. We have developed a ring-opening, halogenation, ring-closing sequence that temporarily transforms pyridines into a reactive series of alkenes. These Zincke imine intermediates undergo highly regioselective halogenation reactions under mild conditions. Experimental and computational mechanistic studies indicate that the selectivity-determining step changes based on the halogen electrophile. Using this method, we formed a diverse set of 3-halopyridines and demonstrated late-stage halogenation of complex pharmaceuticals and agrochemicals. | Benjamin T. Boyle; Jeffrey N. Levy; Louis de Lescure; Robert S. Paton; Andrew McNally | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c88e41244ce0240f4094d7/original/3-selective-halogenation-of-pyridines-via-zincke-imine-intermediates.pdf |
63d0e49a112596738079d5ba | 10.26434/chemrxiv-2023-2xkpc | Gaussian Approximation Potentials for Accurate Thermal
Properties of Two-Dimensional Materials | Two-dimensional materials (2DMs) continue to attract a lot of attention, particularly for their extreme flexibility and superior thermal properties. Molecular dynamics simulations are among the most powerful methods for computing these properties, but their reliability depends on the accuracy of interatomic interactions. While first principles approaches provide the most accurate description of interatomic forces, they are computationally expensive. In contrast, classical force fields are computationally efficient, but have limited accuracy in interatomic force description. Machine learning interatomic potentials, such as Gaussian Approximation Potentials, trained on density functional theory (DFT) calculations offer a compromise by providing both accurate estimation and computational efficiency. In this work, we present a systematic procedure to develop Gaussian approximation potentials for selected 2DMs, graphene, buckled silicene, and <i>h</i>-XN (X = B, Al, and Ga, as binary compounds) structures. We validate our approach through calculations that require various levels of accuracy in interatomic interactions. The calculated phonon dispersion curves and lattice thermal conductivity, obtained through harmonic and anharmonic force constants (including fourth order) are in excellent agreement with DFT results. HIPHIVE calculations, in which the generated GAP potentials were used to compute higher-order force constants instead of DFT, demonstrated the first-principles level accuracy of the potentials for interatomic force description. Molecular dynamics simulations based on phonon density of states calculations, which agree closely with DFT-based calculations, also show the success of the generated potentials in high-temperature simulations. | Tuğbey Kocabaş; Murat Keceli; Álvaro Vázquez-Mayagoitia; Cem Sevik | Materials Science; Nanoscience; Thermal Conductors and Insulators; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d0e49a112596738079d5ba/original/gaussian-approximation-potentials-for-accurate-thermal-properties-of-two-dimensional-materials.pdf |
60c759b6842e650caedb4a8c | 10.26434/chemrxiv.14724147.v1 | Potential Dependence of the Ionic Structure at the Ionic Liquid/water Interface Studied Using MD Simulation | <div>
<p>The structure at the electrochemical
liquid/liquid interface between water (W) and trioctylmethylammonium bis (nonafluorobutanesulfonyl)amide,
a hydrophobic ionic liquid (IL), was studied using molecular dynamics (MD) simulation
in which the interfacial potential difference was controlled. On the IL side of the IL|W interface, ionic
multilayers were found in the number density distribution of IL ions whereas monolayer-thick
charge accumulation was found in the charge density distribution. This suggests
that the potential screening is completed within the first ionic layer and the effect of
overlayers on the potential is marginal. The W side of the interface showed the
diffuse electric double layer as expected, and also unveiled a density depletion
layer, indicating that the IL surface is hydrophobic enough to be repelled by
water. The IL ions in the first ionic layer showed anisotropic orientation even
at the potential of zero charge, in which the polar moieties were oriented to
the W side and the non-polar moieties preferred parallel to the interface. When
an electric field is applied across the interface so that the IL ions are more
accumulated, the non-polar moieties changed the parallel preference to more
oriented to the IL side due to the dipolar nature of the IL ions. The ionic orientations at the IL|W
interface were compared with those at other two IL interfaces, the vacuum and graphene
interfaces of the IL. The parallel preference of the non-polar moieties was
similar at the IL|graphene interface but different from the perpendicular
orientation toward the vacuum side at the IL|vacuum interface. The
comparison suggests that water behaves like a wall repelling IL ions like a
solid electrode.</p></div> | Kosuke Ishii; Tetsuo Sakka; Naoya Nishi | Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Physical and Chemical Properties; Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759b6842e650caedb4a8c/original/potential-dependence-of-the-ionic-structure-at-the-ionic-liquid-water-interface-studied-using-md-simulation.pdf |
6241fbbdbdebba39556f90f7 | 10.26434/chemrxiv-2022-6m0wp | Zero-gap bipolar membrane electrolyzer for carbon dioxide reduction using acid-tolerant molecular electrocatalysts | The scaling-up of electrochemical CO2 reduction requires circumventing the CO2 loss as carbonates under alkaline conditions. Zero-gap cell configurations with a reverse-bias bipolar membrane (BPM) represent a possible solution, but the catalyst layer in direct contact with the acidic environment of a BPM usually leads to H2 evolution dominating. Here we show that using acid-tolerant Ni molecular electrocatalysts selective (> 60%) CO2 reduction can be achieved in a zero-gap BPM device using a pure water and CO2 feed. At higher current density (100 mA cm-2), CO selectivity de-creases, but was still >30%, due to reversible product inhibition. This study demonstrates the importance of developing acid-tolerant catalysts for use in large-scale CO2 reduction devices. | Bhavin Siritanaratkul; Mark Forster; Francesca Greenwell; Preetam K. Sharma; Eileen H. Yu; Alexander J. Cowan | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6241fbbdbdebba39556f90f7/original/zero-gap-bipolar-membrane-electrolyzer-for-carbon-dioxide-reduction-using-acid-tolerant-molecular-electrocatalysts.pdf |
654bce78dbd7c8b54bddaac8 | 10.26434/chemrxiv-2023-2w7w7 | Phase diagrams of alloys and their hydrides via on-lattice graph neural networks and limited training data | Efficient prediction of sampling-intensive thermodynamic properties in both closed and open systems is needed to evaluate material performance and permit high-throughput materials discovery for a diverse array of technology applications, from rational design of low-density high entropy alloys, to optimizing battery cathodes, to modulating hydrogen absorption equilibria in complex metals. To alleviate the prohibitive computational expense of high-throughput configurational sampling with density functional theory (DFT), surrogate modeling strategies like cluster expansion are many orders of magnitude more efficient, but can be difficult to construct in systems with high compositional complexity. We therefore employ minimal-complexity graph neural network models that accurately predict, and can even extrapolate to out-of-train-distribution, formation energies of DFT-relaxed structures from an ideal (unrelaxed) crystallographic representation. This enables the large-scale sampling necessary for various thermodynamic property predictions that may otherwise be intractable and can be achieved with small training datasets. Two exemplars, optimizing thermodynamic stability of low-density high entropy alloys and the modulating the plateau pressure of hydrogen in metal alloys, demonstrate the power of this approach, which will be extendable to a variety of materials discovery and modeling problems. | Matthew Witman; Norman Bartelt; Sanliang Ling; Pinwen Guan; Lauren Way; Mark Allendorf; Vitalie Stavila | Theoretical and Computational Chemistry; Materials Science; Energy; Hydrogen Storage Materials; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654bce78dbd7c8b54bddaac8/original/phase-diagrams-of-alloys-and-their-hydrides-via-on-lattice-graph-neural-networks-and-limited-training-data.pdf |
63848f3e0949e1dd4f58c527 | 10.26434/chemrxiv-2022-b1pt5 | Neural Network Potentials for Accelerated Metadynamics of Oxygen Reduction Kinetics at Au-Water Interfaces | The application of ab-initio molecular dynamics (AIMD) for the explicit modeling of reactions at the solid- liquid interfaces can provide new understandings towards the reaction mechanisms. However, prohibitive computational cost severely restricts the time- and length-scale of AIMD. Equiv- ariant graph neural network (GNN) based accurate surrogate potentials can accelerate the speed of performing molecular dynamics after learning on representative structures in a data efficient manner. In this study, we combined uncertainty- aware GNN potentials and enhanced sampling to investigate the reactive process of the oxygen reduction reaction (ORR) at Au(100)-water interface. By using a well-established active learning framework based on CUR matrix decomposition, we can evenly sample equilibrium structures from MD simulations and non-equilibrium reaction intermediates that are rarely vis- ited during the reaction. The trained GNNs have shown excep- tional performance in terms of force prediction accuracy, the ability to reproduce structural properties, and the low uncer- tainties when performing MD and metadynamics simulations. Furthermore, the collective variables employed in this work en- ables an automatic search of reaction pathways and provide a detailed understanding towards the ORR reaction mechanism on Au(100). Our simulations identify an associative reaction mechanism where adsorbed O2 reacts with water to form hy- droxyls through an *OOH transition state. The reaction pro- ceeds without formation of *O with a low reaction barrier of 0.3 eV. The low barrier agrees with the fast reaction kinetics observed experimentally. The methodology employed in this study can pave the way for modeling complex chemical reac- tions at electrochemical interfaces with an explicit solvent at ambient conditions. | Xin Yang; Arghya Bhowmik; Tejs Vegge; Heine Anton Hansen | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Machine Learning; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63848f3e0949e1dd4f58c527/original/neural-network-potentials-for-accelerated-metadynamics-of-oxygen-reduction-kinetics-at-au-water-interfaces.pdf |
631b2822be03b20eacefabbb | 10.26434/chemrxiv-2022-44sjw | Enhanced metal exsolution at the non-polar (001) surfaces of multi-faceted epitaxial thin films | Metal exsolution is a dynamic process that is driven under reducing atomosphere and at elevated temperatures, which results in the self-assembly of nanoparticles at the surface of complex perovskite catalysts. The nanoparticle characteristics of metal exsolution catalysts can be subject to considerable inhomogeneity, where the anisotropic surface properties of ceramic oxides were identified to have a major influence on the exsolution behavior. We systematically reveal the orientation-dependent anisotropy of the exsolution behavior of Ni in SrTi0.9Nb0.05Ni0.05O3-ẟ using multi-faceted epitaxial thin films, that represent a material system with properties in between functional ceramics and single-crystalline perovskite thin film model systems. Using an approach of combined orientation mapping and surface imaging we study the exsolution behavior with particular focus on the initial exsolution reponse i.e. after short annealing times. We find orientation-specific variations in the surface morphology of the thin film facets. In the as-prepared state, surface reconstructions cause the formation of patterned surface structures for all thin film facets apart from (001) surfaces, which exhibit a plain surface morphology as well as an enhanced exsolution response. Surface reconstructions and their inherent energy landscape may hence cause an additional energy barrier for the exsolution reaction that results in orientation-dependent differences in the exsolution kinetics. | Moritz Weber; Moritz Kindelmann; Egbert Wessel; Alexandros Sarantopoulos; Norbert H. Menzler; Regina Dittmann; Rainer Waser; Olivier Guillon; Christian Lenser; Felix Gunkel | Materials Science; Catalysis; Nanoscience; Composites; Nanostructured Materials - Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631b2822be03b20eacefabbb/original/enhanced-metal-exsolution-at-the-non-polar-001-surfaces-of-multi-faceted-epitaxial-thin-films.pdf |
60c75089bdbb896f95a39f3a | 10.26434/chemrxiv.12301934.v4 | Predicting Elemental Boiling Points from First Principles | <div>The normal boiling point (NBP) is a fundamental property of liquids and marks the intersection of the Gibbs energies of the liquid and the gas phase at ambient pressure.</div><div>This work provides the first comprehensive demonstration of the calculation of boiling points of atomic liquids through first-principles molecular-dynamics simulations.</div><div>To this end, thermodynamic integration (TDI) and perturbation theory (TPT) are combined with a density-functional theory (DFT) Hamiltonian, which provides absolute Gibbs energies, internal energies, and entropies of atomic liquids with an accuracy of a few meV/atom. </div><div>Linear extrapolation to the intersection with the Gibbs energy of a non-interacting gas phase eventually pins-down the NBPs. While these direct results can already be quite accurate, they are susceptible to a systematic over- or underbinding of the employed density functional. We show how the resulting errors can be strongly reduced by increasing the robustness of the method through a simple linear correction based on a high-level theoretical or experimental cohesive energy termed $\lambda$-scaling.</div><div>By carefully tuning the technical parameters, the walltime per element could be reduced from weeks to about a day (10-20k core-hours), which enabled extensive testing for B, Al, Na, K, Ca, Sr, Ba, Mn, Cu, Xe and Hg. </div><div>This comprehensive benchmark demonstrates the excellent performance and robustness of the approach with a mean absolute deviation (MAD) of less than 2% from experimental NBPs and very similar accuracy for liquid entropies (MAD 2.3 J/(mol*K), 2% relative). In some cases, the uncertainty in the predictions are several times smaller than the variation between literature values, allowing us to clear out ambiguities in the NBPs of B and Ba.</div> | Jan-Michael Mewes; Odile Smits | Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75089bdbb896f95a39f3a/original/predicting-elemental-boiling-points-from-first-principles.pdf |
62b212918c552323a91c4ab3 | 10.26434/chemrxiv-2022-mjnp6 | 2D Conjugated Polymers: Exploiting Topological Properties for the Rational Design of Metal-Free Photocatalysts | Solar-to-hydrogen conversion is one of the most promising avenues to provide emission-free fuels and long-term chemical energy storage. Wide-range application crucially requires high-performance photocatalysts that are environmentally benign and free of precious metals. With high robustness, controllable composition, tunable electronic structure and high porosity, two-dimensional conjugated polymers (2DCPs) are among the most appealing candidates. We provide rational design principles for 2DCPs which are suitable for water splitting, highlight progress and open challenges in synthesis, and review the recent theory-based investigations on 2DCPs for photocatalysis. The role of theory as indispensable tool is highlighted, as it promotes the understanding of the inner relationship between geometry, electronic structure and photocatalytic performance of 2DCPs and therefore enables rational design of new photocatalysts. | Yu Jing; Xinyue Zhu; Sabine Maier; Thomas Heine | Theoretical and Computational Chemistry; Materials Science; Catalysis; Catalysts; Nanostructured Materials - Materials; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b212918c552323a91c4ab3/original/2d-conjugated-polymers-exploiting-topological-properties-for-the-rational-design-of-metal-free-photocatalysts.pdf |
66817c185101a2ffa8ef9b5d | 10.26434/chemrxiv-2024-cb2sk | Enhanced Electrochemical Oxygen Evolution Reaction Enabled by Ni Cavity-Arrayed Electrodes | The water electrolysis is mostly limited by the slow kinetics of the oxygen evolution reaction (OER) including the interfacial electron and mass transfer and autoionization reactions. Especially in the neutral pH condition, slow rate of the autoionization reaction of water molecules also limits the electrolysis. The vibrational strong coupling, where the matter excitation is coupled to the cavity vacuum field mediated by a virtual photon, can be expected to modulate the physicochemical properties of water. Here, we utilized the cavity-arrayed electrode for the promotion of the OER. The OER activities of Ni cavity-array electrodes were evaluated from the oxygen bubble growth behavior. The Tafel slopes from the bubble analyses were modulated from 120 mV per decade to 30 mV per decade and the OER activity was enhanced by the cavity-arrayed electrode. This enhancement was explained with regards to the acceleration of autoionization of water molecules under the vibrational strong coupling. This study demonstrates that the cavity systems modulate the thermodynamic equilibrium of water autoionization under the vibrational strong coupling of liquid water at room temperature, leading to enhanced OER. | Daiki Ashizawa; Masaki Itatani; Tomohiro Fukushima; Kei Murakoshi | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Optics; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66817c185101a2ffa8ef9b5d/original/enhanced-electrochemical-oxygen-evolution-reaction-enabled-by-ni-cavity-arrayed-electrodes.pdf |
60c74ca94c89195ee4ad3694 | 10.26434/chemrxiv.12501281.v1 | Basal Plane Activation in Monolayer MoTe2 for Hydrogen Evolution Reaction via Phase Boundaries | <p>Two-dimensional transition metal
dichalcogenides (2D TMDCs) have attracted tremendous interest as one prominent
material group promising inexpensive <a>electrocatalysts
for hydrogen evolution reaction (HER)</a>. In the present study, using <a>monolayer MoTe<sub>2</sub> as a representative, we
demonstrated that </a>phase boundaries can provide a viable pathway to activate
the basal plane of 2D TMDCs for enhanced HER performance. Comprehensive
first-principles calculations have been performed to examine the energetics and
structural stabilities of possible 2H/1T’ phase boundary configurations. Three
categories of sites, Te, Mo and hollow sites, have been identified in
energetically stable phase boundaries, as potential catalytic centers for HER,
all indicating enhanced HER activity than the pristine basal lattice. In
particular, the hollow sites, a new group of sites induced by phase boundaries,
show great promise by exhibiting a Gibbs free energy near the thermoneutral value for
hydrogen adsorption, comparable to that of Pt. The mechanisms underlying hydrogen
adsorption at phase boundaries were then revealed, shown to be attributed to
the unique local hydrogen adsorption geometries and electronic structures at
phase boundaries. Our study clarifies the important mechanistic aspects
underlying hydrogen activation at phase boundaries, providing valuable
theoretical insights towards designing new class of
high-performance HER electrocatalysts based on 2D TMDCs.</p> | Yiqing Chen; Pengfei Ou; Xiaohan Bie; Jun Song | Catalysts; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ca94c89195ee4ad3694/original/basal-plane-activation-in-monolayer-mo-te2-for-hydrogen-evolution-reaction-via-phase-boundaries.pdf |
660cacf0e9ebbb4db93ab666 | 10.26434/chemrxiv-2024-dv2jf | Photoelectric properties of composite materials based on ultrathin porphyrin-based 2D lanthanide MOF nanosheets grown on TiO2 nanowire arrays through epitaxial growth | Ultrathin Two-dimensional (2D) metal-organic framework (MOF) nanosheets have attracted the attention of researchers because of large specific surface area, and TiO2 nanowire arrays based on semiconductor materials can utilize solar energy and have broad application prospects in the energy and environmental fields. In this paper, needle-shaped TiO2 (n type) nanowire arrays are synthesized through the optimization and control of reaction conditions, and stable TiO2 nanowire arrays are obtained with a diameter of about 10-20 nm and a length of about 4-5 μm. In addition, through the improvement of solvothermal synthesis, 2D ultrathin Eu-TCPP MOF nanosheets (p type) are synthesized, with a thickness of 1.25 nm and ultrathin nanosheets with an area of more than 20 μm2. Through the compounding of the two materials, a new composite material (TiO2@Eu-TCPP nanowire arrays) was obtained, and the Photoelectric properties are 140 times higher than the original two materials, response time is within 2s, due to the semiconductor p-n heterojunction effect. | BING Wang; Yuqing Zhang | Materials Science; Nanoscience; Composites; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660cacf0e9ebbb4db93ab666/original/photoelectric-properties-of-composite-materials-based-on-ultrathin-porphyrin-based-2d-lanthanide-mof-nanosheets-grown-on-ti-o2-nanowire-arrays-through-epitaxial-growth.pdf |
60cbde0fa5b6af1a7075494b | 10.26434/chemrxiv-2021-308fg | Impact of deamidation on the structure and function of anti-apoptotic Bcl-xL.
