id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
60d2df47c62295e1a41a9daf | 10.26434/chemrxiv-2021-3f144-v2 | Reproducing the invention of a named reaction: zero-shot
prediction of unseen chemical reactions | While state-of-art models can predict reactions through the transfer learning of thousands of samples with the same reaction types as those of the reactions to predict, how to prepare such models to predict "unseen" reactions remain an unanswered question. We aim to study the Transformer model's ability to predict "unseen" reactions following "zero-shot reaction prediction (ZSRP)", a concept derived from zero-shot learning and zero-shot translation. We reproduce the human invention of the Chan-Lam coupling reaction where the inventor was inspired by the Suzuki reaction when improving Barton's bismuth arylation reaction. After being fine-tuned with the samples from these two "existing" reactions, the USPTO-trained Transformer can predict "unseen" Chan-Lam coupling reactions with 55.7% top-1 accuracy. Our model also mimics the later stage of the history of this reaction, where the initial case of this reaction was generalized to more reactants and reagents via the "one-shot/few-shot reaction prediction(OSRP/FSRP)" approaches. | An Su; Ling Wang; Xinqiao Wang; Chengyun Zhang; Yejian Wu; Hongliang Duan | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d2df47c62295e1a41a9daf/original/reproducing-the-invention-of-a-named-reaction-zero-shot-prediction-of-unseen-chemical-reactions.pdf |
64c80862658ec5f7e58252b2 | 10.26434/chemrxiv-2023-d2cg5 | Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops | Access to the three-dimensional structure of RNA enables an ability to gain a more profound understanding of its biological mechanisms, as well as the ability to design RNA-targeting drugs, which can take advantage of the unique chemical environment imposed by a folded RNA structure. Due to the dynamic and structurally complex properties of RNA, both experimental and traditional computational methods have difficulty in determining RNA’s 3D structure. Herein, we introduce TAPERSS (Theoretical Analyses, Prediction, and Evaluation of RNA Structures from Sequence), a physics-based fragment assembly method for predicting 3D RNA structures from sequence. Using a fragment library created using discrete path sampling calculations of RNA dinucleoside monophosphates, TAPERSS can sample the physics-based energy landscapes of any RNA sequence with relatively low computational complexity. We have benchmarked TAPERSS on 21 RNA tetraloops, using a combinatorial algorithm as a proof-of-concept. We show that TAPERSS was successfully able to predict the apo-state structures of all 21 RNA hairpins, with 16 of those structures also having low predicted energies as well. We demonstrate that TAPERSS performs most accurately on GNRA-like tetraloops with mostly stacked loop-nucleotides, while having limited success with more dynamic UNCG and CUYG tetraloops, most likely due to the influence of the RNA force field used to create the fragment library. Moreover, we show that TAPERSS can successfully predict the majority of the experimental non-apo states, highlighting its potential in anticipating biologically significant yet unobserved states. This holds great promise for future applications in drug design and related studies. With discussed improvements and implementation of more efficient sampling algorithms, we believe TAPERSS may serve as a useful tool for a physics-based conformational sampling of large RNA structures. | ILYAS YILDIRIM; Ivan Riveros | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c80862658ec5f7e58252b2/original/prediction-of-3d-rna-structures-from-sequence-using-energy-landscapes-of-rna-dimers-application-to-rna-tetraloops.pdf |
60c74cb4337d6c50eae27cb5 | 10.26434/chemrxiv.12473501.v2 | Accelerating Battery Manufacturing Optimization by Combining Experiments, In Silico Electrodes Generation and Machine Learning | Both the society and the market calls for safer, high-performing and cheap Li-ion batteries (LIBs) in order to speed up the transition from oil-based to electric-based economy. One critical aspect to be taken into account in this modern challenge is LIBs manufacturing process, whose optimization is time and resources consuming due to the several interdependent physicochemical mechanisms involved. In order to tackle rapidly this challenge, digital tools able to accelerate LIBs manufacturing optimization are crucially needed for both well assessed and recently discovered chemistries. The methodology presented here encompasses experimental characterizations, in silico generation of electrode mesostructures and machine learning algorithms to track the effect of manufacturing over a wide array of mesoscale electrode properties critically linked to the electrochemical performance. Particularly, features as the interconnectivity of the particles network, the electrolyte tortuosity and effective ionic conductivity, the percentage of current collector surface covered by either active material or carbon-binder domain particles and the active material surface in contact with electrolyte were analysed and discussed in detail. This approach was tested and validated for the case of LiNi1/3Mn1/3Co1/3O2-based cathodes calendering, proving its capability to ease the process parameters-electrode properties interdependencies analysis, paving the way to deeper understanding and then faster optimization of LIBs manufacturing. | Marc Duquesnoy; Teo Lombardo; Mehdi Chouchane; Emiliano Primo; Alejandro A. Franco | Materials Processing; Machine Learning; Artificial Intelligence; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cb4337d6c50eae27cb5/original/accelerating-battery-manufacturing-optimization-by-combining-experiments-in-silico-electrodes-generation-and-machine-learning.pdf |
67a17b7afa469535b9fa75aa | 10.26434/chemrxiv-2025-mtmkb | Predicting the Ionic Conductivity and Obtaining Mechanistic Insights of Plasticized Solid Polymer Electrolytes Using a Data-Driven Approach | Solid polymer electrolytes (SPEs) are critical for the development of safe and high-performance solid-state lithium batteries powering the next generation of electric vehicles, drones, and robotics. To date, one of the major disadvantages of SPEs limiting their wide applications is the low ionic conductivity. The use of ionic liquid as plasticizers in SPEs has been demonstrated as a promising strategy to enhance the ionic conductivity of SPEs at room temperature while maintaining their safety features and mechanical properties. However, the optimization of plasticizers is largely intuition-based, without general design rules and predictive design strategies. Therefore, in this work, we developed a fast and low-cost data-driven workflow that advances the design and optimization of ionic liquid plasticizers for SPEs. Using this approach, we successfully identified a new plasticized SPE material that showed high ionic conductivity and superior cycling stability. Our data-driven model revealed important design factors correlated to highly effective plasticizers, providing insights into the conduction mechanism of plasticized SPEs. More importantly, we found that these key factors are transferrable and applicable in other plasticized SPEs beyond our dataset, highlighting the generality of the findings obtained by our data-driven approach. | Zhen-Nan Shen; Wenda Bao; Zhengzheng Dang; He Li; Rongliang Shang; Mengyu Hu; Yanming Wang; Jin Xie; Bo Qiao | Polymer Science; Energy; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a17b7afa469535b9fa75aa/original/predicting-the-ionic-conductivity-and-obtaining-mechanistic-insights-of-plasticized-solid-polymer-electrolytes-using-a-data-driven-approach.pdf |
60c74c5bbb8c1a77dd3db3d6 | 10.26434/chemrxiv.12465176.v1 | One-Pot Thiol-Amine Bioconjugation to Maleimides; Simultaneous Stabilisation and Dual Functionalisation | Maleimide chemistry is widely used in the site-selective modification of proteins. However, hydrolysis of the resultant thiosuccinimides is required to provide robust stability to the bioconjugates. Herein, we present an alternative approach that affords simultaneous stabilisation and dual functionalisation in a one pot fashion. By consecutive conjugation of a thiol and an amine to dibromomaleimides, we show that aminothiomaleimides can be generated extremely efficiently. Furthermore, the amine serves to deactivate the electrophilicity of the maleimide, precluding further reactivity and hence generating stable conjugates. We have applied this conjugation strategy to peptides and proteins to generate stabilised trifunctional conjugates. We propose that this stabilisation-dual modification strategy could have widespread use in the generation of diverse conjugates. <br /> | Archie Wall; Alfie Wills; Nafsika Forte; Calise Bahou; Lisa Bonin; Karl Nicholls; Michelle Ma; Vijay Chudasama; James Baker | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c5bbb8c1a77dd3db3d6/original/one-pot-thiol-amine-bioconjugation-to-maleimides-simultaneous-stabilisation-and-dual-functionalisation.pdf |
627baaf443d1f03c11289077 | 10.26434/chemrxiv-2022-zxn90 | A chemical catalyst enabling histone acylation with endogenous Acyl-CoA | Post-translational modifications (PTMs) of proteins, e.g., epigenetic acetylation of lysine residues in histones, are crucial to cellular functions and related to diseases. Chemical tools to directly introducing epigenetic lysine acetylation hold promise for elucidating the PTM’s functions and treating diseases. Although several chemical catalysts introducing protein acetylation in live cells were reported, there is no precedent promoting in-cell acetylation of epigenetically important but often low-reactive histone proteins using endogenous acetyl-CoA, as histone acetyltransferases (HATs) do. Herein, we developed a chemical catalyst mBnA enabling selective in-cell histone lysine acylation (H2BK120ac) using endogenous acyl-CoA as a sole acyl donor. A hydroxamic acid of proper electronic characteristics as a nucleophilic catalytic site combined with a thiol-thioester exchange process enabled mBnA to activate low concentration of acyl-CoAs in cells, promoting histone lysine acylations (acetylation and malonylation). This chemical catalyst will be a small-molecule surrogate to HAT and thus a unique tool to synthetic epigenetics. | Misuzu Habazaki; Shinsuke Mizumoto; Hidetoshi Kajino; Tomoya Kujirai; Hitoshi Kurumizaka; Shigehiro Kawashima; Kenzo Yamatsugu; Motomu Kanai | Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627baaf443d1f03c11289077/original/a-chemical-catalyst-enabling-histone-acylation-with-endogenous-acyl-co-a.pdf |
628d291c809e32e9e19b799e | 10.26434/chemrxiv-2022-vh04c | Synthesis of Multifunctional Amorphous Metallic Shell on Crystalline Metallic Nanoparticles | Colloidal nanoparticles can be coated with a conformal shell to form multifunctional nanoparticles. For instance, plasmonic, magnetic, and catalytic properties, chemical stability and biocompatibility can be mixed and matched. Here, a facile synthesis for depositing metal boride amorphous coatings on colloidal metallic nanocrystals is introduced. The synthesis is independent of core size, shape, capping ligand, and composition. Shell thickness can be as thin as 3 nm with no apparent pinholes. High pressure studies show that the coatings are highly resistant to crystallization and are strongly bonded to the crystalline core. By choosing either CoB or NiB for the coating, the composite nanoparticles can be either ferromagnetic or paramagnetic at room temperature, respectively. | Abhinav Parakh; Mehrdad Toussi Kiani; Emily Lindgren; Anabelle Colmenares; Andrew Curtis Lee; Yuri Suzuki; Xun Wendy Gu | Materials Science; Nanoscience; Coating Materials; Core-Shell Materials; Materials Processing; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628d291c809e32e9e19b799e/original/synthesis-of-multifunctional-amorphous-metallic-shell-on-crystalline-metallic-nanoparticles.pdf |
65d66b9e66c138172931b057 | 10.26434/chemrxiv-2024-rk4qx | Machine Learning-driven models for predicting CO2 Uptake in Metal-Organic Frameworks (MOFs) | This study advances the discourse on the application of machine learning (ML) algorithms for the predictive analysis of CO2 uptake in Metal-Organic Frameworks (MOFs), with a nuanced focus on the CATBoost model's capability to navigate the complexities inherent in MOFs' heterogeneous landscape. Building upon and extending the comparative analysis, our investigation underscores the CATBoost model's remarkable predictive prowess, characterized by a significant reduction in root mean square error (RMSE) and an enhanced R-squared (R²) value, thereby affirming its superior accuracy and reliability in forecasting CO2 adsorption. A pivotal aspect of our research is the integration of SHAP values for a detailed assessment of feature importance, which not only corroborated 'Pressure' and 'Surface Area' as pivotal determinants of CO2 uptake but also illuminated the model's advanced analytical capabilities in handling categorical features and mitigating overfitting, even within a dataset marked by intricate and non-linear patterns. Our quantitative and conceptual analysis, showcasing up to a 15% improvement in (RMSE) over previous models, reveals the CATBoost model’s unparalleled efficiency in discerning the multifaceted interplay of factors influencing CO2 adsorption. This is crucial for the strategic engineering of MOFs with optimized properties. Beyond 'Pressure' and 'Surface Area', our SHAP analysis highlighted other descriptors with substantial values, elucidating their nuanced contributions to CO2 uptake and providing invaluable insights for the MOF design process. Through this work, we aim to foster a deeper understanding and application of ML algorithms in environmental sustainability, thereby building upon the foundational research of Abdi et al. and pushing the boundaries of machine learning applications in the field. | Sofiene Achour; Zied Hosni | Materials Science | CC BY NC 4.0 | CHEMRXIV | 2024-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d66b9e66c138172931b057/original/machine-learning-driven-models-for-predicting-co2-uptake-in-metal-organic-frameworks-mo-fs.pdf |
6491a97c853d501c00321a94 | 10.26434/chemrxiv-2023-mwkp3 | Automated Analysis of Nano-Impact Single-Entity Electrochemistry Signals using Unsupervised Machine Learning and Template Matching | Nano-impact single-entity electrochemistry (NIE) is an emerging technique that enables electrochemical investigation of individual entities, ranging from metal nanoparticles to single cells and biomolecules. To extract meaningful information from NIE experiments, statistical analysis of large datasets is necessary. In this study, we developed a method for the automated analysis of NIE data based on unsupervised machine learning and template matching approaches. Template matching not only facilitates downstream processing of the NIE data but also provides a more accurate analysis of the NIE signal characteristics and variations that are difficult to discern with conventional data analysis techniques, such as the height threshold method. The developed algorithm enables fast automated processing of large experimental datasets recorded with different systems, requiring minimal human intervention and thereby eliminating human bias in data analysis. As a result, it improves the standardization of data processing and NIE signal interpretation across various experiments and applications. | Ziwen Zhao; Arunava Naha; Sagar Ganguli; Alina Sekretareva | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Electrochemical Analysis; Machine Learning; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6491a97c853d501c00321a94/original/automated-analysis-of-nano-impact-single-entity-electrochemistry-signals-using-unsupervised-machine-learning-and-template-matching.pdf |
625044ef5b9009c63d08476e | 10.26434/chemrxiv-2022-npslc | Identification of three new inhibitor classes against Plasmodium falciparum | In this study, we identified three novel compound classes with potent activity against Plasmodium falciparum, the most dangerous human malarial parasite. Resistance of this pathogen to known drugs is increasing and compounds with different modes of action are urgently needed. One promising drug target is the enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) of the methylerythritol 4-phosphate (MEP) pathway for which we have previously identified three active compound classes against Mycobacterium tuberculosis. The close structural similarities in the active sites of the DXPS enzymes of P. falciparum and M. tuberculosis prompted investigation of its antiparasitic action, displaying good cell-based activity for all classes. Through structure-activity relationship studies we increased their antimalarial potency, and two classes also show good metabolic stability and low toxicity against human liver cells. The most active compound 1 inhibits the growth of blood-stage P. falciparum with an IC50 of 600 nM. The results from three different methods for target validation of compound 1 suggest intracellular polypharmacy. Similarity-based searches revealed two other possible target enzymes for this compound, which were further analyzed by docking calculations. All inhibitor classes are active against chloroquine resistant strains, confirming a new mode of action. | Sandra Johannsen; Robin M. Gierse; Arne Krüger; Rachel L. Edwards; Vittoria Nanna; Anna Fontana; Di Zhu; Tizina Masini; Lais Pessanha de Carvalho; Mael Poizat; Bart Kieftenbelt; Dana M. Hodge; Sophie Alvarez; Daan Bunt; Kamila Anna Meissner; Edmarcia Elisa de Souza; Melloney Dröge; Bernard van Vliet; Jack de Hartog; Michael C. Hutter; Jana Held; Audrey R. Odom John; Carsten Wrenger; Anna K. H. Hirsch | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625044ef5b9009c63d08476e/original/identification-of-three-new-inhibitor-classes-against-plasmodium-falciparum.pdf |
615748109f1b44c44adc7418 | 10.26434/chemrxiv-2021-x9bjv | Targeted Activation in Localized Protein Environments via Deep Red Photoredox Catalysis | State-of-the art photoactivation strategies in chemical biology provide spatiotemporal control and visualization of biological processes. However, using high energy light (λ < 500 nm) for substrate or photocatalyst sensitization can lead to background activation of photoactive small molecule probes and reduce its efficacy in complex biological environments. Here we describe the development of targeted aryl azide activation via deep red light (λ = 660 nm) photoredox catalysis and its use in photocatalyzed proximity labeling. We demonstrate that aryl azides are converted to triplet nitrenes via a novel redox-centric mechanism and show that its spatially localized-formation requires both red light and a photocatalyst-targeting modality. This technology was applied in different colon cancer cell systems for targeted protein environment labeling of epithelial cell adhesion molecule (EpCAM). We identified a small subset of proteins with previously known and unknown association to EpCAM, including CDH3, a clinically relevant protein that shares high tumor selective expression with EpCAM. | Nicholas Tay; Keun Ah Ryu; John Weber; Aleksandra Olow; David Reichman; Rob Oslund; Olugbeminiyi Fadeyi; Tomislav Rovis | Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.); Bioinformatics and Computational Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615748109f1b44c44adc7418/original/targeted-activation-in-localized-protein-environments-via-deep-red-photoredox-catalysis.pdf |
646d9142ccabde9f6e4327a8 | 10.26434/chemrxiv-2023-x8899 | Theoretical Analysis of the Electronic Structure and Optical Properties of DNA-Stabilized Silver Cluster Ag16Cl2 in Aqueous Solvent | DNA-stabilized silver nanoclusters with 10 to 30 silver atoms are by construction ideal candidates for biocompatible bright fluorescent emitters but their electronic structure is not well understood. Here, using density functional theory (DFT), we analyze the ground-state electronic structure and optical absorption of a bright NIR-emitting cluster Ag16Cl2 which is stabilized by two DNA strands of 9-base sequence 5’-CACCTAGCG-3’ and whose atomic structure was very recently confirmed to have two chlorides bound to the silver core. We are able to (i) unambiguously assign the charge of this cluster in aqueous solvent, (ii) analyze the details of silver–DNA interactions and their effect on the cluster charge, (iii) analyze the character of low-energy optical absorption peaks and the involved electron orbitals and make a first assessment on circular dichroism, and (iv) evaluate the suitability of various DFT exchange-correlation functionals via benchmarking to experimental optical data. This work lays out a baseline for all future theoretical work to understand the electronic, chiroptical and fluorescence properties of these fascinating bio-compatible nanostructures. | Hannu Häkkinen; Sami Malola; Maria Francisca Matus | Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646d9142ccabde9f6e4327a8/original/theoretical-analysis-of-the-electronic-structure-and-optical-properties-of-dna-stabilized-silver-cluster-ag16cl2-in-aqueous-solvent.pdf |
60c750a7567dfe73e1ec58db | 10.26434/chemrxiv.13066061.v1 | Drug and Drug-like Molecule Binding to Interface of SARS-CoV-2 Sprotein:human ACE2 Complex: A Density Functional Theory Study | SARS-CoV-2
S-protein:human ACE2 complex models.<div>QM-MM optimized active site model of SARS-CoV-2 S-protein:human ACE2 interface.</div><div>ONIOM(B3LYP/6-31G*:PM7)
method is the chosen QM-MM method. </div><div> DFT B3LYP/6-31G* level data on energetics is reported for drug-receptor interaction.</div><div>Several FDA approved drugs and traditional herbal isolates are modelled.</div><div>Used Gaussian16 to model the systems.</div><div><br /></div><div><br /></div><p>The interface cavity of SARS-CoV-2 S-protein:human
ACE2 complex (<b>M</b>) for ligand (<b>L</b>) binding is modelled using a two layer ONIOM(B3LYP/6-31G*:PM7) method for
sixteen traditional herbal isolates (THI) and nineteen drugs. The binding energy (E<sub>b</sub>) of <b>ML</b> complexes increased with increase in
dipole moment of <b>L</b>s. E<sub>b</sub> better than -80.0 kcal/mol is
observed for digallic acid and adenosine 3',5'-bisphosphate whereas myricetin,
glucogallin, sapropterin, tetrahydrobiopterin,
