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6386e7d30146ef60a70b3604 | 10.26434/chemrxiv-2022-pv5zx | Transition-State Analysis Reveals Unexpected Coordination-Specific Reactivity that Drives Alkene Dimerization by Sulfated Metal–Organic Frameworks | Metal–organic frameworks (MOFs) with metal nodes and organic linkers have significant potential as reaction catalysts. However, one major factor impeding the development and use of MOFs as organic reaction catalysts is the detailed under-standing of catalytically active sites and their molecular reaction mechanism and selectivity. Experimentally, sulfated and Brønsted acidic MOF-808 catalyzes isobutylene dimerization. Here we report a density functional theory (DFT) based mul-ti-chemical model (cluster and periodic) transition-state study that reveals the likely active catalytic sites/species and the resulting reaction mechanism and selectivity for isobutylene dimerization catalyzed by sulfated MOF-808. Surprisingly, while there are dozens of acidic sites within a single MOF crystal, catalysis is likely the result of only a few specific active sites. Of the two-dozen acidic sites we extensively examined, only one aqua group from the tri-sulfated MOF-808 Zr6 node exhibits strong enough acidity to produce a dimerization barrier consistent with the experiment. Reaction coordinate and transition state models indicate a novel concerted dimerization process that couples C–C bond formation, C–H bond cleav-age, and proton shuttling. The selectivity between terminal and internal alkene dimerization products is likely kinetically controlled with negligible influence from the steric effects of the MOF framework. | Bo Yang; Jose Mendez-Arroyo; Camille May; Jianhua Yao; Daniel Ess | Inorganic Chemistry; Catalysis; Theory - Inorganic; Acid Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6386e7d30146ef60a70b3604/original/transition-state-analysis-reveals-unexpected-coordination-specific-reactivity-that-drives-alkene-dimerization-by-sulfated-metal-organic-frameworks.pdf |
61a78a5303232f41de21d660 | 10.26434/chemrxiv-2021-gg41j | Olefin Metathesis in Confinement: Towards Covalent Organic Framework Scaffolds for Increased Macrocyclization Selectivity | Covalent organic frameworks (COFs) offer vast structural and chemical diversity enabling a wide and growing range of applications. While COFs are well-established as homogeneous catalysts, so far, their high and ordered porosity has scarcely been utilized to its full potential when it comes to spatially confined reactions in COF pores to alter the outcome of reactions. Here, we present a highly porous and crystalline, large-pore COF as catalytic support in diene ring-closing metathesis reactions, leading to increased macrocylization selectivity. COF pore-wall modification by immobilization of a Grubbs-Hoveyda-type catalyst via a mild silylation reaction provides a molecularly precise heterogeneous metathesis catalyst. An increased macro(mono)cyclization (MMC) selectivity over oligomerization (O) for the heterogeneous COF-catalyst (MMC:O = 1.30) of up to 44% compared to the homogeneous catalyst (MMC:O = 0.90) was observed along with a substrate-size dependency in selectivity, pointing to diffusion limitations induced by the pore confinement. | Sebastian T. Emmerling; Felix Ziegler; Felix R. Fischer; Roland Schoch; Matthias Bauer; Bernd Plietker; Michael R. Buchmeiser; Bettina V. Lotsch | Organic Chemistry; Catalysis; Supramolecular Chemistry (Org.); Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a78a5303232f41de21d660/original/olefin-metathesis-in-confinement-towards-covalent-organic-framework-scaffolds-for-increased-macrocyclization-selectivity.pdf |
60c74470337d6cd99ee26da2 | 10.26434/chemrxiv.9788975.v1 | Hooking Together Sigmoidal Monomers into Supramolecular Polymers | <div><div><div><p>Supramolecular polymers have a lot of potential in the development of new materials because of their inherent recyclability and their self-healing and stimuli-responsive properties. Supramolecular conductive polymers are generally obtained by the assembly of individual disk-like π-conjugated molecules into columnar arrays that provide an optimal channel for electronic transport. We report a new approach to prepare supramolecular polymers by hooking together sigmoidal monomers into 1D arrays of π-stacked anthracene and acridine units, which give rise to micrometer-sized fibrils that show pseudoconductivities in line with other conducting materials. This approach paves the way for the design of new supramolecular polymers constituted by acene derivatives with enhanced excitonic and electronic transporting properties.</p></div></div></div> | Marco Carini; Mauro Marongiu; Karol Strutyński; Akinori Saeki; Manuel Melle-Franco; Aurelio Mateo-Alonso | Supramolecular Chemistry (Org.); Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74470337d6cd99ee26da2/original/hooking-together-sigmoidal-monomers-into-supramolecular-polymers.pdf |
6703cbf512ff75c3a1b489a1 | 10.26434/chemrxiv-2024-k9mq6-v3 | Vibrational frequencies utilized for the assessment of exchange-correlation functionals in the description of metal-adsorbate systems: C2H2 and C2H4 on transition-metal surfaces | Describing the interaction between reactive species and surfaces is crucial for designing catalyst materials. Density-functional approximation is able to quantitatively model such interaction, but its accuracy strongly depends on the choice of exchange-correlation (XC) functional approximation. In this work, we assess the performance of XC functionals for describing the interaction of C2H2 and C2H4 with (111) surfaces of Cu, Pt, Pd, and Rh by particulary focusing on RPBE and mBEEF functionals. We study the geometry and the vibrational frequencies associated with the adsorbed molecules, as well as the adsorption energies and the reaction enthalpy of semi-hydrogenation of C2H2 in the gas phase. Crucially, experimental values for vibrational frequencies of molecules adsorbed on the metal surfaces are available for more system compared to physical quantities typically used to benchmark of XC functionals, such as adsorption energies. Thus, vibrational frequencies can be utilized as reference to assess the reliability of the exchange-correlation functionals. We find that the mean percentage errors (MPEs) of RPBE and mBEEF with respect to reported experimental values of vibrational frequencies are 0.64% and -3.88 %, respectively (36 data points). For adsorption enthalpy, RPBE and mBEEF provide MPEs of 27.61 and -59.81%, respectively, with respect to reported experimental values (7 data points). Therefore, the performance of RPBE is superior to that of mBEEF for the considered systems. | Ray Miyazaki; Somayeh Faraji; Sergey V. Levchenko; Lucas Foppa; Matthias Scheffler | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6703cbf512ff75c3a1b489a1/original/vibrational-frequencies-utilized-for-the-assessment-of-exchange-correlation-functionals-in-the-description-of-metal-adsorbate-systems-c2h2-and-c2h4-on-transition-metal-surfaces.pdf |
6542353848dad23120d687c2 | 10.26434/chemrxiv-2023-djc05-v2 | Spiro[3.3]heptane as a Non-collinear Benzene Bioisostere | Spiro[3.3]heptane can mimic the mono-, meta- and para-substituted phenyl rings in drugs. | Kateryna Prysiazhniuk; Oleksandr Datsenko; Oleksandr Polishchuk; Stanislav Shulha; Oleh Shablykin; Liza Nikandrova; Kateryna Horbatok; Iryna Bodenchuk; Petro Borysko; Dmytro Shepilov; Iryna Pishel; Vladimir Kubyshkin; Pavel Mykhailiuk | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6542353848dad23120d687c2/original/spiro-3-3-heptane-as-a-non-collinear-benzene-bioisostere.pdf |
661ece1921291e5d1df988e6 | 10.26434/chemrxiv-2024-x1k47 | A Mitochondrial-Targeted Activity-Based Sensing Probe for Ratiometric Imaging of Formaldehyde Reveals Key Regulators of the Mitochondrial One-Carbon Pool | Formaldehyde (FA) is both a highly reactive environmental genotoxin and an endogenously produced metabolite that functions as a signaling molecule and one-carbon (1C) store to regulate 1C metabolism and epigenetics in the cell. Owing to its signal-stress duality, cells have evolved multiple clearance mechanisms to maintain FA homeostasis, acting to avoid the established genotoxicity of FA while also redirecting FA-derived carbon units into the biosynthesis of essential nucleobases and amino acids. The highly compartmentalized nature of FA exposure, production, and regulation motivates the development of chemical tools that enable monitoring of transient FA fluxes with subcellular resolution. Here we report a mitochondrial-targeted, activity-based sensing probe for ratiometric FA detection, MitoRFAP-2, and apply this reagent to monitor endogenous mitochondrial sources and sinks of this 1C unit. We establish the utility of subcellular localization by showing that MitoRFAP-2 is sensitive enough to detect changes in mitochondrial FA pools with genetic and pharmacological modulation of enzymes involved in 1C and amino acid metabolism, including the pervasive, less active genetic mutant aldehyde dehydrogenase 2*2 (ALDH2*2), where previous, non-targeted versions of FA sensors are not. Finally, we used MitoRFAP-2 to comparatively profile basal levels of FA across a panel of breast cancer cell lines, finding that FA-dependent fluorescence correlates with expression levels of enzymes involved in 1C metabolism. By showcasing the ability of MitoRFAP-2 to identify new information on mitochondrial FA homeostasis, this work provides a starting point for the design of a broader range of chemical probes for detecting physiologically important aldehydes with subcellular resolution and a useful reagent for further studies of 1C biology. | Logan Tenney; Vanha Pham; Thomas Brewer; Christopher Chang | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661ece1921291e5d1df988e6/original/a-mitochondrial-targeted-activity-based-sensing-probe-for-ratiometric-imaging-of-formaldehyde-reveals-key-regulators-of-the-mitochondrial-one-carbon-pool.pdf |
60c749a2ee301cd83cc79adb | 10.26434/chemrxiv.12049377.v2 | Fe-Catalyzed Conjunctive Cross-Couplings of Unactivated Alkenes with Grignard Reagents | The first iron-catalyzed three-component cross-coupling of unactivated olefins with alkyl halides and Grignard reagents is reported. The reaction operates under fast turnover frequency and tolerates a diverse range of sp2-hybridized nucleophiles, alkyl halides, and unactivated olefins bearing diverse functional groups to yield the desired 1,2-alkylarylated products with high regiocontrol. Further, we demonstrate that this protocol is amenable for the synthesis of new (hetero)carbocycles including tetrahydrofurans and pyrrolidines via a three-component radical cascade cyclization/arylation that forges three new C-C bonds. | Lei Liu; Wes Lee; Cassandra R. Youshaw; Mingbin Yuan; Michael B. Geherty; Peter Y. Zavalij; Osvaldo Gutierrez | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749a2ee301cd83cc79adb/original/fe-catalyzed-conjunctive-cross-couplings-of-unactivated-alkenes-with-grignard-reagents.pdf |
63bc6a17d19cc558a9ff063b | 10.26434/chemrxiv-2022-n2z1c-v2 | Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field | We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes easily to highly diverse sets of chemistries based on substructure queries.
Like the previous OpenFF iterations, the Sage generation of OpenFF force fields was validated in protein-ligand simulations to be compatible with AMBER biopolymer force fields. In this paper we detail the methodology used to develop this force field, as well as the innovations and improvements introduced since the release of Parsley 1.0.0. One particularly significant feature of Sage is a set of improved Lennard-Jones (LJ) parameters retrained against condensed phase mixture data, the first refit of LJ parameters in the OpenFF small molecule force field line.
Sage also includes valence parameters refit to a larger database of quantum chemical calculations than previous versions, as well as improvements in how this fitting is performed. Force field benchmarks show improvements in general metrics of performance against quantum chemistry reference data such as root mean square deviations (RMSD) of optimized conformer geometries, torsion fingerprint deviations (TFD), and improved relative conformer energetics (ΔΔ𝐸). We present a variety of benchmarks for these metrics against our previous force fields as well as in some cases other small molecule biomolecular force fields. Sage also demonstrates improved performance in estimating physical properties, including comparison against experimental data from various thermodynamic databases for small molecule properties such as Δ𝐻_𝑚𝑖𝑥, ρ(𝑥), Δ𝐺_𝑠𝑜𝑙𝑣 and Δ𝐺_𝑡𝑟𝑎𝑛𝑠. Additionally, we benchmarked against protein-ligand binding free energies (Δ𝐺_𝑏𝑖𝑛𝑑), where Sage yields results statistically similar to previous force fields. All the data is made publicly available along with complete details on how to reproduce the training results at https://github.com/openforcefield/openff-sage. | Simon Boothroyd; Pavan Kumar Behara; Owen Madin; David Hahn; Hyesu Jang; Vytautas Gapsys; Jeffrey Wagner; Joshua Horton; David Dotson; Matthew Thompson; Jessica Maat; Trevor Gokey; Lee-Ping Wang; Daniel Cole; Michael Gilson; John Chodera; Christopher Bayly; Michael Shirts; David Mobley | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bc6a17d19cc558a9ff063b/original/development-and-benchmarking-of-open-force-field-2-0-0-the-sage-small-molecule-force-field.pdf |
60c746a4842e6521f3db2851 | 10.26434/chemrxiv.11365025.v1 | Thermodynamic and Kinetic Parameters for Calcite Nucleation on Peptoid and Model Scaffolds - a Step Toward Nacre Mimicry. | To establish an approach for a bulk upscaling of a composit material consisting of calcium carbonate and tunable peptoids we
here combined three distinct approaches to thoroughly access the underlying
kinetic and thermodynamic driving forces for CaCO3 formation on peptoid polymers.
We derived the net interfacial free energy for calcite formation on the
nanosheets and self-assemblage monolayers of the sheets constituent functional
groups (carboxyl, amine and a 1:1 mix) using: nucleation experiments, dynamic
force spectroscopy and theoretical modeling (COSMO-RS). We applied nucleation theory to the results and obtain insight into conditions were we can obtain favorable nucleation conditions on the polymers in a highly controlled manner. | Anne Rath Nielsen; Stanislav Jelavic; Daniel Murray; Behzad Rad; Martin Andersson; Marcel Ceccato; Andrew Mitchell; Susan Stipp; Ron N. Zuckermann; Karina Sand | Composites; Geochemistry; Industrial Manufacturing; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746a4842e6521f3db2851/original/thermodynamic-and-kinetic-parameters-for-calcite-nucleation-on-peptoid-and-model-scaffolds-a-step-toward-nacre-mimicry.pdf |
60c74e01bb8c1a2c2c3db6a5 | 10.26434/chemrxiv.12686012.v1 | Theoretical Description of the Physical/chemical Contributions Determining the Stability of Transition-Metal Doped Phosphorene Nanosheets | In this report, we explore the stability of doped-phosphorene nanosheets with first-row transition metals in the framework of density functional theory and by using a bonding characterization and energy decomposition analyses. | Sasha Gazzari; Kerry Wrighton-Araneda; Diego Cortes-Arriagada | Interfaces; Physical and Chemical Properties; Quantum Mechanics; Structure; Surface | CC BY 4.0 | CHEMRXIV | 2020-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e01bb8c1a2c2c3db6a5/original/theoretical-description-of-the-physical-chemical-contributions-determining-the-stability-of-transition-metal-doped-phosphorene-nanosheets.pdf |
60c74750567dfee171ec47e9 | 10.26434/chemrxiv.8217143.v2 | Thermodynamic Driving Forces and Chemical Reaction Fluxes; Reflections on the Steady State | Molar
balances of continuous and batch reacting systems with a simple reaction are
analyzed from the point of view of finding relationships between the thermodynamic
driving force and the chemical reaction rate. Special attention is focused on
steady state, which has been the core subject of previous similar work. It is
argued that such relationships should contain, besides the thermodynamic driving
force, also a kinetic factor, and are of a specific form for a specific
reacting system. More general analysis is provided by means of the non-equilibrium
thermodynamics of linear fluid mixtures. Then, the driving force can be
expressed either in Gibbs energy (affinity) form or on the basis of chemical
potentials. The relationships can be generally interpreted in terms of
force-resistance-flux. | Miloslav Pekař | Chemical Kinetics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74750567dfee171ec47e9/original/thermodynamic-driving-forces-and-chemical-reaction-fluxes-reflections-on-the-steady-state.pdf |
652256868bab5d2055deb7ef | 10.26434/chemrxiv-2023-smkqb | Digital DNA Strand Displacement for Molecular Computing | Multiplexed analysis of feature biomarkers enhances the accuracy of molecular diagnostic results. Molecular computing systems exhibited potentials for intelligent analysis of multiplexed biomarkers. However, the chemical reaction networks of current molecular computing systems suffer from the use of large number of oligonucleotides and limited encoding capability. Here, we developed a molecular computing platform termed as Digital DNA Strand Displacement (DDSD), utilizing the features of DNA polymerase-mediated strand extension and displacement to achieve robust linear weight encoding as well as exponential weight encoding. This approach not only ensures precise molecular diagnostics but also enables precise identification of specific infection types. The DNA polymerase-based digital DNA strand displacement guaranteed high specificity in molecular reactions and reduced the number of DNA strands used in molecular computing. We conducted double-blind experiments to diagnose and identify bacterial or viral infection samples accurately. Furthermore, we demonstrated two approaches (cascade strand displacement and multi-way DNA junction) for computing capability upgradation, enabling weighted calculations for at least 15 feature biomarkers. Digital DNA strand displacement lays the foundation for more intricate and accurate molecular computing and diagnostics. | Linghao Zhang; Huixiao Yang; Xinmiao Kang; Yumin Yan; Jiong Huang; Hongyang Zhao; Jiayu Yang; Xin Su | Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Biochemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652256868bab5d2055deb7ef/original/digital-dna-strand-displacement-for-molecular-computing.pdf |
641dff93647e3dca9973f174 | 10.26434/chemrxiv-2022-jn0mj-v2 | Injectable and photocurable macromonomers synthesized using a heterometallic magnesium-titanium metal-organic catalyst for elastomeric polymer networks | Injectable and in situ photocurable biomaterials are receiving a lot of attention due to their ease of application via syringe or dedicated applicator and ability to be used in laparoscopic and robotic minimally invasive procedures. The aim of this work was to synthesize photocurable ester-urethane macromonomers using a heterometallic magnesium-titanium catalyst, magnesium-titanium (IV) butoxide for elastomeric polymer networks. The progress of the two-step synthesis of macromonomers was monitored using infrared spectroscopy. The chemical structure and molecular weight of the obtained macromonomers were characterized using nuclear magnetic resonance spectroscopy and gel permeation chromatography. The dynamic viscosity of the obtained macromonomers was evaluated by a rheometer. Next, the photocuring process was studied under both air and argon atmospheres. Both the thermal and dynamic mechanical thermal properties of the photocured soft and elastomeric networks were investigated. Finally, in vitro cytotoxicity screening of polymer networks based on ISO10993-5 revealed high cell viability (over 77%) regardless of curing atmosphere. Overall, our results indicate that this heterometallic magnesium-titanium butoxide catalyst can be an attractive alternative to commonly used homometallic catalysts for the synthesis of injectable and photocurable materials for medical applications. | Malwina Niedzwiedz; Wojciech Ignaczak; Peter Sobolewski; Agata Goszczyńska; Gokhan Demirci; Miroslawa El Fray | Materials Science; Polymer Science; Biocompatible Materials; Polymerization (Polymers); Polymerization catalysts | CC BY 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641dff93647e3dca9973f174/original/injectable-and-photocurable-macromonomers-synthesized-using-a-heterometallic-magnesium-titanium-metal-organic-catalyst-for-elastomeric-polymer-networks.pdf |
653d1099c573f893f1526c21 | 10.26434/chemrxiv-2023-7h0sd | Low Part-Per-Trillion, Humidity Resistant Detection of Nitric Oxide Using Microtoroid Optical Resonators | The nitric oxide radical plays pivotal roles in physiological as well as atmospheric contexts. Although the detection of dissolved nitric oxide in vivo has been widely explored, highly sensitive (i.e. low part-per-trillion level), selective, and humidity resistant detection of gaseous nitric oxide in air remains challenging. In the field, humidity can have dramatic effects on the accuracy and selectivity of gas sensors, confounding data and leading to overestimation of gas concentration. Highly selective and humidity resistant gaseous NO sensors based on laser-induced graphene (LIG) were recently reported, displaying a limit of detection (LOD) of 8.3 ppb. Although highly sensitive (LOD = 590 ppq) single-wall carbon nanotube NO sensors have been reported, these sensors lack selectivity and humidity resistance. In this report, we disclose a highly sensitive (LOD = 2.34 ppt), selective, and humidity resistant nitric oxide sensor based on a whispering-gallery mode (WGM) microtoroid optical resonator. Excellent analyte selectivity was enabled via novel ferrocene-containing polymeric coatings synthesized via RAFT polymerization. Utilizing a Frequency Locked Optical Whispering Evanescent Resonator (FLOWER) system, the microtoroid’s real-time resonance frequency shift response to nitric oxide, was tracked with sub-femtometer resolution. The lowest concentration experimentally detected was 6.4 ppt, which is the lowest reported to date. Additionally, the performance of the sensor remained consistent across different humidity environments. Lastly, the impact of the chemical composition and molecular weight of the novel ferrocene-containing polymeric coatings on sensing performance was evaluated. We anticipate that our results will have impact on a wide variety of fields where NO sensing is important such as medical diagnostics through exhaled breath, determination of planetary habitability, marine science, climate change, air quality monitoring, and treating cardiovascular and neurological disorders.
