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62bcb67abe884bcd82f54d88 | 10.26434/chemrxiv-2022-x76g3 | Substituent effects in iron porphyrin catalysts for the hydrogen evolution reaction | For a future hydrogen economy, non precious metal catalysts for the water splitting reactions are needed that can be implemented on a global scale. MNC catalysts with MN4 active sites show promising performance, but an optimization rooted in structure property relationships has been hampered by their low structural definition. Porphyrin model complexes are studied to transfer insights from well-defined molecules to MNC systems. This work combines experiment and theory to evaluate the influence of porphin substituents on the electronic and electrocatalytic properties of MN4 centers with respect to the hydrogen evolution reaction (HER) in aqueous electrolyte. We found that the choice of substituent affects their utilization on the carbon support and their electrocatalytic performance. We propose an HER mechanism for supported iron porphyrin complexes involving a [FeII(P▪)]- radical anion intermediate, in which a porphinic nitrogen atom acts as an internal base. While this work focuses on the HER, the limited influence of a simultaneous interaction with the support and an aqueous electrolyte will likely be transferrable to other catalytic applications. | Nils Heppe; Charlotte Gallenkamp; Stephen Paul; Nicole Segura-Salas; Niklas von Rhein; Bernhard Kaiser; Wolfram Jaegermann; Atefeh Jafari; Ilya Sergeev; Vera Krewald; Ulrike I. Kramm | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Small Molecule Activation (Inorg.); Heterogeneous Catalysis; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bcb67abe884bcd82f54d88/original/substituent-effects-in-iron-porphyrin-catalysts-for-the-hydrogen-evolution-reaction.pdf |
622cfe2f835f773b77003bac | 10.26434/chemrxiv-2022-vs1t1 | Fabrication of Boehmite Nanofiber Aerogels by a Phosphate Gelation Process for Optical Applications | A transparent wet gel was obtained in a few minutes at room temperature by adding an aqueous phosphoric acid solution of appropriate concentration to boehmite nanofiber sol. After room temperature aging and supercritical carbon dioxide drying, low bulk density aerogels with visible light transmittance of over 90 % at 10 mm thickness were obtained. These aerogels exhibited superior mechanical properties and visible light transmittance, while having the same bulk density as the samples obtained by a conventional gelation process using a base. The optical properties of the aerogel were hardly lost even at high humidity because the phosphorylation of the skeletal surface reduced the percentage of hydroxyl groups. The three-dimensional imaging inspection of the exterior and interior of the aerogel and the laser processing method were also demonstrated. The various developments reported in this paper make aerogels with ultralow bulk density and high visible light transmission even more promising for applications in the physical field. | Gen Hayase; Keita Yamazaki; Tetsuya Kodaira | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622cfe2f835f773b77003bac/original/fabrication-of-boehmite-nanofiber-aerogels-by-a-phosphate-gelation-process-for-optical-applications.pdf |
6656038321291e5d1d7b0102 | 10.26434/chemrxiv-2024-j9rdv | Irreversible Inhibition of DNMT3A by an N-Mustard Analog of S-Adenosyl-L-methionine | DNA methylation, an important epigenetic modification, is catalyzed by DNA methyltransferases and is essential in the regulation of gene expression. Here, the utility of an N-mustard analog designed to mimic the native methyl donor, S-adenosyl-L-methionine (SAM), was explored with the DNA methyltransferase 3A catalytic domain (DNMT3AC). In lieu of the expected analog transfer to DNA, methyltransferase activity was instead inhibited in a concentration dependent manner. Further investigation into the mechanism of analog inhibition did not reveal a typical competitive mechanism. Instead, mass spectrometry analysis provided direct evidence of two cysteine residues in the SAM binding site covalently modified by the SAM analog and confirmed its’ function as an irreversible inhibitor of DNMT3A. | Nichanun Sirasunthorn; Isabelle Roseto; Lindsay Pecor; Lindsay Comstock | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6656038321291e5d1d7b0102/original/irreversible-inhibition-of-dnmt3a-by-an-n-mustard-analog-of-s-adenosyl-l-methionine.pdf |
67536de3085116a1339bcc81 | 10.26434/chemrxiv-2024-rzqmh | A Machine-Learned "Chemical Intuition" to Overcome Spectroscopic Data Scarcity | Machine learning models for predicting IR spectra of molecular ions (infrared ion spectroscopy, IRIS) have yet to be reported owing to the relatively sparse experimental datasets available. To overcome this limitation, we employ the Graphormer-IR model for neutral molecules as a knowledgeable starting point, then employ transfer learning to refine the model to predict the spectra of gaseous ions. A library of 10,336 computed spectra and a small dataset of 312 experimental IRIS spectra is used for model fine-tuning. Nonspecific global graph encodings that describe the molecular charge state (i.e., (de)protonation, sodiation), combined with an additional transfer learning step that considers computed spectra for ions, improved model performance. The resulting Graphormer-IRIS model yields spectra that are 21% more accurate than those produced by commonly employed DFT quantum chemical models, while capturing subtle phenomena such as spectral red-shifts due to sodiation. Dimensionality reduction of model embeddings demonstrate derived “chemical intuition” of functional groups, trends in molecular electron density, and the location of charge sites. Our approach will enable fast IRIS predictions for determining the structures of unknown small molecule analytes (e.g., metabolites, lipids) present in biological samples. | Cailum M. K. Stienstra; Teun van Wieringen; Liam Hebert; Patrick Thomas; Kas J. Houthuijs; Giel Berden; Jos Oomens; Jonathan Martens; W. Scott Hopkins | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Artificial Intelligence; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67536de3085116a1339bcc81/original/a-machine-learned-chemical-intuition-to-overcome-spectroscopic-data-scarcity.pdf |
61ea79984a603d5a6d37e575 | 10.26434/chemrxiv-2022-xg9bd | Importance of Molecular Symmetry for Enantiomeric Excess Recognition by NMR | Recently prochiral solvating agents (pro-CSA) became a spotlight for the detection of enantiopurity by NMR. Chemical shift non-equivalency in achiral hosts introduced by the presence of chiral guest yields observable resonance signal splitting correlating to the enantiomeric excess (e.e.). In this work, symmetry is our lens to explain porphyrin-based supramolecular receptors’ activity in a chiral environment. Based on extensive NMR analyses of the atropisomeric receptors, host symmetry is shown to be affected by porphyrin nonplanarity and further desymmetrized in the presence of a chiral guest. We have formulated a simple, symmetry-based protocol that can be used to identify pro-CSA candidates. As such, the exposed porphyrin inner core (N–H), with its strong hydrogen bond abilities, for the first time, has been exploited in enantiomeric composition analysis. Our approach in e.e. detection by N–H signals appearing in a previously underutilized region of the spectrum (below 0 ppm.), shows chemical shifts (the e.e. dependent splitting) three times more sensitive to enantiomeric compositions than previously reported systems. The findings are complemented by extensive 2D NMR studies, including the first reporting of e.e. dependent in non-hydrogen NMR, and supporting by density functional theory (DFT) calculations. | Karolis Norvaisa; John E. O'Brien; Irina Osadchuk; Brendan Twamley; Victor Borovkov; Mathias O. Senge | Organic Chemistry; Analytical Chemistry; Stereochemistry; Spectroscopy (Anal. Chem.); Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2022-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ea79984a603d5a6d37e575/original/importance-of-molecular-symmetry-for-enantiomeric-excess-recognition-by-nmr.pdf |
60c73f5dee301cb154c788ba | 10.26434/chemrxiv.7245167.v2 | A Concise Total Synthesis of (±)-Vibralactone | Disclosed is a four-step synthesis of (<i>±</i>)-vibralactone, a biologically active terpenoid natural product. A key photochemical valence isomerization of 3-prenyl-pyran-2-one forges both the all-carbon quaternary stereocenter and the β-lactone at an early stage. Cyclopropanation of the resulting bicyclic β-lactone furnishes a strained housane structure that is converted to the natural product through a sequential ring expansion and reduction strategy. Our concise and modular route to the natural product provides the shortest total synthesis of (<i>±</i>)-vibralactone reported to date. <br /> | Sepand Nistanaki; Luke A. Boralsky; Roy D. Pan; Hosea Nelson | Natural Products; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5dee301cb154c788ba/original/a-concise-total-synthesis-of-vibralactone.pdf |
60c74da8567dfef3f5ec53ad | 10.26434/chemrxiv.12646244.v1 | Exploring the Use of Gas Chromatography Coupled to Chemical Ionization Mass Spectrometry (GC-CI-MS) for Stable Isotope Labelling in Metabolomics | <p>Isotopic labelling experiments have been utterly
valuable to monitor the flux of metabolic reactions in biological systems,
which is crucial to understand homeostatic alterations with disease.
Experimental determination of metabolic fluxes can be inferred from a
characteristic rearrangement of stable isotope tracers (e.g., 13C or 15N) that
can be detected by mass spectrometry (MS). Metabolites measured are generally
members of well-known metabolic pathways, and most of them can be detected using
both gas chromatography (GC)-MS and liquid chromatography (LC)-MS. In here, we
show that GC methods coupled to chemical ionization (CI) MS have a clear
advantage over alternative methodologies due to GC’s superior chromatography
separation efficiency and the fact that CI is a soft ionization technique that
yields identifiable protonated molecular ion peaks. We tested diverse GC-CI-MS
setups, including methane and isobutane reagent gases, triple quadrupole (QqQ)
MS in SIM mode or selected ion clusters using optimized narrow-windows (~10 Da)
in scan mode, and standard full scan methods using high resolution GC-(q)TOF
and GC-Orbitrap systems. Isobutane as reagent gas in combination with both low-resolution
(LR) and high-resolution (HR) MS showed the best performance, enabling precise
detection of isotopologues in most metabolic intermediates of central carbon
metabolism. Finally, with the aim of overcoming manual operations, we developed
an R-based tool called isoSCAN that automatically quantifies all isotopologues
of intermediate metabolites of glycolysis, TCA cycle, amino acids, pentose
phosphate pathway and urea cycle from LRMS and HRMS data.</p> | Jordi Capellades; Alexandra Junza; Sara Samino; Maria Vinaixa; Oscar Yanes | Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74da8567dfef3f5ec53ad/original/exploring-the-use-of-gas-chromatography-coupled-to-chemical-ionization-mass-spectrometry-gc-ci-ms-for-stable-isotope-labelling-in-metabolomics.pdf |
60c755fdbdbb893a20a3a92e | 10.26434/chemrxiv.14189012.v1 | Graphene-Oxide Based Fluorescent DNA Aptasensor for Liver Cancer Diagnosis and Therapy | Graphene-oxide based
fluorescent DNA aptasensors for the <i>in vivo </i>application remain a challenging task. We demonstrate for the first time such a nanomaterial for <i>in vivo</i> diagnosis and
therapy of liver tumor with good biocompatibility and high selectivity. This DNA nanomaterial
comprising of
DNA tetrahedron and aptamers, aggregation-induced emission luminogen (AIEgens)
and antitumor drug doxorubicin,
is fabricated and attached on
GO surface. Additionally, this GO-based fluorescent DNA nanodevice is
also constructed by using microfluidic chip for liver
tumor cell screening. | Ke Ma; Wei Xie; Wei Liu; Lei Wang; Dong Wang; Ben Zhong Tang | Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755fdbdbb893a20a3a92e/original/graphene-oxide-based-fluorescent-dna-aptasensor-for-liver-cancer-diagnosis-and-therapy.pdf |
66edb5b951558a15ef98542f | 10.26434/chemrxiv-2024-3r6z4 | Ni-Catalyzed Enantioselective Desymmetrization: Development of Divergent Acyl and Decarbonylative Cross-Coupling Reactions | Ni-catalyzed asymmetric reductive cross-coupling reactions provide rapid and modular access to enantioenriched building blocks from simple electrophile precursors. Reductive coupling reactions that can diverge through a common organometallic intermediate to two distinct families of enantioenriched products are particularly versatile but underdeveloped. Here, we describe the development of a bis(oxazoline) ligand that enables the desymmetrization of meso-anhydrides. When secondary benzylic electrophiles are employed, doubly stereoselective acyl cross-coupling proceeds to give ketone products with catalyst control over three newly formed stereogenic centers. Alternatively, use of primary alkyl halides in the presence of an additional halogen atom transfer catalyst results in decarbonylative alkylation to give enantioenriched beta-alkyl acids. Analysis of reaction rates for a range of both catalysts and substrates supports the notion that tuning the different electrophile activation steps with the two catalysts is required for enhanced reaction performance. These studies illustrate how reaction design can diverge a common Ni-acyl intermediate to either acyl or decarbonylative coupling products and highlight how dual ligand systems can be used to engage unactivated alkyl halides in Ni-catalyzed asymmetric reductive coupling. | Ángel Hernández-Mejías; Alexander Shimozono; Avijit Hazra; Sven Richter; Zhengjia Tong; Neil Langille; Kyle Quasdorf; Andrew Parsons; Matthew Sigman; Sarah Reisman | Organic Chemistry; Catalysis; Organometallic Chemistry; Stereochemistry; Ligand Design; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66edb5b951558a15ef98542f/original/ni-catalyzed-enantioselective-desymmetrization-development-of-divergent-acyl-and-decarbonylative-cross-coupling-reactions.pdf |
64382b6808c86922ffec7abe | 10.26434/chemrxiv-2023-sc931-v2 | Time-frequency signatures of electronic coherence of colloidal CdSe quantum dot dimer assemblies probed at room temperature by 2-dimensional electronic spectroscopy
| Electronic coherence signatures can be directly identified in the time-frequency maps measured in 2 dimensional spectroscopy (2DES). We demonstrate the theory and discuss the advantages of this approach by a detailed application to the fast femtosecond beatings of a wide variety of electronic coherences in dimers of size-dispersed (8%) 3nm quantum dots (QDs). The observed and computed results can be consistently characterized directly in the time-frequency domain by probing the polarization in a 2DES set-up. Experimental and computed time-frequency maps are found in very good agreement and several electronic coherences are characterized at room temperature in solution before extensive dephasing due to the size-dispersion kicks in. As compared to the frequency-frequency maps that are commonly used in 2DES, the time-frequency maps allow for exploiting electronic coherences without additional post processing and with fewer 2DES measurements. Towards quantum technology applications, we also report on the modeling of the time-frequency photocurrent response of these electronic coherences, which opens the way to integrating QD devices with classical architectures thereby enhancing the quantum advantage of such technologies for parallel information processing at room temperature. | James Hamilton; Edoardo Amarotti; Carlo Dibenedetto; Marinella Striccoli; Raphael Levine; Elisabetta Collini; Francoise Remacle | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanodevices; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64382b6808c86922ffec7abe/original/time-frequency-signatures-of-electronic-coherence-of-colloidal-cd-se-quantum-dot-dimer-assemblies-probed-at-room-temperature-by-2-dimensional-electronic-spectroscopy.pdf |
613814f8fc08e30cce8d8c1a | 10.26434/chemrxiv-2021-qtq8d | InFrag: Using Attribution-based Explainability to Guide Deep Molecular Optimization | The recently proposed Genetic expert guided learning (GEGL) framework has demonstrated impressive performances on several \textit{de novo} molecular design tasks. Despite the displayed state-of-the art results, the proposed system relies on an expert-designed Genetic expert. Although hand-crafted experts allow to navigate the chemical space efficiently, designing such experts requires a significant amount of effort and might contain inherent biases which can potentially slow down convergence or even lead to sub-optimal solutions. In this research, we propose a novel genetic expert named \textit{InFrag} which is free of design rules and can generate new molecules by combining promising molecular fragments. Fragments are obtained by using an additional graph convolutional neural network which computes attributions for each atom for a given molecule. Molecular substructures which contribute positively to the task score are kept and combined to propose novel molecules. We experimentally demonstrate that, within the GEGL framework, our proposed attribution-based genetic expert is either competitive or outperforms the original expert-designed genetic expert on goal-directed optimization tasks. When limiting the number of optimization rounds to one and three rounds, a performance increase of approximately 43% and 20% respectively is observed compared to the baseline genetic expert. Furthermore, we empirically show that combining several experts that share a fixed sampling budget at each optimization round generally improves or maintains the overall performance of the framework. | Pierre Wüthrich; Jun Jin Choong; Shinya Yuki | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; 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/613814f8fc08e30cce8d8c1a/original/in-frag-using-attribution-based-explainability-to-guide-deep-molecular-optimization.pdf |
60c741af842e65485cdb1f60 | 10.26434/chemrxiv.8118377.v1 | Multiscale Electrolyte Transport Simulations for Lithium Ion Batteries | Establishing a link between atomistic processes and battery cell behavior is a major challenge for lithium ion batteries. Focusing on liquid electrolytes, we describe parameter-free molecular dynamics predictions of their mass and charge transport properties. The simulations agree quantitatively with experiments across the full range of relevant ion concentrations and for different electrolyte compositions. We introduce a simple analytic form to describe the transport properties. Our results are used in an extended Newman electrochemical model, including a cell temperature prediction. This multi-scale approach provides quantitative agreement between calculated and measured discharge voltage of a battery and enables the computational optimization of the electrolyte formulation. | Felix Hanke; Nils Modrow; Reinier Akkermans; Ivan Korotkin; Felix Mocanu; Verena Neufeld; Max Veit | Solid State Chemistry; Computational Chemistry and Modeling; Energy Storage; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741af842e65485cdb1f60/original/multiscale-electrolyte-transport-simulations-for-lithium-ion-batteries.pdf |
64d4bd20dfabaf06ff0a8e5a | 10.26434/chemrxiv-2023-2kdbk-v4 | Intramolecular electron transfer in multi-redox systems based on cyclic [3]spirobifluorenylene compound | Cyclic [3]spirobifluorenylene with bulky alkyl groups at the ends (1) was designed and synthesized to investigate the electron transfer phenomena in a -conjugated system including orthogonal -conjugated chains. The three bifluorenyl units in 1 are conjugated to each other via spiro-conjugation, resulting in the splitting of the HOMO levels to a small extent. Therefore, the SOMO–HOMO gap of the radical cation species is small, which is considered to allow the facile intramolecular electron transfer. The electronic properties of 1 and its partial structures were characterized by absorption and fluorescence measurements and electrochemical analysis. From the electrochemical oxidation, the interchain Coulombic repulsion was observed. In the TD-DFT calculations for the radical cation species of 1, the geometry-featured interchain electronic transitions were visualized by NTO calculations. The radical cation species of 1 generated by chemical oxidation with SbCl5 exhibited a broadened and lower-energy shifted NIR absorption band compared to those of its partial structures. Considering the results of the TD-DFT calculations, the NIR band of the radical cation of 1 was attributed to the intramolecular electron transfer processes among the bifluorenyl units in the macrocycle. ESR experiments also indicated the delocalization of a spin of 1·+ in the whole molecule via hole hopping. This work demonstrates the usefulness of spiro-conjugation as a bridging unit in molecular wires to facilitate smooth electron transfer. | Tomoya Imai; Daisuke Sakamaki; Shinobu Aoyagi; Toru Amaya | Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d4bd20dfabaf06ff0a8e5a/original/intramolecular-electron-transfer-in-multi-redox-systems-based-on-cyclic-3-spirobifluorenylene-compound.pdf |