protirelin and fidarestat<b> </b>showed
E<sub>b</sub> better than -60.0 kcal/mol. Multiple noncovalent interactions emanating
from arginine, histidine, tyrosine, lysine, carboxylate and amide units (total
around 6 - 8) of <b>L</b>, S-protein and ACE2 receptors provide the high
binding energy. The sugar substitute aspartame modified with myricetin unit
showed the best E<sub>b</sub> -91.7 kcal/mol. ONIOM-linked DFT study is
effective, affordable and reliable for a quantum chemical rational design
approach to model drug-receptor binding process for COVID-19 drug development which
sheds light upon the noncovalent binding features of receptor cavity.</p> | CH Suresh | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750a7567dfe73e1ec58db/original/drug-and-drug-like-molecule-binding-to-interface-of-sars-co-v-2-sprotein-human-ace2-complex-a-density-functional-theory-study.pdf |
60c74818bdbb893643a38f36 | 10.26434/chemrxiv.11708364.v2 | Divergent Adsorption-Dependent Luminescence of Amino- Functionalized Lanthanide Metal-Organic Frameworks for Highly Sensitive NO2 Sensors | A novel gas sensing mechanism exploiting the luminescence modulation upon NO2 adsorption is here demonstrated. Two isostructural lanthanide based-metal-organic frameworks are used including a recognition center (aminogroup) that provides high selectivity for NO2 molecules. Energy transfer from the organic ligands to Ln is strongly dependent on the presence of NO2, resulting in an unprecedented photoluminescent sensing scheme. Thereby, NO2 exposition triggers either a reversible enhancement or a decrease of the luminescence intensity, depending on the lanthanide ion (Eu or Tb). Our experimental studies combined with DFT and complete active space self-consistent field calculations, provide understanding of the nature and effects of NO2 interactions within the MOFs and the signal transduction mechanism.<br /> | Arturo Gamonal; Chen Sun; A. Lorenzo Mariano; Estefania Fernandez-Bartolome; Elena SanVicente; Bess Vlaisavljevich; Javier Castells-Gil; Carlos Martí-Gastaldo; Roberta Poloni; Reinhold Wannemacher; Juan Cabanillas-Gonzalez; José Sanchez Costa | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.); Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74818bdbb893643a38f36/original/divergent-adsorption-dependent-luminescence-of-amino-functionalized-lanthanide-metal-organic-frameworks-for-highly-sensitive-no2-sensors.pdf |
60c750c3ee301c0c35c7a913 | 10.26434/chemrxiv.13079078.v1 | Stoichiometric Excess of H2O2 as Strategy of Oxidant Dosing for Intensifying Both Degradation and Mineralization of the Hydrochlorothiazide via UVCH2O2, Dark-Fenton, and Photo-Fenton | <div>Hydrochlorothiazide (HCT) is a pharmaceutical micropollutant highly toxic to the
environment, being strictly mandatory to oxidize it completely toward CO2. In this context, how
could the HCT oxidation via advanced oxidative processes benefit from the accelerated oxidation
rates promoted by the mineralization stoichiometric excess of H2O2 ? Overall, this work
elucidates the role of stoichiometric H2O2 concentration on promoting fast
degradation/mineralization rates across Advanced Oxidative Processes (AOP). Employing 0.68
excess of H2O2, it was found absolute (100%) HCT degradation within 60 minutes and 95%
within 30 min for UVC-H2O2 oxidation; however, the mineralization of HCT suffered limited
optimization even at high H2O2 excess, being at the best performance 26.76% HCT mineralized
via UVC photo-Fenton within 60 min at initial 2.00 H2O2 excess. Very presumably, the
evaporation of H2O2 was the underlying reason for a low mineralization performance. Together
with a detailed mathematical methodology, the time-synchronized evolution of both the residual
H2O2 concentration and the TOC depletion were employed to infer the quantity of radical ∙OH
that effectively was consumed by the micropollutant mineralization. The global mean efficiency
of radicals •OH consumption by the HCT mineralization laid around 15% for UVC Fenton
considering H2O2 excess of 2.00. Under these conditions, the residual H2O2 concentration
depletes significantly within 30 minutes of UVC photo-Fenton oxidation, which indicates that
either the solution heating or stirring is very likely to promote a substantial loss of H2O2 by
evaporation in the beaker-assembled reactor<br /></div> | Fernando J. Cunha-Filho; Andressa Mota-Lima; claudio A. Oller do Nascimento; Osvaldo Chiavone-Filho | Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750c3ee301c0c35c7a913/original/stoichiometric-excess-of-h2o2-as-strategy-of-oxidant-dosing-for-intensifying-both-degradation-and-mineralization-of-the-hydrochlorothiazide-via-uvch2o2-dark-fenton-and-photo-fenton.pdf |
60c758c09abda253d3f8e981 | 10.26434/chemrxiv.14197457.v3 | Analytic Gradients for Restricted Active Space Second-order Perturbation Theory (RASPT2) | The computational cost of analytic derivatives in multireference perturbation theory is strongly affected by the size of the active space employed in the reference self-consistent field calculation. To overcome previous limits on active space size, the analytic gradients of single-state restricted active space second-order perturbation theory (RASPT2) and its complete active space variant (CASPT2) have been developed and implemented in a local version of OpenMolcas. Similar to previous implementations of CASPT2, the RASPT2 implementation employs the Lagrangian or Z-vector method.<br />The numerical results show that restricted active spaces with up to 20 electrons in 20 orbitals can now be employed for geometry optimizations.<br /> | Yoshio Nishimoto | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758c09abda253d3f8e981/original/analytic-gradients-for-restricted-active-space-second-order-perturbation-theory-raspt2.pdf |
65007e50b6ab98a41c5299a0 | 10.26434/chemrxiv-2023-31ctw | Transition metal free continuous flow synthesis of 2,5-diaryl furans: access to medicinal building blocks and optoelectronic materials | The direct transformation of 1,3-dienes into valuable 2,5-diarylfurans using transition metal-free conditions is presented. By employing a simple oxidation - dehydration sequence on readily accessible 1,3-dienes, important 2,5-diarylfuran building blocks frequently used in medicinal and materials chemistry are prepared. The oxidation step is realised using singlet oxygen, and the intermediate endoperoxide is dehydrated under metal-free conditions and at ambient temperature using the Appel reagent. Notably, this sequence can be streamlined into continuous flow, thereby eliminating the isolation of the intermediate, often unstable endoperoxide. This leads to a significant improvement in isolated yields (ca. 27% average increase) of the 2,5-diarylfurans, while also increasing safety and reducing waste. Our transition metal-free synthetic approach to 2,5-diarylfurans delivers several important furan building blocks used commonly in medicinal chemistry and as optoelectronic materials, including short chain linearly conjugated furan oligomers. Consequently, we also complete a short study of the optical and electrochemical properties of a selection of these novel materials. | Helena Grantham; Robert Lee; Grzegorz Wardas; Jai-Ram Mistry; Mark Elsegood; Iain Wright; Gareth Pritchard; Marc Kimber | Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65007e50b6ab98a41c5299a0/original/transition-metal-free-continuous-flow-synthesis-of-2-5-diaryl-furans-access-to-medicinal-building-blocks-and-optoelectronic-materials.pdf |
6519a1f5ade1178b247a3b71 | 10.26434/chemrxiv-2023-sx2hz-v2 | Exploiting Grain Boundary Diffusion to Minimize Dendrite
Formation in Lithium Metal-Solid State Batteries
| Maintaining interfacial contact between the Li metal anode and the solid electrolyte is a key challenge in developing Li metal-based solid-state batteries (LMSSB). At moderate discharge rates, relatively slower diffusion within the anode results in roughening and void formation in Li near this interface. The resulting reduction in interfacial contact focuses the Li-ion current during plating to a reduced number of contact points, generating high local current densities that nucleate dendrites. One approach to minimize void formation is to apply high stack pressure, which enhances plastic flow in the anode. Nevertheless, the use of pressure has drawbacks, as it facilitates fracture within the solid electrolyte. Here, an alternative strategy for minimizing void formation is described. Using a multi-scale model, it is shown that targets for capacity and current density in LMSSBs can be achieved by reducing the grain size of Li to exploit fast grain boundary (GB) diffusion. Diffusion rates along a diverse sampling of 55 tilt and twist GBs in Li were predicted using molecular dynamics, and found to be 3 to 6 orders of magnitude faster than in the bulk. Using these atomic-scale data as input, a meso-scale model of Li depletion in the anode during discharge was developed. The model predicts that smaller, columnar grains are desirable, with grain sizes of approximately 1 μm or less needed to meet performance targets. As micron-sized grains are two orders of magnitude smaller than those in common use, strategies for controlling grain size are discussed. In total, the model highlights the importance of the anode’s microstructure on the performance of LMSSBs. | Jeong Seop Yoon; Hafeez Sulaimon; Donald J. Siegel | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6519a1f5ade1178b247a3b71/original/exploiting-grain-boundary-diffusion-to-minimize-dendrite-formation-in-lithium-metal-solid-state-batteries.pdf |
659bffa266c1381729fae1c7 | 10.26434/chemrxiv-2024-p6wkk | Structural isomerism-tuned magnetisation relaxation dynamics in lanthanide coordination complexes | The eigenspectrum and eigenvectors of the 2F7/2 ground multiplets of two structural isomer coordination complexes, Yb(trenovan) (H3trenovan = tris(((3-methoxysaliclidene)amino)ethyl)amine) and Yb(trenpvan) (H3trenpvan = tris(((5-methoxysaliclidene)amino)ethyl)amine), were determined by use of magnetometry and electron paramagnetic resonance and luminescence spectroscopies. The two 4f complexes crystallise in the trigonal 𝑃3̅ space group, have identical chemical formulas and differ only in the placement of the methoxy group on the aromatic ring of salicylaldehyde, with it being either ortho, Yb(trenovan), or para, Yb(trenpvan), to the phenoxo group. This structural isomerism is found to have a profound influence on the solid state static and dynamic magnetic properties of the complexes. In the bulk, both isomers display a combination of direct and raman magnetisation relaxation procceses, however, at vastly different rates. Magnetic dilution in an isostructural diamagnetic host supresses the occurrence of the direct procces suggesting that the direct process observed in the bulk originates from Yb(III) centres coupled by magnetic dipole interactions. The eigenspectrum, eigenvectors and spin lattice relaxation of Yb(trenpvan) are found to be closer to the ones found in Yb(trensal) (H3trensal = tris(((saliclidene)amino)ethyl)amine) where the methoxy group is substituted by an H atom, than to those of Yb(trenovan) where the methoxy group is in the ortho position. Thus, the position of chemical modifications has a tremendous influence on the static and dynamic solid state magnetic properties of 4f coordination complexes. Our detailed study on single crystals, demonstrates that the rarely studied effect of modifications of the position of second coordination sphere chemical groups on the dynamic magnetic properties can in fact be used to chemically tune the magnetisation dynamics of 4f spin systems. | Steen Hansgaard Hansen; Christian Dirk Buch; Stergios Piligkos | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659bffa266c1381729fae1c7/original/structural-isomerism-tuned-magnetisation-relaxation-dynamics-in-lanthanide-coordination-complexes.pdf |
65029868b6ab98a41c69836b | 10.26434/chemrxiv-2023-52ppc | Ultra-Low Loaded Platinum Bonded Hexagonal Boron Nitride as Stable Electrocatalyst for Hydrogen Generation | Chemical stability of hexagonal boron nitride (hBN) ultra-thin layers in harsh electrolytes and the availability of nitrogen site to stabilize metals like Pt are used here to develop a high intrinsic activity hydrogen evolution reaction (HER) catalyst having low loaded Pt (5 weight% or < 1 atomic%). A catalyst having non-zero oxidation state for Pt (with a Pt-N bonding) is shown to be HER active even with low catalyst loadings (0.114 mgcm-2). Electronic modification of the shear exfoliated hBN sheets is achieved by Au nanoparticle-based surface decoration (hBN_Au), and further anchoring with Pt develops a catalyst (hBN_Au_Pt) with high turnover frequency for HER (~15), which is ~1.8 times higher than the benchmarked Pt/C HER catalyst. The hBN_Au_Pt is shown to be a highly durable catalyst even after the accelerated durability test for 10000 cycles and temperature annealing of 100 oC. Density functional theory-based calculations gave insights in to the electronic modifications of hBN with Au and the catalytic activity of the hBN_Au_Pt system, in line with the experimental studies, indicating the demonstration of a new class of catalyst system devoid of issues such as carbon corrosion and Pt leaching. | Narayanan Tharangattu Narayanan; Rayantan Sadhukhan; Amar Kumar; Ponnappa K. Prasanna; Anku Guha; Raul Arenal; Sudip Chakraborty | Catalysis; Energy; Acid Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65029868b6ab98a41c69836b/original/ultra-low-loaded-platinum-bonded-hexagonal-boron-nitride-as-stable-electrocatalyst-for-hydrogen-generation.pdf |
60f954b9c0c36e69d4cc13fc | 10.26434/chemrxiv-2021-plbj8 | Sterically Stabilized End-On Superoxocopper(II) Complexes and Mechanistic Insights Into Their Reactivity With O-H, N-H and C-H Substrates. | Instability of end-on superoxocopper(II) complexes, with respect to conversion to the corresponding peroxo-bridged complexes, has largely constrained their study to very low temperatures (< -80°C). This limits their kinetic capacity to oxidize substrates. In response, we have developed a series of ligand systems bearing bulky aryl substituents that are primarily directed away from the metal centre, Ar3-TMPA (Ar = tpb, dpb, dtbpb), and used them to support [Cu(Ar3-TMPA)(NCMe)]+ copper(I) complexes. Solutions of all three react with O2 to yield [Cu(η1-O2•−)(Ar3-TMPA)]+ complexes that are stable against dimerization at all temperatures. Full binding of O2 is observed at sub-ambient temperatures and can be reversed by warming. The onset of oxygenation is ligand dependent, but can be observed at 25°C in the case of Ar = tpb and dpb. Furthermore, all three [Cu(η1-O2•−)(Ar3-TMPA)]+ complexes are stable against self-decay at temperatures ≤ -20°C. This provides a wide temperature window over which these complexes can be studied, which was exploited by performing extensive reaction kinetics measurements for [Cu(η1-O2•−)(tpb3-TMPA)]+ with a broad range of O-H, N-H, and C-H bond substrates. This includes correlation of second order rate constants (k2 values) versus oxidation potentials (Eox) for a range of phenols (i.e., a Marcus plot), construction of Eyring plots, and temperature-dependent kinetic isotope effect (KIE) measurements. The data obtained indicates that reaction with all substrates proceeds via H-atom transfer (HAT) to [Cu(η1-O2•−)(tpb3-TMPA)]+. In addition, evidence suggests that HAT reaction with the phenols studied proceeds with significant charge transfer, and that it involves full tunelling of both H and D atoms in the case of 1,2-diphenylhydrazine (DPH) and 4-methoxy-2,6-di-tert-butylphenol (MeO-ArOH). Consistent with expectations for HAT, large entropic barriers (ΔS‡) were measured for the substrates MeO-ArOH, DPH, triphenylhydrazine (TPH), and 1-benzyl-1,4-dihydronicotinamide (BNAH). Despite having the lowest X-H bond dissociation energy (BDE) amongst these substrates, the C-H substrate BNAH exhibits both the largest ΔS‡ and the second largest enthalpic barrier (ΔH‡) to reaction. This is congruent with the expectation that oxidation of C-H bonds is kinetically challenging and the experimental observation that [Cu(η1-O2•−)(tpb3-TMPA)]+ is only able to oxidize very weak C-H bonds, whereas it can oxidize moderately strong N-H bonds. | Sebastian Quek; Suman Debnath; Shoba Laxmi; Maurice van Gastel; Jason England | Inorganic Chemistry; Bioinorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f954b9c0c36e69d4cc13fc/original/sterically-stabilized-end-on-superoxocopper-ii-complexes-and-mechanistic-insights-into-their-reactivity-with-o-h-n-h-and-c-h-substrates.pdf |
6723b619f9980725cfb5014b | 10.26434/chemrxiv-2024-75cb8 | Triblock architecture and PEG hydrophilic blocks enable efficient thermogelation of poly(2-phenyl-2-oxazine)-based worm-gels | Previously, the cooling-induced thermogelation of an amphiphilic ABA type triblock copolymer comprising a central poly(2-phenyl-2-oxazine) (pPheOzi) block flanked by hydrophilic poly(2-methyl-2-oxazoline) (pMeOx) blocks was reported. This process is based on an unusual, cooling-induced transition in polymer self-assembly from spherical to worm-like micelles, for which the PheOzi units are decisive. Here, we investigate this phenomenon further by introducing new variants of amphiphilic pPheOzi-based copolymers to explore the variability of the system. Changing the arrangement of the MeOx and PheOzi constitutional repeat units enables to investigate the influence of the polymer architecture on the thermogelation. We found that a triblock architecture is superior to diblock, gradient and star-like polymer architectures in terms of efficient order-order transition-based thermogelation. In addition, a coupling procedure based on copper-catalyzed azide-alkyne cycloaddition is presented that allows for a direct comparison of pMeOx and PEG as hydrophilic blocks in pPheOzi-based triblocks. Interestingly, PEG hydrophilic blocks also enable rapid worm-formation and show faster gelation as well as increased gel strength. Altogether, our findings provide basic design criteria for improved (pPheOzi-based) worm-gels. The introduced small library of pPheOzi-based copolymer variants can be used for further fundamental studies regarding thermo-responsive transitions in polymer self-assembly. | Anna-Lena Ziegler; Andrew Kerr; Florian T. Kaps; Robert Luxenhofer | Materials Science; Polymer Science; Biocompatible Materials; Hydrogels; Polymerization catalysts; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6723b619f9980725cfb5014b/original/triblock-architecture-and-peg-hydrophilic-blocks-enable-efficient-thermogelation-of-poly-2-phenyl-2-oxazine-based-worm-gels.pdf |
650f16cfb927619fe7aed0fc | 10.26434/chemrxiv-2023-9b906 | In Silico Screening and Evolution of Promising Novel Anti-Virulents Against Salmonella ATPase | Our current treatments for bacterial infections are under threat by the growth of antibiotic resistance in many different pathogens. Of these pathogens, Salmonella is a particularly widespread microbe, infecting over a million people annually as the leading source of food-borne diseases. One potential solution for antibiotic-resistant Salmonella is virulence inhibition of the bacteria’s T3SS injection system, which has been shown to destroy Salmonella’s proliferative abilities. Here, we identify fourteen compounds, primarily novel ligands, that exhibit high in-vitro potential as Salmonella inhibitors by attacking the ATPase InvC protein vital for T3SS injection–an enzyme that has not been previously evaluated for small-molecule inhibition. We also present a statistical analysis of AutoGrow4, a virtual structure-based molecular design tool that evolves ligands to better suit a target protein using Autodock Vina binding affinity calculations. Together, these create an entirely open-source workflow towards computational identification and evaluation of novel chemical treatments.
| Lexi Xu; Norah Shen | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Education; Chemical Education - General; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650f16cfb927619fe7aed0fc/original/in-silico-screening-and-evolution-of-promising-novel-anti-virulents-against-salmonella-at-pase.pdf |
60c757fb702a9bff8518cbe1 | 10.26434/chemrxiv.14479698.v1 | Diels-Alder Additions to 2,2’-Biaceanthrylene | A series of Diels-Alder reactions between the diene 2,2’-biaceanthylene and several dienophiles is presented. The diene is a cyclopenta-fused polycyclic aromatic hydrocarbon with anthracene units linked by two cyclopentene rings. Depending on the dienophile, the major product was the result of a single addition (dimethyl acetylenedicarboxylate) or double addition (quinone, benzyne) to the diene. Single crystal X-ray analysis of the quinone-derivative shows a propeller-like structure composed of mixed enantiomers. The synthesis and photophysical properties of these compounds is presented.<br /> | Yachu Du; Kyle Plunkett | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757fb702a9bff8518cbe1/original/diels-alder-additions-to-2-2-biaceanthrylene.pdf |
668ef5265101a2ffa803d7d8 | 10.26434/chemrxiv-2024-rcvcc | Multistage and Multicolor Liquid Crystal Reflections using a Chiral
Triptycene Photoswitchable Dopant | The photomodulation of the helical pitch of cholesteric liquid crystals (CLCs) results in
dynamic and colored canvases that can potentially be used in applications ranging from energyefficient
displays to color filters, anti-counterfeiting tags and LC lasers. The challenge in attaining
these functions though is the development of photoswitchable chiral dopants with optimal
properties that can modulate the CLCs in a controllable and multistage manner, to afford longlived
multi-color reflections from the LC surface. Here we report on the structure property analysis
of a series of photoswitchable chiral dopants that combine the large geometrical change and
bistabilty of hydrazone switches with the efficient helical pitch induction of the new chiral motif,
triptycene. These studies have elucidated the effects that conformational flexibility, dispersion
forces, and - interactions have on the chirality transfer ability of the dopant. Finally, we used
the best performing dopant in designing LC surfaces whose reflected wavelength (450-800 nm)
can be controlled and tuned as a function of irradiation wavelength or time dependent isomer ratio.