| Yinchao Xu; Allison Stanko; Chloe Cerione; Trevor Lohrey; Euan McLeod; Brian Stoltz; Judith Su | Analytical Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653d1099c573f893f1526c21/original/low-part-per-trillion-humidity-resistant-detection-of-nitric-oxide-using-microtoroid-optical-resonators.pdf |
6703ea1b51558a15ef5cdfef | 10.26434/chemrxiv-2024-vljqw-v2 | An Extension of the Stern-Volmer Equation for Thermally Activated Delayed Fluorescence (TADF) Photocatalysts | Fluorescence quenching experiments are essential mechanistic tools in photoredox catalysis, allowing to elucidate the first step in the catalytic cycle that occurs after photon absorption. Thermally activated delayed fluorescence (TADF) photocatalysts, however, yield non-linear Stern-Volmer plots, thus requiring an adjustment to this widely used method to determine the efficiency of excited state quenching. Here, we derive an extension of the Stern-Volmer equation for TADF-fluorophores that considers quenching from both the singlet and triplet excited states, and experimentally verify it with fluorescence quenching experiments using the commonly employed TADF-photocatalyst 4CzIPN with three different quenchers in three solvents. The experimental data is perfectly described by this new equation, which in addition to the Stern-Volmer constants of quenching allows for the determination of the product of intersystem and reverse intersystem crossing quantum yields, a quantity that is independent of the quencher. | Bart Limburg | Physical Chemistry; Organic Chemistry; Catalysis; Physical Organic Chemistry; Photocatalysis; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6703ea1b51558a15ef5cdfef/original/an-extension-of-the-stern-volmer-equation-for-thermally-activated-delayed-fluorescence-tadf-photocatalysts.pdf |
60c749b4337d6ce75de27771 | 10.26434/chemrxiv.12098670.v1 | A Paramagnetic NMR Spectroscopy Toolbox for the Characterisation of Paramagnetic/Spin-Crossover Coordination Complexes and Metal-Organic Cages | <div>
<p>The
large paramagnetic shifts and short relaxation times resulting from the
presence of a paramagnetic centre complicate NMR data acquisition and
interpretation in solution. In contrast to the large number of standard NMR
methods for diamagnetic compounds, the number of paramagnetic NMR methods is
limited and spectral assignment often relies on theoretical models. We report a
toolbox of 1D (<sup>1</sup>H, proton-coupled <sup>13</sup>C, selective <sup>1</sup>H‑decoupling
<sup>13</sup>C, steady-state NOE) and 2D (COSY, NOESY, HMQC) paramagnetic NMR
methods for the straightforward structural characterisation of paramagnetic
complexes in solution and demonstrate its general applicability for fields from
coordination chemistry to spin‑crossover complexes and supramolecular chemistry
through the characterisation of Co<sup>II</sup> and high-spin Fe<sup>II</sup>
mononuclear complexes as well as a Co<sub>4</sub>L<sub>6</sub> cage. The
toolbox takes advantage of the reduced signal overlap, decreased instrument
time and greater sensitivity from the presence of the paramagnetic centre while
overcoming the loss of structural information from the wide chemical shift
dispersion and broad signals. In some circumstances, more structural
information was revealed in the COSY spectra than would be observable for a
diamagnetic analogue; as well as the expected through-bond cross-peaks,
through-space and exchange cross-peaks were also observed for mononuclear
complexes with multiple ligand environments and fast ligand exchange. With this
toolbox, the standard characterisation of paramagnetic complexes and cages is
now possible using NMR spectroscopic methods. </p>
</div>
<br /> | Marc Lehr; Tobias Paschelke; Eicke Trumpf; Anna-Marlene Vogt; Christian Näther; Frank Sönnichsen; Anna McConnell | Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749b4337d6ce75de27771/original/a-paramagnetic-nmr-spectroscopy-toolbox-for-the-characterisation-of-paramagnetic-spin-crossover-coordination-complexes-and-metal-organic-cages.pdf |
6538fe66c573f893f10a8aea | 10.26434/chemrxiv-2023-rtjcx | Utilization of AlphaFold Models for Drug Discovery: Feasibility and Challenges. Histone Deacetylase 11 as a Case Study | Histone deacetylase 11 (HDAC11), an enzyme that is cleaving acyl groups from acylated lysine residues, is the sole member of class IV of HDAC family with no reported crystal structure so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms which complicates the conventional template based homology modeling. AlphaFold is a neural network machine learning approach for predicting the 3D structures of proteins with atomic accuracy even in absence of similar structures. However, the structures predicted by AlphaFold are missing small molecules as ligands and cofactors. In our study, we first optimized the HDAC11 AlphaFold model by adding the catalytic zinc ion followed by assessment of the usability of the model by docking of the selective inhibitor FT895. Minimization of the optimized model in presence of transplanted inhibitors, previously described as HDAC11 inhibitors for which X-ray structures with the related HDAC8 are available was performed. Four complexes were generated and proved to be stable using three replicas of 50 ns MD simulations and were successfully utilized for docking of the selective inhibitors FT895 and MIR002 and SIS17 The most reasonable pose was selected based on structural comparison between HDAC6, HDAC8 and the HDAC11 optimized AlphaFold model. The manually optimized HDAC11 model is thus able to explain the binding behavior of known HDAC11 inhibitors and can be used for further structure based optimization. | Fady Baselious; Dina Robaa; Wolfgang Sippl | Theoretical and Computational Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6538fe66c573f893f10a8aea/original/utilization-of-alpha-fold-models-for-drug-discovery-feasibility-and-challenges-histone-deacetylase-11-as-a-case-study.pdf |
6479ec8e4f8b1884b7b7d67f | 10.26434/chemrxiv-2023-mjgd8 | Scalable air-tolerant μL-volume synthesis of thick poly(SPMA) brushes using SI-ARGET-ATRP | We present a straightforward procedure for preparing thick (up to 300 nm) poly(3-sulfopropyl methacrylate) brushes using SI-ARGET-ATRP by conducting the reaction in a fluid film between the substrate and a coverslip. This method is advantageous in a number of ways: it does not require deoxygenation of the reaction solution, and the monomer conversion is much higher than usual since only a minimal amount of solution (microliters) is used, resulting in a tremendous reduction (~50x) of wasted reagents. Moreover, this method is particularly suited for grafting brushes to large substrates. | Lars Veldscholte; Sissi de Beer | Materials Science; Polymer Science; Polyelectrolytes - Polymers; Polymer brushes; Polymerization (Polymers); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6479ec8e4f8b1884b7b7d67f/original/scalable-air-tolerant-l-volume-synthesis-of-thick-poly-spma-brushes-using-si-arget-atrp.pdf |
656a203929a13c4d4773f681 | 10.26434/chemrxiv-2023-3fj7g | Dissolution heterogeneity observed in anisotropic ruthenium dioxide nanocrystals via liquid-phase transmission electron microscopy | Noble metal oxides such as ruthenium dioxide are highly active electrocatalysts for anodic reactions in acidic electrolytes, but dissolution during electrochemical operation impedes wide-scale application in renewable energy technologies. Improving the fundamental understanding of the dissolution dynamics of application-relevant morphologies such as nanocrystals is critical for grid-scale implementation of these materials. Herein we report the nanoscale heterogeneity observed via liquid phase transmission electron microscopy during ruthenium dioxide nanocrystal dissolution under oxidizing conditions. Single-crystalline ruthenium dioxide nanocrystals enabled direct observation of dissolution along different crystallographic facets, allowing an unprecedented direct comparison of crystal facet stability. The nanoscale observations revealed substantial heterogeneity in the relative stability of crystallographic facets across different nanocrystals, attributed to nanoscale strains present in these crystals. These findings highlight the importance of nanoscale heterogeneity in determining macroscale properties such as electrocatalyst stability and provide a characterization methodology that can be integrated into next-generation electrocatalyst discovery efforts. | S. Avery Vigil; Ivan A. Moreno-Hernandez | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656a203929a13c4d4773f681/original/dissolution-heterogeneity-observed-in-anisotropic-ruthenium-dioxide-nanocrystals-via-liquid-phase-transmission-electron-microscopy.pdf |
666747cd409abc034518cf9a | 10.26434/chemrxiv-2024-bthcz | Chromophore Optimization in Organometallic Au(III) Cys Arylation of Peptides and Proteins for 266 nm Photoactivation | Cysteine is the most reactive naturally occurring amino acid due to the presence of a free thiol, presenting a tantalizing handle for covalent modification of peptides/proteins. Although many mass spectrometry experiments could benefit from site-specific modification of Cys, the utility of direct arylation has not been thoroughly explored. Recently, Spokoyny and coworkers reported a Au(III) organometallic reagent that robustly arylates Cys and tolerates a wide variety of solvents and conditions. Given the chromophoric nature of aryl groups and the known susceptibility of carbon-sulfur bonds to photodissociation, we set out to identify an aryl group that could efficiently cleave Cys carbon-sulfur bonds at 266 nm. A streamlined workflow was developed to facilitate rapid examination of a large number of aryls with minimal sample using a simple test peptide, RAAACGVLK. We were able to identify several aryl groups that yield abundant homolytic photodissociation of the adjacent Cys carbon-sulfur bonds with short activation times (<10 ms). In addition, we characterized the radical products created by photodissociation by subjecting the product ions to further collisional activation. Finally, we tested Cys arylation with human hemoglobin, identified reaction conditions that facilitate efficient modification of intact proteins, and evaluated the photochemistry and activation of these large radical ions. | Jacob Silzel; Chengwei Chen; Colomba Sanchez-Marsetti; Phillip Farias; Veronica Carta; W. Hill Harman; Ryan Julian | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666747cd409abc034518cf9a/original/chromophore-optimization-in-organometallic-au-iii-cys-arylation-of-peptides-and-proteins-for-266-nm-photoactivation.pdf |
60c74a1c842e6539addb2e8d | 10.26434/chemrxiv.12005988.v2 | Identification of SARS-CoV-2 Cell Entry Inhibitors by Drug Repurposing Using in Silico Structure-Based Virtual Screening Approach | The rapidly spreading, highly contagious and pathogenic SARS-coronavirus 2 (SARS-CoV-2) associated Coronavirus Disease 2019 (COVID-19) has been declared as a pandemic by the World Health Organization (WHO). The novel 2019 SARS-CoV-2 enters the host cell by binding of the viral surface spike glycoprotein (S-protein) to angiotensin converting enzyme 2 (ACE2). The virus specific molecular interaction with the host cell represents a promising therapeutic target for identifying SARS-CoV-2 antiviral drugs. The repurposing of drugs can provide a rapid and potential cure towards exponentially expending COVID-19. Thereto, high-throughput virtual screening approach was used to investigate FDA approved LOPAC library drugs against both the S-protein and ACE2 host cell receptor. Primary screening identified a few promising drugs for both the targets, which were further analyzed in details by their binding energy, binding modes through molecular docking, dynamics and simulations. Evidently, Eptifibatide acetate, TNP, GNF5, GR 127935 hydrochloride hydrate and RS504393 were found binding to virus binding motifs of ACE2 receptor. Additionally, KT185, KT203 GSK1838705A, BMS195614, and RS504393 were identified to bind at the receptor binding site on the viral S-protein. These identified drug molecules may effectively assist in controlling the rapid spread of SARS-COV-2 by not only potentially inhibiting the virus at entry step but also as anti-inflammatory agents which could impart relief in lung injuries. Timely identification and determination of an effective drug to combat and tranquilize the COVID-19 global crisis is the utmost need of hour. Further, prompt in vivo testing to validate the anti-SARS-COV-2 inhibition by these drugs could save lives is justified. | Shweta Choudhary; Yashpal S. Malik; Shailly Tomar | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a1c842e6539addb2e8d/original/identification-of-sars-co-v-2-cell-entry-inhibitors-by-drug-repurposing-using-in-silico-structure-based-virtual-screening-approach.pdf |
60c73dd4337d6c754ce2622f | 10.26434/chemrxiv.6157451.v1 | Catalytic Ring Closing Reactions of Gold Compounds Containing Bis(phosphino)ferrocene Ligands | A variety of gold compounds containing bis(phosphino)ferrocene ligands were examined as catalysts in the ring closing reaction of (Z)-3-methylpent-2-en-4-yn-1-ol | Toni A. Michaels; Justine Dell; Chip Nataro | Homogeneous Catalysis; Catalysis; Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd4337d6c754ce2622f/original/catalytic-ring-closing-reactions-of-gold-compounds-containing-bis-phosphino-ferrocene-ligands.pdf |
661dba1b91aefa6ce1a3c46f | 10.26434/chemrxiv-2024-5kzm8 | Discovery of 3-((4-benzylpyridin-2-yl)amino)benzamide Derivatives as Potent GPR52 G Protein-Biased Agonists. | Orphan GPR52 is emerging as a promising neurotherapeutic target. Optimization of previously reported lead 4a employing an iterative drug design strategy led to identification of a series of unique GPR52 agonists, such as 10a (PW0677), 15b (PW0729) and 24f (PW0866), with improved potency and efficacy. Intriguingly, compounds 10a and 24f showed greater bias for G protein/cAMP signaling and induced significantly less in vitro desensitization than parent compound 4a, indicating that reducing GPR52 β-arrestin activity with biased agonism results in sustained GPR52 activation. Further exploration of compounds 15b and 24f indicated improved potency and efficacy, excellent target selectivity, but limited brain exposure warranting further optimization. These balanced and biased GPR52 agonists provide important pharmacological tools to study GPR52 activation, signaling bias, and therapeutic potential for neuropsychiatric and neurological diseases. | Ryan Murphy; Pingyuan Wang; Sagir Ali; Hudson Smith; Daniel Felsing; Haiying Chen; Jia Zhou; John Allen | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661dba1b91aefa6ce1a3c46f/original/discovery-of-3-4-benzylpyridin-2-yl-amino-benzamide-derivatives-as-potent-gpr52-g-protein-biased-agonists.pdf |
60c74a96f96a007f8228747a | 10.26434/chemrxiv.12227363.v1 | Combined Deep Learning and Molecular Docking Simulations Approach Identifies Potentially Effective FDA Approved Drugs for Repurposing Against SARS-CoV-2 | <p></p><p>The ongoing pandemic of Coronavirus Disease 2019
(COVID-19), the disease caused by the severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2), has posed a serious threat to global public health.
