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60c73d68337d6c2cdee26147 | 10.26434/chemrxiv.5328235.v2 | The Significance of the Amorphous Potential Energy Landscape for Dictating Glassy Dynamics and Driving Solid-State Crystallisation | <div>
<div>
<div>
<p>The fundamental origins surrounding the dynamics of disordered solids near their characteristic glass transitions continue to be fiercely debated, even though a vast number of materials
can form amorphous solids, including small-molecule organic, inorganic, covalent, metallic, and
even large biological systems. The glass-transition temperature, Tg, can be readily detected by
a diverse set of techniques, but given that these measurement modalities probe vastly different
processes, there has been significant debate regarding the question of why Tg can be detected
across all of them. Here we show clear experimental and computational evidence in support of
a theory that proposes that the shape and structure of the potential-energy surface (PES) is the
fundamental factor underlying the glass-transition processes, regardless of the frequency that experimental methods probe. Whilst this has been proposed previously, we demonstrate, using ab
initio molecular-dynamics (AIMD) simulations, that it is of critical importance to carefully consider
the complete PES – both the intra-molecular and inter-molecular features – in order to fully un-
derstand the entire range of atomic-dynamical processes in disordered solids. Finally, we show
that it is possible to utilise this dependence to directly manipulate and harness amorphous dynamics in order to control the behaviour of such solids by using high-powered terahertz pulses to
induce crystallisation and preferential crystal-polymorph growth in glasses. Combined, these findings provide direct evidence that the PES landscape, and the corresponding energy barriers, are
the ultimate controlling feature behind the atomic and molecular dynamics of disordered solids,
regardless of the frequency at which they occur. </p>
</div>
</div>
</div> | Michael T. Ruggiero; Marcin Krynski; Eric Ofosu Kissi; Juraj Sibik; Daniel Markl; Nicholas Y. Tan; Denis Arslanov; Wim van der Zande; Britta Redlich; Timothy M. Korter; Holger Grohganz; Korbinian Lobmann; Thomas Rades; Stephen R. Elliott; J. Axel Zeitler | Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2017-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d68337d6c2cdee26147/original/the-significance-of-the-amorphous-potential-energy-landscape-for-dictating-glassy-dynamics-and-driving-solid-state-crystallisation.pdf |
632998b1fee74ebb56435801 | 10.26434/chemrxiv-2022-tls8v | Lewis Acidity Trend of Boron Trihalides: If
Not π Back-Bonding, What Else? | Lewis acidity trend of boron trihalides is a subject that has received a variety of explanations, and still the simple π back-bonding based one is believed by most, perhaps
because of its simplicity, irrespective of opposing findings. Herein we try to give an alternative explanation based on qualitative Molecular Orbital (MO) theory, and support
that quantitatively by Generalized Kohn-Sham Energy Decomposition Analysis. While the role of orbital overlap on the orbital interaction energy is widely known, the role
of electronegativity of the atoms involved is often overlooked. Here we find that the Lewis acidity trend of boron and aluminum halides can be explained by the WolfsbergHelmholz (W-H) formula for resonance integral . The MO theory based predictions are valid only when the orbital interactions are strong enough. In the weakly interacting systems the effect of orbital interactions can be overshadowed by other effects such as Pauli repulsion, dispersion etc. Thus the Lewis acidity trend of boron and aluminum halides can vary depending on the strength of interacting Lewis base. We believe that this work would enable one to gain a better understanding not only on the Lewis acidity of boron trihalides and its heavy analogs, but also on a variety of related problems such as the stronger π acidity of CS compared to CO and weaker π bonding between heavy atoms. | Ashith Thayyil; Priyakumari Chakkingal Parambil | Inorganic Chemistry; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632998b1fee74ebb56435801/original/lewis-acidity-trend-of-boron-trihalides-if-not-back-bonding-what-else.pdf |
60c7567fbdbb8992eda3aa2a | 10.26434/chemrxiv.14256599.v1 | Refinement and Extension of COSMO-RS-Trained Fragment Contribution Models for Predicting Partition Properties of C10–20 Chlorinated Paraffin Congeners | COSMO-RS-trained fragment contribution models (FCMs) to predict partition properties of chlorinated paraffin (CP) congeners were refined and extended. The improvement includes (i) the use of an improved conformer generation method for COSMO-RS, (ii) extension of training and validation sets for FCMs up to C<sub>20</sub> congeners covering short-chain (SCCPs), medium-chain (MCCPs) and long-chain CPs (LCCPs), and (iii) more realistic simulation of industrial CP mixture compositions by using a stochastic algorithm. Extension of the training set markedly improved the accuracy of model predictions for MCCPs and LCCPs, as compared to the previous study. The predicted values of the log octanol/water partition coefficients (<i>K</i><sub>ow</sub>) for CP mixtures agreed well with experimentally determined values from the literature. Using the established FCMs, this study provided a set of quantum chemically based predictions for 193 congener groups (C<sub>10–20</sub>, Cl<sub>0–21</sub>) regarding <i>K</i><sub>ow</sub>, air/water (<i>K</i><sub>aw</sub>), and octanol/air (<i>K</i><sub>oa</sub>) partition coefficients, subcooled liquid vapor pressure (VP) and aqueous solubility (<i>S</i><sub>w</sub>) in a temperature range of 5–45 °C as well as the respective enthalpy and internal energy changes.<br /><br />This is a preprint version and has not yet been peer reviewed. | Satoshi Endo | Physical Organic Chemistry; Environmental Science; Wastes; Chemoinformatics; Environmental Analysis; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7567fbdbb8992eda3aa2a/original/refinement-and-extension-of-cosmo-rs-trained-fragment-contribution-models-for-predicting-partition-properties-of-c10-20-chlorinated-paraffin-congeners.pdf |
672375c97be152b1d091fb67 | 10.26434/chemrxiv-2024-l36zv | An amide-to-chloroalkene substitution improves the peptide permeability | This study highlights the novel application of Chloroalkene Dipeptide Isosteres (CADIs) in enhancing peptide membrane permeability. Replacing the peptide bond with CADIs in model dipeptides significantly improved passive permeability. This enhancement is attributed to the increased lipophilicity provided by the CADI substitution, as confirmed by AlogP calculations and HPLC retention times. Molecular dynamics simulations further indicated that CADI substitution reduces water interaction, potentially lowering hydration energy. Our findings demonstrate that CADI incorporation can effectively improve the permeability of peptides, offering a valuable approach for developing bioactive peptidomimetics with enhanced pharmacological properties including permeability and hydrolytic stability. | Sayuri Takeo; Chihiro Iio; Ai Sakakibara; Mio Takeda; Yuki Yamazaki; Kohei Sato; Nobuyuki Mase; Mizuki Watanabe; Tetsuo NARUMI | Biological and Medicinal Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672375c97be152b1d091fb67/original/an-amide-to-chloroalkene-substitution-improves-the-peptide-permeability.pdf |
66db016f51558a15ef3b271b | 10.26434/chemrxiv-2024-1sxfh | A lipid-based delivery platform for pulsatile delivery of teriparatide | Teriparatide (and analogue peptides) are the only FDA approved anabolic treatments for osteoporosis. Current therapies are administered as a daily subcutaneous injection, which limits patient adherence and clinical efficacy. To achieve the desired anabolic effect, a controlled delivery system must ensure a pulsatile release profile over a prolonged period. Thermo-responsive formulations (e.g. liposomes) can undergo a temperature-related phase-transition which can allow active control of drug release. Herein, thermo-responsive liposomes were developed to permit precise control over the teriparatide release rate through modulation of temperature. Entrapment of hydrophilic molecules, including peptides within liposomes remains challenging due to the large volume of hydration. In this work, hydrophobic ion pairing was employed for the first time to enhance peptide entrapment within liposomes. The method resulted in a hydrophobic complex that achieved high teriparatide entrapment (>75%) in sub-200 nm, monodispersed liposomes. Hydrophobic ion pairing outperformed other entrapment approaches. Several liposomal formulations with transition temperatures between 38 – 50 °C were obtained by modulation of the phospholipid composition. In vitro release assays demonstrated temperature-dependent release kinetics with faster rates of release observed at/above the transition temperature. The maintenance of biological activity of released teriparatide was demonstrated in a cell-based assay utilising the PTH1R receptor. Overall, this provides the first proof-of-concept of the suitability of thermo-responsive systems for pulsatile delivery of teriparatide and similar peptides. | Corinna Schlosser; Wojciech Rozek; Ryan Mellor; Szymon Manka; Christopher Morris; Steve Brocchini; Gareth Williams | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66db016f51558a15ef3b271b/original/a-lipid-based-delivery-platform-for-pulsatile-delivery-of-teriparatide.pdf |
63623674cf6de985122c4332 | 10.26434/chemrxiv-2022-rf742 | Algorithmic graph theory, reinforcement learning and game theory in MD simulations: from 3D-structures to topological 2D-MolGraphs and backwards | This paper reviews graph theory-based methods that were recently developed in our group for post-processing molecular dynamics trajectories.
We show that the use of algorithmic graph theory not only provides a direct and fast methodology to identify conformers sampled over time but also allows to follow the interconversions between the conformers through graphs of transitions in time.
Examples of gas phase molecules and inhomogeneous aqueous solid interfaces are presented to demonstrate the power of topological 2D graphs and their versatility for post-processing molecular dynamics trajectories.
An even more complex challenge is to predict 3D structures from topological 2D graphs. Our first attempts to tackle such a challenge are presented with the development of game theory and reinforcement learning methods for predicting the 3D structure of a gas-phase peptide.
| Sana Bougueroua; Marie Bricage; Ylène Aboulfath; Dominique Barth; Marie-Pierre Gaigeot | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63623674cf6de985122c4332/original/algorithmic-graph-theory-reinforcement-learning-and-game-theory-in-md-simulations-from-3d-structures-to-topological-2d-mol-graphs-and-backwards.pdf |
60c7480fee301c3f4fc797f2 | 10.26434/chemrxiv.11855031.v1 | Unravelling the Keto-Enol Tautomer Dependent Photochemistry and Degradation Pathways of the Protonated UVA Filter Avobenzone | Avobenzone (AB) is a widely used UVA filter known to undergo irreversible photodegradation. Here, we investigate the detailed pathways by which AB photodegrades by applying UV laser-interfaced mass spectrometry to protonated AB ions. Gas-phase infrared multiple-photon dissociation (IRMPD) spectra obtained with the free electron laser for infrared experiments, FELIX, (600-1800 cm-1) are also presented to confirm the geometric structures. The UV gas-phase absorption spectrum (2.5-5 eV) of protonated AB contains bands that correspond to selective excitation of either the enol or diketo forms, allowing us to probe the resulting, tautomer-dependent photochemistry. Numerous photofragments (i.e. photodegradants) are directly identified for the first time, with m/z 135 and 161 dominating, and m/z 146 and 177 also appearing prominently. Analysis of the production spectra of these photofragments reveals that that strong enol to keto photoisomerism is occurring, and that protonation significantly disrupts the stability of the enol (UVA active) tautomer. Close comparison of fragment ion yields with the TDDFT-calculated absorption spectra give detailed information on the location and identity of the dissociative excited state surfaces, and thus provide new insight into the photodegradation pathways of avobenzone, and photoisomerisation of the wider class of β-diketone containing molecules.<br /> | Jacob A. Berenbeim; Natalie Wong; Martin C. R. Cockett; Giel Berden; Jos Oomens; Anouk Rijs; Caroline E. H. Dessent | Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7480fee301c3f4fc797f2/original/unravelling-the-keto-enol-tautomer-dependent-photochemistry-and-degradation-pathways-of-the-protonated-uva-filter-avobenzone.pdf |
672a2db6f9980725cf2de22d | 10.26434/chemrxiv-2024-rg1xg | Quantum Tunneling of 7Li Spins in Argyrodite-Type Solids | The irregular movement of atoms or ions, known as self-diffusion, is a widespread phenom-enon in solids. In crystalline Li6.6P0.4Ge0.6S5I, the triplet arrangements within the Li-rich cag-es allow for ultrafast localized Li+ exchange processes. This feature leads us to consider whether, in addition to classical over-barrier hopping, quantum effects — commonly ob-served for electrons, protons, and deuterons — should also be taken into account for the heavier 7Li nuclei. To explore this hypothesis, we investigated 7Li spin fluctuations using nu-clear magnetic resonance (NMR) spin-lattice relaxation (SLR) measurements at cryogenic temperatures, down to T = 9 K. Our findings reveal signatures in the SLR NMR data that we attribute to (coherent) quantum tunneling of the Li spins within the triplet arrangement. These insights not only enhance our understanding of atomic jump processes but also sug-gest potential future quantum applications involving 7(6)Li+ tunneling. | H. Martin R. Wilkening | Physical Chemistry; Inorganic Chemistry; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a2db6f9980725cf2de22d/original/quantum-tunneling-of-7li-spins-in-argyrodite-type-solids.pdf |
61a16f1df93ad33aecb57cdc | 10.26434/chemrxiv-2021-jv2cc | Remote Oxidative Activation of a [Cp*Rh] Monohydride | Half-sandwich rhodium monohydrides are often proposed as intermediates in catalysis, but little is known regarding the redox-induced reactivity accessible to these species. Here, the κ2-bis-diphenylphosphinoferrocene (dppf) ligand has been used to explore the reactivity that can be induced when a [Cp*Rh] monohydride undergoes remote (dppf-centered) oxidation by 1e–. Chemical and electrochemical studies showed that one-electron redox chemistry is accessible to Cp*Rh(dppf), including a unique quasi-reversible RhII/I process at –0.96 V vs. ferrocenium/ferrocene (Fc+/0). This redox manifold was confirmed by isolation of an uncommon Rh(II) species that was characterized by EPR spectroscopy. Protonation of Cp*Rh(dppf) with anilinium triflate yielded an isolable and inert monohydride, and this species was found to undergo a quasireversible electrochemical oxidation at +0.41 V vs Fc+/0 that corresponds to iron-centered oxidation in the dppf backbone. Thermochemical analysis predicts that this dppf-centered oxidation drives a dramatic increase in acidity of the Rh–H moiety by 23 pKa units, a reactivity pattern confirmed by in situ 1H NMR studies. Taken together, these results show that remote oxidation can effectively induce M–H activation and suggest that ligand-centered redox activity could be an attractive feature for design of new systems relying on hydride intermediates. | Emily Boyd; Julie Hopkins Leseberg; Emma Cosner; Davide Lionetti; Wade Henke; Victor Day; James Blakemore | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Electrochemistry - Organometallic; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a16f1df93ad33aecb57cdc/original/remote-oxidative-activation-of-a-cp-rh-monohydride.pdf |
61d5c82f90fc8a74ceeb10b8 | 10.26434/chemrxiv-2022-4cn0f | Ion-shift reagent binding energy and the shift-mass correlation in ion mobility spectrometry
| Ion mobility spectrometry is widely used for the detection of illegal substances and explosives in airports, ports, custom, some stations and many other important places. This task is usually complicated by false positives caused by overlapping the target peaks with that of interferents, commonly associated with samples of interest. Shift reagents (SR) are species that selectively change ion mobilities through adduction with analyte ions when they are introduced in IMS instruments. This characteristic can be used to discriminate false positives because the interferents and illegal substances respond differently to SR depending on the structure and size of analytes and their interaction energy with SR. This study demonstrates that ion mobility shifts upon introduction of SR depend, not only on the ion masses, but on the interaction energies of the ion:SR adducts. In this study, we introduced five different SRs using ESI-IMS-MS to study the effect of the interaction energy and size on mobility shifts. The mobility shifts showed a decreasing trend as the molecular weight increased for the series of compounds ethanolamine, valinol, serine, threonine, phenylalanine, tyrosine, tributylamine, tryptophan, desipramine, and tribenzylamine. It was proved that the decreasing trend was partially due to the inverse relation between the mobility and drift time and hence, the shift in drift time better reflects the pure effect of SR on the mobility of analytes. Yet the drift time shift exhibited a mild decrease with the mass of ions. Valinol pulled out from this trend because it had a low binding energy interaction with all the SR and, consequently, its clusters were short-lived. This short lifetime produced fewer collisions against the buffer gas and a drift time shorter compared to those of ions of similar molecular weight. Analyte ion:SR interactions were calculated using Gaussian. IMS with the introduction of SR could be the choice for the free-interferents detection of illegal drugs, explosives, and biological and warfare agents. The suppression of false positives could facilitate the transit of passengers and cargos, rise the confiscation of illicit substances, and save money and distresses due to needless delays.
