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6170c5acd7e1ee4ddb2bab2d | 10.26434/chemrxiv-2021-q6z1p | Crystal Structure of the Intermediate Na2V2(PO4)3 Phase and Electrochemical Reaction Mechanisms in NaxV2(PO4)3 (1 ≤ x ≤ 4) System | The Na-superionic-conductor (NASICON) Na3V2(PO4)3 is an important positive electrode material for Na-ion batteries. Here, we investigate the mechanisms of phase transition in NaxV2(PO4)3 (1 ≤ x ≤ 4) upon a non-equilibrium battery cycling. Unlike the widely believed two-phase reaction in Na3V2(PO4)3 – Na1V2(PO4)3 system, we determine a new intermediate Na2V2(PO4)3 phase using operando synchrotron X-ray diffraction. Density functional theory calculations further support the existence of the Na2V2(PO4)3 phase. We propose for the first time two possible crystal structures of Na2V2(PO4)3 analyzed by Rietveld refinement. The two structure models with the space groups P21/c or P2/c for the new intermediate Na2V2(PO4)3 phase show similar unit cell parameters but different atomic arrangements, including a vanadium charge ordering. As the appearance of the intermediate Na2V2(PO4)3 phase is accompanied by symmetry reduction, Na(1) and Na(2) sites split into several positions in Na2V2(PO4)3, in which one of the splitting Na(2) position is found to be a vacancy whereas the Na(1) positions are almost fully filled. The intermediate Na2V2(PO4)3 phase reduces the lattice mismatch between Na3V2(PO4)3 and Na1V2(PO4)3 phases facilitating a fast phase transition. This work paves the way for a better understanding of great rate capabilities of Na3V2(PO4)3. | Sunkyu Park ; Ziliang Wang; Zeyu Deng; Iona Moog; Pieremanuele Canepa; François Fauth ; Dany Carlier ; Laurence Croguennec ; Christian Masquelier; Jean-Noël Chotard | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6170c5acd7e1ee4ddb2bab2d/original/crystal-structure-of-the-intermediate-na2v2-po4-3-phase-and-electrochemical-reaction-mechanisms-in-nax-v2-po4-3-1-x-4-system.pdf |
661ca29391aefa6ce192bede | 10.26434/chemrxiv-2024-lc1sz | Optimal Flow and Scaling Laws for Power-Law Fluids in Elliptical Cross-Section Self-Similar Tree-Like Networks | Tree-like self-similar branching networks with power-law fluid flow in elliptical cross-sectional tubes are ubiquitous in nature and engineered systems. This study optimizes flow conductance within these networks under tube-volume and tube's surface-area constraints for fully developed laminar power-law fluid flow in elliptical cross-sectional tubes. We identify key network parameters influencing flow conductance and find that the efficient flow occurs when a specific ratio of the semi-major or semi-minor axis lengths is achieved. This ratio depends on the number of daughter branches splitting at each junction (bifurcation number $N$) and the fluid's power-law index $n$. This study extends the Hess-Murray's law to non-Newtonian fluids (thinning and thickening fluids) with arbitrary branch numbers for elliptical cross-sectional tubes. We find that the maximum flow conductance occurs when a non-dimensional semi-major or semi-minor axis length ratio $\beta^*$ satisfies $\beta^* = N^{-1/3}$, and $\beta^* = N^{-(n+1)/(3n+2)}$ under constrained-volume and constrained tube's surface-area, respectively. When semi-major and semi-minor axis are equal, our findings are validated through experiments, and theory under limiting case of circular tube. These insights provide important design principles for developing efficient and optimal transport and flow systems inspired by nature's and engineered intricate networks. | Ashish Garg; Himanshu Mishra; Sudip K. Pattanayek | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Theory - Computational; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661ca29391aefa6ce192bede/original/optimal-flow-and-scaling-laws-for-power-law-fluids-in-elliptical-cross-section-self-similar-tree-like-networks.pdf |
6750257a5a82cea2faf0c9bf | 10.26434/chemrxiv-2024-wtd2k | Peptide Backbone Cleavage and trans-Amidation via Thioester-to-Imide Acyl Transfer | Cysteine thioesters are involved in a myriad of cen-tral biological transformations because of their unique reactivity. Despite their well-studied proper-ties, we discovered an unexpected trans-amidation reaction of cysteine thioesters that leads to peptide backbone cleavage. S-Acylcysteine-containing pep-tides were found to spontaneously fragment by cleavage of the amide bond in the i-1 position to the acylated cysteine residue at pH 8–10. We pre-sent compelling evidence for a mechanism involv-ing a central reversible thioester-to-imide acyl transfer step. The discovered trans-amidation reac-tion was found to be highly sequence dependent and was found to proceed in peptides containing post-translational modifications (PTMs) such as cysteine S-acetylation and S-palmitoylation as well as in peptide–peptide branched thioesters, mimick-ing class I intein splicing. Thus, the inherent reac-tivity of peptide backbones containing S-acylcysteine residues should represent a starting point for investigation of endogenous protein be-havior and may serve as a foundation for the dis-covery mild new peptide and protein transfor-mations. | Bengt Herbert Gless; Sabrina Schmied; Christian Adam Olsen | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6750257a5a82cea2faf0c9bf/original/peptide-backbone-cleavage-and-trans-amidation-via-thioester-to-imide-acyl-transfer.pdf |
60c74d7d842e6507b3db34aa | 10.26434/chemrxiv.12624722.v1 | Optimal Anchoring of a Urea-based Foldamer Inhibitor of ASF1 Histone Chaperone Through Backbone Plasticity | <p><b>Sequence-specific
oligomers with predictable folding patterns, i.e. foldamers provide new
opportunities to mimic α-helical peptides and design inhibitors of
protein-protein interactions. One major hurdle of this strategy is to retain
the correct orientation of key side chains involved in protein surface
recognition. Here, we show that the structural plasticity of a foldamer
backbone may significantly contribute to the required spatial adjustment for
optimal interaction with the protein surface. By using oligoureas as α-helix
mimics, we designed a foldamer/peptide hybrid inhibitor of histone chaperone
ASF1, a key regulator of chromatin dynamics. The crystal structure of its
complex with ASF1 reveals a striking plasticity of the urea backbone, which
adapts to the ASF1 surface to maintain the same binding interface. One additional
benefit of generating ASF1 ligands with non-peptide oligourea segments is the resistance
to proteolysis in human plasma which was highly improved compared to the
cognate α-helical peptide. </b></p> | Johanne Mbianda; May Bakail; Christophe André; Gwenaëlle Moal; Marie E. Perrin; Raphaël Guerois; François Becher; Pierre Legrand; Seydou Traore; Céline Douat; Gilles GUICHARD; Francoise OCHSENBEIN | Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d7d842e6507b3db34aa/original/optimal-anchoring-of-a-urea-based-foldamer-inhibitor-of-asf1-histone-chaperone-through-backbone-plasticity.pdf |
639a4e4cb9c5f6b786d33159 | 10.26434/chemrxiv-2022-1fp1v | Automated Parameterization of Coarse-Grained Polyethylenimine Under Martini Framework | As a versatile polymer in many applications, synthesized polyethylenimine (PEI) is polydisperse with diverse branched structures that attain pH-dependent protonation states. Understanding the structure-function relationship of PEI is necessary for enhancing its efficacy in various applications. Coarse-grained (CG) simulations can be performed at length- and timescales directly comparable with experimental data while maintaining the molecular perspective. However, manually developing CG forcefields for complex PEI structures is time-consuming and prone to human errors. This article presents a fully automated algorithm that can coarse-grain any branched architecture of PEI from its all-atom (AA) simulation trajectories and topology. The algorithm is demonstrated by coarse-graining a branched 2 kDa PEI, which can replicate the AA diffusion coefficient, radius of gyration, and end-to-end distance of the longest linear chain. Commercially available 25 kDa and 2 kDa Millipore-Sigma PEIs are used for experimental validation. Specifically, branched PEI architectures are proposed, coarse-grained using the automated algorithm, and then simulated at different mass concentrations. The CG-PEIs can reproduce existing experimental data on PEI’s diffusion coefficient and Stokes-Einstein radius at infinite dilution, as well as its intrinsic viscosity. This suggests a strategy where probable chemical structures of synthetic PEIs can be inferred computationally using the developed algorithm. The coarse-graining methodology presented here can also be extended to other polymers. | Subhamoy Mahajan; Tian Tang | Theoretical and Computational Chemistry; Polymer Science; Polyelectrolytes - Polymers; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639a4e4cb9c5f6b786d33159/original/automated-parameterization-of-coarse-grained-polyethylenimine-under-martini-framework.pdf |
65734a9629a13c4d470128ba | 10.26434/chemrxiv-2023-wptvg | The value of ammonia towards integrated power and heat system decarbonisation | As UK is legally bound to Net Zero goal, deep decarbonisation of wide power and heat systems constitutes a focal point of research. With heat being the biggest energy consumer in the UK, sector coupling emerges as imperative towards cost-efficient decarbonisation. Pathways including dense energy carriers (DEC), which can store excessive intermittent renewable energy, offer alternative options for optimal system's operation. In this work, the role of hydrogen and ammonia as energy vectors in Great Britain’s (GB) power system planning is examined. Dense energy carriers' pathways are modelled to offer additional energy storage, transport and electricity generation options for the system. A spatially-explicit snapshot model is developed, whose temporal resolution captures the short- and long-term dynamics of demands and renewable sources through a novel fine-grained chronological clustering. Ultimately, integrated capacity planning and operational optimisation in GB is conducted for a target year via the snapshot model. Regional power and heat demands are determined as the heat fuel consumption mix is optimised. Key findings include that under various scenarios up to 80\% heat electrification can be cost effectively achieved through the flexibility offered by up to 6 TWh of ammonia storage for annual inter-seasonal storage. | Georgios Bounitsis; Vassilis M. Charitopoulos | Energy; Energy Storage; Power | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65734a9629a13c4d470128ba/original/the-value-of-ammonia-towards-integrated-power-and-heat-system-decarbonisation.pdf |
654d5b9cdbd7c8b54bf9885e | 10.26434/chemrxiv-2023-tp76q | Pyrolytic Conversion of Glucose into Hydroxymethylfurfural and Furfural: A Survey of Mechanisms and Benchmark Quantum-Chemical Calculations | Quantum chemical methods have been intensively applied to study the pyrolytic conversion of glucose into hydroxymethylfurfural (HMF) and furfural (FF). Herein, we collect the most relevant mechanistic proposals from the recent literature and organize them into a single reaction network. The transition structures (TSs) and intermediates are characterized using high level ab initio methods that predict relative energies within chemical accuracy. The reaction pathways are assessed in terms of the Gibbs free energy differences of the TSs and intermediates with respect to β-glucopyranose, selecting a 2D ideal-gas standard state at 773K to represent the usual pyrolysis conditions. After having scored all the possible pathways throughout the network assuming reversible reaction steps, several pathways, which present various changes with respect to the former proposals, can lead to the formation of both HMF and FF passing through rate-determining TSs that have ∆G‡ values of ~ 49-50 kcal/mol. Interestingly, the catalysis by auxiliary water molecules and the non-specific environmental effects as modelled by solvent continuum methods, have only a minor impact on the Gibbs free energy profiles of the most favoured routes. Since the HMF fragmentation (HMF→FF+CH2O) is predicted to have a small ∆rxnG value and an accessible ∆G‡ barrier, the HMF/FF molecular ratio may be partly determined by equilibrium conditions. In addition, the benchmark energies and structures are employed to study the performance of density functional methodologies. Finally, we show that the computational results are in consonance with the kinetic parameters derived from lumped models, the results of isotopic labelling experiments and the reported HMF/FF molecular ratios. Eventually, they could be useful in future computational studies focused on the kinetic modelling of the pyrolysis mechanisms including non-equilibrium kinetic effects, which could render much more detailed information about product yields and the importance of the various pathways. | Roberto López; Dimas Suárez | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654d5b9cdbd7c8b54bf9885e/original/pyrolytic-conversion-of-glucose-into-hydroxymethylfurfural-and-furfural-a-survey-of-mechanisms-and-benchmark-quantum-chemical-calculations.pdf |
6645125391aefa6ce118982e | 10.26434/chemrxiv-2024-368wd | PerQueue: Managing Complex and Dynamic Workflows | Workflow managers play a critical role in the efficient planning and execution of complex workloads. A handful of these already exist within the world of computational materials discovery, but their dynamic capabilities are somewhat lacking. The PerQueue workflow manager is the answer to this need. By utilizing modular and dynamic building blocks to define a workflow explicitly before starting, PerQueue can give a better overview of the workflow while allowing full flexibility and high dynamism. To exemplify its usage, we present four use cases at different scales within computational materials discovery. These encapsulate high-throughput screening with Density Functional Theory, using active learning to train a Machine-Learning Interatomic Potential with Molecular Dynamics and reusing this potential for kinetic Monte Carlo simulations of extended systems. Lastly, it is used for an active- learning-accelerated image segmentation procedure with a human-in-the-loop. | Benjamin Sjølin; William Hansen; Armando Antonio Morin-Martinez; Martin Hoffmann Petersen; Laura Hannemose Rieger; Tejs Vegge; Juan Maria Garcia-Lastra; Ivano Eligio Castelli | Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Theory - Computational; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6645125391aefa6ce118982e/original/per-queue-managing-complex-and-dynamic-workflows.pdf |
60c7532cf96a0071c42883ba | 10.26434/chemrxiv.13414931.v1 | Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts | The new R739×5 data set from the Non-Covalent Interactions Atlas series (www.nciatlas.org) focuses on repulsive contacts in molecular complexes, covering organic molecules, sulfur, phosphorus, halogens and noble gases. Information on the repulsive parts of the potential energy surface is crucial for the development of robust empirically parametrized computational methods. We use the new data set of highly accurate CCSD(T)/CBS interaction energies to test existing DFT and semiempirical quantum-mechanical methods. On the example of the PM6 method, we analyze the source of the error and its relation to the difficulties in the description of conformational energies, and we also devise an immediately applicable correction that fixes the most serious uncorrected issues previously encountered in practical calculations. | Kristian Kříž; Martin Nováček; Jan Řezáč | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7532cf96a0071c42883ba/original/non-covalent-interactions-atlas-benchmark-data-sets-3-repulsive-contacts.pdf |
65234cd745aaa5fdbb91fef4 | 10.26434/chemrxiv-2023-rftqg | Up Up Down Down Left Right Left Right B A Start for the Catalytic Hackers of Programmable Materials
| The valuable information of catalysis for the past century has been the composition and structure of high-performing catalytic materials. But a new class of programmable catalysts that change the electronic characteristics of their active sites on the time scale of the surface reaction are changing the catalyst design process by requiring additional information describing the input program that directs the temporal changes in the catalyst surface. Catalyst programs vary in complexity associated with the number of combined waveforms required to optimize surface chemistry rates and selectivity to products. The path forward for writing and optimizing catalyst programs will combine together the methods of parameter screening, rational design based on molecular models, and machine learning. This new approach to catalysis will change the nature of catalysis science, with researchers pursuing dynamic catalytic programs with improved catalytic performance over static catalyst compositions. | Paul Dauenhauer | Materials Science; Catalysis; Catalysts; Materials Processing; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65234cd745aaa5fdbb91fef4/original/up-up-down-down-left-right-left-right-b-a-start-for-the-catalytic-hackers-of-programmable-materials.pdf |
624bd9fc3b5f9924cacea797 | 10.26434/chemrxiv-2022-lqkgn | Merging bioresponsive release of insulin-like growth factor I
with 3D printable thermogelling hydrogels
| 3D printing of biomaterials enables spatial control of drug incorporation during automated manufacturing. This study links bioresponsive release of the anabolic biologic, insulin-like growth factor-I (IGF-I) in response to matrix metalloproteinases (MMP) to 3D printing using the block copolymer of poly(2-methyl-2-oxazoline) and thermoresponsive poly(2-n-propyl-2-oxazine) (POx-b-POzi). For that, a chemo-enzymatic synthesis was deployed, ligating IGF-I enzymatically to a protease sensitive linker (PSL), which was conjugated to a POx-b-POzi copolymer. The product was blended with the plain thermogelling POx-b-POzi hydrogel. MMP exposure of the resulting hydrogel triggered bioactive IGF-I release. The bioresponsive IGF-I containing POx-b-POzi hydrogel system was further detailed for shape control and localized incorporation of IGF-I via extrusion 3D printing for future applications in biomedicine and biofabrication. | Matthias Beudert; Lukas Hahn; Anselm Horn; Niklas Hauptstein; Heinrich Sticht; Lorenz Meinel; Robert Luxenhofer; Marcus Gutmann; Tessa Lühmann | Biological and Medicinal Chemistry; Organic Chemistry; Polymer Science; Drug delivery systems; Hydrogels; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624bd9fc3b5f9924cacea797/original/merging-bioresponsive-release-of-insulin-like-growth-factor-i-with-3d-printable-thermogelling-hydrogels.pdf |
60c746f44c89192887ad2c09 | 10.26434/chemrxiv.11444877.v1 | X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists | <div>
<div>
<div>
<p>Nowadays, rigorous free energy calculations are routinely considered in pharmaceutical design strategies. One typical sce-
nario is the lead-optimization based on well-defined protein-ligand binding modes, inferred by pharmacological data in com-
putational models and ultimately revealed by structural data. In this work, we reveal the molecular determinants of antago-
nist binding to the adenosine A2A adenosine receptor (AR), an emerging target in immuno-oncology, via a robust protocol that
connects structural and pharmacological data through free energy perturbation (FEP) calculations. Eight A2AAR binding site
mutations from biophysical mapping experiments were initially analyzed with FEP simulations of each side-chain mutation,
performed on alternate binding modes previously proposed in the literature. The results strongly suggested that only one
binding mode could explain this experimental data, which was used to subsequently design a series of 11 chromone deriva-
tives. The experimental affinities of these new compounds were linked through a cycle of ligand-FEP calculations around
selected ligand pairs, which allowed the identification of the optimal positioning of the different chemical substituents in the
proposed binding model. Subsequent X-ray crystallography of the A2AAR with a low and high affinity chromone derivative
confirmed the predicted binding orientation, and provided new insights in the role of the explored substituents in the chro-
</p>
</div>
</div>
<div>
<div>
<p>mone scaffold.
