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60c75a08f96a0053da2890f1 | 10.26434/chemrxiv.14208446.v2 | Prediction of Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis | <div>There is growing consensus that the optimization of the kinetic parameters for drug-protein binding leads to improved drug efficacy. Therefore, computational methods have been developed to predict kinetic rates and to derive quantitative structure-kinetic relationships (QSKRs). Many of these methods are based on crystal structures of ligand-protein complexes. However, a drawback is that each protein-ligand complex is usually treated as having a single structure. Here, we present a modification of COMparative BINding Energy (COMBINE) analysis, which uses the structures of protein-</div><div>ligand complexes to predict binding parameters. We introduce the option to use multiple structures to describe each ligand-protein complex into COMBINE analysis and</div><div>apply this to study the effects of protein flexibility on the derivation of dissociation rate constants (k<sub>off</sub>) for inhibitors of p38 mitogen-activated protein (MAP) kinase, which has a flexible binding site. Multiple structures were obtained for each ligand-protein complex by performing docking to an ensemble of protein configurations obtained from molecular dynamics simulations. Coefficients to scale ligand-protein interaction energies determined from energy-minimized structures of ligand-protein complexes were obtained by partial least squares regression and allowed the computation of k<sub>off</sub> values. The QSKR model obtained using single, energy minimized crystal structures for each ligand-protein complex had a higher predictive power than the QSKR model obtained with multiple structures from ensemble docking. However, the incorporation of protein-ligand flexibility helped to highlight additional ligand-protein interactions that lead to longer residence times, like interactions with residues Arg67 and Asp168, which are close to the ligand in many crystal structures. These results show that COMBINE analysis is a promising method to guide the design of compounds that bind to flexible proteins with improved binding kinetics. </div> | Ariane Nunes Alves; Fabian Ormersbach; Rebecca Wade; Ariane Nunes-Alves | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75a08f96a0053da2890f1/original/prediction-of-drug-target-binding-kinetics-for-flexible-proteins-by-comparative-binding-energy-analysis.pdf |
60c7484e842e6523a5db2b8c | 10.26434/chemrxiv.11888205.v1 | Uncovering Alternate Pathways to Nafion Membrane Degradation in Fuel Cells with First-Principles Modeling | Polymer electrolyte membrane fuel cells (PEMFCs) represent promising energy storage solutions, but challenges remain to maximize their utility. Nafion is frequently employed as the PEMFC membrane material, but degradation of Nafion can limit the life of PEMFCs. Using hybrid density functional theory (DFT), we carry out reaction pathway analysis on a range of candidate degradation pathways on both pristine and defect-containing models of Nafion. Degradation of pristine Nafion initiated by hydrogen radicals involves moderate (ca. 20 kcal/mol) barriers lower than alternative pathways initiated by hydroxyl radicals. We propose a new pathway for continued Nafion degradation after initial H radical attack in the presence of H<sub>2</sub>O<sub>2</sub>. This pathway has a modest barrier and provides a mechanistic basis for the production of experimentally observed trifluoroacetic acid and hydrogen fluoride. Our work suggests inherent limits to mechanistic studies that use hydroxyl radical as the sole radical source to model Nafion degradation under operating conditions. We observe that hydroxyl radical-only degradation mechanisms have barriers competitive with hydrogen radical species only for initiation at carboxylic acid defects on the main chain or sulfonic acid functional groups on the Nafion side chain. We confirm our observations with DFT by comparison to correlated wavefunction theory. Our study highlights the importance of thorough first-principles modeling to identify the most probable, low energy pathways for materials degradation. | Akash Bajaj; Fang Liu; Heather Kulik | Polymers; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7484e842e6523a5db2b8c/original/uncovering-alternate-pathways-to-nafion-membrane-degradation-in-fuel-cells-with-first-principles-modeling.pdf |
61e53e030121b997c02f50fe | 10.26434/chemrxiv-2022-htmn0-v2 | The Effect of Chemical Representation on Active Machine Learning Towards Closed-Loop Optimization | Multivariate chemical reaction optimization involving catalytic systems is a non-trivial task due to the high number of tuneable parameters and discrete choices. Closed-loop optimization featuring active Machine Learning (ML) represents a powerful strategy for automating reaction optimization. However, the translation of chemical reaction conditions into a machine-readable format comes with the challenge of finding highly informative features which accurately capture the factors for reaction success and allow the model to learn efficiently. Herein, we compare the efficacy of different calculated chemical descriptors for a high throughput generated dataset to determine the impact on a supervised ML model when predicting reaction yield. Then, the effect of featurization and size of the initial dataset within a closed-loop reaction optimization was examined. Finally, the balance between descriptor complexity and dataset size was considered. Ultimately, tailored descriptors did not outperform simple generic representations, however, a larger initial dataset accelerated reaction optimization. | Alexander Pomberger; Antonio Pedrina McCarthy; Ahmad Khan; Simon Sung; Connor Taylor; Matthew Gaunt; Lucy Colwell; David Walz; Alexei Lapkin | Theoretical and Computational Chemistry; Organic Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e53e030121b997c02f50fe/original/the-effect-of-chemical-representation-on-active-machine-learning-towards-closed-loop-optimization.pdf |
656a146b29a13c4d47737e05 | 10.26434/chemrxiv-2023-8r6g7 | Repurposing Drugs: Unraveling Anti-Cancer Interactions
with the Kinase Domain of Human HER2 | Human epidermal growth factor receptor 2 (HER2) is a transmembrane tyrosine kinase
receptor that is overexpressed in many types of cancer, including breast cancer. HER2
overexpression is associated with poor prognosis and resistance to therapy. Therefore,
HER2 is a promising target for cancer therapy.
In this study, we investigated the binding and stability of a number of drugs with the
kinase domain of HER2 using computational docking and molecular dynamics
simulations. The drugs included oxycodone, methylamino luvinilate, ciclesonide,
salicylic acid, melphalan, ibuprofen, N-acetyl tyrosine, and aspirin. All drugs except
phenylalanine and methylamino luvinilate docked with HER2 and formed stable
complexes.
The molecular dynamics simulations showed that the drug-HER2 complexes remained
stable throughout the simulation time of 100 ns. The drugs interacted with HER2
through a variety of interactions, including hydrogen bonding, hydrophobic interactions,
and electrostatic interactions.
The results of this study suggest that these drugs could be potential candidates for
HER2-targeted cancer therapy. However, further in vitro and in vivo studies are needed
to validate these findings. | Arslan Hameed | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656a146b29a13c4d47737e05/original/repurposing-drugs-unraveling-anti-cancer-interactions-with-the-kinase-domain-of-human-her2.pdf |
625c518b368ab6b49f82fb4c | 10.26434/chemrxiv-2022-tskhp-v2 | Digital chromatography: separating amino acids into spatially discrete containers
| Separation of amino acids (AAs) in a mixture has been conventionally done with chromatography or electrophoresis; separation usually occurs over some continuous space. The present communication proposes a digital method with a 20-stage pipeline for separating (and counting) single AA molecules in a mixture, with each of the 20 proteinogenic AAs ending up in its own discrete and spatially distinct container. Presently the method is designed for samples with a few molecules on up to the atto-mole level and can be used with samples collected from single cells. It is based on the superspecificity property of transfer RNAs (tRNAs): an AA can bind only with a cognate tRNA and not with any other; the binding error rate is about 1 in 350. Four necessary conditions for accurate separation are noted; it is shown informally that they can be satisfied. The method can also be used for peptide sequencing by feeding terminal residues cleaved from a peptide into the first stage of the pipeline.