Currently no approved
drug or vaccine exists against SARS-CoV-2. Drug repurposing, represented as an effective drug discovery strategy from
existing drugs, is a time efficient approach to find effective drugs against
SARS-CoV-2 in this emergency situation. Both experimental and computational approaches are being
employed in drug repurposing with computational approaches becoming
increasingly popular and efficient. In this study, we present a robust
experimental design combining deep learning with molecular docking experiments to
identify most promising candidates from the list of FDA approved drugs that can
be repurposed to treat COVID-19. We have employed a
deep learning based Drug Target Interaction (DTI) model, called DeepDTA, with
few improvements to predict drug-protein binding affinities, represented as KIBA
scores, for 2,440 FDA approved and 8,168 investigational drugs against 24
SARS-CoV-2 viral proteins. FDA approved drugs with the highest KIBA scores were
selected for molecular docking simulations. We ran docking simulations for 168
selected drugs against 285 total predicted and/or experimentally proven active
sites of all 24 SARS-CoV-2 viral proteins. We used a recently published open source AutoDock based high
throughput screening platform virtualflow to reduce the time required to run
around 50,000 docking simulations. A list of 49 most promising FDA approved
drugs with best consensus KIBA scores and AutoDock vina binding affinity values
against selected SARS-CoV-2 viral proteins is generated. Most importantly, anidulafungin,
velpatasvir, glecaprevir, rifabutin, procaine penicillin G, tadalafil,
riboflavin 5’-monophosphate, flavin adenine dinucleotide, terlipressin,
desmopressin, elbasvir, oxatomide, enasidenib, edoxaban and selinexor
demonstrate highest predicted inhibitory potential against key SARS-CoV-2 viral
proteins.</p><p></p> | Muhammad Umer Anwar; Farjad Adnan; Asma Abro; Muhammad Rayyan Khan; Asad Ur Rehman; Muhammad Osama; Saad Javed; Ahmadullah Baig; Muhammad Raffey Shabbir; Muhammad Zaman Assir | Bioinformatics and Computational Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a96f96a007f8228747a/original/combined-deep-learning-and-molecular-docking-simulations-approach-identifies-potentially-effective-fda-approved-drugs-for-repurposing-against-sars-co-v-2.pdf |
65ddfee29138d23161279bc1 | 10.26434/chemrxiv-2024-ksg1l | Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ | Human polymerases are vital for genetic information management. Their function involves catalyzing the synthesis of DNA strands with unparalleled accuracy, which ensures the fidelity and stability of the human genomic blueprint. Several disease-associated mutations and their functional impact on DNA polymerases have been reported. One particular polymerase, human DNA polymerase kappa (Pol κ), has been reported to be susceptible to several cancer-associated mutations. The Y432S mutation in Pol κ, which is associated with various cancers, is of interest due to its impact on polymerization activity and markedly reduced thermal stability. Here, we have used computational simulations to investigate the functional consequences of the Y432S by means of classical molecular dynamics (MD) and coupled quantum mechanics/molecular mechanics (QM/MM) methods. Our results suggest that Y432S results in structural effects on domains involved in nucleotide addition and ternary complex stabilization while maintaining catalytic competence. Calculation of the minimum energy path associated with the reaction mechanism of wild type (WT) and Y432S Pol κ indicate that while both enzymes are catalytically competent, the cancer mutation results in a slightly endoergic reaction and an increase in the catalytic barrier. Interactions with a third magnesium ion and environmental effects on non-bonded interactions, particularly involving key residues, contribute to the kinetic and thermodynamic distinctions between the WT and mutant during the catalytic reaction. The energetics and electronic findings suggest that active site residues favor the catalytic reaction with dCTP3– over dCTP4–. | Yazdan Maghsoud; Arkanil Roy; Emmett M. Leddin; G. Andrés Cisneros | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Biophysics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ddfee29138d23161279bc1/original/effects-of-the-y432s-cancer-associated-variant-on-the-reaction-mechanism-of-human-dna-polymerase.pdf |
62d091e34e76bf66078e5a96 | 10.26434/chemrxiv-2022-fgq9l | Characterizing the Behavior of Bitumen-Water Systems with the Hydrophilic-Lipophilic Difference (HLD) Framework | Emulsions of water in bitumen, even in solvent-diluted bitumen, are notorious for their stability. Such stability affects the removal of water in the Froth Treatment Process prior to upgrading of bitumen extracted from mining operations. The literature presents various examples of the use of the Hydrophilic-Lipophilic Difference (HLD) framework to formulate demulsifiers for conventional crude oils, reducing the emulsion stability from hours to minutes when HLD=0 (phase inversion point). To apply this approach to bitumen emulsions, the HLD of these systems needs to be assessed. A previous attempt to obtain the HLD of bitumen emulsions was incomplete because the suspected surfactant-like and oil-like behavior of polar oils in bitumen, particularly asphaltenes and naphthenic acids (NAs), could not be resolved. This question was revisited using a newly established framework for the HLD of polar oils. To this end, microemulsion phase behavior studies were conducted involving mixtures of ionic and nonionic surfactants with asphaltenes, diluted bitumen, and deasphalted bitumen (maltenes), which led to the realization that asphaltenes do not play a role in HLD when other surfactants are present in the system. Instead, NAs and their dissociation into naphthenates dominate the phase behavior of bitumen emulsions. It was determined that a gradual change in the degree of dissociation of NAs, induced by sodium hydroxide addition, could substantially change the HLD of the system and the accompanying changes in interfacial tension, emulsion stability, and residual water content in the oil phase. | Amir Ghayour; Rafael Perez Franco; Sujit Bhattacharya; Edgar Acosta | Physical Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Petrochemicals; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d091e34e76bf66078e5a96/original/characterizing-the-behavior-of-bitumen-water-systems-with-the-hydrophilic-lipophilic-difference-hld-framework.pdf |
61c366f37284d03776f4f3c8 | 10.26434/chemrxiv-2021-j3qs1-v2 | OS100: A Benchmark Set of 100 Digitized UV-Visible Spectra and Derived Experimental Oscillator Strengths | Excited-state quantum chemical calculations typically report excitation energies and oscillator strengths, ƒ, for each electronic transition. On the other hand, UV-visible spectrophotometric experiments report energy-dependent molar extinction/attenuation coefficients, ε(v), that determine the absorption band line shapes. ε(v) and ƒ are related, but this relation is complicated by various broadening and solvation effects. We fit and integrated experimental UV-visible spectra to obtain ƒexp values for absorption bands and estimated the uncertainty in the fitting. We derived 164 ƒexp values from 100 organic molecules ranging in size from 6-34 atoms. The corresponding computed oscillator strengths (ƒcomp) were obtained with time-dependent density functional theory and a polarizable continuum solvent model. By expressing experimental and computed absorption strengths using a common quantity, we directly compared ƒcomp and ƒexp. While ƒcomp and ƒexp are well correlated (linear regression R2=0. 921), ƒcomp in most cases significantly overestimates ƒexp (regression slope=1.34). The agreement between absolute ƒcomp and ƒexp values was substantially improved by accounting for a solvent refractive index factor, as suggested in some derivations in the literature. The 100 digitized UV-visible spectra are included as plain text files in the supporting information to aid in benchmarking computational or machine-learning approaches that aim to simulate realistic UV-visible absorption spectra. | Astrid Tarleton; Jorge Garcia-Alvarez; Anah Wynn; Cade Awbrey; Tomas Roberts; Samer Gozem | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c366f37284d03776f4f3c8/original/os100-a-benchmark-set-of-100-digitized-uv-visible-spectra-and-derived-experimental-oscillator-strengths.pdf |
66f16b8ecec5d6c142f29bc5 | 10.26434/chemrxiv-2024-44l9s | NHC-Catalyzed Transition-Metal-Free Allylation of Aldehydes with MBH Carbonates and Their Michael Addition-Elimination-Cope Rearrangement Cascade: Facile Access to Sacubitril API | We report herein, a novel NHC-catalyzed transition-metal-free chemoselective allylation of aldehydes with Morita-Baylis-Hillman (MBH) carbonates using inorganic base. Fascinatingly, use of an organic base follows a different mechanism leading to highly functionalized 1,5-dienes via Michael addition-elimination reaction followed by [3,3]-sigmatropic cope rearrangement. The described method harnesses a new Csp2–Csp3 bond to access α-methylene-γ-oxo-γ-substituted ester derivatives paving a way to facile synthesis of potent natural products and APIs. A broad range of aromatic and aliphatic aldehydes with MBH carbonates were employed to provide a variety of interesting butanoate and dienyl ketone scaffolds in good to excellent yields. This chemistry has been extended to the efficient syntheses of sacubitril API and γ-butyrolactone scaffold found in many natural products and APIs. | Tushar Kale; Sayali Jagtap; Santosh Mhaske | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f16b8ecec5d6c142f29bc5/original/nhc-catalyzed-transition-metal-free-allylation-of-aldehydes-with-mbh-carbonates-and-their-michael-addition-elimination-cope-rearrangement-cascade-facile-access-to-sacubitril-api.pdf |
66eb02afcec5d6c1427326ab | 10.26434/chemrxiv-2024-2pdt3 | Phase Separation and Passive Diffusion of Perfluorooctane Sulfonic Acid (PFOS) in Multilamellar and
Unilamellar Vesicles | Perfluorinated alkyl substances (PFAS) are important environmental hazards that enter microorganisms
and animal tissues via their cellular membranes, where they bind to both proteins and lipids1. The
interaction of a prevalent PFAS, perfluorooctane sulfonic acid (PFOS), with a model cell membrane
composed of dipalmitoyl phosphatidylcholine (DPPC) was investigated as a function of molar ratio of
DPPC/PFOS in both multilamellar vesicles (MLVs) and large unilamellar vesicles (LUVs). The PFOS was both
prepared and incubated with the vesicles and its incorporation into the LUVs and MLVs was monitored by
nano- differential scanning calorimetry (for phase transition temperatures, Tm) and by dynamic light
scattering (DLS) or optical microscopy for size. For MLVs and LUVs prepared with PFOS, no pretransition
was observed. The LUVs and MLVs remained intact for up to 30 days with sizes ~ 100nm for LUVs and ~
10-100 μm for MLVs. At DPPC/PFOS ~ 75/1 to 7.5/1, there was a single Tm, that decreased and broadened
as the DPPC/PFOS molar ratio decreased, as previously observed.2 At higher PFOS concentrations,
DPPC/PFOS < 5/1, two or three phase transitions were observed, with one Tm at a temperature close to
that of the neat MLVs/LUVs and one at lower temperature. This was interpreted as phase separation into
PFOS rich and PFOS poor domains. When MLVs were incubated with PFOS, both the main (Tm) and
pretransition (Tpre), characteristic of neat DPPC, were observed, indicating the presence of bilayers with
no incorporated PFOS. The intensity of Tm decreased with increased time, temperature (i.e. faster above
than below Tm) and the external PFAS concentration, and Tpre increased (T = Tm - Tpre decreased).
Concurrently, a phase transition in the MLVs at lower temperature was observed and disappeared with
time. These results indicate that there was progressive penetration of the PFOS from the outer leaflets
(that had incorporated PFOS) to the interior bilayers (that had no incorporated PFOS) of the MLVs, and by
implication that there was passive diffusion of PFOS across (not just into) the DPPC bilayers, which
occurred more quickly above than below Tm. While diffusion of PFOS across cellular membranes has
previously been observed, this effect has been attributed to association with membrane proteins. | Tutan Das Aka; Thomas Boller; Graham Dobereiner; Stephanie L. Wunder | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Aggregates and Assemblies; Bioengineering and Biotechnology; Environmental biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66eb02afcec5d6c1427326ab/original/phase-separation-and-passive-diffusion-of-perfluorooctane-sulfonic-acid-pfos-in-multilamellar-and-unilamellar-vesicles.pdf |
60c740e1842e656bffdb1d77 | 10.26434/chemrxiv.7851587.v1 | When Current Does Not Follow Bonds: Current Density in Saturated Molecules | <div>
<div>
<div>
<p>The tools commonly used to understand structure-property relationships in molecular conductance, inter-atomic currents and conductance eigenchannels, generally give
us a sense of familiarity, with the chemical bonding framework and molecular orbitals
reflected in the current. Here we show that while this picture is true for conjugated
molecules, it breaks down in saturated systems. We investigate the current density in
saturated chains of alkanes, silanes and germanes and show that the current density
does not follow the bonds, but rather the nuclei define the diameter of a pipe through
which the current flows. We discuss how this picture of current density can be used
to understand details about the electron transport properties of these molecules. Understanding the spatial distribution of current through molecules, rather than simply
the magnitude, provides a powerful tool for chemical insight into physical properties of
molecules that are related to current flow.
</p>
</div>
</div>
</div> | Anders Jensen; Marc Hamilton Garner; Gemma C. Solomon | Theory - Computational; Physical and Chemical Properties; Structure; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e1842e656bffdb1d77/original/when-current-does-not-follow-bonds-current-density-in-saturated-molecules.pdf |
64ca54eb69bfb8925a3c221b | 10.26434/chemrxiv-2023-4df3z | Insights in Molybdenum Composite Catalysts for High Performance Hydrazine monopropellant Decomposition in Thrusters, for Spacecraft, Satellites, Space probes, Launch Vehicles’ technologies, and Beyond. | Launch Vehicles, satellites, Spacecraft, energy storage technologies constitute an important human endeavour, which requires big investment and highly crucial actions to fulfill the well being of our societies. So, hydrazine is largely used as a liquid propellant in the launch vehicles technologies, which is known to decompose over a shell 405 commercial catalyst to make done the space mission successful. Catalytic hydrazine decomposition over catalysts happens in two ways, indirect pathway which goes via (NH3/N2) intermediate to yield (H2/N2), and direct pathway to (N2/H2). This reaction products might be influenced by catalysts selectivity and reaction conditions such as temperature in the reactor room. Especially, in the satellite motor thruster, it is well known nowadays that metallic supported irridium catalyst plays a fantastic job to make this fuel decomposition, as the shell 405 case. Analysis shows that monometallic (Ir/Al2O3) and bimetallic (Ir-Ru/Al2O3) catalysts behave similarly as to shell 405 catalyst for hydrazine decomposition reaction (HzDR) in the satellite thruster. Also, forms of Ir composite catalysts have shown as powerful candidate for this special catalytic reaction. But, an effective and cheap catalysts based on molybdenum (Mo) catalysts revealed higher catalytic performances for this issue. Here, a significant ways of molybdenum catalysts engineering are fully shown, which exhibited advanced features of molybdenum based composites. In fact, allowing higher catalytic performance in the disintegration of hydrazine in satellite thrusters technologies. Also, these Mo-Catalysts showed a good hydrazine oxidation reaction (HzOR) activity in fuel cell technology, hydrogen evolution (HER) through water splitting, and act as environmental hydrazine sensing platform. Therefore, Mo-based materials could be suggested as the resolver of many catalytic and environmental issues via Mo-hybrid materials engineering technologies. | Mamadou Kalan DIALLO | Catalysis; Earth, Space, and Environmental Chemistry; Environmental Science; Space Chemistry; Heterogeneous Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca54eb69bfb8925a3c221b/original/insights-in-molybdenum-composite-catalysts-for-high-performance-hydrazine-monopropellant-decomposition-in-thrusters-for-spacecraft-satellites-space-probes-launch-vehicles-technologies-and-beyond.pdf |
61718ed28acf7ee7a1c6778c | 10.26434/chemrxiv-2021-6lmr3 | Dual-State Emission in Molecular Rotors with Reorientable Benzotriazole Acceptors | Dual-State Emission (DSE) of organic molecules in both solution and solid-state is an elusive property that has recently drawn significant interest. In this work, we report two molecular rotors 1 and 2 with exceptional photoluminescence (PL) in solution (ФPL = 0.53 and ФPL = 0.43) and in the solid state (ФPL = 0.92 and ФPL = 0.84). To the best of our knowledge, this is the first report containing Donor-pi-Acceptor-pi-Donor (D-pi-A-pi-D) compounds with high quantum yields in both states that features a rotary acceptor. Furthermore, we describe the marked variations in PL in solution upon polarity and viscosity changes. TD-DFT computations indicate that these changes are facilitated by the fast molecular rotation in these molecules. The symmetry (or lack of it) in 1 and 2 plays a crucial role in producing noticeable differences in the X-ray crystal arrays with variations in the solid-state PL. We attribute this DSE behavior to the favorable combination of the D--A--D architecture and the twisted conformations adopted in the solid state. | Lizbeth Rodríguez-Cortés; Federico Hernández; Mario Rodríguez; Rubén Toscano; Arturo Jiménez-Sánchez; Rachel Crespo-Otero; Braulio Rodríguez-Molina | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61718ed28acf7ee7a1c6778c/original/dual-state-emission-in-molecular-rotors-with-reorientable-benzotriazole-acceptors.pdf |
60c7495c469df4070af43bbf | 10.26434/chemrxiv.12055716.v1 | Identification of Compounds from Nigella Sativa as New Potential Inhibitors of 2019 Novel Coronasvirus (Covid-19): Molecular Docking Study. | <p>The spread of the global COVID-19 pandemic,
the lack of specific treatment and the urgent situation requires use of all
resources to remedy this scourge. In the present study, using molecular
docking, we identify new probable inhibitors of COVID-19 by molecules from <i>Nigella
sativa L</i>, which is highly reputed healing herb in North African societies
and both Islamic and Christian traditions.
The discovery
of the M<sup>pro</sup>
protease
structure in COVID-19 provides a great opportunity to identify potential drug
candidates for treatment. Focusing on the main proteases in CoVs (3CL<sup>pro</sup>/M<sup>pro</sup>) (PDB ID 6LU7 and 2GTB); docking of compounds from <i>Nigella Sativa</i> and drugs under
clinical test was performed using Molecular Operating Environment software
(MOE). Nigelledine docked into 6LU7 active site gives energy complex about -6.29734373
Kcal/mol which is close to the energy score
given by chloroquine (-6.2930522 Kcal/mol) and better than energy score given by
hydroxychloroquine (-5.57386112 Kcal/mol)
and favipiravir (-4.23310471 kcal/mol). Docking into 2GTB active site
showed that α- Hederin gives energy score about-6.50204802 kcal/mol whcih is better energy score given by chloroquine (-6.20844936 kcal/mol), hydroxychloroquine (-5.51465893 kcal/mol)) and
favipiravir (-4.12183571kcal/mol). Nigellidine and α- Hederin appeared to have the best potential to act as COVID-19
treatment. Further, researches are necessary to testify medicinal use of
identified and to encourage preventive use of <i>Nigella Sativa </i>against
coronavirus infection.</p> | Salim Bouchentouf; Noureddine Missoum | Biochemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7495c469df4070af43bbf/original/identification-of-compounds-from-nigella-sativa-as-new-potential-inhibitors-of-2019-novel-coronasvirus-covid-19-molecular-docking-study.pdf |
64f4ef5cdd1a73847f1d969a | 10.26434/chemrxiv-2023-swkp8 | Detection of Micron-Sized Chemical Droplets Using a Commodity Digital Camera Setup | The availability, portability, and low cost of electronic devices have made them a prime candidate for the rapid detection of chemical particles. Here we designed a chemical particle detection system based on a Raspberry Pi camera to detect micron droplets generated by ultrasonic atomizers. Through the analysis of sample photos and droplet size, we found that the detection system could clearly image micron-sized particles and accurately measure the particle size. The devices used in this system were all low-cost widely accessible digital cameras, so this detection technique could meet the requirements of low-cost and rapid detection technology, and widely deployed as a practical readout method in chemistry experiments. | Hongli Jiang; S. Hessam M. Mehr | Analytical Chemistry; Imaging; Microscopy; High-throughput Screening | CC BY 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f4ef5cdd1a73847f1d969a/original/detection-of-micron-sized-chemical-droplets-using-a-commodity-digital-camera-setup.pdf |
60c744b39abda21482f8c3ef | 10.26434/chemrxiv.9878948.v1 | Metalloporphyrins into Mesoporous Photonic Crystals: Towards Nanostructured Sensing Devices | <p>Metalloporphyrins
are molecules capable of optically sensing targets due to their
specific reactivity. Shifts in metalloporphyrins spectra are usually
in the order of 30 nm, requiring a spectrophotometer for transducing
the analyte concentration. Mesoporous oxide thin films photonic
crystals (PC) act as optical filters, while their pores can host
molecular moieties. In this work used a metalloporphyrin, Mn<sup>III</sup>
meso-tetra(N-methyl-4-pyridyl) porphyrin (MP), to add a recognition
functionality to a PC and, at the same time, retain their pore
network, in order to develop a versatile and portable sensing device
for volatile amines. The hybrid material MP@PC was prepared by
immersion of the PC, synthesized from two mesoporous oxides with
different refractive index, in an MP solution. The system was
characterized by UV-Vis absorption and FTIR spectroscopies, and SEM
microscopy. Sensing of small molecules was tested using
ethylenediamine (EDA) as a volatile amine model, showing an
absorbance increase in the PC spectral window with promising
analytical parameters. The hybrid material presents enhanced sensing
capabilities compared to MP or PC alone.
A
prototype device was built, aiming for a future design of simple,
low-cost equipment, with a light emitting diode and a light-dependent
resistor, including the MP@PC
sensor.