Keywords: Adduction, ion mobility spectrometry, mass spectrometry, shift reagent, valinol, buffer gas modifier
| Roberto Fernandez-Maestre; Mahmoud Tabrizchi; Dairo Meza-Morelos | Analytical Chemistry; Analytical Chemistry - General | CC BY NC 4.0 | CHEMRXIV | 2022-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d5c82f90fc8a74ceeb10b8/original/ion-shift-reagent-binding-energy-and-the-shift-mass-correlation-in-ion-mobility-spectrometry.pdf |
646c8f15ccabde9f6e390fe8 | 10.26434/chemrxiv-2022-m2z57-v2 | Meso-Aminomethyl-BODIPY as a Scaffold for Nitric Oxide Photo-Releasers | Nitric oxide (NO) is a unique biochemical mediator involved in the regulation of vital processes. Its short lifetime in physiological conditions and local action impede direct application in medicine because highly targeted NO-delivery systems are required. Light-controllable NO releasers are promising for the development of smart therapies. Here we present simply prepared meso-aminomethyl BODIPY derivatives containing N-nitroso moiety, which show the photoinduced generation of NO in a solution. These compounds can additionally generate singlet oxygen, and NO/1O2 generation efficiency can be tuned by substituents. As an example of NO-mediated effect, we demonstrate light-dependent inhibition of platelet activation in vitro. The presented compounds could serve as the basis for the development of novel hybrid therapeutic methods. | Mikhail Panfilov; Tatyana Karogodina; Anastasiya Sibiryakova; Irina Tretyakova; Alexey Vorob’ev; Alexander Moskalensky | Biological and Medicinal Chemistry; Organic Chemistry; Materials Science; Photochemistry (Org.); Controlled-Release Systems; Dyes and Chromophores | CC BY 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646c8f15ccabde9f6e390fe8/original/meso-aminomethyl-bodipy-as-a-scaffold-for-nitric-oxide-photo-releasers.pdf |
615df5138b620d96e646c2d1 | 10.26434/chemrxiv-2021-mt8jt | Identification of photocrosslinking peptide ligands by mRNA display | Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific crosslinker can require significant optimisation. We report a novel mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that photocrosslink to a target of interest. As a proof of concept, we generated a benzophenone-containing library and applied XL-RaPID screening against a model target, the second bromodomain of BRD3. This crosslinking screening gave two optimal candidates that selectively labelled the target protein in cell lysate. Overall, this work introduces direct photocrosslinking screening as a versatile technique for identifying covalent peptide ligands from mRNA display libraries incorporating reactive warheads. | Yuteng Wu; M. Teresa Bertran; Dhira Joshi; Sarah Maslen; Catherine Hurd; Louise Walport | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2021-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615df5138b620d96e646c2d1/original/identification-of-photocrosslinking-peptide-ligands-by-m-rna-display.pdf |
672883497be152b1d0ec114b | 10.26434/chemrxiv-2024-7s826 | Mechanistic Insights into GTP Hydrolysis by the RhoA Protein: Catalytic Impact of Glutamine Tautomerism | We present a systematic evaluation of different possible reaction mechanisms for GTP hydrolysis in RhoA, a member of the Ras superfamily of enzymes that uses this reaction to switch from an active to an inactive conformation. These enzymes are activated by the presence of GTPase activating protein (or GAP) that forms an intimate complex with residues of the two proteins present in the active site. We have explored the multidimensional reactional free energy landscape in the active site of the complex formed by RhoA and p50RhoGAP. Our Molecular Dynamics simulations show that the activating enzyme p50RhoGAP establishes catalytically important interactions with the phosphate groups of GTP through its so-called arginine finger (Arg85) and also with RhoA residue Gln63. This is a key residue because it does not only interact with the nucleophilic water molecule but also participates actively in the reaction mechanism. Adaptive String Method simulations using hybrid QM/MM potentials with both Tight-Binding and Density Functional hamiltonians show that GTP hydrolysis proceeds through formation of a metaphosphate metastable species. Mechanistic proposals differ in the proton transfer rearrangements required to form the inorganic phosphate ion. Our simulations discard a solvent assisted mechanism and point to the participation of Gln63 in the proton transfer process by means of the side chain tautomerism from the amide to the imide form. The proton transfer required to recover the amide form of Gln63 requires the participation of the inorganic phosphate and it is the rate-limiting step of the process, with a free energy barrier of 20.2 kcal mol-1 at the B3LYPD3/MM level, in good agreement with the experimentally derived value. The amide-imide tautomerism could be relevant also in other enzymes, facilitating proton transfer events in complex mechanisms. | Jorge Pardos; Adrián García-Martínez; J. Javier Ruiz-Pernia; Iñaki Tuñón | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672883497be152b1d0ec114b/original/mechanistic-insights-into-gtp-hydrolysis-by-the-rho-a-protein-catalytic-impact-of-glutamine-tautomerism.pdf |
60c74891469df4778cf43a5e | 10.26434/chemrxiv.11917800.v1 | Ultrafast Humidity Sensing by Anisotropic Deformation of Carbon Nitride Nanoribbons for Real-Time Respiratory Monitoring | Developing humidity sensing materials with fast response and high sensitivity was of great interest for many applications from industrial field to human healthcare. Here, we report a carbon nitride nanoribbons (CNNRs)-based humidity sensor. Thanks to the delicate humidity-responsive anisotropic deformation and well-balanced hydrophilic surfaces/hydrophobic framework with rapid adsorption/desorption of water molecules by CNNRs, this humidity sensor possessed an ultrafast response of ca. 50 ms, high reproducibility and selectivity, and linearity in an almost full humidity range. As an example, this sensor was successfully applied to real-time breathing detection, and the as-obtained breathing graphic waveforms exhibited a higher sensitivity than that by the traditional clinic measurements. This work would pave a new way for ultrafast and sensitive humidity sensing by using anisotropic deformation of CNNRs and introduce a new application scheme of humidity sensors in more user-friendly respiratory monitoring with higher resolution.<br /> | Yuye Zhang; Yongxiu Song; Hong Yang; Kaiyang Chen; Qing Zhou; Yanqin Lv; Ensheng Xu; Songqin Liu; Yanfei Shen; Lei Liu; Yuanjian Zhang | Carbon-based Materials; Nanostructured Materials - Materials; Polymer morphology; Analytical Chemistry - General; Nanostructured Materials - Nanoscience; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74891469df4778cf43a5e/original/ultrafast-humidity-sensing-by-anisotropic-deformation-of-carbon-nitride-nanoribbons-for-real-time-respiratory-monitoring.pdf |
60c7578ef96a00930d288cb1 | 10.26434/chemrxiv.14417759.v1 | Thermoelectric Properties of the As/P-Based Zintl Compounds EuIn2As2−xPx (X = 0 to 2) and SrSn2As2 | Zintl compounds containing Sb have been studied extensively because of their promising thermoelectric properties. In this study, we prepared As/P-based Zintl compounds, EuIn2As2-xPx (x = 0 to 2) and SrSn2As2, and examined their potential for use as thermoelectric materials. These compounds show hole carrier concentrations of ~10^19 /cm3 for EuIn2As2-xPx and ~10^21 /cm3 for SrSn2As2 at 300 K. The high carrier concentration of SrSn2As2 is likely owing to self-doping by hole-donating Sn vacancies. The electrical power factor reaches ~1 mW/mK2 at ~600 K for EuIn2As2-xPx with x = 0.1 and 0.2. The lattice thermal conductivity is determined to be 1.6–2.0 W/mK for EuIn2As2 and SrSn2As2, and 2.8 W/mK for EuIn2P2 at 673 K. The dimensionless figure of merit reaches ZT = 0.29 at 773 K for EuIn2As2-xPx with x = 0.2. First-principles calculations show that EuIn2As2 and SrSn2As2 are topologically nontrivial materials with band inversion, while EuIn2P2 is a conventional semiconductor with a bandgap. The present study demonstrates that As/P-based Zintl compounds can also show promising thermoelectric properties, thus expanding the frontier for efficient thermoelectric materials. | Keisuke Shinozaki; Yosuke Goto; Kazuhisa Hoshi; Ryosuke Kiyama; Naoto Nakamura; akira miura; Chikako Moriyoshi; Yoshihiro Kuroiwa; Hidetomo Usui; Yoshikazu Mizuguchi | Piezoelectricity and Thermoelectricity | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7578ef96a00930d288cb1/original/thermoelectric-properties-of-the-as-p-based-zintl-compounds-eu-in2as2-x-px-x-0-to-2-and-sr-sn2as2.pdf |
62a03fc02e62693b3b7b9ace | 10.26434/chemrxiv-2022-ng823 | Non-Directed Pd-Catalyzed Electrooxidative Olefination of Arenes | The Fujiwara-Moritani reaction is a powerful tool for the olefination of arenes by Pd-catalyzed C–H activation. However, the need for superstoichiometric amounts of toxic chemical oxidants makes the reaction unattractive from an environmental and atom-economical view. Herein, we report the first non-directed and regioselective olefination of simple arenes via an electrooxidative Fujiwara-Moritani reaction. The versatility of this operator-friendly approach was demonstrated by a broad substrate scope that includes arenes, heteroarenes and a variety of olefins. Electroanalytic studies suggest the involvement of a Pd(II)/Pd(IV) catalytic cycle via a Pd(III) intermediate. | Subir Panja; Salman Ahsan; Tanay Pal; Simon Kolb; Wajid Ali; Sulekha Sharma; Chandan Das; Jagrit Grover; Arnab Dutta; Daniel B. Werz; Amit Paul; Debabrata Maiti | Organic Chemistry; Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a03fc02e62693b3b7b9ace/original/non-directed-pd-catalyzed-electrooxidative-olefination-of-arenes.pdf |
67ddaaf681d2151a0256a9fa | 10.26434/chemrxiv-2025-p9fk9 | Covalent Adaptable Networks with Associative Siloxane Exchange Enabled by Amide-Based Internal Catalysis: Designing for Reprocessability and Extrudability by Increasing the Cross-link Density
| Replacing non-recyclable thermosets with covalent adaptable networks (CANs) that recover cross-link density after reprocessing will reduce waste and contribute to a circular polymer economy. Many CANs undergoing associative dynamic exchange require catalysis. External catalysis often leads to harmful effects, e.g., increased creep, accelerated material aging, and catalyst leaching. Herein, we demonstrate internally catalyzed siloxane dynamic chemistry resulting from amides covalently linked through alkyl chains to siloxanes. Small-molecule studies show the formation of exchange products resulting from the reaction of two amide-containing siloxane molecules. From the rubbery plateau modulus, each siloxane-exchange-based CAN exhibits a cross-link density that is temperature-invariant, or nearly so, characteristic of associative CANs. The alkyl length in the siloxane-containing monomer tunes the network cross-link density. Cross-link density recovery after reprocessing is achieved, with the required reprocessing time and temperature decreasing with increasing cross-link density. Stress relaxation is also faster with increasing cross-link density. The faster dynamics and reprocessability with increasing cross-link density arise because associative exchange is second order in siloxane (i.e., cross-linker) concentration. Capitalizing on this, we demonstrate the melt-extrusion of our highest cross-link density CAN, achieving the same cross-link density in extruded and compression-molded CANs. Using identical conditions, the next-highest cross-link density CAN is not extrudable. | Nathan S. Purwanto; Tong Wang; Xiaoyang Liu; Linda J. Broadbelt; Tapas Debsharma; John Torkelson | Materials Science; Polymer Science; Materials Processing; Polymerization catalysts; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ddaaf681d2151a0256a9fa/original/covalent-adaptable-networks-with-associative-siloxane-exchange-enabled-by-amide-based-internal-catalysis-designing-for-reprocessability-and-extrudability-by-increasing-the-cross-link-density.pdf |
62430d6981e6497f2dec3588 | 10.26434/chemrxiv-2022-b04k0 | Silicon Substitution Expands the Repertoire of Si-Rhodamine Fluorescent Probes | Fluorescent dyes such as rhodamines are widely used to assay the activity and image the location of otherwise invisible molecules. Si-rhodamines, in which the bridging oxygen of rhodamines is replaced with a dimethyl silyl group, are increasingly the dye scaffold of choice for biological applications, as fluorescence is shifted into the near-infrared while maintaining high brightness. Despite intense interest in Si-rhodamines, there has been no exploration of the scope of silicon substitution in these dyes, a potential site of modification that does not exist in conventional rhodamines. Here we report a broad range of silyl modifications that enable brighter dyes, further red-shifting, new ways to modulate fluorescence, and the introduction of handles for dye attachment, including fluorogenic labeling agents for nuclear DNA, SNAP-tag and HaloTag labeling. Modifications to the bridging silicon are therefore of broad utility to improve and expand the applications of all Si-dyes. | Desaboini Nageswara Rao; Xincai Ji; Stephen Miller | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Imaging; Microscopy; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62430d6981e6497f2dec3588/original/silicon-substitution-expands-the-repertoire-of-si-rhodamine-fluorescent-probes.pdf |
60c74ebbbdbb895a48a39c04 | 10.26434/chemrxiv.11894904.v2 | Triptolide Self-Assembling Nanoparticles Engineering with Modified Erythrocyte Membranes for Targeting and Remodeling Inflammatory Microenvironment in Arthritis | Rheumatoid arthritis (RA) is an autoimmune disease causing severe joint damage, disability and decreased quality of life. Pathologically, numerous blood-derived cells infiltrating in synovium and cytokine secret necessitating formation of new blood vessels to generate pannus together form an inflammatory microenvironment. Triptolide with immunosuppressive activities is a potential drug to treat RA. However, it is still lack of an effective targeting system to deliver triptolide to RA site safely. Herein an inflammatory microenvironment targeting and remodeling nanoplatform is developed to achieve significantly effective RA treatment. In this system we synthesized a self-assembling triptolide nanoparticles (TPNs) mediated by dipeptide diphenylalanine which is the simplest self-assembly building block, then TPNs were entrapped by mannose-modified erythrocyte membranes to form engineering manRTPNs. For targeting, the immunological molecule of erythrocytes was firstly introduced to target T cells by ligand binding of LFA-3/LFA-2, and the coated mannose modified erythrocyte membrane also conferred the capacity of targeting to macrophages by mannose and its receptor CD206; for remodeling inflammatory microenvironment, TPNs could selectively exert its suppressive effects on different cells of RA including lymphocytes and synovial fibroblasts. In collagen<br />induced arthritis mice, manRTPNs showed excellent targeting effect and prolonged accumulation at inflamed joint. After manRTPNs treatment, swollen paws of CIA considerably shrunk to normal, boss loss even recovered healthy level and cartilage preserved at synovium cavity, because of systemically conventional cytokine reduction and expression shift of core genes in networks of RA microenvironment. Therefore, this well-defined manRTPNs might be a well promising systematic therapeutic agent for RA.<br /> | Jing Li; Sanpeng Li; Chunbin Li; Hongfeng Li; Chuangjun Liu; qi zhao; Pengfei Zhang; Ping Gong; Lintao Cai | Natural Products; Biopolymers; Drug delivery systems; Imaging; Nanofabrication; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ebbbdbb895a48a39c04/original/triptolide-self-assembling-nanoparticles-engineering-with-modified-erythrocyte-membranes-for-targeting-and-remodeling-inflammatory-microenvironment-in-arthritis.pdf |
60c742424c89190ce4ad2414 | 10.26434/chemrxiv.7497053.v2 | The Impact of Bioconjugation on the Interfacial Activity of a Protein Biosurfactant | Biosurfactants, are
surface active molecules that can be produced by renewable, industrially
scalable biologic processes. DAMP4, a designer biosurfactant, enables the
modification of interfaces via genetic or chemical fusion to functional
moieties. However, bioconjugation of addressable amines introduces
heterogeneity that limits the precision of functionalization as well as the resolution
of interfacial characterization. Here we designed DAMP4 variants with cysteine
point mutations to allow for site-specific bioconjugation. The DAMP4 variants
were shown to retain the structural stability and interfacial activity characteristic
of the parent molecule, while permitting efficient and specific conjugation of
polyethylene glycol (PEG). PEGylation results in a considerable reduction on
the interfacial activity of both single and double mutants. Comparison of
conjugates with one or two conjugation sites shows that both the number of
conjugates as well as the mass of conjugated material impacts the interfacial activity
of DAMP4. As a result, the ability of DAMP4 variants with multiple PEG
conjugates to impart colloidal stability on peptide-stabilized emulsions is
reduced. We suggest that this is due to steric constraints on the structure of
amphiphilic helices at the interface. Specific and efficient bioconjugation permits
the exploration and investigation of the interfacial properties of designer
protein biosurfactants with molecular precision. Our findings should therefore
inform the design and modification of biosurfactants for their increasing use
in industrial processes, and nutritional and pharmaceutical formulations. | Hossam H Tayeb; Marina Stienecker; Anton Middelberg; Frank Sainsbury | Bioengineering and Biotechnology; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742424c89190ce4ad2414/original/the-impact-of-bioconjugation-on-the-interfacial-activity-of-a-protein-biosurfactant.pdf |
638db9027b7c915771e3fac6 | 10.26434/chemrxiv-2022-63ms2-v3 | Adsorption of Carbamazepine in All-Silica Zeolites Studied with Density Functional Theory Calculations | The anticonvulsant drug carbamazepine (CBZ) is an emerging contaminant of considerable concern due to its hazard potential and environmental persistence. Some previous experimental studies proposed hydrophobic zeolites as promising adsorbents for the removal of carbamazepine from water, but only a few framework types were considered in those investigations. In the present work, electronic structure calculations based on dispersion-corrected density functional theory (DFT) were used to study the adsorption of CBZ in eleven all-silica zeolites having different pore sizes and connectivities of the pore system (AFI, ATS, BEA, CFI, DON, FAU, IFR, ISV, MOR, SFH, SSF framework types). It was found that some zeolites with one-dimensional channels formed by twelve-membered rings (IFR, AFI) exhibit the highest affinity towards CBZ. A “good fit” of CBZ into the zeolite pores that maximises dispersion interactions was identified as the dominant factor determining the interaction strength. Further calculations addressed the role of temperature, performing DFT-based molecular dynamics simulations for selected systems, and of guest-guest interactions between coadsorbed CBZ molecules. In addition to predicting zeolite frameworks of particular interest as materials for selective CBZ removal, the calculations presented here also contribute to the atomic-level understanding of the interaction of functional organic molecules with all-silica zeolites. | Michael Fischer | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry; Crystallography | CC BY 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638db9027b7c915771e3fac6/original/adsorption-of-carbamazepine-in-all-silica-zeolites-studied-with-density-functional-theory-calculations.pdf |
610cc4734cb479f8b7297aff | 10.26434/chemrxiv-2021-hp2p9-v2 | Drug-target affinity prediction using applicability domain based on data density | In the pursuit of research and development of drug discovery, the computational prediction of the target affinity of a drug candidate is useful for screening compounds at an early stage and for verifying the binding potential to an unknown target. The chemogenomics-based method has attracted increased attention as it integrates information pertaining to the drug and target to predict drug-target affinity (DTA). However, the compound and target spaces are vast, and without sufficient training data, proper DTA prediction is not possible. If a DTA prediction is made in this situation, it will potentially lead to false predictions. In this study, we propose a DTA prediction method that can advise whether/when there are insufficient samples in the compound/target spaces based on the concept of the applicability domain (AD) and the data density of the training dataset. AD indicates a data region in which a machine learning model can make reliable predictions. By preclassifying the samples to be predicted by the constructed AD into those within (In-AD) and those outside the AD (Out-AD), we can determine whether a reasonable prediction can be made for these samples. The results of the evaluation experiments based on the use of three different public datasets showed that the AD constructed by the k-nearest neighbor (k-NN) method worked well, i.e., the prediction accuracy of the samples classified by the AD as Out-AD was low, while the prediction accuracy of the samples classified by the AD as In-AD was high. | Shunya Sugita; Masahito Ohue | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610cc4734cb479f8b7297aff/original/drug-target-affinity-prediction-using-applicability-domain-based-on-data-density.pdf |
664c60fa21291e5d1dda87a7 | 10.26434/chemrxiv-2024-0qn5p | Different Nucleation Mechanisms during Atomic Layer Deposition of HfS2 on Cobalt Oxide Surfaces | We investigated the atomic layer deposition (ALD) of HfS2 on atomically defined CoO(100) and CoO(111) surfaces under ultrahigh-vacuum (UHV) conditions. The ALD process was performed by sequential dosing of the precursors tetrakis(dimethylamido)hafnium (TDMAH) and deuterium sulfide (D2S) separated by purging periods. The growth and nucleation reactions were monitored by in situ infrared reflection absorption spectroscopy (IRAS). HfS2 films nucleate and grow on both cobalt oxide surfaces, despite the fact that CoO(100) lacks acidic protons and CoO(111) exposes only very few OH groups at defects. On these OH- free or OH-lean surfaces, the nucleation step involves a Lewis acid-base reaction instead. The stoichiometry of the –Hf(NMe2)x nuclei changes during the first ALD half cycle. On CoO(100), the split-off ligands bind as –NMe2 to surface cobalt ions. The nucleation on CoO(111) is more complex and the split-off ligands undergo dehydrogenation to form various surface species with C=N double and C≡N triple bonds and surface OH. Our findings reveal a new nucleation mechanism for ALD in the absence of acidic protons and show that other factors such as Lewis acidity, surface structure, and surface reactivity must also be considered in the nucleation event. | Georg Fickenscher; Nikolai Sidorenko; Kira Mikulinskaya; Joerg Libuda | Physical Chemistry; Interfaces; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664c60fa21291e5d1dda87a7/original/different-nucleation-mechanisms-during-atomic-layer-deposition-of-hf-s2-on-cobalt-oxide-surfaces.pdf |
60c73f9eee301c3adbc7894d | 10.26434/chemrxiv.7442303.v1 | On the Chemistry and Mobility of Hydrogen in the Interstitial Space of Layered Crystals H-BN, MoS2 and Graphite | <div><div><div><p>Recent experiments have demonstrated transport and separation of hydrogen isotopes in layered materials, such as hexagonal boron nitride and molybdenum disulphide. Here, based on first-principles calculations combined with well-tempered metadynamics simulations, we report the chemical interactions and mobility of protons (H+) and protium (H atoms) in the interstitial space of these layered materials. We show that both H+ and H can be transported between the layers of h-BN and MoS2 with low free energy barriers, while they are immobilized in graphite, in accordance with the experimental observations. In h-BN and MoS2, the transport mechanism involves a hopping process between the adjacent layers, which is assisted by the low- energy phonon shear modes. Defects present in MoS2 suppress the transport and act as traps for H species.</p></div></div></div> | Agnieszka Kuc; Yun An; Petko Petkov; Marcelo Lozada-Hidalgo; Thomas Heine | Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Theory - Computational; Surface; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2019-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9eee301c3adbc7894d/original/on-the-chemistry-and-mobility-of-hydrogen-in-the-interstitial-space-of-layered-crystals-h-bn-mo-s2-and-graphite.pdf |
64fec0a8b338ec988a460e91 | 10.26434/chemrxiv-2023-g9vv5 | Solution-driven processing of calcium sulfate: the mechanism of the reversible transformation of gypsum to bassanite in brines | Here, we show that calcium sulfate dihydrate (gypsum) can be directly, rapidly and reversibly converted to calcium sulfate hemihydrate (bassanite) in high salinity solutions (brines). The optimum conditions for the efficient production of bassanite in a short time (< 5 min) involve the use of brines with [NaCl] > 4 M and maintaining a temperature, T > 80 °C. When the solution containing bassanite crystals is cooled down to around room temperature, eventually gypsum is formed. When the temperature is raised again to T > 80 °C, bassanite is rapidly re-precipitated. This contrasts with the typical behaviour of the bassanite phase in low salt environments. Traditionally, hemihydrate is obtained from gypsum through a solid state thermal treatment at 150 °C < T < 200 °C, to remove some of the structural water. This is because, bassanite is considered to be metastable with respect to gypsum and anhydrite in aqueous solutions, and therefore gypsum-to-bassanite conversion should not occur in water. Interestingly, the high-salinity transformation of gypsum-to-bassanite has been reported by many authors and used in practice for several decades, although its very occurrence actually contradicts numerical thermodynamic predictions regarding solubility of calcium sulfate phases. By following the evolution of crystalline phases with in situ and time-resolved X-ray diffraction/scattering and Raman spectroscopy, we demonstrated that the phase stability in brines at elevated temperatures is inaccurately represented in the thermodynamic databases. Most notably for [NaCl] > 4 M, and T > 80 °C gypsum becomes readily more soluble than bassanite, which induces the direct precipitation of the latter from gypsum. The fact that these transformations are controlled by the solution provides extensive opportunities for precise manipulation of crystal formation. Our experiments confirmed that bassanite remained the sole crystalline structure for many hours before reverting into gypsum. This property is extremely advantageous for practical processing and efficient crystal extraction in industrial scenarios. | Tomasz Stawski; Stephanos Karafiludis; Carlos Pimentel; German Montes Hernandez; Zdravko Kochovski; Ralf Bienert; Karin Weimann; Franziska Emmerling; Ernesto Scoppola; Alexander Van Driessche | Physical Chemistry; Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry; Kinetics and Mechanism - Inorganic Reactions; Minerals | CC BY 4.0 | CHEMRXIV | 2023-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fec0a8b338ec988a460e91/original/solution-driven-processing-of-calcium-sulfate-the-mechanism-of-the-reversible-transformation-of-gypsum-to-bassanite-in-brines.pdf |
66fe29becec5d6c142ff7bc5 | 10.26434/chemrxiv-2024-c97nr | Rationally Grafting A Synthetic Multinuclear Metal Center into a Cytokine: A Dual-Functional Designer Metalloenzyme | A designer enzyme consisting of an abiological molecule incorporated into a natural protein has been developed as an exceptionally chemoselective catalyst, highlighting that the internal space of proteins is highly beneficial for enhancing catalytic performance. However, other superior features of proteins have received less attention in designer enzymes: e.g., their use as ligands to construct abiological (multinuclear) metal centers and an intrinsic protein function that has often been traded off for a new function.