| G Sampath | Analytical Chemistry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625c518b368ab6b49f82fb4c/original/digital-chromatography-separating-amino-acids-into-spatially-discrete-containers.pdf |
6642105f21291e5d1d2327df | 10.26434/chemrxiv-2024-0m3br | IEV2Mol: Molecular Generative Model Considering Protein-Ligand Interaction Energy Vectors | Generating drug candidates with desired protein‒ligand interactions is a significant challenge in structure-based drug design. In this study, a new generative model, IEV2Mol, is proposed that incorporates interaction energy vectors (IEVs) between proteins and ligands obtained from docking simulations, which quantitatively capture the strength of each interaction type, such as hydrogen bonds, electrostatic interactions, and van der Waals forces. By integrating this IEV into an end-to-end variational autoencoder (VAE) framework that learns the chemical space from SMILES and minimizes the reconstruction error of the SMILES, the model can more accurately generate compounds with the desired interactions. To evaluate the effectiveness of IEV2Mol, we performed benchmark comparisons with randomly selected compounds, unconstrained VAE models (JT-VAE), and compounds generated by RNN models based on interaction fingerprints (IFP-RNN). The results show that the compounds generated by IEV2Mol retain a significantly greater percentage of the binding mode of the query structure than those of the other methods. Furthermore, IEV2Mol was able to generate compounds with interactions similar to those of the input compounds, regardless of structural similarity. The source code and trained models for IEV2Mol, JT-VAE, and IFP-RNN designed for generating compounds active against the DRD2 receptor, as well as the datasets (DM-QP-1M, DRD2 Active, and ChEMBL33) utilized in this study, are released under the MIT License and available at https://github.com/sekijima-lab/IEV2Mol. | Mami Ozawa; NOBUAKI YASUO; Masakazu Sekijima | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6642105f21291e5d1d2327df/original/iev2mol-molecular-generative-model-considering-protein-ligand-interaction-energy-vectors.pdf |
633476eff764e616e7068a4e | 10.26434/chemrxiv-2022-g8v23 | Impact of reversible proton insertion on the electrochemistry of electrode materials operating in mild aqueous electrolytes: a case study with TiO2 | Near-neutral aqueous electrolytes are to be preferred for the development of sustainable electrochemical energy conversion and storage devices. Protons are inherent to these electrolytes and their reactivity towards the electrode material extends beyond their own reduction, especially when reversible proton insertion takes place in the bulk electrode material from acidic or buffered electrolytes. However, a still burning question regards whether reversible proton insertion persists when working in unbuffered mild aqueous electrolytes, and if so, with which consequences on the functioning of the electrode material. Here, we address this issue by examining TiO2 as a model insertion electrode in a range of mild aqueous electrolytes. Through a combination of experiments, modelling and multiphysics simulations, we demonstrate that, in a KCl-based electrolyte, water acts as proton donor to support reversible insertion of protons in TiO2, while in a NH4Cl-based aqueous electrolyte, the proton donor is NH4+. Moreover, we establish that strong pH gradients develop at the electrode interface during proton insertion/disinsertion, highlighting their dependence on the proton donor/acceptor and rationalizing their impact on the electrode voltage. Overall, this work provides a comprehensive framework of proton-insertion coupled electron transfer (PICET) that can be easily generalised to other electrode materials. | Benoît Limoges; Véronique Balland; Nikolina Makivic; Jean-Marie Tarascon; Kenneth D. Harris | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633476eff764e616e7068a4e/original/impact-of-reversible-proton-insertion-on-the-electrochemistry-of-electrode-materials-operating-in-mild-aqueous-electrolytes-a-case-study-with-ti-o2.pdf |
60c74e34ee301ce75cc7a468 | 10.26434/chemrxiv.9248825.v3 | Sensitive and Selective Detection of DNA Fragments Associated with Ganoderma Boninense by DNA-Nanoparticle Conjugate Hybridisation | <u><strong>
</strong></u><p>A colorimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense is reported, which is based on the aggregation of DNA-nanoparticle conjugated in the presence of complementary DNA from the pathogen. Here, various designs of DNA-nanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of double-stranded DNA analyte even in the presence of a large excess of a mixture of non-complementary DNA. The assay was also able to differentiate analyte sequences with three or more single nucleotide mismatches. Overall, this label-free system is rapid, sensitive, selective, simple in design and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results and therefore has the potential to be deployed of agricultural diagnostics in the field.</p><u><strong></strong></u> | Ekta Rani; Siti Akhtar Mohshim; Nor Hidayat Yusof; Muhammad Zamharir Ahmad; Royston Goodacre; Shahrul Ainliah Alang Ahmad; Lu Shin Wong | Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e34ee301ce75cc7a468/original/sensitive-and-selective-detection-of-dna-fragments-associated-with-ganoderma-boninense-by-dna-nanoparticle-conjugate-hybridisation.pdf |
60c7457c4c8919991fad29cc | 10.26434/chemrxiv.10032128.v1 | Third-Generation Method for High Throughput Quantification of Trace Palladium by Color or Fluorescence | Chemists frequently encounter problems associated with trace palladium in synthetic samples because palladium is presumably the most frequently used transition metal in synthetic organic chemistry. We previously reported a colorimetric method for trace palladium quantification, the only high throughput method implemented in the pharmaceutical industry. However, slight changes from the published reaction conditions have caused reproducibility problems, with little understanding of underlying molecular mechanisms. In the current study, we took a combinatorial approach to investigate the method and found that strong basicity was a culprit for the lack of reproducibility. We changed the reaction conditions and procedure accordingly, which substantially improved reproducibility. We discovered that the reaction followed Michaelis-Menten kinetics, allowing for predicting reaction rates on the basis of the substrate concentrations. The current method showed good correlation with inductively coupled plasma mass spectroscopy when 14 synthetic samples with unknown amounts of trace palladium were quantified. | Lydia Lukomski; Ivanna Pohorilets; Kazunori Koide | High-throughput Screening | CC BY 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457c4c8919991fad29cc/original/third-generation-method-for-high-throughput-quantification-of-trace-palladium-by-color-or-fluorescence.pdf |
60c741a90f50dbad44395b79 | 10.26434/chemrxiv.7990910.v2 | Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design | <p>In medicinal chemistry
programs it is key to design and make compounds that are efficacious and safe.
This is a long, complex and difficult multi-parameter optimization process,
often including several properties with orthogonal trends. New methods for the
automated design of compounds against profiles of multiple properties are thus
of great value. Here we present a fragment-based reinforcement learning
approach based on an actor-critic model, for the generation of novel molecules
with optimal properties. The actor and the critic are both modelled with
bidirectional long short-term memory (LSTM) networks. The AI method learns how
to generate new compounds with desired properties by starting from an initial
set of lead molecules and then improve these by replacing some of their
fragments. A balanced binary tree based on the similarity of fragments is used
in the generative process to bias the output towards structurally similar
molecules. The method is demonstrated by a case study showing that 93% of the
generated molecules are chemically valid, and a third satisfy the targeted
objectives, while there were none in the initial set.</p> | Niclas Ståhl; Göran Falkman; Alexander Karlsson; Gunnar Mathiason; Jonas Boström | Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a90f50dbad44395b79/original/deep-reinforcement-learning-for-multiparameter-optimization-in-de-novo-drug-design.pdf |
60c75081469df4ea37f448a1 | 10.26434/chemrxiv.12346823.v5 | Nanometer Scale Spectroscopic Visualization of Catalytic Sites During a Hydrogenation Reaction on a Pd/Au Bimetallic Catalyst | <p>Understanding the mechanism of catalytic hydrogenation at the local environment requires chemical and topographic information involving catalytic sites, active hydrogen species and their spatial distribution. Here, tip-enhanced Raman spectroscopy (TERS) was employed to study the catalytic hydrogenation of chloro-nitrobenzenethiol on a well-defined Pd(sub-monolayer)/Au(111) bimetallic catalyst (<i>p</i><sub>H2</sub>=1.5 bar, 298 K), where the surface topography and chemical fingerprint information were simultaneously mapped with nanoscale resolution (≈10 nm). TERS imaging of the surface after catalytic hydrogenation confirms that the reaction occurs beyond the location of Pd sites. The results demonstrate that hydrogen spillover accelerates hydrogenation at the Au sites within 20 nm from the bimetallic Pd/Au boundary. Density functional theory was used to elucidate the thermodynamics of interfacial hydrogen transfer. We demonstrate that TERS as a powerful analytical tool provides a unique approach to spatially investigate the local structure-reactivity relationship in catalysis.</p> | hao yin; Liqing Zheng; Wei Fang; Yin-Hung Lai; Nikolaus Porenta; Guillaume Goubert; Hua Zhang; Hai-Sheng Su; Bin Ren; Richardson O. Jeremy; Jian-Feng Li; Renato Zenobi | Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75081469df4ea37f448a1/original/nanometer-scale-spectroscopic-visualization-of-catalytic-sites-during-a-hydrogenation-reaction-on-a-pd-au-bimetallic-catalyst.pdf |