The bistability of the hydrazone switch allowed us to lock-in different reflected colors from the
surface including the primary colors red, green, and blue, for extended periods of time. Finally,
irradiation time with visible light (442 nm) combined with a simple digital light processing
microscope projection setup was used in drawing numerous multi-colored images on an LC
canvas, showcasing the fine control this dopant yields over the LC assembly. This work
demonstrates how the combination of a bistable photoswitch with a chiral motif having a strong
helical twisting power can result in adaptive LC surfaces whose properties can be tuned with
exceptional efficiency. | Indu Bala; Joshua Plank; Brandon Balamut; Drake Henry ; Alexander Lippert; Ivan Aprahamian | Physical Chemistry; Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668ef5265101a2ffa803d7d8/original/multistage-and-multicolor-liquid-crystal-reflections-using-a-chiral-triptycene-photoswitchable-dopant.pdf |
60c75436bb8c1a333e3dc1bf | 10.26434/chemrxiv.13626821.v1 | Leveraging Neural Networks and Genetic Algorithms to Refine Electrode Properties in Redox Flow Batteries | Redox flow batteries are a nascent, yet promising, energy storage technology for which widespread deployment is hampered by technical and economic challenges. A performance-determining component in the reactor, present-day electrodes are often borrowed from adjacent electrochemical technologies rather than specifically designed for use in flow batteries. A lack of structural diversity in commercial offerings, coupled with the time constraints of wet-lab experiments, render broad electrode screening infeasible without a modeling complement. Herein, an experimentally validated model of a vanadium redox flow cell is used to generate polarization data for electrodes with different macrohomogeneous properties (thickness, porosity, volumetric surface area, and kinetic rate constant). Using these data sets, we then build and train a neural network with minimal average root-mean squared testing error (17.9 ± 1.8 mA cm<sup>−2</sup>) to compute individual parameter sweeps along the cell polarization curve. Finally, we employ a genetic algorithm with the neural network to ascertain electrode property values for improving cell power density. While the developed framework does not supplant experimentation, it is generalizable to different redox chemistries and may inform future electrode design strategies. | Kevin Tenny; Richard Braatz; Yet- Ming Chiang; Fikile Brushett | Reaction Engineering; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75436bb8c1a333e3dc1bf/original/leveraging-neural-networks-and-genetic-algorithms-to-refine-electrode-properties-in-redox-flow-batteries.pdf |
63c8b0980cc433774bd6dc89 | 10.26434/chemrxiv-2023-jplm7 | Porous film impregnation method for record-efficiency visible-to-UV photon upconversion and subsolar light harvesting | Photon upconversion from visible light to ultraviolet (UV) light is useful for various photochemical reactions such as artificial photosynthesis, but its efficiency has been low under practical film conditions. Here, we demonstrate a film with a record-high visible-to-UV upconversion efficiency of 27.6% by simply soaking a porous film with a low-volatile upconversion solution. Furthermore, by combining this film with a microlens array, a significantly low threshold excitation light intensity of less than 0.60 mW cm−2, at least one order of magnitude lower than solar irradiance, is achieved. | Naoyuki Harada; Masanori Uji; Baljeet Singh; Nobuo Kimizuka; Nobuhiro Yanai | Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c8b0980cc433774bd6dc89/original/porous-film-impregnation-method-for-record-efficiency-visible-to-uv-photon-upconversion-and-subsolar-light-harvesting.pdf |
61d77876db142e078eb6257f | 10.26434/chemrxiv-2021-c603x-v2 | Static and Dynamic Statistical Correlations in
Water: Comparison of Classical Ab Initio
Molecular Dynamics at Elevated Temperature
With Path Integral Simulations at Ambient
Temperature | It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the over-structuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic state are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. We find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-molecule
correlations as well as hydrogen bond dynamics. In many of these cases, the effects of NQEs are the opposite of the effects of carrying out the simulations at an elevated temperature. | Chenghan Li; Francesco Paesani; Gregory A. Voth | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d77876db142e078eb6257f/original/static-and-dynamic-statistical-correlations-in-water-comparison-of-classical-ab-initio-molecular-dynamics-at-elevated-temperature-with-path-integral-simulations-at-ambient-temperature.pdf |
60c744dcee301c0d5ac791e4 | 10.26434/chemrxiv.9917225.v1 | PEPPI-MS: Strategies to Enhance the Extraction of Electrophoretically Separated Proteins from Polyacrylamide Gels and Their Application to Top-Down/native Mass Spectrometry | Polyacrylamide gel electrophoresis (PAGE) is a powerful technique for separating proteins from complex biological samples. However, the difficulty in recovering proteins with high yields from polyacrylamide matrices often precludes further analyses of intact proteins. Here, we propose a novel experimental workflow named Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS (‘PEPPI-MS’), which allows intact mass spectrometry (MS) of PAGE separated proteins. We discovered that staining proteins with certain Coomassie brilliant blue formulations immediately after PAGE improves the efficiency of extraction in a medium with pH 7–11. Post-staining, proteins spanning a broad range of molecular weights were recovered efficiently in a 10-minute procedure. High recovery yields were also obtained from dried and archived gels. This workflow is effective for top-down proteomics analysis of the target molecular region in the gel. An alternative procedure was developed for the extraction of protein complexes exceeding 400 kDa, which were separated using native PAGE, from unstained gels. Non-covalent hemoglobin tetramer, purified from cell lysate with two-dimensional native PAGE and extracted with the mild detergent octyl-β-Dglucopyranoside, was amenable for native MS analysis. We anticipate that the established workflow will facilitate the purification, storage, and transport of proteins destined for detailed characterization by MS. | Ayako Takemori; Lissa C Anderson; Victoria M. Harman; Philip Brownridge; David Butcher; Keisuke Shima; Daisuke Higo; Jun Ishizaki; Hitoshi Hasegawa; Junpei Suzuki; Masakatsu Yamashita; Joseph A. Loo; Rachel R. Ogorzalek Loo; Robert J. Beynon; Nobuaki Takemori | Analytical Chemistry - General; Biochemical Analysis; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744dcee301c0d5ac791e4/original/peppi-ms-strategies-to-enhance-the-extraction-of-electrophoretically-separated-proteins-from-polyacrylamide-gels-and-their-application-to-top-down-native-mass-spectrometry.pdf |
60c74ab3337d6ccdf3e27961 | 10.26434/chemrxiv.12249752.v1 | Machine Learning for Materials Scientists: An Introductory Guide Towards Best Practices | <div>This Editorial is intended for materials scientists interested in performing machine learning-centered research.</div><div><br /></div><div>We cover broad guidelines and best practices regarding the obtaining and treatment of data, feature engineering, model training, validation, evaluation and comparison, popular repositories for materials data and benchmarking datasets, model and architecture sharing, and finally publication.</div><div>In addition, we include interactive Jupyter notebooks with example Python code to demonstrate some of the concepts, workflows, and best practices discussed.</div><div><br /></div><div>Overall, the data-driven methods and machine learning workflows and considerations are presented in a simple way, allowing interested readers to more intelligently guide their machine learning research using the suggested references, best practices, and their own materials domain expertise.</div> | Anthony Wang; Ryan Murdock; Steven Kauwe; Anton Oliynyk; Aleksander Gurlo; Jakoah Brgoch; Kristin Persson; Taylor Sparks | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ab3337d6ccdf3e27961/original/machine-learning-for-materials-scientists-an-introductory-guide-towards-best-practices.pdf |
618587423c169d6f858fefb3 | 10.26434/chemrxiv-2021-drhkb-v2 | Solar-thermal production of graphitic carbon and hydrogen via methane decomposition | This work reports a process in which concentrated irradiation from a simulated solar source converts methane to high-value graphitic carbon and hydrogen gas. Methane flows within a photo-thermal reactor through the pores of a thin substrate irradiated by several thousand suns at the focal peak. The methane decomposes primarily into hydrogen while depositing highly graphitic carbon that grows conformally over ligaments in the porous substrate. The localized solar heating of the porous substrate serves to capture the solid carbon into a readily extractable and useful form while maintaining active deposition site density with persistent catalytic activity. Results indicate a strong temperature dependence with high decomposition occurring in the central heating zone with concentration factors and temperatures above 1000 suns and 1300 K, respectively. Even with a large flow area through regions of lower irradiation and temperature, methane conversion and hydrogen yields of approx. 70\% are achieved, and 58\% of the inlet carbon is captured in graphitic form. | Mostafa Abuseada; Chuyu Wei; R. Mitchell Spearrin; Timothy S. Fisher | Materials Science; Energy; Carbon-based Materials; Nanostructured Materials - Materials; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618587423c169d6f858fefb3/original/solar-thermal-production-of-graphitic-carbon-and-hydrogen-via-methane-decomposition.pdf |
66504a7c91aefa6ce1dd9bc3 | 10.26434/chemrxiv-2024-sqwhs | Fluorene vs. Spirobifluorene: Effect of the π-system on TADF properties | There are many options to design a molecular structure that could result in thermally activated delayed fluorescence (TADF). One promising strategy is to use donor-π-acceptor motive where the electron-donating unit is linked to the electron-acceptor via an aryl moiety which reduces the HOMO-LUMO overlap. While this approach is widely used and well understood, the perfor-mance of the chromophores can be limited by different energy loss pathways, e.g. internal con-version or π-stacking. To circumvent these problems rigid structures with sterically demanding substituents are applied. In this work, we designed two TADF emitters based on phenothiazine and nitrile linked via spirobifluorene or 9,9-dimethylfluorene and compared the effect of the linker on the physical properties of the dyes. | Tim Silies; Nikos Doltsinis; Constantin Daniliuc; Fabio Rizzo | Physical Chemistry; Organic Chemistry; Materials Science; Dyes and Chromophores; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66504a7c91aefa6ce1dd9bc3/original/fluorene-vs-spirobifluorene-effect-of-the-system-on-tadf-properties.pdf |
64da497e69bfb8925aec6cab | 10.26434/chemrxiv-2023-31b3x | Assessment of DLPNO-MP2 Approximations in Double-Hybrid DFT | The unfavorable scaling (N5) of conventional second-order Møller-Plesset theory (MP2) typically prevents the application of double-hybrid (DH) density functionals to large systems with more than 100 atoms. A prominent approach to reduce the computational demand of electron correlation methods is the domain-based local pair natural orbital (DLPNO) approximation that is successfully used in the framework of DLPNO-CCSD(T). Its extension to MP2 [P. Pinski, C. Riplinger, E. F. Valeev and F. Neese, J. Chem. Phys. 143, 034108 (2015)] paved the way for DLPNO-MP2-based double-hybrid methods. In this work, we assess the accuracy of the DLPNO-MP2 approximation compared to conventional double-hybrids on a large number of 7925 data points for thermochemistry and 239 data points for structural features, including main-group and transition-metal systems. It is shown that DLPNO-DH-DFT can be applied successfully to perform energy calculations and geometry optimizations for large molecules at a drastically reduced computational cost. Furthermore, PNO space extrapolation is shown to be applicable, similar to its DLPNO-CCSD(T) counterpart, to reduce the remaining error. | Hagen Neugebauer; Peter Pinski; Stefan Grimme; Frank Neese; Markus Bursch | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64da497e69bfb8925aec6cab/original/assessment-of-dlpno-mp2-approximations-in-double-hybrid-dft.pdf |
632244ffbada3867d0c58fcb | 10.26434/chemrxiv-2022-9shrz | F-tag induced acyl shift in the photochemical cyclization of o-alkynylated N-alkyl-N-acylamides to indoles | A photochemical cyclization of F-tagged, o-alkynylated N-alkylamides to indoles catalyzed by the [Ir(dtbbpy)(ppy)2]PF6 is presented. This straightforward and efficient reaction involves an intramolecular rearrangement due to the presence of fluorine in the acyl moiety and is the first example of photochemically induced 1,3-acyl shift in the cyclization towards 3-acylidoles. A four-step reaction sequence to the desired derivatives including the photoreaction as a key step has been developed and optimized. The compatibility of differently substituted F-tagged precursors with the photocyclization step was investigated and the robustness of this step towards modifications could be shown. In total, 19 so far unknown derivatives with diverse modifications in positions N1 and C2 were synthesized in very good yields and fully characterized. | Nicole Jung; Stefan Bräse; Helena Simek Tosino; Andre Jung; Olaf Fuhr; Claudia Muhle-Goll | Organic Chemistry; Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632244ffbada3867d0c58fcb/original/f-tag-induced-acyl-shift-in-the-photochemical-cyclization-of-o-alkynylated-n-alkyl-n-acylamides-to-indoles.pdf |
60c742f09abda23483f8c0e8 | 10.26434/chemrxiv.8863832.v1 | Nickel-Catalyzed Acylation of Aryl Bromides with Acyl Imidazoles | Alkyl imidazolides were herein found to be viable coupling partners for the Ni-catalyzed acylation of aryl bromides. This cross-coupling reaction features a broad substrate scope and be performed in an extremely cost-efficient fashion. Mechanistically, formation of acyl radicals via reduction of imidazolides represents a major departure from other reported radical acylation reactions. Of particular note, extensive studies revealed an intriguing radical chain mechanism and a remarkable CO-extrusion-recombination phenomenon. Finally, the practicality of this cross-coupling was demonstrated with a gram-scale reaction for the synthesis of a furan diterpenoid natural product. | Junming Zhuo; Yong Zhang; Zijian Li; Chao Li | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f09abda23483f8c0e8/original/nickel-catalyzed-acylation-of-aryl-bromides-with-acyl-imidazoles.pdf |
6190f55a2e10ad59bb4632bb | 10.26434/chemrxiv-2021-qz268 | Switchable radical carbonylation by polarity-regulation | Carbonylation reactions involving CO as readily available C1 synthons have become one of the most important tools for construction of carbonyl compounds from feedstock chemicals in modern chemical synthesis. Whereas numerous catalytic methods for carbonylation reactions proceeding via ionic or radical pathways have been reported, an inherent limitation to these methods is the need to control switchable single and double carbonylative formation of value-added products from the same and simple starting materials. Here we describe a new strategy that exploits simple visible-light-driven photoredox catalysis to regulate the polarity of coupling partners to drive switchable radical carbonylation reactions. Controlled trap of various alkyl radicals by single or double CO thereby proceed smoothly with excellent selectivity in the presence of various amine nucleophiles at room temperature, generating valuable amides and α-ketoamides in a versatile and controlled fashion. Combined experimental and DFT computational studies suggest that trap of the initially formed acyl radical by the second molecule of CO to form α-ketoacyl radical is a facile but reversible process; and photoredox-catalyzed SET oxidation of natural nucleophilic amines into relatively electrophilic nitrogen radical cations is responsible for switchable coupling with such two radical intermediates. | Bin Lu; Xiaotian Qi; Wen-Jing Xiao; Jia-Rong Chen | Organic Chemistry; Catalysis; Photochemistry (Org.); Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6190f55a2e10ad59bb4632bb/original/switchable-radical-carbonylation-by-polarity-regulation.pdf |
66f9ec9051558a15ef89622f | 10.26434/chemrxiv-2024-3sn8n | Molecular Understanding for Motion Modes of Oil Droplets in Aqueous Solutions of Ester- and Amide-Containing Cationic Surfactants | The study of self-propelled motion in soft matter systems has garnered significant interest due to its potential applications in microfluidics, soft robotics, and the design of autonomous systems. Understanding the molecular mechanisms behind such motility is crucial for advancing these applications. This study investigates the self-propelled motion of lauronitrile oil droplets in aqueous surfactant solutions, focusing on the impact of different surfactant molecular structures on droplet dynamics. The research compares surfactants containing ester and amide linkages, which play a critical role in modulating interfacial tension and influencing Marangoni convection—a key factor of droplet movement. surfactants with ester linkages exhibit a higher affinity for lauronitrile and adsorb more rapidly at the oil-water interface, resulting in stronger Marangoni flows and faster droplet motion. In contrast, amide-containing surfactants show slower adsorption and weaker interactions with lauronitrile, leading to reduced or absent motion. These findings provide new insights into the molecular mechanisms underlying self-propelled droplet behavior in non-equilibrium systems, and contribute to a deeper understanding of self-organising phenomena. | Kazuki Ueno; Yuuki Ishiwatari; Ken Sasaki; Tomoya Kojima; Atsuro Takai; Kouichi Asakura; Noriyoshi Arai; Taisuke Banno | Physical Chemistry; Nanoscience; Interfaces; Physical and Chemical Properties; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f9ec9051558a15ef89622f/original/molecular-understanding-for-motion-modes-of-oil-droplets-in-aqueous-solutions-of-ester-and-amide-containing-cationic-surfactants.pdf |
62e45002a8e4dcc94722baf2 | 10.26434/chemrxiv-2022-b276b-v3 | Transport of water and oxygen in epoxy-based coatings | Epoxies are used in various industrial applications as corrosion barriers but quantitative time-dependent predictions of their ability to mitigate corrosion attack at the metal/coating interface remain elusive. Permeability data for water and oxygen through epoxy-based coatings are of particular interest because the coating’s barrier performance in humid environments is directly related to how quickly these reactants get to the metal/coating interface. There is, however, an absence of literature data to explain oxygen transport within coatings in the presence of condensed water and its associated plasticization effects. We show that water is a dominant player in the barrier performance of epoxy coatings because it blocks the transport of other permeants. Through analysis of the sorption isotherms and empirical permeation data, we determined adjustable parameters that explain water vapor plasticization effects in fusion bonded epoxy (FBE) at 65°C. At this temperature, evolution of cavity formation and break-up of water clusters result in high mobility of water molecules inside the epoxy network. We also modeled oxygen transport through FBE in wet-state conditions based on time lag measurements, and with reported literature data on vapor and gas sorption in epoxy. In a mixed gas/vapor system, condensed water in FBE blocks and/or significantly decreases gas permeation in the coating. If the service temperature is low (less than 40°C), water immobilizes the oxygen gas within microvoid regions in the glassy epoxy. Our experimental measurements, combined with Freeman’s theoretical model for upper bound limits, showed that this water-induced blocking mechanism is sufficient to suppress corrosion reactions on the underlying substrate material. At 65°C and above, the synergistic effect of coating plasticization by water molecules and dissolution of oxygen in a mobile water phase results in significant gaseous transport. We applied mathematical models based on proven sorption and transport models to FBE free-standing films and derived adjustable parameters to quantitatively explain this competitive permeation. Our O2 transport data show that, compared to the single-layer FBE, epoxy-based coatings with additional polyolefin layers can improve the barrier performance by deprivation of micropore channels for gas transport. | Hossein Zargar; Parham Zarei; Dennis Wong; Catherine Lam; Edouard Asselin | Materials Science; Polymer Science; Coating Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e45002a8e4dcc94722baf2/original/transport-of-water-and-oxygen-in-epoxy-based-coatings.pdf |
63f0a7ea1d2d184063b31a68 | 10.26434/chemrxiv-2023-l8q0t | Silver(I)-Catalyzed Synthesis of Cuneanes from Cubanes and their Investigation as Isosteres | Bridged or caged polycyclic hydrocarbons have rigid structures that project substituents into precise regions of 3D space, making them attractive as linking groups in materials science and as building blocks for medicinal chemistry. The efficient synthesis of new or underexplored classes of such compounds is therefore an important objective. Herein, we describe the silver(I)-catalyzed rearrangement of 1,4-disubstituted cubanes to cuneanes, which are strained hydrocarbons that have not received much attention from the synthetic community. The synthesis of 2,6-disubstitued or 1,3-disubstituted cuneanes can be achieved with high regioselectivities, with the regioselectivity being dependent on the electronic character of the cubane substituents. A preliminary assessment of cuneanes as scaffolds for medicinal chemistry was also performed, which suggests cuneanes could serve as isosteric replacements of trans-1,4-disubstituted cyclohexanes and 1,3-disubstituted benzenes. | Elliot Smith; Luke O'Brien; Kieran Jones; Stephen Argent; Christophe Salome; Quentin Lefebvre; Alain Valery; Graham Newton; Hon Wai Lam | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f0a7ea1d2d184063b31a68/original/silver-i-catalyzed-synthesis-of-cuneanes-from-cubanes-and-their-investigation-as-isosteres.pdf |