</p>
</div>
</div>
</div> | Willem Jespers; Grégory Verdon; Jhonny Azuaje; maria majellaro; Henrik Keränen; Xerardo García-Mera; Miles Congreve; Francesca Deflorian; Chris de Graaf; Andrei Zhukov; Andy Dore; Jonathan S. Mason; Johan Åqvist; Robert M. Cooke; Eddy Sotelo; Hugo Gutierrez de Teran | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746f44c89192887ad2c09/original/x-ray-crystallography-and-free-energy-calculations-reveal-the-binding-mechanism-of-a2a-adenosine-receptor-antagonists.pdf |
60c74d4b469df40116f44273 | 10.26434/chemrxiv.12609899.v1 | The Photoswitch Dataset: A Molecular Machine Learning Benchmark for the Advancement of Synthetic Chemistry | The space of synthesizable molecules is greater than $10^{60}$, meaning only a vanishingly small fraction of these molecules have ever been realized in the lab. In order to prioritize which regions of this space to explore next, synthetic chemists need access to accurate molecular property predictions. While great advances in molecular machine learning have been made, there is a dearth of benchmarks featuring properties that are useful for the synthetic chemist. Focussing directly on the needs of the synthetic chemist, we introduce the Photoswitch Dataset, a new benchmark for molecular machine learning where improvements in model performance can be immediately observed in the throughput of promising molecules synthesized in the lab. Photoswitches are a versatile class of molecule for medical and renewable energy applications where a molecule's efficacy is governed by its electronic transition wavelengths. We demonstrate superior performance in predicting these wavelengths compared to both time-dependent density functional theory (TD-DFT), the incumbent first principles quantum mechanical approach, as well as a panel of human experts. Our baseline models are currently being deployed in the lab as part of the decision process for candidate synthesis. It is our hope that this benchmark can drive real discoveries in photoswitch chemistry and that future benchmarks can be introduced to pivot learning algorithm development to benefit more expansive areas of synthetic chemistry. | Aditya Raymond Thawani; Ryan-Rhys Griffiths; Arian Jamasb; Anthony Bourached; Penelope Jones; William McCorkindale; Alexander Aldrick; Alpha Lee | Photochemistry (Org.); Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d4b469df40116f44273/original/the-photoswitch-dataset-a-molecular-machine-learning-benchmark-for-the-advancement-of-synthetic-chemistry.pdf |
67369db65a82cea2fa298d81 | 10.26434/chemrxiv-2024-0glrn | Porous halogen-bonded frameworks assembled through hetero-polytopic ion pair templation | Halogen-bonding (XB) interactions have been extensively studied in the preparation of crystalline frameworks, yet porous 3D framework materials built on XBs remain elusive. The donor-acceptor interactions are strengthened by use of anionic XB acceptors; however, the requisite charge-balancing cations typically disrupt the framework and occupy potential void space. In this work, we prepare a tetratopic XB donor bearing a crown ether moiety for sodium cation sequestration. We show that when this ion pair receptor is crystallised with NaCl it gives a 3D framework that is porous to solvent and vapour, and undergoes single-crystal-to-single-crystal reactions. | Jordan Smith; Callum Hunter; Huan Doan; Valeska Ting; Nicholas White | Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67369db65a82cea2fa298d81/original/porous-halogen-bonded-frameworks-assembled-through-hetero-polytopic-ion-pair-templation.pdf |
62eb7ec7659a3f471f33ba8b | 10.26434/chemrxiv-2022-4v1l4 | Non-Covalent Interaction within Catalytic Anionic Donor and Neutral Acceptor to Promote Pd-Catalyzed Distal Site- selective Functionalization of Amines | C‒H activation of simple molecules to provide corresponding functionalized analogues has gained immense prominence. While this is widely applicable to a range of organic motifs, regioselectivity and most importantly site-selectivity of distal C‒H bonds remains a significant challenge. While covalently attached directing groups have been designed to solve the puzzle, their profound impact on the step-economy and substrate biasness cause a significant dent in the applicability of the protocol. To overcome this, weak non-covalent interactions between substrate and ligands have been developed but have been mainly explored with Ir-catalysis. Herein we aim to execute an unprecedented Pd catalyzed meta-selective C‒H functionalization of simple amines harnessing weak non-covalent interactions between anionic H-bond donor and neutral acceptor. Catalytic amount of organic salt acts as an anionic ligand and is suitable for efficient meta-selective C‒H olefination. Experimental and computational studies elucidate the mechanistic understanding and suggest that site-selectivity is governed by the key H-bonding interaction between an anionic donating ligand and a neutral accepting substrate. The protocol can be further extended to amines with variable linker-lengths, outlining the versatility and applicability of our methodology to organic motifs, while utilizing only a catalytic amount of directing ligand for the functionalization. | Nupur Goswami; Soumya Kumar Sinha; Partha Mondal; Adhya Suresh; Ayan Datta; Debabrata Maiti | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eb7ec7659a3f471f33ba8b/original/non-covalent-interaction-within-catalytic-anionic-donor-and-neutral-acceptor-to-promote-pd-catalyzed-distal-site-selective-functionalization-of-amines.pdf |
60e56d6ab95bdd6be25fc4e6 | 10.26434/chemrxiv-2021-fkm3h | A copper(I)-catalyzed sulfonylative Hiyama cross-coupling | An air-tolerant Cu-catalyzed sulfonylative Hiyama cross-coupling reaction enabling the formation of diaryl sulfones is described. Starting from aryl silanes, DABSO and aryliodides, the reaction tolerates a large variety of polar functional groups (amines, ketones, esters, aldehydes). Control experiments coupled with DFT calculations shed light on the mechanism, where the reductive elimination showcases an usual high energy barrier for a Cu(III)/Cu(I) process. | Aurélien Adenot; Lucile Anthore-Dalion; Emmanuel Nicolas; Jean-Claude Berthet; Pierre Thuéry; Thibault Cantat | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e56d6ab95bdd6be25fc4e6/original/a-copper-i-catalyzed-sulfonylative-hiyama-cross-coupling.pdf |
65087d2599918fe5372f70de | 10.26434/chemrxiv-2023-x3l64 | New Window of Opportunities for CvFAP photodecarboxylation by Violet Light Irradiation | In this study, we describe a light-driven photocatalytic decarboxylation of palmitic acid and related fatty acids using Chlorella variabilis fatty acid photodecarboxylase (CvFAP). By utilizing violet LED light (50 W; 397 nm), we achieved a remarkable conversion efficiency of 99% within just 4 minutes, surpassing the previous 79% conversion achieved in 60 minutes using blue LED light (300 W; 439 nm). Importantly, the use of 50 W violet LED light also resulted with lower enzyme photoinactivation rate when compared to 300 W blue LED. Comparing the whole-cell biocatalyst with the enzymatic extract, we found that the former demonstrated superior catalytic performance and reduced susceptibility to photoinactivation. Furthermore, through fed-batch reactions using three pulses of 13 mM palmitic acid, we achieved the production of 39 mM of pentadecane within 1 hour, highlighting a promising strategy for enhanced productivity. These findings represent a significant advancement in CvFAP photodecarboxylation processes, utilizing an alternative light source, with potential implications for biofuel production. | Rodrigo Octavio Mendonça Alves de Souza; Gabriela Breda; Alexandre França; Kleber de Oliveira; Rodrigo Almeida | Organic Chemistry; Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65087d2599918fe5372f70de/original/new-window-of-opportunities-for-cv-fap-photodecarboxylation-by-violet-light-irradiation.pdf |
620c0f877d068a0c3a210db0 | 10.26434/chemrxiv-2022-6pc2z | Photoswitching neutral homoaromatic hydrocarbons | The identification and characterization of homoaromatic compounds bearing an interrupted -system are fundamental challenges for the understanding of electronic interactions in organic molecules. This is further hampered by the fact that no stable neutral homoaromatic hydrocarbon is known. We present the preparation of a new class of neutral homoaromatic compounds, which are supported by experimental evidence (ring current observed by NMR spectroscopy, equalization of bond lengths through X-ray structure analysis) as well as computational analysis (NICS and ACID). Furthermore, we show that one homoaromatic hydrocarbon is a photoswitch through a reversible photochemical [1,11] sigmatropic rearrangement. We provide evidence that the local 6 homoaromatic state vanishes upon photoswitching to produce a purely global 10 homoaromatic state. These results of stable and accessible homoaromatic neutral hydrocarbons and their photoswitching behaviour provide new insights for the understanding and study of homoconjugative interactions in organic molecules, and for the design of new responsive molecular materials. | Trung Tran Ngoc; Niklas Grabicki; Elisabeth Irran; Oliver Dumele; Teichert Johannes | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620c0f877d068a0c3a210db0/original/photoswitching-neutral-homoaromatic-hydrocarbons.pdf |
66ead258cec5d6c1426f3bed | 10.26434/chemrxiv-2024-qgsl2 | Bifunctional photocatalysts display proximity-enhanced catalytic activity in metallaphotoredox C–O coupling | Dual catalytic reactions may be made more effective through an improved integration of the catalytic cycles achieved using bifunctional catalysts. Herein we describe new bifunctional photocatalysts consisting of a photoactive donor-acceptor cyanoarene unit linked to a bipyridine ligand moiety that can bind transition metals. The bifunctional photocatalysts were synthesized in 3-5 steps form commercially available compounds and fully characterized in terms of photophysical properties, which are strongly affected by the type of linkage used (C vs. O) to connect the cyanoarene core to the ligand. Catalytic tests carried out in the Nicatalyzed C-O cross-coupling of alcohols to aryl bromides promoted by visible light have shown that the bifunctional systems are more active than the corresponding ‘dual catalytic systems’ (i.e., not covalently bound), taking advantage of the proximity between the two catalytic moieties (Ni-complex and photocatalyst). The best bifunctional dyes were tested with several alcohols and aryl halides, giving good yields at low catalytic loading (0.5-2 mol%). | Luigi Dolcini; Andrea Solida; Daniele Lavelli; Andrés Mauricio Hidalgo-Núñez; Tommaso Gandini; Matthieu Fornara; Alessandro Colella; Alberto Bossi; Marta Penconi; Daniele Fiorito; Cesare Gennari; Alberto Dal Corso; Luca Pignataro | Organic Chemistry; Catalysis; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ead258cec5d6c1426f3bed/original/bifunctional-photocatalysts-display-proximity-enhanced-catalytic-activity-in-metallaphotoredox-c-o-coupling.pdf |
60c74934842e6519fbdb2cce | 10.26434/chemrxiv.12040518.v1 | Deferasirox (ExJade): A Fluorescent Pro-Chelator Active Against Antibiotic Resistant Bacteria | <p>Deferasirox,<b>
ExJade</b>, an FDA-approved treatment for iron overload disorders has been
shown to inhibit the growth of both gram-positive and -negative bacteria
through iron (Fe(III)) chelation. Modification of the <b>ExJade</b> framework led to the identification
of a new fluorescent platform <b>ExPh </b>and
<b>ExBT</b>. Functionalization of the
phenol moieties on <b>ExBT</b> with
phosphate units afforded a ratiometric fluorescent pro-chelator (<b>ExPhos</b>),
which was effective in the inhibition of two clinically relevant
antibiotic-resistant bacteria, (MRSA (ATCC 43300) and VRE (ATCC 51299)), and
allowed the fluorescent imaging of MRSA. <a>Remarkably,
this pro-chelation strategy proved selective towards bacteria with no
cytotoxicity observed for <b>ExPhos</b> treated A549 cells (72 h incubation). This
work represents a new pro-chelator antibiotic strategy that </a><a>can be modified
with a chosen reactive chemical trigger to provide a diagnostic signal in
conjunction with a therapeutic response</a> with a potential of minimal
off-target toxicities.</p> | Adam Sedgwick; Kai-Cheng Yan; Daniel N. Mangel; Ying Shang; Axel Steinbrueck; Hai-Hao Han; James T. Brewster; Xi-Le Hu; Dylan W. Snelson; Vincent M. Lynch; He Tian; Xiao-Peng He; Jonathan L. Sessler | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74934842e6519fbdb2cce/original/deferasirox-ex-jade-a-fluorescent-pro-chelator-active-against-antibiotic-resistant-bacteria.pdf |
66aab10601103d79c55f1010 | 10.26434/chemrxiv-2024-vw2dm-v2 | Temperature-Induced Phase Transition in 2D Alkylammonium Lead Halide Perovskites: A Molecular Dynamics Study | Molecular dynamics simulations are utilized to unravel the temperature-driven phase transition in double-layered butylammonium (BA) methylammonium (MA) lead halide perovskite (BA)$_{2}$(MA)Pb$_{2}$I$_{7}$, which holds great promise in a wide range of optoelectronics and sensor applications. The simulations successfully capture the structural transition from low to high symmetry phases with rising temperatures, consistent with experimental observations. The phase transition initiates at two critical interfaces: the first is between the inorganic and organic layers, where the melting of N-H bonds in BA leads to significant reduction in hydrogen bonding between BA and iodides, and the second is at the interface between top and bottom organic layers, where the melting of the tail bonds in BA triggers the phase transition. Following this, BA cations exhibit a patterned and synchronized motion reminiscent of a conical pendulum, displaying a mix of ordered and disordered behaviors, prior to evolving into a completely molten and disordered state. While the melting of BA cations is the primary driver of the phase transition, the rotational dynamics of MA cations also plays a critical role in determining the phase transition temperature, influenced by the BA-MA interaction. Such interaction alters the polarization patterns of MA cations across the phase transition. In particular, an anti-parallel polarization pattern is observed in low temperature phase. Additionally, displacive elements of the phase transition are identified in the simulations, characterized by the shear and distortion of the inorganic octahedra. Notably, at lower temperatures, the octahedral distortion follows a bimodal distribution, reflecting significant variations in distortion among octahedra. This variation is attributed to an anisotropic hydrogen bonding network between iodides and BA cations. Our study reveals new phenomena and mechanisms extending beyond the order-disorder transition mechanism, shedding new light on potential phase engineering through strategic tuning of organic and inorganic components. | Reza Namakian; Maria Alejandra Garzon; Qing Tu; Ali Erdemir; Wei Gao | Theoretical and Computational Chemistry; Materials Science; Nanostructured Materials - Materials; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aab10601103d79c55f1010/original/temperature-induced-phase-transition-in-2d-alkylammonium-lead-halide-perovskites-a-molecular-dynamics-study.pdf |
6482e1fdbe16ad5c57af76eb | 10.26434/chemrxiv-2023-6ldv7 | Understanding the effects of ethanol on structural changes in liposomes using microfluidic-based time-resolved small-angle X-ray scattering and MD simulations | Lipid nanoparticles (LNPs) are essential carrier particles in drug delivery systems, particularly in ribonucleic acid delivery. In preparing lipid-based nanoparticles, microfluidic-based ethanol injection may produce precisely size-controlled nanoparticles. Ethanol is critical in LNP formation and post-treatment processes and affects liposome size, structure, lamellarity, and drug-loading efficiency. However, the effects of time-dependent changes in the ethanol concentration on the structural dynamics of liposomes are not clearly understood. Herein, we investigated ethanol-induced structural changes in liposomes on a time scale from microseconds to tens of seconds using a microfluidic-based small-angle X-ray scattering (SAXS) measurement system coupled with molecular dynamics (MD) simulations. The time-resolved SAXS measurement system revealed that single unilamellar liposomes converted to multilamellar liposomes within 0.8 s of contact with ethanol, and the d-spacing was decreased from 6.1 (w/o ethanol) to 4.4 nm (80% ethanol) with increasing ethanol concentration. We conducted 1 µs MD simulations to understand the molecular-level structural changes in the liposomes. The MD simulations revealed that the changes in the lamellar structure caused by ethanol at the molecular level could explain the structural changes in the liposomes observed via time-resolved SAXS. Therefore, the post-treatment process to remove residual ethanol is critical in liposome formation. | Masatoshi Maeki; Niko Kimura; Yuto Okada; Kazuki Shimizu; Kana Shibata; Yusuke Miyazaki; Akihiko Ishida; Kento Yonezawa; Nobutaka Shimizu; Wataru Shinoda; Manabu Tokeshi | Materials Science | CC BY 4.0 | CHEMRXIV | 2023-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6482e1fdbe16ad5c57af76eb/original/understanding-the-effects-of-ethanol-on-structural-changes-in-liposomes-using-microfluidic-based-time-resolved-small-angle-x-ray-scattering-and-md-simulations.pdf |
65295aa545aaa5fdbbefc830 | 10.26434/chemrxiv-2023-rrpkw-v2 | Markov state models: to optimize or not to optimize | Markov state models (MSM) are a popular statistical method for analyzing the conformational dynamics of proteins, including protein folding. With all statistical and machine learning (ML) models choices must be made about the modeling pipeline that cannot be directly learned from the data. These choices, or hyperparameters, are often evaluated by expert judgment or, in the case of MSMs, by maximizing variational scores such as the VAMP-2 score. Modern ML and statistical pipelines often use automatic hyperparameter selection techniques ranging from the simple: choosing the best score from a random selection of hyperparameters to the complex: optimization via e.g., Bayesian optimization. In this work, we ask whether it is possible to automatically select MSM models this way by estimating and analysing over 16'000'000 observations from over 280'000 estimated MSMs. We find that differences in hyperparameters can change the physical interpretation of the optimization objective making automatic selection difficult. In addition, we find that enforcing conditions of equilibrium in the VAMP scores can result in inconsistent model selection. However, other parameters which specify the VAMP-2 score (lag time and number of relaxation processes scored) have only negligible influence on model selection. We suggest that model observables and variational scores should only be a guide to model selection and that a full investigation of the MSM properties be undertaken when selecting hyperparameters. | Robert Arbon; Yanchen Zhu; Antonia S. J. S. Mey | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Chemical Kinetics | CC BY 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65295aa545aaa5fdbbefc830/original/markov-state-models-to-optimize-or-not-to-optimize.pdf |
635fca4fac45c728c79f713f | 10.26434/chemrxiv-2022-qkrrh | Asymmetric [3,3]-Sigmatropic Rearrangement of Sulfoniums for the Synthesis of Quaternary Center-Containing Polycyclic Molecules: Application to the Total Synthesis of Myrmenaphthol A | The asymmetric total synthesis of myrmenaphthol A, a natural product isolated from a Hawaiian sponge of the genus myrmekioderma, has been achieved in 12 steps. The key transformation of this synthesis is a gold-catalyzed [3,3]-sigmatropic rearrangement of sulfonium, starting from a chiral sulfoxide substrate and propargyl silane. The development of the methodology included the synthesis of benz[e]inden-2-one derivatives with quaternary centers (51-78% yield, 90-99% ee). | Weiping ZHOU; Arnaud Voituriez | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635fca4fac45c728c79f713f/original/asymmetric-3-3-sigmatropic-rearrangement-of-sulfoniums-for-the-synthesis-of-quaternary-center-containing-polycyclic-molecules-application-to-the-total-synthesis-of-myrmenaphthol-a.pdf |
65c684e766c13817294e53ec | 10.26434/chemrxiv-2024-hd8t4 | Appending polyamines on MOFs as an efficient strategy for selective removal of H2S under humid conditions | Removal of highly toxic and corrosive hydrogen sulphide from gas flows is of paramount importance for the environment and in industrial processes. This contribution reports a simple strategy to obtain materials for efficient hydrogen sulphide removal under humid conditions by functionalization of open-metal sites in metal-organic frameworks (MOFs) with polyamines. | Guillaume Esser; Robin Crits; Gabriella Barozzino-Consiglio; Yaroslav Filinchuk; Sophie Hermans; Timothy Steenhaut | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c684e766c13817294e53ec/original/appending-polyamines-on-mo-fs-as-an-efficient-strategy-for-selective-removal-of-h2s-under-humid-conditions.pdf |
67aea27e6dde43c908c749e8 | 10.26434/chemrxiv-2025-3dn5z | Synthesis of α,α-Difluoro-β-amino Amides using Aldimines and Bromodifluoroacetamides via Zinc-Promoted Reformatsky Reaction | α,α-Difluoro-β-amino amides are one of the attractive building blocks of biologically active compounds such as fluorinated pharmaceutical mimics and oligopeptides. Herein, we describe zinc-promoted Reformatosky reaction of aldimines using bromodifluoroacetamides provides a directly synthetic approach to α,α-difluoro-β-amino amides. This method gave various N-PMP protected α,α-difluoro-β-amino-β-aryl amides in 64–95% yields. | Ryota Ozawa; Tetsuya Yamamoto | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aea27e6dde43c908c749e8/original/synthesis-of-difluoro-amino-amides-using-aldimines-and-bromodifluoroacetamides-via-zinc-promoted-reformatsky-reaction.pdf |