| Bcl-xL is an anti-apoptotic mitochondrial trans-membrane protein, known to play a crucial role in the
survival of tumor cells. The deamidation of Bcl-xL is a pivotal switch that regulates its biological
function. The potential impact of deamidation on the structure and dynamics of Bcl-xL is directly
linked to the intrinsically disordered region (IDR), which is the main site for post-translational
modifications (PTMs). In this study, we explored deamidation-induced conformational changes in Bcl-
xL to gain insight into its loss of function by performing microsecond-long molecular dynamics (MD)
simulations. MD simulation outcomes showed that the IDR motion and interaction patterns have
changed notably upon deamidation. Principal component analysis (PCA) demonstrates significant
differences between wild type and deamidated Bcl-xL and suggests that deamidation affects the
structure and dynamics of Bcl-xL. Differences in contact patterns and essential dynamics in the
binding groove (BG) are clear indications of deamidation-induced allosteric affects.
| Gamze Tanriver; Gerald Monard; Saron Catak | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cbde0fa5b6af1a7075494b/original/impact-of-deamidation-on-the-structure-and-function-of-anti-apoptotic-bcl-x-l.pdf |
672256e95a82cea2fa881776 | 10.26434/chemrxiv-2024-165mk | Fine-Tuning a Genetic Algorithm for CAMD: A Screening-Guided Warm Start | More sustainable chemical processes require the selection of suitable molecules, which can be supported by computer-aided molecular design (CAMD). CAMD often generates and evaluates molecular structures using genetic algorithms. However, genetic algorithms can suffer from slow convergence, and might yield suboptimal solutions. In response to these challenges, this work presents a method to fine-tune a genetic algorithm for CAMD. The proposed method builds on the COSMO-CAMD framework that utilizes a genetic algorithm for solving optimization-based molecular design problems and COSMO-RS for predicting physical properties of molecules. The key idea of the proposed method is to integrate results from a fast large-scale molecular screening into the molecular design framework, thereby enabling targeted initialization of the genetic algorithm, referred to as warm-start. The proposed method is applied in two case studies to design solvents for extracting gamma-valerolactone and phenol, respectively, from aqueous solutions. Compared to the benchmark method, the warm-started COSMO-CAMD framework reduces computing time by up to 70%, discovers fourfold more top performing candidate molecules, and identifies seven tailored molecular fragments, culminating in the discovery of two novel solvents specifically for the phenol case. The optimal solvent is found in all computational runs. Overall, the warm-started COSMO-CAMD framework significantly improves efficiency, effectiveness, and robustness of molecular design. | Yifan Wang; Lorenz Fleitmann; Lukas Raßpe-Lange; Niklas von der Assen; André Bardow; Kai Leonhard | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672256e95a82cea2fa881776/original/fine-tuning-a-genetic-algorithm-for-camd-a-screening-guided-warm-start.pdf |
60c74a6c567dfea2a5ec4d9c | 10.26434/chemrxiv.12200495.v1 | In Silico Identification of a Potent Arsenic Based Approved Drug Darinaparsin against SARS-CoV-2: Inhibitor of RNA dependent RNA polymerase (RdRp) and Necessary Proteases | The work demonstrate screening of several arsenical compounds against RdRp of coronavirus. The study implies out of all arsenical compounds, darinaparsin shows its most effective results based on <i>in silico</i> docking analysis. This study also confirmed the significant interaction between the active site of viral replicase protein, endoribonuclease protein and different proteases with darinaparsin. | Trinath Chowdhury; Gourisankar Roymahapatra; Santi M Mandal | Bioinformatics and Computational Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a6c567dfea2a5ec4d9c/original/in-silico-identification-of-a-potent-arsenic-based-approved-drug-darinaparsin-against-sars-co-v-2-inhibitor-of-rna-dependent-rna-polymerase-rd-rp-and-necessary-proteases.pdf |
6773dc04fa469535b95a7988 | 10.26434/chemrxiv-2024-w4h5s-v2 | Physics-assisted machine learning for slurry drying simulation in manufacturing process of battery electrodes: A hybrid time-dependent VGG16-DEM model | In this study, we present a hybrid Physics-Assisted Machine Learning (PAML) model that integrates Deep Learning (DL) techniques with the classical Discrete Element Method (DEM) to simulate the slurry drying during a lithium ion battery electrode manufacturing process. This model predicts the microstructure evolution leading to the formation of the electrode, as a time-series along the drying process. The hybrid approach consists in performing a certain amount of DEM simulation steps, n_DEM, after every DL prediction, mitigating the risk of unphysical predictions, like overlapping particles. Our PAML model was rigorously tested by evaluating different functional metrics of the predicted electrodes, including density, porosity, tortuosity factor, and radial distribution function. We conducted an in-depth analysis of performance versus accuracy, particularly focusing on the impact of the n_DEM hyperparameter, which represents the number of DEM steps executed between two subsequent DL predictions. Despite the model being trained on a specific formulation (96 % of Active Material, AM, and 4 % of Carbon Binder Domain, CBD), it demonstrated exceptional generalization capability when used to extrapolate to a different formulation (94 % AM and 6 % CBD). This adaptability highlights the robustness of our PAML hybrid approach. Furthermore, the integration of DL significantly reduced the computational cost versus the original DEM model simulation, decreasing the calculation time from 615 minutes to 36 min for the whole slurry drying simulation process. Our findings underscore the potential of combining ML with traditional simulation methods to enhance efficiency and accuracy in the field of electrode manufacturing.
| Diego Eduardo Galvez-Aranda; Francisco Fernandez; Alejandro A. Franco | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6773dc04fa469535b95a7988/original/physics-assisted-machine-learning-for-slurry-drying-simulation-in-manufacturing-process-of-battery-electrodes-a-hybrid-time-dependent-vgg16-dem-model.pdf |
634a23e64a1876b53ae4569c | 10.26434/chemrxiv-2022-dzn5h-v2 | Minimal Active Space: NOSCF and NOSI in
Multistate Density Functional Theory | In this Perspective, we introduce a minimal active space (MAS) for the lowest N
eigenstates of a molecular system in the framework of a multistate density functional
theory (MSDFT), consisting of no more than N2 nonorthgonal Slater determinants. In
comparison with some methods in wave function theory in which one seeks to expand the ever increasing size of an active space to approximate the wave functions,
it is possible to have an upper bound in MSDFT because the auxiliary states in a
MAS are used to represent the exact N-dimensional matrix density D(r). In analogy
to Kohn-Sham DFT, we partition the total Hamiltonian matrix functional H[D] into
an orbital-dependent part, including multistate kinetic energy and Coulomb-exchange energy plus an external potential energy, and a correlation matrix density functional Ec[D]. The latter accounts for the part of correlation
energy not explicitly included in the minimal active space. However, a major difference from Kohn-Sham DFT is that state interactions are necessary to represent the
N-matrix density D(r) in MSDFT, rather than a non-interacting reference state for the
scalar ground-state density. Two computational approaches are highlighted. We
first derive a set of non-orthogonal multistate self-consistent-field (NOSCF) equations
for the variational optimization of H[D]. We introduce the multistate correlation potential, as the functional derivative of Ec[D], which includes both correlation effects
within the MAS and that from the correlation matrix functional. Alternatively, we
describe a non-orthogonal state interaction (NOSI) procedure, in which the determinant functions are optimized separately. Both computational methods are useful for
determining the exact eigenstate energies and for constructing variational diabatic
states, provided that the universal correlation matrix functional is known. It is hoped
that this discussion would stimulate developments of approximate multistate density
functionals both for the ground and excited states. | Yangyi Lu; Ruoqi Zhao; Jun Zhang; Meiyi Liu; Jiali Gao | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634a23e64a1876b53ae4569c/original/minimal-active-space-noscf-and-nosi-in-multistate-density-functional-theory.pdf |
60c746ca9abda23631f8c7e0 | 10.26434/chemrxiv.9917948.v2 | What Do We Learn from the Classical Turning Surface of the Kohn-Sham Potential as Electron Number Is Varied Continuously? | The classical turning radius Rt of an atom can be defined as the radius where the KS potential is equal to the negative ionisation potential of the atom, i.e. where v_s(R_t)=\epsilon_h. It was recently shown [P.N.A.S. 115, E11578 (2018)] to yield chemically relevant bonding distances, in line with known empirical values. In this work we show that extension of the concept to non-integer electron number yields additional information about atomic systems, and can be used to detect the difficulty of adding or subtracting electrons. Notably, it reflects the ease of bonding in open p-shells, and its greater difficulty in open s-shells. The latter manifests in significant discontinuities in the turning radius as the electron number changes the principal quantum number of the outermost electronic shell (e.g. going from Na to Na^{2+}). We then show that a non-integer picture is required to correctly interpret bonding and dissociation in H_2^+. Results are consistent when properties are calculated exactly, or via an appropriate approximation. They can be interpreted in the context of conceptual density functional theory. | Tim Gould; Benjamin Libereles; John P. Perdew | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ca9abda23631f8c7e0/original/what-do-we-learn-from-the-classical-turning-surface-of-the-kohn-sham-potential-as-electron-number-is-varied-continuously.pdf |
654220d248dad23120d576f0 | 10.26434/chemrxiv-2023-c3qf2 | Mapping the Distribution of Electronic States within the 5D4 and 7F6 Levels of Tb3+ Complexes with Optical Spectroscopy | The Tb(III) ion has the most intense luminescence of the trivalent lanthanide(III) ions. In contrast to Eu(III), where the two levels only include a single state, the high number of electronic states in the ground (7F6) and emitting (5D4) levels makes detailed interpretations of the electronic structure—the crystal field—difficult. Here, luminescence emission and excitation spectra of Tb(III) complexes with 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA, [Tb(DOTA)(H2O)]-), ethylenediaminetetraacetic acid (EDTA, [Tb(EDTA)(H2O)3]-) and diethylenetriaminepentaacetic acid (DTPA, [Tb(DTPA)(H2O)]2-) as well as the Tb(III) aqua ion ([Tb(H2O)9]3+) were were recorded at room temperature and in frozen solution. Using these data the electronic structure of the 5D4 multiplets of Tb(III) was mapped by considering the transitions to the singly degenerate 7F0 state. A detailed spectroscopic investigation was performed and it was found that the 5D4 multiplet could accurately be described as a single band for [Tb(H2O)9]3+, [Tb(DOTA)(H2O)]- and [Tb(EDTA)(H2O)3]-. In contrast, for [Tb(DTPA)(H2O)]2- two bands were needed. These results demonstrated the ability of describing the electronic structure of the emitting 5D4 multiplet using emission spectra. This offers an avenue for investigating the relationship between molecular structure and luminescent properties in detailed photophysical studies of Tb(III) ion complexes. | Nicolaj Kofod; Margrete Juel Henrichsen; Thomas Just Sørensen | Physical Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Solvates; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654220d248dad23120d576f0/original/mapping-the-distribution-of-electronic-states-within-the-5d4-and-7f6-levels-of-tb3-complexes-with-optical-spectroscopy.pdf |
60c747629abda27787f8c8d3 | 10.26434/chemrxiv.11639931.v1 | Fluorescence of BODIPY Dyes in Gas Phase at near Ambient Conditions | Molecular fluorescence is a phenomenon that is usually observed in condensed phase. It is strongly affected by molecular interactions. The study of fluorescence spectra in the gas phase can provide a nearly-ideal model for the evaluation of intrinsic properties of the fluorophores. Unfortunately, most conventional fluorophores are not volatile enough to allow study of their fluorescence in the gas phase. Here we report very bright gas phase fluorescence of simple BODIPY dyes that can be readily observed at atmospheric pressure using conventional fluorescence instrumentation. To our knowledge, this is the first example of visible range gas phase fluorescence at near ambient conditions. Evaporation of the dye in vacuum allowed us to demonstrate organic molecular electroluminescence in gas discharge excited by electric field produced by a Tesla coil. | Kseniya A. Mariewskaya; Denis Larkin; Yuri Samoilichenko; Vladimir Korshun; Alex Ustinov | Photochemistry (Org.); Physical Organic Chemistry; Dyes and Chromophores | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747629abda27787f8c8d3/original/fluorescence-of-bodipy-dyes-in-gas-phase-at-near-ambient-conditions.pdf |
60c75677ee301ce267c7b365 | 10.26434/chemrxiv.14252351.v1 | Crystalline Covalent Organic Framework Aerogels | Covalent organic frameworks (COFs) are crystalline
organic materials of interest for a wide range of applications due to their
porosity, tunable architecture, and precise chemistry. However, COFs are
typically produced in powder form and are difficult to process. Herein, we
report a simple and versatile approach to fabricate macroscopic, crystalline
COF gels and foams. Our method involved the use of dimethyl sulfoxide as a
solvent and acetic acid as a catalyst to first produce a COF gel. The COF gel
was then washed, dried, and reactivated to produce a macroscopic, crystalline,
porous COF foam. We demonstrated this synthesis for six different imine COFs
and found that the crystallinities and porosities of the COF foams matched
those of COF powders. Electron microscopy revealed a robust hierarchical pore
structure, and we showed that the COF foams can be used as absorbents in
oil-water separations, for the removal of organic and inorganic
micropollutants, and for the capture and retention of iodine. This study
provides a versatile and simple approach for the fabrication of COF foams and
will provide novel routes for incorporating COFs in applications that require
macroscopic, porous materials. | Dongyang Zhu; Yifan Zhu; Qianqian Yan; Fangxin Liu; Pingfeng Yu; Chia-Ping Tseng; Nicholas Tjahjono; Po-Chun Huang; Muhammad M. Rahman; Eilaf Egap; Pulickel
M. Ajayan; Rafael Verduzco | Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75677ee301ce267c7b365/original/crystalline-covalent-organic-framework-aerogels.pdf |
60c7473f9abda237e2f8c88d | 10.26434/chemrxiv.11422095.v2 | Localization of Spiropyran Activation | Functionalization of planar and curved glass surfaces with spiropyran (SP) molecules and localized UV-induced activation of the mechanophore are demonstrated. Fluorescence spectra of UV-irradiated SP-functionalized surfaces reveal that increases in surface roughness or curvature produces more efficient conversion of the mechanophore to the open merocyanine (MC) form. Further, force-induced activation of the mechanophore is achieved at curved glass-polymer interfaces and not planar interfaces. Minimal fluorescence signal from UV-irradiated SP-functionalized planar glass surfaces precluded mechanical activation testing. Curved glass-polymer interfaces are prepared by SP functionalization of E-glass fibers, which are subsequently embedded in a poly(methyl methacrylate) (PMMA) matrix. Mechanical activation is induced through shear loading by a single fiber microbond testing protocol. In situ detection of SP activation at the interface is monitored by fluorescence spectroscopy.<br /> | Martha Grady; Cassandra Birrenkott; Preston A. May; ScottR. White; Jeffrey S. Moore; Nancy