60c758cf567dfe0f75ec6900 | 10.26434/chemrxiv.14609985.v1 | On the Fly” Characterization of YbIII:ErIII Co-Doped Upconversion Nanoparticle Nonlinear Optical Response from Single-Particle Trajectories | <p> Spectroscopic characterization of individual nanoparticles is essential for
understanding their structure-property relationship and for applications. Upconversion
nanoparticles (UCNPs) in condensed phases can undergo both nonlinear optical and stochastic
dynamics when interacting with near-infrared sources. By integrating optical trapping microspectroscopy, stochastic dynamics and light-matter interactions experiments and simulations, in
the present work we study how individual trajectories of YbIII:ErIII co-doped UCNPs can be
used to perform “on the fly” characterization of their nonlinear optical power-law response upon
near-infrared excitation. We illustrate the methodology in the case of freely diffusing and
optically trapped UCNPs as well as with particles bound to the substrate. The approach
presented in this work can be applied to UCNPs with varying composition and morphological
features, particularly in single-particle studies.</p> | Isabela Cavalcante; María Claudia Marchi; Fernando Sigoli; Paulo Cesar de Sousa Filho; Beatriz C. Barja; RENE NOME | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758cf567dfe0f75ec6900/original/on-the-fly-characterization-of-yb-iii-er-iii-co-doped-upconversion-nanoparticle-nonlinear-optical-response-from-single-particle-trajectories.pdf |
65196165ade1178b247739db | 10.26434/chemrxiv-2023-vc1x4 | A polynomial equation devised using machine learning to predict the antibacterial activity of silver nanoparticles | The antibacterial activity of silver nanoparticles has been well-researched throughout the years, and massive data has been generated describing a specific nanoparticle sample and its antibacterial activity by performing laboratory experiments; however, none have utilized this data to create a means of predicting the antibacterial activity. In this paper, we developed a polynomial equation using machine learning that predicts the antibacterial activity of silver nanoparticles against S. aureus and E. coli. Only studies featuring spherical silver nanoparticles without any surface modifications that may enhance the antibacterial activity were considered, and the studies must test the antibacterial activity in terms of the number of bacterial colonies left after treatment to calculate the efficiency. The equation takes the size and amount of the nanoparticles in a particular sample as inputs and predicts its antibacterial activity in terms of the percentage of bacterial colonies left after treatment. The equation was validated for its accuracy and was found to accurately predict the antibacterial activity based on the values of the relevant features. The study is the first of its kind and contributes to the field by reducing the effort and resource consumption in laboratories and providing a simple and efficient means of predicting antibacterial activity. | Tarun Mateti; Venkat Tummala; Veera Raghav Reddy Y; Rekha Gopalkrishna Pai; Praveen Kumar; Prasoon Agarwal | Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65196165ade1178b247739db/original/a-polynomial-equation-devised-using-machine-learning-to-predict-the-antibacterial-activity-of-silver-nanoparticles.pdf |
66b5805801103d79c54c695e | 10.26434/chemrxiv-2024-vj26z | Accessing Sulfonamides via Formal SO2 Insertion into C–N Bonds | Functional group interconversions of abundant substructures that accommodate the often-complex molecular architectures seen in pharmaceuticals are particularly sought after by medicinal chemists as a means to enable both lead optimization and library diversification. Here, we report a conceptually new strategy that enables net SO<sub>2</sub>-insertion into the C–N bond of primary amines, enabling the direct synthesis of primary sulfonamides without pre-activation and effectively inverting the nitrogen’s properties (acidity, hydrogen bonding, etc.). The key to realizing this overall transformation is the implementation of an anomeric amide as a dual-function reagent which both serves to cleave the initial C–N bond and deliver a nitrogen atom to the product after SO<sub>2</sub> incorporation. The process tolerates a wide array of functionalities and can be run in an automated fashion thus allowing libraries of amines to be viable progenitors to highly desirable sulfonamides. Mechanistic studies support an isodiazene radical chain mechanism that generates an intermediate sulfinate which reacts with the anomeric amide to forge the S–N bond. As a proof of concept, our protocol was used to conduct a high-throughput library diversification campaign, was applied to the synthesis and modification of approved active pharmaceutical ingredients and was used to enable a net CO-to-SO<sub>2</sub> “isosteric replacement” approach. Conceptually, this successful translation of a reagent originally developed for atom deletion into a protocol for atom insertion has important implications for skeletal editing. | Myojeong Kim; Carys Obertone; Christopher Kelly; Christopher Reiher; Cristina Grosanu; James Robertson; Mark Levin | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b5805801103d79c54c695e/original/accessing-sulfonamides-via-formal-so2-insertion-into-c-n-bonds.pdf |
64363c690784a63aeef69ace | 10.26434/chemrxiv-2023-rpjld | Bicyclic Bioisosteres of Piperidine: Version 2.0 | 1-Azaspiro[3.3]heptanes were synthesized, characterized, and validated biologically in vivo as a new generation of saturated piperidine bioisosteres. | Alexander Kirichok; Hennadii Tkachuk; Yevhenii Kozyriev; Oleh Shablykin; Oleksandr Datsenko; Dmitry Granat; Tetyana Yegorova; Yuliya Bas; Vitalii Semirenko; Iryna Pishel; Vladimir Kubyshkin; Dmytro Lesyk; Oleksii Klymenko-Ulianov; Pavel Mykhailiuk | Organic Chemistry; Agriculture and Food Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64363c690784a63aeef69ace/original/bicyclic-bioisosteres-of-piperidine-version-2-0.pdf |
60c74665842e65038cdb27c7 | 10.26434/chemrxiv.11316842.v1 | Synthesis of Tetrasubstituted Allenes via Palladium-Catalyzed Cross-Coupling of Vinyl Bromides with Diazo Compounds | A highly efficient palladium-catalyzed cross-coupling of 2,2-diarylvinyl bromides with diazo compounds was developed, providing a convenient approach for the synthesis of tetrasubsti-tuted allenes. Both aryl diazo carbonyl compounds and N-tosylhydrazones are competent carbene precursors in this reaction. An unprecedented hydrogen elimination of the π-allyl palladium intermediate is proposed to be the key step. | Ge Zhang; Ze-Jian Xue; Fang Zhang; Shu-Sheng Zhang; Meng-Yao Li; Bin-Bin Zhu; Chen-Guo Feng; Guo-Qiang Lin | Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74665842e65038cdb27c7/original/synthesis-of-tetrasubstituted-allenes-via-palladium-catalyzed-cross-coupling-of-vinyl-bromides-with-diazo-compounds.pdf |
67a0eb5e81d2151a020ceaaa | 10.26434/chemrxiv-2025-pjbfg | Intactness of Synthetic vs. Natural Polymeric Micelles in Physiological Conditions: A Comparative Review | Typical synthetic polymeric micelles are nano-sized core/shell structures of self-assembled aggregates of amphiphilic molecules. The hydrophilic "head" sections of the molecules form a shell in contact with water, whereas the hydrophobic "tails" are sequestered in the aggregate’s core, which has the potential to capture and protect water-insoluble drugs. However, these structures are shown to lose their integrity in body fluids due to dilution and protein interactions. The natural polymeric micelles (such as chitosan, alginate, collagen etc.) have attracted significant interest in recent years as drug delivery agents in the pharmaceutical field as they provide controlled release, drug targeting, hydrophobic active material solubilization, and high cell uptake efficiency due to their small size, with the added advantage of intrinsic biocompatibility and biodegradability, which is always a question with synthetic polymers. However, biopolymers in their natural form are not suitable for self-assembly, and they require assistance through the chemical modification of biopolymer molecules to obtain hydrophobic functional groups for self-assembly. However, recent studies have shown that the stability problem of synthetic polymeric micelles that encapsulate drugs physically still remains for natural polymeric micelles in the presence of proteins, even though they maintain their integrity with dilution in blood plasma, unlike synthetic polymeric micelles. This requires additional surface modifications to make the natural polymeric micelles protein resistant in the blood. Sometimes, the chemical modification of biopolymeric molecules is provided by the chemical bonding of hydrophobic drug molecules for self-assembly and to maintain the integrity of these types of micelles. However, this type of chemical bonding requires a detailed study on the efficiency of drug molecules that may be affected. | Onur K. Polat; Hurriyet Polat; Merve C. Eren; Mehmet Polat; Nuket Zeybek; Kyle M. Koss | Physical Chemistry; Biological and Medicinal Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a0eb5e81d2151a020ceaaa/original/intactness-of-synthetic-vs-natural-polymeric-micelles-in-physiological-conditions-a-comparative-review.pdf |
60c7592cf96a000f54288f8a | 10.26434/chemrxiv.14653395.v1 | The Periodic Transient Kinetics Method for Investigation of Kinetic Process Dynamics Under Realistic Conditions: Methanation as an Example | Due to rising interest for the integration of chemical energy storage into the electrical power grid, the unsteady-state operation of chemical reactors is gaining more and more attention with emphasis on heterogeneously catalyzed reactions. The transient response of those reactions is influenced by effects on different length scales, ranging from the active surface via the individual porous catalyst particle up to the full-scale reactor. The challenge, however, is to characterize unsteady-state effects under realistic operation conditions and to assign them to distinct transport processes. Therefore, the periodic transient kinetics (PTK) method is introduced, which allows for the separation of kinetic process dynamics at different length scales experimentally under realistic operation conditions. The methodology also provides the capability for statistical analysis of the experimental results and therefore improved reliability of the derived conclusions. Therefore, the PTK method provides the experimental basis for model-based derivation of reaction kinetics valid under dynamic conditions. The applicability of the methodology is demonstrated for the methanation reaction chosen as an example process for heterogeneously catalyzed reactions relevant for chemical energy storage purposes. <br /> | Dominik Meyer; Jens Friedland; Jannik Schumacher; Robert Güttel | Reaction Engineering; Heterogeneous Catalysis; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7592cf96a000f54288f8a/original/the-periodic-transient-kinetics-method-for-investigation-of-kinetic-process-dynamics-under-realistic-conditions-methanation-as-an-example.pdf |
622d303c3599de1678fdd718 | 10.26434/chemrxiv-2022-38v1l | Post-Synthesis Boron Doping of Silicon Quantum Dots via Hydrosilsesquioxane-Capped Thermal Diffusion | Doped silicon quantum dots (SiQDs) with defined dopant distribution, size, and surface chemistry are highly sought-after as a scientific curiosity because their unique properties offer a wide array of potential applications including multi-modal medical imaging and photovoltaic devices. This report describes a diffusion based post-synthesis doping method for incorporating high concentrations of B (2.5 – 5.0 atomic %) into pre-formed SiQDs of predefined sizes while simultaneously maintaining their structure and morphology. The processing temperature, atmosphere, and QD size all strongly influence the resulting B-doped SiQDs. The as-synthesized doped SiQDs exhibit size-dependent photoluminescence spanning the visible to near-infrared spectral regions, are compatible with aqueous environments and are readily rendered compatible with organic solvents upon functionalization with appropriate alkoxide surface groups. | Sarah Milliken; I Teng Cheong; Kai Cui; Jonathan Veinot | Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622d303c3599de1678fdd718/original/post-synthesis-boron-doping-of-silicon-quantum-dots-via-hydrosilsesquioxane-capped-thermal-diffusion.pdf |
60c741a94c8919b101ad2331 | 10.26434/chemrxiv.8097542.v1 | Sterically Unprotected Nucleophilic Boron Cluster Reagents | Herein, we demonstrate that the bench stable <i>closo</i>-hexaborate cluster anion can
engage in a nucleophilic substitution reaction with a wide array of organic and
main group electrophiles. The resulting molecules containing B‒C bonds can be further
converted to tricoordinate boron species widely used in organic synthesis.<br /> | Xin Mu; Jonathan C. Axtell; Nicholas Bernier; Kent Kirlikovali; Dahee Jung; Alexander Umanzor; Kevin Qian; Xiangyang Chen; Katherine Bay; Monica Kirollos; Arnold L. Rheingold; K. N. Houk; Alexander Spokoyny | Organic Synthesis and Reactions; Stereochemistry; Main Group Chemistry (Inorg.); Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a94c8919b101ad2331/original/sterically-unprotected-nucleophilic-boron-cluster-reagents.pdf |
67af6e80fa469535b952dab3 | 10.26434/chemrxiv-2025-4vn1q-v4 | Design and Construction of a Fully Functionalised Probe Library for Mode of Action Studies | The lack of novel drug targets is a barrier to the development of therapeutics for infectious diseases. In this paper the design and construction of a diverse set of small molecule fragments attached to functionalised linkers is discussed. The functionalised linkers are comprised of a diazirine photo crosslinking moiety alongside an acetylene group to facilitate target pulldown. These are designed to be probes to find new targets, though phenotypic screening, followed by cross coupling and pull-down of the target. They also have the potential to be used in screening programmes against whole cells, enzymes and receptors. To help reduce the number of false positives, a set of the fragments with an un-reactive acetamide has also been prepared, which will allow competition studies. | Yaroslav Holik; Dinakaran Murugesan; Stephen Patterson; Susan Wyllie; Ian, H. Gilbert; Fabio Zuccotto; Gary, J. Tarver | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af6e80fa469535b952dab3/original/design-and-construction-of-a-fully-functionalised-probe-library-for-mode-of-action-studies.pdf |
677c94376dde43c9088fb27e | 10.26434/chemrxiv-2025-3rdw8 | RDRP of β-alanine for DOX-release as a Proof-of-Concept dye Encapsulation for Nanoparticle Synthesis. | pH-responsive amphiphilic poly(β alanine acrylamide)-block-poly( methyl methacrylate)-umbelliferon
(PBAAM-b-PMMA) diblock copolymer biohybrids, based of hydrophilic PBAAM and hydrophobic
PMAA segments, is developed via direct switching from Zn-mediated RDRP. EbiB was used to mediate
RDRP of a β-alanine derived monomer, PBAAM, yielding a series of (PBAAM-b-PMMA)-The
copolymer's stimuli response has been assessed against pH changes. The translation of this structure into
a synthetic polymer was the aim of this investigation. This copolymer is capable of dye encapsulation as
a proof of concept of Beta-alanine Nanoparticle (NPs) DOX-release | Subrata Dolui | Polymer Science | CC BY 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677c94376dde43c9088fb27e/original/rdrp-of-alanine-for-dox-release-as-a-proof-of-concept-dye-encapsulation-for-nanoparticle-synthesis.pdf |
662fff6f91aefa6ce1c2db6c | 10.26434/chemrxiv-2024-mvrmf | Boron Nitride Nanotube and Nanosheet Synthesis by Flash Joule Heating | Boron nitride nanotubes (BNNTs) and boron nitride nanosheets (BNNSs), known as structural analogs of carbon nanotubes (CNTs) and graphene, respectively, have garnered significant interest due to their outstanding inherent properties and broad applications. However, the rapid synthesis of these materials with high yield and quality poses a challenge, hindering their practical application advancements. In this study, we report the synthesis of highly crystalline BNNTs and BNNSs through a solid-state catalytic flash Joule heating (FJH) method, using ammonia borane as the precursor. The catalytic growth process was achieved under atmospheric conditions at easily attained FJH temperatures (~1500 °C) within seconds. By adjusting the reaction temperature and variety of catalysts, the selectivity to BNNTs can reach ~30% of the total product composition. Furthermore, the nucleated growth of BNNT on iron(0) is mediated by the introduction of carbon and sulfur. This study demonstrates a convenient and scalable synthesis pathway for BNNTs and BNNSs and provides critical insights into the mechanism of rapid synthesis techniques enabled by electrical heating. | Jinhang Chen; John Li; Weiyin Chen; Kevin Wyss; Yi Cheng; Qiming Liu; Obinna Onah; James Tour | Materials Science; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662fff6f91aefa6ce1c2db6c/original/boron-nitride-nanotube-and-nanosheet-synthesis-by-flash-joule-heating.pdf |
60c744afbb8c1a57573da528 | 10.26434/chemrxiv.9197957.v2 | Accelerating the Discovery of Multilayer Nanostructures with Analytic Differentiation of the Transfer Matrix Equations | <div>Multilayer nanostructures represent an important class of materials with tunable optical and thermal radiative properties that can be leveraged for a wide range of energy applications. We present a theoretical framework for optimizing the geometry of such structures that utilizes gradients of various objective functions that are enabled through analytic differentiation of the transfer matrix equations. We demonstrate the usefulness of this method by applying it to the optimization of structures for incandescent light sources, and the global optimization of anti-reflective solar cell coatings.</div> | James F. Varner; Dayanara Wert; Aya Matari; Raghad Nofal; Jonathan Foley | Coating Materials; Multilayers; Nanostructured Materials - Materials; Optical Materials; Thin Films; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Theory - Computational; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744afbb8c1a57573da528/original/accelerating-the-discovery-of-multilayer-nanostructures-with-analytic-differentiation-of-the-transfer-matrix-equations.pdf |
67a74432fa469535b9831b10 | 10.26434/chemrxiv-2024-hsldj-v2 | NiFe on CeO2, TiO2 and ZrO2 Supports as Efficient Oxygen Evolution Reaction Catalysts in Alkaline Media | The high cost and low energy efficiency of conventional water electrolysis methods continue to restrict the widespread adoption of green hydrogen. Anion exchange membrane (AEM) water electrolysis is a promising technology that can produce hydrogen using cost-effective transition metal catalysts at high energy efficiency. Herein, we investigate the catalytic activity of nickel and iron nanoparticles dispersed on metal-oxide supports for the oxygen evolution reaction (OER), employing electrochemical testing with an anion exchange ionomer to evaluate their potential for application in AEM electrolyzers. We report the electrochemical performance of NiFe nanoparticles of varying Ni:Fe ratios on CeO2 for OER reaction, assessing the overpotential, Tafel slope and electrochemical stability of the catalysts. Our findings indicate that Ni90Fe10 has the highest catalytic activity as well as stability. To further understand the role of different supports, we assess the electrocatalytic performance of Ni90Fe10 nanoparticles on two more supports - TiO2 and ZrO2. While CeO2 has the lowest overpotential, the other supports also show high activity and good performance at high current density. TiO2 exhibits superior stability and its overpotential after chronopotentiometry measurements approaches that of CeO2 at high current densities. These results underscore the critical role of iron addition in enhancing nickel nanoparticles' catalytic activity and further emphasize the importance of metal oxide supports in improving catalyst stability and performance. | Neethu Kochukunnel Varghese; Elina Mkrtchian; Anshika Singh; Letizia Savio; Massimiliano Boccia; Vincenza Marzocchi; Antonio Comite | Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a74432fa469535b9831b10/original/ni-fe-on-ce-o2-ti-o2-and-zr-o2-supports-as-efficient-oxygen-evolution-reaction-catalysts-in-alkaline-media.pdf |
67c1434afa469535b9442256 | 10.26434/chemrxiv-2025-t9njm-v2 | Beyond Lithium Lanthanum Titanate: Toward Metal-Stable Perovskite Electrolytes | According to Chambers et. al., the tetragonal I4/mcm LLTO is the ground-state polymorph.1 Thus, we retrieved the tetragonal I4/mcm SrTiO3 (mp-4651) from the materials project (MP) repository as a reference pristine perovskite structure.2 We chose SrTiO3 because its A-site ionic radius (Sr2+) is close to the ionic radius of La3+.3 At different stages of the study, two distinct working-ion concentration regimes were analyzed: a computationally efficient low concentration (lc) A’0.125A”0.625□0.25B1X3 (A’1A”5□2B8X24) for compositional screening with 38-atom unit cell and a high concentration (hc) A’0.3125A”0.5625□0.125B1X3 (A’5A”9□2B16X48) for the in-depth study stage with 78-atom unit cell. A’, A”, □, B, and X are the working-ion, large-ionic-radius cation, A-site vacancy, small-ionic-radius cation, and anion, respectively. | Ahmed Biby; Basant Ali; Charles Musgrave | Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1434afa469535b9442256/original/beyond-lithium-lanthanum-titanate-toward-metal-stable-perovskite-electrolytes.pdf |
60c7426b0f50db0f23395cd7 | 10.26434/chemrxiv.8279681.v1 | ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution | <p>Molecular dynamics (MD) simulations have become
increasingly popular in studying the motions and functions of biomolecules. The