60c742a7469df420f8f42ffc | 10.26434/chemrxiv.8320985.v1 | Orientational Order in the Splay Nematic Ground State | <p>Modulated nematic liquid crystal phases,
which lack positional order but have some periodic variation in the direction
of average orientation present in a classical nematic, have attracted
significant interest. In the recently discovered splay nematic (N<sub>S</sub>)
phase the average orientational order is augmented with a periodic splay
deformation of orientation perpendicular to the director. We use X-ray
scattering experiments to measure the orientational order parameters in the
nematic (N) and splay nematic (N<sub>S</sub>) phases of the liquid crystalline material
RM734. The degree of orientational order is somewhat larger in the N<sub>S</sub>
phase than in the preceding nematic and temperature dependent. We reconstruct
the orientational distribution function and find it to be nematic-like in the N<sub>S</sub>
phase, indicating the change in orientation between neighbouring molecules due
to the splay modulation is very small. A small splay angle implies that the
splay modulation period is larger than the few tens of nanometers originally
envisaged. The method described herein can be used to assist in unambiguous
identification of the splay-nematic phase.</p> | Richard Mandle; Alenka Mertelj | Liquid Crystals; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742a7469df420f8f42ffc/original/orientational-order-in-the-splay-nematic-ground-state.pdf |
63e11c1aa8f79476ca6f64eb | 10.26434/chemrxiv-2023-x5pp8 | Proton activation in the presence of a weak acid facilitated via second coordination effects in iron porphyrins | The catalytic activity of two iron-based porphyrin complexes containing pyridine-functionalized second coordination spheres, referred to as Py2XPFe and CuPy2XPFe have been investigated for the hydrogen evolution reaction (HER) and compared with the unsubstituted analog TMPFe in MeCN. The CuPy2XPFe incorporates a second metal center within the pyridine residues and represents a heterodinuclear system, while the structurally analogous Py2XPFe lacks an additional metal in the second coordination sphere. Both the Py2XFe and CuPy2XPFe complexes are observed to activate the weak acid, acetic acid (AcOH) at the FeII/I couple rather than at the more energy intensive FeI/0 couple observed for the TMPFe species at low acid concentrations. The ability of the monometallic Py2XPFe complex to activate the weak proton source at the FeII/I couple manifests as an ECEC(E) type electrochemical mechanism, rather than an EECC(E) type mechanism as observed for the unsubstituted TMPFe. The CuPy2XPFe displays improved reactivity compared with the Py2XPFe and TMPFe under the same substrate conditions; however the mechanistic nuances into the bimetallic CuPy2XPFe system are currently unclear. The concentration of AcOH was incrementally increased and the rate constants of the initial protonation step i.e. formation of a hydridic species (k1,app), as well as of the protonation of the hydric species to produce dihydrogen (k2,app) were calculated using the Foot-of-the-wave and KS zone rate equation methodologies, respectively. The kinetic analysis indicates that the activation of protons through the ECEC(E) type mechanism results in a system in which k1,app < k2,app. As both the monometallic Py2XPFe and bimetallic CuPy2XPFe activate the AcOH at less cathodic potentials than the TMPFe under identical conditions, the overpotential (TOF/2) for these complexes is thus dramatically lower. The reactivity difference of the Py2XPFe when compared to the TMPFe due to the hanging groups influence is postulated to be either a result of the pyridine residues acting as hydrogen bonding promoters to the active site or aiding to stabilize a catalytic intermediate species during catalysis. Interestingly, a mechanistic change for the TMPFe is also observed at higher AcOH concentrations, underlying perhaps an increased HER reactivity of iron-porphyrins in MeCN. | Anthony Ramuglia; Vishal Budhija; Hoang Khoa Ly; Matthias Schwalbe; Inez Weidinger | Physical Chemistry; Catalysis; Organometallic Chemistry; Electrocatalysis; Redox Catalysis; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e11c1aa8f79476ca6f64eb/original/proton-activation-in-the-presence-of-a-weak-acid-facilitated-via-second-coordination-effects-in-iron-porphyrins.pdf |
60c74bdbbb8c1a1b913db2e4 | 10.26434/chemrxiv.12383768.v1 | Thermodynamics and Kinetics of Protonated Merocyanine Photoacids in Water | Metastable-state photoacids (mPAHs) are chemical species whose photo-activated state is long-lived enough to allow for proton diffusion. Liao’s photoacid (1) represents the archetype of mPAHs, and is being widely used on account of its unique capability to change the acidity of aqueous solutions reversibly. The behavior of 1 in water, however, still remains poorly understood. Herein, we provide in-dept insights on the thermodynamics and kinetics of 1 in water through a series of comparative 1H NMR and UV-Vis studies and relative modelling. Under dark conditions, we quantified a three-component equilibrium system where the dissociation (Ka) of the open protonated form (MCH) is followed by isomerization (Kc) of the open deprotonated form (MC) to the closed spiropyran form (SP) – i.e., in the absence of light, the ground state acidity can be expressed as KaGS = Ka(1+Kc). On the other hand, under powerful and continuous light irradiation we were able to assess, for the first time experimentally, the dissociation constant (KaMS) of the protonated metastable state (cis-MCH). In addition, we found that thermal ring-opening of SP is always rate-determining regardless of pH, whereas hydrolysis is reminiscent of what is found for Schiff bases. The proposed methodology is general, and it was applied to other two compounds bearing a shorter (ethyl, 2) and a longer (butyl, 3) alkyl-1-sulfonate bridge. We found that the pKa remains constant, whereas both pKc and pKaMS linearly increase with the length of the alkyl bridge. Importantly, all results are consistent with a four-component model cycle, which describes perfectly the full dynamics of proton release/uptake of 1‒3 in water. The superior hydrolytic stability and water solubility of compound 3, together with its relatively high pKaGS (low Kc), allowed us to achieve fully reversible jumps of 2.5 pH units over 18 consecutive cycles (6 hours). | Cesare Berton; Daniel Maria Busiello; Stefano Zamuner; Euro Solari; Rosario Scopelliti; Farzaneh Fadaei Tirani; Kay Severin; Cristian Pezzato | Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bdbbb8c1a1b913db2e4/original/thermodynamics-and-kinetics-of-protonated-merocyanine-photoacids-in-water.pdf |
66db2a6912ff75c3a198629a | 10.26434/chemrxiv-2024-8tnrx-v2 | A General Synthesis of Cyclic Bottlebrush Polymers With Enhanced Mechanical Properties via Graft-Through Ring Expansion Metathesis Polymerization | Bottlebrush polymers represent an important class of macromolecular architectures, with applications ranging from drug delivery to organic electronics. While there is an abundance of literature describing the synthesis, structure, and applications of linear bottlebrush polymers using ring-opening metathesis polymerization (ROMP), there are comparatively less reports on their cyclic counterparts. This lack of research is primarily due to the difficulty in synthesizing cyclic bottlebrush polymers, as extensions of typical routes towards linear bottlebrush polymers (i.e., “grafting-through” polymerizations of macromonomers with ROMP) produce only ultrahigh molar mass cyclic bottlebrush polymers with poor molar mass control. Herein, we report a ring-expansion metathesis polymerization (REMP) approach to cyclic bottlebrush polymers via a “grafting-through” approach utilizing the active pyr-CB6 initiator developed in our lab. The resulting polymers, characterized via GPC-MALS-IV, are shown to have superior molar mass control across a range of target backbone lengths. The cyclic materials are also found to have superior mechanical properties when compared to their linear counterparts, as assessed by ball-mill grinding and compression testing experiments. | Matthew Elardo; Adelaide Levenson; Ana Paula Kitos Vasconcelos; Meredith Pomfret; Matthew Golder | Organic Chemistry; Polymer Science; Organic Polymers; Polymer brushes; Polymerization (Polymers); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66db2a6912ff75c3a198629a/original/a-general-synthesis-of-cyclic-bottlebrush-polymers-with-enhanced-mechanical-properties-via-graft-through-ring-expansion-metathesis-polymerization.pdf |
60c7451dbdbb896e96a3894e | 10.26434/chemrxiv.9968375.v1 | Impact of Dehydroamino Acids on the Structure and Stability of Incipient 3₁₀ Helical Peptides | <div>A comparative study of the impact of small, medium-sized, and bulky Δ,Δ-dehydroamino acids (ΔAAs) on the structure and stability of Balaram’s incipient 3₁₀ -helical peptide (1) is reported. Replacement of the N-terminal Aib residue of 1 with a ΔAA afforded peptides 2a–c that maintained the 310-helical shape of 1 in solution. In contrast, installation of a ΔAA in place of Aib-3 yielded peptides 3a–c that preferred a Δ-sheet-like conformation. The impact of the ΔAA on peptide structure was independent of size, with small (ΔAla), medium-sized (Z-ΔAbu), and bulky (ΔVal) ΔAAs exerting similar effects. The proteolytic stabilities of 1 and its analogs were determined by incubation with Pronase. Z-ΔAbu and ΔVal increased the resistance of peptides to proteolysis when incorporated at the 3-position and had negligible impact on stability when placed at the 1-position, whereas ΔAla-containing peptides degraded rapidly regardless of position. Exposure of peptides 2a–c and 3a–c to the reactive thiol cysteamine revealed that ΔAla-containing peptides underwent conjugate addition at room temperature, while Z-ΔAbu- and ΔVal-containing peptides were inert even at elevated temperatures. These results suggest that both bulky and the more synthetically accessible medium-sized ΔAAs should be valuable tools for bestowing rigidity and proteolytic stability on bioactive peptides.</div> | Daniel Joaquin; Michael A. Lee; David W. Kastner; Jatinder Singh; Shardon T. Morrill; Gracie Damstedt; Steven Castle | Bioorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7451dbdbb896e96a3894e/original/impact-of-dehydroamino-acids-on-the-structure-and-stability-of-incipient-310-helical-peptides.pdf |
60c740e4842e6564e9db1d89 | 10.26434/chemrxiv.7327019.v2 | Application of ESMACS Binding Free Energy Protocols to Diverse Datasets: Bromodomain-Containing Protein 4 | <div>We investigate the robustness of our ensemble molecular dynamics binding free energy protocols, known as ESMACS, to different choices of forcefield, starting structure and analysis. ESMACS is based on MMPBSA and we examinge the influence of multiple trajectories, explicit water molecules and estimates of the entropic contribution to the binding free energy.</div><div><br /></div><div>Simulation input and binding affinity calculation data:</div>https://doi.org/10.5281/zenodo.1484050 | David Wright; Shunzhou Wan; Christophe Meyer; Herman Van Vlijmen; Gary Tresadern; Peter Coveney | Biochemistry; Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2019-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e4842e6564e9db1d89/original/application-of-esmacs-binding-free-energy-protocols-to-diverse-datasets-bromodomain-containing-protein-4.pdf |
64efc1ea3fdae147fa27a33d | 10.26434/chemrxiv-2023-jb23k | Fast and controlled Ring-Opening Polymerization of N-carboxyanhydrides via a cooperative bifunctional amino acid | The Ring-Opening Polymerization (ROP) of amino acid N-Carboxyanhydrides (NCAs) offers a straightforward method for preparing polypeptide-like polymers that display characteristics of their natural counterparts, e.g. secondary structure, and enables rapid in vitro screenings. Although recent publications have progressed in achieving water tolerance, a universally user-friendly solu-tion has yet to be achieved. In this communication, we provide a new polymerization set-up that uses an amino acid salt as an initiator. The bifunctional initiator is key for a fast and controlled polymerization, as the carboxylate opens the NCA in the initiation step, and the acyl group is fur-ther transferred to the nitrogen atom in the amine functionality via a concerted low-barrier mecha-nism. Then, it undergoes accelerated chain propagation via the newly generated carbamate rest in the N-acylated chain, as revealed by theoretical calculations at the DFT level and experimental observations. The fast polymerization kinetics enables the polymerization process to be carried out even in the presence of water. In addition, different amino acids can be used as initiators. The concerted O→N acyl shift and the fast and controlled kinetics shed light on cooperative initiating phenomena. | Héctor Soria-Carrera; Julen Munárriz; Pilar Romero; Jesús M. de la Fuente; Rafael Martín-Rapún | Theoretical and Computational Chemistry; Organic Chemistry; Polymer Science; Polymerization (Polymers); Polymerization kinetics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64efc1ea3fdae147fa27a33d/original/fast-and-controlled-ring-opening-polymerization-of-n-carboxyanhydrides-via-a-cooperative-bifunctional-amino-acid.pdf |
655486b32c3c11ed716e86bd | 10.26434/chemrxiv-2023-hn6n1 | Catalysis of C-N Coupling on High-Entropy Alloys | Catalyzing carbon-nitrogen (C-N) coupling using small abundant nitrogenous molecules is of
growing interest to lessen the environmental impact of the industrial process. High-entropy
alloys hold the potential to have surface sites optimized for each of the coupling intermediates
and by varying the alloy composition of the catalyst it provides tunability to the adsorption
energy distribution. We model the C-N coupling using adsorption energies of CO and NO and
assume that *CO couples with an *NO-reduced intermediate. As more mechanistic inside is
needed, we limit the model to the coverage of pairs of *CO and *NO, providing a necessary but
not sufficient condition for catalytic activity. Two limiting cases for simulating the adsorption
process are presented: one considering thermodynamic equilibrium and one considering out-of-
equilibrium conditions. A Monte Carlo method connecting the two limits is suggested which
reproduce trends observed in experiments. By varying the partial pressure of NO the shape
of the pair coverage function in the composition space as well as its optima are altered. Our
method finds a ternary AuCuPd optimum at equal CO/NO partial pressures and copper to be
the optimum at low NO partial pressures. | Mads Kastrup Plenge; Jack Kirk Pedersen; Alexander Bagger; Jan Rossmeisl | Materials Science; Catalysis; Alloys; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655486b32c3c11ed716e86bd/original/catalysis-of-c-n-coupling-on-high-entropy-alloys.pdf |
6615896121291e5d1d79d225 | 10.26434/chemrxiv-2024-7tf66 | UNRAVELING THE IMPACT OF NITROGEN DOPED GRAPHENE ON
THE SENSING OF VOLATILE ORGANIC COMPOUNDS: A DFT
STUDY | Understanding the interaction mechanisms between volatile organic compounds (VOCs) with
graphene-based materials is the primary and crucial step for human health and the advancement
of digital olfaction. In this study, we investigated the adsorption behavior of four common odor
molecules (toluene, ethanol, 2-Furfurylthiol, and guaiacol) on various graphene-based substrates,
including pristine graphene, graphene doped with single graphitic-N atom (GR-N), and multiple
pyrodinic-N atoms (1pd-N, 2pd-N, 3pd-N, and 4pd-N) using density functional theory. The adsorption
energies and Bader charge analysis for all adsorption cases demonstrated that the molecules were
weak physisorbed on all substrates. Through the work function change comparison, 2pd-N and N-gra
presents likely promising sensing performance towards the odor molecules, while the selectivity
declines by further introducing 3 and 4 pyrodinic-N atoms into graphene. The surface dipole moment
analysis shed light on the underlying mechanism of work function change and explained the reduced
sensitivity and selectivity observed for 3pd-N and 4pd-N, which can be attributed to a decrease in the
molecule-induced dipole moment and increase in spatial charge redistribution. These findings could
contribute to the fundamental understanding of odor molecule-graphene interactions and provide
insights for the design and optimization of graphene-based electronic olfaction devices. | Li Chen; David Bodesheim; Ahmad Ranjbar; Arezoo Dianat; Robert Biele; Rafael Gutierrez; Mohammad Khazaei; Gianaurelio Cuniberti | Physical Chemistry; Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6615896121291e5d1d79d225/original/unraveling-the-impact-of-nitrogen-doped-graphene-on-the-sensing-of-volatile-organic-compounds-a-dft-study.pdf |
61cb1e9e5b23d474f90cea85 | 10.26434/chemrxiv-2021-m2hvl | Manganese Catalysed Dehydrogenative Synthesis of Urea Derivatives and Polyureas | Urea derivatives are prevalent intermediates in the synthesis of resin precursors, dyes, agrochemicals, and pharmaceutical drugs. Furthermore, polyureas are useful plastics with applications in coating, adhesive, and biomedical industries and have a current annual market of USD 885 million. However, the conventional methods for the synthesis of urea derivatives and polyureas involve toxic reagents such as (di)isocyanates, phosgene, CO, and azides. We present here the synthesis of (poly)ureas using much less toxic reagents - (di)amines, and methanol via a catalytic dehydrogenative coupling process. The reaction is catalyzed by a pincer complex of an earth-abundant metal, manganese, and liberates H2 gas, valuable by itself, as the only by-product making the overall process atom-economic, and sustainable. A broad variety of symmetrical, and unsymmetrical urea derivatives and polyureas have been synthesized in moderate to quantitative yields using this catalytic protocol. Mechanistic insights have also been provided using experiments and DFT computation suggesting that the reaction proceeds via an isocyanate intermediate. | Aniekan Owen; Annika Preiss; Angus McLuskie; Chang Gao; Gavin Peters; Michael Bühl; Amit Kumar | Catalysis; Organometallic Chemistry; Polymer Science; Polymerization (Polymers); Homogeneous Catalysis; Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cb1e9e5b23d474f90cea85/original/manganese-catalysed-dehydrogenative-synthesis-of-urea-derivatives-and-polyureas.pdf |
63934f0cb103af0f251209a3 | 10.26434/chemrxiv-2022-rr818 | Water increases Faradaic selectivity of Li-mediated nitrogen reduction. | The lithium-mediated system catalyses nitrogen to ammonia under ambient conditions. Herein we discover that trace amount of water - in contrast to prior reports from the literature – can effect a dramatic improvement in the Faradaic selectivity of N2 reduction to NH3. We report an optimal water concentration of 35.5 mM and LiClO4 salt concentration of 0.8 M allows a Faradaic efficiency up to 27.7% at ambient pressure. We attribute the increase in Faradaic efficiency to the incorporation of Li2O in the solid electrolyte interphase, as suggested by our X-ray photoelectron spectroscopy measurements. Our results highlight the extreme sensitivity of lithium mediated N2 reduction to small changes in the experimental conditions. | Matthew Spry; Olivia Westhead; Romain Tort; Benjamin Moss; Yu Katayama; Magda Titirici; Ifan Stephens; Alexander Bagger | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63934f0cb103af0f251209a3/original/water-increases-faradaic-selectivity-of-li-mediated-nitrogen-reduction.pdf |
6274ee8af053df515211659f | 10.26434/chemrxiv-2022-k8jwb-v2 | Advances in the Development of Novel Green Liquids: Thymol/Water, Thymol/Urea and Thymol/Phenylacetic Acid as Innovative Hydrophobic Natural Deep Eutectic Solvents | Deep Eutectic Solvents (DESs) are increasing their relevance thanks to their ecologically favourable properties, their interesting structural features and their catalytic properties.