66b222dd5101a2ffa8405826 | 10.26434/chemrxiv-2024-q0ng5 | Strategies and Tactics for Site Specific Deuterium Incorporation at Each Available Carbon Atom of a-Pinene | The development of several unique strategies and tactics for the synthesis of a-pinene isotopologues that has culminated in access to all eight possible isomers with deuterium incorporated selectively at each available carbon atom is described. Access to this library of isotopologues provides new tools to more fully investigate the atmospheric autoxidation of a-pinene, a complex process that plays a major role in the formation of secondary organic aerosol (SOA) in the Earth’s atmosphere. | Regan Thomson; Jingyi Luo; Mary Alice Upshur; Marvin Vega; Nicolle Doering; Jonathan Varelas; Zhouyang Ren; Franz Geiger; Richmond Sarpong | Organic Chemistry; Earth, Space, and Environmental Chemistry; Natural Products; Organic Synthesis and Reactions; Atmospheric Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b222dd5101a2ffa8405826/original/strategies-and-tactics-for-site-specific-deuterium-incorporation-at-each-available-carbon-atom-of-a-pinene.pdf |
651b1179a69febde9e1bf429 | 10.26434/chemrxiv-2023-9s46z | Effect of ligand and shell densities on surface structure of core-shell nanoparticles self-assembled from function-spacer-lipid constructs | Biomolecular corona is the major obstacle in clinical translation of nanomedicines. To overcome this problem, comprehensive studies of the processes leading to the formation of a biomolecular corona are required. Since such dynamical studies require high spatial and temporal resolution, nanoparticles utilized in it should enable combined experimental and simulation studies. Interactions at nano-bio interface are defined by nanoparticle surface properties such as topography, charge and surface chemistry. Hence, as the preliminary step towards deep understanding of the processes of corona formation it is necessary to develop nanoparticles employing various biocompatible materials and characterize their surface properties. In this work, we applied molecular dynamics simulation to study surface structure of organic core-shell nanoparticles formed by self-assembly of synthetic molecules composed of DOPE lipid, carboxymethylglycine spacer and biotin. Lipid moieties form the hydrophobic core, spacer motifs serve as a hydrophilic shell and biotin residues function as targeting ligand. By mixing such function-spacer-lipid, spacer-lipid and lipid-only constructs at various molar ratios, densities of the ligand and spacer on nanoparticle surface were modified. For convenient analysis of the structure and dynamics of all regions of nanoparticles’ surface, we compiled topography maps based on atomic coordinates. It was shown that an increase in the density of the shell does not reduce exposure of the core, but increases shell average thickness. Biotin, due to its alkyl valeric acid chain and spacer flexibility, is localized primarily near the hydrophobic core and its partial presentation on the surface occurs only in nanoparticles with higher ligand densities. However, an increase in biotin density leads to its clustering. In turn, ligand clustering diminishes stealth properties of the shell and targeting efficiency. Based on nanoparticle surface structures we determined the optimal density of biotin. Experimental studies reported in the literature confirm these conclusions. We also suggest design tips to achieve preferred biotin presentation. Simulation results are consistent with the synchrotron SAXS profile. We believe that such studies will contribute to the better understanding of nano-bio interactions towards the rational design of efficient drug delivery systems. | Ivan Vaskan; Veronika Dimitreva; Maxim Petoukhov; Eleonora Shtykova; Nicolai Bovin; Alexander Tuzikov; Marina Tretyak; Vladimir Oleinikov; Anton Zalygin | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651b1179a69febde9e1bf429/original/effect-of-ligand-and-shell-densities-on-surface-structure-of-core-shell-nanoparticles-self-assembled-from-function-spacer-lipid-constructs.pdf |
65f2fe62e9ebbb4db9b0c185 | 10.26434/chemrxiv-2024-4btcl | Lignin-based Mucin-mimicking Antiviral Hydrogels with Enzyme Stability and Tunable Porosity | Mucus is a complex hydrogel acting as a defensive and protective barrier in various parts of the human body. The structure and composition of mucus play an important role in maintaining barrier properties by acting as a filter for the diffusion of biomolecules and pathogens. The rise in viral infections has underscored the importance of advancing research into mucus-mimicking hydrogels for the efficient design of antiviral agents. However, the performance of an antiviral strategy should not only be assessed based on its efficacy in inhibiting infections but also based on its sustainability. Herein, we demonstrate the gram-scale synthesis of biocompatible, lignin-based virus-binding inhibitors that reduce waste and ensure long-term availability. The lignin-based inhibitors were equipped with sulfate moieties, which are known binding partners for many viruses including SARS-CoV-2 and herpes viruses. In addition, crosslinking the synthesized inhibitors yielded hydrogels that mimicked native mucus with respect to surface functionality and rheology. It is found that the degree of sulfation has a very strong impact on the mesh size distribution of the hydrogels, which provides a new means to fine-tune steric and electrostatic contributions of the virus-hydrogel interaction. This feature strongly impacts the sequestration capability of the lignin-based hydrogels, which is demonstrated by infection inhibition assays involving human herpes simplex virus-1, influenza A viruses, and the bacterium Escherichia coli (E. coli). For HSV-1 and E. coli, these measurements showed a reduction in plaque (HSV-1) and colony-forming units (E. coli) by more than 4 orders of magnitude, indicating potent inhibition by the lignin-based hydrogels. Taken together, the sulfated lignin hydrogel is an excellent scaffold for large-scale synthesis of sustainable, biocompatible, and highly efficient pathogen-binding inhibitors.
| Sanjam Chandna; Tatyana L. Povolotsky; Chuanxiong Nie; Stefanie Wedepohl; Elisa Quaas; Kai Ludwig; Yulia Boyakova; Sumati Bhatia; Klas Meyer; Jana Falkenhagen; Rainer Haag; Stephan Block | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f2fe62e9ebbb4db9b0c185/original/lignin-based-mucin-mimicking-antiviral-hydrogels-with-enzyme-stability-and-tunable-porosity.pdf |
666c37675101a2ffa8950cc3 | 10.26434/chemrxiv-2024-fvcvk | Analyzing Fusion Pore Dynamics and Counting the Number of Acetylcholine Molecules Released by Exocytosis | Acetylcholine (ACh) is a critical neurotransmitter influencing various neurophysiological functions. Despite its significance, there is a lack of quantitative methods with adequate spatiotemporal resolution for recording single exocytotic efflux of ACh. In this study, we present an ultrafast amperometric ACh biosensor enabling electrochemical recording that captures spontaneous bursts of single presynaptic exocytosis events at axon terminals of cholinergic cells with sub-millisecond temporal resolution. Characterization of the recorded amperometric time trace revealed seven distinct current spike types, each displaying variations in both spike shape, time scale and quantities of ACh released through the synaptic vesicle fusion pore. This observation suggests the presence of multiple exocytosis modes at these cells. Quantifying the absolute number of ACh molecules released at single exocytosis events was achieved through sensor calibration using electroanalytical measurements of synthetic lipid vesicles containing varying concentrations of ACh. Notably, the largest quantal release was estimated at approximately 8000 ACh molecules, likely representing full exocytosis, while the fractional release of roughly 5000 ACh molecules correspond to a partial exocytosis mode. Following a local administration of bafilomycin A1, a V-ATPase inhibitor, the cholinergic cells exhibited both a higher frequency and larger quantity of ACh released during exocytosis events. Hence, this ACh sensor introduces means to monitor minute amounts of ACh and investigate regulatory mechanisms at single-cell level, which is vital for understanding healthy brain function, pathologies, and optimizing drug treatment for disorders. | Yuanmo Wang; Ajay Pradhan; Pankaj Gupta; Jörg Hanrieder; Henrik Zetterberg; Ann-Sofie Cans | Biological and Medicinal Chemistry; Materials Science; Analytical Chemistry; Nanostructured Materials - Materials; Electrochemical Analysis; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666c37675101a2ffa8950cc3/original/analyzing-fusion-pore-dynamics-and-counting-the-number-of-acetylcholine-molecules-released-by-exocytosis.pdf |
6100ca157bf0c9e87861589a | 10.26434/chemrxiv-2021-tb31g | Topology-Mediated Enhanced Polaron Coherence
in Covalent Organic Frameworks | We employ the Holstein model for polarons to investigate the relationship among defects, topology, Coulomb trapping, and polaron delocalization in covalent organic frameworks (COFs). We find that intra-sheet topological connectivity and pi-column density can override disorder-induced deep traps and significantly enhance polaron migration by several orders of magnitude in good agreement with recent experimental observations. The combination of percolation networks and micropores makes trigonal COFs ideally suited for charge transport followed by kagome/tetragonal, and hexagonal structures. By comparing the polaron spectral signatures and coherence numbers of large 3D frameworks having a maximum of 180 coupled chromophores, we show that controlling nanoscale defects and the location of the counter anion is critical for the design of new COF-based materials yielding higher mobilities. Our analysis establishes design strategies for enhanced conductivity in COFs which can be readily
generalized to other classes of conductive materials such as metal-organic frameworks and perovskites. | Raja Ghosh; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6100ca157bf0c9e87861589a/original/topology-mediated-enhanced-polaron-coherence-in-covalent-organic-frameworks.pdf |
60c74229bb8c1a27713da078 | 10.26434/chemrxiv.8222492.v1 | A Highly Crystalline Anthracene-Based MOF-74 Series Featuring Electrical Conductivity and Luminescence | Recently, a small group of metal-organic frameworks (MOFs) has been discovered featuring substantial charge transport properties and electrical conductivity, hence promising to broaden the scope of potential MOF applications in fields such as batteries, fuel cells and supercapacitors. In combination with light emission, electroactive MOFs are intriguing candidates for chemical sensing and optoelectronic applications. Here, we incorporated anthracene-based building blocks into the MOF-74 topology with five different divalent metal ions, that is, Zn2+, Mg2+, Ni2+, Co2+ and Mn2+, resulting in a series of highly crystalline MOFs, coined ANMOF-74(M). This series of MOFs features substantial photoluminescence, with ANMOF-74(Zn) emitting across the whole visible spectrum. The materials moreover combine this photoluminescence with high surface areas and electrical conductivity. Compared to the original MOF-74 materials constructed from 2,5-dihydroxy terephthalic acid and the same metal ions Zn2+, Mg2+, Ni2+, Co2+ and Mn2+, we observed a conductivity enhancement of up to six orders of magnitude. Our results point towards the importance of building block design and the careful choice of the embedded MOF topology for obtaining materials with desired properties such as photoluminescence and electrical conductivity. | Patricia Scheurle; Andre Mähringer; Andreas Jakowetz; Pouya Hosseini; Alexander Richter; Gunther Wittstock; Dana D. Medina; Thomas Bein | Hybrid Organic-Inorganic Materials; Optical Materials; Physical and Chemical Properties; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74229bb8c1a27713da078/original/a-highly-crystalline-anthracene-based-mof-74-series-featuring-electrical-conductivity-and-luminescence.pdf |
60c74f990f50db7d7b397425 | 10.26434/chemrxiv.12924200.v1 | A Nonconjugated Radical Polymer with Stable Red Luminescence in Solid State | <p><b>Luminescent
organic radicals have attracted much attention due to its distinctive
open-shell structure and all-in-one properties on optoelectronics</b><b>,
electronics</b><b>,
and magnetics</b><b>.
However, organic radicals are usually instable</b><b> and only very limited stable structures with π-radicals can </b><b>exhibit luminescent property</b><b>
in the isolated state, most of which originate from the family of
triphenylmethyl derivatives</b><b>.
Here, we report an unusual radical luminescence phenomenon that nonconjugated
radical polymer can readily emits red luminescence at ~635 nm in the solid
state. A traditional luminescence quencher, 2,2,6,6-tetramethylpiperidine
1-oxyl (TEMPO)</b><b>,
was turned into a red chromophore when grafted onto a polymer backbone.
Experimental data confirms the emission is associated with the nitroxide
radicals and is also affected by the packing of polymer. As a proof of concept,
a biomedical application in intracellular ascorbic acid visualization is
demonstrated. This work discloses a novel class of luminescent radicals and
provides a distinctive and simple pathway for stable radical luminescence. </b></p> | Zhaoyu Wang; Xinhui Zou; Yi Xie; Haoke Zhang; lianrui hu; Christopher C. S. Chan; Ruoyao Zhang; Jing Guo; Ryan Tsz Kin Kwok; Jacky W. Y. Lam; ian duncan williams; Zebing Zeng; Kam Sing Wong; c. david sherrill; Ruquan Ye; Ben Zhong Tang | Aggregates and Assemblies; Dyes and Chromophores; Nanostructured Materials - Materials; Oligomers; Optical Materials | CC BY NC 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f990f50db7d7b397425/original/a-nonconjugated-radical-polymer-with-stable-red-luminescence-in-solid-state.pdf |
66e98b63cec5d6c142572268 | 10.26434/chemrxiv-2024-3q21n | Selective Ni-Catalyzed Cross-Electrophile Coupling of Heteroaryl Chlorides and Aryl Bromides at 1:1 Substrate Ratio | Nickel-catalyzed cross-electrophile coupling (XEC) reactions of (hetero)aryl electrophiles represent appealing alternatives to palladium-catalyzed methods for biaryl synthesis, but they often generate significant quantities of homocoupling and/or proto-dehalogenation side products. In this study, an informer library of heteroaryl chloride and aryl bromide coupling partners is used to identify Ni-catalyzed XEC conditions that access high selectivity for the cross-product when using equimolar quantities of the two substrates. Two different catalyst systems are identified that show complementary scope and broad functional-group tolerance, and time-course data suggest the two methods follow different mechanisms. A NiBr2/terpyridine catalyst system with Zn as the reductant converts the aryl bromide into an aryl-zinc intermediate that undergoes in situ coupling with 2-chloropyridines, while a NiBr2/bipyridine catalyst system with tetrakis(dimethylamino)ethylene as the reductant uses FeBr2 and NaI as additives to achieve selective cross-coupling. | Zhi-Ming Su; Darren L. Poole; Mohammad Rafiee; Robert S. Paton; Daniel J. Weix; Shannon Stahl | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e98b63cec5d6c142572268/original/selective-ni-catalyzed-cross-electrophile-coupling-of-heteroaryl-chlorides-and-aryl-bromides-at-1-1-substrate-ratio.pdf |
6613c165418a5379b061c634 | 10.26434/chemrxiv-2024-78mtl | The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis | Natural products, also known as specialized or secondary metabolites, show extraordinary chemical diversity and potent biological activities. Their biosynthesis usually first encompasses scaffold generation, followed by additional tailoring and maturation steps, leading to the mature compound. The latter steps are often performed by accessory enzymes known as tailoring enzymes or maturases. While knowledge about reaction and substrate specificities of these enzymes is essential for natural product biosynthesis, it is often scattered in the literature, hampering understanding and computational processing. Here, we conceptualize the Minimum Information about a Tailoring Enzyme/Maturase (MITE) data standard. We envision this data standard to serve in collecting experimentally verified data on reaction, substrate specificity, and other metadata of tailoring enzymes. Closely associated with the previously established Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard, MITE will aim to capture tailoring enzyme reaction information that is currently not systemized. We anticipate that MITE will accelerate natural product structure predictions from sequence, evolutionary analyses of biosynthetic pathways and synthetic biology engineering of specialized metabolic pathways. | Mitja M. Zdouc; David Meijer; Friederike Biermann; Jonathan Holme; Aleksandra Korenskaia; Annette Lien; Nico L. L. Louwen; Jorge C. Navarro-Muñoz; Giang-Son Nguyen; Adriano Rutz; Anastasia Sveshnikova; Judith Szenei; Barbara Terlouw; Rosina Torres Ortega; Marc Feuermann; Alan J. Bridge; Justin J. J. van der Hooft; Tilmann Weber; Nadine Ziemert; Kai Blin; Marnix H. Medema | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6613c165418a5379b061c634/original/the-minimum-information-about-a-tailoring-enzyme-maturase-data-standard-for-capturing-natural-product-biosynthesis.pdf |
662b7200418a5379b0c6d495 | 10.26434/chemrxiv-2024-x2q9h | Novel superhard tetragonal hybrid sp3/sp2 carbon allotropes Cx (x = 5, 6, 7): Crystal chemistry and ab initio studies | Novel superhard tetragonal carbon allotropes C5, C6, and C7, characterized by the presence of sp3- and sp2-like carbon sites, have been predicted from crystal chemistry and extensively studied by quantum density functional theory (DFT) calculations. All new allotropes were found to be cohesive, with crystal densities and cohesive energies decreasing along the C5 C6 C7 series due to the greater openness of the structures resulting from the presence of C=C ethene and C=C=C propadiene subunits, and mechanically stable with positive sets of elastic constants. The Vickers hardness evaluated by different models qualifies all allotropes as superhard. Phonon band structures confirm that the new allotropes are also dynamically stable. The electronic band structures reveal their metallic-like behavior due to the presence of sp2-hybridized carbon. | Samir F. Matar; Vladimir L. Solozhenko | Inorganic Chemistry; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662b7200418a5379b0c6d495/original/novel-superhard-tetragonal-hybrid-sp3-sp2-carbon-allotropes-cx-x-5-6-7-crystal-chemistry-and-ab-initio-studies.pdf |
624eee7e02f70158cada75d5 | 10.26434/chemrxiv-2022-2hhqw-v3 | Synthesis of π-Extended Thiele's and Chichibabin's Hydrocarbons and Effect of the π-congestion on Conformations and Electronic States | The biradicaloid of Chichibabin’s hydrocarbon exits in a unique thermal equilibrium between closed-shell singlet and open-shell triplet forms. Conceptually, the incorporation of non-planar aromatic groups, such as anthraquinodimethane (AQD), in these species could bring about stabilization of the individual singlet and triplet spin biradicaloids by creating a high energy barrier for con-formational interconversion between folded (singlet) and twisted (triplet) forms. Moreover, this alteration could introduce the possibility of controlling spin states through conformational changes induced by chemical and physical processes. Herein, we report the preparation of AQD containing, π-extended Thiele's (A-TH) and Chichibabin's (A-CH) hydrocarbons, which have highly π-congested structures resulting from the presence of bulky 9-anthryl units. The π-congestion in these substances leads to steric frustration about carbon-carbon double bonds, and creates flexible dynamic motion with a moderate activation barrier between folded singlet and twisted triplet states. These constraints make it possible to isolate the twisted triplet state of A-CH. In addition, simple mechanical grinding of the folded singlet of A-CH produces the twisted triplet. | Tomohiko Nishiuchi; Seito Aibara; Hiroyasu Sato; Takashi Kubo | Organic Chemistry; Physical Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624eee7e02f70158cada75d5/original/synthesis-of-extended-thiele-s-and-chichibabin-s-hydrocarbons-and-effect-of-the-congestion-on-conformations-and-electronic-states.pdf |
63d8cf94d1632f652bea6026 | 10.26434/chemrxiv-2023-tjhkw | AI4Green: An Open-Source ELN for Green and Sustainable Chemistry | An Electronic Laboratory Notebook (ELN) combining features, including data archival, collaboration tools, and green and sustainability metrics for organic chemistry, is presented. AI4Green is a web-based application, available as open-source code and free to use. It offers the core functionality of an ELN, namely the ability to store reactions securely and share them among different members of a research team. As users plan their reactions and record it in the ELN, green and sustainable chemistry is encouraged by automatically calculating green metrics and color-coding hazards, solvents, and reaction conditions. The interface links a database constructed from data extracted from PubChem, enabling the automatic collation of information for reactions. The application's design facilitates the development of auxiliary sustainability applications, such as our Solvent Guide. As more reaction data is captured, subsequent work will include providing "intelligent" sustainability suggestions to the user. | Samuel Boobier; Joseph Davies; Ivan Derbenev; Christopher Handley; Jonathan Hirst | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d8cf94d1632f652bea6026/original/ai4green-an-open-source-eln-for-green-and-sustainable-chemistry.pdf |