accuracy of the simulation, however, is highly determined by the molecular
mechanics (MM) force field (FF), a set of functions with adjustable parameters
to compute the potential energies from atomic positions. However, the overall
quality of the FF, such as our previously published ff99SB and ff14SB, can be
limited by assumptions that were made years ago. In the updated model presented
here (ff19SB), we have significantly improved the backbone profiles for all 20
amino acids. We fit coupled ϕ/ψ parameters using 2D ϕ/ψ conformational scans
for multiple amino acids, using as reference data the entire 2D quantum
mechanics (QM) energy surface. We address the polarization inconsistency during
dihedral parameter fitting by using both QM and MM in solution. Finally, we
examine possible dependency of the backbone fitting on side chain rotamer. To
extensively validate ff19SB parameters, we have performed a total of ~5 milliseconds
MD simulations in explicit solvent. Our results show that after amino-acid
specific training against QM data with solvent polarization, ff19SB not only reproduces
the differences in amino acid specific Protein Data Bank (PDB) Ramachandran
maps better, but also shows significantly improved capability to differentiate
amino acid dependent properties such as helical propensities. We also conclude that
an inherent underestimation of helicity is present in ff14SB, which is
(inexactly) compensated by an increase in helical content driven by the TIP3P
bias toward overly compact structures. In summary, ff19SB, when combined with a
more accurate water model such as OPC, should have better predictive power for
modeling sequence-specific behavior, protein mutations, and also rational
protein design. </p> | Chuan Tian; Koushik Kasavajhala; Kellon Belfon; Lauren Raguette; He Huang; Angela Migues; John Bickel; Yuzhang Wang; Jorge Pincay; Qin Wu; Carlos Simmerling | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426b0f50db0f23395cd7/original/ff19sb-amino-acid-specific-protein-backbone-parameters-trained-against-quantum-mechanics-energy-surfaces-in-solution.pdf |
60c7463f9abda2064af8c6fd | 10.26434/chemrxiv.11214386.v1 | Thermal Spin Crossover in Fe(II) and Fe(III). Accurate Spin State Energetics at the Solid State | <p>The thermal Spin Crossover (SCO) phenomenon refers to an
entropy-driven spin transition in some materials based on d<sub>6</sub>-d<sub>9</sub>
transition metal complexes. While its molecular origin is well known, intricate
SCO behaviours
are increasingly common, in which the spin transition occurs concomitantly to <i>e.g.</i> phase transformations, solvent
absorption/desorption, or order-disorder processes. The computational modelling
of such cases is challenging, as it requires
accurate spin state energies in the solid state. Density Functional Theory
(DFT) is the best framework, but most DFT functionals are unable to balance the spin state energies. While few hybrid functionals perform
better, they are still too expensive solid-state minima searches in
moderate-size systems. The best alternative is to dress cheap local (LDA) or
semi-local (GGA) DFT functionals with a Hubbard-type correction (DFT+<i>U</i>). However, the
parametrization of U is not
straightforward due to the lack of reference values, and because ab initio parametrization methods
perform poorly. Moreover, SCO complexes undergo notable structural changes upon
transition, so intra- and inter-molecular interactions might play an important
role in stabilizing either spin state. As a consequence, the U parameter depends strongly on the
dispersion correction scheme that is used. In this paper, we parametrize U for nine reported SCO compounds (five
based on Fe<sup>II</sup>, <b>1</b>-<b>5</b> and four based on Fe<sup>III</sup>, <b>6</b>-<b>9</b>)
when using the D3 and D3-BJ dispersion corrections. We analyze the impact of
the dispersion correction treatments on the SCO energetics, structure, and the
unit cell dimensions. The average U
values are different for each type of metal ion (Fe<sup>II</sup> vs. Fe<sup>III</sup>), and dispersion correction
scheme (D3 vs. D3-BJ) but they all
show excellent transferability, with mean absolute errors (MAE) below chemical accuracy (i.e. MAE < 4 kJ/mol). This enables a
better description of SCO processes and, more generally, of spin state
energetics, in materials containing Fe<sup>II</sup> and Fe<sup>III</sup> ions.</p> | Sergi Vela; Maria Fumanal; Jordi Cirera; Jordi Ribas | Theory - Inorganic; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7463f9abda2064af8c6fd/original/thermal-spin-crossover-in-fe-ii-and-fe-iii-accurate-spin-state-energetics-at-the-solid-state.pdf |
63d40293112596fe237c98d4 | 10.26434/chemrxiv-2023-90vhh | Linker functionalised phosphinate metal-organic frameworks: Adsorbents for the removal of emerging pollutants | Metal-organic frameworks (MOFs) are attracting increasing attention as adsorbents of contaminants of emerging concern which are difficult to remove by conventional processes. However, common carboxylate-based MOFs suffer from low stability in water environment, which limits their environmental applications. In this study, we use phosphinate-based MOFs with higher hydrolytic stability and we focus on the influence of functional groups covering the pore walls on the adsorption of pharmaceutical pollutants present in water – diclofenac, cephalexin and sulfamethoxazole. We present a synthesis of new structures isoreticular to the phosphinate MOF ICR-7. The presented MOFs contain phenyl rings facing the pore walls modified with dimethylamino groups (ICR-8) and ethyl carboxylate groups (ICR-14). These functionalized MOFs were obtained from two newly synthetized phospinate linkers containing the respective functional groups. Generally, the presence of additional functional groups resulted in higher affinity to the tested pollutants in comparison with ICR-7 or activated carbon, however, it also decreased the sorption capacity. | Jan Hynek; Soňa Ondrušová; Daniel Bůžek; Matouš Kloda; Jan Rohlíček; Miroslav Pospíšil; Pavel Janoš; Jan Demel | Materials Science; Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Hybrid Organic-Inorganic Materials; Environmental Science; Ligands (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d40293112596fe237c98d4/original/linker-functionalised-phosphinate-metal-organic-frameworks-adsorbents-for-the-removal-of-emerging-pollutants.pdf |
64e1430100bbebf0e677315c | 10.26434/chemrxiv-2023-km48t | Hammett Structural Relationships Revealed in Chalcogen Bonded Co-crystals of Electron Rich Pyridines with 4′-Substituted Ebselen Derivatives | In this work, a detailed Hammett structure-structure correlation was applied to a range of chalcogen bonded co-crystals prepared by combining 4′-substituted derivatives of the selenium-based drug ebselen with three different 4-amino-substituted pyridine based chalcogen bond acceptors of differing basicities. This established that the N · · · Se chalcogen bond distance is well within the sum of the van der Waals radii of Se and N and is sensitive to the electronic nature of the substituent. Thus N · · · Se distances ranging from 2.2424(5)–2.4496(9) Å were observed with the shorter distances being observed in co-crystals of ebselen substituted with electron withdrawing groups. Associated with trends of the N · · · Se distance as a function of the 4′-substituent was lengthening of the internal Se−N bond distance consistent with a significant covalent contribution to N · · · Se chalcogen bonding in these derivatives. We define a covalency quotient for the chalcogen bond as the negative slope of the plot of the internal Se−N bond distance vs the external N · · · Se chalcogen bond distance. A value of 0.31 was obtained implying a significant covalent contribution to N · · · Se chalcogen bond. A similar result was obtained by an analysis of chalcogen bonded selenium containing molecules harvested from the Cambridge Crystallographic Database. The covalency quotient is extended to the general case for sigma-hole interactions including halogen bonding and hydrogen bonding, and we show that the covalent component of such interactions can be inferred from the lengthening of the donor bond. The degree of charge transfer in a smaller number of chalcogen bonded co-crystals of ebselen was established by measuring experimental electron density using high-resolution x-ray diffraction to more accurately measure the degree of electron transfer and hence covalency. This showed that in the most strongly bound systems, up to 1 electron worth of charge is transferred from the Lewis base to the Ch-bond donor, which again clearly points to significant covalent character. | Thomas Fellowes; Eric Lee; Jennifer Tran; Ruyi Xu; Alec Barber; Samuel Brydon; Jack Clegg; Jonathan White | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Structure; Materials Chemistry; Crystallography – Organic | CC BY NC 4.0 | CHEMRXIV | 2023-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e1430100bbebf0e677315c/original/hammett-structural-relationships-revealed-in-chalcogen-bonded-co-crystals-of-electron-rich-pyridines-with-4-substituted-ebselen-derivatives.pdf |
60c74ea5702a9bc45018ba2f | 10.26434/chemrxiv.12777359.v1 | Charge Accumulation Kinetics in Multi-redox Molecular Catalysts Immobilised on TiO2 | Multi-redox catalysis requires the transfer of more than one charge
carrier and is crucial for solar energy conversion into fuels and valuable
chemicals. In photo(electro)chemical systems, however, the necessary
accumulation of multiple, long-lived charges is challenged by recombination
with their counterparts. Herein, we investigate charge accumulation in two model
multi-redox molecular catalysts for proton and CO<sub>2</sub> reduction
attached onto mesoporous TiO<sub>2</sub> electrodes. Transient absorption
spectroscopy and spectroelectrochemical techniques have been employed to study
the kinetics of photoinduced electron transfer from the TiO<sub>2</sub> to the
molecular catalysts in acetonitrile, with triethanolamine as the hole
scavenger. At high light intensities, we detect charge accumulation in the millisecond
timescale in the form of multi-reduced species. The redox potentials of the
catalysts and the capacity of TiO<sub>2</sub> to accumulate electrons play an
essential role in the charge accumulation process at the molecular catalyst.
Recombination of reduced species with valence band holes in TiO<sub>2</sub> is
observed to be faster than microseconds, while electron transfer from
multi-reduced species to the conduction band or the electrolyte occurs in the
millisecond timescale. Finally, under light irradiation, we show how charge
accumulation on the catalyst is regulated as a function of the applied bias and
the excitation light intensity. | Carlota Bozal-Ginesta; Camilo A. Mesa; Annika Eisenschmidt; Ravi Shankar; Laia Francàs; Daniel Antón-García; julien Warnan; Janina Willkomm; Anna Reynal; Erwin Reisner; James R Durrant | Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ea5702a9bc45018ba2f/original/charge-accumulation-kinetics-in-multi-redox-molecular-catalysts-immobilised-on-ti-o2.pdf |
67974b856dde43c9088fbefb | 10.26434/chemrxiv-2025-wcbc3 | In vivo multiplexed analysis of aminopeptidase activities by hyperpolarized molecular probes for tumor diagnostic applications | Aminopeptidases (APs) in the renin-angiotensin system (RAS) and their activity balance play a crucial role in regulating vascular functions. Multiplexed analysis of RAS-related AP activities is useful for diagnosing diseases, including cancer. Dynamic nuclear polarization coupled magnetic resonance imaging (DNP-MRI) enables simultaneous detection of multiple enzymatic activities in vivo. However, developing practical DNP-MRI probes, especially for multiplexed detection, remains challenging. Here, we report the design of DNP-MRI probes for in vivo multiplexed analysis of AP activities. By integrating quantum mechanical calculations, organic synthesis, and physicochemical/biochemical evaluations, we developed a series of AP-responsive DNP-MRI probes with high enzymatic reactivities and distinguishable chemical shifts. Using these probes, we successfully detected and visualized multiple AP activities in vivo. Furthermore, we performed in vivo multiplex analysis of RAS-related AP activities in tumor-bearing mice, demonstrating the potential of this approach for monitoring the efficacy of anti-angiogenic cancer therapy and for accurate discrimination of tumor types. | Hiroyuki Yatabe; Keita Saito; Ayumi Koike; Yoichi Takakusagi; Abdelazim Elhelaly; Fuminori Hyodo; Masayuki Matsuo; Wataru Mizukami; Maki Sugaya; Tsuyoshi Osawa; Murali Krishna; Kazutoshi Yamamoto; Yutaro Saito; Shinsuke Sando | Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67974b856dde43c9088fbefb/original/in-vivo-multiplexed-analysis-of-aminopeptidase-activities-by-hyperpolarized-molecular-probes-for-tumor-diagnostic-applications.pdf |
62f0cadfd62bc08b693dbd70 | 10.26434/chemrxiv-2022-rxgqd | Azide modification of single-walled carbon nanotubes for near-infrared defect photoluminescence by luminescent sp2 defect formation | Azide functionalization produced luminescent sp2-type defects on single-walled carbon nanotubes, by which defect photoluminescence appeared in near infrared regions (1116 nm). Changes in exciton properties were induced by localization effects at the defect sites, creating exciton-engineered nanomaterials based on the defect structure design. | Keita Hayashi; Yoshiaki Niidome; Tamehito Shiga; Boda Yu; Yasuto Nakagawa; Dawid Janas; Tsuyohiko Fujigaya; Tomohiro Shiraki | Physical Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f0cadfd62bc08b693dbd70/original/azide-modification-of-single-walled-carbon-nanotubes-for-near-infrared-defect-photoluminescence-by-luminescent-sp2-defect-formation.pdf |
6536b87687198ede071d68bd | 10.26434/chemrxiv-2023-9g3gr | Resonance Enhancement of Vibrational Polariton Chemistry Obtained from the Mixed Quantum-Classical Dynamics Simulations | We applied a variety of mixed quantum-classical (MQC) approaches to simulate the VSC-influenced reaction rate constant. All of these MQC simulations treat the key vibrational levels associated with the reaction coordinate in the quantum subsystem (as quantum states), whereas all other degrees of freedom (DOFs) are treated inside the classical subsystem. We find that as long as we have the quantum state descriptions for the vibrational DOFs, one can correctly describe the VSC resonance condition when the cavity frequency matches the bond vibrational frequency. This correct resonance behavior can be obtained regardless of the detailed MQC methods one uses. The results suggest that the MQC approaches can generate semi-quantitative agreement with the exact results for rate constant changes when changing the cavity frequency, the light-matter coupling strength, or the cavity lifetime. The finding of this work suggests that one can use computationally economic MQC approaches to explore the collective coupling scenario when many molecules are collectively coupled to many cavity modes in the future. | Deping Hu; Wenxiang Ying; Pengfei Huo | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Chemical Kinetics; Optics | CC BY 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6536b87687198ede071d68bd/original/resonance-enhancement-of-vibrational-polariton-chemistry-obtained-from-the-mixed-quantum-classical-dynamics-simulations.pdf |
62c6ed6efb638140a8cffadd | 10.26434/chemrxiv-2022-x4sq9 | A computational bird's eye view of redox reactivity in the formation of cysteine-lysine covalent linkages | Recently, a new naturally occurring covalent linkage in peptides was characterised, involving a cysteine and a lysine, bridged through a single oxygen atom. The latter was dubbed as the NOS bond, reflecting the individual atoms directly involved in this rather uncommon bond which finds little parallel in lab chemistry. It is found to form under oxidising conditions and reversible upon addition of reducing agents. Further studies have shown that this bond is found over a large variety of systems and organisms, potentially playing an important role in regulation, cellular defense and replication. Not only that, double NOS bonds have been identified and even found to be competitive in relation to the formation of disulfide bonds. This raises several questions about how this exotic bond comes to be, what are the intermediates involved in its formation and how it competes with other pathways of sulfide oxidation (e.g., sulfinic acid formation, disulfide linkage). With this objective in mind, we revisited our first proposed mechanism for the reaction with model electronic structure calculations, adding information about the reactivity with alternative reactive oxygen species (ROS) and other potential competing products of oxidation. We present a reaction network with more than 30 intermediates which provides one of the most encompassing pictures for cysteine oxidation pathways to date. | Jin Ye; Sophia Bazzi; Tobias Fritz; Ricardo A. Mata; Jon Uranga | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c6ed6efb638140a8cffadd/original/a-computational-bird-s-eye-view-of-redox-reactivity-in-the-formation-of-cysteine-lysine-covalent-linkages.pdf |
66a1627a01103d79c58aaa83 | 10.26434/chemrxiv-2024-hb013 | Flash Separation of Metals by Electrothermal Chlorination | Metal recycling plays a crucial role in mitigating the critical metals shortage and reducing reliance on primary mining. Current liquid hydrometallurgy involves significant water and chemical consumption with troublesome secondary waste streams, while pyrometallurgy lacks selectivity and requires substantial energy input. Here we develop an electrothermal chlorination and carbochlorination process, and a specialized compact reactor, for the selective separation of individual critical metals from electronic waste. Our approach uses programmable, pulsed current input to achieve precise control over a wide temperature range (from room temperature to 2400 °C), short reaction duration of seconds, and rapid heating/cooling rates (103 °C s-1) during the process. The method capitalizes on the differences in the free energy formation of the metal chlorides. Once conversion to a specific metal chloride is achieved, that compound distills from the mixture in seconds. This allows for both thermodynamic and kinetic selectivity for desired metals with minimization of impurities. | Bing Deng; Shichen Xu; Lucas Eddy; Jaeho Shin; Yi Cheng; Carter Kittrell; Khalil JeBailey; Justin Sharp; Long Qian; Shihui Chen; James Tour | Materials Science; Inorganic Chemistry; Materials Processing; Kinetics and Mechanism - Inorganic Reactions; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a1627a01103d79c58aaa83/original/flash-separation-of-metals-by-electrothermal-chlorination.pdf |
6226297291a2e6f3b6e7fe6d | 10.26434/chemrxiv-2022-jd607 | Insights into chemically-fueled supramolecular polymers | Supramolecular polymerization can be controlled in space and time by chemical fuels. A non-assembled monomer is activated by the fuel and subsequently self-assembles into a polymer. Deactivation of the molecule either in solution or inside the polymer leads to disassembly. Whereas biology has already mastered this approach, fully artificial examples have only appeared in the past decade. Here, we map the available literature examples into four distinct regimes depending on their activation/deactivation rates and the equivalents of deactivating fuel. We present increasingly complex mathematical models, first considering only the chemical activation/deactivation rates (i.e., Transient Activation), and later including the full details of the isodesmic or cooperative supramolecular processes (i.e., Transient Self-assembly). We finish by showing that sustained oscillations are possible in chemically fueled cooperative supramolecular polymerization and provide mechanistic insights. We hope our models encourage the exact quantification of activation, deactivation, assembly, and disassembly kinetics in future studies. | Anastasiia Sharko; Dimitri Livitz; Serena De Piccoli; Kyle Bishop; Thomas Hermans | Physical Chemistry; Polymer Science | CC BY NC 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6226297291a2e6f3b6e7fe6d/original/insights-into-chemically-fueled-supramolecular-polymers.pdf |
63776ee420798161532be93f | 10.26434/chemrxiv-2022-rx3hw | [Pd(2-pymo)2]n/Al2O3 as MOF single site catalyst for the selective hydrogenation of acetylene | Despite the great potential of metal-organic frameworks
(MOFs) in catalysis, industrial applications are still scarce. This is mainly due to a lack of performance when changing from idealized lab conditions towards realistic conditions of the actual application. In this work, we demonstrate the applicability and outstanding catalytic performance of an alumina-supported [Pd(2-pymo)2]n MOF catalyst in the selective hydrogenation of acetylene to ethylene under industrial front-end conditions. It shows a competitive performance to an industrial benchmark catalyst and even exceeds it in terms of ethane selectivity due to the combination of well-defined isolated Pd active sites and synergies due to MOF-support-interactions. The high stability was proven for up to 60 h time-on-stream and supported by XPS and XRD structural analysis. | Sebastian Hock; Martin Lucas; Eva Kolle-Görgen; Maximilian Mellin; Jan P. Hofmann; Marcus Rose | Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63776ee420798161532be93f/original/pd-2-pymo-2-n-al2o3-as-mof-single-site-catalyst-for-the-selective-hydrogenation-of-acetylene.pdf |