64b7802ab605c6803bfaaf94 | 10.26434/chemrxiv-2023-pg444 | Novel Oxidative Coupling-Based Chromogenic Substrates for Horseradish Peroxidase-Enhanced Lateral Flow Immunoassays: A Highly Sensitive and Economical Alternative to Conventional Substrates | Lateral flow immunoassays (LFIAs) have become indispensable in point-of-care diagnostics, but improving their sensitivity remains a critical challenge. Here, we present a strategy to enhance LFA sensitivity by introducing novel oxidative coupling-based chromogenic substrates for horseradish peroxidase (HRP) enhancement. Motivated by the need for more sensitive and cost-effective LFAs, we developed substrates inspired by oxidative permanent hair dyes. These substrates consist of two components: a primary intermediate and a coupler that undergo an oxidative coupling reaction in the presence of HRP and H2O2 to generate an intensely coloured dye. Our LFAs employing these substrates outperform conventional substrates (3,3'-diaminobenzidine (DAB) and 3,3',5,5'-tetramethylbenzidine (TMB)) and achieve an unprecedented sub-ng/mL limit of detection (LoD) for Human IgG. LFAs employing these novel substrates could detect Human IgG at 0.2 ng/mL, significantly surpassing reported sensitivities in the literature. Compared to gold nanoparticle based LFAs, our substrates exhibit over 30 times higher sensitivity. Moreover, these substrates offer substantial cost savings, making them a compelling choice for point-of-care diagnostics. | Karan Saxena; Bhushan Toley | Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b7802ab605c6803bfaaf94/original/novel-oxidative-coupling-based-chromogenic-substrates-for-horseradish-peroxidase-enhanced-lateral-flow-immunoassays-a-highly-sensitive-and-economical-alternative-to-conventional-substrates.pdf |
60c73d0e567dfe5562ec35c3 | 10.26434/chemrxiv.5382781.v1 | Fluorous photosensitizers enhance photodynamic therapy with perfluorocarbon nanoemulsions | <p>Photodynamic therapy (PDT) requires photosensitizer,
light, and oxygen to induce cell death. The majority of efforts to advance PDT focus
only on the first two components. Here, we employ perfluorocarbon nanoemulsions
to simultaneously deliver oxygen and photosensitizer. We find that the
implementation of fluorous soluble photosensitizers enhances the efficacy of
PDT. </p> | Ellen Sletten; Rachael A. Day; Daniel A. Estabrook; Jessica K. Logan | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e567dfe5562ec35c3/original/fluorous-photosensitizers-enhance-photodynamic-therapy-with-perfluorocarbon-nanoemulsions.pdf |
61cc8c56d6dcc20535490815 | 10.26434/chemrxiv-2021-kl8rf | Computational Design of Stapled Peptide Inhibitor against SARS-CoV-2 Receptor Binding Domain | Since its first detection in 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been the cause of millions of deaths worldwide. Despite the development and administration of different vaccines, the situation is still worrisome as the virus is constantly mutating to produce newer variants some of which are highly infectious. This raises an urgent requirement to understand the infection mechanism and thereby design therapeutic-based treatment for COVID-19. The gateway of the virus to the host cell is mediated by the binding of the Receptor Binding Domain (RBD) of the virus spike protein to the Angiotensin-Converting Enzyme 2 (ACE2) of the human cell. Therefore, the RBD of SARS-CoV-2 can be used as a target to design therapeutics. The α1 helix of ACE2 which forms direct contact with the RBD surface has been used as a template in the current study to design stapled peptide therapeutics. Using computer simulation, the mechanism and thermodynamics of the binding of six stapled peptides with RBD have been estimated. Among these, the one with two lactam stapling agents has shown binding affinity, sufficient to overcome RBD-ACE2 binding. Analyses of the mechanistic detail reveal that a reorganization of amino acids at the RBD-ACE2 interface produces favorable enthalpy of binding whereas conformational restriction of the free peptide reduces the loss in entropy to result in higher binding affinity. The understanding of the relation of the nature of the stapling agent with their binding affinity opens up the avenue to explore stapled peptides as therapeutic against SARS-CoV-2. | Asha Rani Choudhury; Atanu Maity; Sayantani Chakraborty ; Rajarshi Chakrabarti | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cc8c56d6dcc20535490815/original/computational-design-of-stapled-peptide-inhibitor-against-sars-co-v-2-receptor-binding-domain.pdf |
60c7483c0f50db7f06396734 | 10.26434/chemrxiv.11862900.v1 | Anion Templated Crystal Engineering of Halogen Bonding Tripodal Tris(halopyridinium) Compounds | <div>In this work four new tripodal tris(halopyridinium) receptors containing potentially halogen</div><div>bonding groups were prepared. The ability of the receptors to bind anions in competitive</div><div>CD<sub>3</sub>CN/d<sub>6</sub>-DMSO was studied using <sup>1</sup>H NMR titration experiments, which revealed that the</div><div>receptors bind chloride anions more strongly than more basic acetate or other halide ions.</div><div>The solid state self–assembly of the tripodal receptors with halide anions was investigated by</div><div>X-ray crystallography. The nature of the structures was dependent on the choice of halide</div><div>anion, as well as the crystallisation solvent. Halogen bond lengths as short as 80% of the sum</div><div>of the van der Waals radii were observed, which is shorter than any halogen bonds involving</div><div>halopyridinium receptors in the Cambridge Structural Database.</div> | Emer Foyle; Nicholas White | Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.); Crystallography – Inorganic; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7483c0f50db7f06396734/original/anion-templated-crystal-engineering-of-halogen-bonding-tripodal-tris-halopyridinium-compounds.pdf |
6414a71e2bfb3dc251ef6e27 | 10.26434/chemrxiv-2023-1zzs0 | Enhancement of CO2 adsorption on activated carbons produced from avocado seeds by combined solvothermal carbonization and thermal KOH activation | A new strategy for ultramicroporous activated carbons production from avocado seeds was developed. Combined solvothermal carbonization and thermal KOH activation was conducted. Solvothermal carbonizations were performed in a stainless-steel autoclave lined with Teflon at the temperature of 180oC for 12 hours in three different liquids (water, methanol, isopropyl alcohol). Chars were activated by KOH. The carbonization combined with activation took place in the oven at 850 oC for one hour. All the samples were very good CO2 sorbents. The highest CO2 adsorption at a pressure of 1 bar was achieved for activated carbon produced using isopropanol. The best carbon dioxide adsorption was equal to 6.47 mmol/g at 0oC and 4.35 mmol/g at 20 oC. | Joanna Siemak; Beata Michalkiewicz | Inorganic Chemistry; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6414a71e2bfb3dc251ef6e27/original/enhancement-of-co2-adsorption-on-activated-carbons-produced-from-avocado-seeds-by-combined-solvothermal-carbonization-and-thermal-koh-activation.pdf |
65f446a89138d231618557eb | 10.26434/chemrxiv-2024-cgxp1 | Porphyrin-decorated bistable rotaxanes: Molecular folding governs switchable singlet oxygen photoproduction | Bistable rotaxanes were used to develop pH-switchable systems for singlet dioxygen photoproduction. Based on the combination of a Zn(II)-tetraphenylporphyrin photosensitizer, which was attached to the macrocycle, and a black-hole-quencher, which was used as one of the rotaxane-stoppers, singlet oxygen production could be switched on/off ((Δ= 0.15/0.03) by the addition of base/acid. However, we found that only a sufficiently long linker between both stations on the thread enabled switchability, and that the direction of switching was inversed with regard to the original design. This unexpected behavior was attributed to intramolecular folding of the rotaxanes, as indicated by extensive theoretical calculations. This evidences the importance to take into account the conformational flexibility of large molecular structures when designing functional switchable systems. | Jan Riebe; Benedikt Bädorf; Sarah Löffelsender; Matias Ezequiel Gutierrez Suburu; María Belén Rivas Aiello; Cristian Alejandro Strassert; Stefan Grimme; Jochen Niemeyer | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f446a89138d231618557eb/original/porphyrin-decorated-bistable-rotaxanes-molecular-folding-governs-switchable-singlet-oxygen-photoproduction.pdf |