60c75240842e65b256db3cd3 | 10.26434/chemrxiv.13274936.v1 | Organ-Specific Treatment for COVID-19: Rationale, Evidence, and Potential Candidates | <div><b>Background and Purpose:</b> COVID-19 has become the ongoing public health crisis of our time. Although it was first presented as a respiratory infection, extrapulmonary manifestations are increasingly reported. However, no effective therapeutic strategy for COVID-19 extrapulmonary involvement is currently available. The current study aims to analyze the pathogenesis of COVID-19 extrapulmonary complications to evaluate the rationale for proposing organ-specific treatment as a novel therapeutic strategy to manage these multisystemic complications.</div><div><b>Experimental Approach:</b> In this study, differentially expressed genes (DEGs) of SARS-CoV-2 infected extrapulmonary organs including human pluripotent stem cells (hPSCs)-derived liver organoids, hPSCs-derived pancreatic endocrine cells, and human-induced pluripotent stem cells (hiPSCs)-derived choroid plexus organoids were analyzed. First, pathway enrichment analysis is done based on the identified DEGs to compare the underlying biological pathways enriched upon SARS-CoV-2 infection in different organs to confirm the need for developing organ-specific treatment strategies. Then, these lists of DEGs are used in a connectivity map-based drug repurposing experiment to propose novel organ-specific therapeutic options.</div><div><b>Key Results:</b> The results reveal different biological pathways and networks responsible for SARS-CoV-2 multisystemic pathogenesis based on the organ involved that highlight the need for considering organ-specific treatments. Besides, some FDA-approved drugs are proposed as the potential therapeutic candidates for each infected cell line.</div><div><b>Conclusion and Implications:</b> Although COVID-19 extrapulmonary manifestations are increasing, management of these complications is still challenging. Traditional therapeutic strategies and already repurposed antiviral agents are not effective. In this situation, organ-specific treatment, or in other words personalized therapy might be a promising solution.</div> | mojdeh rahmanian; seyedeh zahra mousavi; Ashkan Sami | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75240842e65b256db3cd3/original/organ-specific-treatment-for-covid-19-rationale-evidence-and-potential-candidates.pdf |
60c73e3f0f50db75843955ff | 10.26434/chemrxiv.6752867.v1 | Ligand-Enabled, Palladium-Catalyzed Beta-C (sp3)–H Arylation of Weinreb Amides | <em>
</em><p>We
report the development of Pd(II)-catalyzed C(sp<sup>3</sup>)–H arylation of
Weinreb amides. A pyridinesulfonic acid ligand is designed to accommodate the
weak, neutral coordinating property of Weinreb amides via preserving the
cationic character of Pd center through zwitterionic assembly of Pd/ligand
complexes. DFT studies of the C–H cleavage step indicate that the superior
reactivity of 3-pyridinesulfonic acid ligand compared to pyridine, Ac-Gly-OH,
and ligandless conditions originates from the stabilization of overall
substrate-bound Pd species.</p><em>
</em> | Hojoon Park; Nikita Chekshin; Peng-Xiang Shen; jin-quan yu | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e3f0f50db75843955ff/original/ligand-enabled-palladium-catalyzed-beta-c-sp3-h-arylation-of-weinreb-amides.pdf |
66421a43418a5379b025fccb | 10.26434/chemrxiv-2024-frs38 | Sr dope rutile-RuO2 for enhanced Proton exchange membrane electrolyzed water | As an OER catalyst under acidic conditions, Ir has a high cost and poor activity. Ru is the most promising Ir substitute due to its lower cost and higher catalytic activity, and the development of Ir substitutes has become an urgent need. Herein, we have designed and prepared Sr-doped RuO2 to achieve an ultra-low overpotential (197 mV@ 10 mA cm-2).In the PEM single cell, a low pool voltage (1.686 V) was achieved at a current density of 1 A cm-2, together with a high stability retention over 400 h of testing. In addition, the catalytic degradation rates (4.63 ng h-1) were significantly lower than those of commercial RuO2, and the activity is attributed to the increased number of Ru3+ active sites and the very small size (5.10 nm). This work provides a new approach for the development of non-Ir-based catalysts with high activity and stability for acidic oxygen precipitation. | tianyu wu; jinbo wang; mengyi qiu; yubin jiang; chi song; junyi zheng; ru chen | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Fuels - Energy Science; Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66421a43418a5379b025fccb/original/sr-dope-rutile-ru-o2-for-enhanced-proton-exchange-membrane-electrolyzed-water.pdf |
60c73cc0337d6cd8afe26065 | 10.26434/chemrxiv.14627745.v1 | Fully Lignocellulose-Based PET Analogues for the Circular Economy | Polyethylene terephthalate (PET) is one of the most abundantly used polymers, but also a significant pollutant in oceans. Due to growing environmental concerns, novel PET alternatives are highly sought after. Here we present readily recyclable PET analogues made entirely from woody biomass. Central to the concept is a two-step noble metal free catalytic sequence (Cu20-PMO catalyzed reductive catalytic fractionation and Raney Ni mediated catalytic funneling) that allows for obtaining a single aliphatic diol (PC) in 56.4% efficiency as well as other product streams convertible to fuels. The diol PC is co-polymerized with methyl esters of terephthalic acid (TPA) and furan dicarboxylic acid (FDCA), both of which can be derived from the cellulose residues, to obtain polyesters with competitive Mw and thermal properties (Tg of 70–90 °C). The new polymers show excellent chemical recyclability in methanol and are thus promising candidates for the circular economy.<br /> | Xianyuan Wu; Maxim Galkin; Zhuohua Sun; Katalin Barta | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc0337d6cd8afe26065/original/fully-lignocellulose-based-pet-analogues-for-the-circular-economy.pdf |
65b2bd37e9ebbb4db9fba70d | 10.26434/chemrxiv-2024-k5mdb | [n]Cycloparaphenylenes as Compatible Fluorophores for Melt Electrowriting | Abstract: Fluorescent probes are an indispensable tool in the realm of bioimaging technologies, providing valuable insights into the assessment of biomaterial integrity and structural properties. However, incorporating fluorophores into scaffolds made from melt electrowriting (MEW) poses a challenge due to the sustained, elevated temperatures that this processing technique requires. In this context, we report that [n]cycloparaphenylenes ([n]CPPs) serve as excellent fluorophores for MEW processing with the additional benefit of customizable emissions profiles with the same excitation wavelength. We use three fluorescent blends with distinct [n]CPPs with emission wavelengths of either 466 nm, 494 nm, or 533 nm, identifying 0.01 wt.% as the preferred concentration. We discover that [n]CPPs disperse well within poly(ε-caprolactone) (PCL) and maintain their fluorescence even after a week of continuous heating at 80°C. The [n]CPP-PCL blends show no cytotoxicity and support counterstaining with commonly used DAPI (Ex/Em: 359nm/457nm), rhodamine- (Ex/Em: 542/565 nm), and fluorescein-tagged (Ex/Em: 490/515 nm) phalloidin stains. Using different color [n]CPP-PCL blends, we sequentially deposit different MEW fibers into a semi-woven scaffold and onto a solution electrospun membrane containing [8]CPP as a contrasting substrate for the [10]CPP MEW fibers. In general, [n]CPPs are potent fluorophores for MEW, providing new imaging options for this technology.
Introduction
| Patrick Hall; Harrison Reid; Ievgenii Liashenko; Biranche Tandon; Kelly O'Neill; Gabriella Lindberg; Ramesh Jasti; Paul Dalton | Polymer Science; Polymer blends; Polymer scaffolds | CC BY 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b2bd37e9ebbb4db9fba70d/original/n-cycloparaphenylenes-as-compatible-fluorophores-for-melt-electrowriting.pdf |
62dfa08c7f3aa6da5af79086 | 10.26434/chemrxiv-2022-7xf8p-v2 | Tapered Cross-Section Photoelectron Spectroscopy Provides Insights into the Buried Interfaces of III-V Semiconductor Devices | Interfaces are key elements that define electronic properties of the final device. Inevitably, most of the active interfaces of III-V semiconductor devices are buried and it is therefore not straightforward to characterize them. The Tapered Cross-Section Photoelectron Spectroscopy (TCS-PES) approach is promising to address such a challenge. We demonstrate here that the TCS-PES can be used to study the relevant heterojunction in epitaxial III-V architectures prepared by metalorganic chemical vapor deposition. A MULTIPREPTM polishing system that enables controlling the angle between the sample holder and the polishing plate has been employed to improve the reproducibility of the polishing procedure. With this procedure, we demonstrate that preparing the TCS of III-V semiconductor devices with tapering angles lower than 0.02° is possible. The PES provides then information about the buried interfaces of Ge|GaInP and GaAs|GaInP layer stacks. Both, chemical and electronic properties have been measured by PES. It evidences that the preparation of the TCSs under an uncontrolled atmosphere modifies the pristine properties of the critical buried heterointerfaces. Surface states and reaction layers are created on the TCS surface, which restrict unambiguous conclusions on buried interface energetics. | Clément Maheu; Mohammad Amin Zare Pour; Iban Damestoy; David Ostheimer; Maximilian Mellin; Dominik C. Moritz; Agnieszka Paszuk; Wolfram Jaegermann; Thomas Mayer; Thomas Hannappel; Jan Philipp Hofmann | Materials Science | CC BY 4.0 | CHEMRXIV | 2022-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62dfa08c7f3aa6da5af79086/original/tapered-cross-section-photoelectron-spectroscopy-provides-insights-into-the-buried-interfaces-of-iii-v-semiconductor-devices.pdf |
60c7506dbb8c1a41753dbafc | 10.26434/chemrxiv.13040699.v1 | Cooperative Activation of Cellulose with Natural Calcium | Naturally
occurring metals such as calcium catalytically activate the inter-monomer
β-glycosidic bonds in long chains of cellulose initiating reactions to volatile
oxygenates for renewable applications. In this work, the millisecond kinetics
of calcium catalyzed reactions were measured via the method of pulse-heated
analysis of solid/surface reactions (PHASR) at high temperature (370-430 °C) to
reveal accelerated glycosidic ether scission with a second order rate
dependence on Ca<sup>2+</sup> ions. First principles density functional theory
(DFT) calculations were used to identify stable binding configurations for two
Ca<sup>2+</sup> ions that demonstrated accelerated transglycosylation kinetics
with an apparent activation barrier of 50 kcal mol<sup>-1</sup> for a
cooperative calcium catalyzed cycle. The agreement of mechanism with calcium
cooperativity to the experimental barrier (48.7 ± 2.8 kcal mol<sup>-1</sup>)
suggests that calcium enhances reactivity through a dual role of disrupting
native H-bonding and stabilizing charged transition states. | Gregory G. Facas; Vineet Maliekkal; Cheng Zhu; Matthew Neurock; Paul Dauenhauer | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7506dbb8c1a41753dbafc/original/cooperative-activation-of-cellulose-with-natural-calcium.pdf |
667c65f6c9c6a5c07a76df0c | 10.26434/chemrxiv-2024-rt585-v3 | Natural Fragment Bond Orbital Method for Inter-Fragment Bonding Interaction Analysis | A complex chemical system is often examined based on their fragments, so fragment-based analysis is the key to chemical understanding. We report the natural fragment bond orbital (NFBO) method for inter-fragment bonding interaction analysis, as an extension to the well-known natural bond orbital method. NFBOs together with their corresponding natural fragment hybrid orbitals (NFHOs) allow us to derive local bonding and anti-bonding orbitals among fragments from the delocalized canonical molecular orbitals. In this paper, we provide the algorithm for finding NFBOs and showcase its application to several chemically interesting systems featuring significant inter-fragment bonding interactions. Through these examples, the NFBO method is shown to be a powerful tool for molecules possessing strong inter-fragment bonding interactions. | Yichi ZHANG; Fu Kit Sheong; Zhenyang Lin | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Coordination Chemistry (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c65f6c9c6a5c07a76df0c/original/natural-fragment-bond-orbital-method-for-inter-fragment-bonding-interaction-analysis.pdf |
61b1adcf02d90d02df5a1f6c | 10.26434/chemrxiv-2021-z08zx | Dissociation pathways of the p53 DNA binding domain from DNA and critical roles of key residues elucidated by dPaCS-MD/MSM | The dissociation process of the DNA binding domain of p53 (p53-DBD) from a DNA duplex that contains the consensus sequence, which is the specific target of p53-DBD, was investigated by a combination of dissociation parallel cascade selection molecular dynamics (dPaCS-MD) and the Markov state model (MSM). Based on an all-atom model including explicit solvent, we first simulated the p53-DBD dissociation processes by 75 trials of dPaCS-MD, which required an average simulation time of 11.2 ± 2.2 ns per trial. By setting the axis of the DNA duplex as the Z-axis and the binding side of p53-DBD on DNA as the + side of the X-axis, we found that dissociations took place along the +X and −Y directions (−Y directions) in 93% of the cases, while 7% of the cases moved along +X and +Y directions (+Y directions). Toward the −Y directions, p53-DBD dissociated first from the major groove and then detached from the minor groove, while unbinding from the minor groove occurred first in dissociations along the +Y directions. Analysis of the free energy landscape by MSM showed that loss of the minor groove interaction with p53-DBD toward the +Y directions incurred a relatively high energy cost (1.1 kcal/mol) upon a critical transition, whereas major groove detachment more frequently occurred with lower free energy costs. The standard binding free energy calculated from the free energy landscape was −10.9 ± 0.4 kcal/mol, which agrees with an experimental value of –11.1 kcal/mol. These results indicate that the dPaCS-MD/MSM combination can be a powerful tool to investigate dissociation mechanisms of two large molecules. Minor groove binding is mainly stabilized by R248, identified as the most important residue that tightly binds deep inside the minor groove. Analysis of the p53 key residues for DNA binding indicates high correlations with cancer-related mutations, confirming that impairment of the interactions between p53-DBD and DNA can be frequently related to cancer. | Mohamed Sobeh; Akio kitao | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b1adcf02d90d02df5a1f6c/original/dissociation-pathways-of-the-p53-dna-binding-domain-from-dna-and-critical-roles-of-key-residues-elucidated-by-d-pa-cs-md-msm.pdf |
62b151c7486c984d6aacb1d3 | 10.26434/chemrxiv-2022-kkjvx | Data-Driven Many-Body Potential Energy Functions for Generic Molecules: Linear Alkanes as a Proof-of-Concept Application | We present a generalization of the many-body energy (MB-nrg) theoretical/computational framework that enables the development of data-driven potential energy functions (PEFs) for generic covalently bonded molecules, with arbitrary quantum mechanical accuracy. The “nearsightedness of electronic matter” is exploited to define monomers as “natural building blocks” based on their distinct chemical identity. The energy of generic molecules is then expressed as a sum of individual many-body energies of incrementally larger subsystems. The MB-nrg PEFs represent the low-order n-body energies, with n = 1 − 4, using permutationally invariant polynomials derived from electronic structure data carried out at an arbitrary quantum mechanical level of theory, while all higher-order n-body terms (n > 4) are represented by a classical many-body polarization term. As a proof-of-concept application of the general MB-nrg framework, we present MB-nrg PEFs for linear alkanes. The MB-nrg PEFs are shown to accurately reproduce reference energies, harmonic frequencies, and potential energy scans of alkanes, independently of their length. Since, by construction, the MB-nrg framework introduced here can be applied to generic covalently bonded molecules, we envision future computer simulations of complex molecular systems using data-driven MB-nrg PEFs, with arbitrary quantum mechanical accuracy. | Ethan F. Bull-Vulpe; Marc Riera; Sigbjørn L. Bore; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b151c7486c984d6aacb1d3/original/data-driven-many-body-potential-energy-functions-for-generic-molecules-linear-alkanes-as-a-proof-of-concept-application.pdf |
60c752960f50db62a63979ee | 10.26434/chemrxiv.12971942.v2 | RetroPrime: A Chemistry-Inspired and Transformer-based Method for Retrosynthesis Predictions | Retrosynthesis prediction is a crucial task for organic synthesis. In this work, we propose a template-free and Transformer-based method dubbed RetroPrime, integrating chemists’ retrosynthetic strategy of (1) decomposing a molecule into synthons then (2) generating reactants by attaching leaving groups. These two steps are accomplished with versatile Transformer models, respectively. While RetroPrime performs competitively against all state-of-the art models on the standard USPTO-50K dataset, it manifests remarkable generalizability and outperforms the only published result by a non-trivial margin of 4.8% for the Top-1 accuracy on the large-scale USPTO-full dataset. It is known that outputs of Transformer-based retrosynthesis model tend to suffer from insufficient diversity and high invalidity. These problems may limit the potential of Transformer-based methods in real practice, yet no prior works address both issues simultaneously. RetroPrime is designed to tackle these challenges. Finally, we provide convincing results to support the claim that RetromPrime can more effectively generalize across chemical space. | Xiaorui Wang; Jiezhong Qiu; Yuquan Li; Guangyong Chen; Huanxiang Liu; Ben Liao; Chang-Yu Hsieh; Xiaojun Yao | Organic Synthesis and Reactions; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752960f50db62a63979ee/original/retro-prime-a-chemistry-inspired-and-transformer-based-method-for-retrosynthesis-predictions.pdf |
649e8f65ba3e99daef490af1 | 10.26434/chemrxiv-2023-kjcl6 | Exploring Adverse Outcome Pathways for Nanomaterials with semantic web technologies | Adverse Outcome Pathways (AOPs) have been proposed to facilitate mechanistic understanding of interactions of chemicals/materials with biological systems. Each AOP starts with a molecular initiating event (MIE) and possibly ends with adverse outcome(s) (AOs) via a series of key events (KEs). So far, the interaction of engineered nanomaterials (ENMs) with biomolecules, biomembranes, cells, and biological structures, in general, is not yet fully elucidated yet. There is also a huge lack of information on which AOPs are ENMs-relevant or -specific, despite numerous published data on toxicological endpoints they trigger, such as oxidative stress and inflammation. We propose to integrate related data and knowledge recently collected. Our approach combines the annotation of nanomaterials and their MIEs with ontology annotation to demonstrate how we can then query AOPs and biological pathway information for these materials. We conclude that a FAIR (Findable, Accessible, Interoperable, Reusable) representation of the ENM-MIE knowledge simplifies integration with other knowledge. | Jeaphianne van Rijn; Marvin Martens; Ammar Ammar; Mihaela-Roxana Cimpan; Valerie Fessard; Peter Hoet; Nina Jeliazkova; Sivakumar Murugadoss; Ivana Vinković Vrček; Egon Willighagen | Biological and Medicinal Chemistry; Materials Science; Biocompatible Materials; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649e8f65ba3e99daef490af1/original/exploring-adverse-outcome-pathways-for-nanomaterials-with-semantic-web-technologies.pdf |
60d24a46e211330acae048c1 | 10.26434/chemrxiv-2021-b53wx-v2 | A Favorable Path to Domain Separation in the Orange Carotenoid Protein | The Orange Carotenoid Protein (OCP) is responsible for nonphotochemical quenching (NPQ) in cyanobacteria, a defense mechanism against potentially damaging effects of excess light conditions. Domain separation is a critical step in the photocycle of OCP because it exposes the N-terminal domain to perform quenching of the phycobilisomes. Details regarding the mechanism and energetics of OCP domain separation remain unknown. In this work, we apply metadynamics to elucidate the protein rearrangements that lead to the active, domain-separated form of OCP. We find that translocation of the ketocarotenoid canthaxanthin has a profound effect on the energetic landscape and that domain separation only becomes favorable following translocation. Through pathway optimization methods, we characterize the most probable pathway to domain separation and reveal the barriers along that pathway. We find that the free energy barriers are relatively small (<5 kcal/mol), but the overall estimated kinetic rate is consistent with experimental measurements (>1 ms). | Mahmoud Sharawy; Natalia B. Pigni; Eric R. May; José A. Gascón | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d24a46e211330acae048c1/original/a-favorable-path-to-domain-separation-in-the-orange-carotenoid-protein.pdf |