67ca46c66dde43c908d53d90 | 10.26434/chemrxiv-2025-2p16l | OptiDots_v1.0: A Comprehensive Database for Machine Learning-Driven Optimization of Green Synthesis Carbon Dots | Understanding the relationships between the physicochemical properties of Carbon Dots (CDs) and synthesis parameters is crucial for optimizing their use and accelerating the development of CDs. However, this task is complex due to the diversity of materials, heterogeneity of published data, and limited sampling in individual studies. This work addresses this gap by introducing OptiDots_v1.0, a comprehensive database designed to support the scientific community in optimizing the synthesis of CDs thought machine learning (ML) or by integrating other analytical techniques. From a comprehensive set of 157 publications on the synthesis of CDs derived from green precursors and hydrothermal synthesis, we meticulously obtained data samples related to characteristics such as particle size, quantum yield, synthesis yield, maximum emission and excitation, fluorescence, elemental composition, and applications of 199 CDs, as well as experimental conditions of time, temperature, and precursor type. As a case study, we applied exploratory data analysis and ML techniques to OptiDots_v1.0 to demonstrate its potential in predictive modeling and experimental design. We show the relationships between continuous variables such as synthesis yield and nitrogen contente, as well as particle size and photolumiscence, and with machine learning methods, it was possible to make inferences about emission wavelenght. This approach, integrating quantitative and qualitative data, provides a roadmap to investigate the data on the properties of CDs in the literature and suggests that meta-analysis can help develop methods to predict and optimize the applications of these nanomaterials. | Kelvin Goularte dos Santos; Humberto Gracher Riella; Cíntia Soares; Natan Padoin | Materials Science; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca46c66dde43c908d53d90/original/opti-dots-v1-0-a-comprehensive-database-for-machine-learning-driven-optimization-of-green-synthesis-carbon-dots.pdf |
60c74b6e337d6c2564e27aa1 | 10.26434/chemrxiv.12333077.v1 | Discovery of Record-Breaking Metal-Organic Frameworks for Methane Storage using Evolutionary Algorithm and Machine Learning | In the past decade, there has been a rise in a number of computational screening works to facilitate finding optimal metal-organic frameworks (MOF) for variety of different applications. Unfortunately, most of these screening works are limited to its initial set of materials and result in brute-force type of a screening approach. In this work, we present a systematic strategy that can find materials with desired property from an extremely diverse and large MOF set of over 100 trillion possible MOFs using machine learning and evolutionary algorithm. It is demonstrated that our algorithm can discover 964 MOFs with methane working capacity over 200 cm<sup>3</sup> cm<sup>−3</sup> and 96 MOFs with methane working capacity over 208 cm<sup>3</sup> cm<sup>−3</sup>, which is the current world record. We believe that this methodology can facilitate a new type of a screening approach that takes advantage of the modular nature in MOFs, and can readily be extended to other important applications as well. | Sangwon Lee; Baekjun Kim; Jihan Kim | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b6e337d6c2564e27aa1/original/discovery-of-record-breaking-metal-organic-frameworks-for-methane-storage-using-evolutionary-algorithm-and-machine-learning.pdf |
617f12efad7f7cb7305035ea | 10.26434/chemrxiv-2021-sgmp1 | Environment-dependent Emission Tuning in the Multicolor Nitrogen-doped Carbon Quantum Dots | Carbon quantum dots (CQDs) are fascinating luminous materials from the carbonaceous family and are increasingly being investigated in many optoelectronic applications due to their unique photoluminescence (PL) characteristics. Herein, we report the synthesis of nitrogen-doped carbon quantum dots (NCQDs) from citric acid and m-phenylenediamine using a one-pot hydrothermal approach. The environment-dependent emission changes of NCQDs were extensively investigated in various solvents, in solid-state, and in physically assembled PMMA-PnBA-PMMA copolymer gels in 2-ethyl hexanol. The NCQDs display bright emission in various solvents as well as in solid-state and a temperature-dependent enhanced emission in gels. In detail, these NCQDs exhibit multicolor PL emission across the visible region and its enhancement upon changing the environment (solutions and polymer matrices). The NCQDs also exhibit excitation-dependent PL and solvatochromism, which are rarely observed in CQDs. Most CQDs are non-emissive in the aggregated or solid-state due to the aggregation-caused quenching (ACQ) effect, limiting their solid-state applications. However, these NCQDs display a strong solid-state emission centered at 568 nm ascribed to the presence of abundant surface functional groups, which helps to prevent the - interaction between the NCQDs and to overcome the ACQ effect in the solid-state. Interestingly, the NCQD containing gels display a significant fluorescence enhancement than the NCQDs in 2-ethyl hexanol solution because of the interaction between the polar PMMA blocks and NCQDs. This research opens up the development of large-scale, low-cost multicolor phosphor for the fabrication of optoelectronic devices, sensing, and bioimaging applications. | Dineshkumar Sengottuvelu; Abdul Kalam Shaik; Satish Mishra; Mahsa Abbaszadeh; Nathan Hammer; Santanu Kundu | Materials Science; Polymer Science; Nanoscience; Carbon-based Materials; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617f12efad7f7cb7305035ea/original/environment-dependent-emission-tuning-in-the-multicolor-nitrogen-doped-carbon-quantum-dots.pdf |
65a48f479138d23161ed8b6a | 10.26434/chemrxiv-2023-4hn4s-v3 | Scoring Methods in Lead Optimization of Molecular Glues | Efficiency metrics are a simple and effective medicinal chemistry tool to track small molecule progress toward a preferred profile in lead optimization. Targeted protein degradation can be mediated by small molecules that act as a molecular glue between an E3 ligase and a protein target. Molecular glue compounds are characterized by the potency and the depth of their protein degradation dose response measurement, representing additional complexity toward identifying drug candidates. We developed degradation efficiency metrics that are based on both potency and depth of degradation. They serve as basic scoring functions to effectively track lead optimization objectives. In recent years, applying machine learning (ML) has effectively accelerated lead optimization. We established a comprehensive scoring function to guide molecular glue design. This manuscript describes how such a merit score was retrospectively applied to track optimization of a clinical molecular glue degrader series that resulted in the identification of Golcadomide (CC-99282). The application of these efficiency metrics in conjunction with a ML based merit score may accelerate identification of glue molecules development candidates. | Lei Jia; Dahlia Weiss; Benjamin Shields; Brian Claus; Veerabahu Shanmugasundaram; Stephen Johnson; Jennifer Riggs; Christoph Zapf | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a48f479138d23161ed8b6a/original/scoring-methods-in-lead-optimization-of-molecular-glues.pdf |
63cd8111fa87eb17f35091f0 | 10.26434/chemrxiv-2022-mmj3v-v2 | In-House Fabrication of 1.3 to 7 mm MAS Drive Caps using Desktop 3D Printers | The 3D-printing technology has emerged into a well-developed method to fabricate parts with considerably low cost and yet with high precision (< 100 um). It was shown in the recent literature that the 3D-printing technology can be exploited to fabricate magic-angle spinning (MAS) system in solid-state nuclear magnetic resonance (NMR) spectroscopy. In particular, the 3.2 mm MAS drive caps with intricate features are well fabricated using an outsourced 3D printing service, and the caps were demonstrated to spin > 20 kHz. Here, we show that not only lab-affordable benchtop 3D printers can produce equal-quality drive caps as the commercialized version, but also smaller 2.5 mm and 1.3 mm MAS drive caps—despite slight compromise in performances. All in-house fabricated drive caps (1.3 to 7 mm) can be consistently reproduced (> 90 %) and achieved excellent spinning performances. In summary, the > 3.2 mm systems have similar performances as the commercial systems, while the 2.5 and 1.3 mm spun up to 26 kHz 2 Hz, and 46 kHz 1 Hz, respectively. The low-cost and fast in-house fabrication of MAS drive caps allows easy prototyping of new MAS drive cap models and, possibly, new NMR applications. For instance, we have fabricated a 4 mm drive cap with a hollow center to allow better light penetration or sample insertion during MAS. | Cyriaque Amerein; Utsab Banerjee; Zhenfeng Pang; Wenqing Lu; Vanessa Pimenta; Kong Ooi Tan | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cd8111fa87eb17f35091f0/original/in-house-fabrication-of-1-3-to-7-mm-mas-drive-caps-using-desktop-3d-printers.pdf |
64a5f5af9ea64cc16783b106 | 10.26434/chemrxiv-2023-zmbcn | Green Chemistry and Engineering for Our Future | The principles of Green Chemistry and Engineering were formalised more than 20 years ago to guide us toward a safe and sustainable future. This framework is as important as ever in the development of chemical technologies that support human well-being while addressing the complex challenges we face in sustainability. This perspective is a reflection on the duty of chemists and engineers to integrate these principles into their practice, and how doing so can help confront diverse problems such as climate change, sustainable food production, pollution control, renewable construction materials, and green energy production and storage. | Justin Chalker; Rumana Hossain; Veena Sahajwalla | Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a5f5af9ea64cc16783b106/original/green-chemistry-and-engineering-for-our-future.pdf |
611bb501ff39afff15edc51b | 10.26434/chemrxiv-2021-2h7x5 | Effect of Mono-Vacant Defects on the Adsorption Properties of Deep Eutectic Solvents onto Hexagonal Boron-Nitride Nanoflakes | Hexagonal boron nitride is a promising material for a variety of electronic, optical, and material science applications. Both the synthesis of the material through exfoliation, and its various applications almost inevitably require its solvation. Deep eutectic solvents (DES) are extremely useful solvents for these types of applications due to their non-volatility, inflammability, biocompatibility, and reasonable cost. There are many different deep eutectic solvents available, and their suitability for any given application is particularly dependent on the specific of their structure. DES have been examined computationally for use with boron nitride, but these calculations use idealized, perfect boron nitride sheets instead of the more realistic, defect-containing systems. In this report, we investigated four DESs with two experimentally observed defective boron nitride, one with a single boron vacancy, the other with a single nitrogen vacancy. All DESs bound with higher affinity to the defective boron nitride than to the pristine surface. Charge transfer was minimal in all cases although the surfaces tended to donate electron density to the solvents. The interactions between the solvents and the surfaces are primarily non-covalent although in several cases natural bond order analysis indicates a partial covalent interaction that helps explain the higher-than-expected affinity for particular DES. The DESs have little effect on the predicted optical behaviour of the pristine boron nitride but do significantly change the adsorption spectrum of the defective boron nitride nanoflakes; the effect on bulk material might be limited. Together these results suggest that the choice of DES can either be made to limit any effect on the properties of the material (urea-choline chloride) or to affect the optical and electronic nature of the material (benzoic acid-choline chloride). | Mehdi Shakourian-Fard; S. Maryamdokht Taimoory; Hamid Reza Ghenaatian; Ganesh Kamath; John Trant | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Nanostructured Materials - Materials; Optical Materials; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611bb501ff39afff15edc51b/original/effect-of-mono-vacant-defects-on-the-adsorption-properties-of-deep-eutectic-solvents-onto-hexagonal-boron-nitride-nanoflakes.pdf |
6621dfd091aefa6ce1dd27ac | 10.26434/chemrxiv-2024-nbzhr | Oxygen vacancy formation as the rate-determining step in the Mars-van Krevelen mechanism | The Mars-van Krevelen mechanism (MvK) is a widely recognized model for describing the role of lattice oxygen in catalysis. Following the MvK mechanism, the formation and conversion of surface oxygen vacancy (VO) are considered as the key steps. CeO2-ZrO2 (CZ) mixed oxides are the typical catalyst support in MvK mechanism. They have the unique property of hosting remarkable amount of VO without significant change in lattice structure, offering O storage and release capability that maintains the required concentration of active O on the catalytic surface. In this regard, the rate of VO formation and conversion directly affect their catalytic performance. In this work, we obtained the VO formation and conversion kinetics by measuring the rate of the Ce4+ reduction and oxidation via operando energy dispersive Extended X-ray Absorption Fine Structure (EDE). The main conclusions are: 1) VO formation is 10 times faster than VO conversion; 2) VO formation rates are comparable with the CO oxidation rates, thereby serving as the rate-determining step in CO oxidation; 3) Pd and Cu serve as catalysts for VO formation by significantly improving its rate by 50 times at 250 C by weakening the metal-O bonding strength, whereas the activation energy have been reduced to 58.4 kJ/mol and 36.5 kJ/mol, respectively. Our method in measuring and analysing partial reaction rates within a turnover is therefore important for all chemical reactions. | Hao Gu; Takuro Yokoya; Liqun Kang; Sushila Marlow; Xinlian Su; Manxi Gong; Jay Yan; Yifei Ren; Zhipeng Wang; Xuze Guan; Longxiang Liu; Zhangyi Yao; Luke Keenan; Asakura Hiroyuki; Feng Ryan Wang | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6621dfd091aefa6ce1dd27ac/original/oxygen-vacancy-formation-as-the-rate-determining-step-in-the-mars-van-krevelen-mechanism.pdf |
66524bb491aefa6ce1fd50f3 | 10.26434/chemrxiv-2024-md0hn | Colossal Core/Shell CdSe/CdS Quantum Dot Emitters | Single-photon sources are essential for advancing quantum technologies, with scalable integration being a crucial requirement. To date, deterministic positioning of single-photon sources in large-scale photonic structures remains a challenge. In this context, colloidal quantum dots (QDs), particularly core/shell configurations, are attractive due to their solution processability. However, traditional QDs are typically small, about 3 to 6 nm, which restricts their deterministic placement and utility in large-scale photonic devices. The largest existing core/shell QDs are the family of giant CdSe/CdS QDs, with total diameters ranging from about 20 to 50 nm. Pushing beyond this size limit, we introduce a synthesis strategy for colossal CdSe/CdS QDs, with sizes ranging from 30 to 100 nm, using a stepwise high-temperature continuous injection method. Electron microscopy reveals a consistent hexagonal diamond morphology composed of twelve semipolar {101 ̅1} facets and one polar (0001) facet. We also identify conditions where shell growth is disrupted, leading to defects, islands, and mechanical instability, which suggest synthetic requirements for growing crystalline particles beyond 100 nm. The stepwise growth of thick CdS shells on CdSe cores enables the synthesis of emissive QDs with long photoluminescence lifetimes of a few microseconds and suppressed blinking at room temperature. Notably, QDs with 100 CdS monolayers exhibit high single-photon emission purity with second-order photon correlation g(2)(0) values below 0.2. Our findings indicate that colossal core/shell QDs can efficiently emit single photons, which paves the way for quantum photonic applications that require deterministic placement of single-photon sources. | Hao Nguyen; Benjamin Hammel; David Sharp; Jessica Kline; Griffin Schwartz; Samantha Harvey; Emily Nishiwaki; Soren Sandeno; David Ginger; Arka Majumdar; Sadegh Yazdi; Gordana Dukovic; Brandi Cossairt | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66524bb491aefa6ce1fd50f3/original/colossal-core-shell-cd-se-cd-s-quantum-dot-emitters.pdf |
651d663abda59ceb9adbcdf3 | 10.26434/chemrxiv-2023-1vnnr | Rigid PN Cages as 3-Dimensional Building Blocks for Crystalline or Amorphous Networked Materials | Three-dimensional covalent connectors are valuable synthons for accessing crystalline or amorphous networks. Currently, fused polycyclic alkanes are employed as connectors in this context. We debut phosphorus-nitrogen (PN) cages as new 3-dimensional inorganic connectors that yield crystalline MOFs and amorphous networks that can feature gas porosity. We show that the high tunability of PN cages accelerates network diversification and the presence of a responsive 31P NMR spectroscopic handle provides structural insight. Collectively, this work unlocks a new and convenient high-dimensionality synthon for reticular chemistry. | Mohsen Shayan; Maryam Abdollahi; Mason Lawrence; Etienne Guinand; Maxime Goulet; Tanner George; Jason Masuda; Michael Katz; Audrey Laventure; Saurabh Chitnis; Ulrike Werner-Zwanziger | Inorganic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651d663abda59ceb9adbcdf3/original/rigid-pn-cages-as-3-dimensional-building-blocks-for-crystalline-or-amorphous-networked-materials.pdf |
60c74bb8bdbb89e376a39637 | 10.26434/chemrxiv.12376745.v1 | Specificity of Biomarker Detection in Microfluidic Sensors | <p>The microfluidics based point-of-care (POC) sensing
devices offer unmatched possibilities of fast and high throughput diagnosis
over conventional strategies. A major challenge for the early detection of
disease is the significantly lower concentration of biomarkers as compared to the
interfering noise molecules. In this work, we
investigate the ‘reaction parameter’ phase space to identify suitable reaction parameters
to enhance biomarker detection specificity. Under similar target biomarker and
noise concentration levels, we show that a target biomarker is more likely to
be detected at low concentrations and weak target and noise-receptor binding
kinetics. Importantly, a
simulation verified time-scale based methodology is developed to guide the appropriate
choice of biomarkers for specific detection. This study demonstrates the prospect of successful POC
diagnostic devices during early stage of diseases such as cancer. </p> | Praneet Prakash; Manoj Varma | Fluid Mechanics; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bb8bdbb89e376a39637/original/specificity-of-biomarker-detection-in-microfluidic-sensors.pdf |
6282499843d1f0102c2e0e08 | 10.26434/chemrxiv-2022-1zrjl | A Quantum Mechanical Description of the Diffusion Properties of C1-C2 Hydrocarbon Molecules in MOF-74-Mg | Among the numerous metal organic framework (MOF) families, of significant importance is the MOF-74-M series (M = metal, -also known as CPO-27-M), characterized by a high density of not fully coordinated open metal site centers; this peculiarity has been demonstrated to translate into a higher hydrocarbons’ separation potential than other known MOFs and zeolites. To provide a more comprehensive description of the behavior of the hydrocarbon molecules within the MOF-74 cavity, diffusion processes and corresponding diffusion barriers of small hydrocarbons in the MOF-74-Mg were modeled. This work provides a description of the molecular transport processes of CH4, C2H2, C2H4 and C2H6 within and along the cavity of MOF-74-Mg; in addition, the influence of pre-adsorbed water molecules is also addressed. Density functional theory (DFT), as implemented within a plane-wave (PW) approach under periodic boundary conditions (PBC), has been used to investigate the diffusion mechanisms using the climbing-image nudge elastic band (CI-NEB) method, coupled with the van der Waals functional (vdW-DF) and ultra-soft pseudopotentials. Two transport mechanisms were identified: M1, referring to the molecular migrations within the MOF cavity; and M2, referring to the molecular migrations along the MOF longitudinal channel. The M1 transport mechanism was further analyzed to address the molecular migration from one metal atom to its adjacent one (M1a), and with respect to the second metal over (M1b). All the transport mechanisms considered show that the diffusion of paraffin molecules in MOF-74-Mg is energetically more favorable than that of olefin molecules. An interesting trend is observed across all the diffusion mechanisms where the stronger the molecule binds to the open metal site, the higher the diffusion barrier it needs to overcome. For all the small hydrocarbons considered in this study, transport mechanism M1a is significantly more energetically favorable than M1b, showing that it is easier for molecules to drift along the longitudinal cavity than to remain trapped cross-sectionally within the cavity itself. This work shows how this computational approach can be successfully applied not only to reveal the molecular transport in other MOF-74 isostructural species, but also in the fundamental understanding of the screening of MOFs and other nano-porous materials for gas separation applications. | Gemechis Degaga; Amanda Studinger; Loredana Valenzano-Slough | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Processes; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6282499843d1f0102c2e0e08/original/a-quantum-mechanical-description-of-the-diffusion-properties-of-c1-c2-hydrocarbon-molecules-in-mof-74-mg.pdf |