The device is capable of sensing with only 1.52 μg of MP on a 1 cm<sup>2</sup>
glass slide and it is easily prepared and showed a very small
detection limit.</p> | Rolando M. Caraballo; Diego Onna; Nicolás López Abdala; Galo J.A.A. Soler-Illia; Mariana Hamer | Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b39abda21482f8c3ef/original/metalloporphyrins-into-mesoporous-photonic-crystals-towards-nanostructured-sensing-devices.pdf |
618977fc3c169d46129395c2 | 10.26434/chemrxiv-2021-22c7z | Comparison of Linear Response Theory,
Projected Initial Maximum Overlap Method, and
Molecular Dynamics Based Vibronic Spectra:
The Case of Methylene Blue | Simulation of optical spectra is essential to molecular characterization and, in many cases, critical for interpreting experimental spectra. The most common method for simulating vibronic absorption spectra relies on the geometry optimization and computation of normal modes for ground and excited states. In this report, we show that utilization of such a procedure within an adiabatic linear response theory framework may lead to state mixings and a breakdown of the Born-Oppenheimer approximation, resulting in a poor description of absorption spectra. In contrast, computing excited states via a self-consistent eld method in conjunction with a maximum overlap model produces states that are not subject to such mixings. We show that this latter method produces vibronic spectra much more aligned with vertical excitation procedures, such as those computed from a vertical gradient or molecular dynamics trajectory-based approach. For the methylene blue chromophore, we compare vibronic absorption spectra computed with: an adiabatic Hessian approach with linear response theory optimized
structures and normal modes, a vertical gradient procedure, the Hessian and normal modes of maximum overlap method optimized structures, and excitation energy time correlation functions generated from a molecular dynamics trajectory. Due to mixing between the bright S1 and dark S2 surfaces near the S1 minimum, computing the adiabatic Hessian with linear response theory time-dependent density functional theory with the B3LYP density functional predicts a large vibronic shoulder for the absorption spectrum that is not present for any of the other methods. Spectral densities are analyzed and we compare the behavior of the key normal mode that in linear response theory strongly couples to the optical excitation while showing S1/ S2 state mixings. Overall, our study provides a note of caution in computing vibronic spectra using the excited state adiabatic Hessian of linear response theory optimized structures and also showcases three alternatives that are not as subject to adiabatic state mixing effects. | Ali Abou Taka; Shao-Yu Lu; Duncan Gowland; Tim J. Zuehlsdorff; Hector H. Corzo; Aurora Pribram-Jones; Liang Shi; Hrant P. Hratchian; Christine M. Isborn | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2021-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618977fc3c169d46129395c2/original/comparison-of-linear-response-theory-projected-initial-maximum-overlap-method-and-molecular-dynamics-based-vibronic-spectra-the-case-of-methylene-blue.pdf |
65bd56289138d231614da27a | 10.26434/chemrxiv-2024-z6xsv | A Beginner’s Guide to Simulation of Electroanalytical Experiments using COMSOL Multiphysics® | Electroanalytical methods are fundamental in exploring the kinetics and mechanisms of electrochemical reactions, with widespread applications across the pharmaceutical, corrosion and metal industries, as well as in environmental laboratories. For analytical chemistry students, proficiency in both electroanalytical experiments and simulations is crucial. Simulations allow for the comparison with empirical data, thereby informing experimental design and elucidating reaction mechanisms. This guide caters to analytical chemistry students eager to master electroanalytical simulation using COMSOL Multiphysics. We show how relevant electrochemical equations and principles are implemented in COMSOL. In particular, we cover the simulation of steady-state current, cyclic voltammetry, and differential pulse voltammetry by utilizing the Transport of Diluted Species physics module of COMSOL. | Baosen Zhang; Aliaksei Boika | Theoretical and Computational Chemistry; Analytical Chemistry; Chemical Education; Electrochemical Analysis | CC BY NC 4.0 | CHEMRXIV | 2024-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bd56289138d231614da27a/original/a-beginner-s-guide-to-simulation-of-electroanalytical-experiments-using-comsol-multiphysics.pdf |
679286d081d2151a02a68220 | 10.26434/chemrxiv-2025-1z9j7 | Defluorination Mechanisms and Real-Time Dynamics of Per- and Polyfluoroalkyl Substances on Electrified Surfaces | Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants found in groundwater sources and a wide variety of consumer products. In recent years, electrochemical approaches for the degradation of these harmful contaminants have garnered significant attention due to their efficiency and chemical-free modular nature. However, these electrochemical processes occur in open, highly non-equilibrium systems, and a detailed understanding of PFAS degradation mechanisms in these promising technologies is still in its infancy. To shed mechanistic insight into these complex processes, we present the first constant-electrode potential (CEP) quantum calculations of PFAS degradation on electrified surfaces. These advanced CEP calculations provide new mechanistic details on the intricate electronic processes that occur during PFAS degradation in the presence of an electrochemical bias, which cannot be gleaned from conventional DFT calculations. We complement our CEP calculations with large-scale ab initio molecular dynamics simulations in the presence of an electrochemical bias to provide timescales for PFAS degradation on electrified surfaces. Taken together, our CEP-based quantum calculations provide critical reaction mechanisms for PFAS degradation in open electrochemical systems, which can be used for pre-screening candidate material surfaces and optimal electrochemical conditions for remediating PFAS and other environmental contaminants. | Kamal Sharkas; Bryan Wong | Theoretical and Computational Chemistry; Materials Science; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679286d081d2151a02a68220/original/defluorination-mechanisms-and-real-time-dynamics-of-per-and-polyfluoroalkyl-substances-on-electrified-surfaces.pdf |
627942ab3f1e7c544ab78435 | 10.26434/chemrxiv-2022-cfqhh-v2 | Conformational energy benchmark for longer n-alkane chains | We present the first benchmark set focusing on the conformational energies of highly flexible, long n-alkane chains, termed ACONFL. Unbranched alkanes are ubiquitous building blocks in nature, so the goal is to be able to calculate their properties most accurately to improve the modeling of, e.g, complex (biological) systems. Very
accurate DLPNO-CCSD(T1)/CBS reference values are provided, which allow for a statistical meaningful evaluation of even the best available density functional methods. The performance of established and modern (dispersion corrected) density functionals is comprehensively assessed. The recently introduced r²SCAN-V functional
shows excellent performance, similar to efficient composite DFT methods like B97-3c and r²SCAN-3c, which provide an even better cost-accuracy ratio, while almost reaching the accuracy of much more computationally demanding hybrid or double hybrid functionals with large QZ AO basis sets. In addition, we investigated the performance of common wavefunction methods, where MP2/CBS surprisingly performs worse compared to simple D4 dispersion corrected Hartree–Fock. Furthermore, we investigate the performance of several semiempirical and force field methods, which are commonly used for the generation of conformational ensembles in multilevel workflows or in large scale molecular dynamics studies. Outstanding performance is obtained by the recently introduced general force field, GFN-FF, while other commonly applied methods like the universal force field yield large errors. We recommend the ACONFL as a helpful benchmark set for parameterization of new semiempirical or force field methods and machine learning potentials as well as a meaningful validation set for newly developed DFT or dispersion methods. | Sebastian Ehlert; Stefan Grimme; Andreas Hansen | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627942ab3f1e7c544ab78435/original/conformational-energy-benchmark-for-longer-n-alkane-chains.pdf |
6644f2ee21291e5d1d5d2faa | 10.26434/chemrxiv-2024-v95dn | Path-independent all-visible orthogonal photoswitching for applications in multi-photochromic polymers and molecular computing | Synthetic molecular photoswitches have taken center stage as high-precision tools to introduce light-responsiveness at the smallest scales. Today they are found in all areas of applied chemistry, covering materials research, chemical biology, catalysis, or nanotechnology. For a next step of applicability truly orthogonal photoswitching is highly desirable but to date such fully independent addressability of different photoswitches remains to be extremely challenging. In this work we present the first example of all-visible, all-light responsive, path independent, and fully orthogonal photoswitching. By combining two recently developed indigoid photoswitches - peri-anthracenethioindigo and rhodanine-based chromophore - a four-state system is established and each state can be accessed in very high yields completely independently and also with visible light irradiation only. The four states give rise to four different colors, which can be transferred to a solid polymer matrix yielding a multi-state photochromic material of high versatility. Further, combination with a fluorescent dye as third component is possible elevating applicability in all-photonic molecular logic behavior and information processing with this orthogonal photoswitching system. | Laura Köttner; Henry Dube | Physical Chemistry; Organic Chemistry; Nanoscience; Photochemistry (Org.); Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6644f2ee21291e5d1d5d2faa/original/path-independent-all-visible-orthogonal-photoswitching-for-applications-in-multi-photochromic-polymers-and-molecular-computing.pdf |
60c74ba40f50db74b9396c8b | 10.26434/chemrxiv.12367334.v1 | Ferromagnetic Chain Based on Verdazyl-Nitroxide Diradical | <p>Verdazyl-nitroxide
diradicals were synthesized using the palladium-catalyzed cross-coupling
reaction of the corresponding iodoverdazyls with a nitronyl nitroxide-2-ide
gold(I) complex with high yields (up to 82%). The synthesized diradicals were
found to be highly thermally stable and have a singlet (D<i>E</i><sub>ST</sub> » -64 cm<sup>–1</sup>) or triplet ground state (D<i>E</i><sub>ST</sub> ³ 25 and 100 cm<sup>–1</sup>), depending on which
canonical hydrocarbon diradical type they belong to. Upon crystallization,
triplet diradicals form unique one-dimensional (1D) spin <i>S</i> = 1 chains of organic diradicals with intrachain ferromagnetic
coupling of <i>J</i>′/<i>k</i><sub>B</sub> from 3 to 6 K.</p> | Evgeny Tretyakov; Svetlana Zhivetyeva; Pavel Petunin; Dmitry Gorbunov; Nina Gritsan; Irina Bagryanskaya; Artem Bogomyakov; Pavel Postnikov; Maxim Kazantsev; Marina Trusova; Inna Shundrina; Elena Zaytseva; Dmitriy Parkhomenko; Elena Bagryanskaya; Victor Ovcharenko | Organic Compounds and Functional Groups; Physical Organic Chemistry; Quantum Computing; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ba40f50db74b9396c8b/original/ferromagnetic-chain-based-on-verdazyl-nitroxide-diradical.pdf |
60c742e8337d6cd03ce26af6 | 10.26434/chemrxiv.8797871.v1 | Green Exfoliation of Graphite Flakes to Efficiently Synthesize Biographene | <p>A new simple, rapid, and efficient methodology to produce undamaged graphene sheets from graphite flakes in water by a bio-exfoliation technology is described. The methodology consists in the application of a lipase, with a very exclusive mechanism of interaction with hydrophobic surfaces, combined with a previous mechanical sonication, to selectively generate biographene in water. The adsorption of the lipase on the graphene sheets permits to keep the sheets separated in comparison with other methods. It is possible to obtain more than 80% of graphene (in the form of Few Layer Graphene) from low-cost graphite and with less damage compared to commercial graphene oxide (GO) or reduced GO. Experimental analysis demonstrated the formation of bilayer graphene mainly using lipase from Thermomyces lanuginosus (TLL).</p> | Noelia Losada-Garcia; Angel Berenguer-Murcia; Diego Cazorla-Amorós; Jose M Palomo | Coating Materials; Nanostructured Materials - Materials; Environmental Science; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742e8337d6cd03ce26af6/original/green-exfoliation-of-graphite-flakes-to-efficiently-synthesize-biographene.pdf |
66a10d8501103d79c5803768 | 10.26434/chemrxiv-2024-p5jb1 | Identification of Peptide-Based Hepatitis B Virus Capsid Inhibitors Based on the Viral Core Protein | In this study, we have identified two novel peptides, 19Ac (comprising residues 91-105) and 20Ac (encompassing residues 96-110), from a systematically designed peptide library based on the Hepatitis B virus (HBV) core protein, that inhibit the assembly of HBV capsid. Peptide 20Ac exhibited about twofold the inhibitory potency of 19Ac and proved effective against both standard and morphothiadin (GLS4)-resistant HBV strains. Molecular dynamics simulations revealed that despite their overlapping sequence, 19Ac and 20Ac bonded to different regions of the core protein, thereby inhibiting capsid assembly through distinct mechanisms. These peptides could serve as valuable seed compounds for the further development of HBV capsid inhibitors, including GLS4-resistant strains. | Kazutoshi Kawahara; Junko Fujimoto; Sayuri Takeo; Kohei Sato; Kenji Nakashima; Nobuyuki Mase; Masaru Yokoyama; Tetsuro Suzuki; Tetsuo NARUMI | Biological and Medicinal Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a10d8501103d79c5803768/original/identification-of-peptide-based-hepatitis-b-virus-capsid-inhibitors-based-on-the-viral-core-protein.pdf |
671a57fc83f22e421406ff4f | 10.26434/chemrxiv-2024-hfgls | Hybrid model development emulating linear polarization resistance method towards optimizing dosages of corrosion inhibitors | Models that have been developed for optimizing dosages of a corrosion inhibitor are based on corrosion inhibition efficiencies quantified using costly and time-consuming measurements. The current study proposes a methodology for using corrosion data regularly generated from cooling water circuits of large-scale chemical plants to analyse corrosion mechanisms, predict the corrosion rate, and to potentially optimise dosages of multiple corrosion inhibitors. The hybrid model was developed based on an adaptation of the Butler-Volmer equation. Butler-Volmer parameters such as the anodic charge transfer coefficient were modeled as nonlinear functions of a single component of partial least squares (PLS), containing inhibitor concentrations. A suitable indicator of corrosion inhibition efficiency was identified from the model. Adequately capturing the relationship between inhibitors and the corrosion rate facilitates optimizing dosages of corrosion inhibitors using daily recorded data, without heavily relying on case-specific models and experiments. | Chamanthi Denisha Jayaweera; Ivaylo Hitsov; David Fernandes del Pozo; Elias De Ketelaere; Tom Depover; Sarah Müller; Thomas Diekow; Arne Verliefde; Ingmar Nopens | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Artificial Intelligence; Process Control; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a57fc83f22e421406ff4f/original/hybrid-model-development-emulating-linear-polarization-resistance-method-towards-optimizing-dosages-of-corrosion-inhibitors.pdf |
62c21cfc9ca5bba296f08cf0 | 10.26434/chemrxiv-2022-1ps85 | Synthesis of End-Cap Enabled Self-Immolative Photoresists for Extreme Ultraviolet Lithography | Conventional chemically amplified resists (CARs) rely on the usage of photoacid generators to serve as the source of chemical amplification. However, acid diffusion inevitably accompanies CARs and has led to the resolution, line edge roughness, and sensitivity (RLS) tradeoff, which is the most challenging technical problem for modern photoresists. Herein, we take advantage of the self-immolative property of polyphthalaldehyde (PPA) derivatives to create end-cap enabled chain scissionable resists for extreme ultraviolet (EUV) lithography. The feasibility of this strategy was demonstrated under UV photodegradation experiments. The dose-to-clear (DTC) under EUV radiation was 90 mJ/cm2 for the most promising resist, representing more than a hundredfold improvement over previous PPA resists. Density functional theory (DFT) calculations were conducted to understand the structural origin of end-cap EUV sensitivity. | Jingyuan Deng; Sean Bailey; Ruiwen Ai; Anthony Delmonico; Gregory Denbeaux; Shaoyi Jiang; Christopher Ober | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c21cfc9ca5bba296f08cf0/original/synthesis-of-end-cap-enabled-self-immolative-photoresists-for-extreme-ultraviolet-lithography.pdf |
67d937abfa469535b9a13207 | 10.26434/chemrxiv-2025-nr4f2 | Laser-Engineered Iridium-Based Nanoparticles with High Activity and Stability | Designing high-performance, stable catalysts is essential for electrochemical hydrogen production. Crystalline iridium oxide is one of the few materials that remain stable under the harsh acidic conditions of polymer electrolyte membrane water electrolysis (PEMWE). However, its low activity and iridium scarcity require strategies to enhance atomic utilization. Conventional high-temperature post-synthetic processing increases the share of rutile-phase iridium oxide while promoting particle growth, reducing catalytic activity due to a diminished surface area. Here we present a laser-induced nano oven method using a silicon dioxide matrix as a nanoscale reaction chamber, enabling solid-state nanoparticle synthesis under ambient conditions while preventing agglomeration and allowing precise size control. The synthesized ultra-small crystalline rutile iridium oxide of ~2 nm achieves a high mass activity of 350 ± 15 A gIr-1 at 300 mV overpotential. Analysis using a channel flow cell with on-line inductively coupled plasma mass spectrometry confirms that laser-engineered iridium oxide exhibits superior stability compared to commercial iridium oxide, achieving an optimal balance of activity and stability. Operando electron impact mass spectrometry provided the synthesis mechanistic insights, demonstrating the potential of this strategy for synthesizing ultra-small crystalline metals and metal oxides for various applications. | Huize Wang; Philipp Pfeifer; Wenwei Lai; Andreas Göpfert; Sumin Lim; Wei Zhao; A.Lucía Morales; Mattis Goßler; Marko Malinovic; Pallabi Bhuyan; Walter Parada; Pavlo Nikolaienko; Karl Mayrhofer; Guilherme V. Fortunato; Andreas Hutzler; Marc Ledendecker | Materials Science; Catalysis; Nanoscience; Catalysts; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d937abfa469535b9a13207/original/laser-engineered-iridium-based-nanoparticles-with-high-activity-and-stability.pdf |
60c74421469df45efcf432ab | 10.26434/chemrxiv.9746582.v1 | Ordered B-Site Vacancies in an ABX3 Formate Perovskite | <p>We report the synthesis and structural characterisation of a series of aliovalently doped metal–formate ABX<sub>3</sub> perovskite frameworks [C(NH<sub>2</sub>)<sub>3</sub>]Mn<sup>2+</sup><sub>1–<i>x</i></sub>(Fe<sup>3+</sup><sub>2<i>x</i>/3</sub>,V<sub><i>x</i>/3</sub>)(HCOO)<sub>3</sub> (V = B-site vacancy). For sufficiently large <i>x</i>, the vacancies order, lowering the crystal symmetry from orthorhombic <i>Pnna</i> to monoclinic <i>P</i>2/<i>n</i>. This system establishes B-site vacancies as a new type of defect in formate perovskites, and one with important chemical, structural, and functional implications. Monte Carlo simulations driven by a nearest-neighbour vacancy repulsion model show checkerboard vacancy order to emerge for <i>x</i> > 0.6, in accord with experiment.</p> | Hanna Boström; Jonas Bruckmoser; Andrew Goodwin | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74421469df45efcf432ab/original/ordered-b-site-vacancies-in-an-abx3-formate-perovskite.pdf |
63949e6704bc6663b910730b | 10.26434/chemrxiv-2022-18jdz | A single-crystal copper (111) current collector for anode-free lithium batteries | Anode-free lithium (Li) batteries that function via direct Li plating/stripping from cathodes have led to a surge of interest in metallic lithium as an ideal negative electrode. Despite its great promise, its practical use has been hampered by dendritic growth of Li metal, which results in low coulombic efficiencies and cell shorting. In addition, such dendritic growth of Li makes a larger unoccupied space in the battery, which causes dramatic reduction in volumetric energy density. We report that Li plating is a collective motion of Li adatoms influenced by the crystallographic orientation of the Cu substrate, and that Li adatoms can be redistributed by interacting with individual Cu grains via surface migration. By comparing centimeter-sized single-crystal Cu(111) and Cu(410) foils, we found that Cu(111) foil inhibits dendritic growth of metallic Li and that, per our modeling, this is likely due to the near-zero migration barrier of Li adatoms. We suggest that understanding, and ‘controlling’ the Li adatom surface migration ‘behavior’ opens a new avenue for achieving high-performance anode-free Li batteries. | Min-Ho Kim; Dong Yeon Kim; Yunqing Li; Jeongwoo Seo; Juyoung Kim; Myeong Seon Kim; Minhyeok Kim; Taewon Kim; Ukhyun Jung; Sang-Wook Park; Rodney Ruoff; Dong-Hwa Seo; Sunghwan Jin; Hyun-Wook Lee | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63949e6704bc6663b910730b/original/a-single-crystal-copper-111-current-collector-for-anode-free-lithium-batteries.pdf |
6681746e01103d79c58f2ef5 | 10.26434/chemrxiv-2024-z5cw0 | Regiodivergent Functionalization of Protected and Unprotected Carbohydrates via an Adaptive Activating Strategy | The selective functionalization of carbohydrates holds a central position in synthetic carbohydrate chemistry, driving the ongoing quest for ideal approaches to manipulate these compounds. In this study, we introduce a general strategy that enables the regiodivergent functionalization of saccharides. The use of electron-deficient photoactive 4-tetrafluoropyridinylthio (SPyf) fragment as an adaptable activating group, facilitated efficient functionalization across all saccharide sites. More importantly, this activating group can be directly installed at the C1, C5 and C6 positions of biomass-derived carbohydrates in a single step and in a site-selective manner, allowing for the efficient and precision-oriented modification of unprotected saccharides and glycans. | Shen Cao; Haobo Zhang; Mingshuo Chen; Niming Zhu; Beibei Zhan; Peng Xu; Xiaoping Chen; Biao Yu; Xiaheng Zhang | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6681746e01103d79c58f2ef5/original/regiodivergent-functionalization-of-protected-and-unprotected-carbohydrates-via-an-adaptive-activating-strategy.pdf |