In this paper we present three novel hydrophobic DESs mixtures prepared by mixing thymol with water, with urea and with phenylacetic acid. These natural DESs represent important advances in the development of green DESs liquids: Thymol/Water mixture is the first binary, water-based DES with hydrophobic properties; in Thymol/Urea DES, urea and its chelating properties were put in a water-separable phase; finally, Thymol/Phenylacetic acid DES is a mixture of two hydrogen-bond donor molecules showing hydrophobic and slightly acidic properties. The hydrogen bond properties within the different mixtures were investigated via DFT, while ab initio molecular dynamics results showed a substantial interaction between thymol and water in the Thymol/Water DES. Moreover, the investigated DESs show excellent extraction properties of heavy metal salts and phenols from aqueous phases. | Matteo Tiecco; Antonio Grillo; Edoardo Mosconi; Waldemar Kaiser; Tiziana Del Giacco; Raimondo Germani | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6274ee8af053df515211659f/original/advances-in-the-development-of-novel-green-liquids-thymol-water-thymol-urea-and-thymol-phenylacetic-acid-as-innovative-hydrophobic-natural-deep-eutectic-solvents.pdf |
60c73d519abda2963ef8b6cb | 10.26434/chemrxiv.5728286.v1 | O6C-20-nor-SalA is a stable and potent KOR agonist | Salvinorin A (SalA) is a potent and selective agonist of the kappa-opioid receptor (KOR), but its instability has frustrated medicinal chemistry efforts. Treatment of SalA with weak bases like DBU leads to C8 epimerization with loss of receptor affinity and signaling potency. Here we show that replacement of C20 with H and replacement of O6 with CH2 stabilizes the SalA scaffold relative to its C8 epimer, so much so that epimerization is completely suppressed. This new compound, O6C-20-nor-SalA, retains high potency for agonism of KOR. <br /> | Ryan Shenvi; Shun Hirasawa; Min Cho; Tarsis F. Brust; Jeremy J. Roach; Larua M. Bohn | Natural Products; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d519abda2963ef8b6cb/original/o6c-20-nor-sal-a-is-a-stable-and-potent-kor-agonist.pdf |
60c74c784c8919cde7ad3642 | 10.26434/chemrxiv.12485810.v1 | From Abstract to Manipulatable – The Hybridization Explorer, A Digital Interactive for Studying Orbitals | <p>The abstract nature of atomic and hybrid orbitals makes it a challenging concept for students to understand. Presented is the Hybridization Explorer, a web-based interactive learning tool, for manipulating and experimenting with hybridization concepts. Through the explorer students can explore both the combination of atomic orbitals, and the visual representation of both atomic and hybrid orbitals and corresponding bond formation. Case studies from an undergraduate and graduate-level demonstration of the explorer are described. Finally, self-reported student confidence levels on solving hybridization questions both before and after use of the explorer are analyzed and discussed.</p> | Sarah Wegwerth; Jason S. Overby; Christopher J. Douglas; Julia Winter; Gianna Manchester; Joseph Engalan | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c784c8919cde7ad3642/original/from-abstract-to-manipulatable-the-hybridization-explorer-a-digital-interactive-for-studying-orbitals.pdf |
62348dd0a4ed957158249609 | 10.26434/chemrxiv-2022-bn5nt | Bidirectional Graphormer for Reactivity Understanding: neural network trained to reaction atom-to-atom mapping task | This work introduces GraphormerMapper – a new algorithm for reactions atom-to-atom mapping (AAM) based on a distance-aware BERT neural network. In benchmarking studies with IBM RxnMapper, the best AAM algorithm according to our previous study, we demonstrate that our AAM algorithm is superior on our “Golden” benchmarking dataset. The mapper is implemented in Chython [https://github.com/chython/chython] and Chytorch [https://github.com/chython/chytorch, https://github.com/chython/chytorch-rxnmap] Python packages which are freely available for out-the-box use. Chython is a cheminformatics library with a simple interface for processing reaction and molecular data. The key features of Chython are: chemical functional groups standardization, checking atom valence errors, substructure search, and advanced reaction manipulation, for example, generating products from reactants and reaction atom-to-atom mapping. Chytorch provides a PyTorch-like interface for graph-based neural networks developed specifically for chemical tasks. | Ramil Nugmanov; Natalia Dyubankova; Andrey Gedich; Joerg Kurt Wegner | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62348dd0a4ed957158249609/original/bidirectional-graphormer-for-reactivity-understanding-neural-network-trained-to-reaction-atom-to-atom-mapping-task.pdf |
61275a66abeb633060c0bac4 | 10.26434/chemrxiv-2021-v51mb | Stereospecific, Pyrylium Salt-Catalyzed O-Glycosylations of Phenols and Alkyl Alcohols | Despite many years of invention, the field of carbohydrate chemistry remains rather inaccessible to non-specialists, which limits the scientific impact and reach of the discoveries made in the field. Aiming to increase the availability of stereoselective glycosylation chemistry for non-specialists, we have discovered that several commercially available pyrylium salts catalyze stereospecific O-glycosylations of a wide range of phenols and alkyl alcohols. This catalytic reaction utilizes trichloroacetimidates, an easily accessible and synthetically proven electrophile, takes place under air and only initiates when all three reagents are mixed, which should provide better reproducibility by non-specialists. The reaction is stereospecific, resulting in β-specific glycosylations from α-trichloroacetimidates, whilst an α-selective glycosylation proceeds from β-trichloroacetimidates. A mechanistic study revealed that the reaction likely proceeds via an SN2-like substitution on the protonated electrophile. | Michael Martin Nielsen; Thomas Holmstrøm; Christian Marcus Pedersen | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Acid Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61275a66abeb633060c0bac4/original/stereospecific-pyrylium-salt-catalyzed-o-glycosylations-of-phenols-and-alkyl-alcohols.pdf |
60c74d51ee301cec50c7a280 | 10.26434/chemrxiv.12609896.v1 | Potential Zeolites Related to Faujasite (FAU): Structures and Energetics. | We present a small set hypothetical zeolite frameworks that are structurally related to faujasite. They are found by examination of the <b>-t</b> nets of the Frank-Kasper phases, which optimize the conditions for regular-tetrahedral nets. The new frameworks have plausible framework energy, as estimated by empirical potential in the GULP program. One of the new frameworks, <b>fav</b>, has framework energy, as a pure silicate, that is only slightly higher than faujasite itself. These present appealing zeolite synthesis targets. | Olaf Delgado Friedrichs; Martin D. Foster; Michael O'Keeffe; Michael Treacy | Coordination Chemistry (Inorg.); Solid State Chemistry; Theory - Inorganic; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d51ee301cec50c7a280/original/potential-zeolites-related-to-faujasite-fau-structures-and-energetics.pdf |
60c746d2842e655190db28ad | 10.26434/chemrxiv.11418075.v1 | Melanogenesis: A Search for Pheomelanin and Also, What Is Lurking Behind Those Dark Colors? | <p>We investigated the
synthesis of melanin-like materials from DOPA, dopamine, norepinephrine and
epinephrine in the presence of L-cysteine. We observed that L-cysteine delayed
the formation of pigment from these catecholamines and that the presence of
L-cysteine yielded darker-colored reaction mixtures. No reddish pigment was
observed that would indicate the synthesis of pheomelanin-like material. The
reactions were performed in the presence of Na<sub>2</sub>CO<sub>3</sub> and
through the addition of CaCl<sub>2</sub> at the end of the reaction; the black,
eumelanin-like material was co-precipitated with CaCO<sub>3</sub>. The
remaining supernatant solutions were observed to be light-yellow to
rusty-orange in color depending on the catecholamine used in the reaction. Size
exclusion chromatography (SEC) analyses indicated that the removal of the black
pigment left behind an oligomeric material that exhibited a strong absorbance
band around 280nm. Our experimental and analytical observations prompt us to
raise a number of points of discussion or hypotheses. 1) The
presence of L-cysteine during the air-mediated oxidation of catecholamines
leads to darker-colored pigments; not reddish or lighter-colored pigments that
would visually resemble pheomelanin-like pigments, 2) SEC analyses suggested
that the black pigment generated during the air-mediated oxidation of
catecholamines is not necessarily the main reaction product, 3) The pre-formed,
dark-colored pigments obtained through the air-mediated oxidative melanogenesis
process can readily be deposited on insoluble mineral surfaces using an <i>in situ</i> co-precipitation procedure, 4)
The air-mediated oxidation of catecholamines leads to a binary product that
contains an insoluble, melanin-like substance and a soluble, oligo- or
polymeric substance containing unoxidized precursor units, 5) The melanogenesis
process leads to a binary product involving a non-covalently bonded combination
of dark-colored pigment and a lighter-colored or colorless substance; the
latter being understudied or ignored in the <i>in
vitro</i> or <i>in vivo</i> studies of the
melanogenesis process, 6) The kinetics of the melanogenesis process may
determine the balance between insoluble and soluble components of the binary
product generated; the slower the reaction the more dark-colored, insoluble
pigment generated, 7) One should consider the possibility of intermolecularly,
N-to-C, bonded units of catecholamines when evaluating the structure of
melanins, polydopamines, etc. and 8) There is a need for a systematic study of
the effect of amino acids (beyond just L-cysteine) and amines in general on the
melanogenesis process.</p> | Koen Vercruysse; Venise Govan | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746d2842e655190db28ad/original/melanogenesis-a-search-for-pheomelanin-and-also-what-is-lurking-behind-those-dark-colors.pdf |
612674048e38a36331407e6a | 10.26434/chemrxiv-2021-x0h4m-v2 | An evaluation of palladium-based catalysts for the base-free borylation of alkenyl carboxylates
| Synthesis of organoboron derivatives is a key application of catalytic cross-coupling, with the Pd-catalyzed Miyaura borylation among the most versatile methods available. We have evaluated several Pd-based systems for borylation of alkenyl acetates and pivalates, with the optimal system heavily dependant on the substrate structure. | Gregory Gaube; Nahiane Pipaon Fernandez; David Leitch | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612674048e38a36331407e6a/original/an-evaluation-of-palladium-based-catalysts-for-the-base-free-borylation-of-alkenyl-carboxylates.pdf |
6644946c91aefa6ce10fc94f | 10.26434/chemrxiv-2024-6h5m8 | Cell-permeable nicotinamide adenine dinucleotides for exploration of cellular protein ADP-ribosylation | Posttranslational modifications (PTMs) greatly enhance the functional diversity of proteins, surpassing the number of gene-encoded variations. One intriguing PTM is ADP-ribosylation, which utilizes nicotinamide adenine dinucleotide (NAD+) as a substrate and is essential in cell signaling pathways regulating cellular responses. Here, we report the first cell-permeable NAD+ analogs and demonstrate their utility for investigating cellular ADP-ribosylation. Using a desthiobiotin-labelled analog for affinity enrichment of proteins that are ADP-ribosylated in living cells under oxidative stress, we identified protein targets associated with host-virus interactions, DNA damage and repair, protein biosynthesis, and ribosome biogenesis. Most of these targets have been noted in various literature sources, highlighting the potential of our probes for cellular ADP-ribosylome studies. | Renata Kasprzyk; Sonja Rieth; Peter Heid; Florian Stengel; Andreas Marx | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6644946c91aefa6ce10fc94f/original/cell-permeable-nicotinamide-adenine-dinucleotides-for-exploration-of-cellular-protein-adp-ribosylation.pdf |
65980a3166c1381729c7cfba | 10.26434/chemrxiv-2024-sv4m0 | Room-Temperature Cu-Catalyzed Etherification of Aryl Bromides | Transition-metal-catalyzed C–O coupling reactions of aryl halides and alcohols represent a useful alternative to classical aromatic substitution methods due to their improved functional group tolerance and substrate scope. Despite these benefits, many existing protocols rely on harsh reaction conditions or necessitate the use of a significant molar excess of alcohol to facilitate efficient C–O bond formation, thereby limiting their utility with complex substrates. Herein, we disclose the development of a Cu-catalyzed C–O coupling method utilizing a new N1,N2-diarylbenzene-1,2-diamine ligand, L8. Under optimized reaction conditions, a structurally diverse set of aryl and heteroaryl bromides underwent efficient coupling with a variety of alcohols at room temperature using an L8-based catalyst. Notably, the L8-derived catalyst exhibited enhanced activity when compared to the L4-based system previously disclosed for C–N coupling, most notably including the ability to functionalize aryl bromides containing acidic functional groups. Mechanistic studies demonstrate that C–O coupling utilizing the catalyst derived from L8 involves rate-limiting alkoxide transmetallation, resulting in a mechanism of C–O bond formation that is distinct from previously described Pd-, Cu-, or Ni-based systems. Consequently, this lower energy pathway leads to rapid C–O bond formation; a 7-fold increase relative to what it seen with other ligands. The results presented in this report overcome limitations in previously described transition-metal-catalyzed C–O coupling methods, expand the utility of this ligand family, and introduce a new ligand that we anticipate may be useful in other Cu-catalyzed C–heteroatom and C–C bond-forming reactions. | Michael Strauss; Megan Greaves; Seoung-Tae Kim; Christiana Teijaro; Michael Schmidt; Paul Scola; Stephen Buchwald | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65980a3166c1381729c7cfba/original/room-temperature-cu-catalyzed-etherification-of-aryl-bromides.pdf |
60c74833702a9b19bf18af2c | 10.26434/chemrxiv.11618127.v2 | Locating Conical Intersections Using the Quasidegenerate Partially and Strongly Contracted NEVPT2 Methods | Conical intersections (CIs) play an important role in photochemistry because they sometimes govern the non-radiative decay process. However, accurate characterizations of CIs are not always straightforward. In this study, analytic gradients and interstate coupling vectors for the quasidegenerate partially and strongly contracted n-electron valence state second-order perturbation theory (QD-PC-NEVPT2 and QD-SC-NEVPT2) were developed and applied to locating CIs of benzene. The pilot application demonstrates that the results of both the methods are similar to the extended multistate complete active space second-order perturbation theory (XMS-CASPT2), while the lack of dynamic electron correlation resulted in a deviation of 0.7 eV. | Yoshio Nishimoto | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74833702a9b19bf18af2c/original/locating-conical-intersections-using-the-quasidegenerate-partially-and-strongly-contracted-nevpt2-methods.pdf |
613b6b1665db1e025bb2e273 | 10.26434/chemrxiv-2021-zkz9w | Site-Specific DNA Functionalization through the Tetrazene-Forming Reaction in Ionic Liquids | Development of multiple chemical tools for deoxynucleic acid (DNA) labeling has facilitated wide use
of their functionalized conjugates, but significant practical and methodological challenges remain to
achievement of site-specific chemical modification of the biomacromolecule. As covalent labeling
processes are more challenging in aqueous solution, use of nonaqueous, biomolecule-compatible
solvents such as an ionic liquid consisting of a salt with organic molecule architecture, could be
remarkably helpful in this connection. Herein, we demonstrate site-specific chemical modification of
DNAs through a tetrazene-forming amine-azide coupling reaction using an ionic liquid. This ionic
liquid-enhanced reaction process has good functional group tolerance and precise chemoselectivity,
and enables incorporation into DNA of various useful functionalities such as biotin, cholesterol and
fluorophores which could be incorporated into DNA through this method. A site-specifically labeled
single stranded nucleotide, or aptamer interacting with a growth factor receptor (Her2) was
successfully used in the fluorescence imaging of breast cancer cell lines. The non-traditional medium-promoted labeling strategy described here provides an alternative design paradigm for future
development of chemical tools for applications involving DNA functionalization. | Seiya Ishizawa; Munkhtuya Tumurkhuu; Elizabeth Gross; Jun Ohata | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613b6b1665db1e025bb2e273/original/site-specific-dna-functionalization-through-the-tetrazene-forming-reaction-in-ionic-liquids.pdf |
65a92baee9ebbb4db973701e | 10.26434/chemrxiv-2023-ddrh7-v2 | The odd-number cyclo[13]carbon and its dimer cyclo[26]carbon | Cyclo[N]carbons (CN) are molecular rings of N carbon atoms. These exotic carbon allotropes are excellent benchmarking systems for testing quantum chemical theoretical methods, and they may be valuable precursors to other carbon-rich materials. Odd-N cyclocarbons, elusive to date, are predicted to be even less stable than even-N ones, and their structures are unknown. Here we report the on-surface synthesis of cyclo[13]carbon, C13. We elucidate its properties by scanning probe microscopy and theoretical modelling. C13 adopts an open-shell configuration with a triplet ground state and a kinked geometry, which shows different degrees of pronunciation related to different degrees of carbene localization. Moreover, we prepare and characterize the C13 dimer, yielding cyclo[26]carbon, demonstrating the potential of cyclocarbons as precursors to novel carbon allotropes. | Florian Albrecht; Igor Rončević; Yueze Gao; Fabian Paschke; Alberto Baiardi; Ivano Tavernelli; Shantanu Mishra; Harry L. Anderson; Leo Gross | Theoretical and Computational Chemistry; Organic Chemistry; Nanoscience; Organic Synthesis and Reactions; Theory - Computational; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a92baee9ebbb4db973701e/original/the-odd-number-cyclo-13-carbon-and-its-dimer-cyclo-26-carbon.pdf |
60c74a27842e6574dfdb2eb4 | 10.26434/chemrxiv.12162135.v1 | Chemical Fueling Enables Molecular Complexification of Assembly-Driven Self-Replicators | This work addressed how self-replicating molecules can evolve to become more complex. Subjecting a system in which two self-replicating molecules compete for a common food source to a regime in which they are both degraded leads to survival of the most complex of the two replicators, even though this replicator is less efficient at replicating. These results show that chemical fueling of a replication process can drive the complexification of the replicator. The more complex replicator is also more proficient at catalyzing a model reaction, showing that complexification can also enhance (catalytic) function. <br /> | Gael Schaeffer; Elio Mattia; Omer Markovitch; Kai Liu; Andreas S. Hussain; Jim Ottelé; Ankush Sood; Sijbren Otto | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Aggregates and Assemblies | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a27842e6574dfdb2eb4/original/chemical-fueling-enables-molecular-complexification-of-assembly-driven-self-replicators.pdf |
66d16dd220ac769e5f557476 | 10.26434/chemrxiv-2024-t88k2 | [18F]CF3I – Enabling Photoredox-mediated Radical [18F]Trifluoromethylation for Positron Emission Tomography | The development of new tracers for positron emission tomography (PET) is highly dependent on the available synthetic tools for their radiosynthesis. Herein, we present the first radiosynthesis and application of [18F]trifluoroiodomethane – the first reagent for broad scope radical [18F]trifluoromethylation chemistry in high molar activity. [18F]CF3I can be prepared from [18F]fluoroform with 67±5% AY and >99% RCP. Its synthetic utility is demonstrated by the radiosynthesis of previously unprecedented 18F-labeled -trifluoromethyl ketones and trifluoromethyl sulfides, important motifs that are present in a range of bioactive compounds. Both protocols are Ru- and photo-mediated and proceed under mild reaction conditions. They show good functional group tolerance evidenced by the respective reaction scopes and make use of easily obtainable starting materials. The products can be isolated in 8.3-11.1 GBq/μmol (starting from ca. 5 GBq [18F]fluoride). The applicability to PET tracer synthesis is shown by the radiolabeling of bioactive compounds, such as derivatives of probenecid and febuxostat. In a broader context, this work opens the door to the utilization of radical [18F]trifluoromethylation chemistry for the radiolabeling of PET tracers in high molar activity. | Lukas Veth; Albert D. Windhorst; Danielle J. Vugts | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d16dd220ac769e5f557476/original/18f-cf3i-enabling-photoredox-mediated-radical-18f-trifluoromethylation-for-positron-emission-tomography.pdf |
674915cb7be152b1d047a13e | 10.26434/chemrxiv-2024-m8wth | Evaluation of SULT1A1-activated alkylators as cytotoxic agents against liver cancer cells | A quantitative high throughput screen (qHTS) of 7,988 compounds with annotated libraries using biliary tract cancer cell lines with or without isocitrate dehydrogenase I (IDH1) mutations had identified YC-1 as being selectively cytotoxic against the IDH1 mutant cell lines. We present the structure-activity relationship study of YC-1 analogs and identify the key structural motifs that are essential for activity. We highlight the narrow SAR around the furfuryl alcohol that has been reported as a critical motif that is activated by the sulfotransferase enzyme SULT1A1. Drug-like properties of key analogs are evaluated. We also show the SAR of a smaller subset of 2-choloro-4-amino benzyl alcohols from the NCI compound collection with a similar benzyl alcohol motif. We also demonstrate the ability of key analogs to act as substrates of SULT1A1 in a colorimetric biochemical assay. | Ke Kong; Wei Zhao; Jonathan H. Shrimp; Marius Vava; Rohan Sinha; Shweta Sharma; Tobie D Lee; Jacob S Roth; Olivia W Lee; Devin Lewis; Sara E. Kearney; Jason Rohde; Mindy I. Davis; Pranav Shah; Amy Wang; Xin Xu; Lei Shi; Min Shen; Matthew Boxer ; Nabeel Bardeesy; Matthew D. Hall; Samarjit Patnaik | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674915cb7be152b1d047a13e/original/evaluation-of-sult1a1-activated-alkylators-as-cytotoxic-agents-against-liver-cancer-cells.pdf |