60c75686842e657db7db4509 | 10.26434/chemrxiv.14261903.v1 | Bolaamphiphilic Bis-Dehydropeptide Hydrogels as Potential Drug Release Systems | <div>The self-assembly of nanometric structures from molecular building blocks is an effective</div><div>way to make new functional materials for biological and technological applications. In this work</div><div>four symmetrical bolaamphiphiles based on dehydrodipeptides</div><div>(phenylalanyldehydrophenylalanine and tyrosyldehydrophenylalanine) linked through phenyl</div><div>or naphthyl linkers (terephthalic acid and 2,6-naphthalenedicarboxylic acid) were prepared and</div><div>their self-assembly properties studied. The results showed that all compounds with the exception</div><div>of the bolaamphiphile of tyrosyldehydrophenylalanine and 2,6-naphthalene dicarboxylic acid</div><div>gave self-standing hydrogels with critical gelation concentrations of 0.3 and 0.4 wt% using a pH</div><div>trigger. The self-assembly of these hydrogelators was investigated using STEM microscopy,</div><div>which revealed a network of entangled fibres. According to rheology the dehydrodipeptide</div><div>bolaamphiphile hydrogelators are viscoelastic materials with an elastic modulus G’ that falls in</div><div>the range of native tissue (0.37 kPa brain – 4.5 kPa cartilage). In viability and proliferation studies,</div><div>it was found that these compounds were non-toxic towards the human keratinocyte cell line,</div><div>HaCaT. In sustained release assays, we studied the effects of the charge present on the model</div><div>drug compound on the rate of cargo release from the hydrogel networks. Methylene blue (MB),</div><div>methyl orange (MO) and ciprofloxacin were chosen as cationic, anionic and overall neutral cargo,</div><div>respectively. These studies have shown that the hydrogels provide a sustained release of methyl</div><div>orange and ciprofloxacin, while the methylene blue is retained by the hydrogel network.</div> | Carolina Amorim; Sergio R.S. Veloso; Elisabete M.S. Castanheira; Loic Hilliou; Renato B. Pereira; David M. Pereira; José A. Martins; Peter
J. Jervis; Paula Ferreira | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75686842e657db7db4509/original/bolaamphiphilic-bis-dehydropeptide-hydrogels-as-potential-drug-release-systems.pdf |
66eda1c012ff75c3a1f16335 | 10.26434/chemrxiv-2024-7mnqb | Nano Trees: Nanopore signal processing and sublevel fitting using Decision Trees | As the complexity of solid-state nanopore experiments increases, analysis of the resulting electrical signals to determine biomolecular details becomes a challenge. State of the art techniques for this task perform poorly when transient signal characteristics approach the bandwidth limitations of the measurement electronics. In this work, we address this challenge through an algorithm, called Nano Trees, for fitting piecewise constant functions. Nano Trees leverages machine learning algorithms to provide accurate fits to the noisy piecewise constant data that is characteristic of nanopore ionic current signals, producing accurate fits on transients as short as twice the rise time of the measurement system. We demonstrate the performance of our algorithm on several real and synthetic datasets. These findings underscore the generalizability and accuracy of this approach in the regime of fast molecular translocations. | Deekshant Wadhwa; Philipp Mensing; James Harden; Paula Branco; Vincent Tabard-Cossa; Kyle Briggs | Theoretical and Computational Chemistry; Analytical Chemistry; Nanoscience; Biochemical Analysis; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66eda1c012ff75c3a1f16335/original/nano-trees-nanopore-signal-processing-and-sublevel-fitting-using-decision-trees.pdf |
65d8bca79138d23161d15ed1 | 10.26434/chemrxiv-2024-zr2vr | Molecular Fingerprints Optimization for Enhanced Predictive Modeling | The human exposome is represented by a vast number of chemicals, the fate and behavior of which remain largely unexplored. While modeling approaches are commonly employed to address this challenge, there is a recognized need for alternative molecular representations, such as molecular fingerprints. However, existing algorithms for computing molecular fingerprints may incorporate irrelevant or insufficient information for accurate activity prediction. In this study, we present an algorithm designed to optimize molecular fingerprints. This algorithm combines the relevant bits of information, aiming to enrich the final fingerprint for predicting specific behavioral properties. To achieve this, relevant variables (i.e. bits) for prediction were collected from six non-hashed fingerprints and fused into a master fingerprint. We used fish toxicity as a proof of concept. The RFR model was developed based on the master fingerprint. It demonstrated comparable results to conventional descriptor-based models with R$^2$ $\approx 0.9$ for the training set and R$^2$ $\approx 0.6$ for the test set. The molecular fingerprints have the advantage of being consistent and interpretable. Consequently, we were able to confirm the relevance of variables to the toxicity prediction. The final model outperformed each of the models based on individual fingerprints in the number of chemicals with prediction error, that fell in the range of +/- one standard deviation of residuals. The number of cases with the lower prediction error was on average four times higher for the master fingerprint-based model. The algorithm developed for optimizing molecular fingerprints is universal and can be applied to various case studies. | Viktoriia Turkina; Melanie R.W. Messih; Etienne Kant; Jelle Gringhuis; Annemieke Petrignani; Garry Corthals; Jake W. O'Brien; Saer Samanipour | Theoretical and Computational Chemistry; Analytical Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d8bca79138d23161d15ed1/original/molecular-fingerprints-optimization-for-enhanced-predictive-modeling.pdf |
63184aebfaf4a45d77093b0c | 10.26434/chemrxiv-2022-6trwf | Rapid and scalable halosulfonylation of strain-release reagents | Sulfonylated aromatics are commonplace motifs in drugs and agrochemicals. However, methods for the direct synthesis of sulfonylated non-classical arene bioisosteres, which could improve the physico-chemical properties of drug and agrochemical can-didates, are limited. Here we report a solution to this challenge: a one-pot halosulfonylation of [1.1.1]propellane, [3.1.1]propellane and bicy-clo[1.1.0]butanes that proceeds under practical, scalable and mild conditions. The sulfonyl halides used in this chemistry feature aryl, heteroaryl and alkyl substituents, and are conveniently generated in situ from readily available sulfinate salts and halogen atom sources. This methodology enables the syn-thesis of an array of pharmaceutically and agro-chemically relevant sulfonyl BCP, BCHep and cyclo-butyl halides, on milligram to decagram scales. | Helena Pickford; Vasyl Ripenko; Ryan McNamee; Serhii Holovchuk; Amber Thompson; Russell Smith; Pavel Mykhailiuk; Edward Anderson | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63184aebfaf4a45d77093b0c/original/rapid-and-scalable-halosulfonylation-of-strain-release-reagents.pdf |
63448abd0847002ebf9ccc17 | 10.26434/chemrxiv-2022-3kzsz | Prebiotic Synthesis on Meteorite Parent Bodies:
Insights from Hydrogen and Carbon Isotope Models | Several mechanisms could produce the biorelevant compounds in carbonaceous meteorites. These include radiation-driven reactions in the interstellar medium, gas-phase mineral-catalyzed reactions in the solar nebula, and aqueous chemistry in meteorite parent bodies. The ratio of heavy-to-light isotopes in a compound can constrains its formation history: a reaction’s substrates, mechanisms, and physiochemical conditions impact isotope ratios. Studies of the stable isotope compositions of meteoritic organic compounds have focused on sample- and molecular-average isotope measurements and have interpreted those data via qualitative or semi-quantitative models. Here we create quantitative models (i.e., explicitly fit to measurements) for hydrogen and carbon isotope compositions of organic compounds in primitive carbonaceous meteorites and use these models to reach broader conclusions regarding the environments, substrates, and chemical processes that contributed to pre- and early-solar-system organic synthesis.
The hydrogen model fits measured molecular-average deuterium concentrations in a compound class (e.g., amines, carboxylic acids) as linear combinations of hydrogens with similar chemical environments. In the chondrites studied, methyl hydrogens are amongst the most deuterium-enriched moiety and hydrogens attached to α-carbons are the least. Deuterium enrichment is inversely related to both a compound class’s water solubility and a meteorite sample’s degree of aqueous alteration and terrestrial weathering. These values suggest that ISM-sourced compounds reacted to form deuterium-enriched molecules on meteorites’ parent bodies and the enrichments were attenuated through exchange with water during aqueous alteration on the parent body and subsequent terrestrial processing.
The carbon model fits the δ13CVPDB of products from various reaction mechanisms by applying isotope effects to reactant δ13C measurements. The model with the most accurate δ13C fits of the compounds in the Murchison meteorite (62 % of previous measurements fit by model) and the lowest average residuals (5 ‰) uses the integrated aldehyde network (oxidation, reductive amination, and Strecker synthesis on aldehydes and ketones) to produce straight-chain compounds that undergo formaldehyde addition to create branched-chain compounds. Formaldehyde addition has not been previously considered in prebiotic chemical reaction networks, but the best-fit network’s ability to fit compounds that span over 100 ‰ in carbon isotope abundances makes it an attractive chemistry to explore. | Laura Chimiak; John Eiler | Earth, Space, and Environmental Chemistry; Geochemistry; Space Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63448abd0847002ebf9ccc17/original/prebiotic-synthesis-on-meteorite-parent-bodies-insights-from-hydrogen-and-carbon-isotope-models.pdf |
60e65814b95bddf9e660010a | 10.26434/chemrxiv-2021-l6zzm | Chemoselective, Scalable Nickel-Electrocatalytic O-Arylation of Alcohols | The formation of aryl-alkyl ether bonds through cross coupling of alcohols with aryl halides represents a useful strategic departure from classical SN2 methods. Numerous tactics relying on Pd-, Cu-, and Ni-based catalytic systems have emerged over the past several years. Herein we disclose a Ni-catalyzed electrochemically driven protocol to achieve this useful transformation with a broad substrate scope in an operationally simple way. This electrochemical method does not require strong base, exogenous expensive transition metal catalysts (e.g. Ir, Ru), and can easily be scaled up in either a batch or flow setting. Interestingly, e-etherification exhibits an enhanced substrate scope over the mechanistically related photochemical variant as it tolerates tertiary amine functional groups in the alcohol nucleophile. | phil baran; Hai-Jun Zhang; Longrui Chen; Martins Oderinde; Jacob Edwards; yu Kawamata | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e65814b95bddf9e660010a/original/chemoselective-scalable-nickel-electrocatalytic-o-arylation-of-alcohols.pdf |
64ee676b3fdae147fa18ec35 | 10.26434/chemrxiv-2023-ghh52 | Tuning the electrochemical performance of covalent organic framework cathodes for Li- and Mg-based batteries: the influence of electrolyte and binder | Covalent organic frameworks (COFs) are crystalline porous organic polymers that have recently emerged as promising electrode materials for rechargeable batteries. Herein, we present an approach to improve the electrochemical performance of an anthraquinone-based COF (DAAQ-TFP-COF) cathode material in metal anode (Li, Mg) based batteries through proper selection of the electrolyte and binder. Our results show that the combination of lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) in tetraethylene glycol dimethyl ether (TEGDME) as electrolyte and poly(tetrafluoroethylene) (PTFE) as binder led to the best electrochemical performance with high utilisation efficiency of the redox sites and specific capacities close to the theoretical value. Using such electrolyte and binder, cyclable symmetric cells consisting of two DAAQ-TFP-COF organic electrodes exemplify 82% capacity retention after 1300 cycles at a high current density of 500 mAh g-1. The high reversibility and stability of the COF electrode material upon cycling were confirmed by ex situ IR spectroscopy. In addition, DAAQ-TFP-COF was explored as cathode in magnesium cells using two different Mg electrolytes; one based on MgCl2 and one containing weakly coordinating anions. Electrochemical characterisation reveals significant differences in the performance of COF in terms of achievable capacities and voltage profiles, pointing towards hindered transport. Our findings demonstrate that the appropriate choice of electrolyte and binder is crucial to maximise the performance of COF-based materials in different post-lithium-ion metal anode batteries. | Olivera Luzanin; Raquel Dantas; Robert Dominko; Jan Bitenc; Manuel Souto | Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ee676b3fdae147fa18ec35/original/tuning-the-electrochemical-performance-of-covalent-organic-framework-cathodes-for-li-and-mg-based-batteries-the-influence-of-electrolyte-and-binder.pdf |
648b41c1be16ad5c57f901b0 | 10.26434/chemrxiv-2023-zj9ld | The Fluorine Toolbox: from Molecular Design to Advanced Batteries | The increasing demand for high-performance rechargeable batteries, particularly in energy storage applications such as electric vehicles, has driven the development of advanced battery technologies with improved energy density, safety, and cycling stability. In this regard, fluorine has emerged as a crucial element in achieving these goals with fluorinated materials being employed in a wide range of battery applications, including solid and liquid electrolytes, electrolyte additives, solvents, binders, and protective layers for electrodes. This review explores the design and utilization of fluorine-containing materials in advanced batteries, focusing on the significance of controlling their chemical structure and understanding their impact on battery performance. A key aspect is the role of fluorinated materials in facilitating the formation of a thin, protective film of corrosion products at the metal-electrolyte interface, which serves as a barrier against further chemical reactions with the electrolyte. The electron-withdrawing property of fluorine endows these fluorinated materials with high oxidative stability at high voltages. Moreover, the non-flammable nature of fluorinated compounds contributes to the design of batteries with enhanced safety and prolonged lifespan. Additionally, we discuss the current challenges and future directions in harnessing the battery-related aspects of fluorinated materials, with a focus on the regulatory landscape surrounding the use of fluorinated compounds. | Yiqing Wang; Zhenzhen Wu; Faezeh Azad; Yutong Zhu; Lianzhou Wang; Craig Hawker; Andrew Whittaker; Maria Forsyth; CHENG ZHANG | Polymer Science; Energy; Fluoropolymers; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648b41c1be16ad5c57f901b0/original/the-fluorine-toolbox-from-molecular-design-to-advanced-batteries.pdf |
65f9128666c1381729466783 | 10.26434/chemrxiv-2024-k0ml1 | New functional form to describe the temperature dependence of liquid phase reaction rates | Chemical reactions in subcritical or near-critical solvents hold significant promise for numerous industrial and environmental applications. The Arrhenius equation is typically used to describe the temperature dependence of reaction rates, yet it often falls short in capturing the behavior of liquid phase reaction rates near critical points of solvents. To address this limitation, we propose a novel functional form that can correctly describe the temperature trends of liquid phase rate constants from room temperature up to the critical temperature of a solvent. The proposed scheme uses four kinetic parameters with physical implications, two accounting for the gas phase contribution and the other two accounting for the solvation effect on reactions. The new functional form can accurately reproduce the anomalous temperature dependence of liquid phase rate constants in subcritical and near-critical regimes that the Arrhenius equation fails to capture. Furthermore, our preliminary finding suggests that the kinetic parameters associated with the solvation terms can be computed with ab initio approaches to estimate the temperature-dependent rate constants of liquid phase reactions based on their corresponding rate constants in gas phase. The proposed functional form provides an alternative approach to describe the non-Arrhenius behavior of diverse liquid phase reactions across a wide range of temperature. | Yunsie Chung; William H. Green | Chemical Engineering and Industrial Chemistry; Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2024-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f9128666c1381729466783/original/new-functional-form-to-describe-the-temperature-dependence-of-liquid-phase-reaction-rates.pdf |
65490d7dc573f893f1ecf20e | 10.26434/chemrxiv-2023-xn5l3 | Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins | Red fluorescent protein (RFP) variants are highly sought after for in-vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield than their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pre-twisted chromophore conformation which provides easier access to conical intersections. The main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance). | Elisa Pieri; Alice R. Walker; Mingning Zhu; Todd J. Martínez | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65490d7dc573f893f1ecf20e/original/conical-intersection-accessibility-dictates-brightness-in-red-fluorescent-proteins.pdf |
6622935521291e5d1d304149 | 10.26434/chemrxiv-2024-6b5pq | Electrochemical surface nanostructuring of copper using fluoride and chloride | Copper is an active electrocatalyst for different energy conversion reactions which performance depends on the structure of the surface active sites. Here we propose a simple strategy to generate (n10) or (100)x(110) motifs on copper with tailored roughness. We electrochemically oxidize and reduce a copper electrode in solutions containing a mixture of sodium fluoride and sodium chloride with total concentration of 0.1 M: (0.1 -x) M NaF + x M NaCl. Chloride acts as a ligand agent inducing surface re-faceting and the growth of (n10) sites. Fluoride, which weakly adsorbs on copper, mainly causes an increase of the electroactive area and surface rugosity. With fluoride and chloride mixtures, we form (n10) motifs that appear covered by nanometric clusters, progressively increasing the density of defects. The nanoscale clusters almost coalesce with very high fluoride/chloride molar ratio solutions. To address the change in surface geometry on copper, we recorded the voltametric fingerprints of the modified surfaces with lead underpotential deposition (UPD) and compared them with the lead UPD-response of model copper single facets. Our work provides a direct link between an electrochemical response and ex-situ structural characterization describing, in detail, the effect of halides on the surface nanostructuring of copper. | Vicente Pascual Llorens; Albert Serrà Ramos; Pedro Mazaira-Couce; María Escudero-Escribano; Paula Sebastián-Pascual | Materials Science; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6622935521291e5d1d304149/original/electrochemical-surface-nanostructuring-of-copper-using-fluoride-and-chloride.pdf |
60c74e40bb8c1a05673db707 | 10.26434/chemrxiv.12594191.v2 | Machine Learning for Absorption Cross Sections | We present a machine learning (ML) method to accelerate the nuclear ensemble
approach (NEA) for computing absorption cross sections. ML-NEA is used to
calculate cross sections on vast ensembles of nuclear geometries to reduce the
error due to insufficient statistical sampling. The electronic properties —
excitation energies and oscillator strengths — are calculated with a reference electronic
structure method only for relatively few points in the ensemble. Kernel-ridge-regression-based
ML combined with the RE descriptor as implemented in MLatom is used to predict
these properties for the remaining tens of thousands of points in the ensemble
without incurring much of additional computational cost. We demonstrate for two
examples, benzene and a 9-dicyanomethylene derivative of acridine, that ML-NEA can
produce statistically converged cross sections even for very challenging cases
and even with as few as several hundreds of training points. | Bao-Xin Xue; Mario Barbatti; Pavlo O. Dral | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e40bb8c1a05673db707/original/machine-learning-for-absorption-cross-sections.pdf |
60c73d0df96a005d94285cf1 | 10.26434/chemrxiv.14759991.v2 | Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse Grain Force Field | Phosphoinositides are a family of membrane phospholipids that play crucial roles in membrane regulatory events. As such, these lipids are often a key part of molecular dynamics simulation studies of biological membranes, in particular of those employing coarse-grain models because of the potential long times and sizes of the involved membrane processes. Version 3 of the widely used Martini coarse grain force field has been recently published, greatly refining many aspects of biomolecular interactions. In order to properly use it for lipid membrane simulations with phosphoinositides, we put forth the Martini 3-specific parameterization of inositol, phosphatidylinositol, the seven physiologically relevant phosphorylated derivatives of phosphatidylinositol. Compared to parameterizations for earlier Martini versions, focus was put on a more accurate reproduction of the behavior seen in both atomistic simulations and experimental studies, including the signaling relevant phosphoinositide interaction with divalent cations. The models we develop improve upon the conformational dynamics of phosphoinositides in the Martini force field and provide stable topologies at typical Martini timesteps. They are able to reproduce experimentally known protein-binding poses as well as phosphoinositide aggregation tendencies. The latter were tested both in the presence and absence of calcium, and include correct behavior of PI(4,5)P2 calcium-induced clusters, which can be of relevance for regulation. | Luis Borges-Araújo; Paulo Souza; Fábio Fernandes; Manuel N. Melo | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0df96a005d94285cf1/original/improved-parameterization-of-phosphatidylinositide-lipid-headgroups-for-the-martini-3-coarse-grain-force-field.pdf |
60c74126bb8c1a57a53d9ece | 10.26434/chemrxiv.7868927.v2 | Effects of π-Extension on Pyrrole Hemithioindigo Photoswitches | The most red-shifted hemithioindigo
photoswitches have been identified through systematic introduction of aryl
units to a parent pyrrole hemithioindigo photoswitch. Increasing the size of
the 5’-aryl substituent is ineffective at producing further redshifted chromophores.