Here, grafting a synthetic trinuclear zinc complex inside a human cytokine macrophage migration inhibitory factor (MIF) scaffold using solely amino-acid side chains led to a designer multi-metalloenzyme with extrinsic and intrinsic functions. The crystal structure of the designer tri-zinc enzyme verified the high accuracy of our design process based on geometry optimizations and quantum-chemical calculations. The extrinsic catalytic performance of this designer enzyme is of the highest class and comparable to that of previously reported designer zinc hydrolases. Importantly, an intrinsic function of MIF, i.e., its tautomerase activity, was maintained in this designer tri-zinc enzyme.
Considering that cytokines are originally expressed in response to in vivo events, this cytokine-based designer metalloenzyme shows promising potential as a synthetic biological tool for the self-adaptive regulation of life phenomena. | Akiko Ueno; Fumiko Takida; Tomoki Kita; Takuro Ishii; Tomoki Himiyama; Takuya Mabuchi; Yasunori Okamoto | Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fe29becec5d6c142ff7bc5/original/rationally-grafting-a-synthetic-multinuclear-metal-center-into-a-cytokine-a-dual-functional-designer-metalloenzyme.pdf |
674720707be152b1d0119c06 | 10.26434/chemrxiv-2024-9mkbg | Enzyme-based Nanoparticle Biosensors for Rapid Detection of Heavy Metals in Food Samples | Heavy metal contamination of food and water samples is a serious environmental and health problem that requires rapid and sensitive detection methods. In this study, we developed an enzyme-based nano biosensor for detecting heavy metals using sol-gel synthesis of selenium oxide nanoparticles and crude protease enzyme extract from chicken intestine. The biosensor works by measuring the change in temperature after dipping the biosensor in a sample, which reflects the interaction between the heavy metals and the enzyme. We tested our biosensor on five common heavy metal salts (chromic chloride, copper (II) sulfate, mercuric chloride, cadmium carbonate, and arsenic chloride) and observed different responses in terms of temperature change and color change. Our biosensor showed high efficiency and accuracy for detecting heavy metal contamination at 1% concentration, but it also had some limitations such as low selectivity and sensitivity. We suggested some potential improvements and applications of our biosensor, such as coupling it with electronic devicessuch as thermometer or modifying it with different enzymes or nanoparticles. Our biosensor has a wide range of applications for various industrial sectors, such as pharmaceutical, cosmetic, waste water treatment, battery, paper, textile, coal, oil, leather, steel, thermal power, and dye intermediaries. | Areej Nosher; Hira Yasmeen; Sidra Tul Muntaha; Saria Nasir; Umme Salma | Analytical Chemistry; Biochemical Analysis; Spectroscopy (Anal. Chem.) | CC BY 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674720707be152b1d0119c06/original/enzyme-based-nanoparticle-biosensors-for-rapid-detection-of-heavy-metals-in-food-samples.pdf |
61eadae81fd2743c81165739 | 10.26434/chemrxiv-2021-9nsft-v2 | Multimodal Plasmonic Hybrids: Efficient and Selective Photocatalysts | Important efforts are currently under way in order to implement plasmonic phenomena in the growing field of photocatalysis, striving for improved efficiency and reaction selectivity. A significant fraction of such efforts has been focused on distinguishing, understanding and enhancing specific energy transfer mechanisms from plasmonic nanostructures to their environment. Herein we report a synthetic strategy that brings together two of the main physical mechanisms driving plasmonic photocatalysis into an engineered system by rationally combining the photochemical features of energetic charge carriers and the electromagnetic field enhancement inherent to the plasmonic excitation. We do so by creating hybrid photocatalysts that integrate multiple plasmonic resonators in a single entity, controlling their joint contribution through spectral separation and differential surface functionalization. This strategy allows us to study the combination of different photosensitization mechanisms when activated simultaneously. Our results show that hot electron injection can be combined with an energy transfer process mediated by near-field interaction, leading to a significant increase of the final photocatalytic response of the material. In this manner, we overcome the limitations that hinder photocatalysis driven only by a single energy transfer mechanism, and move the field of plasmonic photocatalysis closer to energy-efficient applications. Furthermore, our multimodal hybrids offer a test system to probe the properties of the two targeted mechanisms in energy-related applications such as the photocatalytic generation of hydrogen and open the door to wavelength-selective photocatalysis and novel tandem reactions. | Yoel Negrín-Montecelo; Xiang-Tian Kong; Lucas Besteiro; Enrique Carbo-Argibay; Zhiming Wang; Moisés Pérez-Lorenzo; Alexander Govorov; Miguel Comesana-Hermo; Miguel A. Correa-Duarte | Catalysis; Nanoscience; Energy; Nanocatalysis - Catalysts & Materials; Plasmonic and Photonic Structures and Devices; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61eadae81fd2743c81165739/original/multimodal-plasmonic-hybrids-efficient-and-selective-photocatalysts.pdf |
60c74f080f50db7dda39731a | 10.26434/chemrxiv.12546479.v2 | Computer Simulation of Collision Induced Dissociation and Isolobal Analogy: The Case of Biotin and Its Analogues | We have studied how collision induced dissociation (CID) products and associated
mechanism are modified when a chemical group is modified by isolobal groups, and in
particular S, O, NH and CH2. At this end, we have considered protonated biotin (vitamin
B7) and corresponding oxybiotin, N-biotin and C-biotin, which have the same structures
except for one chemical group (the S in biotin which is substituted with the
aforementioned isolobal ones). Collisional simulations with Ar were performed to model
CID fragmentations and to have directly access to related mechanisms. Simulations have
shown that the CID fragmentation of the four compounds were similar and the resulting
fragments involve in a similar way the isolobal groups. Details on the mechanisms as
obtained from simulations are reported and discussed. This result shows that it is possible
in principle to predict, with a reasonable confidence, mass spectra of unknown molecules
based on mass spectrum of the known one when isolobal modifications are done.<br /> | Yanghune Ha; Riccardo Spezia; Kihyung Song | Mass Spectrometry; Computational Chemistry and Modeling; Chemical Kinetics; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f080f50db7dda39731a/original/computer-simulation-of-collision-induced-dissociation-and-isolobal-analogy-the-case-of-biotin-and-its-analogues.pdf |
6321c4f30429d6f23e9e3ddd | 10.26434/chemrxiv-2022-v9czt | Foam aging under free drainage analysed using associated operando techniques | Liquid foams are multi-scale structures whose structural characterization requires the combination of very different techniques. This inherently complex task is made more difficult by the fact that foams are also intrinsically unstable systems and that their properties are highly dependent on the production protocol and sample container. To tackle these issues, a new device has been developed that enables the simultaneous time-resolved investigation of foams by small-angle neutron scattering (SANS), electrical conductivity, and bubbles imaging. This device allows the characterization of the foam and its aging from nanometer up to centimeter scale on a single experiment. A specific SANS model was developed to quantitatively adjust the scattering intensity from the dry foam. Structural features such as the liquid fraction, specific surface area of the Plateau borders and inter-bubble films, thin film thickness were deduced from this analysis and some of them compared with extracted from the other applied techniques. This approach has been applied to a surfactant-stabilized liquid foam under free drainage and the underlying foam destabilization mechanisms were discussed with unprecedented detail. For example, the information extracted from the image analysis and SANS data allow for the first time to determine the disjoining pressure vs thickness isotherm in a real, draining foam. | Julien Lamolinairie; Benjamin Dollet; Jean-Luc Bridot; Pierre Bauduin; Olivier Diat; Leonardo Chiappisi | Physical Chemistry; Interfaces | CC BY NC 4.0 | CHEMRXIV | 2022-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6321c4f30429d6f23e9e3ddd/original/foam-aging-under-free-drainage-analysed-using-associated-operando-techniques.pdf |
60c75321469df4269df44cbb | 10.26434/chemrxiv.13213526.v4 | Biodiesel Production from Sunflower Oil Using K2CO3 Impregnated Kaolin Novel Solid Base Catalyst | <div><div><div><div><p>Kaolin clay material was loaded with potassium carbonate by impregnation method as a novel effective and economical heterogeneous catalyst for biodiesel production of sunflower oil via the transesterification reaction. The structural and chemical properties of the produced catalysts were analyzed by several characterization tests including the BET-BJH, XRD, SEM and FTIR. Influence of the K2CO3 impregnation level was examined by comparing the catalytic activity of different produced catalysts. To expand the efficiency of transesterification reaction, parameters of reaction were optimized including; the molar ratio between methanol and oil, concentration of catalyst, and duration of the reaction. The highest yield of biodiesel over the K2CO3/kaolin catalyst was around 95.3 ± 1.2%. It was achieved using kaolin supports impregnated with 20 wt.% of K2CO3. The optimum reaction conditions were found to be catalyst reactor loading of 5 wt.%, reaction temperature of 65 °C, methanol: oil molar ratio of 6:1 and reaction duration time of 4 h.</p></div></div></div></div> | Shayan Jalalmanesh; Mohammad Kazemeini; Mohamad Hosein Rahmani; Milad Zehtab Salmasi | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75321469df4269df44cbb/original/biodiesel-production-from-sunflower-oil-using-k2co3-impregnated-kaolin-novel-solid-base-catalyst.pdf |
60c745419abda2bf4ef8c51c | 10.26434/chemrxiv.10002020.v1 | Size-Extensive Molecular Machine Learning with Global Descriptors | <div>
<div>
<div>
<p>Machine learning (ML) models are increasingly used to predict molecular prop-
erties in a high-throughput setting at a much lower computational cost than con-
ventional electronic structure calculations. Such ML models require descriptors that
encode the molecular structure in a vector. These descriptors are generally designed
to respect the symmetries and invariances of the target property. However, size-
extensivity is usually not guaranteed for so-called global descriptors. In this contri-
bution, we show how extensivity can be build into ML models with global descriptors
such as the Many-Body Tensor Representation. Properties of extensive and non-
extensive models for the atomization energy are systematically explored by training
on small molecules and testing on small, medium and large molecules. Our result
shows that the non-extensive model is only useful in the size-range of its training
set, whereas the extensive models provide reasonable predictions across large size
differences. Remaining sources of error for the extensive models are discussed.
</p>
</div>
</div>
</div> | Hyunwook Jung; Sina Stocker; Christian Kunkel; Harald Oberhofer; Byungchan Han; Karsten Reuter; Johannes T. Margraf | Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745419abda2bf4ef8c51c/original/size-extensive-molecular-machine-learning-with-global-descriptors.pdf |
60c74eee469df4c090f4459a | 10.26434/chemrxiv.12597935.v2 | DFT-D4 Counterparts of Leading Meta-GGA and Hybrid Density Functionals for Energetics and Geometries | <div>
<div>
<div>
<p>Previously, we introduced DFT-D3(BJ) variants of the B97M-V, ωB97X-V and
ωB97M-V functionals and assessed them for the GMTKN55 database [Najibi and Go-
erigk, <i>J Chem. Theory Comput.</i> <b>2018</b>, <i>14</i>, 5725]. In this study, we present DFT-D4
damping parameters to build the DFT-D4 counterparts of these functionals and assess
these in comparison. We extend our analysis beyond GMTKN55 and especially turn
our attention to enzymatically catalysed and metal-organic reactions. We find that
B97M-D4 is now the second-best performing meta-GGA functional for the GMTKN55
database and it can provide noticeably better organometallic reaction energies com-
pared to B97M-D3(BJ). Moreover, the aforementioned DFT-D3(BJ) based functionals
have not been thoroughly assessed for geometries and herein we close this gap by
analysing geometries of noncovalently bound dimers and trimers, peptide conformers,
water hexamers and transition-metal complexes. We find that several of the B97(M)-
based methods—particularly the DFT-D4 versions—surpass the accuracy of previously
studied methods for peptide conformer, water hexamer, and transition-metal complex geometries, making them safe-to-use, cost-efficient alternatives to the original methods.
The DFT-D4 variants can be easily used with ORCA4.1 and above. </p>
</div>
</div>
</div> | Asim Najibi; LARS GOERIGK | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eee469df4c090f4459a/original/dft-d4-counterparts-of-leading-meta-gga-and-hybrid-density-functionals-for-energetics-and-geometries.pdf |
66826401c9c6a5c07adf23de | 10.26434/chemrxiv-2024-nmnzp | Automated Processing of Chromatograms: A comprehensive Python Package with GUI for Intelligent Peak Identification and Deconvolution in Chemical Reaction Analysis | Reaction screening and high-throughput experimentation (HTE) coupled with liquid chromatography
(HPLC, UHPLC) are becoming more important than ever in synthetic chemistry. With growing
number of experiments, it is increasingly difficult to ensure correct peak identification and integration,
especially due to unknown side components which often overlap with the peaks of interest.