617586480c0480187a42ef5a | 10.26434/chemrxiv-2021-516z8 | Polymorphism of Garnet Solid Electrolytes and Its
Implications on Grain Level Chemo-Mechanics | Understanding and mitigating filament formation, short-circuit, and solid electrolyte fracture is a key necessity towards achieving practical SSBs. Herein, we employ
a coupled far-fi eld high energy diffraction microscopy -tomography approach for assessing chemo-mechanical behavior for dense, polycrystalline garnet (Li7La3Zr2O12, LLZO) solid electrolytes with grain-level resolution. Tracking the stress response for individual
grains through in situ testing, failure onset and short-circuit mechanism is confirmed to be a stochastic, isolated process governed by the presence of local phase heterogenity. Coupling high energy X-ray diffraction and far eld high energy diffraction microscopy measurements, these local regions are proposed to be regions with the presence of a
cubic polymorph of LLZO arising potentially from local dopant concentration variation. Interplay of mechanics and transport is evaluated and coupled tomography and
FF-HEDM dataset is employed to illustrate the degradation of polycrystalline garnet
solid electrolyte. The results showcase pathways for processing high performing SSBs. | Marm Dixit; Bairav Vishugopi; Wahid Zaman; Peter Kenesei; Jun-Sang Park; Jon Almer; Partha Mukherjee; Kelsey Hatzell | Energy; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617586480c0480187a42ef5a/original/polymorphism-of-garnet-solid-electrolytes-and-its-implications-on-grain-level-chemo-mechanics.pdf |
60c750ed0f50dbd8f339767f | 10.26434/chemrxiv.13100546.v1 | 2D Rigid Benzoxazole-Linked Covalent Organic Framework Films with High-Strength, High-Modulus Mechanical Behavior | <p>Two-dimensional (2D) benzoxazole-linked covalent organic frameworks (COFs) provide an opportunity to incorporate the strength and modulus of corresponding 1D rigid-rod polymers into multiple directions by extending covalent bonding into two dimensions while simultaneously reducing density. Thus far, this potential has been elusive because of the challenge of producing high-quality COF films, particularly those with irreversible, rigid benzazole linkages. The majority of COF syntheses use a single-step process approach where polymerization occurs faster than crystallization and typically result in a poorly ordered and insoluble powder. Here, we present a one-step synthesis and two-step process that allows the deposition of a uniform intermediate film via reversible, non-covalent interactions. This network then undergoes an annealing step that facilitates the irreversible conversion to 2D covalently-bonded polymer product. The resulting films are semi-crystalline with platelet-like crystals embedded in an amorphous matrix with sharp crystal-amorphous interfaces. By this approach, we achieve free-standing films for which we demonstrate the first example of mechanical testing of benzazole-linked COFs. These initial films have promising mechanical properties with an in-plane ultimate tensile strength of nearly 50 MPa and axial tensile and transverse compressive elastic moduli on the scale of several GPa. These mechanical properties already rival the performance of solution-cast films of 1D polybenzoxazole (PBO).<i></i></p> | Kristen Miller; Lawrence
B. Alemany; Edwin L. Thomas; Eilaf Egap | Nanostructured Materials - Materials; Thin Films; Organic Polymers; Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750ed0f50dbd8f339767f/original/2d-rigid-benzoxazole-linked-covalent-organic-framework-films-with-high-strength-high-modulus-mechanical-behavior.pdf |
650c9717b927619fe793ec91 | 10.26434/chemrxiv-2023-9jkx5-v2 | Metallomimetic C-F activation catalysis by simple phosphines | Delivering metallomimetic reactivity from simple p-block compounds is highly desirable in the search to replace expensive, scarce precious-metals by cheap and abundant elements in catalysis. This contribution demonstrates that metallomimetic catalysis, involving facile redox cycling between the P(III) and P(V) oxidation states, is possible using only simple, cheap and readily available trialkylphosphines with no need for complex ligand architectures or external oxidising/reducing agents. Hydrodefluorination and aminodefluorination of a range of fluoroarenes was realised with good to very good yields under mild conditions. Experimental and computational mechanistic studies show that the phosphines undergo oxidative addition of the fluoroaromatic substrate, via a Meisenheimer-like transition state, to form a fluorophosphorane. This undergoes a pseudo-transmetallation step with a silane, via initial fluoride transfer from P to Si, to give experimentally observed phosphonium ions. Hydride transfer from a hydridosilicate counterion then leads to a hydridophosphorane, which undergoes reductive elimination of the product to re-form the phosphine catalyst. This behaviour is analogous to many classical transition-metal catalysed reactions and so is a rare example of both functional and mechanistically metallomimetic behaviour in catalysis by a main-group element system. Crucially, the reagents used are cheap, readily available commercially and easy to handle, making these reactions a realistic prospect in a wide range of academic and industrial settings. | Sara Bonfante; Christian Lorber; Jason M. Lynam; Antoine Simonneau; John M. Slattery | Organic Chemistry; Inorganic Chemistry; Catalysis; Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650c9717b927619fe793ec91/original/metallomimetic-c-f-activation-catalysis-by-simple-phosphines.pdf |
645d350bfb40f6b3ee6c97d3 | 10.26434/chemrxiv-2023-3j7dv | Zipper-like linker self-assembly to obtain low interfacial tensions with partially neutralized naphthenic acids. | The presence of naphthenic acid in crude oil is considered one of the most important factors in the formation and stabilization of water in bitumen emulsions. While naphthenic acids (NAs) are oil-soluble lipophilic amphiphiles, their neutralized form, sodium naphthenates (NaNs), has highly hydrophilic components. The right NA/NaN proportion should produce a balanced, net-zero curvature at the oil-water interface, leading to ultra-low interfacial tensions (IFTs<0.1 mN/m). A previous study showed that such an expectation is not achievable in model oil systems with NA and NaN, likely because of the partition of NA and NaN species. This work explores the hypothesis that it is possible to achieve ultralow IFTs using surfactants with balanced hydrophilic-lipophilic interactions that can trigger a "zipper-like" self-assembly of hydrophilic and lipophilic amphiphiles at the interface. A second hypothesis is that by producing these ultralow IFTs one can achieve fast dewatering of emulsions of oil containing partially neutralized NAs. After introducing sodium dihexyl sulfosuccinate (SDHS) and sodium dioctyl sulfosuccinate (Aerosol OT or AOT) as balanced surfactants, it was noted that one could produce ultralow IFTs in partially neutralized NAs. Using the hydrophilic-lipophilic difference (HLD) and net-average curvature (NAC) framework, it was possible to reproduce the experimental trends when using appropriate values for the critical micelle concentration (CMC) for NaN and SDHS. The best zipper assembly performance was obtained when the intrinsic HLD of the balanced surfactant is near zero. Under those conditions, it was possible to find ultralow IFTs and fast dewatering of emulsions with NA content and pH relevant to diluted bitumen emulsions obtained during naphthenic froth treatment. | Rafael Perez; Edgar Acosta | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Interfaces; Self-Assembly | CC BY NC 4.0 | CHEMRXIV | 2023-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645d350bfb40f6b3ee6c97d3/original/zipper-like-linker-self-assembly-to-obtain-low-interfacial-tensions-with-partially-neutralized-naphthenic-acids.pdf |
60c747de469df41c1af438fb | 10.26434/chemrxiv.11813262.v1 | Geometric Landscapes for Material Discovery within Energy-Structure-Function Maps | Porous molecular crystals are an emerging class of porous materials formed by crystallisation of molecules with weak intermolecular interactions, which distinguishes them from extended nanoporous materials like metal-organic frameworks (MOFs). To aid discovery of porous molecular crystals for desired applications, energy-structure-function (ESF) maps were developed that combine a priori prediction of both the crystal structure and its functional properties. However, it is a challenge to represent the high-dimensional structural and functional landscapes of an ESF map and to identify energetically favourable and functionally interesting polymorphs among the 1,000s-10,000s of structures typically on a single ESF map. Here, we introduce geometric landscapes, a representation for ESF maps based on geometric similarity, quantified by persistent homology. We show that this representation allows the exploration of complex ESF maps, automatically pinpointing interesting crystalline phases available to the molecule. Furthermore, we show that geometric landscapes can serve as an accountable descriptor for porous materials to predict their performance for gas adsorption applications. A machine learning model trained using this geometric similarity could reach a remarkable accuracy in predicting the materials' performance for methane storage applications. | Seyed Mohamad Moosavi; Henglu Xu; Linjiang Chen; Andrew
I. Cooper; Berend Smit | Physical Organic Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747de469df41c1af438fb/original/geometric-landscapes-for-material-discovery-within-energy-structure-function-maps.pdf |
677be9be6dde43c9087f5cf6 | 10.26434/chemrxiv-2025-bd0d8 | Formation and Reactivity of Silicon Oxyhydrides in Nickel Hydrogenation Catalysts Supported on Silica | Silica is generally regarded as an inert support in the field of heterogeneous catalysis, including hydrogenation-dehydrogenation catalysis, on which hydrogen spillover is debated. Since supported hydrogenation and dehydrogenation catalysts are generally activated in H2 as reducing gas at medium-high temperatures (350–500 °C), we suspected that hydride formation could occur during such catalyst pretreatments. In this work, we investigated silicon oxyhydride (SiHxOy, SiHx for brevity) formation during the reduction pretreatment of a set of Ni/SiO2 catalyst materials using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). We observed two distinct vibrational bands located at ~ 2275 and ~ 2257 cm−1, which we assigned to SiH and SiH2 species, as supported by density functional theory (DFT) calculations. Since these vibrational bands are absent after hydrogenation of pure silica, we propose that the formation of hydrides was caused by hydrogen spillover from Ni metal nanoparticles supported on silica. The decrease in the band areas with rising temperature was used in a van t ‘Hoff plot to yield enthalpy values of ~ 26 and ~ 42 kJ/mol for the apparent reaction of hydride species, suggesting an equilibrium with IR-inactive or very mobile species. The reactivity of the SiHx species was also investigated, by dosing methanol, water and CO2 as probe molecules on the pre-reduced Ni/SiO2 catalysts. Methanol reacted the fastest with the hydride species, followed by water, while CO2 did not show any interaction with the hydrides. We anticipate this work will contribute to changing the view of silica as an inert support material, and to the understanding of H spillover in more general. | Bram T. Kappé; Robin Vogel; Jaap N. Louwen; Bettina Baumgartner; Bert M. Weckhuysen; Matteo Monai | Inorganic Chemistry; Catalysis; Spectroscopy (Inorg.); Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677be9be6dde43c9087f5cf6/original/formation-and-reactivity-of-silicon-oxyhydrides-in-nickel-hydrogenation-catalysts-supported-on-silica.pdf |
60c74ac09abda209a4f8cf15 | 10.26434/chemrxiv.12251138.v1 | Diagonal Born-Oppenheimer Corrections to the Ground Electronic State Potential Energy Surfaces of Ozone: Improvement of Ab Initio Vibrational Band Centers for the 16O3, 17O3 and 18O3 Isotopologues | <div>Mass-dependent diagonal Born-Oppenheimer corrections (DBOC) to the ab initio electronic ground state potential energy surface for tseveral isotopologues of the ozone molecule are reported for the first time. The comparison with experimental band centers shows a significant improvement of the accuracy with respect to the best Born-Oppenheimer (BO) ab initio calculations reducing the total root-mean-squares (calculated - observed) deviations by about factor of two. For the set of 16O3 vibrations up to five bending and four stretching quanta, the mean (calculated - observed) deviations drop down from 0.7 cm-1 (BO) to about 0.1 cm-1, with the most pronounced improvement seen for bending states and for mixed bend-stretch polyads. In case of bending band centers directly observed under high spectral resolutions, the errors are reduced by more than order of magnitude from observed levels, approaching nearly experimental accuracy. New sets of ab initio vibrational states can be used for improving spectroscopic effective models for analyses of observed high-resolution spectra, particularly in cases of accidental resonances with ,,dark'' states requiring accurate theoretical predictions.</div> | Attila Tajti; Péter Szalay; Roman V. Kochanov; Vladimir G. Tyuterev | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ac09abda209a4f8cf15/original/diagonal-born-oppenheimer-corrections-to-the-ground-electronic-state-potential-energy-surfaces-of-ozone-improvement-of-ab-initio-vibrational-band-centers-for-the-16o3-17o3-and-18o3-isotopologues.pdf |
60c73f59bdbb8926a9a37f98 | 10.26434/chemrxiv.7301453.v1 | Directed, Nickel-Catalyzed Umpolung 1,2-Carboamination of Alkenyl Carbonyl Compounds | We report a regioselective, nickel-catalyzed <i>syn</i>-1,2-carboamination of non-conjugated alkenyl carbonyl compounds with <i>O</i>-benzoyl hydroxylamine (N–O) electrophiles and aryl/alkylzinc nucleophiles to afford β- and γ-amino acid derivatives. This method enables preparation of products containing structurally diverse tertiary amine motifs, including heterocycles, and can also be used to form quaternary carbon centers. The reaction takes advantage of a tethered 8-aminoquinoline directing group to control the regiochemical outcome and suppress two-component coupling between the N–O electrophile and organozinc nucleophile. | Vincent van der Puyl; Joseph Derosa; Keary Engle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f59bdbb8926a9a37f98/original/directed-nickel-catalyzed-umpolung-1-2-carboamination-of-alkenyl-carbonyl-compounds.pdf |
66c776e1a4e53c48764325c4 | 10.26434/chemrxiv-2024-kqt51-v2 | A Supramolecular–Quantum Dot System for Broad-Spectrum Detection of Fentanyl Analogues | Synthetic opioids, especially fentanyl and its analogues, have led to an epidemic of abuse and a significant increase in overdose deaths in the United States. Current detection methods have significant drawbacks in their sensitivity, scalability, and portability that limit use in field- based applications to promote public health and safety. The need to detect trace amounts of fentanyl in complex mixtures with other drugs or interferents, and the continued emergence of new fentanyl analogues, further complicates detection efforts. Accordingly, there is an urgent need to develop convenient, rapid, and reliable sensors for fentanyl detection. In this study, a sensor is prepared based on competitive displacement of a fluorescent dye from the cavity of a supramolecular macrocycle, with subsequent fluorescence quenching from graphene quantum dots. This approach can detect and quantify small quantities of fentanyl along with 58 fentanyl analogues, including highly potent variants like carfentanil that are of increasing concern. Furthermore, selective detection of these agents is possible even when at 0.01 mol% in the presence of common interferents. Results are provided within seconds, with stable performance over time. This simple, rapid, reliable, sensitive, and cost-effective approach couples supramolecular capture with graphene quantum dot nanomaterial quenchers to create a tool with the potential to advance public health and safety in the context of field based detection of drugs in the fentanyl class. | Yanjing Gao; Farbod Shirinchi; Audrey Hansrisuk; Runyao Zhu; Sijie Xian; Marya Lieberman; Matthew Webber; Yichun Wang | Materials Science; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c776e1a4e53c48764325c4/original/a-supramolecular-quantum-dot-system-for-broad-spectrum-detection-of-fentanyl-analogues.pdf |
6757ca12f9980725cf91c7e0 | 10.26434/chemrxiv-2024-nvmnr | CoRE MOF DB: a curated experimental metal-organic framework database with machine-learned properties for integrated material-process screening | We present an updated version of the CoRE MOF database, which includes a curated set of computation-ready MOF crystal structures designed for high-throughput computational materials discovery. Data collection and curation procedures were improved from the previous version to enable more frequent updates in the future. Machine learning-predicted properties, such as stability metrics and heat capacities, are included in the dataset to streamline screening activities. An updated version of MOFid was developed to provide detailed information on metal nodes, organic linkers, and topologies of a MOF structure. DDEC06 partial atomic charges of MOFs were assigned based on a machine learning model. Gibbs-Ensemble Monte Carlo simulations were used to classify the hydrophobicity of MOFs. The finalized dataset was subsequently used to perform integrated material-process screening for various carbon capture conditions using high-fidelity temperature-swing adsorption (TSA) simulations. Our workflow identified multiple MOF candidates that are predicted to outperform CALF-20 for these applications. | Guobin Zhao; Logan Brabson; Saumil Chheda; Ju Huang; Haewon Kim; Kunhuan Liu; Kenji Mochida; Thang Pham; Prerna Prerna; Gianmarco Terrones; Sunghyun Yoon; Lionel Zoubritzky; François-Xavier Coudert; Maciej Haranczyk; Heather Kulik; Mohamad Moosavi; David Sholl; Ilja Siepmann; Randall Snurr; Yongchul Chung | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6757ca12f9980725cf91c7e0/original/co-re-mof-db-a-curated-experimental-metal-organic-framework-database-with-machine-learned-properties-for-integrated-material-process-screening.pdf |
64baa206ae3d1a7b0d1b17ac | 10.26434/chemrxiv-2023-54wkx | Experimental and theoretical investigation of hydrogen sorption by SnO2 nanostructures in a metal-organic framework scaffold | SnO2 nanostructures decorated with Pd clusters were installed in the porous metal-organic framework (MOF) material NU-1000 and investigated as hydrogen storage materials. The proposed concept was to store atomic hydrogen – dissociated by the Pd clusters – within the nanostructured metal oxide to achieve reversible storage of hydrogen at near-ambient temperature and modest pressure using the MOF as a template for the nanostructures. Temperature programmed reduction and X-ray absorption spectroscopy (XANES) provided evidence for the reduction of SnO2 upon exposure to hydrogen. Hydrogen sorption in or on several idealized SnO2 nanostructures was studied using density functional theory (DFT), including the (110) surface of crystalline SnO2 surface and bulk SnO2 to assess the thermodynamic feasibility of hydrogen sorption under the conditions of the experiments, i.e., 1 bar and ambient temperature. Also evaluated computationally was the thermodynamic feasibility of reducing tin by extracting an oxygen atom with H2 and creating a lattice oxygen vacancy with generation of water in the vapor phase. The combined computational and experimental results point to the benefits of metal oxide nanostructuring in enabling reversible dissociative uptake of molecular hydrogen at ambient temperature and moderate pressures. | Rebecca Goncalves; Zhihengyu Chen; Karena Chapman; Randall Snurr; Joseph Hupp | Theoretical and Computational Chemistry; Inorganic Chemistry; Energy; Bonding; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64baa206ae3d1a7b0d1b17ac/original/experimental-and-theoretical-investigation-of-hydrogen-sorption-by-sn-o2-nanostructures-in-a-metal-organic-framework-scaffold.pdf |
60c750b6842e654da7db3a70 | 10.26434/chemrxiv.13073348.v1 | Mass Transport in Catalytic Pores of GDE-Based CO2 Electroreduction Systems | Gas diffusion electrode (GDE)-based setups have shown promising performance for CO<sub>2</sub> electrocatalysis and further development of these systems will be important on the path to industrial feasibility. In this article, we model an effective catalyst pore within a GDE-based flow-cell to study the influence of the catalyst structure and operating conditions on the reaction environment for CO<sub>2</sub> electrocatalysis at practically relevant current densities. Using a generalized modified Poisson-Nernst-Planck (GMPNP) 3D model of the nanoporous catalyst layer, we show that the length of the catalyst pore as well as the boundary conditions at the gas-electrolyte and electrolyte-electrolyte interfaces across this length are highly influential parameters for determining the conditions within the catalyst pore. Pores with the same catalytic surface area can have very different reaction environments depending primarily on the pore length and not the pore radius. Properties such as electrolyte pH and buffer breakdown, ionic strength and CO<sub>2</sub> concentration are also highly-sensitive to the catalyst layer thickness, gas pressure, electrolyte flow rate and the flow-channel geometry. The applied potential impacts the concentration of ionic species in the pore, which in turn determines the solubility of CO<sub>2</sub> available for the reaction. Our results underline the need to understand and manage transport within GDE-based electrocatalysis systems as an essential means to control catalyst performance. Benchmarking of GDE-based electrocatalytic systems against their structural and operational parameters will be important for achieving improvements in performance that can be ultimately translated to large-scale operation. | Divya Bohra; Jehanzeb Chaudhry; Thomas Burdyny; Evgeny Pidko; Wilson Smith | Catalysts; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Transport Phenomena (Chem. Eng.); Electrocatalysis; Energy Storage; Interfaces | CC BY NC 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b6842e654da7db3a70/original/mass-transport-in-catalytic-pores-of-gde-based-co2-electroreduction-systems.pdf |