R. Sottos | Coating Materials; Composites; Thin Films; Organic Polymers; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7473f9abda237e2f8c88d/original/localization-of-spiropyran-activation.pdf |
60c74c380f50dba1db396de7 | 10.26434/chemrxiv.12453533.v1 | In silico Insights on the Allosteric Modulation of the µ-Opioid Receptor and G protein Complex in the Presence of Agonist Ligand BU72 and Potential Positive Allosteric Modulator BMS-986121 | <div>The G protein-coupled receptor (GPCR) µ-opioid receptor (µOR) is one of several drug targets of commercially available therapeutics for pain. Various opioid drugs like morphines have been associated to numerous substance abuse-related deaths around the world. A better alternative to avoid this undesirable side effect is by targeting allosteric sites. In addition, understanding the underlying mechanism of allosteric ligands in µOR is highly sought for better drug optimizations. Using molecular dynamics, the allosteric behavior of the µOR and G protein complex in the presence of agonist ligand BU72 and potential positive allosteric modulator (PAM) BMS-986121 was probed by observing residue-residue contacts formation and breakage. It was found that G protein residues D959, L349, and K963 participate in the interprotein contact formation between µOR and G protein. Moreover, orthosteric binding site residues D83, Y84, and H233 polar interactions were verified to be critical not only on the agonist ligand binding, but also in the allosteric communication of the protein complex. Also, the overall decrease on the number of contacts was observed after mutations, which can trigger the opening of the orthosteric binding site. Rationalization of allosteric modulation in µ-opioid receptor-G protein complex may improve drug discovery schemes and strategies for allosteric drugs including other targets in the GPCR protein families.</div> | Mac Kevin Braza; Ricky Nellas | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c380f50dba1db396de7/original/in-silico-insights-on-the-allosteric-modulation-of-the-opioid-receptor-and-g-protein-complex-in-the-presence-of-agonist-ligand-bu72-and-potential-positive-allosteric-modulator-bms-986121.pdf |
6781048a6dde43c908fe0104 | 10.26434/chemrxiv-2025-9t733 | Comprehensive Analysis for Low-cost and Highly Efficient Perovskite Solar Cells Using SCAPS-1D with Inexpensive Hole Transport Material, Electron Transport Material and Back Contact Considering the Toxicity | Perovskite solar cells are gaining popularity day by day due to the continuous effort of solar scientists. However, there are several barriers to the commercialization of this solar cell. Various materials can be used to achieve higher efficiency of perovskite solar cell design. Some of these materials may also contain lead (Pb), which harms human life and the environment. Another crucial hindrance for perovskite solar cells is the cost regarding hole transport material (HTM), electron transport material (ETM), and back contact; most of the common HTM, ETM, and back contact materials are expensive. In this study, we have chosen inexpensive HTM, ETM, and back contact to determine highly efficient and less expensive cell structures. Eleven non-toxic and three Pb-based absorber materials have been simulated using SCAPS-1D simulator where ETM (ZnO) and HTM (PEDOT: PSS+WO3) are constant to determine the best absorber material. Later the effect of thickness, temperature, back and front contact, electron affinity, defect density, and series resistance are also considered. After simulation and optimization, it is found that Ni is the least expensive back contact material for providing optimal efficiency, MAPbI3 is the best Pb-based absorber material with open circuit voltage (Voc) =1.10V, short circuit current (Jsc) =28.47 mA/cm2, fill factor (FF) =86.42%, power conversion efficiency (eta(%)) =27.10%. In contrast, the best non-toxic material is MASnI3 with Voc =0.97V, Jsc =34.89mA/cm2, FF =82.51% and eta (%) =27.98%. | Rukon Uddin; Sayem Ul Alam; Subrata Bhowmik | Energy; Photovoltaics | CC BY 4.0 | CHEMRXIV | 2025-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6781048a6dde43c908fe0104/original/comprehensive-analysis-for-low-cost-and-highly-efficient-perovskite-solar-cells-using-scaps-1d-with-inexpensive-hole-transport-material-electron-transport-material-and-back-contact-considering-the-toxicity.pdf |
60c74c27f96a00338b28772a | 10.26434/chemrxiv.12436637.v1 | What Is Discoverable and Why We Need Diversity in Science | This essay tackles the topic of what is discoverable by humans and why it is essential to have diversity of cultural, ethnic, and gender backgrounds in science. | Andrei Yudin | Bioorganic Chemistry; Combinatorial Chemistry; Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry; Process Chemistry; Stereochemistry; Supramolecular Chemistry (Org.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c27f96a00338b28772a/original/what-is-discoverable-and-why-we-need-diversity-in-science.pdf |
64027fe863e8d44e59547b43 | 10.26434/chemrxiv-2023-1ncv5 | Regioselective Fluorohydrin Synthesis from Allylsilanes | Allysilanes can be regioselectively transformed into the corresponding 3-silylfluorohydrin in good yield using a sequence of epoxidation followed by treatment with HF-Et3N with or without isolation of the intermediate epoxide. Various silicon-substitution is tolerated, resulting in a range of 2-fluoro-3-silylpropan-1ol products from this method. Whereas other fluorohydrin syntheses by epoxide opening using HF-Et3N generally require more forcing conditions (e.g. higher reaction temperature), opening of allylsilane-derived epoxides with this reagent occurs at room temperature. We attribute this rate acceleration along with the observed regioselectivity to a beta-silyl effect that stabilizes a proposed cationic intermediate. The use of enantioenriched epoxides produces similarly enantioenriched fluorohydrins suggestive of an SN2-type mechanism. | Alexie W. Clover; Adam P. Jones; Gregory O'Neil | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64027fe863e8d44e59547b43/original/regioselective-fluorohydrin-synthesis-from-allylsilanes.pdf |
60c73cc9469df42751f42616 | 10.26434/chemrxiv.14709351.v1 | A Potential Practical Process for Remdesivir | A four-step synthesis of Remdesivir (1) is presented. This work focuses on the yield improvement of step 1, flow chemistry development of step 2 and 3, process optimization of step 4. The literatures reported (https://dx.doi.org/10.1021/acs.oprd.0c00310 and https://dx.doi.org/10.1021/acs.oprd.0c00172: SI part) step 1 was repeated, but failed in the crystallization, eventually step 1 product was obtained by column chromatography with >98% HPLC purity and 40% IY. The flow chemistry development of step 2(IY: 84%) and 3 (IY: 63%) was achieved and the release of toxic HCN was avoided, the process robustness was improved by flow chemistry. Step 4 was simplified to apply primary alcohol 6 directly (without protection) to react with chiral SM 8. Lewis acid catalysts were screened by HTS and MgI2 gave 50% AY. Cheap and commercially available MgCl2 and NaI were used to replace MgI2, finally Remdesivir (1) was obtained in >99% purity with 40.3% IY. | Chen Liujuan; Guowei Zhang; Jinguang Liu; Jianye Jiao; Han Lin; Miao Wu; Xin Zhang; Liujuan Chen | Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9469df42751f42616/original/a-potential-practical-process-for-remdesivir.pdf |
677f8e3181d2151a026a35c3 | 10.26434/chemrxiv-2025-df42c | Exploring Photophysical Properties and Sensitivity to Dioxygen in Anisolyl-Picolinate Antenna Conjugated to Azamacrocycles | An anisolyl-picolinate antenna grafted onto different macrocyclic ligands such as tacn, pyclen or cyclen renders the resulting terbium (III) complexes highly sensitive towards oxygen in aqueous solutions, enabling the design of ratiometric or lifetime-based molecular sensors. The underlying sensitization mechanism was investigated on analogous Gd(III) complexes and the oxygen sensitivity was studied using transient absorption spectroscopy. The antenna-based triplet lifetime increased up to 900-fold upon degassing, underscoring the role of the ligand excited states in designing highly sensitive oxygen probes. | Lucile Bridou; Loeza Collobert; Kyangwi Malikidogo; Salauat Kiraev; Maher Hojorat; Nadège Hamon; Anh-Thy Bui; François Riobé; Akos Banyasz; Maryline Beyler; Raphael Tripier; Olivier Sénèque; Olivier Maury | Physical Chemistry; Inorganic Chemistry; Analytical Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677f8e3181d2151a026a35c3/original/exploring-photophysical-properties-and-sensitivity-to-dioxygen-in-anisolyl-picolinate-antenna-conjugated-to-azamacrocycles.pdf |
60c758709abda20c9ff8e8e9 | 10.26434/chemrxiv.14551266.v1 | InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics | Interactive molecular dynamics in virtual reality (IMD-VR) simulations provide a digital molecular playground for students as an alternative or complement to traditional molecular modelling kits or 2D illustrations. Previous IMD-VR studies have used molecular mechanics to enable simulations of macromolecules such as proteins and nanostructures for the<br />classroom setting with considerable success. Here, we present the INTERACHEM molecular visualizer, intended for reactive IMD-VR simulation using semiempirical and ab initio methods.<br />INTERACHEM visualizes not only the molecular geometry, but also 1) isosurfaces such as molecular orbitals and electrostatic potentials, and 2) two-dimensional graphs of time-varying<br />simulation quantities such as kinetic/potential energy, internal coordinates, and user-applied force. Additionally, INTERACHEM employs speech recognition to facilitate user interaction and introduces a novel “atom happiness” visualization using emojis to indicate the energetic<br />feasibility of a particular bonding arrangement. We include a set of accompanying exercises that we have used to teach chemical reactivity in small molecular systems. | Stefan Seritan; Yuanheng Wang; Jason E. Ford; alessio Valentini; Tom Gold; Todd J. Martínez | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758709abda20c9ff8e8e9/original/intera-chem-virtual-reality-visualizer-for-reactive-interactive-molecular-dynamics.pdf |
60c74de9702a9bb85c18b937 | 10.26434/chemrxiv.12673691.v1 | A Three Component-Based Van Der Waals Surface Vertically Designed for Biomolecular Recognition Enhancement | <p>Graphene-based vertical electrodes may
have applications in biomolecular recognition for producing low-cost biodevices
with high electronic conductivity. However, they are unsuitable for measuring small
interfacial capacitance variations because graphene is mostly composed of basal
sp<sup>2</sup> carbon surface, which limits its sensitivity as an
electrochemical biosensor. Herein, we introduce an unconventional device alternative
based on a three-component vertically designed (TCVD) surface comprising
ferrocene/graphene/gold deposited on SiO<sub>2</sub>/Si wafers. Ferrocene is
the top layer that promotes reversible redox communication with the electrolyte,
while graphene–gold is the strategically projected layer underneath. Bader
charge analysis indicated that graphene donates electronic density to the gold
surface, thereby significantly increases the charge transfer exchange rate with
ferrocene. The TCVD surface is much more reactive and sensitive to charge variations
compared with pristine graphene, and it maintains excellent conductive
properties. The TCVD device was used to detect DNA hybridization in solutions,
since this is well-known to be a challenging process on a pristine graphene
vertical device. A TCVD device can detect small interfacial charge perturbations
from DNA hybridization. Based on quantum mechanics calculations combined with spectromicroscopy
data, it was realized that the unique synergic interaction between gold and graphene
amplified biomolecular recognition, whereby DNA in nanomolar range
concentration correlated to 0.8 ± 0.1 µF cm<sup>-2</sup>, which was effortlessly
detected. This result is promising since 3.0 µF cm<sup>-2</sup> is the limit of
quantum capacitance for bare graphene. Notably, these results open a new
possibility for next-generation TCVD bioelectronics based on van der Waals
surfaces, while further innovation and material scrutiny may lead to the
achievement of TCVD devices with robust biomolecular recognition abilities.</p> | Ayaz Hassan; Lucyano Macedo; Isabela A. Mattioli; Rafael J. G. Rubira; Carlos J. L. Constantino; Rodrigo G. Amorim; Filipe Lima; Frank Crespilho | Carbon-based Materials; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de9702a9bb85c18b937/original/a-three-component-based-van-der-waals-surface-vertically-designed-for-biomolecular-recognition-enhancement.pdf |
639ad684a53ea618a04b8db7 | 10.26434/chemrxiv-2022-mm62h | Chemical RNA Crosslinking: Mechanisms, Computational Analysis and Biological Applications | In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical crosslinking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough review on the past and future of this field is provided. In particular, the various RNA crosslinkers and their mechanisms, the computational analysis and challenges and illustrative examples from recent literature are discussed. | Willem Velema; Zhipeng Lu | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639ad684a53ea618a04b8db7/original/chemical-rna-crosslinking-mechanisms-computational-analysis-and-biological-applications.pdf |
60c753e4702a9b0f1818c435 | 10.26434/chemrxiv.11955870.v2 | Imide Condensation as a Strategy for the Synthesis of Core Diversified G-Quadruplex Ligands with Anti-Cancer and Anti-Parasitic Activity | <p>A facile imide coupling strategy for the one-step preparation of G‑quadruplex ligands with varied core chemistries is described. The G‑quadruplex stabilization, anticancer and antiparasitic activity of a library of nine compounds was examined, identifying a nanomolar inhibitor of <i>T. brucei</i> with 78‑fold selectivity over MRC5 cells, and strong stabilization of G‑quadruplex nucleic acids. </p> | Steven T. G. Street; pablo Peñalver; Michael O'Hagan; Gregory J. Hollingworth; Juan Carlos Morales; M. Carmen Galan | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753e4702a9b0f1818c435/original/imide-condensation-as-a-strategy-for-the-synthesis-of-core-diversified-g-quadruplex-ligands-with-anti-cancer-and-anti-parasitic-activity.pdf |
629762401959599d27bcd7cb | 10.26434/chemrxiv-2022-vvrrf-v2 | Ab Initio to activity: Machine learning assisted optimization of high-entropy alloy catalytic activity. | High-entropy alloys are slowly making their debut as a platform for catalyst discovery, but conventional methods, theoretical as well as experimental, may fall short of screening the vast composition space inhabited by this class of materials. New theoretical approaches are needed to gauge the catalytic activity of high-entropy alloys and optimize the alloy composition within a feasible time frame as a prerequisite for further experimental studies.
Herein, we establish a workflow for simulations of catalysis on high-entropy alloy surfaces. For each step of the modeling we present our choice of method, however, we also acknowledge that alternative options are available.
We apply the developed methodology to predict the net catalytic activity of any alloy composition, within the composition space spanned by Ag-Ir-Pd-Pt-Ru, for the oxygen reduction reaction. Based on first-principle calculations, a graph convolution neural network is used to predict adsorption energies of *OH and *O. Subsequently, taking competitive co-adsorption of reaction intermediates into account, we couple the net adsorption energy distribution of a high-entropy alloy surface to the expected current density. Lastly, this procedure is used in conjunction with a Bayesian optimization scheme to search for optimal alloy compositions, which yields several promising compositions.