67dd556981d2151a02501490 | 10.26434/chemrxiv-2025-dpptg | Stress Distribution and Scaling Laws for Optimized Fluid Flow in Tree-Like Networks with Triangular Cross-Sections | This study presents an analytical framework for modeling Newtonian fluid flow in an equilateral triangular channel network with a self-similar tree-like structure. The network is characterized by varying bifurcation levels \(N\) and generation stages \(m\), with optimization based on two primary constraints: volume and surface area limitation. The study assumes fully developed laminar flow, neglecting secondary flow effects and junction losses. The analysis evaluates non-dimensional flow resistance \(\mathcal{R}\) and conductance \(E\), considering their dependence on the channel side ratio \(\beta\), length ratio \(\gamma\), bifurcation number \(N\), and branching levels \(m\). The results indicate that flow conductance decreases with increasing generation levels, with different scaling laws under volume and surface-area constraints. For volume constraints, the optimal width ratio follows \( \beta^* = N^{-1/3} \), leading to \( Q_k \propto a_k^3 \), whereas for surface-area constraints, the scaling follows \( \beta^* = N^{-2/5} \), yielding \( Q_k \propto a_k^{5/2} \), where $a$ is the length of the side of triangular channel. Stress distribution in the conduit exhibits symmetry, with higher stresses near the walls. As generation levels increase, stress magnitudes reduce more significantly under surface-area constraints compared to volume constraints. This study excludes junction flow resistance and secondary flows, which can further refine the model. The findings extend Murray’s Law to equilateral triangular networks, offering insights into optimal flow structures and paving the way for applications in fluidic engineering. | Ashish Garg | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd556981d2151a02501490/original/stress-distribution-and-scaling-laws-for-optimized-fluid-flow-in-tree-like-networks-with-triangular-cross-sections.pdf |
64542f4f07c3f02937394e16 | 10.26434/chemrxiv-2023-rpcn4 | Formulation of a Target Plastic Model to estimate critical plastic burdens of toxicants. | Plastic pollution has become a widespread problem affecting multiple environmental compartments, with associated chemicals having harmful effects on living organisms. Here, we developed a Target Plastic Model (TPM) to estimate the critical plastic burden of various toxicants in five types of plastics, namely polydimethylsiloxane (PDMS), polyoxymethylene (POM), polyacrylate (PA), low-density polyethylene (LDPE), and polyurethane ester (PU), following the Target Lipid Model (TLM) framework. The critical plastic burdens of baseline (n=115), less-inert (n=73), and reactive (n=75) toxicants ranged from 0.17-51.33, 0.04-26.62, and 1.00 × 10^-6 - 6.78 × 10^-4 mmol/kg of plastic, respectively. While critical plastic burdens were also estimated for other plastic phases, such as polypropylene (PP), polystyrene (PS), polyvinyl chloride (PVC), ultra-high molecular weight polyethylene (UHMWPE), and high-density polyethylene (HDPE), the findings were less reliable due to a lack of experimental data. Our study showed that PDMS, PA, POM, PE, and PU are similar to biomembranes in mimicking the exchange of chemicals with the water phase. Using the TPM, median lethal concentration (LC50) values for fish exposed to baseline toxicants were predicted, and the results agreed with experimental values, with RMSE ranging from 0.311-0.538 log unit. For less inert chemicals, predictions were within a factor of 5 of experimental values. The TPM's performance was comparable to other widely used models, such as the TLM, ECOSAR, and Abraham Solvation Model. However, like other models, TPM was not effective in predicting the toxicities of reactive toxicants, with RMSE exceeding 1 log unit. TPM can provide valuable insights into the toxicities of chemicals associated with environmental plastic phases, assisting in selecting the best polymeric phase for passive sampling and designing better passive dosing techniques for toxicity experiments. Moreover, TPM can assist in selecting the best plastic phase for developing animal alternatives for toxicity measurement and determining the toxicity of complex mixtures such as those arising during oil spills. | Deedar Nabi; Aaron J. Beck; Eric P. Achterberg | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64542f4f07c3f02937394e16/original/formulation-of-a-target-plastic-model-to-estimate-critical-plastic-burdens-of-toxicants.pdf |
60c752cbbdbb89e3f4a3a362 | 10.26434/chemrxiv.13352324.v1 | Microfluidics Featuring Multilayered Hydrogel Assemblies Enable Real-Time NMR-Monitoring of Enzyme Cascade Reactions | Compartmentalized chemical reactions at the microscale are interesting from many perspectives including (multi)functional surfaces and biotechnology. Monitoring the molecular content as a measure of functional performance at these small scales is challenging. As a means to address this challenge, we leverage microtechnology and biocompatible materials to integrate a compact, reconfigurable reaction cell featuring electrochemical functionality with high-resolution nuclear magnetic resonance spectroscopy (NMR). We demonstrate the operation of this system by monitoring the activity of enzymes immobilized in chemically distinct layers within a multi-layered chitosan hydrogel assembly. As a benchmark, we observed the parallel activities of urease (Urs), catalase (Cat), and glucose oxidase (GOx) by recording NMR spectra to extract reagent and product concentrations in real-time. As a result, simultaneous monitoring of a cooperative enzymatic process (GOx + Cat) together with an independent process (Urs) is achieved. Using Michaelis-Menten progress curve analysis of the NMR data, kinetic data is extracted: in the case of GOx, the Michaelis constants (K<sub>M</sub>) are consistent with previous reports, while for Urs, deviations are observed, attributed to an inhibitory effect under our reaction conditions. The system therefore enables the construction of complex reaction cascades with spatial control, as would be interesting in, for example, metabolic engineering and multiplexed sensing applications. | Nurdiana Nordin; lorenzo bordonali; Hossein Davoodi; Novindi Dwi Ratnawati; Gudrun Gygli; Jan G. Korvink; Vlad Badilita; Neil MacKinnon | Aggregates and Assemblies; Multilayers; Spectroscopy (Anal. Chem.); Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752cbbdbb89e3f4a3a362/original/microfluidics-featuring-multilayered-hydrogel-assemblies-enable-real-time-nmr-monitoring-of-enzyme-cascade-reactions.pdf |
6630440291aefa6ce1c5afd5 | 10.26434/chemrxiv-2024-ctv9p | Design and Manufacturing of Exact Electrospinning Collector | The production of nanofibers has attracted a lot of attention; one of the methods of producing nanofibers is electrospinning, which creates Nano-diameter fibers by applying electric force, which is due to the simplicity of the process, low cost, and the ability to use a wide range of materials, it can replace many manufacturing methods. The applications of nanofibers produced by electrospinning include tissue engineering, energy, filtration, and sensors.
One of the main components of electrospinning is its collector; the produced fibers are collected on this part. The characteristics of this part of the device have many effects on the obtained fibers. Various types of collectors are made and used for multiple applications. Inspired by how 3D printers work, a collector consists of a movable plate that can move in two dimensions and a needle electrode that focuses the fibers on the desired area, according to the movement of the plate, which can create fibers with the desired design. | Kvan Jelodare; Afra Hadjizadeh; Alireza Khodabandeh | Polymer Science; Nanoscience; Nanofabrication; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630440291aefa6ce1c5afd5/original/design-and-manufacturing-of-exact-electrospinning-collector.pdf |
60c75757337d6c869be29002 | 10.26434/chemrxiv.14394602.v1 | Chemoselective Electrosynthesis Using Rapid Alternating Polarity | <div><div><div><p>Challenges in the selective manipulation of functional groups (chemoselectivity) in organic synthesis have historically been overcome using either reagents/catalysts that tunably interact with a substrate or through modification to shield undesired sites of reactivity (protecting groups). Although electrochemistry offers precise redox control to achieve unique chemoselectivity, this approach often becomes challenging in the presence of multiple redox-active functionalities. Historically, electrosynthesis has been performed almost solely by using direct current (DC). In contrast, utilization of alternating current (AC) has been considered as an option to improve reaction efficiency rather than a way to achieve distinctly different reaction outcomes. Here we show how a unique type of waveform employed to deliver electric current – rapid alternating polarity (rAP) – enables control over reaction outcomes in the chemoselective reduction of carbonyl compounds, one of the most widely used reaction manifolds. The reactivity observed cannot be recapitulated using DC electrolysis or chemical reagents. The synthetic value brought by this new method for controlling chemoselectivity is vividly demonstrated in the context of classical reactivity problems such as chiral auxiliary removal and cutting-edge medicinal chemistry topics such as the synthesis of PROTACs.</p></div></div></div> | Yu Kawamata; Kyohei Hayashi; Ethan Carlson; Shobin Shaji; Dirk Waldmann; Bryan Simmons; Jacob Edwards; Christoph Zapf; Masato Saito; Phil Baran | Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75757337d6c869be29002/original/chemoselective-electrosynthesis-using-rapid-alternating-polarity.pdf |
60c73df9469df43f99f427c5 | 10.26434/chemrxiv.6241913.v1 | Nitroxyl Modified Tobacco Mosaic Virus as a Metal-Free High-Relaxivity MRI and EPR Active Superoxide Sensor | Superoxide overproduction is known to occur in
multiple disease states requiring critical care yet non-invasive detection of
superoxide in deep tissue remains a challenge. Herein, we report a metal-free
magnetic resonance imaging (MRI) and electron paramagnetic resonance (EPR)
active contrast agent prepared by “click conjugating” paramagnetic organic
radical contrast agents (ORCAs) to the surface of tobacco mosaic virus (TMV).