We developed a comprehensive Python package with web-based graphical user interface (GUI) for
automated processing of chromatograms, including baseline correction, intelligent peak picking, peak
purity checks, deconvolution of overlapping peaks, and compound tracking. The algorithm accuracy
was benchmarked using three datasets and compared to the previous MOCCA implementation and
published results. The processing is fully automated with the possibility to include calibration and
internal standards. The software supports chromatograms with photo-diode array detector (DAD)
data from most commercial HPLC systems, and the Python package and GUI implementation are
open-source to allow addition of new features and further development. | Julius Hillenbrand; Jan Oboril; Christian P. Haas; Maximilian Lübbesmeyer; Rachel Nicholls; Thorsten Gressling; Klavs F. Jensen; Giulio Volpin | Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Analytical Chemistry - General; High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66826401c9c6a5c07adf23de/original/automated-processing-of-chromatograms-a-comprehensive-python-package-with-gui-for-intelligent-peak-identification-and-deconvolution-in-chemical-reaction-analysis.pdf |
67a5f6bffa469535b9626e6f | 10.26434/chemrxiv-2025-n6d9n-v2 | Entropy-based Regularized Regression for Advanced Distribution of Relaxation Times Deconvolution | Electrochemical impedance spectroscopy (EIS) coupled with distribution of relaxation times (DRT) analysis is a robust framework for characterizing electrochemical systems. However, DRT deconvolution is often plagued by spurious peaks, hindering accurate process identification and quantitative parameter estimation. To overcome this critical limitation, we rigorously evaluate entropy-based regularization within the standard regularized regression framework for DRT deconvolution. Building upon initial investigations, this study provides a detailed and quantitative evaluation of entropy-regularized DRT using a comprehensive suite of simulated impedance spectra, encompassing various impedance models and noise levels, and experimental data from lithium-ion batteries, fuel cells, and solar cells. Our results demonstrate that entropy regularization consistently outperforms conventional ridge regression, achieving significantly improved accuracy in DRT recovery and effectively eliminating spurious peaks. Furthermore, we demonstrate the novel capabilities of the entropy method for Bayesian DRT uncertainty quantification through sampling and for the simultaneous analysis of multiple impedance spectra. These findings establish entropy-based deconvolution as a superior and versatile technique for robust and insightful electrochemical system characterization, advancing the reliability of DRT analysis in electrochemistry. | Baptiste Py; Zilong Wang; Yuhao Wang; Francesco Ciucci | Theoretical and Computational Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Theory - Computational; Machine Learning; Energy Storage | CC BY 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a5f6bffa469535b9626e6f/original/entropy-based-regularized-regression-for-advanced-distribution-of-relaxation-times-deconvolution.pdf |
65732ac0cf8b3c3cd71c2009 | 10.26434/chemrxiv-2023-b70tg | Benchmarking Nitrous Oxide Adsorption and Activation in Metal-Organic Frameworks Bearing Coordinatively Unsaturated Metal Centers | Anthropogenic emissions of N2O, the third most abundant greenhouse gas after CO2 and CH4, are contributing to global climate change. Although metal-organic frameworks (MOFs) have been widely studied as adsorbents for CO2¬ and CH4, less effort has focused on the use of MOFs to remove N2O from emission streams or from air. Further, N2O activation would enable its use as an inexpensive oxidant for fine chemical synthesis. Herein, we identify features that contribute to strong binding and high uptake of N2O at coorinatively unsaturated metal sites in the M2Cl2(btdd) (M= Mn, Co, Ni, Cu; btdd2– = bis(1,2,3-triazolo[4,5-b],[4′,5′-i])dibenzo[1,4]dioxin) and M2(dobdc) (M = Mg, Mn, Fe, Co, Ni, Cu, Zn; dobdc4− = 2,5-dioxido-1,4-benzenedicarboxylate) series of MOFs. Combined experimental and computational studies suggest that N2O adsorption at open-metal-sites is primarily based on electrostatic interactions, rather than π-backbonding, causing MOFs with more Lewis acidic metal centers to be superior N2O adsorbents. As a result, Mg2(dobdc) demonstrates strong binding and record-setting N2O uptake (8.75 mmol/g at 1 bar and 298 K). Using density functional theory (DFT) to characterize reactive intermediates and transition states, we demonstrate that N2O activation to form a M(IV)-oxo species and N2 is thermodynamically favorable in Mn2(dobdc) and Fe2(dobdc) but appears to be kinetically limited in Mn2(dobdc). Our work lays a foundation for understanding N2O adsorption and activation in MOFs, paving the way for the design of promising next-generation materials for N2O capture and utilization. | Tristan Pitt; Haojun Jia; Tyler Azbell; Mary Zick; Aditya Nandy; Heather Kulik; Phillip Milner | Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65732ac0cf8b3c3cd71c2009/original/benchmarking-nitrous-oxide-adsorption-and-activation-in-metal-organic-frameworks-bearing-coordinatively-unsaturated-metal-centers.pdf |
634652ec0322f3fedb47ecd1 | 10.26434/chemrxiv-2022-dhdr8 | Apt-clean: Aptamer-mediated cleavage of extracellular antigen, a new strategy for the inhibition of membrane protein functions | Recently, targeted protein degradation (TPD) has attracted much attention as a powerful strategy for effective inhibition of disease-related proteins. However, development of ligands with high affinity and specificity for a target protein is still a demanding task and poses a particular challenge for designing TPD therapeutics. In this work, we report a novel TPD strategy called aptamer-mediated cleavage of extracellular antigen (Apt-clean), where oligonucleotide-based affinity agents are used for selective recruitment of proteases to target membrane proteins. Our data demonstrate that Apt-clean induces selective degradation of the target protein both in vitro and in cellulo. In addition, potential of Apt-clean was demonstrated through the inhibition of a tumor-related growth factor signaling. This novel TPD modality may serve as an efficient and flexible strategy for targeting membrane proteins. | Junya Hoshiyama; Yuga Okada; Seojung Cho; Ryosuke Ueki; Shinsuke Sando | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634652ec0322f3fedb47ecd1/original/apt-clean-aptamer-mediated-cleavage-of-extracellular-antigen-a-new-strategy-for-the-inhibition-of-membrane-protein-functions.pdf |
67ad478f6dde43c908a631aa | 10.26434/chemrxiv-2025-px2sj | Electron Sextets as Optically Addressable Molecular Qubits: Triplet Carbenes | There is a growing demand in quantum information science and sensing for electron spin purification and readout via a spin-optical interface. This technique, known as optically detected magnetic resonance (ODMR), has been applied on diamond-NV centres and transition metal complexes. Metal-free counterparts of these optically addressable spin qubits promise to be cheaper, more sustainable colour centres with prolonged polarisation lifetimes. However, progress has been hindered by the low ODMR signals of carbon-based π-diradicals, partly due to the lack of a ground singlet-to-triplet intersystem crossing (ISC). In this work, we propose to explore organic systems that are even more electron-deficient: electron sextets. Using triplet carbenes as an example, we illustrate how the ground singlet-triplet gap can be widened beyond thermal energy with the associated singlet-to-triplet ISC made available by vibronic effects. Through careful molecular engineering, this ISC can occur at a rate similar to and with an opposite spin selectivity from the excited-state ISC well-established in π-diradicals, unlocking a new ODMR pathway with potential signal gains. Persistent triplet carbenes is a renascent field with multiple stable molecules being isolated in the past five years. To motivate further development of its emissive properties, we illustrate our design in two realistic carbene candidates that incorporate existing strategies for carbene stabilisation. Ultimately, we believe that a new realm of quantum materials can be uncovered by expanding our scope towards stable electron sextets. | Yong Rui Poh; Xiao Chen; Hai-Ping Cheng; Joel Yuen-Zhou | Theoretical and Computational Chemistry; Organic Chemistry; Inorganic Chemistry; Physical Organic Chemistry; Sensors; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ad478f6dde43c908a631aa/original/electron-sextets-as-optically-addressable-molecular-qubits-triplet-carbenes.pdf |
649ebcfb9ea64cc16737f53c | 10.26434/chemrxiv-2023-pn532-v2 | A modular approach to tuning the charge transfer properties of photoluminescent quinine analogues. | We have shown that Pd-catalysed cascade processes provide molecular access to rigid quinoline-containing tetracylic amines. This enables fine-tuning of the through-space charge transfer (TSCT) state formation by variation of both N-aryl distance and quinoline substitution. It was observed that decreasing the N-aryl distance enhanced the formation of the TSCT species giving control over emission colour and photoluminescence quantum yield. Methoxylation of the quinoline unit decreases the propensity of TSCT formation. This systematic study provides great insight for TSCT formation with impact on further understanding dimeric, excimeric and exciplex species. | Joseph Watson; Ruth Pollard; Marc Etherington; Jonathan Knowles | Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649ebcfb9ea64cc16737f53c/original/a-modular-approach-to-tuning-the-charge-transfer-properties-of-photoluminescent-quinine-analogues.pdf |
6666efb2409abc03451347ed | 10.26434/chemrxiv-2024-58pdc | Magnetron sputtering as a solvent-free method for fabrication of nanoporous ZnO thin films for highly efficient photocatalytic organic pollution degradation | Zinc oxide (ZnO) is one of the most versatile semiconductor materials with many potential applications. Understanding the interactions between the surface chemistry of ZnO along with its physico-chemical properties are essential for the development of ZnO as a robust photocatalyst for the removal of aqueous pollutants. We report on the fabrication of nanoparticle-like porous ZnO films and the correlation between the fabrication process parameters, particle size, surface oxygen vacancies (SOV), photoluminescence and photocatalytic performance. The synthesis route is unique, as highly porous zinc layers with nanoscale grains were first grown via magnetron sputtering, a vacuum-based technique, and subsequently annealed at temperatures of 400 \degree C, 600 \degree C and 800 \degree C in oxygen flow to oxidise them to zinc oxide (ZnO) while maintaining their porosity. Our results show that as the annealing temperature increases, nanoparticle agglomeration increases, and thus there is a decrease in the active sites for the photocatalytic reaction. However, for selected samples the annealing leads to an increase of the photocatalytic efficiency, which we explain based on the analysis of defects in the material, based on photoluminescence (PL). PL analysis showed that in the material the transition between the conduction band and the oxygen vacancy is responsible for the green emission centered at 525 nm, but the photocatalytic activity correlated best with surface states - related emission. | Kamila Ćwik; Jakub Zawadzki; Rafał Zybała; Monika Ożga; Bartłomiej Witkowski; Piotr Wojnar; Małgorzata Wolska-Pietkiewicz; Maria Jędrzejewska; Janusz Lewiński; Michał Borysiewicz | Materials Science; Catalysis; Nanoscience; Nanostructured Materials - Materials; Thin Films; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666efb2409abc03451347ed/original/magnetron-sputtering-as-a-solvent-free-method-for-fabrication-of-nanoporous-zn-o-thin-films-for-highly-efficient-photocatalytic-organic-pollution-degradation.pdf |
67c2a2fd6dde43c908fa9d4f | 10.26434/chemrxiv-2025-j1pnk | Hierarchical Chiral Luminescent Macrocyclic Porous Organic Polymer from Chiral π-Conjugated Macrocycles: Tunable Circularly Polarized Luminescence and Enantiomeric Fluorescent Sensing | Chiral molecules and materials have attracted tremendous research interests owing to their intriguing chiral structure and promising application, whereas precise and modular construction toward chiral structures and frameworks is the cornerstone for their development. Herein, a modular synthetic method toward chiral π-conjugated macrocycles (CCMs) incorporating well-defined helical tetraarylethene (TAE) moiety is established, which can feasibly afford chiral porous organic polymers (POPs) with mirror-imaged chirality and hierarchical porous structure via Yamamoto polymerization. These chiral macrocyclic molecules and chiral macrocyclic POPs all show bright emission in solid states owing to the aggregation-induced emission property of the TAE units, and exhibit mirror-imaged circularly polarized luminescence (CPL) with luminescence asymmetric factor on the level of 10-3. Accommodation of Rhodamine B as guest molecules into chiral POPs has contributed to color-tunable CPL-active materials owing to chirality transfer and energy transfer from chiral porous polymers to non-chiral guest dyes. And the chiral luminescent POPs are further utilized to detect explosive molecules via fluorescent quenching, and display enantio-selective sensing of chiral nitro-aromatics. These results have provided a reliable protocol for developing luminescent chiral porous materials, and will further spur the applications of chiral luminescent polymers. | Shiwei Fu; Yifan Li; Junhao Liang; Qi Wu; Lei Wang; Yi Liu | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c2a2fd6dde43c908fa9d4f/original/hierarchical-chiral-luminescent-macrocyclic-porous-organic-polymer-from-chiral-conjugated-macrocycles-tunable-circularly-polarized-luminescence-and-enantiomeric-fluorescent-sensing.pdf |
64805d0fe64f843f417444a6 | 10.26434/chemrxiv-2023-g4190 | Unveiling polyamorphism and polyamorphic interconversions in pharmaceuticals: the peculiar case of hydrochlorothiazide | Polyamorphism has been a controversial and highly debated solid-state phenomenon in both material and pharmaceutical communities. Although some evidence of this fascinating phenomenon has been reported for several inorganic systems, and more recently also for a few organic compounds, the occurrence of polyamorphism is poorly understood and the molecular-level organization of polyamorphic forms is still unknown. Here we have investigated the occurrence of polyamorphism and polyamorphic interconversions in hydrochlorothiazide (HCT), using both experimental and computational methods. Three distinct HCT polyamorphs, presenting distinct physical and thermal stabilities as well as distinct relaxation properties, were systematically prepared using spray-drying (SD), quench-cooling (QC) and ball milling (BM) methods. HCT polyamorph II (obtained by QC) was found to be more physically stable than polyamorphs I and III (obtained by SD and BM, respectively). Furthermore, polyamorphs I and III could be converted into polyamorph II after QC, while polyamorph II did not convert to any other polyamorph after SD or BM. Molecular dynamics simulations show that HCT dihedral angle distributions are significantly different for polyamorphs I and II, which is postulated as a possible explanation for their different physicochemical properties. | Inês C. B Martins; Anders S. Larsen; Anders Ø. Madsen; Olivia Aalling Frederiksen; Kirsten M. Ø. Jensen; Henrik S. Jeppesen; Thomas Rades | Physical Chemistry; Materials Science; Analytical Chemistry; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64805d0fe64f843f417444a6/original/unveiling-polyamorphism-and-polyamorphic-interconversions-in-pharmaceuticals-the-peculiar-case-of-hydrochlorothiazide.pdf |
60c73dfebdbb894337a37d5a | 10.26434/chemrxiv.5848113.v2 | Bind3P: Optimization of a Water Model with Host-Guest Binding Data | We report a water model, Bind3P (Version 0.1), which was obtained by using sensitivity analysis to readjust the Lennard-Jones parameters of the TIP3P model against experimental binding free energies for six host-guest systems, along with pure liquid properties. Tests of Bind3P against >100 experimental binding free energies and enthalpies for host-guest systems distinct from the training set show a consistent drop in the mean signed error, relative to matched calculations with TIP3P. Importantly, Bind3P also yields some improvement in the hydration free energies of small organic molecules, and preserves the accuracy of bulk water properties, such as density and the heat of vaporization. The same approach can be applied to more sophisticated water models that can better represent pure water properties. These results lend further support to concept of integrating host-guest binding data into force field parameterization. | Jian Yin; Niel M. Henriksen; Hari S. Muddana; Michael K. Gilson | Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dfebdbb894337a37d5a/original/bind3p-optimization-of-a-water-model-with-host-guest-binding-data.pdf |
60c753c8337d6c42d9e288ec | 10.26434/chemrxiv.13550399.v1 | Spatially Encoded Transfer of 1H Polarization to 13C for Uniform 1 JCH-Response in HSQC | Two dimensional (2D) NMR display better resolution than one-dimensional (1D) 1H NMR. However,
2D NMR does not display a straightforward quantitative aspect due to J-dependent
polarization/coherence transfer. 1D 1H NMR is versatile for quantification; however, it displays
significant spectral overlap in biological or organic complex mixtures, which forbids quantification of
a large number of signals in 1D 1H NMR. The significant variations in 1H13C scalar couplings, T1, T2, and
pulse imperfections are the main problems. Although T1, T2 can be suitably chosen to minimize their
adverse effect on quantification, the large variations in 1H -
13C couplings lead to variations in cross
peak intensity, which is more influenced by the amount of polarization transfer rather than the
quantity of metabolites or amount of analytes in a complex mixture. In the present work, we show
that spatial encoding of the polarization transfer periods can be executed in 1H13C HSQC using sweep
frequency pulses in the presence of a magnetic field gradient. As a result, uniform transfer of
polarization from 1H to 13C over a range of 1H -
13C couplings can be performed, subsequently improving
the quantitative aspect of HSQC or improve the intensity of cross-peaks, which are mistuned in regular
HSQC | Bikash Baishya; Rashmi Parihar; Rajeev Verma | Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753c8337d6c42d9e288ec/original/spatially-encoded-transfer-of-1h-polarization-to-13c-for-uniform-1-jch-response-in-hsqc.pdf |
67aedbc1fa469535b941fee8 | 10.26434/chemrxiv-2025-zts13 | Graphically revealing weak interactions in dynamic environments using amIGM method | Visualization of weak interactions is now a very popular kind of analysis methods, which allows chemists to recognize existence, strength, and type of interactions in different regions of a chemical system easily and intuitively. Among these analysis methods, the independent gradient model (IGM) and its variant with better graphical effect, namely IGM based on Hirshfeld partition of molecular density (IGMH), are particularly useful. They can clearly reveal various interactions between specific fragments, and become widely popular in recent years. This chapter first briefly reviews the definition and characteristics of the two methods, and then introduces a new variant of IGM, called modified IGM (mIGM), which, like IGM, only requires atomic coordinate information to perform the analysis and thus the computational cost is fairly low, while its graphical quality in exhibiting weak interactions is almost as good as the markedly more expensive IGMH. This chapter then introduces the averaged mIGM (amIGM) method, which extends mIGM to visual analysis of the weak interactions involved in molecular dynamics trajectories. A series of examples fully demonstrate that amIGM can well display all kinds of weak interactions in dynamic environments, and its image quality and flexibility are all superior to the previously proposed averaged noncovalent interaction (aNCI) method with similar uses. | Tian Lu | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aedbc1fa469535b941fee8/original/graphically-revealing-weak-interactions-in-dynamic-environments-using-am-igm-method.pdf |
67c765976dde43c9088151b7 | 10.26434/chemrxiv-2025-v3blc | The 1.5 um Band of Cyanoacetylene as a Spectroscopic Target in the Hunt for Prebiotic Molecules | The search for prebiotic molecules officially entered a new era with the launch of the James Webb Space Telescope. The capabilities of the near-infrared instrumentation on board offer greater sensitivity and resolution than has ever been available in a space-based instrument. With the planned launch of more near-infrared telescopes---such as SPHEREx in 2025---it is essential to have laboratory data for important molecules on hand to guide observations in this spectral region. We present here the first published line list of the prebiotic cyanoacetylene (HC3N) molecule in the 1.5 um region. Molecules were cooled to 20 K through the use of a cryogenic buffer-gas cooling yielding well-resolved ro-vibrational states of the 2nu1 band that were probed and assigned using cavity-ringdown spectroscopy. Rotational constants were calculated using PGOPHER and spectral line intensities were measured relative to hydrogen cyanide. We recommend the HC3N 1.5um band as an observational target for transmission spectroscopy at Hycean and Super-Earth exoplanetary bodies. | Thomas Howard; Sanjana Maheshwari; Grace Yeh; Shannon Ganley; Leah Dodson | Physical Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c765976dde43c9088151b7/original/the-1-5-um-band-of-cyanoacetylene-as-a-spectroscopic-target-in-the-hunt-for-prebiotic-molecules.pdf |
635adc9631107274c2f2a3ab | 10.26434/chemrxiv-2022-3w06g | Origin of Photoluminescence, Exciton Binding Energy, Exciton-Phonon interaction, and Urbach Energy in γ-CsPbI3 Nanoparticles. | Recently inorganic perovskites have had a deep impact in perovskites-based devices allowing the fabrication of high efficiency and high stability devices. To continue with the development of these technologies a detailed study of the optoelectronic properties of these materials is necessary since this is a fundamental tool for the design of new and more efficient devices. In the present work, the optical properties of γ-CsPbI3 nanoparticles are studied using temperature dependent spectroscopic techniques of transmittance and photoluminescence. The absorption spectrum shows a marked excitonic behavior especially at low temperatures. Analyzing this spectrum with the Elliot function the evolution with temperature of the bandgap and the exciton binding energy is studied. From the evolution of the shape of the excitonic peak, both in the absorption and photoluminescence, we determined the excitonic recombination nature of photoluminescence and exciton-phonon interaction energy. Once proven the excitonic nature of photoluminescence we prove that the Stokes Shift has its origin in excitonic thermalization. Finally, analyzing the low energy region of the absorption spectrum the Urbach energy was determined. The obtained values, which are very low for solution processed nanoparticles, indicates that the nanoparticles present excellent crystallinity and are suitable for the implementation of quantum electronic devices. | Daniel Gau; Isabel Galain; Ivana Aguiar; Ricardo Marotti | Physical Chemistry; Nanoscience; Energy; Nanostructured Materials - Nanoscience; Physical and Chemical Properties; Quasiparticles and Excitations | CC BY NC 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635adc9631107274c2f2a3ab/original/origin-of-photoluminescence-exciton-binding-energy-exciton-phonon-interaction-and-urbach-energy-in-cs-pb-i3-nanoparticles.pdf |
60c752bb567dfe4a44ec5d1d | 10.26434/chemrxiv.13338986.v1 | TD-DFT and Experimental Methods for Unraveling the Energy Distribution of Charge-Transfer Triplet/Singlet States of a TADF Molecule in a Frozen Matrix | Reverse
intersystem crossing (RISC) rate of a thermally activated delayed fluorescence
(TADF) molecule is sensitive to the energy alignment of singlet charge-transfer
state (<sup>1</sup>CT), triplet charge-transfer state (<sup>3</sup>CT), and
locally excited triplet state (<sup>3</sup>LE). However, the energy distribution of the charge-transfer states originating
from the conformational distribution of TADF molecules in a solid matrix
inevitably generated during the preparation of a solid sample due to the
rotatable donor-acceptor linkage is rarely considered. Moreover, the
investigation of the energy distribution of the <sup>3</sup>CT state is both
theoretically and experimentally difficult due to the triplet instabilities of
time-dependent density functional (TD-DFT) calculations and difficulties in phosphorescence
measurements, respectively. As a result, the relation between conformational
distribution, configurations of excited state transition orbitals, and excited
state energies/dynamics have not been clearly explained. In this work, we
determined the energy distribution of CT states of the TADF emitter TPSA in
frozen toluene at 77 K by the measurement of time-resolved spectra in the full
time range (1 ns ~ 30 s) of emission including prompt fluorescence, TADF, <sup>3</sup>CT
phosphorescence, and <sup>3</sup>LE phosphorescence. We obtained the energy
band of CT states where <sup>1</sup>CT and <sup>3</sup>CT states are
distributed in the range of 2.85-3.00 eV and 2.64-2.96 eV, respectively. We
tested various global hybrid and long-range corrected functionals for the TD-DFT calculation of <sup>3</sup>CT energy of TPSA and found
that only the M11 functional shows consistent results without triplet instability.