60c751fe469df4f25ff44ae1 | 10.26434/chemrxiv.13239059.v1 | Dynamics of Ion Locking in Doubly Polymerized Ionic Liquids | <div>In this work, we investigate the dynamics of ion motion in “doubly-polymerized” ionic liquids (DPILs) in which both charged species of an ionic liquid are covalently linked to the same polymer chains. Broadband dielectric spectroscopy is used to characterize these materials over a broad frequency and temperature range, and their behavior is compared to that of conventional “singly-polymerized” ionic liquids (SPILs) in which only one of the charged species is attached to the polymer chains. Polymerization of the DPIL decreases the bulk ionic conductivity by four orders of magnitude relative to both SPILs. The timescales for local ionic rearrangement are similarly found to be approximately four orders of magnitude slower in the DPILs than in the SPILs, and the DPILs also have a lower static dielectric constant. These results suggest that copolymerization of the ionic monomers affects ion motion on both the bulk and the local scales, with ion pairs serving to form strong physical crosslinks between the polymer chains. This study provides quantitative insight into the energetics and timescales of ion motion that drive the phenomenon of “ion locking” currently under investigation for new classes of organic electronics.</div> | Swati Arora; Julisa Rozon; Jennifer Laaser | Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751fe469df4f25ff44ae1/original/dynamics-of-ion-locking-in-doubly-polymerized-ionic-liquids.pdf |
60c7494cbb8c1a705d3dadf2 | 10.26434/chemrxiv.12049554.v1 | A Multifunctional Reagent Designed for the Site-Selective Amination of Pyridines | We report the development
of a multifunctional reagent for the direct conversion of pyridines to
Boc-protected 2-aminopyridines with exquisite site- and chemoselectivity. The
novel reagent was prepared on 200 gram-scale in a single step, reacts in the
title reaction under mild conditions without precautions towards air or
moisture, and is tolerant of nearly all common functionality. Experimental and <i>in-situ </i>spectroscopic<i> </i>monitoring techniques provide detailed insights
and unexpected findings for the unique reaction mechanism. | Patrick Fier; Suhong Kim; Ryan Cohen | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7494cbb8c1a705d3dadf2/original/a-multifunctional-reagent-designed-for-the-site-selective-amination-of-pyridines.pdf |
61dbe0f8636cc9183c456125 | 10.26434/chemrxiv-2022-pq978 | Revisiting the Role of Charge Transfer and Local Excitations in Thermally Activated Delayed Fluorescence | Thermally activated delayed fluorescence (TADF) is a phenomenon that relies on the upconversion of triplet excitons to singlet excitons by means of reverse intersystem crossing (rISC). It has been shown both experimentally and theoretically that the TADF mechanism depends on the interplay between charge transfer and local excitations. However, the difference
between the diabatic and adiabatic character of the involved excited states is rarely discussed in the literature. Here, we develop a diabatization procedure to implement a 4-state model Hamiltonian to a set of TADF molecules. We provide physical interpretation
for the Hamiltonian elements and show their dependence on the electronic state of the equilibrium geometry. We also demonstrate how vibrations affect TADF efficiency by modifying the diabatic decomposition of the molecule. Finally, we provide a simple model that connects the diabatic Hamiltonian to the electronic properties relevant to TADF and show how such relationship translates into different optimization strategies for rISC, fluorescence and overall TADF performance. | Leonardo Evaristo de Sousa; Piotr de Silva | Theoretical and Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dbe0f8636cc9183c456125/original/revisiting-the-role-of-charge-transfer-and-local-excitations-in-thermally-activated-delayed-fluorescence.pdf |
64ad4706ba3e99daefe697f4 | 10.26434/chemrxiv-2023-x0r76 | Combining thermal scanning probe lithography and dry etching for grayscale nanopattern amplification | Grayscale structured surfaces with nanometer-scale features are used in a growing number of applications in optics and fluidics. Thermal scanning probe lithography achieves a lateral resolution below 10 nm and a vertical resolution below 1 nm, but its maximum depth in polymers is limited. Here, we present an innovative combination of nanowriting in thermal resist and plasma dry etching with substrate cooling, which achieves up to 10-fold amplification of polymer nanopatterns into SiO2 without additional surface roughness. Sinusoidal nanopatterns in SiO2 with 400 nm pitch and 150 nm depth are fabricated free of shape distortion after dry etching. To exemplify the possible applications of the proposed method, grayscale dielectric nanostructures are used for scalable manufacturing through nanoimprint lithography and for strain nanoengineering of 2D materials. Such method for high aspect ratio and smooth grayscale nanopatterning has the potential to find application in the fabrication of photonic and nanoelectronic devices. | Berke Erbas; Ana Conde-Rubio; Xia Liu; Joffrey Pernollet; Zenyu Wang; Arnaud Bertsch; Marcos Penedo; Georg Fantner; Mitali Banerjee; Andras Kis; Giovanni Boero; Juergen Brugger | Materials Science; Nanoscience; Thin Films; Nanofabrication; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ad4706ba3e99daefe697f4/original/combining-thermal-scanning-probe-lithography-and-dry-etching-for-grayscale-nanopattern-amplification.pdf |
667a255301103d79c50e3e62 | 10.26434/chemrxiv-2024-kxjgg | iMSminer: A Data Processing and Machine Learning Package for Imaging Mass Spectrometry | Imaging mass spectrometry enables untargeted spatial profiling of compounds in animal tissues. Data preprocessing and mining are central to comprehensively unravel the complexity of hyperspectral imaging mass spectrometry experiments. Herein, we describe a user-friendly, partially GPU- or compiler-accelerated software pipeline that enables multi-ROI, multi-condition, and multi-replicate preprocessing and mining of larger-than-memory imaging mass spectrometry datasets in Python. The package, termed iMSminer, streamlines computational imaging mass spectrometry workflows, from spectral preprocessing to unsupervised exploratory analysis to univariate fold-change statistical analysis. These capabilities enable mining of ions for molecular co-localization, characteristic molecular profiles, and differential expression. Functions include raw imzML import, peak picking, baseline subtraction, mass alignment, peak integration, normalization, ROI selection, calibration, chemical database search, analyte filtering, image processing, box plot visualization, volcano plot and heatmap visualizations, dimensionality reduction, image clustering, and in situ segmentation. Furthermore, data processed by iMSminer can be easily interfaced to standard deep learning packages and other special-purpose modelling tasks in Python for more advanced use cases. | Yu Tin Lin; Haohui Bao; Troy Scoggins; Boone Prentice | Analytical Chemistry; Chemoinformatics; Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667a255301103d79c50e3e62/original/i-m-sminer-a-data-processing-and-machine-learning-package-for-imaging-mass-spectrometry.pdf |
60c73f5a9abda22efef8ba15 | 10.26434/chemrxiv.7312277.v1 | Ion Mobility Mass Spectrometry Uncovers the Impact of the Patterning of Oppositely Charged Residues on the Conformational Distributions of Intrinsically Disordered Proteins | The global dimensions and amplitudes of conformational fluctuations of intrinsically disordered proteins are governed, in part, by the linear segregation versus clustering of oppositely charged residues within the primary sequence. Ion Mobility-Mass Spectrometry (IM-MS) affords unique advantages for probing the conformational consequences of the linear patterning of oppositely charged residues because it measures and separates proteins electrosprayed from solution on the basis of charge and shape. Here, we use IM-MS to measure the conformational consequences of charge patterning on the C-terminal intrinsically disordered region (p27 IDR) of the cell cycle inhibitory protein p27<sup>Kip1</sup>. We report the range of charge states and accompanying collisional cross section distributions for wild-type p27 IDR and two variants with identical amino acid compositions, k14 and k56, distinguished by the extent of linear mixing versus segregation of oppositely charged residues. Wild-type p27 IDR (k31) and k14 where the oppositely charged residues are more evenly distributed, exhibit a broad distribution of charge states. This is concordant with high degrees of conformational heterogeneity in solution. By contrast, k56 with linear segregation of oppositely charged residues, leads to limited conformational heterogeneity and a narrow distribution of charged states. Molecular dynamics simulations demonstrate that the interplay between chain solvation and intra-chain interactions (self-solvation) leads to conformational distributions that are modulated by salt concentration, with the wild-type sequence showing the most sensitivity to changes in salt concentration. These results suggest that the charge patterning within the wild-type p27 IDR may be optimized to sample both highly solvated and self-solvated conformational states. | Rebecca Beveridge; Lukasz Migas; Rahul Das; Rohit Pappu; Richard Kriwacki; Perdita E. Barran | Supramolecular Chemistry (Org.); Mass Spectrometry; Cell and Molecular Biology; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2018-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5a9abda22efef8ba15/original/ion-mobility-mass-spectrometry-uncovers-the-impact-of-the-patterning-of-oppositely-charged-residues-on-the-conformational-distributions-of-intrinsically-disordered-proteins.pdf |
60c7526aee301c7823c7abc7 | 10.26434/chemrxiv.13296521.v1 | Syngas Molecules as Probes for Defects In 2D Hexagonal Boron Nitride: their Adsorption and Vibrations | <div>
<p>Single-layer, defect-laden
hexagonal boron nitride (<i>dh</i>-BN) is attracting
a great deal of attention for its diverse applications: catalysis on the one
hand, and single photon emission on the other. As possible probes for
identifying some common defects in single-layer <i>h</i>-BN, we present results
of <i>ab initio</i> calculations for the adsorption and vibrational
characteristics of syngas molecules (H<sub>2</sub>, CO, CO<sub>2</sub>) on <i>dh</i>-BN containing one of four types of
defects: nitrogen vacancy (V<sub>N</sub>),
boron vacancy (V<sub>B</sub>),
Stone–Wales defect (SW), and nitrogen substituted by boron (B<sub>N</sub>). Through a
comparative examination of adsorption features, charge transfer, electronic
structure, and vibrational spectrum, we obtain a deep understanding of the
interaction of these molecules with <i>dh</i>-BN
and the role of the defect
states. We find that while CO and CO<sub>2</sub> chemisorb, molecular H<sub>2</sub> physisorbs, but dissociative adsorption of H<sub>2</sub>
is feasible on <i>dh</i>-BN. V<sub>N</sub> and V<sub>B</sub> show
strong affinity for CO
and CO<sub>2</sub> since the defect states induced by them lie close to the
Fermi level. SW does not favor adsorption of these small molecules, as the
process for each is endothermic. At B<sub>N </sub>CO adsorbs strongly but CO<sub>2</sub>
only weakly. Vibrational frequencies of notable modes localized at the adsorbed
molecules are analyzed and suggested as measures for identification of the
defect type. Systematically investigating the adsorption of small molecules on
these defects, we predict that <i>dh</i>-BN
with V<sub>N</sub> is a good
catalyst candidate for CO<sub>2</sub> hydrogenation.</p></div> | Tao Jiang; Duy Le; Takat B. Rawal; Talat
S. Rahman | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7526aee301c7823c7abc7/original/syngas-molecules-as-probes-for-defects-in-2d-hexagonal-boron-nitride-their-adsorption-and-vibrations.pdf |
6575d22729a13c4d471e7729 | 10.26434/chemrxiv-2023-v0r6h | Enantioselective Synthesis of Pyrrolidines by Imidodiphosphorimidate (IDPi)-catalysed anti-hydroamination of alkenes | Chiral pyrrolidines are common structural motives in natural products as well as active pharmaceutical ingredients explaining the need for methods for their enantioselective synthesis. While several, often metal-catalyzed, methods do exist, the enantioselective synthesis of pyrrolidines containing quarternary stereocentres remains challenging. Herein, we report a Brønsted acid-catalysed intramolecular hydroamination, which provides such pyrrolidines from simple starting materials in high yield and enantioselectivity. Key to an efficient reaction was the use of an electron-deficient protective group on nitrogen, the common nosyl protecting group, to avoid deactivation of the Brønsted acid by deprotonation. The reaction proceeds as a stereospecific anti-addition suggesting a concerted reaction. Furthermore, kinetic studies show Michaelis-Menten behaviour suggesting the formation of a precomplex similar to those observed in enzymatic catalysis. | Ulrich Hennecke; Sudip Guria; Alexander N. Volkov; Raffi Khudaverdyan; Ruben Van Lommel; Constantin G. Daniliuc; Frank De Proft | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Acid Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6575d22729a13c4d471e7729/original/enantioselective-synthesis-of-pyrrolidines-by-imidodiphosphorimidate-id-pi-catalysed-anti-hydroamination-of-alkenes.pdf |
60c74dd4469df4f975f44372 | 10.26434/chemrxiv.12663065.v1 | Experimental Characterization of the Association of Nine Novel Cyclodextrin Derivatives with Two Guest Compounds | We investigate the binding of native β-cyclodextrin (β-CD) and eight novel β-CD derivatives with two different
guest compounds, using isothermal calorimetry (ITC) and 2D NOESY NMR. In all cases, the stoichiometry is 1:1
and binding is exothermic. Overall, modifications at the 3’ position of β-CD, which is at the secondary face, weaken
binding by several kJ/mol relative to native β-CD, while modifications at the 6’ position (primary face) maintain or
somewhat reduce the binding affinity. The variations in binding enthalpy are larger than the variations in binding
free energy, so entropy-enthalpy compensation is observed. Characterization of the bound conformations with
NOESY NMR shows that the polar groups of the guests may be situated at either face, depending on the host
molecule, and, in some cases, both orientations are populated. The present results were used in the SAMPL7 blinded
prediction challenge whose results are detailed in the same special issue of JCAMD. | Kathryn Kellett; David Slochower; Michael Schauperl; Brendan M. Duggan; Michael Gilson | Supramolecular Chemistry (Org.); Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2020-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dd4469df4f975f44372/original/experimental-characterization-of-the-association-of-nine-novel-cyclodextrin-derivatives-with-two-guest-compounds.pdf |
638e413ccfb5ffc9185e47ad | 10.26434/chemrxiv-2022-nd0bs | The Topology of Molecules with Twelve Fused Phenyl Rings ([12]Circulenes): Rings, Infinitenes, and Möbius Infinitenes | Following the recent preparation of infinitene (J. Am. Chem. Soc. 2022, 144, 862-871), a computational (ωB97XD/6-311G(d)) exploration of 42 isomeric compounds with 12 fused phenyl rings identified structures with linking number of zero (ring, saddle, and ribbon shapes), two (infinitene-like shape), and one (Möbius infinitene shape) is reported. An infinitene isomer composed of two [5]helicene fragments connected to two stacked phenyl rings and a Möbius infinitene isomer are identified that are more stable than the known infinitene. The energies of the structures are examined by assessing their strain energies, π-stacking, and possible aromaticity. Examples of fused phenyl molecules with linking numbers of 3, 4, 5, and 6 are shown, indicating the potential topological range that these molecules can possess. | Steven Bachrach | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638e413ccfb5ffc9185e47ad/original/the-topology-of-molecules-with-twelve-fused-phenyl-rings-12-circulenes-rings-infinitenes-and-mobius-infinitenes.pdf |
66dfb68751558a15ef8e240e | 10.26434/chemrxiv-2024-wmscl | Electrophilic Halogenation of Allenoates and 3-Alkynoates: Syn-thesis of 1,4-Dicarbonyl 3-(E)-Haloalkenes and Mechanistic Investigations | Herein, an electrophilic halogenation of di- or trisubstituted allenoates and 3-alkynoates is demonstrated with NBS and NIS reagents under DABCO catalysis. The protocol affords densely functionalized 1,4-dicarbonyl 3-haloalkenes in good yields with excellent (E)-stereoselectivity (up to 83% yield, >20:1 dr). The role of the Brønsted base in the unusual transformation is demystified through control experiments and computational studies. The deliverables are identified as good synthons for various synthetic transformations and valuable targets for biologically active pyridazine scaffolds. | Paru Jamwal; Yumnam Nganthoinganbi; Ming-Kang Tsai; Ramani Gurubrahamam | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dfb68751558a15ef8e240e/original/electrophilic-halogenation-of-allenoates-and-3-alkynoates-syn-thesis-of-1-4-dicarbonyl-3-e-haloalkenes-and-mechanistic-investigations.pdf |
60c7488b567dfe7043ec49fe | 10.26434/chemrxiv.11923632.v1 | The Total Synthesis of (–)-Scabrolide a | The first total synthesis of the norcembranoid diterpenoid scabrolide A is disclosed. The route begins with the synthesis of two chiral pool-derived fragments, which undergo a convergent coupling to expediently introduce all 19 carbon atoms of the natural product. An intramolecular Diels–Alder reaction and an enone-olefin cycloaddition/fragmentation sequence are then employed to construct the fused [5–6–7] linear carbocyclic core of the molecule and to complete the total synthesis. | Nicholas Hafeman; Steven
A. Loskot; Chris Reimann; Beau P. Pritchett; Scott
C. Virgil; Brian Stoltz | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7488b567dfe7043ec49fe/original/the-total-synthesis-of-scabrolide-a.pdf |
66e4e45a12ff75c3a142efb5 | 10.26434/chemrxiv-2024-mn4wm | OpencanSARchem: chemistry registration and standardization pipeline for FAIR integration of bioassay data | There is an explosion of available chemical and bioactivity information that is used through AI and machine learning for drug discovery. The community needs a computationally efficient and openly available pipeline to harmonize and register disparate sources of chemical structural data to integrate the available bioactivity information. Previously, canSARchem addressed these needs, though it was computationally intensive and required commercial software. Here we describe OpencanSARchem, an open-source and computationally efficient standardization and registration pipeline, which has addressed the limitations of our original pipeline, while still generating chemically valid tautomers. Using DFT and ab initio methods, we the free energy differences of tautomer pairs generated by the two pipelines to understand the energetic consequences of our utility selection. Statistically significant free energy differences were observed between tautomers selected by each utility, with the median difference being approximately 2 kcal/mol. We assess this energetic consequence as an acceptable compromise to democratize this method and meet the needs of the broader community. | Rezvan Chitsazi; Phillip W Gingrich; James P Long; Chong Wu; Bissan Al-Lazikani | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e4e45a12ff75c3a142efb5/original/opencan-sa-rchem-chemistry-registration-and-standardization-pipeline-for-fair-integration-of-bioassay-data.pdf |
60c7538a4c8919ab1dad434c | 10.26434/chemrxiv.13508019.v1 | Electrocatalytic O2 Reduction by an Organometallic Pd(III) Complex via a Binuclear Pd(III) Intermediate | <p>The development of
electrocatalysts for the selective O<sub>2</sub>-to-H<sub>2</sub>O conversion,
the O<sub>2</sub> reduction reaction (ORR), is of great interest for improving
the performance of fuel cells. In this context, molecular catalysts that are known
to mediate the 4H<sup>+</sup>/4e<sup>–</sup> reduction of O<sub>2</sub> to H<sub>2</sub>O
tend to be marred by limited stability and selectivity in controlling the
multi-proton and multi-electron transfer steps. Thus, evaluation of new transition
metal complexes, including organometallic species, for ORR reactivity could
uncover new molecular catalysts with improved properties. We have previously
reported the synthesis and characterization of various organometallic Pd<sup>III</sup>
complexes stabilized by the tetradentate ligand N,N′-di-<i>tert</i>-butyl-2,11-diaza[3.3](2,6)pyridinophane
(<sup>t</sup>BuN4). These complexes were shown to react with O<sub>2</sub> and
undergo oxidatively-induced C–C and C–heteroatom bond formation reactions in
the presence of O<sub>2</sub>. These O<sub>2</sub>-induced oxidative
transformations prompted us to evaluate the ORR reactivity of such
organometallic Pd complexes, which to the best of our knowledge has never been studied
before for any molecular Pd catalyst. Herein, we report the ORR reactivity of
the [(<sup>t</sup>BuN4)Pd<sup>III</sup>MeCl]<sup>+</sup> complex, under both homogeneous
and heterogeneous conditions in a non-aqueous and acidic aqueous electrolyte,
respectively. Cyclic voltammetry and hydrodynamic electrochemical studies for [(<sup>t</sup>BuN4)Pd<sup>III</sup>MeCl]<sup>+</sup>
revealed the electrocatalytic reduction of O<sub>2</sub> to H<sub>2</sub>O proceeds
with Faradaic efficiencies (FE) of 50-70% in the presence of acetic acid (AcOH)
in MeCN. The selectivity toward H<sub>2</sub>O production further improved to a
FE of 80-90% in an acidic aqueous medium (pH 0), upon immobilization of the molecular
catalyst onto edge plane graphite (EPG) electrodes. Analysis of electrochemical
data suggests the formation of a binuclear Pd<sup>III</sup> intermediate in
solution, likely a Pd<sup>III</sup>-peroxo-Pd<sup>III</sup> species, which dictates
the thermochemistry of the ORR process for [(<sup>t</sup>BuN4)Pd<sup>III</sup>MeCl]<sup>+</sup>
in MeCN, and thus being a rare example of a bimolecular ORR process. The maximum
second-order turnover frequency TOF<sub>max</sub><sup>(2)</sup> = 2.76 x 10<sup>8</sup> M<sup>–1</sup>
sec<sup>–1</sup> was determined for 0.32 mM of [(<sup>t</sup>BuN4)Pd<sup>III</sup>MeCl]<sup>+</sup>
in the presence of 1 M AcOH in O<sub>2</sub>-saturated MeCN with an overpotential
of 0.32 V. By comparison, a comparatively lower TOF<sub>max</sub><sup>(2)</sup>
= 1.25 x 10<sup>5</sup> M<sup>–1</sup>
sec<sup>–1</sup> at a higher overpotential of 0.8 V was observed for [(<sup>t</sup>BuN4)Pd<sup>III</sup>MeCl]PF<sub>6</sub>
adsorbed onto EPG electrodes in O<sub>2</sub>-saturated 1 M H<sub>2</sub>SO<sub>4</sub>
aqueous solution. Overall, reported herein is a detailed ORR reactivity study using
a novel Pd<sup>III</sup> organometallic complex and benchmark its selectivity and
energetics toward O<sub>2</sub> reduction in MeCN and acidic aqueous solutions.