While ORCAs are known to be reduced <i>in vivo</i>
to an MRI/EPR silent state, their oxidation is facilitated specifically by
reactive oxygen species—in particular superoxide—and are largely unaffected by
peroxides and molecular oxygen. Unfortunately, single molecule ORCAs typically
offer weak MRI contrast. In contrast, our data confirm that the macromolecular
ORCA-TMV conjugates show marked enhancement for <i>T<sub>1</sub></i> contrast at low field (<3.0 T), and <i>T<sub>2</sub></i> contrast at high field
(9.4 T). Additionally, we demonstrated that the unique topology of TMV allows
for “quenchless fluorescent” bimodal probe for concurrent fluorescence and
MRI/EPR imaging, which was made possible by exploiting the unique inner and
outer surface of the TMV nanoparticle. <a>Finally, we show
TMV-ORCAs do not respond to normal cellular respiration, minimizing the
likelihood for background, yet still respond to enzymatically produced
superoxide in complicated biological fluids like serum.</a> | Madushani Dharmarwardana; André F. Martins; Zhuo Chen; Philip M. Palacios; Chance M. Nowak; Raymond P. Welch; Shaobo Li; Michael A. Luzuriaga; Leonidas Bleris; Brad S. Pierce; A. Dean Sherry; Jeremiah J. Gassensmith | Bioorganic Chemistry; Cell and Molecular Biology | CC BY NC 4.0 | CHEMRXIV | 2018-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73df9469df43f99f427c5/original/nitroxyl-modified-tobacco-mosaic-virus-as-a-metal-free-high-relaxivity-mri-and-epr-active-superoxide-sensor.pdf |
67dd9cd96dde43c908c035d1 | 10.26434/chemrxiv-2025-t5d50 | Elucidating the Geometric and Electronic Structure of a Fully Sulfided Analog of an Anderson Polyoxomolybdate Cluster | The biological activity of transition metal sulfide (TMS) clusters in enzymatic reactions, small molecule reduction, and charge transfer has sparked interest in designing novel TMS clusters for reductive catalysis and other chemical and materials applications. Polyoxometalates (POMs), known for their diverse structures, can be formed into TMS clusters, but these have seldom been isolated in the fully sulfided state, likely due to the tendency of uncapped TMS clusters to agglomerate. Here, we report the geometric and electronic structure of a capping ligand-free fully sulfided analog of heptamolybdate Anderson POM [MoVI7O24]6–, synthesized through the sulfidation of a nanoconfined POM secured within a porous Zr-metal organic framework (NU-1000). A combined computational and experimental analysis indicates that the sulfided counterpart of the Anderson POM is geometrically and electronically more sophisticated than the parent POM. Comparison of experimental pair distribution function (PDF) data with computationally simulated structures confirms that, unlike only oxygen anions in [MoVI7O24]6– cluster, the [MoIV7(3-S)6(2-SH)6(S2)6]2– polythiometalate (PTM) contains various sulfur anions (S2–, HS–, S22–). DFT calculations show that H2S acts as a reducing agent and along with the presence of terminal disulfides (S22–) in the PTM’s structure converts all seven Mo(VI) of the parent POM into seven Mo (IV) in the PTM. X-ray photoelectron spectroscopy (XPS) confirms the presence of Mo (IV) in the PTM cluster. | S. M. Gulam Rabbani; Zhihengyu Chen; Jingyi Sui; Joseph Hupp; Karena Chapman; Rachel Getman | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd9cd96dde43c908c035d1/original/elucidating-the-geometric-and-electronic-structure-of-a-fully-sulfided-analog-of-an-anderson-polyoxomolybdate-cluster.pdf |
673b46ab7be152b1d07caf72 | 10.26434/chemrxiv-2024-0f2t4 | Biomass-based sustainable covalent organic framework (COF) anode for high-performance LIBs | COFs with reversible redox behaviours are promising lithium-ion batteries (LIBs) electrode materials. However, traditional COFs are synthesized from organic monomers primarily derived from fossil fuels, significantly hindering the sustainable development of COF materials. In this study, a novel proof-of-concept COF, named COF@bio, was constructed using two biomass-derived monomers under mild conditions and through a simple synthesis process, aligning with the principles of green sustainable development and showing potential for large-scale preparation. The COF@bio-40 was in-situ grown on carbon nanotubes (CNT) to enhance electronic conductivity. Consequently, COF@bio-40 exhibited satisfactory long-cycle performance and excellent high-rate capability. During the long cycle process, the maximum specific capacity of COF@bio-40 reached 804 mAh g⁻¹ (at 2,000 mA g⁻¹), significantly surpassing most previous reports and commercial graphite anodes. Analysis using X-ray photoelectron spectroscopy (XPS) of the anode during charge and discharge processes, DFT, and capacity contribution revealed that the storage mechanism is governed by 11-electron redox chemistry for the COF monomer, with one lithium ion per benzene ring, one lithium ion per furan ring, and one lithium ion per imine linkage. This work may pave the way for constructing biomass-based sustainable organic electrodes with high performance for organic rechargeable batteries. | Changyu Weng; Hongmei Yuan; Yuxin Ji; Weidong Liu; Longlong Ma; Jianguo liu | Organic Chemistry; Energy; Organic Compounds and Functional Groups; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673b46ab7be152b1d07caf72/original/biomass-based-sustainable-covalent-organic-framework-cof-anode-for-high-performance-li-bs.pdf |
60c74f40702a9b7b1318bb43 | 10.26434/chemrxiv.12867308.v1 | Molecular Docking Studies of Aromatherapy Oils Against SARS-COV-2 | <div>Emerging from Wuhan, China in December 2019, the SARS-CoV-2 virus has spread rapidly, prompting an immediate international response to contain the disease. In this paper, the most abundant volatile compounds in household aromatherapy ointments, namely, methyl salicylate, eucalyptol, α-pinene, menthol, camphor, linalool, and trans-pinocarveol were docked to key structures in SARS-CoV-2 invasion: its spike protein, and the human ACE2 and TMPRSS2 proteins. Based on the molecular docking results, the essential oil compounds methyl salicylate, eucalyptol, and α-pinene exhibit favorable binding to ACE2 and spike proteins. These compounds may be considered for clinical investigation.</div> | Maurice De Jesus; Jokent Gaza; Hiyas A. Junio; Ricky Nellas | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f40702a9b7b1318bb43/original/molecular-docking-studies-of-aromatherapy-oils-against-sars-cov-2.pdf |
61b34aad02d90dca2e5c6575 | 10.26434/chemrxiv-2021-hzkzn | Visible-Light-Mediated Photocatalytic Selective N-Methylation of Amines using CO2 under mild reaction condition via NH2-MIL-125 (Ti) MOF catalyst | We herein describe a facile synthesis method of novel NH2-MIL-125 (Ti) metal organic framework as a photocatalyst, and the photochemical system was firstly developed for the direct N-methylation of amines under very mild reaction conditions of one bar CO2 and NaBH4. According to the optimization of reaction conditions, the selective synthesis of methylamines is achieved in good to excellent conversion and selectivity using visible light mediated photocatalytic system. | Jianguo liu; Xiuzhi Wei; Longlong Ma | Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b34aad02d90dca2e5c6575/original/visible-light-mediated-photocatalytic-selective-n-methylation-of-amines-using-co2-under-mild-reaction-condition-via-nh2-mil-125-ti-mof-catalyst.pdf |
6537e2fe87198ede072ce2ab | 10.26434/chemrxiv-2023-pk99f | Generalizing asymmetric and pseudo-Voigt functions by means of q-Gaussian Tsallis functions to analyze the wings of Raman spectral bands | It is important, for further applying the q-Gaussian Tsallis functions, to discuss how they can generalize asymmetric and pseudo-Voigtian functions. Some remarks about Voigt functions are also stressed, regarding the behavior of the wings of Raman spectral components. The use of Voigt and pseudo-Voigt functions implies the wings as Lorentzian, but this is not observed for the Raman bands. At the same time, the wings are not Gaussians, and for this reason q-Gaussians are fundamental for evidencing the wing behavior. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6537e2fe87198ede072ce2ab/original/generalizing-asymmetric-and-pseudo-voigt-functions-by-means-of-q-gaussian-tsallis-functions-to-analyze-the-wings-of-raman-spectral-bands.pdf |