We performed TD-DFT with the M11* functional optimized for robust dihedral
angle scan of <sup>3</sup>CT states without triplet instability and reproduced
the energy band structure obtained from the experiment. Through TD-DFT and
experimental investigations, it is estimated that the dihedral angle of
donor-acceptor (θ<sub>D-A</sub>) and acceptor-linker (θ<sub>A</sub>) of TPSA in
frozen toluene lie within the range of 70°≤θ<sub>D-A</sub>≤90° and 0°≤θ<sub>A</sub>≤30° respectively. Our results show that the dihedral
angle distribution must be considered for further investigation of the
photophysics of TADF molecules and the development of stable and efficient TADF
emitters. | Seung-Je Woo; Jang-Joo Kim | Dyes and Chromophores; Optical Materials; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752bb567dfe4a44ec5d1d/original/td-dft-and-experimental-methods-for-unraveling-the-energy-distribution-of-charge-transfer-triplet-singlet-states-of-a-tadf-molecule-in-a-frozen-matrix.pdf |
65e53d4266c1381729231a4d | 10.26434/chemrxiv-2024-fxq8c | Advanced Experimental and Computational Approaches for Advanced Reduction of PFAS Contaminants | The elimination of per- and polyfluoroalkyl substances (PFAS) in water continues to garner significant attention due to their enduring presence in the environment and associated health concerns. The emergence of advanced reduction processes (ARPs) holds significant promise in reducing persistent PFAS in water, primarily due to its ability to produce short-lived yet highly reductive hydrated electrons. This concise review offers insights into the latest developments in ARP-based PFAS degradation, encompassing both experimental and theoretical investigations conducted within the last 2 - 5 years. We conclude with an outlook on potential research avenues in this dynamic field and suggest future experimental and computational strategies to enhance ARP capabilities. | Sohag Biswas; Xian Wang; Bryan Wong | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e53d4266c1381729231a4d/original/advanced-experimental-and-computational-approaches-for-advanced-reduction-of-pfas-contaminants.pdf |
60c7451f9abda20f16f8c4cd | 10.26434/chemrxiv.9971054.v1 | Autonomous Discovery of Materials for Intercalation Electrodes | The development of automated computational tools is required to accelerate the discovery of novel battery<br />materials. In this work, we design and implement a workflow, in the framework of Density Functional<br />Theory, which autonomously identifies materials to be used as intercalation electrodes in batteries, based<br />on descriptors like adsorption energies and diffusion barriers. A substantial acceleration for the calculations<br />of the kinetic properties is obtained due to a recent implementation of the Nudged Elastic Bands (NEB)<br />method, which takes into consideration the symmetries of the system to reduce the number of images to<br />calculate. We have applied this workflow to discover new cathode materials for Mg-ion batteries, where<br />two of these materials display a threefold increase in the potential of the Chevrel phase, the state-of-the-art<br />cathode in Mg-ion batteries. | Felix Tim Bölle; Nicolai Rask Mathiesen; Alexander Juul Nielsen; Tejs Vegge; Juan Maria García Lastra; Ivano E. Castelli | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7451f9abda20f16f8c4cd/original/autonomous-discovery-of-materials-for-intercalation-electrodes.pdf |
66e7ff52cec5d6c14236ebdc | 10.26434/chemrxiv-2024-1dchd | Hydration Shell Water Surrounding Citrate-Stabilised Gold Nanoparticles | Presence of gold nanoparticles in an aqueous dispersion perturbs water molecules in their vicinity. Such water molecules form what is known as hydration shell and possess different vibrational attributes than those in the bulk dispersion. Raman spectroscopy was utilised to study these hydration shell water molecules around citrate-stabilised gold nanoparticles. Aqueous dilution series of three sizes of gold nanoparticle samples were prepared. Hydration shell spectral response, recovered by applying multivariate curve resolution technique, were compared against the spectra of the bulk phase. Once correlated with an increasing aqueous content in the respective samples, it could be inferred from the comparison that the hydration shell contains a less extensive hydrogen-bonding network with a smaller number of hydrogen-bonding interactions being possible than that in bulk. The results also suggest the hydrogen-bonding network in the hydration shells to be structurally more rigid and stronger, if compared against the intermolecular hydrogen-bonding prevalent in bulk. | Taritra Mukherjee; Martin Rabe | Physical Chemistry; Interfaces; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e7ff52cec5d6c14236ebdc/original/hydration-shell-water-surrounding-citrate-stabilised-gold-nanoparticles.pdf |
616ae0152aca531d9d65c2df | 10.26434/chemrxiv-2021-d24m3 | Comparison of 2D versus 3D diffusion analysis at Nanowire Electrodes: Finite element analysis and experimental study | In electroanalysis, finite element simulations of electrochemical processes occurring at electrodes are used to provide key insight into experimental design in relation to diffusion profiles and expected currents. The diffusion domain approach (DDA) offers a means of reducing a three dimensional design to two dimensions to ease computational demands. However, the DDA approach can be limited when basic assumptions, for example that all electrodes in an array are equivalent, are incorrect. Consequently, to get a more realistic view of molecular diffusion to nanoelectrodes, it is necessary to undertake simulations in 3D. In this work, two and three dimensional models of electrodes comprising of (i) single nanowires, (ii) arrays of nanowires and (iii) interdigitated arrays of nanowires operating in generator-collector mode, are undertaken and compared to experimental results obtained from fabricated devices. The 3D simulations predict a higher extracted current for a single nanowires and diffusionally independent nanowire arrays when compared to 2D simulations since, unlike the 2D model, they take into account molecular diffusion to and from the nanowire termini. This current difference was observed to increase with increasing electrode width and decrease with electrode length. When the nanowire arrays were diffusionally overlapped, they behaved as an electrode of larger width, and the divergence between the two models increased. By contrast, in generator-collector mode, using interdigitated nanowire arrays, the difference between extracted current values obtained using two models was significantly lower. Simulations indicated however that a higher collection efficiency was predicted by the 2D model when compared to the 3D model. Electrochemical experiments were undertaken to confirm the simulation study and demonstrated that the extracted currents from 3D simulations more closely mapped onto experimentally measured currents. | Benjamin O'Sullivan; Shan O'Sullivan; Tarun Naruyan; Han Shao; Bernardo Patella; Ian Seymour; Rosalinda Inguanta; Alan O'Riordan | Analytical Chemistry; Electrochemical Analysis | CC BY NC 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616ae0152aca531d9d65c2df/original/comparison-of-2d-versus-3d-diffusion-analysis-at-nanowire-electrodes-finite-element-analysis-and-experimental-study.pdf |
63b454cedadddc71b3a45c1f | 10.26434/chemrxiv-2023-xgx5h | Build instructions for Closed-loop Spectroscopy Lab: Light-mixing Demo | Closed-loop Spectroscopy Lab: Light-mixing Demo (CLSLab:Light) is a teaching and prototyping platform for autonomous scientific discovery. It consists of a set of LEDs and a light sensor while encapsulating key principles for "self-driving" (i.e., autonomous) research laboratories, including sending commands, receiving sensor data, physics-based simulation, and advanced optimization. CLSLab:Light is a "Hello, World!" introduction to these topics, accessible by students, educators, hobbyists, and researchers for less than 100 USD, a small footprint, and under an hour of setup time. | Sterling G. Baird; Taylor D. Sparks | Materials Science; Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2023-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b454cedadddc71b3a45c1f/original/build-instructions-for-closed-loop-spectroscopy-lab-light-mixing-demo.pdf |
60c73fa34c891900e7ad1fda | 10.26434/chemrxiv.7468703.v1 | Metal Nanowire Felt as a Flow-Through Electrode for High-Throughput Electrosynthesis | The low productivity of organic electrosynthesis limits the adoption of this green methodology for production of organic chemicals. This work examines to what extent reducing the size of the fibers in a flow-through electrode to the nanoscale can increase the productivity of electrosynthesis. A Cu nanowire felt, made from nanowires 45 times smaller than the 10-μm-wide fibers in carbon paper, achieved a productivity 278 times higher than carbon paper for mass transport-limited reduction of Cu ions. For an intramolecular cyclization reaction that was limited by both mass and charge transfer kinetics, the Cu nanowire felt achieved a productivity 4.2 times higher than carbon paper. This work demonstrates large gains in productivity can be achieved with nanostructured flow-through electrodes, but that potential gains can be limited by charge transfer kinetics. | Myung Jun Kim; Youngran Seo; Mutya Cruz; Benjamin Wiley | Nanostructured Materials - Nanoscience; Electrochemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fa34c891900e7ad1fda/original/metal-nanowire-felt-as-a-flow-through-electrode-for-high-throughput-electrosynthesis.pdf |
674c3e507be152b1d0914b2e | 10.26434/chemrxiv-2024-f0kcq | Data-driven automatic synthesis planning: Synthesis routes of S-Zanubrutinib identified with CDI CASP | Advances in computer-assisted synthesis planning (CASP) are revolutionising how new functional molecules in many chemistry-using industries are being developed. CASP tools allow to assemble and analyse prior knowledge of a specified chemical system (a molecule, a reaction, a synthesis route), to generate hypotheses on experimental campaigns that could either be performed manually or using automated reaction systems. Advanced CASP tools are combining data science, chemoinformatics, machine learning and physical models-based predictive tools. Compared to expert-based synthesis planning, the power of CASP techniques allows for faster and more comprehensive planning, which could significantly improve the efficiencies of chemical process/product development.
This White Paper describes a recent collaboration project between Shionogi & Co. Ltd. and Chemical Data Intelligence (CDI) Ltd. The CASP system developed by CDI (CDI-CASP) was tested in developing a new synthesis of S-Zanubrutinib, a drug for lymphoma treatment. Three types of search in CDI-CASP - “search synthesis routes”, “search analogue routes” and “search chiral reactions” - were iteratively applied for synthesis planning. Setting search criteria requires expert involvement. This ‘human in the middle’ interactive strategy leads to a shorter, greener, and more efficient synthesis route compared to the benchmark route filed in a patent. | Zhen Guo; Akihiro Takada; Alexei Lapkin | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674c3e507be152b1d0914b2e/original/data-driven-automatic-synthesis-planning-synthesis-routes-of-s-zanubrutinib-identified-with-cdi-casp.pdf |
66dddfd112ff75c3a1ca4ba1 | 10.26434/chemrxiv-2024-3h0fn-v2 | Dimensional Analysis of Diffusive Association Rate Equations | Diffusive adsorption/association is a fundamental step in almost all chemical reactions in diluted solutions, such as organic synthesis, polymerization, self-assembly, biomolecular interactions, electrode dynamics, catalysis, chromatography, air and water environmental dynamics, and social and market dynamics. However, predicting the rate of such a reaction is challenging using the equations established over 100 years ago. From dimensional analysis, we can guess a series of equations including historical ones and new ones that have the correct final unit, the number of molecules associated per second, which is constructed from concentration, diffusion coefficient, and size of the molecules only. These equations are roughly divided into two groups, continuous models and discrete models. The continuous models integrate Fick’s concentration gradient in the solution near the target to calculate the association rate, and are the historical solutions reported. The discrete models integrate the probability density function of each probe that is discretely distributed in the solution. I have introduced a key concept of the nearest neighbor diffusion time to stabilize these time-dependent solutions. These models are applied to analyze a set of experimental results for comparison to achieve consistency and clarify assumptions among models. | Jixin Chen | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dddfd112ff75c3a1ca4ba1/original/dimensional-analysis-of-diffusive-association-rate-equations.pdf |
60c73f56bb8c1a3b333d9a97 | 10.26434/chemrxiv.5923786.v3 | Phase-Plane Geometries in Coupled Enzyme Assays | The determination of a substrate or enzyme activity by coupling of one enzymatic reaction with another easily detectable (indicator) reaction is a common practice in the biochemical sciences. Usually, the kinetics of enzyme reactions is simplified with singular perturbation analysis to derive rate or time course expressions valid under the quasi-steady-state and reactant stationary state assumptions. In this paper, the dynamical behavior of coupled enzyme catalyzed reaction mechanisms is studied by analysis of the phase-plane. We analyze two types of time-dependent slow manifolds - Sisyphus and Laelaps manifolds - that occur in the asymptotically autonomous vector fields that arise from enzyme coupled reactions. Projection onto slow manifolds yields various reduced models, and we present a geometric interpretation of the slow/fast dynamics that occur in the phase-planes of these reactions. <br /> | Justin Eilertsen; Wylie Stroberg; Santiago Schnell | Biochemical Analysis; Biophysical Chemistry; Chemical Kinetics; Solution Chemistry | CC BY 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f56bb8c1a3b333d9a97/original/phase-plane-geometries-in-coupled-enzyme-assays.pdf |
63656025ee31866a0b7fc443 | 10.26434/chemrxiv-2022-qggs2 | The internal structure of the velvet worm projectile slime: A small-angle scattering study | Velvet worms capture prey and defend themselves by ejecting an adhesive slime which has been established as a model system for recyclable complex liquids. Triggered by mechanical agitation, the sticky fluid rapidly transitions into solid fibers. The assembly of slime proteins into stiff polymers is fully reversible and recyclable enabling the recovery of the soluble precursors. In order to understand the rapid and reversible mechanoresponsive behavior of this material, here, we study the nanostructural organization of slime components using small-angle scattering with neutrons and x-rays under physiological native conditions, after drying and re-hydration, and mechanical agitation. The scattering intensities are successfully described with a three-component model accounting for proteins of two dominant molecular weight fractions and for protein-based nanoglobules with a radius of ~40-45 nm, which is in line with the literature. However, in contrast to the previous assumption that high molecular weight (HMW) proteins -- the presumed building blocks of the fiber core -- are contained in the nanoglobules, we find that the majority of slime proteins exist as free proteins in solution, including the HMW fiber core precursors. Only less than 10 % of the slime proteins are contained in the nanoglobules, necessitating a reassessment of the previously proposed function of nanoglobules in fiber formation. Exploiting distinct differences in the x-ray and neutron scattering contrast of slime re-hydrated with light and heavy water (D2O) indicates that the majority of lipids available in the slime are contained in the nanoglobules, where they are homogeneously distributed. Surprisingly, mechanical agitation of slime in a completely filled container causes gelification; however, this neither leads to fiber formation nor alters the bulk structure of the slime significantly, suggesting that interfacial phenomena and directional shearing are required for the formation of stiff fibers in velvet worm slime. | Alexander Baer; Ingo Hoffmann; Najet Mahmoudi; Alexandre Poulhazan; Matthew J. Harrington; Georg Mayer; Stephan Schmidt; Emanuel Schneck | Physical Chemistry; Materials Science; Nanoscience; Biological Materials; Nanostructured Materials - Nanoscience; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63656025ee31866a0b7fc443/original/the-internal-structure-of-the-velvet-worm-projectile-slime-a-small-angle-scattering-study.pdf |
6172bcd10c0480fd773f44a4 | 10.26434/chemrxiv-2021-fzjx8 | Mapping Ambiphile Reactivity Trends in the Anti-(Hetero)annulation of Non-Conjugated Alkenes via Pd(II)/Pd(IV) Catalysis | In this study, we systematically evaluate different ambiphilic organohalides for their ability to participate in anti-selective carbo- or heteroannulation with non-conjugated alkenyl amides under Pd catalysis. Detailed optimization of reaction conditions has led to protocols for synthesizing tetrahydropyridines, tetralins, pyrrolidines, and other carbo/heterocyclic cores via [n+2] (n = 3–5) (hetero)annulation. Expansion of scope to otherwise unreactive ambiphilic haloketones through Pd(II)/amine co-catalysis is also demonstrated. Compared to other annulation processes, this method proceeds via a distinct Pd(II)/Pd(IV) mechanism involving Wacker-type directed nucleopalladation. This distinction results in unique reactivity and selectivity patterns, as revealed through assessment of reaction scope and competition experiments. | Hui-Qi Ni; Phillippa Cooper; Shouliang Yang; Fen Wang; Neal Sach; Pranali Bedekar; Joyann Donaldson; Michelle Tran-Dubé; Indrawan McAlpine; Keary Engle | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6172bcd10c0480fd773f44a4/original/mapping-ambiphile-reactivity-trends-in-the-anti-hetero-annulation-of-non-conjugated-alkenes-via-pd-ii-pd-iv-catalysis.pdf |
62d0ab3381efd066fdab1cbd | 10.26434/chemrxiv-2022-xj9rk | A long-wavelength xanthene dye for photoacoustic imaging | Photoacoustic (PA) imaging is a powerful biomedical imaging modality. We designed KeTMR and KeJuR, two xanthene-based dyes that readily obtained through a 2-step synthetic route. KeJuR has low molecular weight, good aqueous solubility, and superior chemical stability compared to KeTMR. KeJuR shows robust PA signal at 860 nm excitation and can be paired with traditional PA dyes for multiplex imaging in blood samples under tissue-mimicking environment. | Xinqi Zhou; Yuan Fang; Viranga Wimalasiri; Cliff Stains; Evan Miller | Analytical Chemistry; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d0ab3381efd066fdab1cbd/original/a-long-wavelength-xanthene-dye-for-photoacoustic-imaging.pdf |
616ec04ef718dffe58e3e06b | 10.26434/chemrxiv-2021-dkf1k | Discovery of a novel class of D-amino acid oxidase (DAO) inhibitors with the Schrödinger computational platform | D-Serine is a co-agonist of the N-methyl D-aspartate (NMDA) receptor, a key excitatory neurotransmitter receptor. In the brain, D-Serine is synthesized from its L-isomer by serine racemase and is metabolized by the D-amino acid oxidase (DAO, DAAO), a flavoenzyme that catalyzes the oxidative degradation of D-amino acids including D-serine to the corresponding α-keto acids. Many studies have linked decreased D-serine concentration and/or increased DAO expression and enzyme activity to NMDA dysfunction and schizophrenia. Thus, many companies have explored the possibility of employing DAO inhibitors for the treatment of schizophrenia and other indications. Powered by the Schrödinger computational modeling platform, we initiated a research program to identify novel DAO inhibitors with best-in-class properties. The program execution leveraged an hDAO FEP+ model to prospectively predict compound hDAO inhibitory potency and prioritize design ideas from both human design and computer enumeration by our AutoDesigner algorithm. A novel class of DAO inhibitors with desirable pharmacokinetic and brain penetration properties was discovered from this effort. In an in vivo mouse PK/PD model, tool compound 37 demonstrated modulation of D-serine concentrations in the plasma and brain through inhibition of DAO function. Continued SAR work has led to significant potency improvement in both DAO biochemical and cell assays. Our modeling technology on this program has not only enhanced the efficiency of medicinal chemistry execution, it has also helped to identify a previously unexplored subpocket for further SAR development. | Haifeng Tang; Kristian Jensen; Evelyne Houang; Fiona McRobb; Sathesh Bhat; Mats Svensson; Art Bochevarov; Markus Dahlgren; Jeff Bell; Tyler Day; Leah Frye; Robert Skene; James Lewis; James Osborne; Jason Tierney; James Gordon; Maria Palomero-Vazquez; Caroline Gallati; Robert Chapman; Daniel Jones; Kim Hirst; Mark Sephton; Alka Chauhan; Andrew Sharpe; Piero Tardia; Elsa Dechaux; Andrea Taylor; Ross Waddell; Andrea Valentine; Holden Janssens; Omar Aziz; Dawn Bloomfield; Sandeep Ladha; Ian Fraser; John Ellard | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2021-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616ec04ef718dffe58e3e06b/original/discovery-of-a-novel-class-of-d-amino-acid-oxidase-dao-inhibitors-with-the-schrodinger-computational-platform.pdf |