This result shows that an unbiased in silico pre-screening and discovery of catalyst candidates is viable and will help scale the otherwise insurmountable challenge of searching for high-entropy alloy catalysts. It is our hope that our computational framework, which is freely available on GitHub, will aid other research groups to efficiently identify promising high-entropy alloy catalysts. | Christian Møgelberg Clausen; Martin Lillebro Striib Nielsen; Jack Kirk Pedersen; Jan Rossmeisl | Theoretical and Computational Chemistry; Materials Science; Catalysis; Alloys; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629762401959599d27bcd7cb/original/ab-initio-to-activity-machine-learning-assisted-optimization-of-high-entropy-alloy-catalytic-activity.pdf |
67884fbefa469535b934827b | 10.26434/chemrxiv-2025-q4t58 | Isomerism and Solvent Interaction in Octamethyl Calix[4]pyrrole Complexed with Formate | We investigate the binding motifs of host-guest complexes of the anion receptor octamethyl calix[4]pyrrole (omC4P) with the formate anion using cryogenic ion vibrational spectroscopy in concert with density functional theory. The resulting IR spectrum in vacuo is compared to that in deuterated acetonitrile and acetone solutions. The formate-omC4P complex has three low energy isomers in vacuo:(i) one with an oxygen atom of formate interacting with three of the NH groups of omC4P and the other oxygen atom interacting with the remaining NH group; (ii) one with a single oxygen atom of formate interacting with all four NH groups of omC4P; and (iii) one with each oxygen atom interacting with two NH groups. Each complex geometry lowers the C4v symmetry of the receptor to C1, Cs, or C2v, respectively, and this symmetry breaking and isomerism is reflected in the broadening and pattern of the NH stretching modes of omC4P. | Lane Terry; Madison Foreman; J. Mathias WEBER | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67884fbefa469535b934827b/original/isomerism-and-solvent-interaction-in-octamethyl-calix-4-pyrrole-complexed-with-formate.pdf |
6211348e7a054a91a9137da7 | 10.26434/chemrxiv-2022-79l4g | Arylation of Pharmaceutically Relevant Strained Rings Using Electronically Tuned Redox-Active Esters | Strained rings are increasingly important for the design of pharmaceutical candidates due to their improved pharmacokinetic and safety profiles, as well as their ability to orient substituents into favorable geometries for the potential improvement of the binding affinity to the biological target. Despite their importance, methodologies to cross-couple strained rings have been underdeveloped. The most abundant source of strained carbocycles and heterocycles is the corresponding carboxylic acid, making methods that employ this substrate pool attractive. Coupling of these carboxylic acids with halides, a second source of abundant building blocks, would allow for rapid access to a diverse set of functionalized carbocyclic and heterocyclic frameworks containing all-carbon quaternary centers. Herein we disclose the development of a nickel-catalyzed cross-electrophile approach that couples a variety of strained ring N-hydroxyphthalimide esters, derived from the carboxylic acid in one step or in situ, with various aryl and heteroaryl halides under reductive conditions. The key to this success was the electronic modification of the NHP ester to make them less reactive, as well as the discovery of a new ligand, t-BuBpyCamCN, that avoids problematic side reactions. This method enables the incorporation of 3-membered rings, 4-membered rings, and bicyclic fragments onto (hetero)arenes derived from (hetero)aryl iodides and (hetero)aryl bromides, allowing for straightforward and direct access to arylated strained rings. | Daniel Salgueiro; Benjamin Chi; Pablo Garcia-Reynaga; Daniel Weix | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6211348e7a054a91a9137da7/original/arylation-of-pharmaceutically-relevant-strained-rings-using-electronically-tuned-redox-active-esters.pdf |
6125cafcd4eb8a6866a11b3c | 10.26434/chemrxiv-2021-grm27 | Palladium-Catalyzed C-C Bond Activation and Regioselective Alkenyla-tion between Cyclopropanol and 1,3-Diyne: One-Step Synthesis of Di-verse Conjugated Enynes | We report here the first example of the use of 1,3-dialkynes in C-C bond activation with any metal. The regio- and stereo-selective synthesis of 1,3-enynes from 1,3-diynes is demonstrated by the palladium-catalyzed C-C bond activation of cyclo-propanol. Exclusive formation of mono-alkenylated adduct was achieved by eliminating the possibility of di-functionalization with high regio- and stereo-selectivity. Indeed, this protocol worked very well with electronically and sterically diverse substrates. Several studies, including deuterium labeling experiments and intermolecular competitive experiments, were carried out to understand the mechanistic details. The atomic-level mechanism followed in the catalytic process was also validated using DFT calculations, and the rate-controlling states in the catalytic cycle were identified. Further, preliminary mechanistic investigations with radical scavengers revealed non-involvement of the radical pathway for this transformation. | Bedadyuti Vedvyas Pati; Asit Ghosh; Komal Yadav; Shyam Kumar Banjare; Upakarasamy Lourderaj; Ponneri C. Ravikumar | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6125cafcd4eb8a6866a11b3c/original/palladium-catalyzed-c-c-bond-activation-and-regioselective-alkenyla-tion-between-cyclopropanol-and-1-3-diyne-one-step-synthesis-of-di-verse-conjugated-enynes.pdf |
659db252e9ebbb4db9cd7280 | 10.26434/chemrxiv-2023-f20bg-v3 | Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates | Fast and accurate prediction of solvent effects on reaction rates are crucial for kinetic modeling, chemical process design, and high-throughput solvent screening. Despite the recent advance in machine learning, a scarcity of reliable data has hindered the development of predictive models that are generalizable for diverse reactions and solvents. In this work, we generate a large set of data with the COSMO-RS method for over 28,000 neutral reactions and 295 solvents and train a machine learning model to predict the solvation free energy and solvation enthalpy of activation (ΔΔG‡solv, ΔΔH‡solv) for a solution phase reaction. On unseen reactions, the model achieves mean absolute errors of 0.71 and 1.03 kcal/mol for ΔΔG‡solv and ΔΔH‡solv, respectively, relative to the COSMO-RS calculations. The model also provides reliable predictions of relative rate constants within a factor of 4 when tested on experimental data. The presented model can provide nearly instantaneous predictions of kinetic solvent effects or relative rate constants for a broad range of neutral closed-shell or free radical reactions and solvents only based on atom-mapped reaction SMILES and solvent SMILES strings. | Yunsie Chung; William H. Green | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Machine Learning; Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659db252e9ebbb4db9cd7280/original/machine-learning-from-quantum-chemistry-to-predict-experimental-solvent-effects-on-reaction-rates.pdf |
643d9dd273c6563f140ddda1 | 10.26434/chemrxiv-2023-w8x3c | Engineering Phosphinate-Containing Rhodamines for Turn-On Photoacoustic Imaging Applications | Photoacoustic imaging (PAI) is an emerging imaging technique with applications in preclinical and point-of-care settings. PAI is a light-in, sound-out technique which uses pulsed laser excitation with near-infrared (NIR) light to elicit local temperature increases through non-radiative relaxation events, ultimately leading to the production of ultrasound waves. The classical xanthene dye scaffold has found numerous applications in fluorescence imaging, however, xanthenes are rarely utilized for PAI since they do not typically display NIR absorbance. Herein, we report the ability of Nebraska Red (NR) dyes to produce photoacoustic (PA) signal and provide a rational design approach to reduce the hydrolysis rate of ester containing dyes. By converting a relatively hydrolytically labile phosphinate ester to a more stable thiophosphinate ester, we were able to reduce the rate of ester hydrolysis 3.6-fold within a new dye, termed SNR700. Leveraging the stabilized NIR absorbance of this dye, we were able to construct the first rhodamine-based, turn-on PAI imaging probe for hypochlorous acid (HOCl) that is compatible with commercial PA instrumentation. This probe, termed SNR700-HOCl, has a limit of detection of 500 nM for HOCl and is capable of producing contrast up to 2.9 cm deep in tissues using PAI. This work provides a new set of rhodamine-based PAI agents as well as a rational design approach to stabilize esterified versions of NR dyes with desirable properties for PAI. In the long term, the reagents described herein could be utilized to enable non-invasive imaging of HOCl in disease-relevant model systems. | Frederik Brøndsted; Yuan Fang; Xinqi Zhou; Cliff Stains | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d9dd273c6563f140ddda1/original/engineering-phosphinate-containing-rhodamines-for-turn-on-photoacoustic-imaging-applications.pdf |
631215955351a39497ec9696 | 10.26434/chemrxiv-2022-43g7d | Gravitational settling of active droplets | The gravitational settling of oil droplets solubilizing in an aqueous micellar solution contained in a capillary channel is investigated. The motion of these active droplets reflects a competition between gravitational and Marangoni forces, the latter due to interfacial tension gradients generated by differences in filled- micelle concentrations along the oil-water interface. This competition is studied by varying the surfactant concentration, the density difference between the droplet and the continuous phase, and the viscosity of the continuous phase. The Marangoni force enhances the settling speed of an active droplet when compared to the Hadamard-Rybczynski prediction for a (surfactant free) droplet settling in Stokes flow. The Marangoni force can also induce lateral droplet motion, suggesting that the Marangoni and gravitational forces are not always aligned. The decorrelation rate (𝛼) of the droplet motion, measured as the initial slope of the velocity autocorrelation and indicative of the extent to which the Marangoni and gravitational forces are aligned during settling, is examined as a function of the droplet size: correlated motion (small values of 𝛼) is observed at both small and large droplet radii, whereas significant decorrelation can occur between these limits. This behavior of active droplets settling in a capillary channel is in marked contrast to that observed in a dish, where the decorrelation rate increases with the droplet radius before saturating at large values of droplet radius. A simple relation for the crossover radius at which the maximal value of 𝛼 occurs for an active settling droplet is proposed. | Alexander C. Castonguay; R. Kailasham; Ciera M. Wentworth; Caleb H. Meredith; Aditya S. Khair; Lauren D. Zarzar | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631215955351a39497ec9696/original/gravitational-settling-of-active-droplets.pdf |
666738ef409abc0345181177 | 10.26434/chemrxiv-2024-x6mm0 | Sickle Cell Hemoglobin Drugged with Cyclic Peptides is Aggregation Incompetent | Sickle cell disease is a monogenic blood disorder associated with a mutation in the HBB gene encoding for the β-globin of normal adult hemoglobin (HbA). This mutation transcribes into a Gluβ6→Val-β6 substitution in the β-globins, inducing the polymerization of this hemoglobin form (HbS) when in the T-state. Despite advances in stem cell and gene therapy and the recent approval of a new anti-sickling drug, therapeutic limitations persist. Herein, we demonstrate through molecular dynamics and umbrella sampling, that (unrestrained) blockage of the hydrophobic pocket involved in the lateral contact of the HbS fibers by 5-mer cyclic peptides (CPs) recently proposed as SCD aggregation inhibitors (J. Med. Chem. 2023, 66, 16062), is enough to turn the dimerization of HbS thermodynamically unfavorable. Amongst these potential drugs, some exhibit an estimated pocket abandonment probability of around 15-20% within the simulations’ timeframe, and an impressive specificity towards the mutated Val-β6. Additionally, we show that the dimerization can be thermodynamically unfavored by blocking a nearby region while the pocket remains undrugged. These results are compared with curcumin, an antisickling molecule and a pan-assay interference compound, with a good binding affinity for different proteins and protein domains. Our results confirm the potential of some of these CPs as anti-sickling drugs to reduce the concentration of aggregation-competent HbS. | Nuno Galamba | Physical Chemistry; Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666738ef409abc0345181177/original/sickle-cell-hemoglobin-drugged-with-cyclic-peptides-is-aggregation-incompetent.pdf |
60c74445702a9b1b4a18a7fa | 10.26434/chemrxiv.9777218.v1 | Nobel Metal Based High Entropy Alloy for Conversion of Carbon Dioxide (CO2) to Hydrocarbon | <p>Conversion of carbon-di-oxide into selective hydrocarbon
using stable catalyst remains a holy-grail in catalysis community. The high
overpotential, stability, and selectivity in use of a single metal-based
catalyst still remain a challenge. In current work, instead of using pure noble
metals (Ag, Au, and Pt) as the catalyst, a novel nanocrystalline high entropy
alloy (HEA: AuAgPtPdCu) has been used for conversion of CO<sub>2</sub> into
gaseous hydrocarbons. Utilizing an approach of multi-metallic HEA, a Faradaic
efficiency of about 100% towards gaseous products is obtained. The reason
behind the superior catalytic activity of high entropy alloy (HEA) was
established through first-principles based density functional theory (DFT) by
comparing it with pristine Cu (111) surface. This is attributed to the
reversal in adsorption trends for two out of the total eight intermediates - <sup>*</sup>OCH<sub>3</sub>
and <sup>*</sup>O on Cu(111) and HEA surfaces<b>.</b></p> | Subramanian Nellaiappan; Nirmal Kumar; Ritesh Kumar; Arko Parui; Kirtiman
Deo Malviya; K. G. Pradeep; Abhishek
Kumar Singh; Sudhanshu Sharma; Chandra Sekhar Tiwary; Krishanu Biswas | Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74445702a9b1b4a18a7fa/original/nobel-metal-based-high-entropy-alloy-for-conversion-of-carbon-dioxide-co2-to-hydrocarbon.pdf |
60c74ce0702a9b4cda18b746 | 10.26434/chemrxiv.12493889.v1 | Solid-State Laser Refrigeration at GPa Pressures | <div>Although solid-state laser-refrigeration recently has been demonstrated to reach cryogenic temperatures in vacuum, to date the solid-state laser refrigeration of materials at elevated pressure conditions has remained unexplored. Here we demonstrate the laser cooling of ytterbium-doped yttirum-lithium-fluoride (10%Yb<sup>3+</sup>:YLiF<sub>4</sub>, or Yb:YLF)</div><div>>17K below room temperature at pressures >4 GPa in a diamond anvil cell using lithium fluoride and ice-VII as a quasi-hydrostatic pressure media. Temperature measurements are quantified using a ratiometric-thermometry approach involving a Boltzmann fit to excited states distribution through 4f-4f Stark-level transitions from the Yb<sup>3+</sup> ions that occur between the <sup>2</sup>F<sub>5/2</sub> and <sup>2</sup>F<sub>7/2</sub> manifolds. At pressures between 7 and 12 GPa the YLF grains are observed to undergo a martensitic phase transition from a tetragonal scheelite phase (space group I41/a, Z = 4, No. 88) to a monoclinic fergusonite phase (space group I2/a, Z = 4, No. 15) which modifies the crys-</div><div>tal field splitting of the ground- and excited- state manifolds, but is observed to not eliminate laser cooling. Solid-state laser refrigeration at extreme pressures could allow researchers to use rapid photothermal cycling to explore temperature-dependent properties of materials, including electronic-structure phase-transitions, without the need for external cryostats.</div> | Abbie S. Ganas; Elena Dobretsova; Anupum Pant; Baptiste Journaux; Xiaojing Xia; Robert G. Felsted; Peter Pauzauskie | Ceramics; Composites; Lanthanides and Actinides; Solid State Chemistry; Spectroscopy (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ce0702a9b4cda18b746/original/solid-state-laser-refrigeration-at-g-pa-pressures.pdf |
64080d006642bf8c8f2571bb | 10.26434/chemrxiv-2023-1bzgp-v2 | The Repeatability and Reproducibility Problem in the CVD Synthesis of 2D Materials:
Towards a More Efficient and Sustainable Synthetic Process
| Though Chemical Vapor Deposition (CVD) is a versatile process that has been widely used for synthesizing graphene, hexagonal boron nitride (h BN) and other 2-D materials, the process is plagued by issues of repeatability and reproducibility, the two important pillars of the scientific method. The primary reason for this is that we do not know or can directly measure the reaction environment inside the reactor (flow and thermal fields and reactant concentrations) that controls the growth process and the final film characteristics. In turn, we are unsure about the external parameters that control this reaction environment and can be measured instead. Consequently, experimental details currently monitored and reported in the literature are insufficient to ensure reproducibility, with process details typically reported only partially, and details about the reactor not included at all, further compounding the problem. In this paper, using the example of a hot-wall tube reactor that is typically used in the laboratory and the Computational Fluid Dynamics toolbox OpenFOAM, we have simulated the reactor environment and identified measurable reactor and process parameters that control this environment and explored its sensitivity to these external parameters. Based on our findings, we have devised a straightforward protocol for experimentalists to use for monitoring and reporting CVD processes in literature so that they become repeatable and reproducible, and, aid in analyzing and studying processes and mechanisms, rapid testing of ideas, process scale-up and an overall faster and more sustainable progress of the field. | Shahana Chatterjee; Thomas Abadie; Meihui Wang; Omar Matar; Rodney Ruoff | Nanoscience; Chemical Engineering and Industrial Chemistry; Nanostructured Materials - Nanoscience; Fluid Mechanics; Process Control | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64080d006642bf8c8f2571bb/original/the-repeatability-and-reproducibility-problem-in-the-cvd-synthesis-of-2d-materials-towards-a-more-efficient-and-sustainable-synthetic-process.pdf |
6536d13f87198ede071eb178 | 10.26434/chemrxiv-2023-pdw1d | Ni-Catalyzed Electrochemical Cross-Electrophile C(sp2)-C(sp3) Coupling via a NiII Aryl Amido Intermediate | Cross-electrophile coupling (XEC) between aryl halides and alkyl halides is a streamlined approach for C(sp2)−C(sp3) bond construction, which is highly valuable in medicinal chemistry. Based on a key NiII aryl amido intermediate, we developed a highly selective and scalable Ni-catalyzed electrochemical XEC reaction between (hetero)aryl halides and primary and secondary alkyl halides. Experimental and computational mechanistic studies indicate that in the presence of a polypyridine primary ligand and an amine secondary ligand, there is in-situ formation of a NiII aryl amido intermediate. The NiII aryl amido intermediate stabilizes the NiII−aryl species to prevent the aryl−aryl homo-coupling side reactions and acts as a catalyst to activate the alkyl bromide substrates. This electrosynthesis system provides a facile and practical platform for the formation of (hetero)aryl−alkyl bonds using standard Ni catalysts under mild conditions, and the system is amenable to scalable flow synthesis. | Jian Luo; Michael Davenport; Daniel Ess; Tianbiao Liu | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Electrocatalysis; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6536d13f87198ede071eb178/original/ni-catalyzed-electrochemical-cross-electrophile-c-sp2-c-sp3-coupling-via-a-ni-ii-aryl-amido-intermediate.pdf |