</p> | Soumalya Sinha; Liviu M. Mirica | Electrocatalysis; Heterogeneous Catalysis; Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7538a4c8919ab1dad434c/original/electrocatalytic-o2-reduction-by-an-organometallic-pd-iii-complex-via-a-binuclear-pd-iii-intermediate.pdf |
61689f3fbe1074ceff9d3c99 | 10.26434/chemrxiv-2021-7gxtw | New Hypercoordinating Organostannanes for the Modular Functionalization of Mono- and Polystannanes: Synthetic and Computational Studies | In this paper we outline two major findings. The first is that we describe how designer hypercoordinate stannanes can be made from simple substitutions, and by extension, designer tin polymers, at least partially, using these methods. The second is that using advanced DFT methods, 119Sn NMR frequencies have been accurately calculated for select hypercoordinate tin compounds. This accuracy provides a means for further investigation of an important bonding interaction in the solution phase, and is of significant interest to small molecule tin chemists. | Jeffrey Pau; Jung-Won Choi; Kaitlyn Silverthorne; Mokhamed Ranne; R. Stephen Wylie; Robert Gossage; Alan Lough; Daniel Foucher | Inorganic Chemistry; Polymer Science; Conducting polymers; Coordination Chemistry (Inorg.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61689f3fbe1074ceff9d3c99/original/new-hypercoordinating-organostannanes-for-the-modular-functionalization-of-mono-and-polystannanes-synthetic-and-computational-studies.pdf |
60dec7e96b8d896a176af408 | 10.26434/chemrxiv-2021-g6j4d-v5 | Failure-experiment-supported optimization of poorly reproducible synthetic conditions for novel lanthanide metal-organic frameworks with two-dimensional secondary building units | A series of novel metal organic frameworks with lanthanide double-layer-based inorganic subnetworks (KGF-3) was synthesized assisted by machine learning. Pure KGF-3 was difficult to isolate in the initial screening experiments. The synthetic conditions were successfully optimized by extracting the dominant factors for KGF-3 synthesis using two machine-learning techniques. Cluster analysis was used to classify the obtained PXRD patterns of the products and to decide automatically whether the experiments were successful or had failed. Decision tree analysis was used to visualize the experimental results, with the factors that mainly affected the synthetic reproducibility being extracted. The water adsorption isotherm revealed that KGF-3 possesses unique hydrophilic pores, and impedance measurements demonstrated good proton conductivities (σ = 5.2 × 10<sup>−4</sup> S cm<sup>−1</sup> for KGF-3(Y)) at a high temperature (363 K) and high relative humidity (95%).<br /> | Yu Kitamura; Emi Terado; Zechen Zhang; Hirofumi Yoshikawa; Tomoko Inose; Hiroshi Uji-i; Masaharu Tanimizu; Akihiro Inokuchi; Yoshinobu Kamakura; Daisuke Tanaka | Inorganic Chemistry; Coordination Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dec7e96b8d896a176af408/original/failure-experiment-supported-optimization-of-poorly-reproducible-synthetic-conditions-for-novel-lanthanide-metal-organic-frameworks-with-two-dimensional-secondary-building-units.pdf |
65de6a1c66c1381729b6d6fc | 10.26434/chemrxiv-2024-gmw9l | Advances in mass spectrometry-enabled multiomics at single-cell resolution | Biological organisms are multifaceted, intricate systems where slight perturbations can result in extensive changes in gene expression, protein abundance and/or activity, and metabolic flux. These changes occur at different timescales, spatially across cells of heterogenous origins, and within single cells. Hence multimodal measurements at the smallest biological scales are necessary to capture dynamic changes in heterogenous biological systems. Of the analytical techniques used to measure biomolecules, mass spectrometry has proven to be a powerful option due to its sensitivity, robustness, and flexibility with regards to breadth of biomolecules that can be analyzed. Recently many studies have coupled mass spectrometry to other analytical techniques with the goal of measuring multiple modalities from the same single-cell. It is with these concepts in mind that we focus this Review on mass spectrometry-enabled multiomic measurements at single-cell or near-single-cell resolution. | Rashmi Kumar; Kevin Zemaitis; James Fulcher; Ljiljana Pasa-Tolic | Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Mass Spectrometry; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65de6a1c66c1381729b6d6fc/original/advances-in-mass-spectrometry-enabled-multiomics-at-single-cell-resolution.pdf |
60c756e50f50db0390398186 | 10.26434/chemrxiv.12915779.v3 | A machine learning platform to estimate anti-SARS-CoV-2 activities | <p>
</p><div>
<div>
<div>
<div>
<p>Strategies for drug discovery and repositioning are an urgent need with respect to COVID-19. Here we present
"REDIAL-2020", a suite of computational models for estimating small molecule activities in a range of SARS-CoV-2
related assays. Models were trained using publicly available, high throughput screening data and by employing different
descriptor types and various machine learning strategies. Here we describe the development and the usage of eleven
models spanning across the areas of viral entry, viral replication, live virus infectivity, in vitro infectivity and human cell
toxicity. REDIAL-2020 is available as a web application through the DrugCentral web portal
(http://drugcentral.org/Redial). In addition, the web-app provides similarity search results that display the most similar
molecules to the query, as well as associated experimental data. REDIAL-2020 can serve as a rapid online tool for
identifying active molecules for COVID-19 treatment.
</p>
</div>
</div>
</div>
</div><br /><p></p> | Govinda KC; Giovanni Bocci; Srijan Verma; Mahmudulla Hassan; Jayme Holmes; Jeremy Yang; suman sirimulla; Tudor
I. Oprea | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756e50f50db0390398186/original/a-machine-learning-platform-to-estimate-anti-sars-co-v-2-activities.pdf |
67b304ed81d2151a02d25a0f | 10.26434/chemrxiv-2025-tl41k | Operando Spectroscopic Insights into the Key Role of Phase
Engineering in Cobalt Diselenide for Overall Water Electrolysis | Identification of the true catalytically active species/sites
holds the key to new catalyst design. In this study, combination of complementary operando surface/bulk sensitive spectroscopic techniques and density functional theory (DFT) calculations establish a clear picture of the structure-activity relations in marcasite- and pyrite-type CoSe2 for overall water splitting. Our results reveal that
under acidic conditions marcasite CoSe2 undergoes slight surface corrosion, producing disordered [CoSe6] motifs with the active Se sites for catalyzing the hydrogen evolution reaction (HER). In contrast, during the alkaline HER, the marcasite CoSe2 initially interacts with the electrolyte to reconstruct an O-rich covered surface, which
subsequently undergoes potential-driven restructuring to generate the metallic cobalt species as the true active species. Such dynamic changes of the active species/sites along with variations in pH values were not observed in pyrite CoSe2, either with or without heteroatom substitution, highlighting the significant importance of phase engineering in managing the HER kinetics. Further operando spectroelectrochemical monitoring demonstrates that the in situ generation of highly disordered Co4+ species is a common denominator of CoSe2 catalysts for the oxygen evolution reaction (OER). This study directly evidences the dynamic influence of local coordination geometries of the catalytic active centers on the underlying catalytic reaction kinetics. | Yonggui Zhao; Nanchen Dongfang; Rolf Erni; Marcella Iannuzzi; Greta R. Patzke | Materials Science; Catalysis; Energy; Catalysts; Electrocatalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b304ed81d2151a02d25a0f/original/operando-spectroscopic-insights-into-the-key-role-of-phase-engineering-in-cobalt-diselenide-for-overall-water-electrolysis.pdf |
6685595d01103d79c5e7d5fa | 10.26434/chemrxiv-2023-xqlv6-v2 | Automatic orbital pair selection for multi-level local coupled-cluster based on orbital maps | We present an automatic, orbital-map based orbital pair selection scheme for multi-level local coupled-cluster approaches that exploits the locality of chemical reactions and concentrates on the part of the molecule directly involved in the reaction. The previously introduced pair-selected multi-level extension to domain-based local pair natural orbital coupled-cluster with singles, doubles, and semi-canonical perturbative triples [DLPNO-CCSD(T0)] partitions the orbital pairs according to relative changes in pair correlation energies [J. Chem. Phys. 157, 064102 (2022)]. To this end, maps between localized orbitals are required which in turn require maps between the atoms of structures along reaction paths. So far, these atom maps have been manually determined, which can be a (human) time-consuming procedure. In order to automatize this procedure, we present an atom mapping algorithm based on the principle of minimum chemical distance that incorporates the orientation through dihedral angles. Within the methodology of this algorithm, linear assignment problems are addressed and explicitly solved, giving rise to the idea of considering the orbital mapping problem as such. This led to a new strategy to obtain orbital maps that proves advantageous over the previously used direct orbital selection. Along with a modified orbital pair prescreening, this results in an improved variant of the pair-selected multi-level DLPNO-CCSD(T0) method. For given combinations of pair selection thresholds, the performance of this approach is demonstrated for various reaction types showing a significant efficiency gain and accurate results due to beneficial, systematic error cancellation. The presented method operates in a black-box manner due to its fully-automatized algorithms with only the need to specify a single target-accuracy parameter. Core orbitals can be included in the correlation treatment in a computationally cheap way such that there is no need for the frozen-core approximation. Additionally, we demonstrate that basis set extrapolation techniques can be applied. In this context, the approach shows deficiencies for the use of large basis sets, especially with diffuse basis functions, which can be traced back to the semi-canonical triples correction. | Lukas Lampe; Johannes Neugebauer | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6685595d01103d79c5e7d5fa/original/automatic-orbital-pair-selection-for-multi-level-local-coupled-cluster-based-on-orbital-maps.pdf |
63f93219897b18336f126115 | 10.26434/chemrxiv-2023-qnn6v | On the inadequacy of Stern-Volmer and FRET in describing quenching in binary donor-acceptor solutions | Quantitative fluorescence quenching is a common analytical approach to studying the mechanism of chemical reactions. The Stern-Volmer (S-V) equation is the most common expression used to analyzing quenching behavior, and can be used to extract kinetics in complex environments. However, the approximations underlying the S-V equation are incompatible with Forster Resonance Energy Transfer (FRET) acting as the primary quenching mechanism. The nonlinear distance dependence of FRET leads to significant departures from standard S-V quenching curves, both by modulating the interaction range of donor species, and increasing the effect of component diffusion. We demonstrate this inadequacy by probing the fluorescence quenching of long-lifetime lead sulfide quantum dots (QDs) mixed with plasmonic covellite copper sulfide (CuS) nanodisks (NDs), which serve as perfect fluorescent quenchers. By applying kinetic Monte-Carlo methods which consider particle distributions and diffusion we are able to quantitatively reproduce experimental data which shows significant quenching at very small concentrations of NDs. Distribution of interparticle distances and diffusion are concluded to play important roles in the fluorescence quenching, particularly in the shortwave infrared, where photoluminescent lifetimes are often long relative to diffusion time-scales. | Xuanheng Tan; Justin Caram | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f93219897b18336f126115/original/on-the-inadequacy-of-stern-volmer-and-fret-in-describing-quenching-in-binary-donor-acceptor-solutions.pdf |
60c74a1af96a000abc287388 | 10.26434/chemrxiv.12152979.v1 | The Solid-State Emission of Bilirubin | <p>Bilirubin (BR)
is a human-biological compound formed during the haem metabolism that is
insoluble in most solvents. BR has shown short emission lifetime with low
quantum yield in limited number of solvents, due to the non-radiative ultrafast
isomerization process. However, in solid-state, red-shifted emission of
long-lived species of BR are detected at room temperature, due to the
aggregation-induced emission formed by Frenkel exciton of J-system. This solid-state emission of BR depends on the
crystal quality of BR as shown by SEM and XRD. This study allows for better
understandings of the photophysics of BR in solid-state, opening opportunities for
its applications in luminescent biological sensors. </p> | Ahmed El-Zohry; Taha Ahmed; Burkhard Zietz | Biophysical Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Surface; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a1af96a000abc287388/original/the-solid-state-emission-of-bilirubin.pdf |
60c758aa842e656672db4890 | 10.26434/chemrxiv.14573148.v1 | Ti(OiPr)4-Enabled Dual Photoredox and Nickel-Catalyzed Arylation and Alkenylation of Cyclopropanols | <p>In this
article, we report an application of cyclopropanols as coupling partners in the
dual photoredox/nickel catalyzed reaction with aryl and vinyl bromides. We
found that this cross-coupling proceeds smoothly in the presence of Ti(OiPr)<sub>4</sub>
as an additive to provide β-aryl or γ,δ-unsaturated ketones. </p> | Nastassia A. Varabyeva; Maryia V. Barysevich; Yauhen Aniskevich; Alaksiej Hurski | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758aa842e656672db4890/original/ti-oi-pr-4-enabled-dual-photoredox-and-nickel-catalyzed-arylation-and-alkenylation-of-cyclopropanols.pdf |
6690f94001103d79c5ccef96 | 10.26434/chemrxiv-2024-z9qcn | A new physical picture to achieve small singlet-triplet energy gaps in high-efficiency polycyclic heteroaromatic emitters | The manipulation of the singlet-triplet energy gap (ΔES1T1) is an active area of research in the field of organic semiconductor materials. In polycyclic heteroaromatic emitters, which possess a great potential for application in ultra-high-definition displays, the origin of a small ΔES1T1 and its relationship with molecular structure still remain poorly established. Here, based on configuration-interaction theory, we derive a new effective expression for ΔES1T1, in which ΔES1T1 positively depends both on 2KHL (where KHL is the exchange energy between the HOMO and LUMO levels) and on the energy gap between the LUMO and LUMO+1 levels (ΔELUMO-LUMO+1). This physical picture of ΔES1T1 goes well beyond the simple HOMO→LUMO description that has been routinely applied in conventional donor-acceptor-type molecules and is validated over a series of more than sixty reported polycyclic heteroaromatic emitters. It allows us to suggest that an appropriate introduction of meta-substituted molecular fragments, which have small KHL and ΔELUMO-LUMO+1 values, is an effective way of designing molecules with smaller ΔES1T1. Importantly, a proof-of-concept molecule, IV-DABNA, was synthesized and demonstrates an extremely small ΔES1T1 (0.02 eV); its rate of reverse intersystem crossing is as fast as 4.4×106 s-1, the highest value reported in such systems. Sky-blue electroluminescent devices exploiting IV-DABNA as an emitter exhibit a remarkable maximum external quantum efficiency (EQE) of 32.1% with a largely suppressed roll-off (5.1%) at 1000 cd m-2. Overall, our work provides a new physical picture to reach a small ΔES1T1 in emerging polycyclic heteroaromatic emitters, which will accelerate the development of high-efficiency systems. | Rajat Walia; Xin Xiong; Xiao‐Chun Fan; Kai Wang; Yi-Zhong Shi; Xun Tang; Jean-Luc Bredas; Chihaya Adachi; Xian-Kai Chen; Xiao-Hong Zhang | Materials Science; Dyes and Chromophores | CC BY NC 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6690f94001103d79c5ccef96/original/a-new-physical-picture-to-achieve-small-singlet-triplet-energy-gaps-in-high-efficiency-polycyclic-heteroaromatic-emitters.pdf |
60c74041469df4ed37f42bf4 | 10.26434/chemrxiv.7679864.v1 | Order Parameters, Orientational Distribution Functions and Heliconical Tilt Angles of Oligomeric Liquid Crystals | We
compare the order parameters, orientational distribution functions (ODF) and
heliconical tilt angles of the TB phase exhibited by a liquid-crystalline dimer
(CB7CB) to a tetramer (O47) and hexamer (O67) by SAXS/WAXS. Following the N-TB
phase transition we find that all order parameters decrease, and while 〈P2 〉 remains positive 〈P4 〉 becomes negative. For all three materials the
order parameter 〈P6 〉 is near zero in both phases. The ODF is
sugarloaf-like in the nematic phase and volcano-like in the TB phase, allowing
us to estimate the heliconical tilt angle of each material and its thermal
evolution. The heliconical tilt angle appears to be largely
independent of the material studied despite the differing number of mesogenic
units. | Richard Mandle; John W. Goodby | Liquid Crystals; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74041469df4ed37f42bf4/original/order-parameters-orientational-distribution-functions-and-heliconical-tilt-angles-of-oligomeric-liquid-crystals.pdf |
6197e5e447f47d54a5a8de0e | 10.26434/chemrxiv-2021-4r4fc | Medium-Length Lipids Facilitate Cell-Permeability and Bioactivity | The majority of bioactive molecules act on membrane proteins or intracellular targets and therefore needs to partition into or cross biological membranes. Natural products often exhibit lipid modifications to facilitate critical molecule-membrane interactions and in many cases their bioactivity is markedly reduced upon removal of a lipid group. However, despite its importance in nature, lipid-conjugation of small molecules is not commonly used in chemical biology and medicinal chemistry, and the effect of such conjugation has not been systematically studied. To understand the composition of lipids found in natural products, we carried out a chemoinformatic characterization of the ‘natural product lipidome’. According to this analysis, lipidated natural products predominantly contain saturated linear medium-length lipids, which are significantly shorter than those found in membranes and lipidated proteins. To study the usefulness of such modifications in probe design, we systematically explored the effect of lipid conjugation on five different small molecule chemotypes and find that permeability, cellular retention, subcellular localization, and bioactivity can be significantly modulated depending on the type of lipid tail used. We demonstrate that medium-length lipid tails can render impermeable molecules cell-permeable and switch on their bioactivity. Saturated medium-length lipids (e.g. C10) are found to be ideal for the bioactivity of small molecules in mammalian cells, while saturated long-chain lipids (e.g. C18) often significantly reduce bioavailability and activity. Together, our findings suggest that conjugation of small molecules with medium-length lipids could be a powerful strategy for the design of probes and drugs. | Johannes Morstein; Alice Capecchi; Konstantin Hinnah; Jerome Petit-Jacques; Jean-Louis Reymond; Dirk Trauner | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2021-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6197e5e447f47d54a5a8de0e/original/medium-length-lipids-facilitate-cell-permeability-and-bioactivity.pdf |