623d80b221e2d025e0b078b6 | 10.26434/chemrxiv-2022-zrnsx | Fast protein modification in the nanomolar concentration range using an oxalyl amide as latent thioester | We show that latent oxalyl thioester surrogates are a powerful means to modify peptides and proteins in highly dilute conditions in purified aqueous media or in mixtures as complex as cell lysates. Designed to be shelf-stable reagents, they can be activated on-demand for enabling ligation reactions down to peptide concentrations as low as a few hundreds nM at rates approaching 30 M-1 s-1. | Benoît Snella; Benjamin Grain; Jérôme Vicogne; Frédéric Capet; Birgit Wiltschi; Oleg Melnyk; Vangelis Agouridas | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623d80b221e2d025e0b078b6/original/fast-protein-modification-in-the-nanomolar-concentration-range-using-an-oxalyl-amide-as-latent-thioester.pdf |
619180c22bf8a90a18dc7404 | 10.26434/chemrxiv-2021-h6b9d | Unveiling the Degradation Nature of Pt/NbOx/C Catalysts for Oxygen Reduction Reaction via in situ X-ray Absorption Spectroscopy | Among various metal nanoparticles supported on metal oxide (MMO) catalysts, the Pt/NbOx/C system has promising oxygen reduction reaction (ORR) activity as cathode for proton exchange membrane fuel cells (PEMFCs). Herein, we study a series of Pt/NbOx/C catalysts with tunable structural and electronic properties via physical vapor deposition and unravel the nature of metal and metal oxide interaction (MMOI) by characterizing this system under reactive conditions. By conducting in situ X-ray absorption spectroscopy (XAS) experiments, we demonstrate the Pt preferably interacts with O but not Nb in the Pt/NbOx/C system and such Pt-O interaction benefits the ORR activity via electronic effect rather than strain effect. We also provide clear evidence for the formation of metallic Nb phase at the early stage of PEMFC operation and identify severe particle growth of Pt after long-term PEMFC operation. These findings deepen our understanding of the degradation mechanism of MMO catalysts during long-term PEMFC operation. | Ershuai Liu; Qingying Jia; Jun Yang; Kai Sun; Li Jiao; Thomas Stracensky; Sanjeev Mukerjee | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Fuel Cells; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619180c22bf8a90a18dc7404/original/unveiling-the-degradation-nature-of-pt-nb-ox-c-catalysts-for-oxygen-reduction-reaction-via-in-situ-x-ray-absorption-spectroscopy.pdf |
6419a4b6aad2a62ca11bc08b | 10.26434/chemrxiv-2023-xhj85 | Deuterium Isotope Probing: a potential game-changer in assessing chemical persistency in soil | Chemical persistency studies are crucial for the regulatory risk assessment of chemicals. One of their major challenges is the formation of so-called non-extractable residues (NERs) in soil as current analytics cannot easily differentiate hazardous xenobiotic NERs from harmless biogenic NERs (bioNERs). Widely-used radiocarbon (14C) tracing allows a rapid quantitation of total NERs whereas stable isotope labeling (13C or 15N) can track bioNERs but is not economically efficient. This study investigated the potential of deuterium isotope probing (DIP) as a new method to simplify the risk assessment associated with xenobiotic NER (xenoNER) formation. Deuterium (D) and 13C tracers were used to study the simulated degradation of three model compounds in soil, the results of which showed negligible incorporation of D into bioNERs as compared to 13C. This indicates the high potential of DIP for a rapid estimation of the hazardous xenoNERs, which could simplify chemical persistency studies in soil. | Sophie Lennartz ; Harriet A. Byrne; Martin Krauss; Steffen Kümmel; Karolina Nowak | Earth, Space, and Environmental Chemistry; Environmental Science; Soil Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6419a4b6aad2a62ca11bc08b/original/deuterium-isotope-probing-a-potential-game-changer-in-assessing-chemical-persistency-in-soil.pdf |
66ebf5e851558a15ef7572f7 | 10.26434/chemrxiv-2024-wc1bc | Interfacial versus confinement effects in the anisotropic frequency-dependent dielectric, THz and IR response of nanoconfined water | We investigate the anisotropic frequency-dependent dielectric, THz and IR response of water confined between two planar graphene sheets with force-field and density-functional-theory-based molecular dynamics simulations. Using spatially resolved anisotropic spectra, we demonstrate the critical role of the volume over which the spectral response is integrated when reporting spatially averaged electric susceptibilities. To analyze the spectra, we introduce a unique decomposition into bulk, interfacial, and confinement contributions, which reveals that confinement effects on the spectra occur only for systems with graphene separation below 1.4 nm, for all frequencies. Based on this decomposition, we discuss the molecular origin of the main absorption features of nanoconfined water from the GHz to the IR regime. We show that, at low frequencies, the 15 GHz Debye peak of interfacial water is red-shifted due to a slowdown of collective water reorientations. At high frequencies the OH stretch at 100 THz blue shifts and a signature of free OH groups emerges, while the HOH bend mode at 50 Thz is red-shifted. Strikingly, in nanoconfinement, the 20 THz libration band shifts to below 15 THz and broadens drastically, spanning two orders of magnitude in frequency. These results are rationalized by the collective water motion and the structure of the hydrogen-bond network at the water-graphene interface and in two-dimensional water layers, which reveals the intricate behavior of nanoconfined water and its spectral properties. | Maximilian Becker; Roland Netz | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ebf5e851558a15ef7572f7/original/interfacial-versus-confinement-effects-in-the-anisotropic-frequency-dependent-dielectric-t-hz-and-ir-response-of-nanoconfined-water.pdf |
66dccad612ff75c3a1ba0d35 | 10.26434/chemrxiv-2024-r6k72 | Different ion maps for the same substance? Glucose analysis by MS Imaging with betaine aldehyde derivatization and NEDC matrix. | Glucose is one of the most essential molecules for sustaining life thus, appropriate and trusted methods of analysis are very welcome. In our study, we have tested two ways of glucose analysis by the MALDI IMS approach: one well-known with NEDC matrix in a negative ionization mode and one developed by us with betaine aldehyde derivatization in positive ionization mode with the aid of CHCA matrix. To our surprise, even though both methods should indicate the localization of the same molecule on adjacent tissue sections and produce the same ion maps, we obtained different results. In this study, we tested the idea that maybe one of the techniques is sensitive to a certain hexose. This would be good news because it would mean having a selective technique for analyzing different hexoses. We performed the dried droplet analyses of glucose, galactose, mannose, and fructose either with betaine aldehyde derivatization or with NEDC matrix and compared the results with the analyses from the tissue. Judging from the MS/MS spectra of analyzed molecules and comparing them with MS/MS spectra from the tissue, it is impossible to distinguish between different hexoses, maybe except fructose. In the article we discussed some ideas that could be responsible for the difference in ion maps of native glucose. Moreover, we highlight the advantages and disadvantages of both analytical approaches. Nevertheless, the question of why ion maps for glucose, obtained by the NEDC matrix and betaine aldehyde derivatization are different, remains open. | Paulina Kret; Przemysław Mielczarek; Giuseppe Grasso; Piotr Suder; Anna Bodzoń-Kułakowska | Analytical Chemistry; Biochemical Analysis; Imaging; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dccad612ff75c3a1ba0d35/original/different-ion-maps-for-the-same-substance-glucose-analysis-by-ms-imaging-with-betaine-aldehyde-derivatization-and-nedc-matrix.pdf |
60c740a4ee301c5d9bc78ae8 | 10.26434/chemrxiv.7800824.v1 | Rapid Intrabacterial Hydrolysis for Activating Antibiotics against Gram-negative Bacteria | <div>Antimicrobial drug resistance demands novel approaches for improving the efficacy of antibiotics, especially against Gram-negative bacteria. Here we report that conjugating a diglycine (GG) to a prodrug of antibiotics drastically accelerates intrabacterial hydrolysis of ester bond for regenerating the antibiotics against E. coli. Specifically, the attachment of GG to chloramphenicol succinate (CLsu) generates a novel conjugate (CLsuGG), which exhibits about an order of magnitude higher inhibitory efficacy than CLsu against E. coli. This work, for the first time, illustrates that dipeptide conjugation modulates intrabacterial hydrolysis for increasing antibiotic efficacy and reducing adverse drug effects.</div> | Jiaqing Wang; Deani L. Cooper; Wenjun Zhan; Difei Wu; Hongjian He; Shenghuan Sun; Susan T. Lovett; Bing Xu | Biological Materials; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a4ee301c5d9bc78ae8/original/rapid-intrabacterial-hydrolysis-for-activating-antibiotics-against-gram-negative-bacteria.pdf |
628b25ee43d1f0a24f35e8ea | 10.26434/chemrxiv-2022-whjg2 | Shear and Solvent-mediated Fabrication of Layered Double Hydroxide Superstructures for High Rate, Stable Supercapacitor Cathodes | The development of sustainable energy economies is blocked by the lack of stable electrical energy sources with high power and energy densities. Next generation supercapacitors utilizing two-dimensional layered double hydroxides (LDHs) promise to fill this need in hybrid and standalone architectures; however, despite their high power and energy densities, LDH supercapacitors have poor stability. New methods for creating robust LDH electrodes are necessary to prevent this degradation. In this study, the recently developed annular microreactor is used to synthesize defect-rich NiCo LDH nanocrystals. A simple, solvent-based method is used to rationally generate binder-free, superstructured-thin films on Ni foam electrodes. Control over crystallite size, thinness and orientation improves contact with the conductive substrate, increase reactivity and improve structural stability. Optimized electrodes are fabricated with specific capacitances from 3,000-5,000 F/g at charging rates as high as 1,000 A/g, a performance that was retained after 20,000 cycles. This is twice as stable at 5,000 times the current density of the most stable reported Ni-based supercapacitor. Ultimately, this study addresses key concerns in electrode development, introduces new approaches through reactor technology and solvent-mediated assembly, and opens new ground for more fundamental inquiries into the mechanisms of electron transport in 2D systems. | Nicholas A. Jose; Mikhail Kovalev; Alexei A. Lapkin | Materials Science; Nanoscience; Energy; Aggregates and Assemblies; Nanostructured Materials - Materials; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628b25ee43d1f0a24f35e8ea/original/shear-and-solvent-mediated-fabrication-of-layered-double-hydroxide-superstructures-for-high-rate-stable-supercapacitor-cathodes.pdf |
63eb94f91d2d1840637bd546 | 10.26434/chemrxiv-2023-5jx42 | Modular Synthesis of Polar Spirocyclic Scaffolds Enabled by Radical Chemistry | Exploration of three-dimensional structural space has become crucial for the development of novel bioactive molecules. In this context, polar spirocycles have emerged as key scaffolds due to their enhanced 3D character and well-defined spatial orientation. Herein, we report the development of a highly modular strategy to access beta-spirocyclic pyrrolidine derivatives from readily available starting materials, i.e., cyclic ketones and amino or oxamic acids. The sequence proceeds through a straightforward Knoevenagel condensation, followed by a domino Giese-type reaction/base-mediated cyclisation process, delivering a broad scope of polar spirocyclic scaffolds in good to excellent yields. The products can be readily diversified to access a wider range of spirocyclic cores (such as lactams or succinimides), thus increasing the versatility of our method to gain rapid access to libraries of potential drug-like molecules. | Khadijah Anwar; Francisco José Aguilar Troyano; Ayham H. Abazid; Oumayma El Yarroudi; Ignacio Funes-Ardoiz; Adrián Gómez-Suárez | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eb94f91d2d1840637bd546/original/modular-synthesis-of-polar-spirocyclic-scaffolds-enabled-by-radical-chemistry.pdf |
6570899e5bc9fcb5c92c1bdf | 10.26434/chemrxiv-2023-21scg | Synthesis and Single Crystal X-ray Diffraction Structure of an Indium Arsenide Nanocluster | The discovery of magic sized clusters as intermediates in the synthesis of colloidal quantum dots has allowed for insight into formation pathways and provided atomically precise, molecular platforms for studying the structure and surface chemistry of those materials. The synthesis of monodisperse InAs quantum dots has been developed through the use of indium carboxylate and As(SiMe3)3 as precursors and documented to proceed through the formation of magic-sized intermediates. Herein, we report the synthesis, isolation, and single-crystal X-ray diffraction structure of an InAs nanocluster that is ubiquitous across reports of InAs quantum dot synthesis. The structure, In26As18(O2CR)24(PR’3)3, is substantially different from previously reported nanocluster structures even within the III-V family. However, it can be structurally linked to III-V and II-VI cluster structures through the anion sublattice. Further spectroscopic analysis using variable temperature absorbance spectroscopy and supported by computation deepens our understanding of the reported structure and InAs nanomaterials as a whole. | Soren Sandeno; Sebastian Krajewski; Ryan Beck; Werner Kaminsky; Xiaosong Li; Brandi Cossairt | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Bonding; Main Group Chemistry (Inorg.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6570899e5bc9fcb5c92c1bdf/original/synthesis-and-single-crystal-x-ray-diffraction-structure-of-an-indium-arsenide-nanocluster.pdf |
64b02207ae3d1a7b0d9e2088 | 10.26434/chemrxiv-2023-zj5q4-v2 | Unveiling the Configurational Landscape of Carbamate: Paving the Way for Designing Functional Sequence-Defined Polymers | Carbamate is an emerging class of polymer backbone for constructing sequence-defined, abiotic polymers. It is expected that new functional materials can be de novo designed by controlling the primary polycarbamate sequence. While amino acids have been actively studied as building blocks for protein folding and peptide self-assembly, carbamates have not been widely investigated from this perspective. Here we combined infrared (IR), vibrational circular dichroism (VCD) and nuclear magnetic resonance (NMR) spectroscopy with density functional theory (DFT) calculations to understand the conformation of carbamate monomer units in a non-polar, aprotic environment (chloroform). Compared with amino acid building blocks, carbamates are more rigid, presumably due to the extended delocalization of π-electrons on the backbones. cis configurations can be energetically stable for carbamates while peptides typically assume trans configurations at low energies. This study lays an essential foundation for future developments of carbamate-based sequence-defined polymer material design. | Ariel F. Perez Mellor; Johanna Brazard; Sara Kozub; Thomas Bürgi; Roza Szweda; Takuji B. M. Adachi | Physical Chemistry; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b02207ae3d1a7b0d9e2088/original/unveiling-the-configurational-landscape-of-carbamate-paving-the-way-for-designing-functional-sequence-defined-polymers.pdf |
6732f95f7be152b1d0cfd3f8 | 10.26434/chemrxiv-2024-8hcwc-v2 | Resorcinol–Formaldehyde/TiO2 Polymer Composites: Efficient Photocatalysts for Water Oxidation to Hydrogen Peroxide | Given its multi-faceted important roles such as aqueous oxidant, chemical platform for environmental remediation, possible liquid fuel and so on, environment friendly approaches to produce hydrogen peroxide (H2O2) are highly desirable. In this context, the photocatalytic generation of hydrogen peroxide (H2O2) from water oxidation has emerged as a promising method, and phenol-formaldehyde based functional resins have been established to be an excellent platform for developing photocatalyst for water oxidation. The present work reports the development of resorcinol−formaldehyde (RF)-TiO2 composites (RF/TiO2) as efficient heterogenous platform for photocatalytic production of H2O2 through water oxidation. The synthesis of RF/TiO2 was accomplished following a simple high-temperature hydrothermal method, and it was characterized to study its microstructures and optical properties. The role of optimum amount of TiO2 in RF/TiO2 composites in improving the photocatalytic activity of resorcinol-formaldehyde resin was established by developing RF/TiO2 composites with varied amount of TiO2. As experimentally established, the RF/TiO2 composites prepared with 1.1-1.6 % (w/w) feed of TiO2 with respect to resorcinol at a temperature of 200 oC under hydrothermal condition was found to be the most efficient ones for the present study. Out of these composites, RF/TiO2-1.2% and RF/TiO2-1.3% resulted in the production of ~ 500 and ~530 µmol of H2O2 per gram of catalyst, respectively, upon 5 h of continuous photoirradiation under the present experimental condition with reaction temperature of ~30-35 ℃. It was observed that the H2O2 production rate can be enhanced by increasing the reaction temperature. | Addisalem Abebe; Ravinder Kaushik; Sunil Kumar; Iswar Chandra Mondal; Subrata Ghosh; Aditi Halder | Catalysis; Heterogeneous Catalysis; Photocatalysis; Redox Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6732f95f7be152b1d0cfd3f8/original/resorcinol-formaldehyde-ti-o2-polymer-composites-efficient-photocatalysts-for-water-oxidation-to-hydrogen-peroxide.pdf |
6746033df9980725cf0bb7ef | 10.26434/chemrxiv-2024-r74jq | Intramolecular Direct Arylation Through Mechanochemistry: Efficient Synthesis of Peri-Annulated Nanographenes | Peri-annulation is recognized as an influential structural motif in accessing functional molecular materials. However, efficient synthetic access to peri-annulated structures remains challenging. Herein, we show that mechanochemistry is a valuable synthetic tool to achieve this goal. It is comparatively better than activation through microwave irradiation and conventional solution-phase reactions. The synthesized materials are molecularly curved nanographenes containing sulfur and selenium atoms. The curvature comes from the use of corannulene as the central building block, upon which the benzothiophene or benzoselenophene are peri-annulated through the palladium-catalyzed direct arylation reactions. Peri-annulation endows the nanographene structures with better optical properties as compared to other annulation chemistries. | Zhongbo Zhang; Mihaiela Stuparu | Organic Chemistry; Organic Synthesis and Reactions; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6746033df9980725cf0bb7ef/original/intramolecular-direct-arylation-through-mechanochemistry-efficient-synthesis-of-peri-annulated-nanographenes.pdf |
6627ec72418a5379b082bc18 | 10.26434/chemrxiv-2024-ncl3q | Osmolyte-Induced Modulation of Hofmeister Series | Natural selection has driven the convergence towards a selected set of osmolytes, endowing them with the necessary efficiency to manage stress arising from salt diversity. This study combines atomistic simulations and experiments to investigate how two osmolytes, glycine and betaine, individually modulate Hofmeister ion ordering of alkali metal salts (LiCl, KCl, CsCl) near a charged silica interface. Both osmolytes are found to prevent salt-induced aggregation of the charged entities, yet their mode and degree of relative modulation depend on their intricate interplay with specific salt-cations. Betaine's ion-mediated surface interaction maintains Hofmeister ion ordering, whereas glycine alters the relative Hofmeister order of cation by salt-specific ion desorption from the surface. Experimental validation through surface-enhanced Raman spectroscopy supports these findings, elucidating osmolyte-mediated alterations in interfacial water structures. These observations based on an inorganic interface are reciprocated in amyloid beta 40 (Abeta40) dimerization dynamics, highlighting osmolyte efficacy in mitigating salt-induced aggregation. | Susmita Sarkar; Anku Guha; Tharangattu Narayanan; Jagannath Mondal | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6627ec72418a5379b082bc18/original/osmolyte-induced-modulation-of-hofmeister-series.pdf |
60c7418b567dfef735ec3dc3 | 10.26434/chemrxiv.8061812.v1 | Synthesis of Idarubicinone via Global Functionalization of Tetracene | Herein, we describe
the realization of this concept, providing a non-annulative strategy to
anthracyclines from a polynuclear arene. Specifically, tetracene was converted
to idarubicinone, the aglycone of the FDA approved anthracycline idarubicin, <a>through </a>the judicious orchestration of Co- and
Ru-catalyzed arene oxidation and arenophile-mediated dearomative hydroboration.