6749ceb35a82cea2fa6594b4 | 10.26434/chemrxiv-2024-nsjlk | Hierarchical Assembly of Conductive Fibers from Coiled-Coil Peptide Building Blocks | Biology provides many sources of inspiration for synthetic and multi-functional nanomaterials. Naturally evolved proteins exhibit unique, sequence-defined functions and self-assembly behavior. Some microbial protein filaments are electronically conductive, evolved to support access to remote electron acceptors outside the cell, which serve as a design platform for bioelectronic materials with applications in biosensors and enzymatic electrocatalysis. Recapitulating their self-assembly and conductive behavior, however, is challenging in de novo proteins. Peptides, on the other hand, represent a more well-defined and rationally designable space with the potential for sequence-programmable, stimuli responsive design for structure and function, making them ideal building blocks of bioelectronic interfaces. In this work, we design peptides that exhibit stimuli-responsive self-assembly and the capacity to transport electrical current over micrometer long distances. A lysine-lysine (KK) motif inserted at solvent exposed positions of a coiled coil forming peptide sequence introduces pH dependent control over a transition from random coil to α-helical peptide structure. The ordered state of the peptide serves as a building block for assembly of coiled coils and higher order assemblies. Cryo-EM structures of these structures reveal a novel organization of α-helical peptides in a cross coiled coil (CCC) arrangement that is unprecedented in de novo and natural protein designs. Structural analysis also reveals a -sheet fiber phase under certain conditions and placements of the KK motif, revealing a complex and sensitive self-assembly pathway. Both solid-state and solution-based electrochemical characterization show that CCC fibers are electronically conductive. Single-fiber conductive AFM measurement indicate that the solid-state electrical conductivity is comparable with bacterial cytochrome filaments. Solution deposited fiber films approximately doubled the electroactive surface area of the electrode, confirming their conductivity in aqueous environments. This work establishes a stimuli-responsive peptide sequence element for balancing the order-disorder transitions in peptides to control their self-assembly into highly organized, electronically conductive nanofibers. | Adam Grosvirt-Dramen; Zachary Urbach ; Paul Hurst; Claire Kwok; Joseph Patterson; Fengbin Wang; Allon Hochbaum | Biological and Medicinal Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6749ceb35a82cea2fa6594b4/original/hierarchical-assembly-of-conductive-fibers-from-coiled-coil-peptide-building-blocks.pdf |
60c74ae1567dfe162cec4e4a | 10.26434/chemrxiv.12120912.v2 | Flawed methods in “COVID-19: Attacks the 1-Beta Chain of Hemoglobin and Captures the Porphyrin to Inhibit Human Heme Metabolism” | <div>This is a critical commentary on an earlier submission by Liu and Li. The preprint from Liu & Li (<a href="https://doi.org/10.26434/chemrxiv.11938173.v7">https://doi.org/10.26434/chemrxiv.11938173.v7</a>) puts forward hypotheses about a proposed role for proteins of SARS-CoV-2, the virus associated with Covid-19, in directly attacking haemoglobin in patients’ blood. Arguments for the hypotheses are based on computational methods: bioinformatics calculations searching for evidence that viral proteins share functional domains related to haem binding with human proteins, molecular modeling of viral proteins, and computational docking of these protein models with models of haem, porphyrin and haemoglobin. No experimental evidence is provided to support any of the conclusions. When interpreted according to accepted standards, these computational results do not hold up and do not provide support for the hypotheses. The interpretation of the search for shared functional domains suffers from a fundamental error in how the significance of the results is judged; when interpreted correctly, there is no evidence for these shared functional domains. Molecular modeling is carried out with tools that are easy to use but not best-in-class, and no allowance is made for uncertainty in the resulting atomic coordinates. Finally, the docking results are invalidated by a catastrophic error in their interpretation: the authors choose the docking trials that have the highest energies, whereas the most stable complexes are actually the ones that have the lowest energies and are therefore least strained. An addendum addresses flaws in a new version 8 from Liu & Li (<a href="https://doi.org/10.26434/chemrxiv.11938173.v8">https://doi.org/10.26434/chemrxiv.11938173.v8</a>), which retracts most of their results from earlier versions but nonetheless continues to put forward the same conclusions on the basis of poorly-controlled docking calculations.</div> | Randy Read | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae1567dfe162cec4e4a/original/flawed-methods-in-covid-19-attacks-the-1-beta-chain-of-hemoglobin-and-captures-the-porphyrin-to-inhibit-human-heme-metabolism.pdf |
60c74705337d6cc6b1e27280 | 10.26434/chemrxiv.11467845.v1 | Visible Light-Promoted Catalytic Ring-Opening Isomerization of 1,2-Disubstituted Cyclopropanols to Linear Ketones | In this article, we report a photocatalytic protocol for the isomerization of 1,2-disubstituted cyclopropanols to linear ketones. The reaction proceeds <i>via</i> radical intermediates and tolerates various functional groups. | Marharyta V. Laktsevich-Iskryk; Nastassia A. Varabyeva; Volha V. Kazlova; Vladimir N. Zhabinskii; Vladimir A. Khripach; Alaksiej Hurski | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74705337d6cc6b1e27280/original/visible-light-promoted-catalytic-ring-opening-isomerization-of-1-2-disubstituted-cyclopropanols-to-linear-ketones.pdf |
64dd24424a3f7d0c0d474b33 | 10.26434/chemrxiv-2023-65m0v | Development of a General Organophosphorus Radical Trap: Deoxyphosphonylation of Alcohols | Here we report the conceptualization and design of a general, redox switchable organophosphorus alkyl radical trap enabling the synthesis of a broad range of C(sp3)–P(V) modalities. This plug-and-play approach relies upon an in-situ activation of alcohols and dialkyl phosphites, two broadly available sources of molecular complexity. The mild, photocatalytic deoxygenative strategy employed here allows for the direct transformation of sugars, nucleosides, and complex pharmaceutical architectures to their organophosphorus analogs, including medicinally relevant phosphonate ester prodrugs. | Noah B. Bissonnette; Niels Bisballe; Andrew V. Tran; James A. Rossi-Ashton; David W. C. MacMillan | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dd24424a3f7d0c0d474b33/original/development-of-a-general-organophosphorus-radical-trap-deoxyphosphonylation-of-alcohols.pdf |
661a0a7891aefa6ce1751c1a | 10.26434/chemrxiv-2024-3b2vc | Crystallographic and spectroscopic studies on persistent triarylpropargyl cations | By acid treatment of precursor alcohols, mesitylethynyl-substituted diarylmethyl cations were isolated as stable solids, X-ray structural analyses of which revealed a planar geometry. Furthermore, the ion pairs including these triarylpropargyl cations form charge-segregated assemblies in the crystal, and effective intermolecular interaction induces a red-shift of absorption in the crystal. | Takuya Shimajiri; Taiga Tsue; Shumpei Koakutsu; Yusuke Ishigaki; Takanori Suzuki | Physical Chemistry; Organic Chemistry; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661a0a7891aefa6ce1751c1a/original/crystallographic-and-spectroscopic-studies-on-persistent-triarylpropargyl-cations.pdf |
63c711317c5fefc675256046 | 10.26434/chemrxiv-2023-z799b | Variable Amine Spacing Determines
Depolymerization Rate in Polydiketoenamines | The design of circular polymers has emerged as a necessity due to the lack of efficient recycling methods for many commodity plastics, particularly those used in durable products. Among the promising circular polymers, polydiketoenamines (PDKs) stand out for their ability to undergo highly selective depolymerization in strong acid, allowing monomers to be recovered from additives and fillers. Varying the triketone monomer in PDK variants is known to strongly affect the depolymerization rate; however, it remains unclear how the chemistry of the crosslinker, far from the reaction center, affects the depolymerization rate. Here, we elucidate design rules for PDK acidolysis from a convergence of simulations and experiments. We demonstrate that a multi-path transition state theory approach to calculating reaction kinetics is essential to accurate modeling of small molecule hydrolysis kinetics and that the computational results match closely to experimental observations of both small molecule hydrolysis kinetics and PDK depolymerization. Notably, we found that a proximal amine in the crosslinker dramatically accelerates PDK depolymerization when compared to crosslinkers obviating this functionality. Moreover, the spacing between this amine and the diketoenamine bond offers a previously unexplored opportunity to tune PDK depolymerization rates. In this way, the molecular basis for PDK circularity is revealed and further suggests new targets for the amine monomer design to diversify PDK properties, while ensuring circularity in chemical recycling. | Alex Epstein; Jeremy Demarteau; Brett Helms; Kristin Persson | Theoretical and Computational Chemistry; Polymer Science; Polymerization (Polymers); Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c711317c5fefc675256046/original/variable-amine-spacing-determines-depolymerization-rate-in-polydiketoenamines.pdf |
60c7536eee301cfe6fc7add0 | 10.26434/chemrxiv.13489656.v1 | Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation | In chemical kinetics research, kinetic models containing hundreds of species and tens of thousands of elementary reactions are commonly used to understand and predict the behavior of reactive chemical systems. Reaction Mechanism Generator (RMG) is a software suite developed to automatically generate such models by incorporating and extrapolating from a database of known thermochemical and kinetic parameters. Here, we present the recent version 3 release of RMG and highlight improvements since the previously published description of RMG v1.0. One important change is that RMG v3.0 is now Python 3 compatible, which supports the most up-to-date versions of cheminformatics and machine learning packages that RMG depends on. Additionally, RMG can now generate heterogeneous catalysis models, in addition to the previously available gas- and liquid-phase capabilities. For model analysis, new methods for local and global uncertainty analysis have been implemented to supplement first-order sensitivity analysis. The RMG database of thermochemical and kinetic parameters has been significantly expanded to cover more types of chemistry. The present release also includes parallelization for reaction generation and on-the-fly quantum calculations, and a new molecule isomorphism approach to improve computational performance. Overall, RMG v3.0 includes many changes which improve the accuracy of the generated chemical mechanisms and allow for exploration of a wider range of chemical systems. | Mengjie Liu; Alon Grinberg Dana; Matthew Johnson; Mark Goldman; Agnes Jocher; A. Mark Payne; Colin Grambow; Kehang Han; Nathan Wa-Wai Yee; Emily Mazeau; Katrin Blondal; Richard West; Franklin Goldsmith; William H. Green | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Reaction Engineering; Heterogeneous Catalysis; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2020-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7536eee301cfe6fc7add0/original/reaction-mechanism-generator-v3-0-advances-in-automatic-mechanism-generation.pdf |
67179e48d433919392d6b626 | 10.26434/chemrxiv-2024-4mvs6 | Separation and detection of charged unilamellar vesicles in vacuum by a frequency-scanned quadrupole mass sensor | Extracellular vesicles (EVs) are membranous particles released by cells considered as a promising source of biomarkers for various diseases. Mass spectrometry (MS) analysis of EVs requires a sample of purified and disintegrated EVs. Purification of EVs is laborious, based on size, density or surface nature and requires large amounts of the source material (e.g., blood, spinal fluid). We have employed synthetically produced large unilamellar lipid vesicles (LUVs) as analogs of EVs to demonstrate a simplified method of vesicle separation for mass spectrometry analysis. Mass-to-charge ratio m/z separation by frequency-scanned quadrupole was employed to filter narrow size distributions of LUVs from a water sample. Lipid vesicles were charged with nano-electrospray and transferred into a vacuum using two wide m/z-range frequency-scanned quadrupoles. The m/z, charges and masses of individual vesicles were obtained by the nondestructive single-pass charge detector. The resolving regime of the second quadrupole with m/z RSD < 10% allowed to separate size selected distributions of vesicles with modal diameters 87, 111, 130, 160, 181 nm at corresponding quadrupole m/z settings 2.5×105, 5×105, 8×105, 1.5×106, 2.5×106 with detection frequencies 20-100 per minute. The presented approach for lipid vesicles separation encourages the development of new techniques for direct mass-spectrometric analysis of biomarkers in MS-separated EVs in a vacuum. | Anatolii Spesyvyi; Marek Cebecauer; Ján Žabka; Agnieszka Olżyńska; Michaela Malečková; Zuzana Johanovská; Miroslav Polášek; Ales Charvat; Bernd Abel | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67179e48d433919392d6b626/original/separation-and-detection-of-charged-unilamellar-vesicles-in-vacuum-by-a-frequency-scanned-quadrupole-mass-sensor.pdf |
618bdc132c7c0b8f04d710e6 | 10.26434/chemrxiv-2021-nppzq | An In Vivo Biocatalytic Cascade Featuring an Artificial Enzyme Catalyzed New-to-Nature Reaction | Artificial enzymes utilizing the genetically encoded non-proteinogenic amino acid p-aminophenylalanine (pAF) as catalytic residue are able to react with carbonyl compounds through an iminium ion mechanism, making reactions possible that have no equivalent in nature. Here, we report an in vivo biocatalytic cascade that is augmented with such an artificial enzyme catalyzed new-to-nature reaction. The artificial enzyme in this study is a pAF containing evolved variant of the Lactococcal multidrug resistance Regulator, designated LmrR_V15pAF_RMH, which efficiently converts in vivo produced benzaldehyde derivatives into the corresponding hydrazone products inside E. coli cells. These in vivo biocatalytic cascades comprising an artificial enzyme catalyzed reactions are an important step towards achieving a hybrid metabolism. | Linda Ofori Atta; Zhi Zhou; Gerard Roelfes | Catalysis; Biocatalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618bdc132c7c0b8f04d710e6/original/an-in-vivo-biocatalytic-cascade-featuring-an-artificial-enzyme-catalyzed-new-to-nature-reaction.pdf |
647dc0fc4f8b1884b7e025b9 | 10.26434/chemrxiv-2023-n1kr5 | Template-induced graphitic nanodomains in nitrogen-doped carbons enable high-performance sodium-ion capacitors | Sodium-ion capacitors (SICs) have great potential in energy storage due to their low cost, the abundance of Na, and the potential to deliver high energy and power simultaneously. This paper demonstrates a template-assisted method to induce graphitic nanodomains and micro-mesopores into nitrogen-doped carbons. This study elucidates that these graphitic nanodomains are beneficial for Na+ storage. The obtained As8Mg electrode achieved a reversible capacity of 254 mA h g−1 at 0.1 A g−1 and excellent cycling stability of 98.7% capacity retention over 350 cycles. Moreover, the As8Mg-based SIC device achieves high combinations of power/energy densities (52 W kg−1 at 204 Wh kg−1 and 10,456 W kg−1 at 51 Wh kg−1) with outstanding cycle stability (99.7% retention over 600 cycles at 0.2 A g−1). Our findings provide insights into optimizing carbon’s microstructure to boost sodium storage in the pseudo-capacitive mode. | Chun Li; Zihan Zong; Mingliang Liu; Enrico Lepre; Markus Antonietti; Junwu Zhu; Jian Liu; Yongsheng Fu; Nieves López-Salas | Materials Science; Nanoscience; Energy; Carbon-based Materials; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647dc0fc4f8b1884b7e025b9/original/template-induced-graphitic-nanodomains-in-nitrogen-doped-carbons-enable-high-performance-sodium-ion-capacitors.pdf |
6683a876c9c6a5c07a0370c2 | 10.26434/chemrxiv-2024-j6gdf-v2 | Rare Earth Mixed Sandwich Complexes with Tetraalkylphospholide and Cyclooctatetraenide Ligands | A series of rare earth (mono)phospholide mixed sandwich complexes of the general form [M(PC4R4)(COT)(THF)n] (M = Sc, Y, La, Lu; R = Me, Et; COT = cyclooctatetraenide, {C8H8}2–; n = 0 to 2) have been isolated by the treatment of iodide precursors, [M(COT)(I)(THF)n], (1M, M = Sc, Y, Lu, n = 2; M = La, n = 3) with potassium phospholide salts, [K(PC4R4)]n (R = Me, Et). The solid-state molecular structures and speciation of these sandwich complexes depends upon both the ionic radius of the rare earth metal, along with small steric and solubility differences which arise between the two per-alkylated phospholide ligands. The smaller {PC4Me4} ligand gave monomeric Lewis-base free [M(C8H8)(PC4Me4)] (2M, M = Sc, Lu) with smaller rare earths Sc(III) and Lu(III), but moving to larger ions Y(III) and La(III), the products were poorly soluble and could only be isolated as THF-adducts, [Y(C8H8)(PC4Me4)(THF)] (3) and [La(C8H8)(PC4Me4)(THF)2] (4). The slightly increased steric demands of {PC4Et4} gave monomeric Lewis-base free complexes for Sc(III), Lu(III), and Y(III) in [M(C8H8)(PC4Et4)] (5M, M = Sc, Y, Lu), whereas for La(III) a dimeric complex was isolated, [La(C8H8)(µ- PC4Et4)]2 (6). We also report the synthesis and molecular structures of 1Sc and 1Lu, as well as [LuI3(THF)3] (7) for the first time. All complexes were characterised by single crystal X-ray diffraction, multi-nuclear NMR, UV-Vis-NIR and ATR-IR spectroscopies in addition to elemental analysis. | Cameron Deakin; Daniel O'Neill; Ralph Adams; George Whitehead; Conrad Goodwin | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6683a876c9c6a5c07a0370c2/original/rare-earth-mixed-sandwich-complexes-with-tetraalkylphospholide-and-cyclooctatetraenide-ligands.pdf |
60c756294c8919b04aad47e2 | 10.26434/chemrxiv.14199443.v1 | Hydrogen Bond Synchronized Dual Activation Enables the Unified β-Selective O-Glycosylation Inside a Molecular Capsule | <div>Carbohydrates are of central importance in biology. The selective chemical synthesis of carbohydrates, however, still poses a challenge; particularly, the selective formation of the</div><div>thermodynamically labile b-glycosidic bond is difficult and depends on the substrate’s substitution pattern. We here demonstrate that a molecular capsule catalyzes the highly</div><div>challenging selective formation of b-glycosides independent of the substrate’s substitution pattern and configuration. We demonstrate the versatility of the catalyst by synthesizing small to medium sized 1,2-cis, 2-deoxy, and 1,2-trans b-glycosides in very high selectivity and good yield. The confined space inside the molecular capsule naturally limits the scope concerning the size of reactants. Interestingly, the proposed mechanism involves the synchronized activation of the glycosyl donor and acceptor inside the supramolecular capsule via a relay involving seven hydrogen bonds. Such an activation is known for enzymes, however, to our knowledge, is unprecedented for man-made catalysts.</div> | Tian-Ren Li; Fabian Huck; GiovanniMaria Piccini; Konrad Tiefenbacher | Supramolecular Chemistry (Org.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756294c8919b04aad47e2/original/hydrogen-bond-synchronized-dual-activation-enables-the-unified-selective-o-glycosylation-inside-a-molecular-capsule.pdf |