A second generation of 3’,5’-diarylated photoswitches which possess increased
tunability is reported. Experimental and computational evidence indicates the
4’ position is electronically isolated from the bulk of the conjugated system. | Timothy Newhouse; Joshua E. Zweig; Tongil Ko; Junrou Huang | Photochemistry (Org.); Physical Organic Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74126bb8c1a57a53d9ece/original/effects-of-extension-on-pyrrole-hemithioindigo-photoswitches.pdf |
649af52a6e1c4c986b6cd8a5 | 10.26434/chemrxiv-2023-1ht31 | Hierarchically doped plasmonic nanocrystal metamaterials | Assembling plasmonic nanocrystals in regular superlattices can produce effective optical properties not found in homogeneous materials. However, the range of these metamaterial properties is limited when a single nanocrystal composition is selected for the constituent meta-atoms. Here, we show how continuously varying doping at two length scales - the atomic and nanocrystal scales - enables tuning of both the frequency and bandwidth of the collective plasmon resonance in nanocrystal-based metasurfaces, while these features are inextricably linked in single-component superlattices. Varying the mixing ratio of indium tin oxide nanocrystals with different dopant concentrations, we use large-scale simulations to predict the emergence of a broad infrared spectral region with near-zero permittivity. Experimentally, tunable reflectance and absorption bands are observed owing to in- and out-of-plane collective resonances. These spectral features and the predicted strong near-field enhancement establish this multiscale doping strategy as a powerful new approach to designing metamaterials for optical applications. | Kihoon Kim; Zachary Sherman; Angela Cleri; Woo Je Chang; Jon-Paul Maria; Thomas Truskett; Delia Milliron | Materials Science; Nanoscience; Metamaterials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649af52a6e1c4c986b6cd8a5/original/hierarchically-doped-plasmonic-nanocrystal-metamaterials.pdf |
60c74533ee301cecf4c79272 | 10.26434/chemrxiv.9947474.v1 | Development of Small-Scale Experiments for the Education of Chemical Engineering and Its Practice for Undergraduates | A series
of small-scale/micro-scale experiments used for the education of undergraduate
students in chemical engineering courses have been developed. Based on the
“small-scale/micro-scale” concept, the experiments were developed to provide an
intuitive understanding of chemical processes, both by increasing the
visibility of these chemical processes and by making the apparatus compact
(desktop size). Nine experiments were developed that are relevant to the fields
of thermal engineering, fluid engineering, unit operations, and reaction
engineering. These experiments were introduced during the educational
experiment course for undergraduates in the chemical engineering program. | Kenji Katayama; Risa Ichinohe; Yuki Konno; Woon Yong Sohn; Shota Kuwahara; Toshitaka Funazukuri | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74533ee301cecf4c79272/original/development-of-small-scale-experiments-for-the-education-of-chemical-engineering-and-its-practice-for-undergraduates.pdf |
60c74dd4567dfe48c5ec53f6 | 10.26434/chemrxiv.12664799.v1 | Smart molecular/MoS2 Heterostructures Featuring Light and Thermally-Induced Strain Driven by Spin Switching | In this work we exploit the ability of spin-crossover molecules to switch between two spin states,
upon the application of external stimuli, to prepare smart molecular/2D heterostructures.
Through the chemical design of the hybrid interface, that involves a covalent grafting between
the two components, we obtain a hybrid heterostructure formed by spin-crossover nanoparticles
anchored on chemically functionalized monolayers of semiconducting MoS2. In the resulting
hybrid, the strain generated by the molecular system over the MoS2 layer, as a consequence of
a thermal or light-induced spin switching, results in a dramatic and reversible change of its
electrical and optical properties. This novel class of smart molecular/2D heterostructures could
open the way towards a novel generation of hybrid multifunctional materials and devices of
direct application in highly topical fields like electronics, spintronics or molecular sensing. | Ramón Torres-Cavanillas; Marc Morant-Giner; Garin Escorcia-Ariza; Julien Dugay; J. Canet-Ferrer; Sergio Tatay; Salvador Cardona-Serra; Dr. Mónica Giménez Marqués; Marta Galbiati; Alicia Forment-Aliaga; Eugenio Coronado | Hybrid Organic-Inorganic Materials; Magnetic Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Magnetism | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dd4567dfe48c5ec53f6/original/smart-molecular-mo-s2-heterostructures-featuring-light-and-thermally-induced-strain-driven-by-spin-switching.pdf |
6358b6c62e0c639cf93c77bc | 10.26434/chemrxiv-2022-rhjcx-v2 | Synthesis and Biological Evaluation of tert-Butyl Ester and Ethyl Ester Prodrugs of L-γ-Methyleneglutamic Acid Amides for Cancer | In cancer cells, glutaminolysis is the primary source of biosynthetic precursors. Recent efforts to develop amino acid analogues to inhibit glutamine metabolism in cancer have been extensive. Our lab recently discovered many L-γ-methyleneglutamic acid amides that were shown to be as efficacious as tamoxifen or olaparib in inhibiting the cell growth of MCF-7, SK-BR-3, and MDA-MB-231 breast cancer cells after 24 or 72 h of treatment. None of these compounds inhibited the cell growth of nonmalignant MCF-10A breast cells. These L-γ-methyleneglutamic acid amides hold promise as novel therapeutics for the treatment of multiple subtypes of breast cancer. Herein we report our synthesis and evaluation of two series of tert-butyl ester and ethyl ester prodrugs of these L-γ-methyleneglutamic acid amides and the cyclic metabolite and its tert-butyl esters and ethyl esters on the three breast cancer cell lines MCF-7, SK-BR-3, and MDA-MB-231 and the nonmalignant MCF-10A breast cell line. These esters were found to suppress the growth of the breast cancer cells, but they were less potent compared to their parent L-γ-methyleneglutamic acid amides. Pharmacokinetic (PK) studies were carried out on the lead L-γ-methyleneglutamic acid amide to establish tissue-specific distribution and other PK parameters. Notably, this lead compound showed moderate exposure to the brain with a half-life of 0.74 h and good tissue distribution, such as in the kidney and liver. Therefore, the L-γ-methyleneglutamic acid amides were then tested on glioblastoma cell lines BNC3 and BNC6 and head and neck cancer cell lines HN30 and HN31. They were found to effectively suppress the growth of these cancer cell lines after 24 or 72 h of treatment in a concentration-dependent manner. These results suggest broad applications of the L-γ-methyleneglutamic acid amides in anticancer therapy. | Md Imdadul Khan; Fakhri Mahdi; Patrice Penfornis; Nicholas Akins; Md Imran Hossain; Seong Jong Kim; Suresh Sulochana; Amna Adam; Tristan Tran; Chalet Tan; Pier Paolo Claudio; Jason Paris; Hoang Le | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6358b6c62e0c639cf93c77bc/original/synthesis-and-biological-evaluation-of-tert-butyl-ester-and-ethyl-ester-prodrugs-of-l-methyleneglutamic-acid-amides-for-cancer.pdf |
62ed3ddcfad4852c5c62c8e0 | 10.26434/chemrxiv-2022-7s8rb | Enhancing Sampling of Water Rehydration upon Ligand Binding using Variants of Grand Canonical Monte Carlo | Water plays an important role in mediating protein-ligand interactions. Water rearrangement upon a ligand binding or modification can be very slow and beyond typical timescales used in molecular dynamics (MD) simulations. Thus, inadequate sampling of slow water motions in MD simulations often impairs the accuracy of the accuracy of ligand binding free energy calculations. Previous studies suggest grand canonical Monte Carlo (GCMC) outperforms normal MD simulations for water sampling, thus GCMC has been applied to help improve the accuracy of ligand binding free energy calculations. However, in prior work we observed protein and/or ligand motions impaired how well GCMC performs at water rehydration, suggesting more work is needed to improve this method to handle water sampling. In this work, we applied GCMC in 21 protein-ligand systems to assess the performance of GCMC for rehydrating buried water sites. While our results show that GCMC can rapidly rehydrate all selected water sites for most systems, it fails in 5 systems. In most failed systems, we observe protein/ligand motions, which occur in the absence of water, combine to close water sites and block instantaneous GCMC water insertion moves. For these 5 failed systems, we both extended our GCMC simulations and tested a new technique named grand canonical nonequilibrium candidate Monte Carlo (GCNCMC). GCNCMC combines GCMC with the nonequilibrium candidate Monte Carlo (NCMC) sampling technique to improve the probability of a successful water insertion/deletion. Our results show that GCNCMC and extended GCMC can rehydrate all target water sites for three of the five problematic systems and GCNCMC is more efficient than GCMC in two out of the three systems. In one system, only GCNCMC can rehydrate all target water sites, while GCMC fails. Both GCNCMC and GCMC fail in one system. This work suggests this new GCNCMC method is promising for water rehydration especially when protein/ligand motions may block water insertion/removal. | Yunhui Ge; Oliver Melling; Weiming Dong; Jonathan Essex; David Mobley | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ed3ddcfad4852c5c62c8e0/original/enhancing-sampling-of-water-rehydration-upon-ligand-binding-using-variants-of-grand-canonical-monte-carlo.pdf |
631f5ea0bada3858dac24ed3 | 10.26434/chemrxiv-2022-0q8rj | Role and Dynamics of Transition Metal Carbides in Methane Coupling | Transition metal carbides have numerous applications and are known to excel in terms of hardness, thermal stability and conductivity. In particular, the Pt-like behavior of Mo and W carbides has led to a popularization of metal carbides in catalysis, ranging from electrochemically-driven reactions to thermal methane coupling. Herein, we show the dynamics of Mo and W carbides and the active participation of carbidic carbon in the formation of C2 products during methane coupling. A detailed mechanistic study reveals that the catalyst performance of these metal carbides can be traced back to its carbon diffusivity and exchange capability upon interaction with gas phase carbon (methane). A stable C2 selectivity over time on stream for Mo carbide (Mo2C) can be rationalized by fast carbon diffusion dynamics, while W carbide (WC) shows loss of selectivity due to slow diffusion leading to surface carbon depletion. This finding showcases that the bulk carbidic carbon of the catalyst plays a crucial role and that the metal carbide is not only responsible for methyl radical formation. Overall, this study supports the presence of a carbon equivalent to the Mars-Van Krevelen type mechanism for non-oxidative coupling of methane, thus introducing guiding principles to design and develop associated catalysts. | Seraphine B.X.Y. Zhang; Quentin Pessemesse; Lukas Lätsch; Konstantin M. Engel; Wendelin J. Stark; Alexander P. van Bavel; Andrew D. Horton; Pierre-Adrien Payard; Christophe Copéret | Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631f5ea0bada3858dac24ed3/original/role-and-dynamics-of-transition-metal-carbides-in-methane-coupling.pdf |
6733a5c67be152b1d0dd9571 | 10.26434/chemrxiv-2024-06ktk | Unraveling the Nanoscopic Strain Evolution in Single Crystal Cathodes | Single-crystal layered oxides (SC-NMC) with grain boundary-free configuration, have effectively addressed the long-standing cracking issue of conventional polycrystalline Ni-rich cathodes (PC-NMC) for lithium-ion batteries, prompting a shift in optimization strategies. However, continued reliance on anisotropic lattice volume change—a well-established failure indicator in PC-NMC—as a metric for understanding lattice strain and guiding compositional designs for SC-NMC becomes contentious. Herein, leveraging multi-scale diagnostic techniques, we unraveled the distinct nanoscopic strain evolution in SC-NMC cathodes, challenging the conventional composition-driven strategies and mechanical degradation indicators used for PC-NMC. Through particle-level chemo-mechanical analysis , we reveal a decoupling between mechanical strain and lattice volume change of SC-NMC, identifying that the structural instability in SC-NMC is primarily driven by multiple-dimension lattice distortions induced by kinetics-driven reaction heterogeneity and progressively deactivating chemical phases. Consequently, the roles of cobalt (Co) and manganese (Mn) in SC-NMC have been redefined based on the newly established mechanical failure mode. Unlike cobalt’s detrimental role in PC-NMC, we find Co to be critical in enhancing the longevity of SC-NMC cathodes by mitigating localized lattice strain along extended diffusion pathway, whereas Mn exacerbates mechanical degradation. Our findings fundamentally redefine the compositional requirements for SC cathodes compared to conventional NMC cathode systems, offering new insights into developing mechanically robust electrode materials with high capacity and superior durability. | Jing Wang; Tongchao Liu; Weiyuan Huang; Lei Yu; Tianyi Li; Xiaojing Huang; Xianghui Xiao; Lu Ma; Tao Zhou; Martin V. Holt; Haozhe Zhang; Rachid Amine; Wenqian Xu; Luxi Li; Jianguo Wen; Ying Shirley Meng; Khalil Amine | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6733a5c67be152b1d0dd9571/original/unraveling-the-nanoscopic-strain-evolution-in-single-crystal-cathodes.pdf |
67bddc326dde43c9086ca5e7 | 10.26434/chemrxiv-2025-fvm85-v2 | Zero-field NMR and millitesla-SLIC spectra for > 200 molecules from density functional theory and spin dynamics | NMR is usually performed at magnetic fields of 1 T and above to obtain sufficient sensitivity and spectral dispersion to identify chemicals based on chemical shifts and J couplings. At lower fields, the advent of hyperpolarization technologies and sensitive low-field detectors can address sensitivity concerns. However, it remains disputed whether spectral signatures at low fields are sufficient for chemical identification. Here, we report an all–electron DFT batch production of J coupling NMR spectra at zero field and 6.5 mT for over 200 small molecules. We found that ultra-low-field NMR can be used for unique chemical identification. In the developed computational tool chain, we first used the all-electron FHI-aims code to calculate the molecular J couplings and chemical shifts. We then fed the calculated NMR parameters into the NMR simulation package SPINACH to simulate both heteronuclear J coupling spectra at zero-field, and spin-lock induced crossing (SLIC) spectra at 6.5 mT. The resulting spectra demonstrate that ultra-low-field NMR spectra can represent unique identifiers of chemical structure for small molecules. | Iuliia Mandzhieva; Franziska Theiss; Xingtao He; Adam Ortmeier; Anuja Koirala; Stephen McBride; Stephen DeVience; Matthew Rosen; Volker Blum; Thomas Theis | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bddc326dde43c9086ca5e7/original/zero-field-nmr-and-millitesla-slic-spectra-for-200-molecules-from-density-functional-theory-and-spin-dynamics.pdf |
Subsets and Splits
No saved queries yet
Save your SQL queries to embed, download, and access them later. Queries will appear here once saved.