60c7502d702a9b3a3218bcfd | 10.26434/chemrxiv.13002965.v1 | An Automatic Differentiation and Diagrammatic Notation Approach for Developing Analytical Gradients of Tensor Hyper-Contracted Electronic Structure Methods | We show how the combination of automatic differentiation (AD) and diagrammatic notation can facilitate the development of analytical nuclear derivatives for tensor hyper-contraction based (THC) electronic structure methods. The automatically-derived gradients are guaranteed to have the same scaling in terms of both operation count and memory footprint as the underlying energy calculations, and the computation of a gradient is roughly three times as costly as the underlying energy. The new AD/diagrammatic approach enables the first cubic scaling implementation of nuclear derivatives for THC tensors fitted in molecular orbital basis (MO-THC). Furthermore, application of this new approach to THC-MP2 analytical gradients leads to an implementation which is at least four times faster than the previously reported, manually-derived implementation. Finally, we apply the new approach to the 14 tensor contraction patterns appearing in the supporting subspace formulation of multireference perturbation theory, laying the foundation for future developments of analytical nuclear gradients and nonadiabatic coupling vectors for multi-state CASPT2. <br /> | Chenchen Song; Todd J. Martínez; Jeffrey B. Neaton | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7502d702a9b3a3218bcfd/original/an-automatic-differentiation-and-diagrammatic-notation-approach-for-developing-analytical-gradients-of-tensor-hyper-contracted-electronic-structure-methods.pdf |
617fef3e7a00210a79425564 | 10.26434/chemrxiv-2021-jh72b | Mechanochemical Ring-Opening Metathesis Polymerization: Development, Scope, and Mechano-Only Copolymer Synthesis | Ruthenium-alkylidene initiated ring-opening metathesis polymerization (Ru-ROMP) was realized under solid-state conditions employing a mechanochemical ball milling method, promoting greenness and broadening scope. High-speed ball milling provided sufficient mixing and energy to the reaction mixture comprised of the catalyst and solid monomers, thus eliminating the need for solvents. Studies on the catalytic species and ball milling parameters (liquid-assisted grinding, vibration frequency, and ball size) revealed that mechanical energy regulated solid-state Ru-ROMP and it follows similar mechanistic features of solution-phase reactions. The solubility and miscibility of monomer and Ru-initiator are not a limitation in solid-state ball milling. Without the use of a solvent, a wide spectrum of solid monomers, including ionomer, fluorous monomer, and macromonomers, were successfully polymerized. Finally, effective direct copolymerization of immiscible monomers such ionic/hydrophobic and ionic/fluorous monomers resulted in a set of copolymers that are difficult to make using traditional solution procedures. | Gue Seon Lee; Hyo Won Lee; Hyun Sub Lee; Taeyang Do; Jean-Louis Do; Jeewoo Lim; Tomislav Friščić; Jeung Gon Kim | Catalysis; Polymer Science; Polymerization (Polymers); Polymerization catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617fef3e7a00210a79425564/original/mechanochemical-ring-opening-metathesis-polymerization-development-scope-and-mechano-only-copolymer-synthesis.pdf |
635b9a58aca1980c8ee8e59c | 10.26434/chemrxiv-2022-vb60d | Density matrix via few dominant observables for the ultrafast non-radiative decay in pyrazine | Unraveling of the density matrix of a non-stationary quantum state as a function of a few observables provides a complementary view of quantum dynamics. Here we pay special attention to the entangled electron-nuclear motion. We have recently developed a practical way to identify the minimal set of the dominant observables that govern the quantal dynamics even in the case of strong non-adiabatic effects and large anharmonicity [Komarova et al., J. Chem. Phys. 155, 204110 (2021)]. Fast convergence in the number of the dominant contributions is achieved when instead of the density matrix we describe the time-evolution of the surprisal, the logarithm of the density operator. In the present work, we illustrate the efficiency of the proposed approach using an example of the early time dynamics in pyrazine in a Hilbert space accounting for up to four vibrational normal modes, {Q10a, Q6a, Q1 , Q9a}, and two coupled electronic states, the optically dark and the bright states. Dynamics in four-dimensional configurational space involve 19600 vibronic eigenstates. Our results reveal that the rate of the ultrafast population decay as well as the shape of the nuclear wave packets in 2D, accounting only for {Q10a, Q6a} normal modes, are accurately captured with only six dominant time-independent observables in the surprisal. Extension of the dynamics to three- and four-dimensional vibrational subspace requires only five additional constraints. The time-evolution of a quantum state in 4D vibrational space on two electronic states is thus compacted to only 11 time-dependent coefficients of these observables. | Ksenia Komarova | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635b9a58aca1980c8ee8e59c/original/density-matrix-via-few-dominant-observables-for-the-ultrafast-non-radiative-decay-in-pyrazine.pdf |
60c7531d337d6c322fe28805 | 10.26434/chemrxiv.13386917.v1 | Oxidative Ring Expansion of Cyclobutanols: Access to Functionalized 1,2-Dioxanes | Cyclobutanols undergo an oxidative ring
expansion into 1,2-dioxanols by using Co(acac)<sub>2</sub> and triplet oxygen (<sup>3</sup>O<sub>2</sub>)
as radical promoters. The formation of an alkoxy radical drives to the
regioselective break of the strained ring with stabilization of a new radical
on the most substituted side. The radical traps then oxygen to form
1,2-dioxanols. The reaction is particularly effective on secondary cyclobutanols
but can work also on tertiary alcohols. Further acetylation generates peroxycarbenium species under
catalytic Lewis acid conditions, which react with neutral nucleophiles. Many original
1,2-dioxanes, which would be difficult to prepare by another method, were then
obtained with a preferred 3,6-<i>cis</i>-configuration.
This method provides an interesting access to the total synthesis of many
natural endoperoxides. | María Martín López Martín López; Nicolas Jamey; Alexis Pinet; Bruno Figadère; Ferrié Laurent | Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7531d337d6c322fe28805/original/oxidative-ring-expansion-of-cyclobutanols-access-to-functionalized-1-2-dioxanes.pdf |
677c0b96fa469535b9fa9dcd | 10.26434/chemrxiv-2025-zrkfn | Impact of Mg2+ and pH on Amorphous Calcium Carbonate Nanoparticle Formation: Implications for Biomineralization and Ocean Acidification | Calcium carbonate biomineralization, crucial for many marine organisms, often proceeds via amorphous calcium carbonate (ACC) as an intermediate. Using a novel in situ small-angle X-ray scattering (SAXS) setup with sub-20 ms resolution, we reveal how magnesium and pH work together to shift ACC nanoparticle formation to the spinodal line, resulting in an exceptionally narrow size distribution. This narrow distribution is essential for forming well-ordered crystals from ACC particles, critical in biomineralization. We also show that small pH changes, such as those from ocean acidification, dramatically impact particle size distribution. These findings highlight the roles of magnesium and pH in controlling ACC crystallization and underscore the vulnerability of marine calcifiers to environmental changes. | Lucas Kuhrts; Hadar Shaked; Johanna Sklar; Elena Prudnikov; Sylvain Prevost; Gouranga Manna; Michael Sztucki; Alexander Katsman; Boaz Pokroy | Physical Chemistry; Materials Science; Inorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677c0b96fa469535b9fa9dcd/original/impact-of-mg2-and-p-h-on-amorphous-calcium-carbonate-nanoparticle-formation-implications-for-biomineralization-and-ocean-acidification.pdf |
667cb3a65101a2ffa897f91d | 10.26434/chemrxiv-2024-60p6l | Kinetic Investigation on Solvating Alkylamine Hofmann Elimination over Brønsted Acidic Zeolites | The presence of solvents can significantly alter the reaction kinetics of catalytic conversions, yet the mechanisms of the solvent effect remain widely debated and could greatly vary between different chemistries. We use vapor phase Hofmann elimination of tert-butylamine (TBA) to systematically investigate how solvents participate catalyzed reaction over Brønsted acid sites of solid acid catalysts and affect a catalytic cycle. Twenty commonly used organic and inorganic solvents were tested to investigate the relationship between solvent identity and their influence on reaction kinetics. Kinetic measurements showed a significant and reversible inhibition in rates of Hofmann elimination in the presence of every tested solvent, with the degrees of reduction vary from less than 10% for non-polar solvents (carbon dioxide, benzene, hexane) to more than 90 % (methanol, ethanol, 1-propanol, acetonitrile), which was found to exhibit a roughly linear against the molecular dipole moment of solvents. Additionally, the degree of reduction is not affected by the size of molecule as the carbon chain length increases, but is negatively related to the degree of substitution by alkyl group on the α-carbon as well as halogen atom on the β-carbon. Despite the significant kinetic inhibition and a 30 kJ mol-1 increase in the measured apparent activation energies, the temperature programmed surface reaction profiles performed with pre-adsorbed TBA with feeding of acetonitrile and methanol showed no change in the peak temperature from the catalyst without solvent feed. Cooperative adsorption complex formed between the surface tert-butylammonium and solvent molecule adsorbed on a neighboring framework oxygen, which is far less reactive towards Hofmann elimination, is proposed to be responsible for the observed rate inhibition. Also, the stability of adsorption complex formation is found to be affected by the proton affinity of solvent, as revealed by the kinetic modeling of experimental rate measurements. | Han Chen; Omar Abdelrahman | Catalysis; Acid Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667cb3a65101a2ffa897f91d/original/kinetic-investigation-on-solvating-alkylamine-hofmann-elimination-over-br-nsted-acidic-zeolites.pdf |
60c751e5337d6ca66fe2861b | 10.26434/chemrxiv.13227782.v1 | Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite | Today's fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future and hence, effective P use is crucial to avoid food shortage. A substantial amount of P from fertilizers gets adsorbed onto soil minerals to become unavailable to plants. Understanding P interaction with these minerals would help efforts that improve P efficiency. To this end we performed a molecular level analysis of the interaction of common organic P compounds (glycerolphosphate [GP] & inositol hexaphosphate [IHP]) with the abundant soil mineral (goethite) in presence of water. Molecular dynamics simulations are performed for goethite-IHP/GP-water complexes using the multiscale quantum mechanics/molecular mechanics method. Results show that GP forms monodentate (M) and bidentate mononuclear (B) motifs with B being more stable than M. IHP interacts through multiple phosphate groups with the \textbf{3M} motif being most stable. The order of goethite-IHP/GP interaction energies is: GP M < GP B < IHP M < IHP 3M. Water is important in these interactions as multiple proton transfers occur and hydrogen bonds are formed between goethite--IHP/GP complexes and water. We also present theoretically calculated infrared spectra which match reasonably well with frequencies reported in literature. | Prasanth Babu Ganta; Oliver Kühn; Ashour A. Ahmed | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751e5337d6ca66fe2861b/original/ab-initio-molecular-dynamics-simulations-of-the-interaction-between-organic-phosphates-and-goethite.pdf |
67ab7769fa469535b9ddb8a0 | 10.26434/chemrxiv-2025-stwm1 | Photochemical Single Electron Transfer Activation of Alkyl- and Aryl-halides by a Cerium(III) Triamidoamine Complex | Procedures for activating and degrading compounds containing carbon-halogen bonds are highly sought after due to the environmental persistence and potential hazards of such compounds. Such activations are challenging because of the high stability of these bonds, particularly those with C-F bonds. Here, we report on the activation of carbon-halogen bonds, including C-F bonds, by the cerium(III)-triamidoamine complex CeIIITRENTIPS (1, TRENTIPS = tris-(2-(tri-iso-propylsilylamidoethyl)amine). Under light irradiation, 1 reaches a strongly negative excited state redox potential, and our measurements enable it to be estimated as 3.2 V relative to Cp2Fe0/+. Hence, the photo-reactivity of 1 with carbon-halogen bonds has been established with numerous examples, including Persistent Organic Pollutants (POPs) and fluorinated compounds. The photoactivation of POPs is rapid, but the photoactive nature of the cerium(IV) products precludes complete conversion. This study provides insight into the activation of POPs that may benefit the future design of photodegradation approaches for these highly problematic compounds. | Adrien Combourieu; Stella Christodoulou; Laurent Maron; Eachann Assendjee; Nicolas Casaretto; Akos Banyasz; Olivier Maury; Matthew Gregson; Ashley Wooles; Stephen Liddle; Cedric Tard; Gregory Nocton; Grégory Danoun | Organic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligands (Organomet.); Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab7769fa469535b9ddb8a0/original/photochemical-single-electron-transfer-activation-of-alkyl-and-aryl-halides-by-a-cerium-iii-triamidoamine-complex.pdf |
61137bcce540bb9f2375af01 | 10.26434/chemrxiv-2021-k8b06 | Supramolecular Catalysis of a Catalysis-Resistant Diels-Alder Reaction: Rapid Dimerization of Cyclopentadiene inside Cucurbit[7]uril | In contrast to Diels-Alder reactions involving heteroatom-containing substrates, the endo dimerization of cyclopentadiene responds only very weakly to changes in microenvironment or the presence of potential catalysts (less than factor of 10 variation), although this pure hydrocarbon reaction has been used as an early model to predict the maximum possible catalytic effect (kcat/kuncat ca. 106 M) due to entropic contributions of a transition-state confinement (Page, M. I.; Jencks, W. P. Proc. Natl. Acad. Sci. USA 1971, 68, 1678). In the presence of cucurbit[n]uril homologues the reaction is selectively and almost maximally (kcat/kuncat ca. 4 × 105 M) accelerated by the intermediary sized cucurbit[7]uril in aqueous solution, while the other macrocyclic homologues display no acceleration or an inhibitory effect. The expected product inhibition due to the strong binding of the dicyclopentadiene reaction product can be overcome by addition of 10% methanol, which affords catalytic turnover numbers above 10. The reaction was monitored using 1H NMR spectroscopy as well as UV spectrophotometry. The analysis of the kinetic data, combined with packing coefficient considerations, modelling of Lennard-Jones potentials, and dispersion-corrected DFT calculations, suggest that the catalysis is due to an entropy-dominated transition-state stabilization in the tightly packed ternary complex. | Foad Tehrani; Khaleel Assaf; Robert Hein; Thomas Nugent; Werner Nau | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61137bcce540bb9f2375af01/original/supramolecular-catalysis-of-a-catalysis-resistant-diels-alder-reaction-rapid-dimerization-of-cyclopentadiene-inside-cucurbit-7-uril.pdf |
60c745de469df4bc50f4358b | 10.26434/chemrxiv.10279208.v1 | Rotaxanes with Dynamic Mechanical Chirality: Systematic Studies on Synthesis, Optical Resolution, Racemization, and Chiral-Prochiral Interconversion | Dynamic mechanical chirality of [2]rotaxane consisting of a <i>C</i><sub>s</sub> symmetric wheel and a <i>C</i><sub>2v</sub> symmetric axle is discussed via the synthesis, optical resolution, racemization, and chiral-prochiral interconversion. This [2]rotaxane is achiral and/or prochiral when its wheel locates at the center of the axle, but becomes chiral when the wheel moves from the center of the axle. These were proved by the experiments on the optical resolution and racemization. The racemization energy of the optically resolved enantiomers was controlled by the bulkiness of the central substituents on the axle. Furthermore, the chiral-prochiral interconversion was achieved by relative positional control of the com-ponents. The present systematic studies will provide new insight into mechanically chiral interlocked compounds as well as the utility as dynamic chiral sources. | Fumitaka Ishiwari; Toshikazu Takata | Organic Synthesis and Reactions; Stereochemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745de469df4bc50f4358b/original/rotaxanes-with-dynamic-mechanical-chirality-systematic-studies-on-synthesis-optical-resolution-racemization-and-chiral-prochiral-interconversion.pdf |
6632a10b21291e5d1d2ea078 | 10.26434/chemrxiv-2024-ww79v | Synergistic Photoenzymatic Catalysis Enables Synthesis of a-Tertiary Amino Acids Using Threonine Aldolases | a-Tertiary amino acids are essential components of drugs and agrochemicals, yet traditional syntheses are step-intensive and provide access to a limited range of structures with vary-ing levels of enantioselectivity. Here, we report the α-alkylation of unprotected alanine and glycine by pyridinium salts using pyridoxal (PLP)-dependent threonine aldolases with a Rose Bengal photoredox catalyst. The strategy efficient-ly prepares various a-tertiary amino acids in a single chemical step as a single enantiomer. UV-vis spectroscopy studies re-veal a ternary interaction between the pyridinium salt, pro-tein, and photocatalyst, which we hypothesize is responsible for localizing radical formation to the protein active site. This method highlights the opportunity for combining photoredox catalysts with enzymes to reveal new catalytic functions for known enzymes. | Yao Ouyang; Claire Page; Catherine Bilodeau; Todd Hyster | Organic Chemistry; Catalysis; Biocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6632a10b21291e5d1d2ea078/original/synergistic-photoenzymatic-catalysis-enables-synthesis-of-a-tertiary-amino-acids-using-threonine-aldolases.pdf |
614da44e39ef6a0fcf285b52 | 10.26434/chemrxiv-2021-bthks | Spatial reactant distribution in CO2 electrolysis: Balancing CO2 utilization and Faradaic Efficiency | The production of value added C1 and C2 compounds within CO2 electrolyzers has reached sufficient catalytic performance that system and process performance – such as CO2 utilization – have come more into consideration. Efforts to assess the limitations of CO2 conversion and crossover within electrochemical systems have been performed, providing valuable information to position CO2 electrolyzers within a larger process. Currently missing, however, is a clear elucidation of the inevitable trade-offs that exist between CO2 utilization and electrolyzer performance, specifically how the Faradaic Efficiency of a system varies with CO2 availability. Such information is needed to properly assess the viability of the technology. In this work, we provide a combined experimental and 3D modelling assessment of the trade-offs between CO2 utilization and selectivity at 200 mA/cm2 within a membrane-electrode assembly CO2 electrolyzer. Using varying inlet flow rates we demonstrate that the variation in spatial concentration of CO2 leads to spatial variations in Faradaic Efficiency that cannot be captured using common ‘black box’ measurement procedures. Specifically, losses of Faradaic efficiency are observed to occur even at incomplete CO2 consumption (80%). Modelling of the gas channel and diffusion layers indicated at least a portion of the H2 generated is considered as avoidable by proper flow field design and modification. The combined work allows for a spatially resolved interpretation of product selectivity occurring inside the reactor, providing the foundation for design rules in balancing CO2 utilization and device performance in both lab and scaled applications. | Siddhartha Subramanian; Joost Middelkoop; Thomas Burdyny | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Transport Phenomena (Chem. Eng.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614da44e39ef6a0fcf285b52/original/spatial-reactant-distribution-in-co2-electrolysis-balancing-co2-utilization-and-faradaic-efficiency.pdf |
654e9bb46e0ec7777fb70293 | 10.26434/chemrxiv-2023-21wtv | ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery | Developing new drugs is an expensive and lengthy endeavor, partly due to the reliance on high-throughput screening (HTS), which involves significant costs and is time-consuming. Virtual screening, particularly molecular docking, offers a more cost-effective and faster alternative for identifying promising drug candidates. However, the effectiveness of molecular docking can vary greatly, which has led to the use of consensus docking approaches. These approaches combine results from different docking methods to improve the identification of active compounds and can reduce the occurrence of false positives. However, many of these methods do not fully leverage the latest advancements in docking technology.