67d9e091fa469535b9ba510e | 10.26434/chemrxiv-2025-r0wcd | Accelerated Chlorination at the Surface of Organic Aerosol | An interface is a distinct chemical environment where reactivity can proceed differently than the bulk. Although organic interfaces are ubiquitous in nature, they have received comparably less attention than their aqueous counterparts. Here we examine the uptake dynamics of chlorine gas at the air/squalene interface to better interpret the anomalous reaction kinetics observed in previous aerosol experiments. Utilizing molecular dynamics simulations and coarse-grained kinetic models, we find evidence that chlorine addition to squalene carbon double bonds at the interface occurs over an order of magnitude faster than in the bulk. This acceleration is due to enhanced probability and frequency of encounter between a chlorine molecule and a double bond at the air-oil interface. | Liron Cohen; Amro Dodin; Kevin Wilson; David Limmer | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Computational Chemistry and Modeling; Interfaces; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d9e091fa469535b9ba510e/original/accelerated-chlorination-at-the-surface-of-organic-aerosol.pdf |
64e32312694bf1540cb71235 | 10.26434/chemrxiv-2023-8p491 | Thermoelectric properties of Pnma and R3m GeS and
GeSe | With ∼60 % of global energy lost as heat, technologies such as thermoelectric generators (TEGs) are an important route to enhancing the efficiency of energy-intensive processes. Optimising thermoelectric (TE) materials requires balancing a set of interdependent physical properties to meet efficiency, cost and sustainability requirements, and is a complex materials-design challenge. In this study, we demonstrate a fully first-principles modelling approach to calculating the properties and thermoelectric figure of merit ZT and apply it to the orthorhombic and rhombohedral phases of GeS and GeSe. We predict a large ZTmax = 2.12 for n-doped Pnma GeSe at 900 K, which would make it a good match for p-type SnSe in a thermoelectric couple. In contrast to the more usual p-type doping, the electrical conductivity σ is largest along the layering direction, which would combine with the low κlatt to produce a much larger ZTmax > 3 if the growth direction could be controlled. We
also predict that p-doped R3m GeS and GeSe can achieve an industrially-viable ZT > 1, through a high σ counterbalanced by a large thermal conductivity, and experiments indicate this can be further improved by alloying. Our results therefore strongly motivate further study of the under-explored Ge chalcogenides as prospective TEs, with particular focus on strategies for n-doping the Pnma phases. | Min Zhang; Joseph Flitcroft; Sophie Guillemot; Jonathan Skelton | Physical Chemistry; Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e32312694bf1540cb71235/original/thermoelectric-properties-of-pnma-and-r3m-ge-s-and-ge-se.pdf |
6632843e21291e5d1d2d4a30 | 10.26434/chemrxiv-2024-b9rw6 | Active learning of ligands that enhance perovskite nanocrystal luminescence | Ligands play a critical role in the optical properties and chemical stability of colloidal nanocrystals (NCs), but identifying ligands that can enhance NC properties is daunting given the high dimensionality of chemical space. Here we use machine learning (ML) and robotic screening to accelerate the discovery of ligands that enhance the photoluminescence quantum yield (PLQY) of CsPbBr3 perovskite NCs. We developed a ML model designed to predict relative PL enhancement of a perovskite NC when it is coordinated with a ligand selected from a pool of 29,904 candidate molecules. Ligand candidates were selected using an active learning (AL) approach that accounted for uncertainty quantified by twin regressors. After seven experimental iterations of batch AL (corresponding to 21 initial and 72 model-recommended ligands), the uncertainty of the model decreased, demonstrating increased confidence in the model predictions. Feature importance and counterfactual analyses on model predictions illustrate the potential use of ligand field strength in designing PL enhancing ligands. Our versatile AL framework can be readily adapted to screen the effect of ligands on a wide range of colloidal nanomaterials. | Min A Kim; Qianxiang Ai; Alexander J. Norquist; Joshua Schrier; Emory M Chan | Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6632843e21291e5d1d2d4a30/original/active-learning-of-ligands-that-enhance-perovskite-nanocrystal-luminescence.pdf |
60c747bbbdbb893b65a38e65 | 10.26434/chemrxiv.6955355.v2 | Chemical targeting of voltage sensitive dyes to specific cells and molecules in the brain | Voltage sensitive fluorescent dyes (VSDs) are important tools for probing signal transduction in neurons and other excitable cells. These sensors, rendered highly lipophilic to anchor the conjugated pi-wire molecular framework in the membrane, offer several favorable functional parameters including fast response kinetics and high sensitivity to membrane potential changes. The impact of VSDs has, however, been limited due to the lack of cell-specific targeting methods in brain tissue or living animals. We address this key challenge by introducing a non-genetic molecular platform for cell- and molecule-specific targeting of synthetic voltage sensitive dyes in the brain. We employ a dextran polymer particle to overcome the inherent lipophilicity of voltage sensitive dyes by dynamic encapsulation, and high-affinity ligands to target the construct to specific neuronal cells utilizing only native components of the neurotransmission machinery at physiological expression levels. Dichloropane, a monoamine transporter ligand, enables targeting of dense dopaminergic axons in the mouse striatum and sparse noradrenergic axons in the mouse cortex in acute brain slices. PFQX in conjunction with ligand-directed acyl imidazole chemistry enables covalent labeling of AMPA-type glutamate receptors in the same brain regions. Probe variants bearing either a classical electrochromic ANEP dye or state-of-the-art VoltageFluor-type dye respond to membrane potential changes in a similar manner to the parent dyes, as shown by whole-cell patch recording. We demonstrate the feasibility of optical voltage recording with our probes in brain tissue with one-photon and two-photon fluorescence microscopy and define the signal limits of optical voltage imaging with synthetic sensors under a low photon budget determined by the native expression levels of the target proteins. We envision that modularity of our platform will enable its application to a variety of molecular targets and sensors, as well as lipophilic drugs and signaling modulators. This work demonstrates the feasibility of a chemical targeting approach and expands the possibilities of cell-specific imaging and pharmacology. | Tomas Fiala; Jihang Wang; Matthew Dunn; Peter Šebej; Se Joon Choi; Ekeoma Nwadibia; Eva Fialova; Diana M. Martinez; Claire E. Cheetham; Keri J. Fogle; Michael J. Palladino; Zachary Freyberg; David Sulzer; Dalibor Sames | Imaging; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747bbbdbb893b65a38e65/original/chemical-targeting-of-voltage-sensitive-dyes-to-specific-cells-and-molecules-in-the-brain.pdf |
667591f85101a2ffa8265ff0 | 10.26434/chemrxiv-2024-txqzj | Deciphering the Energy Use Channels in Soil Organic Matter: Impacts of Long-term Farmyard Manure Addition and Microbial Necromass Revealed by LC-FT-ICR-MS | Soil organic matter (SOM) plays a central role in the global carbon cycle and contributes to storage of C and energy in soils. Farmyard manure (FYM) addition to arable soils is a measure to increase SOM content, microbial activity and abundance of microbial metabolites (e.g., necromass (NM) markers). However, understanding the mechanistic links between soil dynamics and energy storage is hampered due to the chemical complexity of SOM. Non-targeted molecular-level methods like liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FT-ICR-MS) can be used to explore the complex dynamics of SOM, revealing energetic fingerprints and long-term changes in SOM due to FYM addition. We compared water-extractable organic matter (WEOM) from soils of four long-term FYM addition experiments with representative WEOM signatures from maize, bacterial and fungal NM. Long-term FYM addition increased the complexity of WEOM, most pronounced in polar, unsaturated, oxidised and energy-poor compounds. These changes were linked to a 2-3-fold increase in bacterial, plant and fungal NM signatures. Especially bacterial NM in FYM-amended WEOM indicated a shift in dominant energy use channels. Control soils showed a much lower overlap with all NMs, but indicated a higher dominance of fungal energy-use channels, especially for N-containing compounds. A large fraction of WEOM signals (79% in FYM-amended, 94% in control soils) was unrelated to any of the three NM signatures, and was also mainly responsible for the shift in nominal oxidation state of carbon (NOSC) between the fertilisation treatments. LC-FT-ICR-MS provided access to ~600 novel microbial NM markers which are readily soluble and compositionally distinct from classical NM markers (ergosterol, aminosugars, etc.). Overall, we highlight novel insights into NM contribution to SOM by LC-FT-ICR-MS, and how it can assist to constrain compositional and energetic impacts of FYM addition on soils. | Konstantin Stumpf; Carsten Simon; Anja Miltner; Thomas Maskow; Oliver Lechtenfeld | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Soil Science; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667591f85101a2ffa8265ff0/original/deciphering-the-energy-use-channels-in-soil-organic-matter-impacts-of-long-term-farmyard-manure-addition-and-microbial-necromass-revealed-by-lc-ft-icr-ms.pdf |
64dfdd7e694bf1540c968aca | 10.26434/chemrxiv-2023-1sdz7 | Isolation and Characterization of a U≡C Triple Bond in Isolable Fullerene Compounds | Despite decades of efforts, the actinide-carbon triple bond has remained an elusive target, defying isolation in any compound. Herein, we report the successful stabilization of uranium-carbon triple bonds in carbide-bridged bimetallic [U≡C−Ce] units encapsulated inside fullerene cages of C72 and C78. The molecular structures of UCCe@C2n and the nature of the U≡C triple bond were characterized through X-ray crystallography and various spectroscopic analyses, revealing very short uranium-carbon bonds of 1.921(6) and 1.930(6) Å, with the metals existing in their highest oxidation states of +6 and +4 for uranium and cerium, respectively. Quantum-chemical studies further demonstrate that the C2n cages are crucial for stabilizing the [UVI≡C−CeIV] units through covalent and coordinative interactions. This work offers a new fundamental understanding of the elusive uranium-carbon triple bond and informs the design of complexes with similar bonding motifs, opening up new possibilities for creating distinctive molecular compounds and materials. | Yang-Rong Rao; Jing Zhao; Qingyu Meng; Hu Han-Shi; Min Guo; Yingjing Yan; Jiaxin Zhuang; Shangfeng Yang; Skye Fortier; Luis Echegoyen; Eugen Schwarz; Jun Li; Ning Chen | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bonding; Lanthanides and Actinides; Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dfdd7e694bf1540c968aca/original/isolation-and-characterization-of-a-u-c-triple-bond-in-isolable-fullerene-compounds.pdf |
62ba0ae658b3d6613461d1f2 | 10.26434/chemrxiv-2022-n304h-v2 | Best Practice DFT Protocols for Basic Molecular Computational Chemistry | Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties.
The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets.
This work provides best-practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts:
Firstly, we set the stage and introduce a step-by-step decision tree to choose a computational protocol that models the experiment as closely as possible.
Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand.
A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi-level approaches.
Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices. | Markus Bursch; Jan-Michael Mewes; Andreas Hansen; Stefan Grimme | Theoretical and Computational Chemistry; Chemical Education; Chemical Education - General; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ba0ae658b3d6613461d1f2/original/best-practice-dft-protocols-for-basic-molecular-computational-chemistry.pdf |
60c747f9337d6c5bf2e27446 | 10.26434/chemrxiv.11826771.v1 | Highly Basic Solid Catalyst Obtained by Spray Drying of a NaAlO2 and Boehmite Suspension for the Upgrading of Glycerol to Acetins | <p>In
here, we present the low-cost production of NaAlO<sub>2</sub>-Al<sub>2</sub>O<sub>3</sub>
catalysts, which exhibit high activity in the transesterification of methyl
acetate with glycerol to obtain acetins. The catalyst preparation procedure is
based on the spray drying of a colloidal boehmite suspension, supplemented with
a sodium aluminate (NaAlO<sub>2</sub>) solution using a pilot scale spray
drier. Upon subsequent calcination, we obtain spherical micro particles
presenting a homogeneous dispersion of sodium aluminate and featuring high
basicity. The NaAlO<sub>2</sub> loading has a marked impact on the basicity and
textural properties of the final materials. These solids are found to be
efficient heterogeneous base catalysts for the upgrading of glycerol (which is
essentially a waste) to glycerol acetins (which are important bio-based fuel
additives). With 100 mg of the catalyst loaded with 20 wt.% of NaAlO<sub>2</sub>,
a conversion of 96 % is obtained after 4 h of reaction at 60 °C (10 mmol of
glycerol + 100 mmol of methyl acetate). Importantly, the selectivity for
triacetin is as high as 20 % (the rest being 50 % of diacetin and 30 % of
monoacetin). The catalysts act strictly in a heterogeneous way and are
recyclable.</p> | Sreerangappa Ramesh; Makhlouf Amoura; Damien Debecker | Catalysts; Inorganic Acid/Base Chemistry; Base Catalysis; Heterogeneous Catalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747f9337d6c5bf2e27446/original/highly-basic-solid-catalyst-obtained-by-spray-drying-of-a-na-al-o2-and-boehmite-suspension-for-the-upgrading-of-glycerol-to-acetins.pdf |
62bed4f352acb7a3757aa386 | 10.26434/chemrxiv-2022-68g56 | Photoinduced Amyloid Fibril Degradation for Controlled Cell
Patterning
| Amyloid-like fibrils are a special class of self-assembling peptides that have emerged as a promising nanomaterial with rich bioactivity for applications such as cell adhesion and growth. Unlike the extracellular matrix, the intrinsically stable amyloid-like fibrils do not respond nor adapt to stimuli of their natural environment. Here, we designed a self-assembling motif (CKFKFQF), in which a photosensitive o-nitrobenzyl linker (PCL) was inserted. This peptide (CKFK-PCL-FQF) assembled into amyloid-like fibrils comparable to the unsubstituted CKFKFQF and revealed a strong response to UV-light. After UV irradiation, the secondary structure of the fibrils, fibril morphology and bioactivity were lost. Thus, coating surfaces with the pre-formed fibrils and exposing them to UV-light through a photomask generated well-defined areas with patterns of intact and destroyed fibrillar morphology. The unexposed, fibril-coated surface areas retained their ability to support cell adhesion in culture, in contrast to the light-exposed regions, where the cell-supportive fibril morphology was destroyed. Consequently, the photoresponsive peptide nanofibrils provide a facile and efficient way of cell patterning, exemplarily demonstrated for A549 cells. This study introduces photoresponsive amyloid-like fibrils as adaptive functional materials to precisely arrange cells on surface. | Kübra Kaygisiz; Adriana Maria Ender; Jasmina Gačanin; Lara Alix Kaczmarek ; Dimitrios A. Koutsouras; Abin N. Nalakath; Pia Winterwerber; Franz J. Mayer; Hans-Joachim Räder; Tomasz Marszalek; Paul W. M. Blom; Christopher V. Synatschke ; Tanja Weil | Polymer Science; Nanoscience; Biopolymers; Polymer morphology; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bed4f352acb7a3757aa386/original/photoinduced-amyloid-fibril-degradation-for-controlled-cell-patterning.pdf |
62d885925819870883496535 | 10.26434/chemrxiv-2022-h8l06 | Separation of Dissolved Organic Matter (DOM) and Per- and Polyfluoro-Alkyl Substances (PFAS) from Landfill Leachate Using Modified Coal Fly-Ash (CFA) | Per and Poly-fluoroalkyl Substances (PFAS) has been a major subject of research in environmental sector ever since it was found in the environment and blood serums at toxic levels. As landfills are the final disposal method for majority of the waste, PFAS concentration in landfill leachate have been found in the range of few µg/L to mg/L. Only few conventional treatments such as Activated Carbon, Reverse Osmosis, and Ion-Exchange has been proven effective in removing PFAS. However, these treatment methods are proving to be very expensive and generate secondary contamination that needs to be disposed-off or treated. Since the phase out of C8-PFAS compounds, more short chain PFAS compounds are detected in landfill leachate. Hence, an effective treatment strategy is needed to keep up with the rising concentration levels and variety of PFAS compounds. The purpose of this study was to develop a sustainable and cost-effective process using modified Coal Fly-Ash (CFA) that can treat both short chain and long chain PFAS compounds. Previous studies have shown application of CFA in removal of dye and metals from different types of wastewaters. In previous studies CFA was modified to enhance its surface properties, that can improve the adsorption of organic and anionic contaminants. In this study, thermo-chemical modification was used on CFA to remove organic matter and PFAS compounds. Preliminary results showed that, CFA can remove more than 90% UV absorbance, more than 80% TOC and approximately 40% of total PFAS compounds. The maximum adsorption capacity for total PFAS was found to be 84 ng PFAS per g CFA, out of which 70 ng was for short chain PFAS and 14 ng for long chain PFAS compounds. An effective removal of organic matter and PFAS compounds, show a promising application of CFA in leachate treatment. However, further research is needed to analyze the adsorption dynamics, kinetics, post-treatment disposal method, and any possible contamination when mixing CFA with landfill leachate. | Harsh Patel; Myles Greer; Kang Xia; Zhiwu Wang; Brian Brazil; Chamindu Liyanapatirana; Sameer Hamoush; Renzun Zhao | Organic Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d885925819870883496535/original/separation-of-dissolved-organic-matter-dom-and-per-and-polyfluoro-alkyl-substances-pfas-from-landfill-leachate-using-modified-coal-fly-ash-cfa.pdf |
672a243af9980725cf2cc6ad | 10.26434/chemrxiv-2024-6q9mp | DETECTION OF HYDROQUINONE WITH
ELECTROCHEMICAL SENSOR USING
MXene/Poly Alanine MODIFIED ELECTRODE | Phenolic compounds are extensively used in environmental protection, food safety, and human
health, making their detection a critical concern. Hydroquinone, a widely used isomer of dihydroxy
benzene, is classified as a priority pollutant by the US Environmental Protection Agency (EPA)
and the European Union (EU). In this study, we developed a robust and sensitive method for
detecting hydroquinone (HQ). The sensor was created by sequentially depositing Titanium carbide
(Ti3C2Tx, MXene) and L-alanine on a glassy carbon electrode (GCE). The sensor demonstrated a
linear correlation between current and concentration in the range of 30 × 10−6 mol L−1 to 100 ×
10 −6 mol L−1. Additionally, pH and scan rate optimizations were performed to achieve the best
affinity conditions between the analytes and the electrode surface. | Shakib Mahmud Ayon; Ruhul Amin; Romzan Ali; Abdul Khaleque; Zaved Hossain Khan | Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a243af9980725cf2cc6ad/original/detection-of-hydroquinone-with-electrochemical-sensor-using-m-xene-poly-alanine-modified-electrode.pdf |
6518da64ade1178b246fad95 | 10.26434/chemrxiv-2023-1pz58 | Utilizing an Improved EXAFS Structure Analysis Method to Reveal Site-Specific Bonding Properties of Ag44(SR)30 Nanoclusters | Atomically precise nanoclusters (NCs) are of great interest due to their well-defined structures and molecule-like properties. Understanding their structure-property relationship is an important task because it can help tailor their structures to achieve specific desired properties. In this study, the temperature-dependent bonding properties of Ag44(SR)30 have been revealed by the extended X-ray absorption fine structure (EXAFS) with a new structure analysis method, which includes two Ag-S and two Ag-Ag fitting shells. It has been proven that the EXAFS fitting quality can be improved significantly compared with the conventional method. New insights into Ag-S bondings were discovered based on the fitting results obtained from the new method. It allows us to observe two different bonding properties within the Ag-S motifs, which cannot be discovered by using the conventional method. Additionally, the metal core of Ag44(SR)30 exhibits uncommon thermal behavior, which could be connected to the absence of the center atom in the icosahedral core. Our results demonstrate that the new structure analysis method can provide a more reliable comparison of NCs structural changes than the conventional method and it could be applicable to other NCs. The revealed temperature-dependent bonding properties can provide insights into the structure-property relationship of Ag44(SR)30, which can help design new NCs materials with tailored properties. | Ziyi Chen; Daniel Chevrier; Brian Conn; Terry Bigioni; Peng Zhang | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6518da64ade1178b246fad95/original/utilizing-an-improved-exafs-structure-analysis-method-to-reveal-site-specific-bonding-properties-of-ag44-sr-30-nanoclusters.pdf |
65b8d7199138d2316108c7f5 | 10.26434/chemrxiv-2024-5s3qd | Band gap engineering in pyridyl-functionalized two-dimensional (2D) CuSCN coordination polymers | Copper(I) thiocyanate (CuSCN) has emerged as an excellent hole-transporting semiconductor with applications spanning across electronic and optoelectronic fields. The coordination chemistry of CuSCN allows for extensive structural versatility via ligand modification. In this work, we have developed a synthetic method that reliably produces phase pure [Cu(SCN)(3-XPy)]n complexes (Py = pyridyl; X = OMe, H, Br, and Cl) in a 1:1:1 ratio to yield two-dimensional (2D) structures with a Cu-SCN network. The single crystal structure of [Cu(SCN)(3-OMePy)]n is also reported herein. Complexes with X = OMe and H show similar structures, in which the 2D layers are analogous to the buckled 2D sheets of silicene or blue phosphorene. On the other hand, for complexes with X = Br and Cl, their rippled 2D structures resemble the puckered 2D sheets found in black phosphorene. The variation of the electron-withdrawing ability of the substituent group is found to systematically shift the electronic energy levels and band gaps of the complexes, allowing the 2D CuSCN-based materials to display optical absorptions and emissions in the visible range. In addition, first-principles calculations reveal that the drastic change in the electronic levels is a result of the emergence of the Py ligand electronic states below the SCN states. This work demonstrates that the structural, electronic, and optical properties of 2D Cu-SCN networks can be systematically tailored through ligand modification. | Jetnipat Songkerdthong; Thanasee Thanasarnsurapong; Adisak Boonchun; David J. Harding; Pichaya Pattanasattayavong | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b8d7199138d2316108c7f5/original/band-gap-engineering-in-pyridyl-functionalized-two-dimensional-2d-cu-scn-coordination-polymers.pdf |