60e9ea730387b168b6cb10c6 | 10.26434/chemrxiv-2021-cn2z8 | Supervised Machine Learning Classification Algorithms for Detection of Fracture Location in Dissimilar Friction Stir Welded Joints | Machine Learning focuses on the study of algorithms that are mathematical or statistical in nature in order to extract the required information pattern from the available data. Supervised Machine Learning algorithms are further sub-divided into two types i.e. regression algorithms and classification algorithms. In the present study, four supervised machine learning-based classification models i.e. Decision Trees algorithm, K- Nearest Neighbors (KNN) algorithm, Support Vector Machines (SVM) algorithm, and Ada Boost algorithm were subjected to the given dataset for the determination of fracture location in dissimilar Friction Stir Welded AA6061-T651 and AA7075-T651 alloy. In the given dataset, rotational speed (RPM), welding speed (mm/min), pin profile, and axial force (kN) were the input parameters while Fracture location is the output parameter. The obtained results showed that the Support Vector Machine (SVM) algorithm classified the fracture location with a good accuracy score of 0.889 in comparison to the other algorithms. | Akshansh Mishra | Materials Science; Alloys | CC BY NC 4.0 | CHEMRXIV | 2021-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e9ea730387b168b6cb10c6/original/supervised-machine-learning-classification-algorithms-for-detection-of-fracture-location-in-dissimilar-friction-stir-welded-joints.pdf |
6511a7e9ed7d0eccc331c23d | 10.26434/chemrxiv-2023-0f0km | Reverse-Engineered High-Yield Lasso Peptide Production in an Alternative Host | The knotted configuration of lasso peptides confers thermal stability and proteolytic resistance, addressing two shortcomings of peptide-based drugs. However, low isolation yields hinder the discovery and development of lasso peptides. While testing Burkholderia sp. FERM BP-3421 as a bacterial host to produce the lasso peptide capistruin, an overproducer clone was previously identified. In this study, we show that an increase in plasmid copy number partially contributed to the overproducer phenotype. Further, we modulated plasmid copy number to recapitulate titers to an average of 160% relative to the overproducer, which is 1,000-fold higher than previously reported with E. coli, reaching up to 240 mg/L. To probe the applicability of the developed tools for lasso peptide discovery we targeted a new lasso peptide biosynthetic gene cluster from endosymbiont Mycetohabitans sp. B13, leading to the isolation of mycetolassin-15 and mycetolassin-18 in combined titers of 11 mg/L. These results validate Burkholderia sp. FERM BP-3421 as a production platform for lasso peptide discovery. | Hannah Fernandez; Ashley Kretsch; Sylvia Kunakom; Adjo Kadjo; Douglas Mitchell; Alessandra Eustaquio | Biological and Medicinal Chemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6511a7e9ed7d0eccc331c23d/original/reverse-engineered-high-yield-lasso-peptide-production-in-an-alternative-host.pdf |
65e5481f9138d231619c1879 | 10.26434/chemrxiv-2024-vt6z8 | From Eyes to Cameras: Computer Vision for High-Throughput Liquid-Liquid Separation | We present a modular, high-throughput (HT) automation platform for screening Liquid-Liquid Extraction (LLE) workup processes. Our automated hardware platform simultaneously screens up to 12 vials, and is coupled with a computer vision (CV) system for real-time monitoring of macroscopic visual cues. Our CV system, named HeinSight3.0, leverages machine learning and image analysis to classify and quantify multivariate visual cues such as liquid level, phase split clarity, turbidity, homogeneity, volume, and color. These cues, combined with process parameters like stir rate and temperature, enable real-time analysis of key workup processes (e.g., separation time, phase split quality, volume ratio of layers, color, and emulsion presence) to aid in the optimization of separation parameters. We demonstrate our system on three case-studies: impurity recovery, excess reagent removal, and Grignard workup. Our application of HeinSight3.0 on literature data also suggests high potential for generalizability and adaptability across different platforms and contexts. Overall, our work represents a significant step towards achieving end-to-end autonomous LLE screening guided by visual cues, contributing to the realization of a self-driving lab for workup processes. | Rama El-khawaldeh; Abhijoy Mandal; Naruki Yoshikawa; Wenyu Zhang; Ryan Corkery; Paloma Prieto; Alán Aspuru-Guzik; Kourosh Darvish; Jason Hein | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Chemistry; Pharmaceutical Industry | CC BY NC 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e5481f9138d231619c1879/original/from-eyes-to-cameras-computer-vision-for-high-throughput-liquid-liquid-separation.pdf |
613cca45abeb635f96cfcbfd | 10.26434/chemrxiv-2021-4qcqm | A Machine Learning Approach to Calculate Electronic Couplings between Quasi-Diabatic Molecular Orbitals: The Case of DNA | Diabatization of one-electron states in flexible molecular aggregates is a great challenge due to the presence of surface crossings between molecular orbital (MO) levels and the complex interaction between MOs of neighboring molecules. In this work, we present an efficient machine learning approach to calculate electronic couplings between quasi-diabatic MOs without the need of nonadiabatic coupling calculations. Using MOs of rigid molecules as references, the MOs that can be directly regarded to be quasi-diabatic in molecular dynamics are selected out, state tracked, and phase corrected. On the basis of this information, artificial neural networks are trained to characterize the structure-dependent onsite energies of quasi-diabatic MOs and the inter-molecular electronic couplings. A representative sequence of DNA is systematically studied as an illustration. Smooth time evolution of electronic couplings in all base pairs is obtained with quasi-diabatic MOs. Especially, our method can calculate electronic couplings between different quasi-diabatic MOs independently, and thus possesses unique advantages in many applications. | Xin Bai; Xin Guo; Linjun Wang | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613cca45abeb635f96cfcbfd/original/a-machine-learning-approach-to-calculate-electronic-couplings-between-quasi-diabatic-molecular-orbitals-the-case-of-dna.pdf |
64e3054f694bf1540cb613ed | 10.26434/chemrxiv-2023-78z7p | 1,2-Disubstituted Bicyclo[2.1.1]hexanes as Bioisosteres of the ortho-substituted Benzene | 1,2-Disubstitued bicyclo[2.1.1]hexanes have been designed, synthesized, and validated as a new generation of saturated bioisosteres of ortho-substituted benzenes. Incorporation of the bicyclo[2.1.1]hexane core into the structure of agrochemicals Boskalid (BASF), Bixafen (Bayer CS), and Fluxapyroxad (BASF) gave saturated analogs that exhibited a high antifungal activity. | Aleksandr Denisenko; Pavel Garbuz; Yelyzaveta Makovetska; Oleh Shablykin; Dmytro Lesyk; Galeb Al-Maali; Rodion Korzh; Iryna Sadkova; Pavel Mykhailiuk | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e3054f694bf1540cb613ed/original/1-2-disubstituted-bicyclo-2-1-1-hexanes-as-bioisosteres-of-the-ortho-substituted-benzene.pdf |
66d7a8f3cec5d6c1420d38bd | 10.26434/chemrxiv-2023-x66jd-v3 | Isotropic <--> Anisotropic Surface Geometry Transitions Induced by Adsorbed Surfactants at Water/Vapor Interfaces | It is well known that adsorbates at a water/vapor interface change surface geometry through altered surface tension. Yet detailed theoretical studies of surface geometry in the presence of adsorbates are relatively sparse and many applications focus upon ensemble average surface geometric characteristics. Here we demonstrate that different interpretations of surface geometry emerge when considering the distributions of the geometric descriptors of surface curvature and orientation as a function of adsorbed surfactant concentration and sterics. At low surface coverage, the tributyl phosphate (TBP) sorbed water/vapor surface has an increased presence of ridges that are defined by principle curvatures $\kappa_1$ and $\kappa_2$ of opposite signs yet close in magnitude. As the TBP surface coverage increases, the difference in principle curvatures slowly increases. However there is a distinct transition of the surface geometry, where the ridge-like features become much more pronounced, having sides whose orientation is normal to a flat interfacial plane. Thus as the TBP surfactant is added to the surface, the surface curvatures become significantly anisotropic in terms of the difference in magnitude of $\kappa_1$ and $\kappa_2.$ We label this an \textit{isotropic $\rightarrow$ anisotropic} geometric transition. Comparing the surface geometry as a function of carbon tail length of the alkyl phosphate surfactant reveals that smaller surfactants also anisotropically enhance surface curvatures on the surface, and that adsorbed alkyl tails to the surface stabilize and increase the symmetry of surface waves along the two principle curvature axes. We label this an \textit{anisotropic $\rightarrow$ isotropic} geometric transition. These results reflect the opportunity to incorporate more realistic distributions of surface geometry within the collective understanding of statistical theories of surfaces, including capillary wave theory. | Nitesh Kumar; Joshua Bilsky; Aurora Clark | Theoretical and Computational Chemistry; Physical Chemistry; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d7a8f3cec5d6c1420d38bd/original/isotropic-anisotropic-surface-geometry-transitions-induced-by-adsorbed-surfactants-at-water-vapor-interfaces.pdf |
66da2736cec5d6c1424208a5 | 10.26434/chemrxiv-2024-12h5f | Identifying Green Solvent Mixtures for Bioproduct Separation Using Bayesian Experimental Design | Liquid-liquid extraction (LLE) is a widely used technique for the separation and purification of liquid-phase products with applications in various industries, including pharmaceuticals, petrochemicals, and renewable chemistry. A critical step in the design of a LLE process is the selection of appropriate solvents. This study presents a new methodology for identifying solvent mixtures for bioproduct separation using Bayesian Experimental Design (BED). Motivated by the need for environmentally-friendly and effective separation methods, we address the challenge of selecting solvent systems that balance separation efficiency, selectivity, and environmental impact, while also tackling the difficulty of separating multiple bioproducts using complex solvent systems. Our approach specifically seeks to predict product partition coefficients as thermodynamic parameters underlying solvent selection. The iterative approach integrates Bayesian optimization with experimental measurements to guide solvent selection, and leverages COSMO-RS simulations to enhance high-throughput experimentation. Using the design of solvent systems for the separation of lignin-derived aromatic products via centrifugal partition chromatography (CPC) as a case study, we show that within seven iterations/cycles of the methodology, we can identify new mixtures of green solvents that align with CPC design principles. These results demonstrate the efficacy of the BED framework in optimizing green solvent systems for complex separations, highlighting the potential of this method to advance the field of green chemistry and contribute to the development of sustainable industrial processes. | Shiyi Qin; Surajudeen Omolabake; Aminata Diaby; Jianping Li; Leonardo Gonzalez; Christopher Holland; Victor Zavala; Shannon Stahl; Reid Van Lehn | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Thermodynamics (Chem. Eng.) | CC BY NC 4.0 | CHEMRXIV | 2024-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66da2736cec5d6c1424208a5/original/identifying-green-solvent-mixtures-for-bioproduct-separation-using-bayesian-experimental-design.pdf |
655b7e24dbd7c8b54ba6ec30 | 10.26434/chemrxiv-2023-whtvz | MALDI TIMS IMS Reveals Ganglioside Molecular Diversity within Murine S. aureus Soft Tissue Abscesses. | Gangliosides play important roles in innate and adaptive immunity. The high degree of structural
heterogeneity results in significant variability in ganglioside expression patterns and greatly complicates
linking structure and function. Structural characterization at the site of infection is essential in
elucidating host ganglioside function in response to invading pathogens, such as Staphylococcus aureus
(S. aureus). Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables
high-specificity spatial investigation of in-tact gangliosides. Here, ganglioside structural and spatial
heterogeneity within an S. aureus-infected mouse kidney abscess was characterized. Differences in spatial
distributions were observed for gangliosides of different classes and those that differ in ceramide
chain composition and oligosaccharide-bound sialic acid. Furthermore, integrating trapped ion mobility
spectrometry (TIMS) allowed for the gas-phase separation and visualization of monosialylated ganglioside
isomers that differ in sialic acid type and position. The isomers differ in spatial distributions within
the host-pathogen interface, where molecular patterns revealed new molecular zones in the abscess previously
unidentified by traditional histology. | Katerina V. Djambazova; Katherine N. Gibson-Corley; Jeffrey A. Freiberg; Richard M. Caprioli; Eric P. Skaar; Jeffrey M. Spraggins | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655b7e24dbd7c8b54ba6ec30/original/maldi-tims-ims-reveals-ganglioside-molecular-diversity-within-murine-s-aureus-soft-tissue-abscesses.pdf |
634816f8e79b3f4017e7ac9c | 10.26434/chemrxiv-2022-rfmhk-v2 | Resolution of Electronic States in Heisenberg Cluster Models within the Unitary Group Approach | In this work ground and excited electronic states of Heisenberg cluster models, in the form of configuration interaction many-body wave functions, are characterized within the spin-adapted Graphical Unitary Group Approach framework, and relying on a novel combined unitary and symmetric group approach. Finite-size cluster models of well-defined point-group symmetry and of general local-spin Slocal ≥ 1/2 are presented, including J1–J2 triangular and tetrahedral clusters, which are often used to describe magnetic interactions in biological and bio-mimetic polynuclear transition metal clusters with unique catalytic activity, such as nitrogen fixation and photosynthesis. We show that a unique block-diagonal structure of the underlying Hamiltonian matrix in the spin-adapted basis emerges when an optimal lattice site ordering is chosen that reflects the internal symmetries of the model investigated. The block-diagonal structure is bound to the commutation relations between cumulative spin operators and the Hamiltonian operator, that in turn depend on the geometry of the cluster investigated. The many-body basis transformation, in the form of the orbital/site reordering, exposes such commutation relations. These commutation relations represent a rigorous and formal demonstration of the block-diagonal structure in Hamiltonian matrices and the compression of the corresponding spin-adapted many-body wave functions. As a direct consequence of the block-diagonal structure of the Hamiltonian matrix it is possible to selectively optimize electronic excited states without the overhead of calculating the lower-energy states by simply relying on the initial ansatz for the targeted wave function. Additionally, more compact many-body wave functions are obtained. In extreme cases, electronic states are precisely described by a single configuration state function, despite the curse of dimensionality of the corresponding Hilbert space. These findings are crucial in the electronic structure theory framework, for they offer a conceptual route towards wave functions of reduced multi-reference character, that can be optimized more easily by approximated eigensolvers and are of more facile physical interpretation. They open the way to study larger ab initio and model Hamiltonians of increasingly larger number of correlated electrons, while keeping the computational costs at their lowest. | Giovanni Li Manni; Daniel Kats; Niklas Liebermann | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634816f8e79b3f4017e7ac9c/original/resolution-of-electronic-states-in-heisenberg-cluster-models-within-the-unitary-group-approach.pdf |
60c74109842e65c0c9db1de8 | 10.26434/chemrxiv.7914212.v1 | Reversible Insertion of CO into an Aluminium–Carbon Bond | While reversible main-group mediated processes involving H2 and alkenes have been reported and studied for over a decade, no such reversible processes involving CO have been reported. In this paper, we show that a [2.2.1] aluminium metallobicycle is capable of reversibly inserting CO to form a [2.2.2] metallobicycle at 100 °C. Eyring analysis allowed determination of the Gibbs activation energy of the back-reaction, CO elimination reaction with G‡298K = 26.6 ±3.0 kcal mol-1. Computational studies reveal a highly asynchronous, but concerted, transition state for CO insertion. The coordination of CO to aluminium precedes C–C bond formation. The reversible migratory insertion reaction mimics that known for transition-metal and marks an important step forward for main group systems. | Richard Y Kong; Mark Crimmin | Theory - Computational; Kinetics and Mechanism - Organometallic Reactions; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74109842e65c0c9db1de8/original/reversible-insertion-of-co-into-an-aluminium-carbon-bond.pdf |
6762b8c6fa469535b9fa2cf9 | 10.26434/chemrxiv-2024-gmmws | The Interplay of Ion Mobility Mass Spectrometry and Computational Modelling for Structure Elucidation of Small Molecules: An Upper-Level Undergraduate Experiment | A lab-based experiment, combining ion mobility mass spectrometry (IM-MS) with computational modelling techniques for the analysis of small molecules, has been developed for use in undergraduate teaching laboratories over eight years. Students link IM-MS with computational calculations to show how their interplay can elucidate the structures of molecules chosen by the students. This experiment offers an opportunity to gain experience in a wide range of skills including experimental design, sample preparation, instrument tuning, calibration, and an initial familiarisation with computational modelling programs. The work commences with a 4-week planning stage in the first semester (2 x 6-hour days per week) where students are taught IM-MS theory and are asked to choose a set of related small molecules. The subsequent laboratory work, in the following semester, has a 16-day timeframe with each day lasting 6 hours spread across 8 weeks of a semester which can be tailored to different course requirements. Experiments herein have been conducted by groups of four senior year undergraduate students. The assessment involves pre-laboratory preparation discussions including a literature review, a group poster presentation and an individually written laboratory report. | Matthew Venables; Emily Hicks; Jake Bowden; Ferne Deakin; Millie Jones; Izni Mohd Khairi; Rosa Lawrence; Md Kholilur Rahman; James Walkden; Rachelle Black; Radhika Barchha Radia; Thomas Hoare; Ellen Liggett; Dale Stuchfield; Xudong Wang; Carl Poree; Neil Burton; Niklas Geue; Perdita Barran | Analytical Chemistry; Chemical Education; Analytical Chemistry - General; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762b8c6fa469535b9fa2cf9/original/the-interplay-of-ion-mobility-mass-spectrometry-and-computational-modelling-for-structure-elucidation-of-small-molecules-an-upper-level-undergraduate-experiment.pdf |