Such a global functionalization strategy, a combination of site-selective arene
and dearomative functionalization, provided the key anthracycline framework in
five operations and enabled rapid and controlled access to idarubicinone. | David G. Dennis; Mikiko Okumura; David Sarlah | Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7418b567dfef735ec3dc3/original/synthesis-of-idarubicinone-via-global-functionalization-of-tetracene.pdf |
65582ff6dbd7c8b54b7e6e7b | 10.26434/chemrxiv-2023-vpldb | Computationally guided synthesis of carbon coated mesoporous silica materials | Mesoporous silica materials (MSMs) have unique features like large surface area and tunable pore size, making them suitable for biomedical applications. For longer durability, the small pores in MSMs are kept intact by filling them with carbon precursors, which are carbonized to prevent them from interacting with unreacted silicic acid. In this study, we synthesize and heal MSMs using a combination of non-reactive and reactive molecular dynamics (MD) simulations. We use Pluronic® L64 polymers to form micelle assembly in water, which are interpreted from radial distribution function and hydrogen bonding networks of water molecules with the hydrophilic/hydrophobic segments of the polymers. Orthosilicic acid is condensed around the micelle-water assembly using bond-boosted ReaxFF MD simulations. Then, the system is calcinated to burn down the carbonaceous micelle structure with evaporation of water. Subsequently, we perform the healing of MSM surface by carbonizing polymer precursors inside an MSM pore. Polyethylene and lignite are rendered as the most suitable precursors due to their ability to form a network of turbostratic graphene structures. To assess the performance of turbostratic graphene structure-based coatings on the inner surface of the MSM nanopore, we introduce silicic acid precursor inside the pore and monitor its movement. | Nabankur Dasgupta; Qian Mao; Adri van Duin | Theoretical and Computational Chemistry; Polymer Science; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65582ff6dbd7c8b54b7e6e7b/original/computationally-guided-synthesis-of-carbon-coated-mesoporous-silica-materials.pdf |
60c750449abda23565f8d9e3 | 10.26434/chemrxiv.12967655.v2 | Allosteric Regulation of SARS-CoV-2 Protease: Towards Informed Structure-Based Drug Discovery | The Coronavirus Disease of 2019 (COVID-19) is caused by a novel coronavirus known as the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). Despite extensive research since the outset of the pandemic, definitive therapeutic agents for the treatment of the disease are yet to be identified. The main protease (MPro) of SARS-CoV-2 is an enzyme essential for virus replication through viral proteolytic activity and subsequent generation of infectious virus particles. Current computational efforts towards SARS-CoV-2 MPro inhibitor design have generally neglected an allosteric mechanism linked to His41-Cys145 catalytic dyad disruption and thus fail to target the open conformational state. We identify the rare event associated with the allosteric regulation of MPro activity in the orientation of the His41 imidazole side chain away from Cys145. In this work, we show that molecular dynamics and metadynamics simulations are fundamental for performing computer-aided MPro inhibitor design where the sampling of this allosteric mechanism within a computationally feasible timescale is essential. We calculate a 4.2 ± 1.9 kJ/mol free energy difference between the open and closed states of the SARS-CoV-2 MPro active site, indicating that favourable ligand interactions with His41 over the Cys145-His41 dyad interaction can stabilise the open state. | Khaled Abdel-Maksoud; Mohamed Ali al-Badri; Christian Lorenz; Jonathan W. Essex | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750449abda23565f8d9e3/original/allosteric-regulation-of-sars-co-v-2-protease-towards-informed-structure-based-drug-discovery.pdf |
60c756f99abda2860df8e614 | 10.26434/chemrxiv.14257001.v1 | Copper-Palladium Core-Shell Bifunctional Nanoelectrocatalyst for Ethanol Oxidation and Hydrogen Evolution Reactions | <div>We demonstrate the copper-palladium core-shell nanostructures prepared over a pencil graphite substrate towards two important catalytic reactions viz. ethanol oxidation reaction and hydrogen evolution reactions. <br /></div> | B naveen; gajjala Rajendra Kumar Reddy; Suresh Kumar Palathedath | Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756f99abda2860df8e614/original/copper-palladium-core-shell-bifunctional-nanoelectrocatalyst-for-ethanol-oxidation-and-hydrogen-evolution-reactions.pdf |
6498b0694821a835f3642d0d | 10.26434/chemrxiv-2023-sq6gz | A coumarin-based array to discriminate between different types of amyloid fibrils | Self-assembly of misfolded proteins can lead to the formation of amyloids, which are implicated in the onset of many pathologies including Alzheimer’s disease and Parkinson’s disease. The facile detection and discrimination of different amyloids is crucial for early diagnosis of amyloid-related pathologies. Here, we report the development of a fluorescent two-sensor array which is able to correctly discriminate between four different amyloids implicated in amyloid-related pathologies with 100% classification. The array was also applied to mouse models of Alzheimer’s disease and was able to discriminate between samples from mice corresponding to early (6 months) and advanced (12 months) stages of Alzheimer’s disease. Finally, the flexibility of the array was assessed by expanding the analytes to include functional amyloids. The same two-sensor array was able to correctly discriminate between eight different disease-associated and functional amyloids with 100% classification. | Natalie Trinh; Kaustubh R. Bhuskute; Nikhil R. Varghese; Jessica A. Buchanan; Fiona M. McCutcheon; Robert L. Medcalf; Katrina A. Jolliffe; Margaret Sunde; Elizabeth J. New; Amandeep Kaur | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Spectroscopy (Anal. Chem.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6498b0694821a835f3642d0d/original/a-coumarin-based-array-to-discriminate-between-different-types-of-amyloid-fibrils.pdf |
6480c052e64f843f4177b739 | 10.26434/chemrxiv-2023-77mrp | A single-molecule RNA electrical biosensor for
COVID-19 | The COVID-19 pandemic shows a critical need for rapid, inexpensive, and ultrasensitive early detection methods based on biomarker analysis to reduce mortality rates by containing the spread of epidemics. This can be achieved through electrical detection of nucleic acids at the single-molecule level. In particular, the scanning tunneling microscopic-assisted break junction (STM-BJ) method can be utilized to detect individual nucleic acid molecules with high specificity and sensitivity in liquid samples. Herein, we demonstrate single-molecule electrical detection of RNA coronavirus biomarkers, including those of SARS-CoV-2 as well as those of different variants and subvariants. Our target sequences include a conserved sequence in the human coronavirus family, a conserved target specific for the SARS-CoV-2 family, and specific targets at the variant and subvariant levels. Our results demonstrate that it is possible to distinguish between different variants of the COVID-19 virus using electrical conductance signals, as recently suggested by theoretical approaches. Furthermore, we propose a strategy to detect new variants by analyzing electrical fingerprints from multiple sequences. This could allow for a rapid response early in new outbreaks. These results pave the way for future miniaturized single-molecule electrical biosensors that could be game changers for the COVID-19 pandemic, other infectious diseases, and several other public health applications. | Keshani Pattiya Arachchillage; Subrata Chandra; Ajoke Williams; Srijith Rangan; Patrick Piscitelli; Lily Florence; Sonakshi Ghosal Gupta; Juan Artes Vivancos | Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Microscopy; Biochemistry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6480c052e64f843f4177b739/original/a-single-molecule-rna-electrical-biosensor-for-covid-19.pdf |
60c74f6b702a9b65f218bb8e | 10.26434/chemrxiv.12899420.v1 | Identification of P218 as a Potent Inhibitor of Mycobacteria Ulcerans DHFR | <i>Mycobacterium
ulcerans</i> is
the causative agent of Buruli ulcer, a debilitating chronic disease that mainly
affects the skin. Current treatments for Buruli ulcer are efficacious, but rely
on the use of antibiotics with severe side effects. The enzyme dihydrofolate
reductase (DHFR) plays a critical role in the de novo biosynthesis of folate
species and is a validated target for several antimicrobials. Here we describe
the biochemical and structural characterization of <i>M. ulcerans</i> DHFR and
identified P218, a safe antifolate compound in clinical evaluation for malaria,
as a potent inhibitor of this enzyme. We expect our results to advance <i>M.
ulcerans</i> DHFR as a target for future structure-based drug discovery
campaigns. | Gustavo Pelicioli Riboldi; Rachael Zigweid; Peter J. Myler; Stephen J. Mayclin; Rafael Counago; Bart L. Staker | Biochemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f6b702a9b65f218bb8e/original/identification-of-p218-as-a-potent-inhibitor-of-mycobacteria-ulcerans-dhfr.pdf |
6413da49aad2a62ca1e35264 | 10.26434/chemrxiv-2023-lrt19 | High-Concentration Self-Assembly of Zirconium- and Hafnium-Based Metal-Organic Materials | Metal–organic frameworks (MOFs) are crystalline, porous solids constructed from organic linkers and inorganic nodes that are promising for applications in chemical separations, gas storage, and catalysis, among many others. However, a major roadblock to the widespread implementation of MOFs, including highly tunable and hydrolytically stable Zr- and Hf-based frameworks, is their benchtop-scalable synthesis, as MOFs are typically prepared under highly dilute (≤0.01 M) solvothermal conditions. This necessitates the use of liters of organic solvent to prepare only a few grams of MOF. Here-in, we demonstrate that Zr- and Hf-based frameworks (eight examples) can self-assemble at much higher reaction concen-trations than are typically utilized, up to 1.00 M in many cases. Combining stoichiometric amounts of Zr or Hf precursors with organic linkers at high concentrations yields highly crystalline and porous MOFs, as confirmed by powder X-ray diffraction (PXRD) and 77 K N2 surface area measurements. Further, the use of well-defined pivalate-capped cluster pre-cursors avoids the formation of ordered defects and impurities that arise from standard metal chloride salts. These clus-ters also introduce pivalate defects that increase the exterior hydrophobicity of several MOFs, as confirmed by water con-tact angle measurements. Overall, our findings challenge the standard assumption that MOFs must be prepared under highly dilute solvothermal conditions for optimal results, paving the way for their scalable and user-friendly synthesis in the laboratory. | Ronald Jerozal; Tristan Pitt; Samantha MacMillan; Phillip Milner | Materials Science; Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6413da49aad2a62ca1e35264/original/high-concentration-self-assembly-of-zirconium-and-hafnium-based-metal-organic-materials.pdf |
633660f9114b7ebf1a229015 | 10.26434/chemrxiv-2022-dp58c | Direction-based Graph Representation to Accelerate Stable Catalysts Discovery | To realize renewable and sustainable energy cycle, there has been a lot of effort put into discovering catalysts with desired properties from a large chemical space. To achieve this goal, several screening strategies have been proposed, most of which require validation of thermodynamic stability and synthesizability of candidate materials via computationally intensive quantum chemistry or solid-state physics calculations. This problem can be overcome by reducing the number of calculations through machine learning methods, which predict target properties using unrelaxed crystal structures as inputs. However, numerical input representations of most of the previous models are based on either too specific (e.g., atomic coordinates) or too ambiguous (e.g., stoichiometry) information, practically inapplicable to energy prediction of unrelaxed initial structures. In this work, we develop direction-based crystal graph convolutional neural network (D-CGCNN) with the highest accuracy toward formation energy predictions of the relaxed structures using the initial structures as inputs. By comparing with other approaches, we revealed correlations between crystal graph similarities and model performances, elucidating the origin of the improved accuracy of our model. We applied this model to the on-going high-throughput virtual screening project, where the model discovered 1,725 stable materials from 15,318 unrelaxed structures by performing 3,966 structure optimizations (~25 %). | Dong Hyeon Mok; Jongseung Kim; Seoin Back | Theoretical and Computational Chemistry; Materials Science; Catalysis; Alloys; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633660f9114b7ebf1a229015/original/direction-based-graph-representation-to-accelerate-stable-catalysts-discovery.pdf |
65676b065bc9fcb5c9a9b688 | 10.26434/chemrxiv-2023-fqp34-v2 | π-Radical Cascade to a Chiral Saddle-Shaped Peropyrene | Reactions of open-shell molecular graphene fragments are typically thought of as undesired decomposition processes because they lead to the loss of desired features like π-magnetism. Oxidative dimerization of phenalenyl to peropyrene shows, however, that these transformations hold promise as a synthetic tool for making complex structures via formation of multiple bonds and rings in a single step. Here, we explore the feasibility of using this “undesired” reaction of phenalenyl to build up strain and provide access to non-planar polycyclic aromatic hydrocarbons. To this end, we designed and synthesized a diradical system with two phenalenyl units linked via a biphenylene backbone. The design facilitates an intramolecular cascade reaction to a helically twisted saddle-shaped product, where the key transformations—ring-closure and ring-fusion—occur within one reaction. The negative curvature of the final peropyrene product, resulting from the presence of an eight-membered ring, was confirmed by single-crystal X-ray diffraction analysis and the helical twist was validated via resolution of the product’s enantiomers that display circularly polarized luminescence. | Annika Bernhardt; Daniel Čavlović; Maximilian Mayländer; Olivier Blacque; Carlos Moreno Cruz; Sabine Richert; Michal Juríček | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Stereochemistry; Spectroscopy (Physical Chem.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65676b065bc9fcb5c9a9b688/original/radical-cascade-to-a-chiral-saddle-shaped-peropyrene.pdf |
629135424d8b597d2ea14f76 | 10.26434/chemrxiv-2022-8k02q | Environmental Stability of Crystals: Why Be Greedy When You Can Be Exact? | In a recent paper in this journal (Chem. Mater. 2022, 34, 2545-2552), Twyman et al. studied the environmental stability of crystals by introducing a greedy heuristic algorithm for determining possible oxidation reactions. We show how the problem can be solved exactly, with less code and comparable computational time by reformulating it as a linear optimization for the reaction enthalpy. The enthalpy of oxidation and the oxidation products, computed by Twyman et al.’s greedy heuristic is suboptimal in 22504 of 39634 cases (56.8%), with the error in enthalpy of oxidation as large as 1.480 eV/atom. Every one of these quantitative errors also results in qualitative differences in the oxide species formed. Using our exact approach to the problem, we re-evaluate the core results from the paper by Twyman et al. We also describe a minor modification enabling calculations of oxidation free energy minima. | Qianxiang Ai; Joshua Schrier | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629135424d8b597d2ea14f76/original/environmental-stability-of-crystals-why-be-greedy-when-you-can-be-exact.pdf |
652fed8f2431cc1dacd15597 | 10.26434/chemrxiv-2023-9lrzv | A Site-Specific Synthetic Route to Substituted Inda(box) Ligands | Aminoindanol-derived bis(oxazoline) ligands are widely used in metal-catalyzed transformations, but the synthesis of structural derivatives is challenging. We report the gram-scale, seven-step synthesis of five bromine-functionalized in-da(box) ligands that have varied bridge substituents. The bromoinda(box) ligands undergo late-stage modification via Pd-catalyzed cross-couplings, which allows for the synthesis of 12 unique inda(box) ligands. This complementary syn-thetic route could enable the discovery of new asymmetric metal-catalyzed transformations through modification of the inda(box) ligand architecture. | Kimberly Alley; Aidan Clarkson; Ayaka Uehara; Jeffrey Johnson | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652fed8f2431cc1dacd15597/original/a-site-specific-synthetic-route-to-substituted-inda-box-ligands.pdf |
65688d1529a13c4d47581d5d | 10.26434/chemrxiv-2023-mk6js | Deuteration and Tritiation of Pharmaceuticals by Non-Directed Pd Catalyzed C–H Activation in Heavy and Super-Heavy Water | Deuterated and tritiated analogs of drugs are valuable compounds for pharmaceutical and medicinal chemistry. In this work, we present a novel hydrogen isotope exchange reaction of drugs using non-directed homogeneous Pd catalysis. Aromatic C–H activation is achieved by a commercially available pyridine ligand. Using the most convenient and cheapest deuterium source, D2O, as the only solvent 34 pharmaceuticals were labelled with clean reaction profiles and high deuterium uptakes. Additionally, we describe the first application of non-directed homogeneous Pd catalysis for H/T exchange on an aromatic drug scaffold by using T2O as isotopic source, demonstrating the applicability to the synthesis of radiotracers. | Chitrala Teja; Simon Kolb; Pierre Colonna; Jagrit Grover; Goutam Kumar Lahiri; Grégory Pieters; Daniel B. Werz; Debabrata Maiti | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65688d1529a13c4d47581d5d/original/deuteration-and-tritiation-of-pharmaceuticals-by-non-directed-pd-catalyzed-c-h-activation-in-heavy-and-super-heavy-water.pdf |