64712636be16ad5c57f82221 | 10.26434/chemrxiv-2022-r3pkd-v2 | Origins of hydrogen peroxide selectivity during oxygen reduction on organic mixed ionic-electronic conducting polymers | Electrochemical reduction of atmospheric oxygen provides carbon emission-free pathways for the generation of electricity from chemical fuels and for the distributed production of green chemical oxidants like hydrogen peroxide. Recently, organic mixed ionic-electronic conducting polymers (OMIECs) have been reported as a new class of active electrode materials for the oxygen reduction reaction. This work sets out to identify the operative oxygen reduction mechanism of OMIECs through a multi-faceted experimental and theoretical approach. Using a combination of pH-dependent electrochemical characterization, operando UV-Vis and Raman spectroscopy, and ab initio calculations, we find that the n-type OMIEC, p(NDI-T2 P75), displays pH-dependent activity for the selective reduction of oxygen to the 2-electron hydrogen peroxide product. We use microkinetic simulations of the electrochemical behavior to rationalize our experimental observations through a polaron-mediated pathway involving chemical reduction of oxygen to the 1-electron superoxide intermediate followed by pH-dependent catalytic disproportionation to hydrogen peroxide. Finally, this pathway is applied to understand the experimental oxygen reduction reactivity of an expanded set of n- and p-type OMIECs. | Ana De La Fuente Durán; Allen Yu-Lun Liang; Ilaria Denti; Hang Yu; Drew Pearce; Adam Marks; Emily Penn; Karrie Weaver; Lily Turaski; Iuliana P. Maria; Sophie Griggs; Xingxing Chen; Alberto Salleo; William C. Chueh; Jenny Nelson; Alexander Giovannitti; J. Tyler Mefford | Materials Science; Catalysis; Polymer Science; Conducting polymers; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2023-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64712636be16ad5c57f82221/original/origins-of-hydrogen-peroxide-selectivity-during-oxygen-reduction-on-organic-mixed-ionic-electronic-conducting-polymers.pdf |
618022ea8ac7a23aac642014 | 10.26434/chemrxiv-2021-bx0wg | How to Characterize Amorphous Shapes: The Tale of a Reverse Micelle | Aerosol-OT reverse micelles represent a chemical construct where surfactant molecules self-assemble to stabilize water nanodroplets ~1-10 nm in diameter. Although commonly assumed to adopt a spherical shape, all-atom molecular dynamics simulations and some experimental studies predict a non-spherical shape. If these aggregates are not spherical, then what shape do they take? Because the tools needed to evaluate the shape of something that lacks regular structure, order, or symmetry are not well developed, we present a set of three intuitive metrics- coordinate-pair eccentricity, convexity, and the curvature distribution- that estimate the shape of an amorphous object and we demonstrate their use on a simulated Aerosol-OT reverse micelle. These metrics are all well-established methods and principles in mathematics, and each provides unique information about the shape. Together, these metrics provide intuitive descriptions of amorphous shapes, facilitate ways to quantify those shapes, and follow their changes over time. | Christopher Gale; Mortaza Derakhshani-Molayousefi; Nancy E. Levinger | Theoretical and Computational Chemistry; Physical Chemistry; Interfaces; Physical and Chemical Properties; Structure | CC BY NC 4.0 | CHEMRXIV | 2021-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618022ea8ac7a23aac642014/original/how-to-characterize-amorphous-shapes-the-tale-of-a-reverse-micelle.pdf |
60c74762bb8c1af9f03daa5a | 10.26434/chemrxiv.11639985.v1 | Enantiodivergent Formation of C–P Bonds: Synthesis of P-Chiral Phosphines and Methyl-phosphonate Oligonucleotides | <p>A simple limonene-derived P(V)-based reagent for the modular, scalable, and stereospecific synthesis of chiral phosphines and methyl-phosphonate oligonucleotide (MPO) building blocks is presented. Built on a translimonene oxide (TLO) core, this formally triply electrophilic reagent class displays starkly differing reactivity from the cis-limonene oxide derived reagents reported previously [dubbed phosphorus-sulfur incorporation reagents or Ψ (PSI) for short]. These new phosphorus-incorporation reagents (PI, abbreviated as Π) access distinctly different chemical space than Ψ. The P(V)-manifold disclosed herein permits the stereochemically controlled sequential addition of carbon-based nucleophiles (from one to three) to produce a variety of enantiopure C–P bearing building blocks. When three carbon nucleophiles are added, useful P-chiral phosphines can be accessed after stereospecific reduction. When a single methyl group is added, the remaining nucleophiles can be nucleosides thus opening the door to the first stereospecific access to MPO-based oligonucleotide building blocks. Although both enantiomers of Π are available, only one isomer is required as the order of nucleophile addition controls the absolute stereochemistry of the final product through a unique enantiodivergent design.</p> | Dongmin Xu; Nazaret Rivas-Bascón; Natalia M. Padial; Kyle W. Knouse; Bin Zheng; Julien C. Vantourout; Michael A. Schmidt; Martin Eastgate; Phil Baran | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74762bb8c1af9f03daa5a/original/enantiodivergent-formation-of-c-p-bonds-synthesis-of-p-chiral-phosphines-and-methyl-phosphonate-oligonucleotides.pdf |
63f62ddd32cd591f125169b8 | 10.26434/chemrxiv-2023-173tm | Aggregation-induced emission biomaterials for anti-pathogen medical applications: detecting, imaging and killing | Microbial pathogens, including bacteria, fungi, and viruses, greatly threaten the global public health. For pathogen infections, early diagnosis and precise treatment are essential to cut the mortality rate. The emergence of aggregationinduced emission (AIE) biomaterials provides an effective and promising tool for the theranostics of pathogen infections. In this review, the recent advances about AIE biomaterials for anti-pathogen theranostics are summarized. With the excellent sensitivity and photostability, AIE biomaterials have been widely applied for precise diagnosis of pathogens. Besides, different types of anti-pathogen methods based on AIE biomaterials will be presented in detail, including chemotherapy and phototherapy. Finally, the existing deficiencies and future development of AIE biomaterials for anti-pathogen applications will be discussed. | Zicong Zhang; Lixun Zhu; Ziwei Deng; Jialin Zeng; Xu-Min Cai; Zijie Qiu; Zheng Zhao; Ben Zhong Tang | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f62ddd32cd591f125169b8/original/aggregation-induced-emission-biomaterials-for-anti-pathogen-medical-applications-detecting-imaging-and-killing.pdf |
60c741269abda27641f8be32 | 10.26434/chemrxiv.7376081.v2 | Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification | <p>Correct calculation of the variation of free
energy upon base flipping is crucial in understanding the dynamics of DNA
systems. The free energy landscape along the flipping pathway gives the
thermodynamic stability and the flexibility of base-paired states. Although
numerous free energy simulations are performed in the base flipping cases, no
theoretically rigorous nonequilibrium techniques are devised and employed to
investigate the thermodynamics of base flipping. In the current work, we report
a general nonequilibrium stratification scheme for efficient calculation of the
free energy landscape of base flipping in DNA duplex. We carefully monitor the
convergence behavior of the equilibrium sampling based free energy simulation and
the nonequilibrium stratification and determine the empirical length of time
blocks required for converged sampling. Comparison between the performances of
equilibrium umbrella sampling and nonequilibrium stratification is given. The
results show that nonequilibrium free energy simulation is able to give similar
accuracy and efficiency compared with the equilibrium enhanced sampling technique
in the base flipping cases. We further test a convergence criterion we
previously proposed and it comes out that the convergence behavior determined
by this criterion agrees with those given by the time-invariant behavior of PMF
and the nonlinear dependence of standard deviation on the sample size. </p> | Xiaohui Wang; Zhaoxi Sun | Biophysics; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741269abda27641f8be32/original/determination-of-base-flipping-free-energy-landscapes-from-nonequilibrium-stratification.pdf |
60c755830f50db1d41397ef3 | 10.26434/chemrxiv.14115404.v1 | Thiol-methylsulfone-based Hydrogels for Cell Encapsulation: Reactivity Optimization of Aryl-methylsulfone Substrate for Fine-tunable Gelation Rate and Improved Stability | We present novel thiol-methylsulfone hydrogels for cell encapsulation applications. The reactivity of the methylsulfonyl reactive partner has been optimized to improve the properties of the derived hydrogels for cell encapsulation.<br /><b></b> | Julieta Paez; Adrián de Miguel-Jiménez; Rocío Valbuena-Mendoza; Aditi Rathore; Minye Jin; Alisa Gläser; Samuel Pearson; Aranzazu del Campo | Hydrogels | CC BY NC 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755830f50db1d41397ef3/original/thiol-methylsulfone-based-hydrogels-for-cell-encapsulation-reactivity-optimization-of-aryl-methylsulfone-substrate-for-fine-tunable-gelation-rate-and-improved-stability.pdf |