61c0a808d1f66221c33f42e7 | 10.26434/chemrxiv-2021-w5kz4 | Plug-and-Play Heterogeneous Catalysis Enabled by Metal–Organic Cage-Crosslinked Polymers | The immobilization of homogeneous catalysts onto solid supports to improve recyclability while maintaining catalytic efficiency is often a trial-and-error process limited by poor control of the local catalyst environment and a lack of modular strategies to append catalysts to support materials. Here, we introduce a “plug-and-play” heterogenous catalysis platform that overcomes these challenges. Our approach leverages the well-defined interiors of self-assembled Pd12L24 metal–organic cages/polyhedra (MOCs): through a simple combination of catalyst-ligands, polymeric ligands, and spacer ligands, we demonstrate facile self-assembly of a diverse range of polymer gels featuring endohedrally-catalyst-functionalized junctions. Through decoupling catalyst incorporation and environment from the physical properties of the support (polymer matrix), this simple strategy is shown to enhance the recyclability of various catalyst systems (e.g., TEMPO-catalyzed oxidation and Au(I)-catalyzed cyclization) and enable catalysis in environments where homogeneous catalyst analogs are not viable. | Christopher Brown; David Lundberg; Jessica Lamb; Denise Kleinschmidt; Yasmeen AlFaraj; M. Francesca Ottaviani; Nathan Oldenhuis; Jeremiah Johnson | Organic Chemistry; Catalysis; Polymer Science; Supramolecular Chemistry (Org.); Coordination polymers; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2021-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c0a808d1f66221c33f42e7/original/plug-and-play-heterogeneous-catalysis-enabled-by-metal-organic-cage-crosslinked-polymers.pdf |
67bc9edbfa469535b9bd0d65 | 10.26434/chemrxiv-2025-cc0dq | Unsupervised Machine Learning Prediction of Novel 1:3 Intermetallic Phase with Synthesis of TbIr3 (PuNi3-type) as Experimental Validation | Crystal structure classification of binary intermetallic structures with 1:3 stoichiometry was done with simple machine learning algorithms. The successful crystal structure segregation is attributed to the novel set of descriptors comprising both compositional and structural features. The dataset includes 97 features, and a total of 2366 reported compounds adopting six different structure types. The unsupervised learning method based on principal component analysis (PCA) followed by clustering using the K-means method was applied to cluster compounds belonging to different structure types. Using the recommendation engine, we predicted the expansion of the clusters and then identified cluster/structure-type overlap. PuNi3-type was among the clearly segregated structure types according to the unsupervised model, and a novel representative, TbIr3, was selected for experimental validation, adopting this structure. The final supervised machine learning predictions were done with PLS-DA, SVM, and XGBoost confidently predicting the novel TbIr3 to belong to the PuNi3-type with an accuracy of 96.6%, 99.8%, and 99.9% respectively. Analysis of the features reveals that the main contributing features to the AB3 crystal structure segregation are the average shortest distance count of A element, the total number of sites of B atom, and the total number of second shortest distance count of B atom. Given that the predicted PuNi3-type of the TbIr3 phase could be controversial due to the extensive study of the Tb–Ir phase diagram and the reports of the TbIr3 in two different structure types, we conducted two independent experimental structural validations to confirm the existence of the TbIr3 in PuNi3-type structure. Subsequent theoretical validation explains that Ir-Ir contacts are the primary stability factor of TbIr3 in PuNi3-type structure over other structure types. | Siddha Sethi; Arnab Dutta; Emil I. Jaffal; Nishant Yadav; Danila Shiryaev; Brian Hoang; Anirudh Machathi; Sangjoon Lee; Karabi Das; Partha Jana; Anton Oliynyk | Theoretical and Computational Chemistry; Inorganic Chemistry; Solid State Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc9edbfa469535b9bd0d65/original/unsupervised-machine-learning-prediction-of-novel-1-3-intermetallic-phase-with-synthesis-of-tb-ir3-pu-ni3-type-as-experimental-validation.pdf |
6762fa246dde43c90887d782 | 10.26434/chemrxiv-2024-jls7x-v2 | Chemically Triggered Reactive Coacervates Show Life-like Budding and Membrane Formation | Phase separated coacervates can enhance reaction kinetics and guide multi-level self-assembly mimicking early cellular evolution. In this work, we introduce ‘reactive’ complex coacervates that undergo chemically triggered self-immolative transformations directing the self-assembly of the reaction products within their matrix. These frustrated self-assemblies then evolve to show life-like properties such as budding and membrane formation. We find that the coacervate composition critically influences reaction rates, product distribution, and guides the hierarchical self-assembly. This work showcases ‘reactive’ coacervates as versatile platform to influence reaction and self-assembly pathways for controlled supramolecular synthesis and hierarchical self-organization in confined spaces. | Sudeep Koppayithodi; Nishant Singh | Organic Chemistry; Polymer Science; Combinatorial Chemistry; Supramolecular Chemistry (Org.); Polymer scaffolds; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762fa246dde43c90887d782/original/chemically-triggered-reactive-coacervates-show-life-like-budding-and-membrane-formation.pdf |
67a260526dde43c9089713b6 | 10.26434/chemrxiv-2025-hxbm5 | Power Series Representation of Reaction Rates in Chemical Kinetics and Its Physical Interpretation | This paper introduces a power series framework for modeling chemical reaction rates, offering a mathematically flexible and physically interpretable alternative to traditional power-law models. By expressing reaction rates as multivariate power series of reactant concentrations, this approach captures the contributions of multi-molecular interactions and synergistic effects, which are often neglected in conventional models. | Jia Qiu | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a260526dde43c9089713b6/original/power-series-representation-of-reaction-rates-in-chemical-kinetics-and-its-physical-interpretation.pdf |
62ff923958843b7506959a7c | 10.26434/chemrxiv-2022-c03kc-v3 | Synthesis of mono-fluoromethyl 6,5-heteroaromatic bicycles using 1,3-difluoroacetone as a cyclising reagent | The development of facile, wide scope synthetic methodologies providing access to fluorinated motifs is important in medic-inal chemistry; for our purposes, we are interested in developing fluorine-tagged compounds to investigate their utility in Huntington’s disease. Here, we describe a novel, operationally simple and mild procedure for the synthesis of mono-fluoromethyl 6,5-heteroaromatic bicycles using 1,3-difluoroacetone (DFA). The scope of the reaction was investigated, and 27 examples synthesized with yields up to 96%. | Longbin Liu; Brett Cosgrove; Cole Clissold; Karine Malagu; Mark Chambers; Celia Dominguez | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ff923958843b7506959a7c/original/synthesis-of-mono-fluoromethyl-6-5-heteroaromatic-bicycles-using-1-3-difluoroacetone-as-a-cyclising-reagent.pdf |
635afdb2ca86b81d1ac683f4 | 10.26434/chemrxiv-2022-3cj82-v2 | Overcoming the Limitations of Kolbe Coupling via Waveform-Controlled Electrosynthesis | The Kolbe reaction has seen limited applications owing to its extremely poor chemoselectivity and reliance on precious metal-based electrodes, despite its potential to be one of the workhorse reactions of organic synthesis for C–C bond formation in both discovery and process settings. Although hundreds of studies over a century aimed to improve its efficiency and selectivity, general solutions have yet to be found. Herein, an exceedingly simple solution to this long-standing challenge is presented by merely tuning the waveform employed. Thus, switching from classic direct current (DC) to rapid alternating polarity (rAP), a broad range of functional groups can now be tolerated using inexpensive and sustainable carbon-based electrodes. A variety of high-value molecules ranging from useful unnatural amino acids to promising polymer building blocks are now accessible from readily available carboxylic acids, including biomass-derived acids. The practicality of the rAP-Kolbe reaction enables facile implementation of large-scale reactions, realizing access to novel degradable polymers from biomass. Preliminary mechanistic studies implicate the role of waveform in modulating the local pH around electrodes, which in turn affects the underlying redox processes. The ease, efficiency, and chemoselectivity of the rAP-Kolbe reaction finally opens the door to the widespread mainstream adoption of this classic reaction. | Yuta Hioki; Matteo Costantini; Jeremy Griffin; Kaid Harper; Melania Prado Merini; Benedikt Nissl; Yu Kawamata; Phil Baran | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635afdb2ca86b81d1ac683f4/original/overcoming-the-limitations-of-kolbe-coupling-via-waveform-controlled-electrosynthesis.pdf |
60c74c54f96a00ad2c287772 | 10.26434/chemrxiv.11416374.v3 | Deciphering the oxygen absorption pre-edge: a caveat on its application for probing oxygen redox reactions in batteries | <div>The pre-edges of oxygen-K X-ray absorption spectra have been ubiquitous in transition metal (TM) oxide studies in various fields, especially on the fervent topic of oxygen redox states in battery electrodes. However, critical debates remain on the use of the O-K pre-edge variations upon electrochemical cycling as evidences of oxygen redox reactions, which has been a popular practice in the battery field. This study presents an investigation of the O-K pre-edge of 55 oxides covering all 3d TMs with different elements, structures and electrochemical states through combined experimental and theoretical analyses. It is shown unambiguously that the O-K pre-edge variation in battery cathodes is dominated by changing TM-d states. Furthermore, the pre-edge enables a unique opportunity to project the lowest unoccupied TM-d states onto one common energy window, leading to a summary map of the relative energy positions of the low-lying TM states, with higher TM oxidation states at lower energies, corresponding to higher electrochemical potentials. The results naturally clarify some unusual redox reactions, such as Cr<sup>3+/6+</sup>. This work provides a critical clarification on O-K pre-edge interpretation and more importantly, a benchmark database of O-K pre-edge for characterizing redox reactions in batteries and other energy materials.</div> | Subhayan Roychoudhury; Ruimin Qiao; Zengqing Zhuo; Qinghao Li; Yingchun Lyu; Jung-Hyun Kim; Jun Liu; Eungje Lee; Bryant J. Polzin; Jinghua Guo; Shishen Yan; Yongsheng Hu; Hong Li; David Prendergast; Wanli Yang | Spectroscopy (Anal. Chem.); Theory - Computational; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c54f96a00ad2c287772/original/deciphering-the-oxygen-absorption-pre-edge-a-caveat-on-its-application-for-probing-oxygen-redox-reactions-in-batteries.pdf |
60c755504c89192ad5ad4672 | 10.26434/chemrxiv.14069666.v1 | NMR for Mixture Analysis: Concentration Ordered Spectroscopy | A novel approach, concentration ordered NMR spectroscopy (CORDY), is being proposed based on the principle that the ratio of NMR peak area to its associated number of spins is proportional to the concentration of the assigned compound.CORDY generates a pseudo 2-dimensional NMR spectrum with chemical shifts in one axis and concentrations in the other, resulting both in separation and quantitation of components in complex samples. The method was validated by applying on three samples. It was demonstrated that CORDY could successfully provide separation up to two orders of magnitude in concentration dimension, for the samples used in current study.<br /> | Bin Yuan; Zhiming Zhou; Bin Jiang; Ghulam Mustafa Kamal; Xu Zhang; Conggang Li; Xin Zhou; Maili Liu | Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755504c89192ad5ad4672/original/nmr-for-mixture-analysis-concentration-ordered-spectroscopy.pdf |
674ef8bf7be152b1d0cace6b | 10.26434/chemrxiv-2024-thmt9 | Ideal Molecular Sieving with a Dense MOF for Helium Upgrading with Highly Diffusion Selective Mixed Matrix Membranes | Helium is one of the most critical resources of our planet, as it is a finite resource, cannot be produced from radioactive decay in sufficient amounts and escapes our atmosphere, while being extraordinarily important for high tech applications in research and medicine. We demonstrate a concept of using the “dense” metal-organic framework (MOF) MIL-116(Ga) as a molecular sieve specifically allowing diffusion of He. Incorporating up to 20 wt.% MIL-116(Ga) into polysulfone, a chemically stable, mechanically robust, and commercially available polymer, high performance mixed matrix membranes were fabricated and tested in gas permeation. The membranes reach He permeabilities up to 37.4 Barrer and He/CH4 selectivity of 1190, mimicking process conditions with He concentration of 4 % in CH4. With increasing filler content, permeability of He increases, while CH4 permeability decreases. Microstructural analysis of the MIL-116(Ga) reveals that the crystals grew into druse-like hollow crystals, highly beneficial for fast He permeability. CH4, N2 and CO2 cannot enter the crystal, as proven by sorption experiments, providing high diffusional selectivity. Furthermore, polymer filler interactions are investigated by scanning electron microscopy and energy dispersive x-ray spectroscopy. We benchmarked the performance to existing composites and polymers, where MIL-116(Ga)-formate stands out with extraordinary membrane performance. | Ayisha Komal; Laura Calderón Rodríguez; Oksana Smirnova; Eren Grossmann; Aparna Binu Varghese; Karen Marlenne Garcia Alvarez; Andreas Schneemann; Thomas Hoyer; Ralf Wyrwa; Felix Helmut Schacher; Alexander Knebel | Physical Chemistry; Materials Science; Composites; Physical and Chemical Processes; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674ef8bf7be152b1d0cace6b/original/ideal-molecular-sieving-with-a-dense-mof-for-helium-upgrading-with-highly-diffusion-selective-mixed-matrix-membranes.pdf |
66280954418a5379b084d06e | 10.26434/chemrxiv-2024-20kpv | CHARMM Molecular Simulation Observations of Carbonaceous Materials as Possible Templates for Prebiotic Nucleic Acid Oligomer Formation | This research utilizes CHARMM molecular simulations for the purposes of an initial qualitative observational study of diamond-like carbon and related carbonaceous substrates as potential templates for the abiotic formation of RNA polymers,. While a number of research group have looked at nanodiamond, graphite and other carbon and non-carbon-based materials (especially clays) as possible solid templates for early life, we propose that diamond-like carbon (DLC, also known as amorphous diamond or aD) may have been a plausible ideal template. This is due largely to the fact that DLC is a heterogeneous material, essentially an aggregation of various constituent carbon species (for instance, graphene, graphite, CNT, etc.), depending on formation conditions. Further, DLC exhibits a range of superlative material properties shared by diamond and graphitic materials It possesses high thermal diffusivity and conductivity along all planes due to its inherent anisotropism. Internal and surface structure variability could have played a crucial role in facilitating the molecular interactions that accelerated the abiotic formation of RNA oligomers, potentially supporting the RNA World hypothesis. Significant outside energy is not needed to enable oligomer formation. Entropy, in the form of heat, is a driving force that provides conditions necessary for oligomer formation. To reduce computational and financial costs, we investigate artificial intelligence-driven methodologies to inform optimal MD input parameters with the goal of generating key qualitative endpoints. As MD simulations are extremely computationally expensive due to the large quantity of electronegativity and force field interactions for trajectory calculations, we initially used a lightweight MD system combined with a transformer model to better predict the likelihood of achieving collisions between target molecules, and thus increase the chance of observing exemplar endpoints. Various key endpoints were observed, including Van der Waals oligomer-template attachment, translocation/rotation potentially leading to more complex configurations, quasi-elongation and bridging, as well as detachment). The observations of these endpoints suggest that carbonaceous materials such as DLC could plausibly have served as templates for the formation of early nucleic acid oligomers. Further simulations and physical experiments are needed to confirm these results, and to develop a supporting statistical model. | Anna Du; Barnas Monteith | Theoretical and Computational Chemistry; Catalysis; Earth, Space, and Environmental Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66280954418a5379b084d06e/original/charmm-molecular-simulation-observations-of-carbonaceous-materials-as-possible-templates-for-prebiotic-nucleic-acid-oligomer-formation.pdf |
679a770afa469535b956944b | 10.26434/chemrxiv-2025-gwx6v | Xylopyranose ring‐opening by single and double proton
transfers under pyrolysis conditions | This study unveils a new transition state (TS) leading to the acyclic product via synchronous double proton transfer by automatedly exploring the potential energy surface of β‐D‐xylopyranose under pyrolysis conditions. Quantum chemistry methods with multi‐path canonical variational transition state theory, show that the standard activation enthalpy of the new TS (46.4 kcal mol–1) is 1.5 kcal mol–1 lower than that of the well‐established channel; however, the latter’s rate constant (4.36 × 10–2 ‐9.96 × 101 s–1 ) is higher in the 673.15‐873.15 K pyrolytic interval by a factor of 5‐8. This gap narrows to a factor of 2 within 320‐400 K, signifying that the new TS can potentially impact the acyclic product production in this low‐temperature range. This is particularly relevant for β‐D‐xylopyranose trimers, as the interior unit bears different substituents at the C1 and C3 positions. | Jacopo Lupi; Bernardo Ballotta; Leandro Ayarde-Henríquez; Stephen Dooley | Physical Chemistry; Materials Science; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679a770afa469535b956944b/original/xylopyranose-ring-opening-by-single-and-double-proton-transfers-under-pyrolysis-conditions.pdf |
60c75540f96a00cd7b288804 | 10.26434/chemrxiv.14058269.v1 | Total Synthesis, Isolation, Surfactant Properties, and Biological Evaluation of Ananatosides and Related Macrodilactone-Containing Rhamnolipids | <p>Rhamnolipids are a specific class of microbial
surfactants, which hold great biotechnological and therapeutic potential.