6697af37c9c6a5c07a86ffb1 | 10.26434/chemrxiv-2024-4xgxp | Spatially Offset Raman Spectroscopy (SORS) for sustainable Olive Oil authentication - tackling the challenges in on-site food control | While olive oil production faces many challenges and prices are strongly increasing the de-mand for non-invasive analysing methods is high. The spatially offset Raman spectroscopy (SORS) can be a potential method for a sustainable food analysis since it can penetrate dif-ferent kinds of containers while giving a good spectrum of the food of interest. In this study, we developed a SORS-based method for the authentication of olive oils. Based on a dataset of verified oils of four sample groups we developed an analysis strategy using plotting, prin-cipal component analysis as well as a classification and regression model. This analysis strategy was tested in food inspections of different companies. The results show, that our strategy was successful for on-site analysis and earned positive feedback from the involved parties. In an additional validation step, we analysed 30 online retail samples where we were able to differentiate between actual adulterated and authentic olive oil samples. | Anna Lena Horns; Sarah-Marie Barmbold; Markus Weidner; René Bachmann | Analytical Chemistry; Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6697af37c9c6a5c07a86ffb1/original/spatially-offset-raman-spectroscopy-sors-for-sustainable-olive-oil-authentication-tackling-the-challenges-in-on-site-food-control.pdf |
643c03bc73c6563f14fae441 | 10.26434/chemrxiv-2023-sxnbn-v2 | Enhancement of the Solar Water Splitting Efficiency Mediated by Surface Segregation in Ti-doped Hematite Nanorods | Band engineering is employed thoroughly and targets technologically scalable photoanodes for solar water splitting applications. Complex and costly recipes are necessary, often for average performances. Here we report simple photoanode growth and thermal annealing, with effective band engineering results. By comparing Ti-doped hematite photoanodes annealed under Nitrogen to photoanodes annealed in air, we found strongly enhanced photocurrent, of more than 200 % in the first case. Using electrochemical impedance spectroscopy and synchrotron X-rays spectromicroscopies we demonstrate that oxidized surface states and increased density of charge carriers are responsible for the enhanced photoelectrochemical activity. Surface states are found to be related to the formation of pseudo-brookite clusters by surface Ti segregation. Spectro-ptychography is used for the first time at Ti L3 absorption edge to isolate Ti chemical coordination arising from pseudo-brookite clusters contribution. Correlated with electron microscopy investigation and Density Functional Theory (DFT) calculations, the synchrotron spectromicroscopy data prove unambiguously the origin of the better photoelectrochemical activity of N2- annealed Ti-doped hematite nanorods. Finally, we present here a handy and cheap surface engineering method, beyond the known oxygen vacancy doping, allowing a net gain in the photoelectrochemical activity for the hematite-based photoanodes. | Stefan Stanescu; Théo Alun; Yannick J. Dappe; Dris Ihiawakrim; Ovidiu Ersen; Dana Stanescu | Materials Science; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2023-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643c03bc73c6563f14fae441/original/enhancement-of-the-solar-water-splitting-efficiency-mediated-by-surface-segregation-in-ti-doped-hematite-nanorods.pdf |
666fd3ee01103d79c5615cd8 | 10.26434/chemrxiv-2024-rcj48 | Room-Temperature Solution Fluorescence Excitation Correlation Spectroscopy | Single-molecule fluorescence spectroscopy is a powerful tool to investigate the physical properties of individual molecules. Yet, elucidating the fast fluctuation dynamics of freely diffusing single molecules in solution at room temperature, where a variety of chemical and biological processes occur, remains challenging. In this study, we report on fluorescence excitation correlation spectroscopy (FECS) of room-temperature solutions, which enables the study of spontaneous fluctuation of the excitation spectrum with microsecond time resolution. By employing Fourier transform spectroscopy with broadband femtosecond pulses and time-correlated single-photon counting, we achieved fluorescence excitation spectroscopy of a room-temperature solution at the single-molecule level. Building upon this single-molecule measurement, we obtained an excitation wavelength-resolved fluorescence autocorrelation function in the microsecond to millisecond range, demonstrating the potential of this method to elucidate fast, spontaneous, time-dependent changes of excitation spectra in statistically equilibrium systems. With further development, this method will allow the study of spectral exchange associated with transitions between sub-ensembles of solution-phase molecules with unprecedented time resolution. | Yusuke Yoneda; Hikaru Kuramochi | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666fd3ee01103d79c5615cd8/original/room-temperature-solution-fluorescence-excitation-correlation-spectroscopy.pdf |
60c7538cbb8c1a46283dc082 | 10.26434/chemrxiv.13513161.v1 | Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease | <div>
<div>
<div>
<p>Computational analysis of protein-ligand interactions is of crucial importance for drug
discovery. Assessment of ligand binding energy allows us to have a glimpse on the potential
of a small organic molecule to be a ligand to the binding site of a protein target. Available
scoring functions such as in docking programs, we could say that they all rely on equations
that sum each type of protein-ligand interactions to model the binding affinity. Most of the
scoring functions consider electrostatic interactions involving the protein and the ligand.
Electrostatic interactions contribute one of the most important part of total interaction energies
between macromolecules, unlike dispersion forces they are highly directional and therefore
dominate the nature of molecular packing in crystals and in biological complexes and
contribute significantly to differences in inhibition strength among related enzyme inhibitors. In
this paper, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and Darunavir)
have been analysed using charge densities from a transferable aspherical-atom data bank.
Moreover, we analyse the electrostatic interaction energy for an ensemble of structures using
molecular dynamic simulation to highlight the main features related to the importance of this
interaction for binding affinity.
</p>
</div>
</div>
</div> | Prashant Kumar; Paulina Dominiak | Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7538cbb8c1a46283dc082/original/combining-molecular-dynamic-information-and-an-aspherical-atom-data-bank-in-the-evaluation-of-the-electrostatic-interaction-energy-in-multimeric-protein-ligand-complex-a-case-study-for-hiv-1-protease.pdf |
60c773d3f96a0043f328916a | 10.26434/chemrxiv.14747850.v1 | Unveiling Extreme Photoreduction Potentials of Donor-Acceptor Cyanoarenes to Access Aryl Radicals from Aryl Chlorides | Since the seminal work of Zhang
in 2016, donor-acceptor cyanoarene-based fluorophores, such as
1,2,3,5-tetrakis(carbazol-9-yl)-4,6-dicyanobenzene (4CzIPN), have been widely applied
in photoredox catalysis, and used as excellent metal-free alternatives to noble
metal Ir- and Ru-based photocatalysts. However, all the reported photoredox
reactions involving this chromophore family are based on harnessing the energy
from a single visible light photon, with a limited range of redox potentials
from -1.92 V to +1.79 V. Here, we document the unprecedented discovery that
this family of fluorophores can undergo consecutive photoinduced electron
transfer (ConPET) to achieve very high reduction potentials. One of the newly
synthesized catalysts, 2,4,5-tri(9H-carbazol-9-yl)-6-(ethyl(phenyl)amino)isophthalonitrile
(3CzEPAIPN), possesses a long-lived (12.95 ns) excited radical anion form, 3CzEPAIPN<sup>•</sup><sup>−</sup>*, which can be used to activate reductively
recalcitrant aryl chlorides (E<sub>red </sub>≈ -1.9 to -2.9 V) under mild
conditions. The resultant aryl radicals can be engaged in synthetically
valuable aromatic C-B, C-P, and C-C bond formation to furnish arylboronates,
arylphosphonium salts, arylphosphonates, and spirocyclic cyclohexadienes,
respectively. | Jinhui Xu; Jilei Cao; Xiangyang Wu; Han Wang; Xiaona Yang; Xinxin Tang; Ren Wei Toh; Rong Zhou; Edwin K. L. Yeow; Jie Wu | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c773d3f96a0043f328916a/original/unveiling-extreme-photoreduction-potentials-of-donor-acceptor-cyanoarenes-to-access-aryl-radicals-from-aryl-chlorides.pdf |
60c740e5337d6cf58ce267ac | 10.26434/chemrxiv.7873298.v1 | Effect of Symmetric and Asymmetric Substitution on the Optoelectronic Properties of 9,10-Dicyanoanthracene | <div>
<div>
<div>
<p>A set of substituted 9,10-dicyanoanthracenes (DCA) has been synthesized, their photophysical
and electrochemical properties in liquid solution have been characterized and supplemented by
high level ab initio quantum chemical calculations. Three different methoxy-group-containing substituents have been linked to the DCA core in a symmetric and asymmetric fashion to produce six
different species with strong quadrupole and dipole moments, respectively. The major difference
between the symmetrically and asymmetrically substituted species are the enhanced two-photon
absorption intensities of the former. In most of the cases studied, the molecules show reasonably large optical transition probabilities. The fluorescence brightness of these substances makes
them interesting objects for two-photon absorption applications. Additionally, all molecules can be
both easily reduced and oxidized electrochemically and are therefore suitable for optoelectronic
applications.
</p>
</div>
</div>
</div> | Arnulf Rosspeintner; Florian Glöcklhofer; Pakorn Pasitsuparoad; Simon Eder; Johannes Fröhlich; Gonzalo Angulo; Eric Vauthey; Felix Plasser | Organic Synthesis and Reactions; Optical Materials; Photochemistry (Physical Chem.); Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e5337d6cf58ce267ac/original/effect-of-symmetric-and-asymmetric-substitution-on-the-optoelectronic-properties-of-9-10-dicyanoanthracene.pdf |
66a05468c9c6a5c07aae574d | 10.26434/chemrxiv-2024-2xrx4 | DEL+ML paradigm for actionable hit discovery – a cross DEL and cross ML model assessment. | DNA-Encoded Library (DEL) technology allows the screening of millions, or even billions, of encoded compounds in a pooled fashion which is faster and cheaper than traditional approaches. These massive amounts of data related to DEL binders and not-binders to the target of interest enable Machine Learning (ML) model development and screening of large, readily accessible, drug-like libraries in an ultra-high-throughput fashion. Here, we report a comparative assessment of the DEL+ML pipeline for hit discovery using three DELs and five ML models (fifteen DEL+ML combinations using two different feature representations). Each ML model was used to screen a diverse set of drug-like compound collections to identify orthosteric binders of two therapeutic targets, Casein kinase 1𝛼/δ (CK1𝛼/δ). Overall, 10% and 94% of the predicted binders and not-binders were confirmed in biophysical assays, including two nanomolar binders (187 and 69.6 nM affinity for CK1𝛼 and CK1δ, respectively). Our study provides insights into the DEL+ML paradigm for hit discovery: the importance of an ensemble ML approach in identifying a diverse set of confirmed binders, the usefulness of large training data and chemical diversity in the DEL, and the significance of model generalizability over accuracy. We shared our results via an open-source repository for further use and development of similar efforts. | Sumaiya Iqbal; Wei Jiang; Eric Hansen; Tonia Aristotelous; Shuang Liu; Andrew Reidenbach; Cerise Raffier; Alison Leed; Chengkuan Chen; Lawrence Chung; Eric Sigel; Alex Burgin; Sandy Gould; Holly Soutter | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a05468c9c6a5c07aae574d/original/del-ml-paradigm-for-actionable-hit-discovery-a-cross-del-and-cross-ml-model-assessment.pdf |
6754ad507be152b1d04399dc | 10.26434/chemrxiv-2024-n31lx-v2 | MoleCol.py: A Framework to Simulate Molecular Collisions | Although usually ignored for a more intuitive macroscopic understanding, molecular collisions are the foundation of almost every chemical event - from chemical reactions to transport phenomena. On the molecular level, a chemical reaction is an exchange (or sometimes knocking off) of atoms between molecules as a result of energetically significant collisions. The current simulation paradigm is based on simulating bulks of molecules, requiring high computational resources. In such simulations sometimes the molecules are not allowed to react, as in the case of classical MD, or require a significant amount of computational resources and time to conclude, as in the case of ab initio MD. Without any fine-tuning to allow a more outcome-oriented approach, the results of such simulations require even more computational resources and sometimes human effort to analyze for meaningful results. To answer these limitations, a novel methodology is developed based on a more fine-tuned approach for simulations. Its Python implementation based on current state-of-the-art libraries and supporting applications based on globally accessible web technologies is presented as a software framework. Collider.py focuses on fine-tuning the collision parameters before running the simulation. Individual linear velocities, positions, and orientations of the molecules can be defined as well as the impact points on each molecule. Our framework is based on ASE - a computational chemistry library for Python and consists of a web application to design the collisions in detail. | Ömer Özyıldırım | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6754ad507be152b1d04399dc/original/mole-col-py-a-framework-to-simulate-molecular-collisions.pdf |
66105b8821291e5d1d2b6d2e | 10.26434/chemrxiv-2024-trc0j | Towards an Ab-initio Description of Adsorbate Surface Dynamics | The advent of machine learning potentials (MLPs) provides a unique opportunity to access simulation timescales and to directly compute physiochemical properties that are typically intractable using density functional theory (DFT). In this study, we use an active learning curriculum to train a generalizable MLP using the DeepMD-kit architecture. The resulting model, which provides DFT-level accuracy, is used to investigate the diffusion of key surface-bound adsorbates on a Ag(111) facet using sufficiently long MLP-based molecular dynamics (MD) simulations. The MLP/MD-calculated diffusivities, obtained at three different temperatures, demonstrates the potential shortcomings of DFT-based nudged elastic band calculations that are widely employed to study diffusion. While this work has focused on a few simple adsorbates, the resulting model is transferable and can be fine-tuned to study other adsorbates that were not included in the initial training dataset. | Saurabh Sivakumar; Ambarish Kulkarni | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Chemical Kinetics | CC BY 4.0 | CHEMRXIV | 2024-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66105b8821291e5d1d2b6d2e/original/towards-an-ab-initio-description-of-adsorbate-surface-dynamics.pdf |
60c74ebbee301c54fbc7a57f | 10.26434/chemrxiv.12786722.v1 | Navigating through the Maze of Homogeneous Catalyst Design with Machine Learning | <div><div><div><p>The ability to forge difficult chemical bonds through catalysis has transformed society on all fronts, from feeding our ever-growing populations to increasing our life-expectancies through the synthesis of new drugs. However, developing new chemical reactions and catalytic systems is a tedious task that requires tremendous discovery and optimization efforts. Over the past decade, advances in machine learning have revolutionized a whole new way to approach data- intensive problems, and many of these developments have started to enter chemistry. However, similar progress in the field of homogenous catalysis are only in their infancy. In this article, we want to outline our vision for the future of catalyst design and the role of machine learning to navigate this maze.</p></div></div></div> | Gabriel dos Passos Gomes; Robert Pollice; Alan Aspuru-Guzik | High-throughput Screening; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ebbee301c54fbc7a57f/original/navigating-through-the-maze-of-homogeneous-catalyst-design-with-machine-learning.pdf |
643f8b6f7be842788de39eb7 | 10.26434/chemrxiv-2023-fld0x | Insight into the effect of contact ion pairs on C-H bond activation for the synthesis of Ru(III)-NHC complexes: A combined experimental and computational study | The effect of contact ion pairs and comparison of the three halide ions on the C-H activation during the synthesis of Ru(III)-NHC complexes 1a and 1b have been investigated. DFT modeling of two pathways for the formation of Ru(III)-NHC complexes, viz. halide coordination pathway and ion-pair pathway, reveals the effect of ion pairing. The ion-pair path is preferred for azolium salts with Cl- and I-, whereas with Br-, the reaction follows the halide coordination route leading to the mixed halide complex. The higher activation barrier for the reaction with Cl- ions can be explained in terms of greater stabilization of the intermediates, compared to the transition states, due to halide coordination or hydrogen bonding with Cl- ions. Furthermore, the successful synthesis of 1b from the reaction of RuCl3·3H2O and the corresponding imidazolium salt precursor with Cl- in dioxane at 100 °C validates the conclusions of the DFT studies. | Navdeep Srivastava; Nida Shahid; Amrendra K. Singh | Theoretical and Computational Chemistry; Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643f8b6f7be842788de39eb7/original/insight-into-the-effect-of-contact-ion-pairs-on-c-h-bond-activation-for-the-synthesis-of-ru-iii-nhc-complexes-a-combined-experimental-and-computational-study.pdf |
64d4aa29dfabaf06ff09948c | 10.26434/chemrxiv-2023-zksp5 | Electrostatic [FeFe]-Hydrogenase–Carbon Nitride Assemblies for Efficient Solar Hydrogen Production | The assembly of semiconductors as light absorbers and enzymes as redox catalysts offers a promising approach for sustainable chemical synthesis driven by light. However, achieving the rational design of such semi-artificial systems requires a comprehensive understanding of the abiotic-biotic interface, which poses significant challenges. In this study, we demonstrate an electrostatic interaction strategy to interface negatively charged cyanamide modified graphitic carbon nitride (NCNCNX) with an [FeFe]-hydrogenase possessing a positive surface charge around the distal FeS cluster responsible for electron uptake into the enzyme. The strong electrostatic attraction enables efficient solar hydrogen (H2) production via direct interfacial electron transfer (DET), achieving a turnover frequency (TOF) of 18,669 h–1 (4 h) and a turnover number (TON) of 198,125 (24 h). Interfacial characterizations, including quartz crystal microbalance (QCM) and photoelectrochemical impedance spectroscopy (PEIS), have been conducted for the first time on a carbon nitride-enzyme to provide a comprehensive understanding for the future development of photocatalytic hybrid assemblies. | Yongpeng Liu; Carolina Pulignani; Sophie Webb; Samuel Cobb; Santiago Rodriguez Jimenez; Dongseok Kim; Ross Milton; Erwin Reisner | Catalysis; Energy; Biocatalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d4aa29dfabaf06ff09948c/original/electrostatic-fe-fe-hydrogenase-carbon-nitride-assemblies-for-efficient-solar-hydrogen-production.pdf |
644df4b36ee8e6b5ed547d1c | 10.26434/chemrxiv-2023-gx7rw | A critique of the provisional report of the IUPAC Group 3 project | In this article I critique some grounds relied on by Scerri (2021) in provisionally suggesting that IUPAC could perhaps make a ruling that Group 3 of the periodic table should be composed of Sc-Y-Lu-Lr. My concerns have to do with the philosophical meaning of “compromise”; the popularity of periodic tables instead showing group 3 as Sc-Y-La-Ac; and the rarity of the 32-column form of periodic table. IUPAC has further evidenced a long-standing reluctance to issue guidance on the use of any particular form of periodic table, including the table appearing on its own web site. The provisional report of the IUPAC Group 3 project lacks objectiveness on these bases. IUPAC could nevertheless issue some carefully worded guidance to resolve the situation. | Rene Vernon | Inorganic Chemistry; Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644df4b36ee8e6b5ed547d1c/original/a-critique-of-the-provisional-report-of-the-iupac-group-3-project.pdf |
62f3b3f38dba68454c1e480d | 10.26434/chemrxiv-2022-qtncw | Machine learning for yield prediction for chemical reactions using in situ sensors | Machine learning models were developed to predict product formation from time-series reaction data for ten Buchwald-Hartwig coupling reactions. The data was provided by DeepMatter and was collected in their DigitalGlassware cloud platform. The reaction probe has 12 sensors to measure properties of interest, including temperature, pressure, and colour. Colour was a good predictor of product formation for this reaction and machine learning models were able to learn which of the properties were important. Predictions for the current product formation (in terms of % yield) had a mean absolute error of 1.2%. For predicting 30, 60 and 120 minutes ahead the error rose to 3.4, 4.1 and 4.6%, respectively. The work here presents an example into the insight that can be obtained from applying machine learning methods to sensor data in synthetic chemistry. | Joseph Davies; David Pattison; Jonathan Hirst | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f3b3f38dba68454c1e480d/original/machine-learning-for-yield-prediction-for-chemical-reactions-using-in-situ-sensors.pdf |
62da91457aab586d6fcb59f7 | 10.26434/chemrxiv-2022-mx2qd | Nanoporous Au formation on Au substrates via high voltage electrolysis | Nanoporous Au (NPG) films often show distinctly different properties than bare Au electrodes, which make them suitable for various applications in (electro)catalysis or (bio)sensing. A great deal of effort has gone into finding suitable preparation techniques that can be used to target structural properties, such as the pore size or the surface-to-volume ratio. Many of the methods described for preparing these NPG films require complex starting materials such as alloys, multiple synthesis steps, lengthy preparation procedures or a combination of these factors. Here we present an approach that circumvents these difficulties, enabling for a rapid and controlled preparation of NPG films starting from bare Au electrodes.