645907c427fccdb3eab433aa | 10.26434/chemrxiv-2023-0jq0h | First step of the oxygen reduction reaction on Au(111): A computational study of O2 adsorption at the electrified metal/water interface | Local field effects at the electrical double layer change the energies of reaction intermediates in heterogeneous electrocatalysis. The resulting dependence on (absolute) electrode potential can be pivotal to a catalyst's performance in acid or alkaline media. And yet, such local field effects are very difficult to describe theoretically and are often ignored. In this work, we focus on O2 adsorption as the first step of the oxygen reduction reaction (ORR) on Au(111). Different physical effects of the local field are elucidated and compared by systematically improving the model of the double layer: from an applied saw-tooth potential in vacuum, to an implicit solvent model, and explicitly modeled water via ab initio molecular dynamics (AIMD). We find all models predict a dominant dipole-field type interaction that significantly strengthens O2 binding at increasingly reducing conditions. However, only an atomically-resolved solvent model such as provided by AIMD can properly capture the additional stabilization due to explicit H-bonding from the water network. This contribution comes with the formation of a peroxo-like surface species and a more dramatic field response around the ORR onset. Our results overall demonstrate the importance of including local electric field effects in models of the electrochemical interface, while assessing the level of detail that is required to be accounted for. | Alexandra M. Dudzinski; Elias Diesen; Hendrik H. Heenen; Vanessa Jane Bukas; Karsten Reuter | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645907c427fccdb3eab433aa/original/first-step-of-the-oxygen-reduction-reaction-on-au-111-a-computational-study-of-o2-adsorption-at-the-electrified-metal-water-interface.pdf |
67194936d433919392fad904 | 10.26434/chemrxiv-2024-hwpfc | Discovery of Staircase Chirality through the Design of Unnatural Amino Acid Derivatives | Chirality has garnered significant attention in the scientific community since its discovery by Louis Pasteur over a century ago. It has been showing a profound impact on chemical, biomedical, and materials sciences. Significant progress has been made in controlling molecular chirality, as evidenced by the several Nobel Prizes in chemistry awarded in this area, particularly for advancements in the asymmetric catalytic synthesis of molecules with central and axial chirality. However, the exploration of new types of chirality has been largely stagnant for more than half a century, likely due to the complexity and challenges inherent in this field. In this work, we present the discovery of a novel type of chirality—staircase chirality as inspired by the design and synthesis of unnatural amino acid derivatives. The architecture of staircase chirality is characterized by two symmetrical phenyl rings anchored by a naphthyl pier, with the rings asymmetrically displaced due to the influence of chiral auxiliaries at their para positions. This unique staircase chiral framework has been thoroughly characterized using spectroscopic techniques, with its absolute configuration definitively confirmed by X-ray diffraction analysis. Remarkably, one of the staircase molecules exhibits four distinct types of chirality: central, orientational, turbo, and staircase chirality, a combination that has not been previously documented in the literature. Computational studies using density functional theory (DFT) calculations were conducted to analyze the relative energies of individual staircase isomers, and the results are in agreement with our experimental findings. We believe that this discovery will open up a new research frontier in asymmetric synthesis and catalysis, with the potential to make a substantial impact on the fields of chemistry, medicine, and materials science. | Anis Ur Rahman ; Yu Wang; Ting Xu; Kambham Devendra Reddy; Shengzhou Jin; Xianghua Yan; Qingkai Yuan; Daniel Unruh; Ruibin Liang; Guigen Li | Biological and Medicinal Chemistry; Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Stereochemistry; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67194936d433919392fad904/original/discovery-of-staircase-chirality-through-the-design-of-unnatural-amino-acid-derivatives.pdf |
665788c7418a5379b093c3f1 | 10.26434/chemrxiv-2024-9qwm8 | The Role of Double Excitations in Exciton Dynamics of Multiazobenzenes: Trisazobenzenophane as a Test Case | Molecular exciton dynamics underlie energy and charge transfer processes in organic multichromophoric systems. A particularly interesting class of the latter are multiphotochromic systems made of molecules capable of photochemical transformations. Exciton dynamics in assemblies of photoswitches have been recently investigated using either molecular exciton model or supermolecular configuration interaction (CI) singles, both approaches being based on a semiempirical Hamiltonian and combined with surface hopping molecular dynamics. Here, we study how inclusion of double excitations in nonadiabatic dynamics simulations affect exciton dynamics of multiazobenzenes, using trisazobenzenophane as an example. We find that both CI singles and CI singles and doubles yield virtually the same timescale of dynamical exciton localization, ∼50 fs for the studied multiazobenzene. However, inclusion of double excitations considerably affects excited state lifetimes and isomerization quantum yields. | Evgenii Titov | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Quasiparticles and Excitations | CC BY 4.0 | CHEMRXIV | 2024-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665788c7418a5379b093c3f1/original/the-role-of-double-excitations-in-exciton-dynamics-of-multiazobenzenes-trisazobenzenophane-as-a-test-case.pdf |
61c46b2d7284d05b03f5b38a | 10.26434/chemrxiv-2021-jmn9c | Solvation structure and dynamics of Li and LiO2 and their transformation in non-aqueous organic electrolyte solvents from first-principles simulations | Density functional theory calculations together with ab initio molecular dynamics (AIMD) simulations have been used to study the solvation, diffusion and transformation of Li+ and LiO2 upon O2 reduction in three organic electrolytes. These processes are critical for the performance of Li-air batteries. Apart from studying the structure of the solvation shells in detail, AIMD simulations have been used to derive the diffusivity and together with the Blue Moon ensemble approach to explore LiO2 formation from Li+ and O2- and the subsequent disproportionation of 2LiO2 into Li2O2 + O2. By comparing the results of the simulations to gas phase calculations the impact of electrolytes on these reactions is assessed which turns out to be more pronounced for the ionic species involved in these reactions. | Behnaz Rahmani Didar; Axel Gross | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Transport phenomena (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c46b2d7284d05b03f5b38a/original/solvation-structure-and-dynamics-of-li-and-li-o2-and-their-transformation-in-non-aqueous-organic-electrolyte-solvents-from-first-principles-simulations.pdf |
6395db8d0a812702e2dd6191 | 10.26434/chemrxiv-2022-k7ftg | Editing of Polymer Backbones | Polymers are at the epicenter of modern technological progress and ensuing environmental pollution. Considerations of both polymer functionality and lifecycle are crucial in these contexts, and the polymer backbone—the core of a polymer—is at the root of these issues. Just as the meaning of a sentence can be altered through editing the words, so too could the function and sustainability of a polymer be transformed through chemical modification of its backbone. Yet, polymer modification has primarily been focused on the polymer periphery. In this Review, we attempt to bring a greater focus to transformations of the polymer backbone by defining some concepts fundamental to this topic (e.g., “polymer backbone” and “backbone editing”), collecting and categorizing examples of backbone editing scattered throughout a century’s-worth of chemistry literature, and outlining critical directions for further research. In so doing, we lay the foundation for the field of polymer backbone editing and hope to accelerate its development. | Aleksandr Zhukhovitskiy; Rachael Ditzler; Andrew King; Sydney Towell; Maxim Ratushnyy | Polymer Science; Polymer scaffolds | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6395db8d0a812702e2dd6191/original/editing-of-polymer-backbones.pdf |
67580741f9980725cf9740d8 | 10.26434/chemrxiv-2024-0lkqw | Reversed adaptive system of PNIPAM-decorated nanoparticles induced by the ionic strength of the subphase | We investigate the effects of ionic strength on the self-assembly of poly(N-isopropyl acrylamide)-nanoparticles (PSiFe) at the air-water interface. These responsive nanoparticles exhibit temperature-dependent behavior, forming more compact films at high temperatures (above the lower critical solution temperature, LCST). Upon adding potassium chloride (KCl) to the subphase, we observe an unexpected increase in the distance between nanoparticles, attributed to the creation of ionic clouds around them. This shifts the isotherms significantly compared to those formed at pure water, as larger areas of the interface are required to accommodate the same number of particles. Moreover, our findings reveal that increasing ionic strength alters the PNIPAM conformation, inhibiting nanoparticle aggregation even at higher temperatures. Using Langmuir-Blodgett techniques, we confirm that ionic strength modulates particle spacing and assembly dynamics. These results provide new insights into the control of nanoparticle interactions at interfaces, with potential applications in the design of tunable, stimuli-responsive materials. | Rafał Zbonikowski; Asghar Aryanfar; Ali Tayyar; Michalina Iwan; Martin Presselt; Jan Paczesny | Physical Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Nanoscience; Interfaces; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67580741f9980725cf9740d8/original/reversed-adaptive-system-of-pnipam-decorated-nanoparticles-induced-by-the-ionic-strength-of-the-subphase.pdf |
60c759949abda29dddf8eb36 | 10.26434/chemrxiv.14711142.v1 | Sol Gel Technique to Prepare Composite Material of Glass-Dye-Polymers | Herein we describe the synthesis and in-depth characterization of chemically blended hybrid glasses in which polymer molecules are uniformly distributed and covalently bonded to inorganic matrices. This approach uses a monomer with double bonds, which are hydrosilylated with triethoxy silane and co-condensed with silicon tetraalkoxide to afford a molecular composite of SiO2 glass and the polymer. The generated coposites were characterized using SEM, TGA and XRD as well as a host of stability tests. They showed increased stability and uniform distribution of the blend. <br /> | Jayanta Ray; Leena Bhowmik | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Composites; Hybrid Organic-Inorganic Materials; Inorganic Polymers; Organic Polymers; Polymer blends; Polymerization (Polymers); Polymer morphology; Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759949abda29dddf8eb36/original/sol-gel-technique-to-prepare-composite-material-of-glass-dye-polymers.pdf |
61e51d5aa7e31ef5d2567c80 | 10.26434/chemrxiv-2022-l31zf | Not that innocent – ammonium ions boost homogeneous light-driven hydrogen evolution | We report that the homogeneous light-driven hydrogen evolution reaction (HER) can be significantly enhanced by the presence of seemingly innocent ammonium (NH4+) cations. Expermiental studies with different catalysts, photosensitizers and electron donors show this to be a general effect. Preliminary photophysical and mechanistic studies provide initial suggestions regarding the role of ammonium in the HER enhancement. | Magdalena Heiland; Ratnadip De; Sven Rau; Benjamin Dietzek-Ivanšić; Carsten Streb | Inorganic Chemistry; Catalysis; Energy; Homogeneous Catalysis; Photocatalysis; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e51d5aa7e31ef5d2567c80/original/not-that-innocent-ammonium-ions-boost-homogeneous-light-driven-hydrogen-evolution.pdf |
60c74ed1469df4550af44559 | 10.26434/chemrxiv.12408245.v2 | Persistent, Highly Localized, and Tunable [4]Helicene Radicals | <p><a>Persistent organic radicals have gained considerable attention in the </a>fields of catalysis and material sciences. In particular, helical molecules are of great interest for the development and application of novel organic radicals in optoelectronic and spintronic materials. Here we report the syntheses of easily tunable and stable neutral quinolinoacridine radicals under anaerobic conditions by chemical reduction of their quinolinoacridinium cation analogs. The structures of these [4]helicene radicals were determined by X-ray crystallography. Density functional theory (DFT) calculations, supported by Electron paramagnetic resonance (EPR) measurements, indicate that over 40% of spin density is located at the central carbon of the [4]helicene radicals regardless of their structural modifications. The localization of the charge promotes a reversible oxidation to the cation upon exposure to air. This unusual reactivity toward molecular oxygen was monitored via UV-Vis spectroscopy.</p> | Aslam Shaikh; Jules Moutet; Jose M Veleta; Md Mubarak Hossain; jan bloch; Andrei V. Astashkin; thomas Gianetti | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ed1469df4550af44559/original/persistent-highly-localized-and-tunable-4-helicene-radicals.pdf |
60c74a0bee301c08d5c79ba1 | 10.26434/chemrxiv.12143880.v1 | A Dinuclear Copper Based Artificial Metalloenzyme for the Kinetic Resolution of Adrenalin | Incorporation of a copper catalyst within carbonic anhydrase affords artificial metalloenzyme for the oxidation of catechols in aqueous solution at physiological pH. Optimization of the performance can be achieved either by chemical or genetic means. In addition, a model of enzyme/inhibitor is proposed and discussed. | Thibaud Rossel | Biochemistry; Bioengineering and Biotechnology; Chemical Biology; Biocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a0bee301c08d5c79ba1/original/a-dinuclear-copper-based-artificial-metalloenzyme-for-the-kinetic-resolution-of-adrenalin.pdf |
65c0f4f19138d231617cb6e5 | 10.26434/chemrxiv-2024-5cwc9 | Conformational landscapes of rigid and flexible molecules explored with variable temperature ion mobility-mass spectrometry | Understanding the effect of temperature to the structural integrity and dynamics of proteins has relevance for many areas including biotechnology and the maintenance of a stable food supply for the climate emergency. The methods that can explore changes in structure as a function of sub-ambient temperature are scant, and yet many drugs are stored at such temperatures. Here we show how variable temperature ion mobility-mass spectrometry (VT-IM-MS) can provide the role of temperature on conformational landscapes in the form of collision cross sections at discrete temperatures. To delineate collision effects from structural change we report measurements made on four molecules that possess different degrees of rigidity namely: poly (L-lysine) (PLL) dendrimer, ubiquitin, β-casein and α-synuclein from 190-350K. We show that the PLL dendrimer varies with temperature consistent with collision theory, and conclude, as expected, its structure does not alter significantly over this range. By contrast, the structure of each protein is altered by the temperature of the drift gas, with notable unfolding to all charge states at 350 K and also at 250 K, following predicted in vitro stability curves, and with conformational variation that gives qualitative insights to the effect of temperature on the free energy landscape of these proteins. We also show that we can kinetically trap unfolding intermediates at drift temperatures of 210 K and 190 K on a millisecond experimental time scale. For alpha-synuclein, the 13+ ions present two distinct conformers and VT-IM-MS measurements allow us to calculate the transition rate and activation energies for conversion between these. These data exemplify the capability of VT-IM-MS to provide insights to thermodynamics involved in conformational restructuring.
| Xudong Wang; Emma Norgate; Junxiao Dai; Florian Benoit; Jason Kalapothakis; Anthony Bristow; Richard England; Perdita Barran | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Biophysical Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c0f4f19138d231617cb6e5/original/conformational-landscapes-of-rigid-and-flexible-molecules-explored-with-variable-temperature-ion-mobility-mass-spectrometry.pdf |
62e7c408fad485295b5d9c4b | 10.26434/chemrxiv-2022-4pz7v | High-performance iridium thin films for water splitting by CVD using new Ir(I) precursors
| Thin films of iridium can be utilized in a wide range of applications and are particularly interesting for catalytic transformations. For the scalable deposition of functional Ir thin films, metal-organic chemical vapor deposition (MOCVD) is the method of choice, for which organometallic precursors that embody a high volatility and thermal stability need to be specifically tailored. Herein, we report the synthesis, analysis, and evaluation of new volatile Ir(I)-1,5-cyclooctadiene complexes bearing all-nitrogen coordinating guanidinate (DPDMG), amidinate (DPAMD) and formamidinate (DPfAMD) ligands. The amidinate-based Ir complex [Ir(COD)(DPAMD)] together with O2 was implemented in MOCVD experiments resulting in highly crystalline, dense, and conductive Ir films on a variety of substrate materials. The Ir deposits achieved an outstanding electrochemical performance with overpotentials in the range of 50 mV at –10 mA‧cm-2 for catalytic hydrogen evolution reaction (HER) in acidic solution. The ability to deposit Ir layers via MOCVD exhibiting promising functional properties is a significant step towards large scale applications.
| Nils Boysen; Jan-Lucas Wree; David Zanders; Detlef Rogalla; Denis Öhl; Wolfgang Schuhmann; Anjana Devi | Catalysis; Organometallic Chemistry; Electrocatalysis; Coordination Chemistry (Organomet.); Reaction (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e7c408fad485295b5d9c4b/original/high-performance-iridium-thin-films-for-water-splitting-by-cvd-using-new-ir-i-precursors.pdf |
6747bf4af9980725cf40c5f0 | 10.26434/chemrxiv-2023-r5bwq-v5 | From soft ionization mass spectrometry to “chemical bond” and resistance, semiconductor, superconductivity -- the law of charge motion in phase transition under weak electric field | Propose the possible reason of resistance, establish models of conductors, semiconductors, and insulators, and explain the reason why resistance is proportional to temperature. By utilizing models of resistance, conductors, and the research content of soft ionization mass spectrometry, the microscopic mechanism of superconductivity is proposed. Studying the movement of charges under weak electric fields in different states (phase transitions) such as gas, liquid, and solid is helpful for understanding experimental phenomena such as ion sources, mass spectrometers, electrophoresis, resistance, conductors, semiconductors, and superconductivity. | Jiehong Luo | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6747bf4af9980725cf40c5f0/original/from-soft-ionization-mass-spectrometry-to-chemical-bond-and-resistance-semiconductor-superconductivity-the-law-of-charge-motion-in-phase-transition-under-weak-electric-field.pdf |
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