In response, we present ESSENCE-Dock (Effective Structural Screening ENrichment ConsEnsus Dock), a new consensus docking workflow aimed at decreasing false positives and increasing the discovery of active compounds. By utilizing a combination of novel docking algorithms, we improve the selection process for potential active compounds. ESSENCE-Dock has been made to be user-friendly, requiring only a few simple commands to perform a complete screening, while also being designed for use in high-performance computing (HPC) environments.
| Jochem Nelen; Miguel Carmena-Bargueño; Carlos Martínez-Cortés; Alejandro Rodríguez-Martínez; José Manuel Villalgordo-Soto; Horacio Pérez-Sánchez | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654e9bb46e0ec7777fb70293/original/essence-dock-a-consensus-based-approach-to-enhance-virtual-screening-enrichment-in-drug-discovery.pdf |
60c754c04c8919761fad459d | 10.26434/chemrxiv.13580885.v2 | Visualisation of Chemical Shielding Tensors (VIST) to Elucidate Aromaticity and Antiaromaticity | Aromaticity is a central concept in chemistry,
pervading areas from biochemistry to materials science. Recently, chemists also
started to exploit intricate phenomena such as the interplay of local and
global (anti)aromaticity or aromaticity in non-planar systems and three
dimensions. These phenomena pose new challenges in terms of our fundamental
understanding and the practical visualisation of aromaticity. To overcome these
challenges, a method for the visualisation of chemical shielding tensors (VIST)
is developed here that allows for a 3D visualisation with quantitative
information about the local variations and anisotropy of the chemical
shielding. After exemplifying the method in different planar hydrocarbons, we
study two non-planar macrocycles to show the unique benefits of the VIST method
for molecules with competing pi-conjugated systems and conclude with a
norcorrole dimer showing clear evidence of through-space aromaticity. We
believe that the VIST method will be a highly valuable addition to the
computational toolbox. | Felix Plasser; Florian Glöcklhofer | Physical Organic Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754c04c8919761fad459d/original/visualisation-of-chemical-shielding-tensors-vist-to-elucidate-aromaticity-and-antiaromaticity.pdf |
60c741574c89191acead228e | 10.26434/chemrxiv.8011268.v1 | Dyes@BNNT Nanohybrids for Photostable Fluorescence Imaging | <div><div><div><p>Fluorescence is ubiquitous in life science and used in broad fields of research going from ecology to medicine. Among the most common fluorogenic compounds, dyes are being exploited in bioimaging for their outstanding optical properties across a broad range of wavelengths from the UV to the near-IR. However, dye molecules are often toxic to living organisms and photodegradable, giving limited time windows for in vivo monitoring. By encapsulating organic dyes inside a boron nitride nanotube (dyes@BNNT), we achieve a passivation of the dyes against photodegradation and chemical reaction. The dyes@BNNT nanohybrids contain aggregated and ordered dyes exhibiting strong photoluminescence with signal remaining stable and exempt of blinking over a time scale of more than 10^4 compared to free dyes. Our results also suggest reduced toxicity and exceptional chemical robustness even in harsh environments. The use of these 1D dyes@BNNT nanohybrids as fluorescence nanoprobes in bio-imaging is highlighted with in-vivo monitoring experiments on living Daphnia Pulex.</p></div></div></div> | Charlotte Allard; Raffaela Nascimento; Frederic Fossard; Leonard Schué; Emmanuel Flahaut; Annick Loiseau; Patrick Desjardins; Richard Martel; Etienne Gaufres | Dyes and Chromophores; Imaging; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741574c89191acead228e/original/dyes-bnnt-nanohybrids-for-photostable-fluorescence-imaging.pdf |
6118761f7117503f24e99f18 | 10.26434/chemrxiv-2021-bpgxh | Electrochemistry Enabled Selective Vicinal Fluorosulfenylation and Fluorosulfoxidation of Alkenes | Both sulfur and fluorine play important roles in organic synthesis, the life science, and materials science. The direct incorporation of these elements into organic scaffolds with precise control of the oxidation states of sulfur moieties is of great significance. Herein, we report the highly selective electrochemical vicinal fluorosulfenylation and fluorosulfoxidation reactions of alkenes, which were enabled by the unique ability of electrochemistry to dial in the potentials on demand. Preliminary mechanistic investigations revealed that the fluorosulfenylation reaction proceeded through a radical-polar crossover mechanism involving a key episulfonium ion intermediate. Subsequent electrochemical oxidation of fluorosulfides to fluorosulfoxides were readily achieved under a higher applied potential with the adventitious H2O in the reaction mixture. | Yi Yu; Yi-Min Jiang; Shao-Fen Wu; Zhaojiang Shi; Jin-Nan Wu; Yaofeng Yuan; Ke-Yin Ye | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2021-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6118761f7117503f24e99f18/original/electrochemistry-enabled-selective-vicinal-fluorosulfenylation-and-fluorosulfoxidation-of-alkenes.pdf |
6540c716c573f893f17ffd99 | 10.26434/chemrxiv-2023-23g3r | Triple-photoinduced electron transfer (tri-PET) catalysis for activation of super strong bonds | Single electron redox processes allow the formation of highly reactive radicals – valuable intermediates that enable unique transformations in organic chemistry (1,2). An established concept to create radical intermediates is photoexcitation of a catalyst to a higher energy intermediate, subsequently leading to a photoinduced electron transfer (PET) with a reaction partner (3–7). The known concept of consecutive photoinduced electron transfer (con PET) leads to catalytically active species even higher in energy by the uptake of two photons (8). This process has already been used widely for catalytic reductions; however, limitations towards strong bonds and electron rich substrates remain (9,10). Generally speaking, increased photon uptake leads to a more potent reductant. Here, we introduce triple-photoinduced electron transfer catalysis, termed tri-PET, enabled by the three-photon uptake of a dye molecule leading to an excited dianionic super-reductant which is more potent than Li metal (11) – one of the strongest chemical reductants known. Irradiation of the metal-free catalyst by violet light enables the cleavage of strong carbon-fluoride bonds and reduction of other halides even in very electron-rich substrates. The resulting radicals are quenched by hydrogen atoms or engaged in carbon-carbon and carbon-phosphorus bond formations, highlighting the utility of tri-PET for organic chemistry. Thorough spectroscopic, chemical and computational investigations are presented to understand this novel mode of photoredox catalysis. The existence of the dianion which takes up a third photon when irradiated was proven by X-ray diffraction analysis. | Amit Biswas; Simon Kolb; Sebastian Röttger; Arpan Das; Lukas J. Patalag; Swagata Sil; Subir Maji; Soumi Chakrabarty; Anup Bhunia; Daniel B. Werz; Swadhin K. Mandal | Organic Chemistry; Catalysis; Photochemistry (Org.); Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6540c716c573f893f17ffd99/original/triple-photoinduced-electron-transfer-tri-pet-catalysis-for-activation-of-super-strong-bonds.pdf |
66ae3b71c9c6a5c07aec802d | 10.26434/chemrxiv-2024-2g6lk | Abiotic Acyl Transfer Cascades Driven by Aminoacyl Phosphate Esters and Self-Assembly | Biochemical acyl transfer cascades, such as those initiated by the adenylation of carboxylic acids, are central to various biological processes, including protein synthesis and fatty acid metabolism. Designing aqueous cascades outside of biology remains challenging due to the need to control multiple, sequential reactions in a single pot and manage the stability of reactive intermediates. Herein, we developed abiotic cascades using aminoacyl phosphate esters, the synthetic counterparts of biological aminoacyl adenylates, to drive sequential chemical reactions and self-assembly in a single pot. We demonstrated that the structural elements of amino acid side chains (aromatic versus aliphatic) significantly influence the reactivity and half-lives of aminoacyl phosphate esters, ranging from hours to days. This behavior, in turn, affects the number of couplings we can achieve in the network and the self-assembly propensity of activated intermediate structures. The cascades are constructed using bifunctional peptide substrates featuring side chain nucleophiles. Specifically, aromatic amino acids facilitate the formation of transient thioesters, which preorganized into spherical aggregates and further couple into chimeric assemblies composed of esters and thioesters. In contrast, aliphatic amino acids, which lack the ability to form such structures, predominantly lead to hydrolysis, bypassing elongation after thioester formation. Additionally, in mixtures containing multiple aminoacyl phosphate esters and peptide substrates, we achieved selective product formation by following a distinct pathway that favors elongation through self-assembly. By coupling chemical reactions using molecules with varying reactivity timescales, we can drive multiple reaction clocks with distinct lifetimes and self-assembly dynamics, thereby facilitating precise temporal and structural regulation. | Mahesh Pol; Ralf Thomann; Yi Thomann; charalampos Pappas | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ae3b71c9c6a5c07aec802d/original/abiotic-acyl-transfer-cascades-driven-by-aminoacyl-phosphate-esters-and-self-assembly.pdf |
6549c485c573f893f1f7f351 | 10.26434/chemrxiv-2023-9n7ld-v2 | Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases | Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalisation of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by their suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO’s selectivity and inform their design principles. However, most of these studies focused on the substrate binding poses. Few have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom transfer (HAT) step, initiated by the CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantioselectivity. Building on our previous study on CpdI’s formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI’s formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in rationally designing UPOs with enhanced properties. | Gustavo Costa; Abel Egbemhenghe ; Ruibin Liang | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6549c485c573f893f1f7f351/original/computational-characterization-of-the-reactivity-of-compound-i-in-unspecific-peroxygenases.pdf |
678fb52d81d2151a021ef77e | 10.26434/chemrxiv-2024-npkvm-v4 | Non-Linear Damage Response to Voltage Revealed by Operando X-ray Tomography in Polycrystalline NMC811 | To understand fracture behaviour in battery materials, X-ray computed tomography (X-ray CT) has become the primary technique for non-destructive particle analysis. Cracking causes performance decline in polycrystalline NMC811 by exposing new surfaces for parasitic electrolyte reactions and disconnecting active material from the electrode matrix. First cycle crack formation has been documented, but definitive electrochemically induced particle fracture is challenging to assess due to complex sample preparation and high-resolution X-ray imaging requirements. Presented here is an operando X-ray CT technique that enables accurate observation of fracture behaviour during de-/lithiation. A non-linear relationship between fracture behaviour and cell voltage was uncovered, and evidence of particle reformation during re-lithiation. Using a grey level analysis algorithm for fracture detection, we expedite damage evaluation in several thousands of particles throughout the electrochemical process, understanding crack initiation, propagation, and closure on a large, statistical scale and give the ability to track any one of the thousands of particles through its individual electrochemical history. Additionally, we explore the effects of continued volumetric hysteresis on particle damage. For the first time, we demonstrate the complex plurality of fracture behaviour in commercial lithium-ion battery materials, aiding in designing mitigation strategies against particle fracture. | Huw Parks; Matthew Jones; Aaron Wade; Alice Llewellyn; Chun Tan; Hamish Reid; Ralf Ziesche; Thomas Heenan; Shashidhara Marathe; Christoph Rau; Paul Shearing; Rhodri Jervis | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Energy Storage | CC BY 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678fb52d81d2151a021ef77e/original/non-linear-damage-response-to-voltage-revealed-by-operando-x-ray-tomography-in-polycrystalline-nmc811.pdf |
60c75213567dfedfd0ec5b9d | 10.26434/chemrxiv.13250294.v1 | Rapid Construction of Tetralin, Chromane, and Indane Motifs via Cyclative C−H/C−H Coupling: Four-Step Total Synthesis of (±)-Russujaponol F | The development of
practical C−H/C−H coupling reactions remains a challenging yet appealing
synthetic venture because it circumvents the need to prefunctionalize both
coupling partners for the generation of C−C bonds. Herein, we report a cyclative C(sp<sup>3</sup>)−H/C(sp<sup>2</sup>)−H
coupling reaction of free aliphatic acids enabled by a cyclopentane-based mono-<i>N</i>-protected β-amino acid ligand. This
reaction uses inexpensive sodium percarbonate (Na<sub>2</sub>CO<sub>3</sub>·1.5H<sub>2</sub>O<sub>2</sub>)
as the sole oxidant, generating water as the only byproduct. A range of
biologically important scaffolds, including tetralins, chromanes, and indanes,
could be easily prepared by this protocol. Finally, the synthetic application
of this methodology is demonstrated by the concise total synthesis of (±)-russujaponol
F in a four-step sequence starting from readily available phenylacetic acid and
pivalic acid through the sequential functionalizations of four C−H bonds. | Zhe Zhuang; Alastair Herron; Shuang Liu; jin-quan yu | Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75213567dfedfd0ec5b9d/original/rapid-construction-of-tetralin-chromane-and-indane-motifs-via-cyclative-c-h-c-h-coupling-four-step-total-synthesis-of-russujaponol-f.pdf |
67bc72affa469535b9b82372 | 10.26434/chemrxiv-2025-x8b82 | On-Surface Synthesis of Oxygen-Doped Analogues of Higher Acenes | Oxygen doped analogues of higher acenes have been synthesized on Au(111) through the combination of solution chemistry and on-surface synthesis. On the basis of combined bond-resolved scanning tunneling microscopy (BR-STM), scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations two isomers containing heptacene core with benzofuran moieties, i.e. heptaceno[2,3-b:11,12-b′]bis[1]benzofuran and heptaceno[2,1-b:11,10-b']bis[1]benzofuran) have been identified and their structural and electronic properties have been analyzed in detail. We demonstrate that, in contrast to non-substituted parent acenes, oxygen equipped molecules tend to form self-assembled structures driven by electrostatic interactions on Au(111). Furthermore, the detailed analysis of the electronic properties reveals the ability to fine tune the transport gap by changing the position of benzofuran moieties. | Irena Padniuk; Otilia Stoica; Rafal Zuzak; Remi Blieck; Mariusz Krawiec; Antonio M. Echavarren; Szymon Godlewski | Physical Chemistry; Materials Science; Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc72affa469535b9b82372/original/on-surface-synthesis-of-oxygen-doped-analogues-of-higher-acenes.pdf |
60c757fcbb8c1a903e3dc95c | 10.26434/chemrxiv.14483457.v1 | Edge-Hydrogenated Germanene by Electrochemical Decalcification-Exfoliation of CaGe2: Germanene-Enabled Vapor Sensor | <p><a>Two-dimensional germanene
has been recently explored for applications in sensing, catalysis, and energy
storage. The potential of this material lies on its graphene-like
optoelectronic and chemical properties. However, pure free-standing germanene cannot
be found in nature and the synthetic methods are hindering the potentially
fascinating properties of germanene. </a>Herein, <a>we report for the first time a single-step synthesis of
few-layer germanene by electrochemical exfoliation in non-aqueous environment. As
a result of simultaneous decalcification and intercalation of the electrolyte’s
active ions, we achieved a low-level hydrogenation of germanene that occurs at
the edges of the material. The obtained edge-hydrogenated germanene flakes have
a lateral size of several micrometers which possess a cubic structure. We have
pioneered the potential application of edge-hydrogenated germanene for vapor
sensing and demonstrated its specific sensitivity to methanol and ethanol. We have
shown a selective behavior of the germanene-based sensor that appears to
increase the electrical resistance in the vapors where methanol prevails. We
anticipate that these results can provide a new approach for emerging layered
materials with the potential utility in advanced gas sensing.</a></p> | Evgeniya Kovalska; Nikolas Antonatos; Jan Luxa; Zdenek Sofer | Materials Processing; Multilayers; Electrochemistry; Sensors; Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757fcbb8c1a903e3dc95c/original/edge-hydrogenated-germanene-by-electrochemical-decalcification-exfoliation-of-ca-ge2-germanene-enabled-vapor-sensor.pdf |
61bb46bff52bc485e0c30ee8 | 10.26434/chemrxiv-2021-4gtwr | α-Helix in Cystathionine β-Synthase Enzyme Acts as Electron Reservoir | The modulation of electron density at the Pyridoxal 5-phosphate (PLP) catalytic center, due to charge transfer across the α-Helix-PLP interface, is the determining factor for the enzymatic activities in the human Cystathionine β-Synthase (hCBS) enzyme. Applying density-based first-principle calculations in conjunction with the real space density analysis, we investigated the charge density delocalization across the entire Heme-α-Helix-PLP electron communication channels. The hydrogen bonds at the
interfaces, i.e. Heme-α-Helix and α-Helix-PLP interfaces, are found to play the pivotal role in bi-directional electron transfer towards the α-Helix. Moreover, the internal hydrogen bonds of α-Helix that are crucial for its secondary structure also actively participate in the electron redistribution through the structured hydrogen bond network. α-Helix is found to accumulate the electron density
at the ground state from both the cofactors and behaves as an electron reservoir for catalytic reaction at the electrophilic center of PLP. | Aashish Bhatt; Aritra Mukhopadhyaya; Md. Ehesan Ali | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bb46bff52bc485e0c30ee8/original/helix-in-cystathionine-synthase-enzyme-acts-as-electron-reservoir.pdf |
6347680bbb6d8b9cf1568f62 | 10.26434/chemrxiv-2022-28crb | A general alkene aminoarylation enabled by N-centered radical reactivity of sulfinamides | We disclose an intermolecular 1,2-aminoarylation of alkenes using aryl sulfinamide reagents as bifunctional amine and arene donors. This reaction features excellent regio- and diastereoselectivity on a variety of activated and unactivated substrates. Using a weakly oxidizing photoredox catalyst, a sulfinamidyl radical is generated under mild conditions and adds to an alkene to form a new C–N bond. A desulfinylative Smiles-Truce rearrangement follows to form a new C–C bond. In this manner, biologically active arylethylamines and valuable building blocks can be rapidly assembled from abundant alkene feedstocks. Additionally, we demonstrate that chiral information from the sulfinamide can be transferred via rearrangement to a new carbon stereocenter in the product, thus advancing development of traceless asymmetric alkene difunctionalization methodologies. | Efrey Noten; Cody Ng; Robert Wolesensky; Corey Stephenson | Organic Chemistry; Catalysis; Photocatalysis; Redox Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6347680bbb6d8b9cf1568f62/original/a-general-alkene-aminoarylation-enabled-by-n-centered-radical-reactivity-of-sulfinamides.pdf |