One approach is to prepare in a first step a Au oxide film by high voltage (HV) electrolysis in a KOH solution, which in a second step is reduced either electrochemically or in the presence of H₂O₂. The resulting NPG structures as well as their electrochemically active surface areas strongly depend on the reduction procedure, the concentration and temperature of the H₂O₂-containing KOH solution, as well as the applied voltage and temperature during the HV electrolysis. The NPG film can also be prepared directly by applying electrolysis voltages that result in anodic contact glow discharge electrolysis (aCGDE) over an extended period of time. By carefully adjusting the corresponding parameters, the surface area of the final NPG film can be specifically controlled. The structural properties of the electrodes are investigated by means of XPS, SEM and electrochemical methods. | Evelyn Artmann; Lukas Forschner; Konstantin M. Schüttler; Mohammad Al-Shakran; Timo Jacob; Albert K. Engstfeld | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62da91457aab586d6fcb59f7/original/nanoporous-au-formation-on-au-substrates-via-high-voltage-electrolysis.pdf |
60c759a5f96a0094d2289062 | 10.26434/chemrxiv.14717211.v1 | Disorder Classification of the Vibrational Spectra of Modern Glasses | Using the coherent-potential approximation in heterogeneous-elasticity theory with a log-normal distribution of elastic constants for the description of the Raman spectrum and the temperature dependence of the specifi?c heat, we are able to reconstruct the vibrational density of states and characteristic descriptors of the elastic heterogeneity of a wide range of glassy materials. These descriptors are the non-affi?ne contribution to the shear modulus, the mean-square fluctuation of the local elasticity, and its correlation length. They enable a physical classification scheme for disorder in modern, industrially relevant glass materials. <br /><div>We apply our procedure to a broad range of real-world glass compositions, including metallic,oxide, chalcogenide, hybrid and polymer glasses. Universal relationships between the descriptors on the one side, and the height and frequency position of the boson peak, the Poisson ratio and theliquid fragility index on the other side are established.</div> | Zhiwen Pan; Omar Benzine; Shigeki Sawamura; Rene Limbach; Akio Koike; Thomas Bennett; Gerhard Wilde; Walter Schirmacher; Lothar Wondraczek | Elastic Materials; Nanostructured Materials - Materials; Optical Materials; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Statistical Mechanics; Structure; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759a5f96a0094d2289062/original/disorder-classification-of-the-vibrational-spectra-of-modern-glasses.pdf |
60c7577a9abda2637bf8e73d | 10.26434/chemrxiv.14406053.v1 | Diversification of 4ʹ-Methylated Nucleosides by Nucleoside Phosphorylases | The growing demand for 4'-modified nucleoside analogs in medicinal and biological chemistry is contrasted by the challenging synthetic access to these molecules and the lack of efficient diversification strategies. Herein, we report the development of a biocatalytic diversification approach based on nucleoside phosphorylases, which allows the straightforward installation of a variety of pyrimidine and purine nucleobases on a 4'-alkylated sugar scaffold. Following the identification of a suitable biocatalyst as well as its characterization with kinetic experiments and docking studies, we systematically explored the equilibrium thermodynamics of this reaction system to enable rational yield prediction in transglycosylation reactions via principles of thermodynamic control.<br /> | Felix Kaspar; Margarita Seeger; Sarah Westarp; Christoph Köllmann; Anna P. Lehmann; Patrick Pausch; Sebastian Kemper; Peter Neubauer; Gert Bange; Anett Schallmey; Daniel Werz; Anke Kurreck | Bioorganic Chemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2021-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7577a9abda2637bf8e73d/original/diversification-of-4-methylated-nucleosides-by-nucleoside-phosphorylases.pdf |
65731b9acf8b3c3cd71aebc7 | 10.26434/chemrxiv-2023-vspb5 | Steering photoinduced electron transfer in intramolecular photocatalysts by peripheral ligand control | Bridged photosensitizer-catalyst systems are promising models to study photocatalytic hydrogen evolution. However, the systems in literature are structurally diverse and therefore hard to compare. Many systems show highly complex photophysics including several accepting orbitals for the excited state, as a result catalytic activity is hard to predict. Here we present a bimetallic Ru-Pt photocatalyst bearing peripheral spectator ligands at the ruthenium(II) photocenter as a member of the Ru-tpphz-Pt family. Consequently, it features a single acceptor tpphz ligand and socalled unidirectional electron transfer, i.e., electron transfer without co-occurring transfer to peripheral ligands, from the excited state. Thus – and in contrast to recently used peripheral ligands – the new spectator ligands do not disrupt electron transfer towards the catalytic center. By comparison to known systems, this facilitates unprecedented insight into the importance of electron transfer from the bridge to the catalytic center moving towards more rational design of oligonuclear photocatalysts. | Benedikt Bagemihl; Carolin Müller; Georgina E. Shillito; Marco Hartkorn; Alexander K. Mengele; Stephan Kupfer; Benjamin Dietzek- Ivanšić; Sven Rau | Physical Chemistry; Inorganic Chemistry; Catalysis; Theory - Inorganic; Photocatalysis; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65731b9acf8b3c3cd71aebc7/original/steering-photoinduced-electron-transfer-in-intramolecular-photocatalysts-by-peripheral-ligand-control.pdf |
659d8e3366c13817291518a4 | 10.26434/chemrxiv-2024-wqzx4 | Multi-Component Liquid-Infused Systems: A New Approach to Functional Coatings | Antifouling liquid-infused surfaces have generated interest in multiple fields due to their diverse applications in industry and medicine. In nearly all reports to date, the liquid component consists of only one chemical species. However, unlike traditional solid surfaces, the unique nature of liquid surfaces holds the potential for synergistic and even adaptive functionality simply by including additional elements in the liquid coating. In this work, we explore the concept of multi-component liquid-infused systems, in which the coating liquid consists of a primary liquid and a secondary component or components that provide additional functionality. For ease of understanding, we categorize recently reported multi-component liquid-infused surfaces according to the size of the secondary components: molecular scale, in which the secondary components are molecules; nanoscale, in which they are nanoparticles or their equivalent; and microscale, in which the additional components are micrometer size or above. We present examples at each scale, showing how introducing a secondary element into the liquid can result in synergistic effects, such as maintaining a pristine surface while actively modifying the surrounding environment, which are difficult to achieve in other surface treatments. The review highlights the diversity of fabrication methods and provides perspectives on future research directions. Introducing secondary components into the liquid matrix of liquid-infused surfaces is a promising strategy with significant potential to create a new class of multifunctional materials. | Zachary Applebee; Caitlin Howell | Materials Science; Biocompatible Materials; Coating Materials | CC BY NC 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659d8e3366c13817291518a4/original/multi-component-liquid-infused-systems-a-new-approach-to-functional-coatings.pdf |
65b450ee9138d23161d2b97b | 10.26434/chemrxiv-2024-gkjgv | Measuring the Total Photon Economy of Molecular Species through Fluorescent Optical Cycling (FOC) | The total photon economy of a molecule/material is a measure of how light input is converted to light and heat output across energies and timescales. We describe a technique, Fluorescent Optical Cycling (FOC), which allows for simultaneous observation of prompt and delayed emission during and after multiple pulsed excitation, ultimately granting access to multi-state photophysical rates. We exercise control over the excitation pulse train, which allows us to “optically shelve” long-lived intermediate states without the use of diode or flashlamp excitation. By recording all photon arrival times in the visible and shortwave infrared, we can simultaneously resolve fluorescence, phosphorescence, and singlet oxygen sensitization in a single experiment. We use FOC to examine the photophysics of dual emitting bis(di-R-phosphino)alkanethiophene-pyridine-platinum ([Pt(thpy)(dppm)]+) under different solvation conditions, revealing changes in intersystem crossing and phosphorescent rates induced by the external heavy atom effect. Coupling FOC with Decay Associated Fourier Spectroscopy (DAFS), we demonstrate simultaneous correlated spectral and lifetime data in this dual emitting complex. Finally, FOC combined with superconducting nanowire single photon detectors (SNSPDs) allows us to observe the shortwave infrared region (SWIR) phosphorescence of singlet oxygen sensitized by Rose Bengal. Overall, FOC provides a powerful tool to simultaneously study multiple photophysics across timescales, even in weakly populated electronic states. | Anthony Sica; Ash Hua; Belle Coffey; Kierstyn Anderson; Benjamin Nguyen; Alexander Spokoyny; Justin Caram | Physical Chemistry; Materials Science; Optics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b450ee9138d23161d2b97b/original/measuring-the-total-photon-economy-of-molecular-species-through-fluorescent-optical-cycling-foc.pdf |
67d8a50381d2151a02bf94b8 | 10.26434/chemrxiv-2025-rz7bq | Density Matrix Embedding Pair-Density Functional Theory for Molecules | We combine density matrix embedding theory (DMET) with multiconfiguration pair-density functional theory (MC-PDFT) to explore finite systems exhibiting localized strong electron correlation effects. This methodology, termed density matrix embedded pair-density functional theory (DME-PDFT), provides a substantial cost reduction compared to traditional non-embedded MC-PDFT. Additionally, we compare it with second order n-electron valence state perturbation theory within DMET (NEVPT2-DMET). We have validated these methods by computing the bond dissociation in methyl diazine and spin-splitting energy gap in the \ce{[Fe(H_2O)_6]^{2+}} complex, showing that DME-PDFT splitting energies converge faster compared to NEVPT2-DMET to the corresponding non-embedding limits. We finally compare embedding schemes with truncation schemes for transition metal extended complexes, \ce{Fe[N(H)Ar$^*$]_2} and \ce{[NiC_{90}N_{20}H_{120}]^{2+}}, and show that embedding schemes are superior when the transition metal is not fully coordinated. | Shreya Verma; Matthew R. Hermes; Laura Gagliardi | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d8a50381d2151a02bf94b8/original/density-matrix-embedding-pair-density-functional-theory-for-molecules.pdf |
60c74e2f469df456c5f443f8 | 10.26434/chemrxiv.12721490.v1 | Modulating the Biological Function of Protein by Tailoring the Adsorption Orientation on Nanoparticles | <div><div><div><p>Protein orientation in nanoparticle-protein conjugates plays a crucial role in binding to cell receptors and ultimately, defines their targeting efficiency. Therefore, understanding fundamental aspects of the role of protein orientation upon adsorption on the surface of nanoparticles (NPs) is vital for the development of clinically important protein-based nanomedicine. In this work, new insights on the effect of the different orientation of cytochrome c (cyt c) bound to gold nanoparticles (GNPs) using various ligands on its apoptotic activity is reported. Time-of-Flight Secondary-Ion Mass Spectrometry (ToF- SIMS), electrochemical and circular dichroism (CD) analyses are used to investigate the characteristics of cyt c orientation and structure on functionalized GNPs. These studies indicate that the orientation and position of the heme ring inside the cyt c structure can be altered by changing the surface chemistry on the NPs. A difference in the apoptosis inducing capability because of different orientation of cyt c bound to the GNPs is observed. These findings indicate that the biological activity of a protein can be modulated on the surface of NPs by varying its adsorption orientation. This study will impact on the rational design of new nanoscale biosensors, bioelectronics, and nanoparticle-protein based drugs.</p></div></div></div> | Akhil Jain; Gustavo Trindade; Jacqueline M. Hicks; Jordan C. Pott; Ruman Rahman; Richard Hague; David B. Amabilino; Lluïsa Pérez-García; Frankie Rawson | Nanostructured Materials - Materials; Analytical Chemistry - General; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e2f469df456c5f443f8/original/modulating-the-biological-function-of-protein-by-tailoring-the-adsorption-orientation-on-nanoparticles.pdf |
60def87c9986aa60fa547ab1 | 10.26434/chemrxiv-2021-c6v73 | Singlet to triplet conversion in molecular hydrogen and its role in parahydrogen induced polarization | An analysis is reported of singlet-triplet conversion in molecular hydrogen dissolved in solution together with organometallic complexes used in experiments with parahydrogen (the H2 molecule in its nuclear singlet spin state). We demonstrate that this conversion, which gives rise to formation of orthohydrogen (the H2 molecule in its nuclear triplet spin state), is a remarkably efficient process that strongly reduces the resulting NMR (nuclear magnetic resonance) signal enhancement, here of 15N nuclei polarized at high fields using suitable NMR pulse sequences. We make use of a simple improvement of traditional pulse sequences, utilizing a single pulse on the proton channel that gives rise to an additional strong increase of the signal. Furthermore, analysis of the enhancement as a function of the pulse length allows one to estimate the actual population of the spin states of H2. We are also able to demonstrate that the spin conversion process in H2 is strongly affected by the concentration of 15N nuclei. This observation allows us to explain the dependence of the 15N signal enhancement on the abundance of 15N isotopes. | Danil Markelov; Vitaly Kozinenko; Stephan Knecht; Alexey Kiryutin; Alexandra Yurkovskaya; Konstantin Ivanov | Physical Chemistry; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60def87c9986aa60fa547ab1/original/singlet-to-triplet-conversion-in-molecular-hydrogen-and-its-role-in-parahydrogen-induced-polarization.pdf |
655922d56e0ec7777f380579 | 10.26434/chemrxiv-2023-wxpbh-v2 | Barium Ion Sensing with Commercial IPG K+ Molecular Probes | Fluorophores containing azacrown ether ionophores can be assembled as particularly powerful, sensitive, and selective turn-on chemosensors, due to their well-known size specificity of the binding domain. Here we quantify the capability of three commercially available chemosensors, marketed for biologically useful K+ sensing as probes for Ba2+ ions. Results are presented from both bulk spectrofluorimetry in aqueous solution, as well as at the single molecule level using single molecule fluorescence microscopy. | Reagan Miller; Nick Byrnes; Austin Carlson; Enakshi Dey; Karen Navarro; Ryan Madigan; Benjamin Jones; Frank Foss | Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655922d56e0ec7777f380579/original/barium-ion-sensing-with-commercial-ipg-k-molecular-probes.pdf |
66bf8c9cf3f4b0529017ed93 | 10.26434/chemrxiv-2024-90vvx | Hexanitrogen (N6): A Synthetic Leap Towards Neutral Nitrogen Allotropes | The pursuit of nitrogen allotropes is considered a Holy Grail in high-energy-density materials research because they lend themselves as the cleanest envisionable energy storage materials by producing only benign N2 upon energy release. Here, we present the room temperature preparation of N6 (hexanitrogen) in the gas-phase through the reaction of Cl2 or Br2 with AgN3, followed by trapping in argon matrices at 10 K. We also prepared neat N6 as a film at liquid nitrogen temperature (77 K), indicating its unexpectedly high stability. Infrared and UV/Vis spectroscopy, 15N-isotope labelling experiments, and ab initio computations at the CCSD(T)/cc-pVTZ level of theory support our findings. The preparation of a metastable nitrogen allotrope beyond N2 opens new vistas for making long sought after, high-energy materials. | Weiyu Qian; Artur Mardyukov; Peter Richard Schreiner | Organic Chemistry; Inorganic Chemistry; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bf8c9cf3f4b0529017ed93/original/hexanitrogen-n6-a-synthetic-leap-towards-neutral-nitrogen-allotropes.pdf |
659e67a666c1381729205816 | 10.26434/chemrxiv-2024-41x63 | Modular and Automated Synthesis of Oligonucleotide-Small Molecule Conjugates for Cathepsin B Mediated Traceless Release of Payloads | Attachment of small molecules to oligonucleotides is a versatile tool in the development of therapeutic oligonucleotides. However, cleavable linkers in the oligonucleotide field are scarce, particularly with respect to the requirement of traceless release of payload in vivo. Herein, a cathepsin B-cleavable dipeptide phosphoramidite, Val-Ala(NB), is developed for the automated synthesis of oligonucleotide-small molecule conjugates. Val-Ala(NB) was protected by photolabile 2-nitrobenzyl to improve stability of the peptide linker during DNA synthesis. After photolysis, intracellular cathepsin B digests the dipeptide efficiently, releasing the payload-phosphate which is converted to the free payload by endogenous phosphatase enzymes. With the advantages of modular synthesis and stimuli-responsive drug release, we believe Val-Ala(NB) will be a commonly used cleavable linker in the development of oligonucleotide-drug conjugates. | Cheng Jin; Siqi Li; Katherine Vallis; Afaf El-Sagheer; Tom Brown | Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659e67a666c1381729205816/original/modular-and-automated-synthesis-of-oligonucleotide-small-molecule-conjugates-for-cathepsin-b-mediated-traceless-release-of-payloads.pdf |
60c75152f96a00b781287fd5 | 10.26434/chemrxiv.13149893.v1 | Mechanism of Covalent Binding of Ibrutinib to Bruton’s Tyrosine Kinase revealed by QM/MM Calculations | <p>Ibrutinib is the first covalent inhibitor of Bruton’s tyrosine kinase (BTK) to be used in the treatment of B-cell cancers. Understanding the mechanism of covalent inhibition is crucial for the design of safer and more selective covalent inhibitors that target BTK. There are questions surrounding the precise mechanism of covalent bond formation in BTK as there is no appropriate active site residue that can act as a base to deprotonate the cysteine thiol prior to covalent bond formation. To address this, we have investigated several mechanistic pathways of covalent modification of C481 in BTK by ibrutinib using QM/MM reaction simulations. The lowest energy pathway we identified involves a direct proton transfer from C481 to the acrylamide warhead in ibrutinib, followed by covalent bond formation to form an enol intermediate. There is a subsequent rate-limiting keto-enol tautomerisation step (DG<sup>‡</sup>=10.5 kcal mol<sup>-1</sup>) to reach the inactivated BTK/ibrutinib complex. Our results represent the first mechanistic study of BTK inactivation by ibrutinib to consider multiple mechanistic pathways. These findings should aid in the design of covalent drugs that target BTK and related proteins. </p> | Angus Voice; Gary Tresadern; Rebecca Twidale; Herman Van Vlijmen; Adrian Mulholland | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75152f96a00b781287fd5/original/mechanism-of-covalent-binding-of-ibrutinib-to-bruton-s-tyrosine-kinase-revealed-by-qm-mm-calculations.pdf |