60c741c70f50dbffa3395bb9 | 10.26434/chemrxiv.8126879.v1 | A Computational Survey of Semiconductors for Power Electronics | Power electronics (PE) are used to control and convert electrical energy in a wide range of applications from consumer products to large-scale industrial equipment. While Si-based power devices account for the vast majority of the market, wide band gap semiconductors such as SiC, GaN, and Ga2O3 are starting to gain ground. However, these emerging materials face challenges due to either non-negligible defect densities, or high synthesis and processing costs, or poor thermal properties. Here, we report on a broad computational survey aimed to identify promising materials for future power electronic devices beyond SiC, GaN, and Ga2O3. We consider 863 oxides, sulfides, nitrides, carbides, silicides, and borides that are reported in the crystallographic database and exhibit finite calculated band gaps. We utilize ab initio methods in conjunction with models for intrinsic carrier mobility, and critical breakdown field to compute the widely used Baliga figure of merit. We also compute the lattice thermal conductivity as a screening parameter. In addition to correctly identifying known PE materials, our survey has revealed a number of promising candidates exhibiting the desirable combination of high figure of merit and high lattice thermal conductivity, which we propose for further experimental investigations. | Prashun Gorai; Robert McKinney; Nancy Haegel; Andriy Zakutayev; Vladan Stevanovic | Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Power; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741c70f50dbffa3395bb9/original/a-computational-survey-of-semiconductors-for-power-electronics.pdf |
657569e25bc9fcb5c97bed06 | 10.26434/chemrxiv-2023-tc9xx | Functionalized polyamine synthesis with photoredox catalysis | Polyamines, such as putrescine and spermidine, are pivotal in various biological processes across living organisms. Despite their significance, structurally modified polyamines offer a less-explored avenue for discovering bioactive compounds. The limitation is attributed to the synthetic difficulty of accessing functionalized polyamines. In this study, we accomplished photoredox-catalyzed functionalization of polyamines to diversify their structure. The rapid functionalization allows attaching fluorophores to the target polyamine, facilitating the development of molecular probes for advancing chemical biology studies. | Yuta Makihara; Bumpei Maeda; Ryohei Akiyoshi; Daisuke Tanaka; Kei Murakami | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657569e25bc9fcb5c97bed06/original/functionalized-polyamine-synthesis-with-photoredox-catalysis.pdf |
676449d6fa469535b91b2ade | 10.26434/chemrxiv-2024-5xwv0 | N-Heterocyclic Carbene-Based Copolymers for Templated Synthesis and Stabilization of Gold Nanoparticles | Surface functionalization and colloidal stability are pivotal for numerous applications of gold nanoparticles (Au-NPs). Over the past decade, N-heterocyclic carbenes (NHCs) have emerged as promising ligands for stabilizing Au-NPs owing to their ease of synthesis, structural diversity, and strong metal-ligand bonds. Here, we introduce Au(I)-NHC copolymer scaffolds as novel precursors to multidentate NHC-protected Au-NPs. Ring-opening metathesis copolymerization of a norbornene-appended Au(I)-NHC complex with another functionalized norbornene comonomer provides a diverse array of Au(I)-NHC copolymers with modular compositions and structures. Upon reduction, these copolymers yield multidentate polyNHC-coated Au-NPs with varied properties and corona functionalities dictated by the secondary monomer. These nanoparticles exhibit greater size homogeneity compared to those prepared using existing methods for the bottom-up synthesis of polyNHC-Au-NPs and demonstrate exceptional stability against aggregation in various buffers, cell culture media, and under exposure to electrolytes, oxidants, and exogenous thiols over extended periods. Moreover, we showcase the first example of post-synthetic surface functionalization reactions of polyNHC-Au-NPs while maintaining colloidal stability, highlighting their robustness and potential for applications such as bioconjugation. Overall, these findings underscore the potential of our ROMP-derived NHC-containing copolymers as highly tunable and versatile multidentate ligands that may be suitable for other inorganic colloids and flat surfaces with a wide array of applications. | Suong Nguyen; Christopher Brown; Wenxu Zhang; Landon Kilgallon; Jeremiah Johnson | Polymer Science; Nanoscience; Inorganic Polymers; Polymerization (Polymers); Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676449d6fa469535b91b2ade/original/n-heterocyclic-carbene-based-copolymers-for-templated-synthesis-and-stabilization-of-gold-nanoparticles.pdf |
64310de30784a63aeebe2696 | 10.26434/chemrxiv-2023-wrq5d | Rapid Access to Free Phenols by Photocatalytic Acceptorless Dehydrogenation of Cyclohexanones at Room Temperature | Phenols are ubiquitous substructures in natural products and bioactive compounds. However, practical methods for the direct construction of phenols under mild conditions remains challenging. Herein, a photocatalytic acceptorless dehydrogenative aromatization of cyclohexanones or cyclohexenones at room temperature has been developed. The reaction features the visible-light and cobalt co-catalyzed sequential dehydrogenation of in-situ formed enol silyl ethers, which are regarded as a challenging process. This operationally simple method enables a series of phenols with diverse substitution patterns from cyclohexanones or cyclohexenones, providing a general and straightforward method for the synthesis of phenols from simple starting materials under mild conditions. | Wei Shu; Lin Min; Jia-Ni Lin | Organic Chemistry; Catalysis; Homogeneous Catalysis; Photocatalysis; Redox Catalysis | CC BY 4.0 | CHEMRXIV | 2023-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64310de30784a63aeebe2696/original/rapid-access-to-free-phenols-by-photocatalytic-acceptorless-dehydrogenation-of-cyclohexanones-at-room-temperature.pdf |
63d7e620ab681c2c9d20ef3a | 10.26434/chemrxiv-2023-4g7qv | Encapsulated or amphiphilic liposomal Fe(III) coordination complexes for MRI studies of tumor uptake and clearance | Liposomes containing high-spin Fe(III) coordination complexes were prepared towards the production of MRI probes with improved relaxivity and rapid pharmacokinetic clearance in mice. The amphiphilic Fe(III) complexes were anchored into the liposome with two alkyl chains to give a coordination sphere containing mixed amide hydroxypropyl pendant groups. Three types of MRI probes were prepared including those with intraliposomal Fe(III) complex (LipoA) alone, amphiphilic Fe(III) complex (LipoB) or both intraliposomal and amphiphilic complex (LipoC). Water proton relaxivities r1 and r2 were measured and compared to a small molecule macrocyclic Fe(III) complex containing similar donor groups. Liposomes with amphiphilic Fe(III) complex (LipoB) have a per particle relaxivity of 37,000 and a per iron relaxivity of 2.6 mM-1s-1 in solutions with pH 7.2, 34 C at 1.4 T. Liposomes containing both amphiphilic and intraliposomal Fe(III) complexes (lipoC) have reduced per iron relaxivity of 0.8 mM-1s-1 in solution consistent with quenching of the interior Fe(III) complex relaxivity and per particle relaxivity of 42 ,000 mM-1s-1. Liposomes containing only encapsulated Fe(III) complex have a lower relaxivity of 0.46 mM-1s-1 per iron complex. Studies show that lipoB and lipoC produce enhanced signal in the CT26 tumors of BALB/c mice. However, the biodistribution and clearance of the liposomal nanoparticles differs greatly. LipoB is a blood pool agent with a long circulation time whereas lipoC is cleared more rapidly through both renal and hepatobiliary pathways. | MD Saiful I Chowdhury; Elizabeth Kras; Steven G. Turowski; Joseph A Spernyak; Janet Morrow | Biological and Medicinal Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d7e620ab681c2c9d20ef3a/original/encapsulated-or-amphiphilic-liposomal-fe-iii-coordination-complexes-for-mri-studies-of-tumor-uptake-and-clearance.pdf |
6274ac45809e322cba850159 | 10.26434/chemrxiv-2022-xn8dq | Ring-Opening Metathesis Polymerization of Pyridinonorbornenes Synthesized from 2,3-Pyridynes
| Pyridine-containing polymers are promising materials for a variety of applications from the capture of contaminants to the self-assembly of block copolymers. However, the coordinative ability and the innate basicity of the pyridine motif drastically limit the scope of pyridine-based monomers that can undergo living polymerization. For example, processes relying on transition metal catalysts are rarely amenable to controlled polymerizations because of coordination of the pyridine nitrogen to the metal center. Herein, we report the expedient synthesis of a family of pyridinonorbornene monomers via a [4+2] cycloaddition between 2,3-pyridynes and cyclopentadiene. Careful structural design of the monomer allowed the preparation of polypyridinonorbornenes via ring-opening metathesis polymerization (ROMP) with living characteristics. These unusual macromolecules exhibited high Tg and Td. Investigation of the polymerization kinetics and of the reactivity of the chain ends shed light on the influence of monomer coordination on the chain-growth mechanism. | Sarah N. Hancock; Nattawut Yuntawattana; Sara M. Valdez; Quentin Michaudel | Organic Chemistry; Catalysis; Polymer Science; Organic Synthesis and Reactions; Polymerization (Polymers); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6274ac45809e322cba850159/original/ring-opening-metathesis-polymerization-of-pyridinonorbornenes-synthesized-from-2-3-pyridynes.pdf |
60c74127f96a00a99d2863c0 | 10.26434/chemrxiv.7976003.v1 | A Simple Chemical Guide for Finding Novel n-type Dopable Zintl Pnictide Thermoelectric Materials | Computations have predicted good thermoelectric performance for a number of Zintl phases when doped <i>n</i>-type. Combined with the successful experimental realization of <i>n</i>-type KGaSb<sub>4</sub>, KAlSb<sub>4</sub>, and Mg<sub>3</sub>Sb<sub>2</sub> with zT>1, this has fueled efforts to discover novel <i>n</i>-type dopable Zintl phases. However, a majority of Zintl phases exhibit strong proclivity toward <i>p</i>-type doping and prior successes in finding <i>n</i>-type dopable Zintls were largely serendipitous. Herein we use modern first-principles defect calculations to study trends in the dopability of Zintl pnictides and find that the average oxidation state of the anion is a useful chemical guide to identify novel <i>n</i>-type dopable phases. Specifically, we observe that Zintl pnictides with average oxidation of the anion near -1 are<i> n</i>-type dopable. The trend is mainly a consequence of the high formation energy of native acceptor defects (<i>e.g.</i> cation vacancies) and the resulting absence of charge (electron) compensation. Using the oxidation state guide in conjunction with a descriptor of thermoelectric performance, we conduct a large-scale materials search and identify promising candidates that are <i>n</i>-type dopable. | Prashun Gorai; Anuj Goyal; Eric S. Toberer; Vladan Stevanovic | Solid State Chemistry; Theory - Computational; Piezoelectricity and Thermoelectricity; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74127f96a00a99d2863c0/original/a-simple-chemical-guide-for-finding-novel-n-type-dopable-zintl-pnictide-thermoelectric-materials.pdf |
60c75524bdbb89a5faa3a78a | 10.26434/chemrxiv.14034605.v1 | Highly Sensitive Optical Sensor for Selective Detection of Fluoride Level in Drinking Water: Methodology to Fabrication of Prototype Device | <p><b>Excess consumption of fluoride
through drinking water and its detrimental effects on human health have been a serious
global concern. Therefore, frequent monitoring as well as quantitative
determination of fluoride ion (F<sup>-</sup>) concentration in aqueous media is
of vital importance. Herein, we have developed a facile</b> <b>and</b> <b>highly sensitive spectroscopic technique for selective detection of F<sup>-</sup>
in aqueous media using aluminium phthalocyanine chloride (AlPc-Cl) as a sensor.
The absorbance as well as steady-state fluorescence intensity of AlPc-Cl has
been found to decrease in presence of F<sup>-</sup> which has been used as a
marker for the determination of fluoride ion concentration in water. The
structural change in AlPc-Cl after addition of F<sup>-</sup> has been thoroughly
studied by using <sup>19</sup>F NMR (Nuclear Magnetic Resonance) spectroscopy. Our
detailed steady-state as well as time-resolved fluorescence studies reveal that
the quenching mechanism is static in nature due to ground state complexation in
between F<sup>-</sup> and AlPc-Cl molecules. The response of the sensor is
found to be linear over the F<sup>-</sup> concentration regime from 0 to 6 parts
per million (ppm) with a detection limit of 0.05 ppm. Additionally, it shows an
excellent selectivity as well as an insignificant change in sensitivity even in
the presence of interfering iron and aluminium ions. Based on the detailed
photophysical study, we have further developed a low cost and portable
prototype device which shows an excellent sensitivity with the detection limit
of 0.10 ppm. This prototype device has a high prospect for real-time monitoring
of fluoride ion concentration especially in remote areas.</b></p> | Arka Chatterjee; Nivedita Pan; Tuhin Kumar Maji; Sheik Saleem Pasha; Soumendra Singh; Saleh A. Ahmed; Jalal T. Al-Thakafy; Samir Kumar Pal | Optics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75524bdbb89a5faa3a78a/original/highly-sensitive-optical-sensor-for-selective-detection-of-fluoride-level-in-drinking-water-methodology-to-fabrication-of-prototype-device.pdf |
646d58d9ccabde9f6e41a872 | 10.26434/chemrxiv-2023-tws4n | Unsupervised machine learning leads to an abiotic picomolar peptide ligand | Here, we combined unsupervised machine learning (ML), non-natural amino acids, and affinity-selection mass-spectrometry (AS-MS) for the discovery of ultra-high affinity peptidomimetics that bind to a protein target. Peptides and peptidomimetics were discovered using AS-MS, encoded using diverse representations, and decomposed into two-dimensional “maps” of the chemical space by dimensionality reduction. These maps showed well-defined clusters of target-specific binders distinct from the remaining chemical space that included nonspecific and nonbinding peptides. Experimental testing of abiotic peptidomimetics confirmed the discovery of low nanomolar to picomolar binders and the accurate mapping of high-affinity binders across the co-learned sequence space. With ML and AS-MS, we anticipate this cartographic approach will accelerate the definition of chemical design spaces for the prediction and generation of functional peptidomimetics. | Joseph S. Brown; Somesh Mohapatra; Michael A. Lee; Roman Misteli; Yitong Tseo; Nathalie M. Grob; Anthony J. Quartararo; Andrei Loas; Rafael Gomez-Bombarelli; Bradley L. Pentelute | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Bioengineering and Biotechnology; Chemical Biology; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646d58d9ccabde9f6e41a872/original/unsupervised-machine-learning-leads-to-an-abiotic-picomolar-peptide-ligand.pdf |
64ae816fba3e99daeff63268 | 10.26434/chemrxiv-2023-5q5zf-v2 | Curbing chlorine disinfection byproduct formation with a biomimetic iron oxidation catalyst | We demonstrate, by bench-scale chlorination of local tap water containing phenol (16 M, 1.5 ppm) as a model organic micropollutant, that the [Fe(TAML)]– catalyst (TAML = tetra amido macrocyclic ligand) increases the rate of phenol decomposition and suppresses the build-up of chlorophenol disinfection byproducts. Specifically, significantly lower concentrations of trihalomethanes (1.0–2.1 ppb) were formed in the presence of [Fe(TAML)]– compared to those formed in the absence of the catalyst (39–78 ppb). Hydrophobic disinfection byproducts (1–2000 ppb) were monitored in real-time and without any sample preparation using membrane inlet mass spectrometry. This work encourages the incorporation of biomimetic iron catalysts into existing chlorine disinfection processes to harness the oxidative power of chlorine through oxygen- or hydrogen-atom transfer reactions instead of the problematic halogenation reactions which yield disinfection byproducts. | James N. McPherson; Freja Troj Larsen; Maja Juncher Lind; Christopher J. Miller; T. David Waite; Christine J. McKenzie; Frants R. Lauritsen | Inorganic Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Reaction (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ae816fba3e99daeff63268/original/curbing-chlorine-disinfection-byproduct-formation-with-a-biomimetic-iron-oxidation-catalyst.pdf |
63f390b19da0bc6b33405c4f | 10.26434/chemrxiv-2023-h0pmf | Photothermal catalysis: Recycling polymer to monomer with carbon quantum dots | Plastic recycling strategies to combat rapidly increasing waste build-up are of utmost environmental importance. Because of inherent limitations to mechanical recycling, chemical recycling to monomer has emerged as a powerful alternative that enables infinite recyclability through depolymerization. Regeneration of monomer starting materials allows for the reproduction of virgin polymer in a closed-loop fashion. However, methods for chemical recycling to monomer typically rely on bulk heating of polymer, which leads to unselective depolymerization in complex polymer mixtures and the formation of degradation byproducts. Here, we report a selective chemical recycling strategy facilitated by photothermal carbon quantum dots under visible light irradiation. Upon photoexcitation, we found that carbon quantum dots generate thermal gradients that induce bulk depolymerization of various polymer classes, including commercial samples. This method also provides selective depolymerization in mixed polymer waste streams enabled by the spatial control over thermal gradients. Broadly, photothermal catalysis enables thermally mediated bond cleavages, and subsequent depolymerization, with high selectivity, akin to other photocatalytic processes. | Liat Kugelmass; Erin Stache | Organic Chemistry; Catalysis; Polymer Science; Organic Polymers; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f390b19da0bc6b33405c4f/original/photothermal-catalysis-recycling-polymer-to-monomer-with-carbon-quantum-dots.pdf |
60c74bb4f96a00118428766e | 10.26434/chemrxiv.12174879.v2 | Impact of small promoter amounts on coke structure in dry reforming of methane over Ni/ ZrO2 | Coke
deposition is one of the main challenges in the commercialisation of dry
reforming of methane over supported Ni catalysts. Besides the coke quantity,
the structure of the deposits is also essential for the catalyst lifetime.