62c0c054253021b56187743d | 10.26434/chemrxiv-2022-3fklf | Effects of sodium benzoate and heavy metals on biodegradation of 2,2',4,4'-tetrabromodiphenyl ether by Rhodococcus jostii RHA1 | We investigated the effects of co-metabolic substrate, sodium benzoate, and heavy metal ions (i.e., Cd(II), Cr(III), Cu(II), Ni(II), Pb(II)) on the biotransformation of 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47), which is a PBDE congener commonly found in the e-waste contaminated sites, by Rhodococcus jostii RHA1 (RHA1). In the co-metabolic degradation reactors, 1000 ppb and 1200 ppb of BDE-47 were degraded 54.58% and 60.98%, respectively; however, 100 ppb, 250 ppb and 500 ppb of BDE-47 were hardly transformed. With heavy metals co-existing, 1000 ppb of BDE-47 was converted from 6.56% (with 50 ppm of Cu(II) added) to 86.32% (with 1 ppm of Cr(III) added). Meanwhile, 88.40%~100% of heavy metal ions (50ppm) were removed in the extracted aqueous solutions. The co-contaminants of Cd(II)+BDE-47 and Cu(II)+BDE-47 were predicted to threaten the growth of RHA1, while Cr(III)+BDE-47 provided amenable conditions for RHA1 to thrive. As the concentration of heavy metal ions increasing (from 1 ppm to 50 ppm), the critical role of RHA1 transferred from BDE-47 co-metabolism to heavy metal removal (i.e., via absorption, mineralization, and/or uptake). RHA1 can produce extracellular polymeric substances (EPS) matrix under the exposure to BDE-47, which in turn, influenced the bioavailability of BDE-47 and the removal of heavy metal ions in the aqueous environments. These results demonstrated that the presence of dissolved heavy metals is predicted to affect the performance of RHA1 to transform BDE-47 in the contaminated sites. | Chunlei Wang; Teng Ma | Organic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c0c054253021b56187743d/original/effects-of-sodium-benzoate-and-heavy-metals-on-biodegradation-of-2-2-4-4-tetrabromodiphenyl-ether-by-rhodococcus-jostii-rha1.pdf |
660a0e07e9ebbb4db916a7ae | 10.26434/chemrxiv-2024-k6k5n | Engineering Porosity-Tuned Chitosan Beads:
Balancing Porosity, Kinetics, and Mechanical Integrity | Chitosan, a cationic natural polysaccharide derived from the deacetylation of chitin, is known for its solubility in diluted acidic solutions, biodegradability, biocompatibility, and non-toxicity. This study introduces three innovative methods to prepare porous chitosan microsphere particles, which are crucial for enhancing their efficiency in water remediation and medical applications. The methods, solvent extraction, surfactant extraction, and substance decomposition, involve the integration and subsequent extraction or decomposition of materials during the synthesis process, eliminating the need for additional steps. We used state-of-the-art characterization techniques to analyze and evaluate the chemical and physical properties of the particles, such as Fourier-transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), X-ray diffraction (XRD), and especially three-dimensional computed tomography (CT) scanning. The CT scans were used to visualize and measure the porosity of different particle types, ranging from 68.4% to 39.3%. This detailed study extended to evaluate the mechanical properties of the particles under compressive forces in wet and dry conditions, highlighting the influence of porosity on their mechanical integrity and compression pressure behavior. In addition, we explored the adsorptive properties of these chitosan particles, using methylene blue as a model pollutant because of its toxicity, underscoring the significance of porosity in enhancing their pollutant removal efficiency. This study opens the window for developing environmentally sustainable polymer particles and highlights the pivotal role of porosity in optimizing the material’s efficacy for a wide range of applications. | Rouzbeh Tehrani; Astha Upadhyay; Farbod Alimohammadi | Polymer Science; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660a0e07e9ebbb4db916a7ae/original/engineering-porosity-tuned-chitosan-beads-balancing-porosity-kinetics-and-mechanical-integrity.pdf |
63bbcc4f055be719dcc74a75 | 10.26434/chemrxiv-2023-5f009 | Superconformal silicon carbide coatings via precursor pulsed chemical vapor deposition | In this work, silicon carbide coatings (SiC) were successfully grown by pulsed chemical
vapor deposition (CVD). The precursors silicon tetrachloride (SiCl4) and ethylene (C2H4)
were not supplied in a continuous flow, but were pulsed alternately into the growth
chamber with H2 as a carrier and a purge gas. A typical pulsed CVD cycle was SiCl4 pulse
– H2 purge – C2H4 pulse – H2 purge. This led to the growth of superconformal SiC coatings,
which could not be obtained under similar process conditions using a constant flow CVD
process. We propose a two-step mechanism for the SiC growth via pulsed CVD. During
the SiCl4 pulse, a layer of Si is deposited. In the following C2H4 pulse, this Si layer is
carburized, and SiC is formed. The high chlorine surface coverage after the SiCl4 pulse is
believed to enable the superconformal growth via a growth inhibition mechanism. | Jing-Jia Huang; Christian Militzer; Charles Wijayawardhana; Urban Forsberg; Henrik Pedersen | Physical Chemistry; Materials Science; Thin Films; Physical and Chemical Processes; Surface; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bbcc4f055be719dcc74a75/original/superconformal-silicon-carbide-coatings-via-precursor-pulsed-chemical-vapor-deposition.pdf |
67a36a2cfa469535b925ff7b | 10.26434/chemrxiv-2025-3bx69 | NMR- and EPR spectroscopic characterization of S4N4 and (SN)x dissolved in [EMIm][OAc] | This work focuses on the reaction mechanism of poly(sulfur nitride) ((SN)x, (S15N)x), with the ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate [EMIm][OAc]. We compare this with the reaction of the IL with S4N4 or its 15N labeled form S415N4, a precursor for the synthesis of (SN)x and (S15N)x. After purification of the S4N4-IL- and S415N4-system via column chromatography, we characterize the reaction products with 1H, 13C and 15N nuclear magnetic resonance (NMR) spectroscopy and with electron spray ionization time-of-flight mass spectrometry (ESI-ToF-MS). Furthermore, time-resolved electron paramagnetic resonance (EPR) spectroscopy as well as time-resolved ultraviolet-visible (UV/Vis) spectroscopy are carried out. Thus, radical intermediates are detected which are consumed with reaction progress. Finally, we postulate a reaction mechanism for the S4N4-IL- and S415N4-IL system and compare this with the respective data for the (SN)x-IL- and (S15N)x-IL-system. | Julian Radicke; Vanessa Jerschabek; Haleh Hashemi Haeri; Muhammad Abu-Bakar; Dariush Hinderberger; Jörg Kreßler; Karsten Busse | Physical Chemistry; Materials Science; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a36a2cfa469535b925ff7b/original/nmr-and-epr-spectroscopic-characterization-of-s4n4-and-sn-x-dissolved-in-em-im-o-ac.pdf |
6582bc7de9ebbb4db95679ab | 10.26434/chemrxiv-2023-6vfxk | Modeling the freezing process of aqueous solutions considering thermal gradients and stochastic ice nucleation | Despite its importance to multiple scientific fields and industries, the freezing process of aqueous solutions is not yet completely understood. In particular, the relationship between temperature gradients within a solution and the occurrence of stochastic ice nucleation remains elusive. To address this knowledge gap, we have derived a novel stochastic spatial freezing model from first principles. The model predicts with quantitative accuracy how temperature gradients affect the stochastic ice nucleation of sucrose solutions in vials. This motivated a detailed study of the freezing-stage in freeze-drying. In particular, the model enabled a mechanistic assessment of vacuum-induced surface freezing, an emerging approach towards optimized freeze-drying processes. Model predictions revealed both the stochastic nature of this freezing method, and its performance limitations in case highly concentrated solutions are frozen. To ensure that both researchers and practitioners benefit from this modeling work, we provide open source access to it within our python package ethz-snow. | Leif-Thore Deck; Andraž Košir; Marco Mazzotti | Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Pharmaceutical Industry; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6582bc7de9ebbb4db95679ab/original/modeling-the-freezing-process-of-aqueous-solutions-considering-thermal-gradients-and-stochastic-ice-nucleation.pdf |
60c75946842e659d91db49d8 | 10.26434/chemrxiv.14680335.v1 | Integration of Fluorescent Functionality into Pressure Amplifying Metal-Organic Frameworks | The flexibility of soft porous crystals, i.e., their ability to respond to external stimuli with structural changes, is one of the most fascinating features of metal-organic frameworks. In addition to breathing and swelling phenomena of flexible MOFs, negative gas adsorption and pressure amplification is one of the more recent discoveries in this field, initially observed in the cubic DUT-49 framework. In recent years the structural contraction was monitored by physisorption, X‑ray diffraction, NMR and EPR techniques, providing only limited information about the electronic structure of the ligand. In this work we designed a new ligand with a fluorescent core in the linker backbone and synthesized three new MOFs, isoreticular to DUT-49, denoted as DUT‑140(M) (M - Cu, Co, Zn) crystalizing in space group. DUT‑140(Cu) can be desolvated and is highly porous with an accessible apparent surface area of 4870 m2g-1 and a pore volume of 2.59 cm3g-1. Furthermore, it shows flexibility and NGA upon adsorption of subcritical gases. DUT-140(Zn), synthesized using post-synthetic metal exchange, could only be studied with guests in the pores. In addition to the investigation of the adsorption behavior of DUT-140(Cu) spectroscopic and computational methods were used to study the light absorption properties. | Francesco Walenszus; Jack D. Evans; Volodymyr Bon; Friedrich Schwotzer; Irena Senkovska; Stefan Kaskel | Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Solid State Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry; Crystallography; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75946842e659d91db49d8/original/integration-of-fluorescent-functionality-into-pressure-amplifying-metal-organic-frameworks.pdf |
63738f43207981460e279a30 | 10.26434/chemrxiv-2022-gmjw4 | Matrix Isolation and Photorearrangement of Cis– and Trans–1,2-Ethenediol to Glycolaldehyde | 1,2-Ethenediols are deemed key intermediates in prebiotic and interstellar syntheses of carbohydrates. Here we present the gas-phase synthesis of these enediols, the high-energy tautomers of glycolaldehyde, trapped in cryogenic argon matrices. Importantly, upon photolysis at ʎ = 180–254 nm, the enols rearrange to the simplest sugar glycolaldehyde. | Artur Mardyukov; Raffael C. Wende; Peter R. Schreiner | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63738f43207981460e279a30/original/matrix-isolation-and-photorearrangement-of-cis-and-trans-1-2-ethenediol-to-glycolaldehyde.pdf |
6719d97383f22e4214f8b821 | 10.26434/chemrxiv-2024-v8h0j | Physics-based Machine Learning to Predict Hydration Free Energies for Small Molecules with a minimal number of descriptors: Interpretable and Accurate | Hydration free energy (HFE) of molecules is a fundamental property having impor- tance throughout chemistry and biology. Calculation of the HFE can be challenging and expensive with classical molecular dynamics simulation-based approaches. Ma- chine learning (ML) models are increasingly being used to predict HFE. Although the accuracy of ML models for datasets for small molecules is impressive, these models suffer from lack of interpretability. In this work, we have developed a physics-based ML model with only six descriptors, which is both accurate and fully interpretable, and applied it to a database for small molecule HFE, FreeSolv. We have evaluated the electrostatic energy by an approximate closed form of the Generalized Born (GB) model and polar surface area. In addition, we have logP and hydrogen bond acceptor and donors as descriptors along with the number of rotatable bonds. We have used different ML models such as random forest and extreme gradient boosting. The best result from these models has a mean absolute error of only 0.74 kcal/mol. The main power of this model is that the descriptors have clear physical meaning and it was found that the descriptor describing the electrostatics and the polar surface area, followed by the hydrogen bond donors and acceptors, are the most important factors for the calculation of hydration free energy. | Ajeet Kumar Yadav; Marvin V. Prakash; Pradipta Bandyopadhyay | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6719d97383f22e4214f8b821/original/physics-based-machine-learning-to-predict-hydration-free-energies-for-small-molecules-with-a-minimal-number-of-descriptors-interpretable-and-accurate.pdf |
61adb8e9772cb2138a5207b8 | 10.26434/chemrxiv-2021-25n6h | Development and Application of a Single Neural Network Potential for IRMOF-n (n=1,4,6,7,10) | Metal‑organic frameworks (MOFs) with their exceptional porous and organized structures have been subject of numerous applications. Predicting macroscopic properties from atomistic simulations require the most accurate force fields, which is still a major problem due to MOFs’ hybrid structures governed by covalent, ionic and dispersion forces. Application of ab‑initio molecular dynamics to such large periodic systems are thus beyond the current computational power. Therefore, alternative strategies must be developed to reduce computational cost without losing reliability. In this work, we describe the construction of a neural network potential (NNP) for IRMOF‑n series (n=1,4,7,10) trained by PBE-D4/def2-TZVP reference data of MOF fragments. We validated the resulting NNP on both fragments and bulk MOF structures by prediction of properties such as equilibrium lattice constants, phonon density of states and linker orientation. The energy and force RMSE values for the fragments are only 0.0017 eV/atom and 0.15 eV/Å, respectively. The NNP predicted equilibrium lattice constants of bulk structures, which are not included in training, are off by only 0.2-2.4% from experimental results. Moreover, our fragment trained NNP greatly predicts phenylene ring torsional energy barrier, equilibrium bond distances and vibrational density of states of bulk MOFs. Furthermore, NNP allows us to investigate unusual behaviors of selected MOFs such as the thermal expansion properties and the effect of mechanical strain on the adsorption of hydrogen and methane molecules. The NNP based molecular dynamics (MD) simulations suggest the IRMOF‑4 and IRMOF‑7 to have positive‑to‑negative thermal expansion coefficients while the rest to have only negative thermal expansion under the studied temperatures of 200 K to 400 K. The deformation of bulk structure by reduction of unit cell volume has shown to increase volumetric methane uptake in IRMOF‑1 but decrease in IRMOF‑7 due to the steric hindrance. | Omer Tayfuroglu; Abdul Kadir Kocak; Yunus Zorlu | Theoretical and Computational Chemistry; Organometallic Chemistry; Computational Chemistry and Modeling; Machine Learning; Transition Metal Complexes (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61adb8e9772cb2138a5207b8/original/development-and-application-of-a-single-neural-network-potential-for-irmof-n-n-1-4-6-7-10.pdf |
60c73d924c8919c428ad1c0e | 10.26434/chemrxiv.5901178.v1 | The Simplest Patterns of Interpenetrated Honeycomb Layers – Counter examples to the Minimal Transitivity Principle? | The paper calls attention to the most symmetric interpenetration patterns of honeycomb layers. To the best of my knowledge, such patterns remained unknown so far. In my contribution a rigorous derivation of such patterns is given that makes use of a new approach to interpenetrating nets. The results are presented in a broad context of structural chemistry and crystal engineering. | Igor Baburin | Coordination Chemistry (Inorg.); Solid State Chemistry; Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2018-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d924c8919c428ad1c0e/original/the-simplest-patterns-of-interpenetrated-honeycomb-layers-counter-examples-to-the-minimal-transitivity-principle.pdf |
60c756c84c89191ccead48c0 | 10.26434/chemrxiv.14330294.v1 | Magnesium Oxide as an Additive with Polymeric Sulfur Cathode and Modified Glass Fiber Separator for High Performance Lithium-Sulfur Batteries | <p>The lithium ion
technology is now beginning to enter into electric vehicles and grid storage of
renewable energies (solar and wind energy). However, the current lithium ion
technology has reached the limitations of their charge-storage capacity and
energy density. Therefore, alternative cathode and anode materials that offer
higher capacities need to be developed. Lithium- sulfur battery with sulfur
based cathode undergoes conversion reactions while accommodating more ions and
electrons as promising options to overcome the charge-storage limitations of
lithium ion battery. Cost, cycle life, safety, energy, power, and environmental
impact should be considered for commercializing modified lithium-sulfur
batteries. In this study highly
conductive and lightweight cathode materials consist of
poly 1,5-diaminoanthraquinone (PDAAQ) and magnesium oxide (MgO) have
been considered to increase cycle life and performance of lithium-sulfur
batteries. Modified one and double side coated glass fiber separator
also was investigated to improve confinement of active materials on the pores
and prevented dissolution of undesired materials in the electrolyte. The cells
with MgO/PDAAQ/S cathode and uncoated glass fiber separator showed initial
discharge capacity of 1000 mAh g<sup>-1</sup> at 2C. The discharge capacity decreased
at ~ 900 mAh g<sup>-1</sup> for 5C. MgO/PDAAQ/S cathode and double side coated
glass fiber separator showed the higher capacities of ~1250 and 1170 at 2C and 5C
respectively. </p> | Maryam Sadat Kiai | Nanodevices; Nanofabrication; Nanostructured Materials - Nanoscience; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756c84c89191ccead48c0/original/magnesium-oxide-as-an-additive-with-polymeric-sulfur-cathode-and-modified-glass-fiber-separator-for-high-performance-lithium-sulfur-batteries.pdf |
619b6c6662372e14e4c41c9d | 10.26434/chemrxiv-2021-kq32x | Conversion of carboxylic acids to amides under the action of tantalum(V) chloride | It was found that the reaction of aliphatic carboxylic acids with secondary amines under the action of tantalum (V) chloride leads to the selective formation of carboxamides. N,N-Diethyladamantane-1-carboxamide were synthesized with a yield of 73% as well. | Azat Gabdullin; Oleg Mozgovoj; Rita Kadikova; Ilfir Ramazanov; Aliya Amirova; Usein Dzhemilev | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619b6c6662372e14e4c41c9d/original/conversion-of-carboxylic-acids-to-amides-under-the-action-of-tantalum-v-chloride.pdf |
60c73d51ee301c0666c78546 | 10.26434/chemrxiv.5696410.v1 | Application of numerical basis sets with a family of DFT methods to predict the transition states of Diels-Alder reactions: Assessing the accuracy through synchronous transit method | <div>
<table>
<tr>
<td>
<p>Knowledge
of the transition state is crucial in determining the mechanism in order to
diversify the applicability of the reaction. The computational method is the
most convenient way to locate the transition state in the absence any
efficient experimental technique. We have applied the method of the
transition state search on the Diels-Alder reaction computationally by means
of combined linear synchronous transit and quadratic synchronous transit