However, their exploitation at the industrial level is hampered because they
are mainly produced by the opportunistic pathogen <i>Pseudomonas aeruginosa</i>. The non-human pathogenic bacterium <i>Pantoea ananatis</i> is an alternative
producer of rhamnolipid-like metabolites containing glucose instead of rhamnose
residues. Herein, we present the isolation, structural characterization, and
total synthesis of ananatoside A, a 15-membered macrodilactone-containing
glucolipid, and ananatoside B, its open-chain congener, from organic extracts
of <i>P. ananatis</i>. Ananatoside A was
synthesized through three alternative pathways involving either an intramolecular
glycosylation, a chemical macrolactonization or a direct enzymatic
transformation from ananatoside B. A series of diasteroisomerically pure (1®2), (1®3), and (1®4)-macrolactonized rhamnolipids were also
synthesized through intramolecular glycosylation and their anomeric
configurations as well as ring conformations were solved using molecular
modeling in tandem with NMR studies. We show that ananatoside B is a more
potent surfactant than its macrolide counterpart. We present evidence that
macrolactonization of rhamnolipids enhances their cytotoxic and hemolytic
potential, pointing towards a mechanism involving the formation of pores into
the lipidic cell membrane. Lastly, we demonstrate that ananatoside A and
ananatoside B as well as synthetic macrolactonized rhamnolipids can be
perceived by the plant immune system, and that this sensing is more pronounced
for a macrolide featuring a rhamnose moiety in its native <sup>1</sup><i>C</i><sub>4</sub> conformation. Altogether
our results prove that macrolactonization of glycolipids can dramatically
interfere with their surfactant properties and biological activity.</p> | Maude Cloutier; Marie-Joëlle Prévost; Serge Lavoie; Thomas Feroldi; Marianne Piochon; Marie-Christine Groleau; Jean Legault; Sandra Villaume; Jérôme Crouzet; Stéphan Dorey; Mayri Alejandra Dìaz De Rienzo; Eric Déziel; Charles Gauthier | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75540f96a00cd7b288804/original/total-synthesis-isolation-surfactant-properties-and-biological-evaluation-of-ananatosides-and-related-macrodilactone-containing-rhamnolipids.pdf |
60c759ce842e658065db4aa0 | 10.26434/chemrxiv.12728738.v3 | Gas Adsorption in Amorphous Porous Boron Oxynitride: Grand Canonical Monte Carlo Simulations and Experimental Determination | <p>Note: The authors realised errors in the calculations related to this study, which impact the conclusions of the work previously posted.</p> | Ravi Shankar; Sofia Marchesini; Erich A. Muller; Camille Petit | Ceramics | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759ce842e658065db4aa0/original/gas-adsorption-in-amorphous-porous-boron-oxynitride-grand-canonical-monte-carlo-simulations-and-experimental-determination.pdf |
63808cfa6b4e812a6e7f12ed | 10.26434/chemrxiv-2022-b1v2c | eFluorination using cheap and readily available tetrafluoroborate salts | A new practical electrochemical method for the rapid, safe, and mild synthesis of tertiary hindered alkyl fluorides from easily accessed carboxylic acids has been developed without the need for hydrofluoric acid derivatives or non-glass reactors. In this anodic fluorination, collidinium tetrafluoroborate (Coll·HBF4) is advantageous as a supporting electrolyte and fluoride donor. A wide range of functional groups has been shown to be compatible with this new methodology. The possibility of scale-up using flow electrochemistry has also been demonstrated, thus representing a viable procedure for tertiary fluorination on a larger scale. | Kevin Lam; Matthew Leech; Dmitrii Nagornii; Jamie Walsh; Cyrille Kiaku; Darren Poole; Joseph Mason; Iain Goodall; Perry Devo | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63808cfa6b4e812a6e7f12ed/original/e-fluorination-using-cheap-and-readily-available-tetrafluoroborate-salts.pdf |
6798c84581d2151a0247e958 | 10.26434/chemrxiv-2025-h3vxn | Tailoring Peptide Coacervates for Advanced Biotechnological Applications: Enhancing Control, Encapsulation, and Antioxidant Properties | The increasing interest in protein and peptide coacervates is accompanied by the development of various applications, from drug delivery to biosensor preparation. However, the impact of peptide end groups and charges on the coacervation remains unclear. For this purpose, we designed four peptide derivatives with varying end groups and net charges. These inherently fluorescent peptides readily formed coacervates in solution or during evaporation. The ability to control the coacervation process, the coacervate’s appearance, and the encapsulation capabilities were thoroughly investigated. The coacervates displayed significant antioxidant properties, protecting the encapsulated material. Additionally, control of the deposition of the coacervates on surfaces was achieved. These abilities highlight the potential of these coacervates in biotechnological applications, including biosensor development and delivery of compounds such as drugs and dietary supplements. Exploiting the dynamic characteristics of coacervates with the unique properties of these peptides underscores their practical advantages. | Daniel Boas; Meital Reches | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6798c84581d2151a0247e958/original/tailoring-peptide-coacervates-for-advanced-biotechnological-applications-enhancing-control-encapsulation-and-antioxidant-properties.pdf |
639d9158518c16aa152ee95b | 10.26434/chemrxiv-2022-mxd0c-v2 | Alchemical osmostat for MC simulation: Sampling aqueous electrolyte solution in open systems | Molecular simulations involving electrolytes are usually performed at a fixed amount of salt ions in the simulation box, reproducing macroscopic concentration. Although this statement is valid in the bulk, the concentration of an electrolyte confined in a nanoporous materials such as MOFs or zeolites is greatly affected and remains a priori unknown. The nanoporous material in equilibrium with the bulk electrolyte exchange water and ions at a given chemical potential in the semigrand canonical ensemble that must be calibrated in order to determine the concentration in the nanoporous material. In this work, we propose an algorithm based on non-equilibrium candidate Monte Carlo (NCMC) moves to ultimately perform MC simulations in contact with a saline reservoir. First, we adapt the Widom insertion technique to calibrate the chemical potential by alchemically transmuting water molecules into ions by using NCMC moves. The chemical potential defines a Monte carlo osmostat in the semigrand constant volume and temperature ensemble to be added in a Monte Carlo simulation where the number of ions fluctuates. In order to validate the method, we adapted the NCMC move to determine the free energy of water solvation and subsequently explore thermodynamics of electrolyte solvation at infinite dilution in water. Finally, we implemented the osmostat in MC simulations initialized with bulk water that are driven towards electrolytes of similar concencentration as the saline reservoir. Our results demonstrate that alchemical osmostat MC simulation is a promising tool for use to sample electrolyte insertion in nanoporous materials. | Ambroise De Izarra; François-Xavier Coudert; Alain Fuchs; Anne Boutin | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639d9158518c16aa152ee95b/original/alchemical-osmostat-for-mc-simulation-sampling-aqueous-electrolyte-solution-in-open-systems.pdf |
60c755ad567dfe0f83ec6324 | 10.26434/chemrxiv.14135624.v1 | Self-Assembly and Photophysical Studies of an Unusual Red Colored Dye Which Show Green Fluorescence in Cell Imaging | <p>We
report for the very first time self-assembly of a red color dye 7-Amino-6h-anthra[9,1-cd][1,2]thiazol-6-one
(<b>AAT</b>),its photophysical properties and its applications in cell imaging<b>.</b>Interestingly,
<b>AAT </b>show intense red colour in visible light while it shows the orange
colour fluorescence under UV light @312nm.Surprisingly, when this dye was used as
cell imaging agent it revealed only green fluorescence inside cells and not red.
Hence, the photophysical properties of this dye was very intriguing. Further,
when self-assembling properties of this dye was examined it revealed formation
of tree like branched structures which appeared red both under green and red
filter which was again an unexpected result..Interestingly <b>AAT</b>
self-assembly also show morphological transition and the branched tree like
structures changes to straight fibres as the solvent is changed from DMSO to
THF. Hence, the results of self-assembly and cell imaging were contrary to each
other and the photophysical properties of this
dye is very unusual as compared to conventional dyes. Our future
endeavours willaim to understand this anomalous behaviour in greater details in
future through various biophysical assays.</p> | Vivekshinh Kshtriya; Bharti Koshti; Ashadul Haque; Ankit Gangrade; Ramesh Singh; Khashti Ballabh Joshi; Sujoy Bandyopadhyay; Dhiraj Bhatia; Nidhi Gour | Biochemical Analysis; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755ad567dfe0f83ec6324/original/self-assembly-and-photophysical-studies-of-an-unusual-red-colored-dye-which-show-green-fluorescence-in-cell-imaging.pdf |
67d3dd8c81d2151a0255fb11 | 10.26434/chemrxiv-2025-pjb6q-v2 | Photoregulation of the Chiral Nematic Phase by Using a Hexa-Arylazopyrazole-Substituted Co(III) Complex | A photoresponsive hexa-arylazopyrazole-substituted tris(β-diketonato) Co(III) complexes was synthesized and the Λ- or Δ-enantiomers were isolated. The complex shows reversible E/Z isomerization using UV (λmax = 365 nm) or visible light (λmax = 520 nm) respectively. Using the Co(III) complex as a dopant in the commercially available liquid crystal N-(4-methoxybenzylidene)-4-butylaniline (MBBA), the chiral nematic phase can be induced. Upon photoisomerization, the helical pitch of the doped system can be reversibly modulated, leading to very high changes in terms of HTP values. Corresponding to this change the HTP value of the doped liquid crystals varied between 615 µm-1 and 346 µm-1 or between - 563 µm-1 and - 352 µm-1 at 30 °C, where the positive or negative sign corresponds to the P and M helix, respectively. Thus, the Co(III) complex possesses both high HTP values and large changes upon photoisomerization which enables induction of the chiral nematic phase with low dopant concentrations, which can be useful for the development of novel optical applications. | Hoan Quan Tran; Shinichiro Kawano; Jun Yoshida; Kentaro Tanaka; Bart Jan Ravoo | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d3dd8c81d2151a0255fb11/original/photoregulation-of-the-chiral-nematic-phase-by-using-a-hexa-arylazopyrazole-substituted-co-iii-complex.pdf |
627d215aa42e9c58183e3680 | 10.26434/chemrxiv-2022-pgvsc | Micro-flow Size-Exclusion Chromatography for enhanced native Mass Spectrometry of proteins and protein complexes | Native Size-exclusion chromatography (SEC) employing aqueous mobile phases with volatile salts at neutral pH combined with native mass spectrometry (nMS) is a useful tool for the characterization of proteins in their native state. However, in many cases the conditions needed to realize the hyphenation of SEC with MS require relative high activation energy and therefore hinder the analysis of labile protein complexes.
In this work, we are investigating the advantages of narrow SEC columns (1 mm internal diameter) operated at 15 μL/min flow rates coupled directly to nMS for the characterization of proteins, labile protein complexes and their higher-order structures (HOS). Reducing the flow rate, allowed for a significant increase of the MS sensitivity and ionization efficiency, facilitating detection of low-abundant impurities and HOS (up to the limit of the Orbitrap-MS used, i.e. 230 kDa). More-efficient solvent evaporation could be achieved, allowing using softer MS conditions (e.g. lower gas temperature, lower activation energy) that ensured (little or) no structural alterations or denaturation of the proteins and their HOS during their transfer to the gas phase. Furthermore, high-ionic-strength conditions of volatile salts (200-400 mM), are often necessary to ensure (almost) interaction-free SEC analysis of proteins, such as antibodies (mAbs). With this approach the salt tolerance of the MS was much improved. Because of the reduced column dimensions, band broadening effects resulting from the injection volume became more critical. At high injection volumes (exceeding 3% of the column volume) of more dilute samples, the peak shape and width was affected. Therefore, a new set-up was developed to pre-concentrate the injected proteins on an anion and cation-exchange mixed bed trap column prior to SEC-nMS analysis. This “trap-and-elute” set-up was able to eliminate adverse injection-volume effects in SEC and provide additional desalting, while improving MS detection limits.
| Iro Konstantina Ventouri; Sharene Veelders; Marta Passamonti; Patrick Endres; Regina Roemling; Peter J. Schoenmakers; Govert W. Somsen; Rob Haselberg; Andrea F.G. Gargano | Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627d215aa42e9c58183e3680/original/micro-flow-size-exclusion-chromatography-for-enhanced-native-mass-spectrometry-of-proteins-and-protein-complexes.pdf |
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