60c74872f96a00f219287080 | 10.26434/chemrxiv.11909397.v1 | Gas-Phase Oxidation of Reactive Organometallic Ions | Analysis of highly
reactive compounds at very low concentration in solution using electrospray
ionization mass spectrometry requires the use of exhaustively purified
solvents. It has generally been assumed that desolvation gas purity needs to be
similarly high, and so most chemists working in this space have relied upon
high purity gas. However, the increasingly competitiveness of nitrogen
generators, which provide gas purity levels that vary inversely with flow rate,
prompted an investigation of the effect of gas-phase oxygen on the speciation
of ions. For moderately oxygen sensitive species such as phosphines, no
gas-phase oxidation was observed. Even the most reactive species studied, the
reduced titanium complex [Cp<sub>2</sub>Ti(NCMe)<sub>2</sub>]<sup>+</sup>[ZnCl<sub>3</sub>]<sup>–</sup>
and the olefin polymerization precatalyst [Cp<sub>2</sub>Zr(µ-Me)<sub>2</sub>AlMe<sub>2</sub>]<sup>+</sup>
[B(C<sub>6</sub>F<sub>5</sub>)<sub>4</sub>]<sup>–</sup>, only exhibited
detectable oxidation when they were rendered coordinatively unsaturated through
in-source fragmentation. Computational chemistry allowed us to find the most
plausible pathways for the observed chemistry in the absence of observed
intermediates. The results provide insight into the gas-phase oxidation of
reactive species and should assure experimentalists that evidence of
significant oxidation is likely a solution rather than a gas-phase process,
even when relatively low-purity nitrogen is used for desolvation. | Anuj Joshi; Sofia Donnecke; Ori Granot; Dongju Shin; Scott Collins; Irina Paci; J Scott McIndoe | Kinetics and Mechanism - Inorganic Reactions; Organometallic Compounds; Theory - Inorganic; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74872f96a00f219287080/original/gas-phase-oxidation-of-reactive-organometallic-ions.pdf |
60c75801337d6c07c2e2912e | 10.26434/chemrxiv.14485002.v1 | Functional Group Introduction and Aromatic Unit Variation in a Set of π-Conjugated Macrocycles: Revealing the Central Role of Local and Global Aromaticity | π-Conjugated macrocycles are molecules with unique properties that are increasingly exploited for applications and the question of whether they can sustain global aromatic or antiaromatic ring currents is particularly intriguing. However, there are only a small number of experimental studies that investigate how the properties of π-conjugated macrocycles evolve with systematic structural changes. Here, we present such a systematic experimental study of a set of [2.2.2.2]cyclophanetetraenes, all with formally Hückel antiaromatic ground states, and combine it with an in-depth computational analysis. The study reveals the central role of local and global aromaticity for rationalizing the observed optoelectronic properties, ranging from extremely large Stokes shifts of up to 1.6 eV to reversible fourfold reduction, a highly useful feature for charge storage/accumulation applications. A recently developed method for the visualization of chemical shielding tensors (VIST) is applied to provide unique insight into local and global ring currents occurring in different planes along the macrocycle. Conformational changes as a result of the structural variations can further explain some of the observations. The study contributes to the development of structure–property relationships and molecular design guidelines and will help to understand, rationalize, and predict the properties of other π-conjugated macrocycles. | Martina Rimmele; Wojciech Nogala; Maryam Seif-Eddine; Maxie M. Roessler; Martin Heeney; Felix Plasser; Florian Glöcklhofer | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Carbon-based Materials; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75801337d6c07c2e2912e/original/functional-group-introduction-and-aromatic-unit-variation-in-a-set-of-conjugated-macrocycles-revealing-the-central-role-of-local-and-global-aromaticity.pdf |
678a1edbfa469535b9611587 | 10.26434/chemrxiv-2025-7z8s7 | Fast photo-deactivation of chloride transport and cytotoxicity mediated by squaramides | The ability to control anion transporters with precision is crucial to maximise their therapeutic potential while mitigating collateral damage to healthy cells. Consequently, there is a growing interest in light-regulated anion transporters, which offer the advantage of spatio-temporal control over their activity. We have previously reported that the chloride transport activity of an electron-poor squaramide can be inhibited by UV irradiation (365 nm), probably due to the photo-transformation of the transporter. Herein we present a series of diaryl squaramides containing different electron-withdrawing substituents. Using liposome-based assays, all compounds, with similar chloride affinities, have shown to be active chloride transporters at a relatively low concentration (1:10k transporter-lipid ratio). We have studied the efficiency of the light-induced deactivation process, observing how the nature of the electron-withdrawing groups on the aryl rings has a strong effect on the time of irradiation required to completely inhibit the transport activity of the compounds. Remarkably, efficient deactivations have been observed with cyano-substituted squaramides, which have showed complete loss of activity after only 1-2 s of irradiation. Finally, we have performed cell viability studies that show how the cytotoxicity of squaramides can be reduced by irradiation, which can be attributed to the deactivation of an anion transport process in the cell membrane. | Bartomeu Galmés; Manel Vega; Fatima Amine; Atonio Costa; Carmen Rotger; Luis Martínez-Crespo | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Supramolecular Chemistry (Org.); Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a1edbfa469535b9611587/original/fast-photo-deactivation-of-chloride-transport-and-cytotoxicity-mediated-by-squaramides.pdf |
6488c0da4f8b1884b73f357a | 10.26434/chemrxiv-2023-tbvsv | Unlocking Tertiary Acids for Metallaphotoredox C(sp2)-C(sp3) Decarboxylative Cross-Couplings | Dual nickel photoredox catalysis conditions have been developed for the decarboxylative cross-coupling of aryl halides and carboxylic acids containing fully substituted alpha carbons, a valuable but challenging substrate class for C(sp2)–C(sp3) bond-forming reactions. High-throughput experimentation identified Ni(TMHD)2 as the optimal precatalyst for this reaction in contrast to the nickel-bipyridyl complexes typically employed in decarboxylative couplings, which predominantly furnished undesired C–O products. Computational work provides insight into the potential mechanistic underpinnings for the C–C vs. C–O selectivity for the nickel-diketonate complex. | Junqing Guo; Derek Norris; Antonio Ramirez; Jack L. Sloane; Eric M. Simmons; Jacob M. Ganley; Martins S. Oderinde; T. G. Murali Dhar; Geraint H. M. Davies; Trevor C. Sherwood | Organic Chemistry; Catalysis; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6488c0da4f8b1884b73f357a/original/unlocking-tertiary-acids-for-metallaphotoredox-c-sp2-c-sp3-decarboxylative-cross-couplings.pdf |
60c74a040f50db05673969c3 | 10.26434/chemrxiv.12136782.v1 | Gold-Catalyzed Spirocyclization Reactions of N-Propargyl Tryptamines and Tryptophans in Aqueous Media | N-Propargyl tryptamine and tryptophan derivatives that are readily available from both synthetic and biocatalytic approaches, undergo gold-catalyzed dearomative cyclizations in aqueous media to the corresponding spirocyclic derivatives. In addition to the efficiency of the method, operating in aqueous media affords a selective entry to C2-unsubstituted spiroindolenines that have long remained unattainable by Au(I)-catalysis. Moderate to excellent yields of the desired spirocyclic products bearing various substituents were obtained. <br /> | Nazarii Sabat; Feryel Soualmia; Pascal Retailleau; Alhosna Benjdia; Olivier Berteau; Xavier Guinchard | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a040f50db05673969c3/original/gold-catalyzed-spirocyclization-reactions-of-n-propargyl-tryptamines-and-tryptophans-in-aqueous-media.pdf |