methods. Here we have shown that, of various methods adopted, BOP functional
with numerical basis set provides a computationally economical alternative to
the widely used B3LYP functional with higher Gaussian basis sets in the
transition state search. It can reproduce the experimental parameters like
activation energy of the Diels-Alder reaction, and the calculations are much
faster than the corresponding other functional based calculations.</p>
</td>
</tr>
</table>
</div> | Saurav Dutta; Bhabani S. Mallik | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51ee301c0666c78546/original/application-of-numerical-basis-sets-with-a-family-of-dft-methods-to-predict-the-transition-states-of-diels-alder-reactions-assessing-the-accuracy-through-synchronous-transit-method.pdf |
6660deef21291e5d1d2811ac | 10.26434/chemrxiv-2024-kxj6s | Unlocking the chemistry of graphene: the impact of charge carrier concentration on molecular adsorption on graphene | Both intentional and unintentional doping of graphene is a common occurrence, as its carrier concentration can be modulated through various mechanisms. While extensively explored in electronics for achieving desirable conductivity, other aspects of doping remain largely untapped, presenting opportunities for further innovation. This study demonstrates that carrier concentration serves as a powerful and selective tool for modulating the interaction between molecular adsorbates and graphene. The effects are tunable and evident for both n-type and p-type doping, with low-to-medium modulation at doping levels of ±1012 e/cm2 , and substantial enhancements, with interaction strength increases exceeding 150% and hundreds of meV, at doping levels of ±1013 e/cm2 . These effects are also molecule-specific, with significant enhancements for species such as water (H2O), ammonia (NH3), and aluminum chloride (AlCl3 ), while having minimal impact on species like hydrogen (H2 ). This finding not only elucidates the fundamental chemical behavior of graphene but also provides a versatile method to tailor its surface chemistry for applications in sensors, catalysis, and electronic devices. The insights from this research pave the way for advanced material design strategies, leveraging the tunable nature of graphene’s properties to optimize its interaction with various molecular species. | Maciej J. Szary | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Surface; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6660deef21291e5d1d2811ac/original/unlocking-the-chemistry-of-graphene-the-impact-of-charge-carrier-concentration-on-molecular-adsorption-on-graphene.pdf |
6319c71f3e2e362f0d2f13ac | 10.26434/chemrxiv-2022-72rbc-v2 | Probing Methyl Group Dynamics in Proteins by NMR Cross-Correlated Dipolar Relaxation and Molecular Dynamics Simulations | Nuclear magnetic resonance (NMR) spin relaxation is the most informative approach to experimentally probe the internal dynamics of proteins on the picosecond to
nanosecond timescale. At the same time, molecular dynamics (MD) simulations of biological macromolecules are steadily improving through better physical models, enhanced sampling algorithms, and increasing computational power, and they provide exquisite
information about flexibility and its role in protein stability and molecular interactions. Many examples have shown that MD is now adept in probing protein backbone motion,
but improvements are still required towards a quantitative description of the dynamics of side chains, for example probed by the dynamics of methyl groups. Thus far, the comparison of computation with experiment for side chains has primarily focused on the relaxation of 13C and 2H nuclei induced by auto-correlated variation of spin
interactions. However, the cross-correlation of 13C-1H dipolar interactions in methyl groups offers an attractive alternative. Here, we establish a methodological framework
to extract cross-correlation relaxation parameters of methyl groups in proteins from all-atom MD simulations. To demonstrate the utility of the approach, cross-correlation
relaxation rates of ubiquitin are computed from MD simulations performed with the AMBER99SB*-ILDN and CHARMM36 force fields. The simulation results were found
to agree well with those obtained by experiment. Moreover, the data obtained with the two force fields are highly consistent. | Ahmed A. A. I. Ali; Falk Hoffmann; Lars V. Schäfer; Frans A. A. Mulder | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6319c71f3e2e362f0d2f13ac/original/probing-methyl-group-dynamics-in-proteins-by-nmr-cross-correlated-dipolar-relaxation-and-molecular-dynamics-simulations.pdf |
60c74c23469df40468f4400c | 10.26434/chemrxiv.12436487.v1 | Absorption and Circular Dichroism Spectra of Molecular Aggregates with the Full Cumulant Expansion. | The exciton Hamiltonian of multichromophoric aggregates can be probed by spectroscopic techniques such as linear absorption and circular dichroism. In order to compare calculated Hamiltonians to experiments, a lineshape theory is needed, which takes into account the coupling of the excitons with inter- and intramolecular vibrations. This coupling is normally introduced in a perturbative way through the cumulant expansion formalism, and further approximated by assuming a Markovian exciton dynamics, for example with the modified Redfield theory.<br /><br />Here we present an implementation of the full cumulant expansion (FCE) formalism [Ma and Cao, <i>J. Chem. Phys.</i> <b>2015</b>, 142, 094106 ] to efficiently compute absorption and circular dichroism spectra of molecular aggregates beyond the Markov approximation, without restrictions on the form of the exciton-phonon coupling. By employing the LH2 system of purple bacteria as a challenging test case, we compare the FCE lineshapes with the Markovian lineshapes obtained with the modified Redfield theory, showing that the latter present a much poorer agreement with experiments. The FCE approach instead accurately describes the lineshapes, especially in the vibronic sideband of the B800 peak. We envision that the FCE approach will become a valuable tool for accurately comparing model exciton Hamiltonians with optical spectroscopy experiments. | Lorenzo Cupellini; Filippo Lipparini; Jianshu Cao | Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c23469df40468f4400c/original/absorption-and-circular-dichroism-spectra-of-molecular-aggregates-with-the-full-cumulant-expansion.pdf |
60c74160567dfe78eeec3d56 | 10.26434/chemrxiv.8015651.v1 | Highly Robust but Surface-Active: N-Heterocyclic Carbene-Stabilized Au25 Nanocluster as a Homogeneous Catalyst | <div>
<div>
<div>
<p>Surface organic ligands play a critical role in stabilizing atomically precise metal nanoclusters in solutions.
However, it is still challenging to prepare highly robust ligated metal nanoclusters that are surface-active for liquid-phase catalysis
without any pre-treatment. Herein, we report a novel N-heterocyclic carbine-stabilized Au25 nanocluster with high thermal and air
stabilities as a homogenous catalyst for cycloisomerization of alkynyl amines to indoles. The nanocluster, characterized as
[Au25(iPr2-bimy)10Br7]2+ (iPr2-bimy=diisopropyl-benzilidazolium) (1), was synthesized by direct reduction of AuSMe2Cl and iPr2-
bimyAuBr with NaBH4 in one pot. X-ray crystallization analysis revealed that the cluster comprises two centered Au13 icosahedra
sharing a vertex. Cluster 1 is highly stable and can survive in solution at 80 oC for 12 h, which is superior to Au25 nanoclusters
passivated with phosphines or thiols. DFT computations reveal the origins of both electronic and thermal stability of 1 and point to
the probable catalytic sites. This work provides new insights into the bonding capability of N-heterocyclic carbene to gold in a
cluster, and offers an opportunity to probe the catalytic mechanism at the atomic level.
</p>
</div>
</div>
</div> | Hui Shen; Guocheng Deng; Sami Kaappa; Sami Malola; Boon K. Teo; Hannu Hakkinen; Nanfeng Zheng; Tongde Tan; Yinzi Han; Shuichao Lin | Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Theory - Computational; Clusters; Surface | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74160567dfe78eeec3d56/original/highly-robust-but-surface-active-n-heterocyclic-carbene-stabilized-au25-nanocluster-as-a-homogeneous-catalyst.pdf |
66904e27c9c6a5c07a0391d4 | 10.26434/chemrxiv-2024-9js67-v2 | Photophysical properties of donor(D)-acceptor(A)-donor(D) diketopyrrolopyrrole (A) systems as donors for applications to organic electronic devices | Fourteen substituted diketopyrrolopyrrole (DPP) molecules in a donor (D)-acceptor (DPP)-donor (D) arrangement were designed. We employed density functional theory (DFT), time-dependent DFT and the ab initio wave function second-order algebraic diagrammatic construction (ADC(2)) methods to investigate theoretically these systems. The examined aromatic substituents have one, two or three hetero- and non-hetero rings. We comprehensively investigated their optical, electronic and charge transport properties to evaluate potential applications in organic electronic devices. We found that the substituents based on one, two or three aromatic rings bonded to the DPP core functioning as a donor can improve the efficiency of an organic solar cell by fine-tuning the HOMO/LUMO levels to match acceptors in typical bulk heterojunctions acceptors. Several properties of interest for organic photovoltaic devices were computed. We show that the investigated molecules are promising for applications as donor materials when combined with typical acceptors in bulk heterojunctions because they have appreciable energy conversion efficiencies resulting from their low ionization potentials and high electronic affinities. This scenario allows a more effective charge separation and reduces the recombination rates. A comprehensive charge transfer analysis shows that D – A (DDP) – D systems have significant intramolecular charge transfer, further confirming their promise as candidates for donor materials in solar cells. The significant photophysical properties of DPP derivatives, including the high fluorescence emission, also allow these materials to be used in organic light-emitting diodes (OLEDs). | Nathalia Rosa; Itamar Borges Jr | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Photovoltaics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66904e27c9c6a5c07a0391d4/original/photophysical-properties-of-donor-d-acceptor-a-donor-d-diketopyrrolopyrrole-a-systems-as-donors-for-applications-to-organic-electronic-devices.pdf |
656836c35bc9fcb5c9b5e283 | 10.26434/chemrxiv-2023-xglb4-v3 | Understanding β-strand mediated protein-protein interactions using peptidomimetics: tuning binding affinity of intrinsically disordered sequences by covalent backbone modification | A significant challenge in chemical biology is to understand and modulate protein-protein interactions (PPIs). Given that many PPIs involve a folded protein domain and a peptide sequence that is intrinsically disordered in isolation, peptides represent powerful tools to understand PPIs and templates for PPI modulator development. Using the interaction between small ubiquitin-like modifiers (SUMO) and SUMO-interacting motifs (SIMs), here we show that N-methylation of the peptide backbone can effectively restrict accessible peptide conformations, predisposing them for protein recognition. Backbone N-methylation in appropriate locations results in faster target binding, and thus higher affinity, as shown by fluorescence anisotropy, relaxation-based NMR experiments, and computational analysis. We show that such higher affinities occur as a consequence of an increase in the energy of the unbound state, and a reduction in the entropic contribution to the binding and activation energies. Thus, backbone N-Methylation may represent a useful modification within the peptidomimetic toolbox to probe β-strand mediated coupled binding and folding interactions.
| Emma Cawood; Emily Baker; Thomas Edwards; Derek Woolfson; Theodoros Karamanos; Wilson Andrew | Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Biophysics; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656836c35bc9fcb5c9b5e283/original/understanding-strand-mediated-protein-protein-interactions-using-peptidomimetics-tuning-binding-affinity-of-intrinsically-disordered-sequences-by-covalent-backbone-modification.pdf |
62ea24f1659a3f242b329f22 | 10.26434/chemrxiv-2022-kpf0x | Metal-based conducive nano-inks: A review of synthesis and characterisation techniques | In the recent decade, metal-based conductive nano-inks comprising of nanometer-sized metallic particles of high electrical conductivity (mainly Ag and Cu) suspended in a polymer have revolutionized the field of printed electronics. The present review aims to provide an overview of the current state of research in synthesis and characterization techniques for metallic nano-inks and associated challenges. Moreover, the end of the review will discuss future perspectives in this field (from industrial and academic viewpoints). | Mainak Saha | Materials Science; Organometallic Chemistry; Nanoscience; Nanodevices; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ea24f1659a3f242b329f22/original/metal-based-conducive-nano-inks-a-review-of-synthesis-and-characterisation-techniques.pdf |
626ad24c103388755bfe1c0c | 10.26434/chemrxiv-2022-zprf5 | Fluorescence-based Measurement of the Lewis Acidities of Lanthanide Triflates in Solution | Despite the prominence of rare earth complexes to act as Lewis-acid catalysts in organic synthesis, the comprehensive measure of the Lewis-acid strength of such compounds has yet to be performed due to incompatibilities with existing methods. We report our results in measurement of a sequence of lanthanide triflates via our recently established Fluorescent Lewis adduct (FLA) method. The persistence in solution of these Lewis acids as solvated coordination complexes is accurately measurable by the FLA method. However, several of the RE species exhibit fluorescence quenching, which may potentially inhibit the measurement. Nevertheless, meaningful FLA measurements were still able and the results correspond to both periodic trends and were even consistent with previous correlated reported data | Paul Demay-Drouhard; Joshua Gaffen; Christopher Caputo; Thomas Baumgartner | Physical Chemistry; Organic Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Sensors; Solution Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626ad24c103388755bfe1c0c/original/fluorescence-based-measurement-of-the-lewis-acidities-of-lanthanide-triflates-in-solution.pdf |
6298b2f41959595804be4c68 | 10.26434/chemrxiv-2022-srf0s | Thermal and Light Induced Infrared Blackening of ZnO Revisited: Overcoming the Language Border and Rediscovery of Fundamental Scientific Knowledge | A comprehensive and reliable view on the influence of UV light and heat on optical properties of ZnO shall be outlined mainly based on research conducted by scientists from Warsaw Pact countries throughout the 20th century. The problems of language barrier and loss of knowledge are being addressed. An insight into processes of photodesorption and photoadsorption of oxygen and other gas phase molecules leading to changes in charge carrier states is outlined. While desorption of surface adsorbates leads to increased number of conduction electrons and thus increased absorbance of infrared light, adsorption of electronegative gas phase molecules leads to quenching in fluorescence. | Pawel Naliwajko; Tim Peppel; Jennifer Strunk | Physical Chemistry; Materials Science; Chemical Education; Optical Materials; Physical and Chemical Properties; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6298b2f41959595804be4c68/original/thermal-and-light-induced-infrared-blackening-of-zn-o-revisited-overcoming-the-language-border-and-rediscovery-of-fundamental-scientific-knowledge.pdf |
60c74fc0842e658acadb38e2 | 10.26434/chemrxiv.12807167.v1 | Reactions of Ruthenium Cyclopentadienyl Praecursor in the Metal Precursor Pulse of Ru Atomic Layer Deposition | Ruthenium is a
promising material in the semiconductor industry and is investigated as the
interconnect metal or as a seed layer for Cu interconnects. Non-oxidative
reactants are required in a plasma-enhanced atomic layer deposition (PE-ALD) process
for metals to avoid oxygen contamination. The PE-ALD of Ru has been explored
experimentally, but the growth mechanism is not clear. In this paper, the reaction
mechanism of the cyclopentadienyl (Cp, C<sub>5</sub>H<sub>5</sub>) precursor RuCp<sub>2</sub>
and NH<sub>x</sub>-terminated Ru surfaces that result from the plasma cycle is studied
in detail by first-principle calculations. The Cp ligands are eliminated by hydrogen
transfer and desorb from metal surface as CpH. The results show that on the NH<sub>x</sub>-terminated
Ru surface at typical ALD operating condition (temperature range 550K to 650K), the first hydrogen
transfer is the rate-limiting step and has high barriers, which are -1.51eV for
Ru(001) and 2.01eV for Ru(100). Assuming that the initial activation barrier
for the first hydrogen transfer can be overcome, the two Cp ligands will be completely eliminated
completely on Ru(100) surface during the metal precursor pulse, resulting in Ru
atoms on the surface, binding to N atom. But at most only one Cp ligand is
eliminated on Ru(001) surface, resulting in an RuCp termination on (001)
surface. Investigating the precursor
coverage, the final surface coverages of final terminations after the metal
precursor pulse are 0.85 RuCp/nm<sup>2</sup> on the NH<sub>x</sub>-terminated
Ru(001) surface and 2.02 Ru/nm<sup>2</sup> on the NH<sub>x</sub>-terminated
Ru(100) surface. However, if the first H transfer barrier cannot be overcome,
leaving RuCp<sub>2</sub> on NH<sub>x</sub>-terminated Ru surfaces, the maximum coverages
of RuCp<sub>2</sub> on Ru(001) and Ru(100) surfaces are 2.54 RuCp<sub>2</sub>/nm<sup>2</sup>
and 2.02 RuCp<sub>2</sub>/nm<sup>2</sup>.
These structures are vital to model the
following N-plasma step. | Ji Liu; hongliang lu; david wei zhang; Michael Nolan | Thin Films; Computational Chemistry and Modeling; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fc0842e658acadb38e2/original/reactions-of-ruthenium-cyclopentadienyl-praecursor-in-the-metal-precursor-pulse-of-ru-atomic-layer-deposition.pdf |
64118137e53eff1af326e8b7 | 10.26434/chemrxiv-2023-hjqc9 | Visualizing formation and dynamics of a three-dimensional sponge-like network of a coacervate in real time | Coacervates, which are formed by liquid–liquid phase separation, have been extensively explored as models for synthetic cells and membraneless organelles, so their in-depth structural analysis is crucial. However, both the inner structure dynamics and formation mechanism of coacervates remain elusive. Herein, we demonstrate real-time confocal observation of a three-dimensional sponge-like network in a dipeptide-based coacervate. In situ generation of the dipeptide allowed us to capture the emergence of the sponge-like network via unprecedented membrane folding of vesicle-shaped intermediates. We also visualized dynamic fluctuation of the network, including reversible engagement/disengagement of crosslinks and a stochastic network kissing event. Photo-induced transient formation of a multiphase coacervate was achieved with a thermally responsive phase transition. Our findings expand the fundamental understanding of synthetic and biological coacervates, and provide opportunities to manipulate their physicochemical properties by engineering the inner network for potential applications in life-like material fabrication and biomedical research. | Ryou Kubota; Taro Hiroi; Yuchong Liu; Itaru Hamachi | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64118137e53eff1af326e8b7/original/visualizing-formation-and-dynamics-of-a-three-dimensional-sponge-like-network-of-a-coacervate-in-real-time.pdf |
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