634055d7e665bda88021f904 | 10.26434/chemrxiv-2022-gx4xc | Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases Through a Ser/Ile Double Mutation | Polyethylene terephthalate (PET) is the most common polyester plastic in the packaging industry, and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases (PETases), have been found to hydrolyze this polymer at different temperatures, with the enzyme from I. sakaiensis (IsPETase) having optimal catalytic activity at 40ºC. Crystal structures of IsPETase have revealed that the side chain of a conserved tryptophan residue within an active site loop (W185) shifts between 3 conformations to enable substrate binding and product release. This is facilitated by two residues unique to IsPETase, S214 and I218 (S/I). When these residues are inserted into other PETases in place of the otherwise strictly conserved His/Phe (H/F) residues found at their respective positions, they enhance activity and decrease Topt. Herein, we combine conventional molecular dynamics and well-tempered metadynamics simulations to investigate dynamic changes of the S/I and H/F variants of IsPETase, as well as three other mesophilic and thermophilic PETases, at their respective temperature and pH optima. Our simulations show that the S/I insertion both increases the flexibility of active site loop regions harboring key catalytic residues and the conserved Trp, as well as expanding the conformational plasticity of this Trp side chain, allowing the conformational transitions that allow for substrate binding and product release in IsPETase. The observed catalytic enhancement caused by this substitution in other PETases appears to be due to conformational selection, by capturing the conformational ensemble observed in IsPETase. | Alessandro Crnjar; Aransa Griñen; Shina Caroline Lynn Kamerlin; César Ramírez-Sarmiento | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634055d7e665bda88021f904/original/conformational-selection-of-a-tryptophan-side-chain-drives-the-generalized-increase-in-activity-of-pet-hydrolases-through-a-ser-ile-double-mutation.pdf |
67bc14b96dde43c908344b5a | 10.26434/chemrxiv-2025-ls2nr | Development of Indolo-Bicyclo[3.1.1]heptane as a Carbazole Isostere through Radical Indolization of Bicyclo[1.1.0]butanes | Semisaturated ring systems with a balanced fraction of Csp3 have garnered increasing attention in drug development. In this study, we propose indolo-bicyclo[3.1.1]heptane as a potential carbazole isostere and present a novel strategy for synthesizing this new semisaturated polycyclic scaffold. The synthesis involves using bicyclo[1.1.0]butanes (BCBs) as radical precursors/terminators in the Fukuyama radical indolization reaction with 2-alkenylarylisocyanides, providing a highly efficient approach to construct a tricyclic system in a single step. These reactions represent a rare example of two functional groups (isonitrile and alkene) being sequentially involved in the cyclization process within BCB chemistry. | Honggen Wang; Yuan Liu; Jun-Yunzi Wu; Qi Fan; Yifan Yang; Yin Li; Shuang Lin; Jiang-Hao Xue; Qingjiang Li | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc14b96dde43c908344b5a/original/development-of-indolo-bicyclo-3-1-1-heptane-as-a-carbazole-isostere-through-radical-indolization-of-bicyclo-1-1-0-butanes.pdf |
60c74fd7ee301c9693c7a779 | 10.26434/chemrxiv.12945833.v1 | Polypharmacology of Some Medicinal Plant Metabolites Against SARS-CoV-2 and Host Targets: Molecular Dynamics Evaluation of NSP9 RNA Binding Protein | <p><b>Background: </b>Medicinal plants, as rich sources of bioactive compounds with antiviral properties, are now being explored for the development of drugs against SARS-CoV-2.</p><p><b>Aims: </b>Identification of promising compounds for the treatment of COVID-19 from natural products via molecular modelling against NSP9, including some other viral and host targets and evaluation of polypharmacological indications.</p><p><b>Main methods: </b>A manually curated library of 521 phytochemicals (from 19 medicinal plants) was virtually screened using Mcule server and binding interactions were studied using DS Visualiser. Docking thresholds were set based on the scores of standard controls and rigorous ADMET properties were used to finally get the potential inhibitors. Free binding energies of the docked complexes were calculated employing MM-GBSA method. MM-GBSA informed our choice for MD simulation studies performed against NSP9 to study the stability of the drug-receptor interaction. NSP9 structure comparison was also performed. </p><p><b>Key findings: </b>Extensive screening of the molecules identified 5 leads for NSP9, 23 for Furin, 18 for ORF3a, and 19 for interleukin-6. Ochnaflavone and Licoflavone B, obtained from Lonicera japonica (Japanese Honeysuckle) and Glycyrrhiza glabra (Licorice), respectively, were identified to have the highest potential multi-target inhibition properties for NSP9, furin, ORF3a, and IL-6. Additionally, molecular dynamics simulation supports the robust stability of Ochnaflavone and Licoflavone B against NSP9 at the active sites via hydrophobic interactions, H-bonding, and H-bonding facilitated by water.</p><b>Significance:</b> These compounds with the highest drug-like ranking against multiple viral and host targets have the potential to be drug candidates for the treatment of SARS-CoV-2 infection that may possibly act on multiple pathways simultaneously to inhibit viral entry and replication as well as disease progression. | Suritra Bandyopadhyay; Omobolanle Abimbola Abiodun; Blessing Chinweotito Ogboo; Adeola Tawakalitu Kola-Mustapha; Emmanuel Ifeanyi Attah; Lawrence Edemhanria; Ankita Kumari; Ravindran Jaganathan; Niyi Samuel Adelakun | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fd7ee301c9693c7a779/original/polypharmacology-of-some-medicinal-plant-metabolites-against-sars-co-v-2-and-host-targets-molecular-dynamics-evaluation-of-nsp9-rna-binding-protein.pdf |
6705d4cfcec5d6c142a2e30c | 10.26434/chemrxiv-2024-5tt53-v2 | Delocalization error poisons the density-functional many-body expansion | The many-body expansion is a fragment-based approach to large-scale quantum chemistry that partitions a single monolithic calculation into manageable subsystems. This technique is increasingly being used as a basis for fitting classical force fields to electronic structure data, especially for water and aqueous ions, and for machine learning. Here, we show that the many-body expansion based on semilocal density functional theory affords wild oscillations and runaway error accumulation for ion–water interactions, typified by F–(H2O)N with N >= 15. We attribute these oscillations to self-interaction error in the density-functional approximation. The effect is minor or negligible in small water clusters, explaining why it has not been noticed previously, but grows to catastrophic proportion in clusters that are only moderately larger. This behavior can be counteracted with hybrid functionals but only if the fraction of exact exchange is >= 50%, whereas modern meta-generalized gradient approximations including wB97X-V, SCAN, and SCAN0 are insufficient to eliminate divergent behavior. Other mitigation strategies including counterpoise correction, density correction (i.e., exchange-correlation functionals evaluated atop Hartree-Fock densities), and dielectric continuum boundary conditions do little to curtail the problematic oscillations. In contrast, energy-based screening to cull unimportant subsystems can successfully forestall divergent behavior. These results suggest that extreme caution is required when the many-body expansion is combined with density functional theory. | Dustin Broderick; John Herbert | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Machine Learning; Clusters; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6705d4cfcec5d6c142a2e30c/original/delocalization-error-poisons-the-density-functional-many-body-expansion.pdf |
66be63e4a4e53c48767dd069 | 10.26434/chemrxiv-2024-lwczt-v2 | Inverse Relationship Between Ice Nucleation and Ice Growth in Frozen Foods | According to a USDA report, $161 billion worth of food products was not available for human consumption in 2010 due to food loss. One potential way to reduce food loss is to prevent damage to the food product during the freezing process. This study presents quantitative measurements of the two primary processes involved in freezing of foods: ice nucleation and ice growth. Using a newly developed micro-thermography system, we measured in-situ ice nucleation and growth rates. We found that ice nucleation rates in beef and zucchini were significantly higher than those in broccoli and potato, whereas ice growth was faster in broccoli and potato compared to beef and zucchini. Thus, ice nucleation and ice growth in the foods tested here, were found to be opposing processes. By analyzing the chemical composition of these foods, we applied established crystal growth and nucleation principles to explain the reasons causing the inverted relationship between ice nucleation and ice growth. Therefore, designing a customized freezing process for each food product will lead to improved quality of the product, thereby limiting food loss.
| Martin Zalazar; Shriya Jitendra Kalburge; Yining Zhang; Ran Drori | Agriculture and Food Chemistry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66be63e4a4e53c48767dd069/original/inverse-relationship-between-ice-nucleation-and-ice-growth-in-frozen-foods.pdf |
60c74ae4469df482a7f43e24 | 10.26434/chemrxiv.12268517.v1 | Photodissociation of Iso-Propoxy (I-C3H7O) Radical at 248 Nm | <p>Photodissociation of the <i>i</i>-C<sub>3</sub>H<sub>7</sub>O radical is investigated using fast beam photofragment translational spectroscopy. Neutral <i>i</i>-C<sub>3</sub>H<sub>7</sub>O radicals are produced through the photodetachment of a fast beam of <i>i</i>-C<sub>3</sub>H<sub>7</sub>O<sup>-</sup> anions and are subsequently dissociated using 248 nm (5.0 eV). The dominant product channels are CH<sub>3</sub> + CH<sub>3</sub>CHO and OH + C<sub>3</sub>H<sub>6</sub> with some contribution from H + C<sub>3</sub>H<sub>6</sub>O. CH<sub>3</sub> and H loss are attributed to dissociation on the ground electronic state of <i>i</i>-C<sub>3</sub>H<sub>7</sub>O, but in a nonstatistical manner because RRKM dissociation rates exceed the rate of energy randomization. Translational energy and angular distributions for OH loss are consistent with ground state dissociation, but the branching ratio for this channel is considerably higher than predicted from RRKM rate calculations. These results corroborate what has been observed previously in C<sub>2</sub>H<sub>5</sub>O dissociation at 5.2 eV that yields CH<sub>3</sub>, H, and OH loss. Additionally, <i>i</i>-C<sub>3</sub>H<sub>7</sub>O undergoes three-body fragmentation to CH<sub>3</sub> + CH<sub>3</sub> + HCO and CH<sub>3</sub> + CH<sub>4</sub> + CO. These three-body channels are attributed to dissociation of <i>i</i>-C<sub>3</sub>H<sub>7</sub>O to CH<sub>3</sub> + CH<sub>3</sub>CHO, followed by secondary dissociation of CH<sub>3</sub>CHO on its ground electronic state.</p> | Erin Sullivan; Steven Saric; Daniel Neumark | Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae4469df482a7f43e24/original/photodissociation-of-iso-propoxy-i-c3h7o-radical-at-248-nm.pdf |
66293f1b418a5379b09d3b54 | 10.26434/chemrxiv-2024-f0hg7 | Scaling Laws for Optimal Herschel–Bulkley Yield Stress Fluid Flow in Self-Similar Tree-like Branching Networks | This study analyzes optimal flow conditions and structures in tree-like branching networks for yield stress Herschel–Bulkley fluids. We focus on maximizing flow conductance under volume constraints, assuming fully developed laminar flow in circular tubes. We propose a conjecture that if the tube-wall stress, remains the same in the network for all branches, then an optimal solution exists. We find that optimal network geometry depends on the number of branch splits $N$, and independent of the power-law index $n$ and the yield stress $\tau_y$. This optimal condition leads to an equal pressure drop across each branching level. Our results are validated with existing theory and extended to encompass shear-thinning and shear-thickening behaviors for any number of splits $N$ with and without yield stress. Additionally, we derive relationships between geometrical and flow characteristics for parent and daughter tubes, including wall stresses, length ratios. These findings provide valuable design principles for efficient transport systems involving yield stress fluids. | Ashish Garg | Nanoscience; Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66293f1b418a5379b09d3b54/original/scaling-laws-for-optimal-herschel-bulkley-yield-stress-fluid-flow-in-self-similar-tree-like-branching-networks.pdf |
651d32b68bab5d20559fa41e | 10.26434/chemrxiv-2023-41scv | Thermodynamic characterization of amyloid polymorphism by Taylor dispersion analysis | Amyloid fibrils of proteins such as α-synuclein are a hallmark of neurodegenerative diseases and much research has focused on their kinetics and mechanisms of formation. The question as to the thermodynamic stability of such structures has received much less attention. Here, we present a novel experimental method to quantify amyloid fibril stability based on chemical depolymerisation and Taylor dispersion analysis. The relative concentrations of fibrils and monomer at equilibrium are determined through an in situ separation of these species through Taylor dispersion in laminar flow inside a microfluidic capillary. This method is highly sample economical, using much less than a microliter of sample per data point and its only requirement is the presence of aromatic residues because of its label-free nature. Using this method, we investigate the differences in thermodynamic stability between different fibril polymorphs of α-synuclein and quantify these differences for the first time. Importantly, we show that fibril formation can be under kinetic or thermodynamic control and that a change in solution conditions can both stabilise and destabilise amyloid fibrils. Taken together, our results establish the thermodynamic stability as a well-defined and key parameter that can contribute towards a better understanding of the physiological roles of amyloid fibril polymorphism. | Azad Farzadfard; Antonin Kunka; Thomas O. Mason; Jacob A. Larsen; Rasmus K. Norrild; Elisa Torrescasana Dominguez; Soumik Ray; Alexander K. Buell | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Separation Science; Biophysics | CC BY 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651d32b68bab5d20559fa41e/original/thermodynamic-characterization-of-amyloid-polymorphism-by-taylor-dispersion-analysis.pdf |
61c45d387f367e2a475d4436 | 10.26434/chemrxiv-2021-kw8xx | Organocatalytic Silicon-Free SuFEx reactions for modular synthesis of sulfonate esters and sulfonamides | Sulfur(VI) fluoride exchange (SuFEx) click chemistry provides a powerful tool for rapid construction of modular connections. Here, we report a novel catalytic silicon-free SuFEx reaction with sulfonyl fluorides. Under the catalysis of 10 mol% N-heterocyclic carbene (NHC), a range of phenols and alcohols react with different sulfonyl fluorides to afford sulfonate esters in 49-99% yields. In addition, Under the relay catalysis of 10 mol% N-heterocyclic carbene and 10 mol% 1-hydroxybenzotriazole (HOBt), a variety of primary and secondary amines react with different sulfonyl fluorides to produce sulfonamides in 58%-99% yields. More than 140 sulfonylated products, including 17 natural product derivatives have been prepared through this method. Mechanism study showed that NHCs might act as a carbon-centered Brønsted base to catalyse the SuFEx click reactions via the formation of hydrogen bonding with phenols or alcohols. | Muze Lin; JInyun Luo; Yu Xie; Guangfen Du; Zhihua Cai; Bin Dai; Lin He | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2021-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c45d387f367e2a475d4436/original/organocatalytic-silicon-free-su-f-ex-reactions-for-modular-synthesis-of-sulfonate-esters-and-sulfonamides.pdf |
65696557cf8b3c3cd7871603 | 10.26434/chemrxiv-2023-vk9gh | Equivariant Neural Networks Utilizing Molecular Clusters for Accurate Molecular Crystal Binding Energy Predictions | Equivariant neural networks have emerged as prominent models in advancing the construction of interatomic potentials due to their remarkable data efficiency and generalization capabilities for out-of-distribution data. Here, we expand the utility of these networks to the prediction of crystal structures consisting of organic molecules. Traditional methods for computing crystal structure properties, such as plane-wave quantum chemical methods based on density functional theory (DFT), are prohibitively resource-intensive, often necessitating compromises in accuracy and the choice of exchange-correlation functional. We present an approach that leverages the efficiency, and transferability of equivariant neural networks, specifically Allegro, to predict molecular crystal structure energies at a reduced computational cost. Our neural network is trained on molecular clusters using a highly accurate Gaussian-type orbital (GTO)-based method as the target level of theory, eliminating the need for costly periodic DFT calculations, while providing access to all families of exchange-corelation functionals and post-Hartree Fock methods. The trained model exhibits remarkable accuracy in predicting binding energies, aligning closely with those computed by plane-wave based DFT methods, thus representing significant cost reductions. Furthermore, the Allegro network was seamlessly integrated with the USPEX framework, accelerating the discovery of low-energy crystal structures during crystal structure prediction. | Ankur Gupta; Miko Stulajter; Yusuf Shaidu; Jeffrey Neaton; Wibe de Jong | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65696557cf8b3c3cd7871603/original/equivariant-neural-networks-utilizing-molecular-clusters-for-accurate-molecular-crystal-binding-energy-predictions.pdf |
60c75593702a9b798018c726 | 10.26434/chemrxiv.14130080.v1 | Determination of Lithium in Human Serum by Isotope Dilution Atomic Absorption Spectrometry | <p>The therapeutic dose of lithium (Li) compounds, which
are widely used for the treatment of psychiatric and hematologic disorders, is
close to its toxic level; therefore, drug monitoring protocols are mandatory. Herein,
we propose a fast, simple, and low-cost analytical procedure for the traceable determination
of Li concentration in human serum, based on the monitoring of the Li isotope dilution
through the partially resolved isotope shift in its electronic transition
around 670.80 nm using a commercially available high-resolution continuum
source graphite furnace atomic absorption spectrometer. With this technique, serum
samples only require acidic digestion before analysis. The procedure requires
three measurements—an enriched <sup>6</sup>Li spike, a mixture of a certified
standard solution and spike, and a mixture of the sample and spike with a
nominal <sup>7</sup>Li/<sup>6</sup>Li ratio of 0.82. Lanthanum has been used as
an internal spectral standard for wavelength correction. The spectra are
described as the linear superposition of the contributions of the respective
isotopes, each consisting of a spin-orbit doublet, which can be expressed as
Gaussian components with constant spectral position and width and different
relative intensity, reflecting the isotope ratio in the sample. Both, the
spectral constants and the correlation between isotope ratio and relative band
intensity have been experimentally obtained using commercially available materials
enriched with Li isotopes. The procedure has been validated using five human
serum certified reference materials. The results are metrologically comparable and compatible
to the certified values. The measurement uncertainties are comparable to those
obtained by the more complex and expensive technique, isotope dilution mass
spectrometry. </p> | Alexander Winckelmann; Dalia Morcillo; Silke Richter; Sebastian Recknagel; Jens Riedel; Jochen Vogl; Ulrich Panne; Carlos Abad | Analytical Chemistry - General; Chemoinformatics; Spectroscopy (Anal. Chem.); Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75593702a9b798018c726/original/determination-of-lithium-in-human-serum-by-isotope-dilution-atomic-absorption-spectrometry.pdf |
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