Accordingly, in this study, we analysed the effect of Na, K, and Cs promoters
on both these variables over Ni/ ZrO<sub>2</sub> catalysts. Besides blocking
the most active coke-forming sites already at low loading, the promoting effect
of the alkali metals is also contributed by their coke gasification activity.
To evaluate the additional impact of the latter, the behaviour of alkali-doped
catalysts was compared to that for Mn-doped catalysts, exclusively featuring
the site-blocking promotion mechanism. While the conversion is barely affected
by the type of promoter, it has a profound effect on the amount and the
composition of carbon deposits formed during the reaction. Promoting with K or
Mn reduces the coke content to a similar degree but with less carbon fibres
observed in the case of K. The promotion by Cs and Na results in the lowest
coke content. The superior performance of Cs and Na-doped Ni/ZrO<sub>2</sub>
catalysts is attributed to the enhanced coke gasification via carbonate species
on top of the site blocking effects. | Robert Franz; Tobias Kuehlewind; Genrikh Shterk; Edy Abou-hamad; Alexander Parastaev; Evgeny Uslamin; Emiel J.M. Hensen; Freek Kapteijn; Jorge Gascon; Evgeny Pidko | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bb4f96a00118428766e/original/impact-of-small-promoter-amounts-on-coke-structure-in-dry-reforming-of-methane-over-ni-zr-o2.pdf |
66ed710f12ff75c3a1eb9ecc | 10.26434/chemrxiv-2024-skzbn-v3 | Tailoring Mechanical Properties for Additive Manufacturing: Strategic Molecular Design of UV-Curable Bio-based Oligoester Resins via Diacid and Diol Exploration | Digital Light Processing (DLP) is a 3D printing technology that enables the fabrication of complex, high-resolution structures; however, the mechanical properties of DLP-printed objects are often limited by the resins used. This study focuses on developing and characterizing bio-based polyester UV-curable resins with tunable mechanical properties optimized for DLP 3D printing. Bio-based polyester resins were synthesized by direct esterification polycondensation reaction of itaconic and/or succinic acids with 1,2-propane-, 1,4-butane-, and/or 1,8-octanediols followed by blending with triethylene glycol dimethacrylate. The bio-renewable nature of the resin components provides several advantages over traditional petroleum-derived resins. The diacid and diol monomers come from renewable feedstocks such as corn, soybean, and vegetable oils rather than finite fossil fuel reserves. Furthermore, bio-renewable materials lower dependence on petrochemicals and increase the sustainability of 3D printing. The effects of diacid structure and diol chain length on resin properties were systematically investigated. Chemical characteristics were investigated by NMR and FTIR and suggested successful synthesis of the desired bio-based polyesters. By varying the molecular design, diacid, and diol building blocks, the molecular weight, crosslink density, and mechanical performance were tailored. The liquid resins were characterized by gel permeation chromatography and rheological measurements, and solid UV-cured objects were characterized by static and dynamic tensile testing. Rheological studies confirmed all resin formulations displayed shear-thinning behavior ideal for DLP printing. Mechanical testing revealed that varying diacid and diol components could modulate tensile elastic modulus and elongation at break from 0.1-1.0 GPa and 3.5-8.5%, respectively. Printability was assessed by printing a resolution test structure on a DLP 3D printer equipped with a 405 nm LED source. This ability to tailor the properties of bio-based polyester resins by molecular design provides an avenue for fabricating high-performance DLP-printed objects targeted for specific applications ranging from prototypes to end-use products. | Syed Bokhari; Jensen Sevening; Jeffrey Catchmark; Stephen Chmely | Materials Science; Polymer Science; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ed710f12ff75c3a1eb9ecc/original/tailoring-mechanical-properties-for-additive-manufacturing-strategic-molecular-design-of-uv-curable-bio-based-oligoester-resins-via-diacid-and-diol-exploration.pdf |
60c7436c0f50dbe12b395ed3 | 10.26434/chemrxiv.7699853.v3 | The Clinically Used Iron Chelator Deferasirox is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases | Fe(II)- and 2-oxoglutarate (2OG)-dependent JumonjiC domain-containing histone demethylases (JmjC KDMs) are epigenetic eraser enzymes involved in the regulation of gene expression and are emerging drug targets in oncology. We screened a set of clinically used iron chelators and report that they potently inhibit JMJD2A (KDM4A) in vitro. Mode of action investigations revealed that one compound, deferasirox, is a bona fide active site-binding inhibitor as shown by kinetic and spectroscopic studies. Synthesis of derivatives with improved cell permeability resulted in significant upregulation of histone trimethylation and potent cancer cell growth inhibition. Deferasirox was also found to similarly inhibit human 2OG-dependent hypoxia inducible factor prolyl hydroxylase activity. Therapeutic effects of clinically used deferasirox may thus involve transcriptional regulation through 2OG oxygenase inhibition. Deferasirox may provide a useful starting point for the development of novel anticancer drugs targeting 2OG oxygenases and a valuable tool compound for investigations of KDM function.<br /> | Manfred Jung; Martin Roatsch; Inga Hoffmann; Martine I. Abboud; Rebecca L. Hancock; Hanna Tarhonskaya; Kuo-Feng Hsu; Sarah E. Wilkins; Tzu-lan Yeh; Kerstin Lippl; Kerstin Serrer; Isabelle Moneke; Theresa D. Ahrens; Dina Robaa; Sandra Wenzler; Henriette Franz; Wolfgang Sippl; Silke Lassmann; Sven Diederichs; Erik Schleicher; Christopher J. Schofield; Akane Kawamura; Roland Schüle | Biochemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436c0f50dbe12b395ed3/original/the-clinically-used-iron-chelator-deferasirox-is-an-inhibitor-of-epigenetic-jumonji-c-domain-containing-histone-demethylases.pdf |
6438943f08c86922ffeffe57 | 10.26434/chemrxiv-2023-pq197 | Building Block-Based Binding Predictions for DNA-Encoded Libraries | DNA-encoded libraries (DELs) provide the means to make and screen millions of diverse compounds against a target of interest in a single experiment. However, despite producing large volumes of binding data at a relatively low cost, the DEL selection process is susceptible to noise, necessitating computational follow-up to increase signal-to-noise ratios. In this work, we present a set of informatics tools to analyze DEL selection data so that subsequent DEL screens probe productive regions of chemical space. Our approach segments DEL data at the individual building block level to identify productive building blocks in a library. We show how similar building blocks have a similar probability of binding, which we then employ to predict the behavior of untested building blocks. Lastly, we build a model from the inference that the combined behavior of individual building blocks is predictive of the activity of an overall compound. We report a performance of more than an order of magnitude greater than random guessing on a holdout set, demonstrating that our model can serve as a baseline for comparison against other machine learning models on DEL data. | Chris Zhang; Mary Pitman; Anjali Dixit; Sumudu Leelananda; Henri Palacci; Meghan Lawler; Svetlana Belyanskaya; LaShadric Grady; Joe Franklin; Nicolas Tilmans; David Mobley | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6438943f08c86922ffeffe57/original/building-block-based-binding-predictions-for-dna-encoded-libraries.pdf |
628779827087673baa5927d8 | 10.26434/chemrxiv-2022-k123z | Ultra-high-rate CO2 reduction reactions to multicarbon products with a current density of 1.7 A/cm2 in neutral electrolytes | CO2 electrolysis to value-added products is a promising technology to close the carbon cycle and sequester anthropogenic CO2 into chemical feedstocks; an increase of the current density for multicarbon products is one of the requirements for practical implementation. We have successfully increased the partial current density for gaseous CO2 reduction reactions to multicarbon products (C2+) over Cu nanoparticles on gas diffusion electrodes in neutral electrolytes to a record value of 1.7 A/cm2. The faradaic efficiency for multicarbon products increased with the current density and reached 76% at a total current density of 1.6 A/cm2. The turnover frequency for the production of C2+ per Cu atoms exceeded 2.8 s-1. The optimal porosity and thickness of the catalyst layer are confirmed as factors that elicit the high-turnover frequency of Cu atoms, resulting in the record partial current density for C2+. | Asato Inoue; Takashi Harada; Shuji Nakanishi; Kazuhide Kamiya | Physical Chemistry; Energy; Fuels - Energy Science; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628779827087673baa5927d8/original/ultra-high-rate-co2-reduction-reactions-to-multicarbon-products-with-a-current-density-of-1-7-a-cm2-in-neutral-electrolytes.pdf |
678e52f06dde43c908548528 | 10.26434/chemrxiv-2025-jclbt | A Photoswitchable Tryptophan Zipper – (Un)folding Fibrils in Seconds | Peptides and proteins, that have the tendency to form aggregates, are often discussed in the context of Alz-heimer’s, Huntington’s, or Parkinson’s disease. However, studying aggregation processes is inherently challenging due to the due to the diversity of aggregate size and geometry and the lack of control over the aggregation process in space and time. Here, we present a small, synthetic peptide, for which aggregation can be controlled reversibly with light within seconds. Specifically, by incorporating photoswitchable unnatural amino acids into the sequence of a tryptophan zipper, we could cre-ate the A3Tz5 peptide, which can switch its secondary structure between a β-hairpin and a β-sheet-like structure through photoisomerization. We provide a detailed insight into the molecular interactions involved in this process by combining var-ious spectroscopies and microscopy techniques. With A3Tz5 in hand, we overcame the limitation of spatiotemporal control in aggregation processes opening the door towards disease relevant studies. | Elena Rebecca Cotroneo; Tat Cheung Cheng; Lukas Kaltschnee; Patrick Maibach; Moritz Engelke; Niklas Schwegler; Franziska Thomas; Christina M. Thiele; Nadja Simeth | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678e52f06dde43c908548528/original/a-photoswitchable-tryptophan-zipper-un-folding-fibrils-in-seconds.pdf |
6148aa2caeaa6e451df35af4 | 10.26434/chemrxiv-2021-55g6z | Tracking the Catalyst Layer Depth-Dependent Electrochemical Degradation of a Bimodal Pt/C Fuel Cell Catalyst: A Combined Operando Small- and Wide-Angle X-Ray Scattering Study | The combination of operando small- and wide-angle X-ray scattering (SAXS, WAXS) in grazing incidence configuration is presented as a new approach to provide depth-dependent insights into the changes in mean particle sizes and phase fractions occurring for fuel cell catalysts during accelerated stress tests (ASTs). As fuel cell catalyst, a bimodal Pt/C catalyst was chosen that consists of two distinguishable particle size populations. The presence of the two different sizes should favor and uncover electrochemical Ostwald ripening as the major degradation mechanism, i.e., it is expected that the size of the larger particles in the Pt/C catalyst grows at the expense of the smaller particles. The grazing incidence mode performed at the European Synchrotron Radiation Facility (ESRF) at the ID31 beamline revealed an intertwinement of the depth dependent degradation. While the larger particles show the same particle size changes close to the electrolyte-catalyst interface and within the catalyst layer, for the smaller Pt nanoparticles a different degradation scenario is observed. At the electrolyte-catalyst interface, the smaller particles increase in size while their phase fraction decreases during the AST. However, in the inner catalyst layer the phase fraction of smaller particles increases instead of decreases. The results of a depth-dependent degradation strongly suggest to employ a depth-dependent catalyst design for future improvement of the catalyst stability. | Johanna Schröder; Rebecca K. Pittkowski; Isaac Martens; Raphaël Chattot; Jakub Drnec; Jonathan Quinson; Jacob J. K. Kirkensgaard; Matthias Arenz | Physical Chemistry; Nanoscience; Energy; Nanostructured Materials - Nanoscience; Fuel Cells; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6148aa2caeaa6e451df35af4/original/tracking-the-catalyst-layer-depth-dependent-electrochemical-degradation-of-a-bimodal-pt-c-fuel-cell-catalyst-a-combined-operando-small-and-wide-angle-x-ray-scattering-study.pdf |
621da75c7c13f4977b62ee6b | 10.26434/chemrxiv-2022-b3gn1 | Automated Bioanalytical Workflow for Ligand Binding Based Pharmacokinetic Assay Development | The growth of therapeutic monoclonal antibodies continues to accelerate due to their success as treatments for many diseases. As new therapeutics are developed, it is increasingly important to have robust bioanalytical methods to measure the pharmacokinetics of the circulating therapeutic monoclonal antibodies (mAbs) in serum. Ligand-binding assays such as enzyme-linked immunosorbent assays (ELISA) utilizing anti-idiotypic (anti-ID) antibodies against the variable regions of the antibody, are a sensitive and specific bioanalytical method routinely used to measure levels of therapeutic antibodies in a biological matrix. Screening and selecting optimal reagents and assay format are critical steps in the development of robust assays. An additional complication exists for soluble circulating drug, mAb targets that could interfere with the anti-IDs binding to the therapeutic mAb resulting in underestimation of total drug concentrations. Therefore, the selection of anti-IDs and the assay format that are not impacted by soluble antigen is paramount to development of a successful pharmacokinetic (PK) assay. We have developed an automated workflow and scoring system that allows for ranking of candidate anti-IDs on a variety of criteria. A primary generic automated indirect ELISA was utilized to shortlist the anti-IDs that need to be labeled and screened in pairs. A secondary screen using a sandwich ELISA with labeled-anti-ID pairings tested multiple PK assay formats to identify the best anti-ID pairing/PK assay format. We demonstrate the use of automation and a scoring system that allows for screening of anti-IDs and identification of the most robust PK assay format in a significantly reduced timeframe compared to standard approaches. | Brad Evans; Lai Yeung; Armen Beck; Annie Li; Dong Hun Lee; Gaurav Chopra; Kevin Bateman | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; High-throughput Screening; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621da75c7c13f4977b62ee6b/original/automated-bioanalytical-workflow-for-ligand-binding-based-pharmacokinetic-assay-development.pdf |
610ce11b18911d6f04daf652 | 10.26434/chemrxiv-2021-z3jhf | Non-Adiabatic Dynamics Simulations of a Light-Driven Molecular Motor in Solution | Despite molecular motors have numerous potential applications in optoelectronics, where optical properties can be tuned to transform light into mechanical movements, finding relationships between molecular motion and the environment is challenging. Here, we report the first excited state dynamics study of an overcrowded alkene in solution using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach combined with non-adiabatic molecular dynamics simulations. Using QM/MM surface-hopping trajectories, we calculate time-resolved emission and transient absorption spectra. These show the rise of a short-lived Frank-Condon state in the first 150 fs, followed by a formation of a dark state, before the motor relaxes to the ground state in about 1 ps. From the analysis of radial distribution functions we infer that the orientation of the solvent in the electronic excited state is similar to that in the ground state during the photoisomerization. | Jin Wen; Sebastian Mai; Leticia Gonzalez | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610ce11b18911d6f04daf652/original/non-adiabatic-dynamics-simulations-of-a-light-driven-molecular-motor-in-solution.pdf |
63d7cf85ab681c2c9d20bdc6 | 10.26434/chemrxiv-2022-r7rlv-v3 | Diiminium Nucleophile Adducts are Stable and Convenient Lewis Superacids | Strong Lewis acids are essential tools for a manifold of chemical procedures that aim to react weakly basic centres but their scalable deployment is severely limited by their costs and safety concerns. We report that dicationic relatives of guanidinium can be conveniently synthesised in a two-step one-pot procedure from tetramethylurea. Triflic anhydride is used to generate an isouronium intermediate. Substitution of the bound triflate with pyridines yield the dicationic tetramethyldiiminium bis(triflate) nucleophile adducts (TMDINu). Their proposed diiminium character is demonstrated by substituting pyridine from the corresponding adduct with other nucleophiles. The observation of a chelation effect in the 2,2’-bipyridine adducts supports Lewis acidic character of the diiminium π-system and flexibility towards accepting another bond. High fluoride, hydride, and oxide affinities are demonstrated, leading to their classification as soft and hard Lewis superacids. An example reaction is reported which shows that the tetramethyldiiminium bis(triflate) pyridine complex (TMDIPy) is more effective than conventional reagents in the activation of electron-poor amines for amide couplings. | Niklas Bormann; Jas S. Ward; Ann Kathrin Bergmann; Paula Wenz; Kari Rissanen; Wolf-Benedikt Hatz; Alexander Burbaum; Florian F. Mulks | Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Bonding; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d7cf85ab681c2c9d20bdc6/original/diiminium-nucleophile-adducts-are-stable-and-convenient-lewis-superacids.pdf |
635b2c5eee318669ea7567cd | 10.26434/chemrxiv-2022-xm94p | Synthesis and Testing of Analogs of the Tuberculosis Drug SQ109 Against Bacteria and Protozoa: Identification of Lead Compounds Against Mycobacterium abscessus and Malaria | SQ109 is a tuberculosis drug candidate that has high potency against Mycobacterium tuberculosis and is thought to function at least in part by blocking cell wall biosynthesis by inhibiting the MmpL3 transporter. It also has activity against bacteria and protozoan parasites that lack MmpL3, where it can act as an uncoupler, targeting lipid membranes and Ca2+ homeostasis. Here, we synthesized 19 analogs of SQ109 and tested them against bacteria: M. smegmatis, M. tuberculosis, M. abscessus, Bacillus subtilis and Escherichia coli, as well as against the protozoan parasites, Trypanosoma brucei, T. cruzi, Leishmania donovani, L. mexicana and Plasmodium falciparum. Activity against the mycobacteria was generally less than with SQ109 and was reduced by increasing the size of the alkyl adduct, but two analogs were ~4-8 fold more active than was SQ109 against M. abscessus, including a highly drug resistant strain harboring a A309P mutation in MmpL3. There was also better activity than found with SQ109 with other bacteria and protozoa. Of particular interest, we found that the adamantyl C-2 ethyl, butyl, phenyl and benzyl analogs had 4-10x increased activity against P. falciparum asexual blood stages, together with low toxicity to a human HepG2 cell line, making them of interest as new anti-malarial drug leads. We also used surface plasmon resonance to investigate the binding of inhibitors to MmpL3, and differential scanning calorimetry to investigate binding to lipid membranes. There was no correlation between MmpL3 binding and M. tuberculosis or M. smegmatis cell activity, suggesting that MmpL3 is not a major target, in mycobacteria. However, some of the more active species decreased lipid phase transition temperatures, indicating increased accumulation in membranes, expected to lead to enhanced uncoupler activity. | Marianna Stampolaki; Satish Malwal; Nadine Alvarez; Zijun Gao; Mohammad Moniruzzaman; Svitlana Babii; Nikolaos Naziris; André Rey-Cibati; Mariana Valladares-Delgado; Andreea Turcu; Kyung-Hwa Baek; Hyeryon Lee; Matthéo Alcaraz; Savannah Watson; Mariëtte van der Watt; Dina Coertzen; Natasa Efstathiou; Ioannis Stylianakis; Maria Chountoulesi; Carolyn Schoen; Ioannis Papanastasiou; José Brea; Michael Cynamon; Lyn-Marie Birkholtz; Laurent Kremer; Joo Hwan No; Santiago Vazquez; Gustavo Benaim; Costas Demetzos; Helen Zgurskaya; Thomas Dick; Eric Oldfield; Antonios Kolocouris | Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635b2c5eee318669ea7567cd/original/synthesis-and-testing-of-analogs-of-the-tuberculosis-drug-sq109-against-bacteria-and-protozoa-identification-of-lead-compounds-against-mycobacterium-abscessus-and-malaria.pdf |
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