6721e7215a82cea2fa4debeb | 10.26434/chemrxiv-2024-x3sh7 | Study of the Mechanical Recycling Process of Electric Motors for the Recovery and Valorization of NdFeB Magnet Content | The demand for NdFeB permanent magnets, known as the strongest permanent magnets on the market, is projected to rise significantly. These magnets, made from rare earth elements (REEs) such as neodymium (Nd), praseodymium (Pr), and dysprosium (Dy), are essential for various high-tech applications, including electric motors for e-mobility, wind turbines, electronics, and air conditioners. However, their production is heavily reliant on REEs—classified as critical raw materials in the EU due to limited geographic availability and supply risks. Over 60% of global REE production occurs in China, which also controls 91% of REEs refinement and 94% of the permanent magnet market. Given Europe’s lack of internal REEs production and refining capabilities, this dependency on Chinese imports poses a supply risk. To address this problem, Europe must establish alternative REE sources, either by exploiting local mines or implementing recycling. Projections indicate that by 2050, recycling could potentially meet up to 75% of Europe’s REE demand. However, current recycling efforts are limited, with less than 1% of REEs being recovered. This study aims to investigate a recycling method capable of recovering REEs, particularly from NdFeB magnets embedded within electric motors from e-mobility. The focus centers on a mechanical pretreatment approach that combines shredding with physical separation techniques, such as magnetic separation. The primary objective is to isolate a NdFeB-enriched fraction—a material stream containing a substantially higher concentration of NdFeB magnets than the original motor composition. An industrial-scale trial was conducted on electric motors that were initially thermally demagnetized. This demagnetization step is crucial to mitigate issues related to magnet agglomeration during subsequent mechanical processing. The demagnetized motors were then shredded and processed via magnetic separation within an industrial facility. The separated fractions were subjected to laboratory pretreatment, involving sample homogenization, sieving, and magnetic attraction, to concentrate the NdFeB content. The samples were analyzed through MP-AES to quantify the REE content, including Nd, Pr, Ce, Dy, and Gd. This data provided insights into the enrichment of NdFeB magnets in the treated fraction. A material flow analysis (MFA) was conducted to assess the distribution of magnets throughout the process. The MFA revealed that 71.3% of magnets entering the treatment facility were retained in the ferrous fraction, while 28.3% were found in the non-ferrous fraction. The ferromagnetic properties of the NdFeB magnets facilitated their attraction to the magnetic separator, enhancing the concentration of magnets in the ferrous fraction. A significant increase was observed in the magnet concentration in the non-ferrous fraction after additional magnetic separation, with the concentration rising from 9.47% in the initial non-ferrous fraction to 50.8% in the final attracted fraction. The findings of the study provided key information for the future design of an optimized mechanical pretreatment process that could achieve both a higher concentration of NdFeB magnets and an improved process yield. | Gianluca Torta; Leonardo Sparascio; Luca Ciacci; Ivano Vassura; Fabrizio Passarini | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Wastes; Industrial Manufacturing; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6721e7215a82cea2fa4debeb/original/study-of-the-mechanical-recycling-process-of-electric-motors-for-the-recovery-and-valorization-of-nd-fe-b-magnet-content.pdf |
645c45abfb40f6b3ee5fc05e | 10.26434/chemrxiv-2022-28rkk-v2 | The Mechanistic Basis for the Oxoammonium Salt Mediated Tertiary Alcohol Oxidative Transformation Decoded by Computations: Oxoammonium Cation Acts as a Masked Carbocation, and the Previously Believed Addition Mechanism is Ruled Out | Oxoammonium salts have been shown to be superior reagents to mediate various reactions of tertiary alcohols, including eliminative functionalization of tertiary benzylic alcohols, oxidative rearrangement of tertiary allylic alcohols, and oxidative Nazarov cyclization. These reactions have been believed to be triggered by the addition of alcohols to the N–O double bonds of the oxoammonium cation for a long time. In this work, however, combined density functional theory (DFT) and ab-initio molecular dynamics (AIMD) results show that the formation of this adduct is thermodynamically highly disfavored. Instead, through a thorough enumeration of possible mechanisms, it has been shown that the reaction occurs through a surprising ring-opening of oxoammonium cation. The oxoammonium cation acts as a masked tertiary carbocation, which triggers all the following reactions. The computational results were further supported by control experiments and High-Resolution Mass-Spectroscopy (HR-MS) characterization. | Yumiao Ma | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645c45abfb40f6b3ee5fc05e/original/the-mechanistic-basis-for-the-oxoammonium-salt-mediated-tertiary-alcohol-oxidative-transformation-decoded-by-computations-oxoammonium-cation-acts-as-a-masked-carbocation-and-the-previously-believed-addition-mechanism-is-ruled-out.pdf |
61941a8e64a707355272903d | 10.26434/chemrxiv-2021-rvrqv | A Practical and Economical Route to (S)-Glycidyl Pivalate | An efficient method to prepare enantiopure (S)-glycidyl pivalate from (R)-epichlorohydrin and pivalic acid is
reported. This work provides an alternative to the synthesis of this important building block from readily available and inexpensive
materials. | Jeffrey M. Noble; Le Chang; Dan Chen; Binglin Wang; Raymond N. Dominey; Daniel W. Cook; Justina M. Burns; Rodger W. Stringham; Flavio S. P. Cardoso; David R. Snead | Organic Chemistry; Process Chemistry | CC BY 4.0 | CHEMRXIV | 2021-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61941a8e64a707355272903d/original/a-practical-and-economical-route-to-s-glycidyl-pivalate.pdf |
677d8956fa469535b91e263e | 10.26434/chemrxiv-2025-qs33s | Deciphering the unique mechanism whereby bis-sulfonamido-2-phenylbenzoxazole (PBZ) GroEL/ES inhibitors modulate chaperonin ATPase and client protein folding functions. | We previously reported a series of bis-sulfonamido-2-phenylbenzoxazole (PBZ) inhibitors of GroEL/ES and HSP60/10 chaperonin systems that exhibited potent antibiotic effects against bacteria and Trypanosoma brucei parasites, and chemotherapeutic effects against colorectal cancer cells. However, the mechanisms of action of these inhibitors at the protein level and their relative impact on folding in bacterial versus human cells remained unknown. In this study, cryoEM analyses identified a set of 7-fold symmetrical inhibitor binding sites at the GroEL ring-ring interface (RRI). In addition, LC-MS/MS analyses identified two sets of binding sites at the apical domains and the ATP pockets. These findings, coupled with results from biochemical assays evaluating a small panel of PBZ-based inhibitors, allowed the development of a unique mechanistic model that explains how PBZ binding at the three sites modulates the ATPase and client protein folding functions of E. coli GroEL/ES. Screening of our diversity set of structurally distinct GroEL/ES inhibitors highlighted the unique mechanism of PBZ compounds binding to the RRI and disrupting the intra- and inter-ring allostery governing chaperonin function. We further developed complementary intravital reporter assays to measure the targeting of GroEL/ES in S. aureus bacteria and HSP60/10 in the mitochondria of human embryonic kidney (HEK) 293 cells. Compound screening using these assays support the differential engagement of PBZ analogs with chaperonins in bacteria and/or human cells. Together, these results provide a more detailed molecular basis for the findings from our companion study by Godek et al. that elucidated on-target functions of our lead analog, PBZ1038 (compound 1), against GroEL in E. coli. The inhibition model developed here will be invaluable for interpreting the mechanisms of new inhibitors and generating more potent and selective analogs as antibacterial candidates. | Mckayla Stevens; Emma Doud; Javiera Norambuena; Katelyn Tepper; Haddie DeHart; Carlee A. Trindl; Richard Carpenter; Eli Chapman; Jeffrey M. Boyd; Clark Wells; Qiuyan Chen; Steven M. Johnson | Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d8956fa469535b91e263e/original/deciphering-the-unique-mechanism-whereby-bis-sulfonamido-2-phenylbenzoxazole-pbz-gro-el-es-inhibitors-modulate-chaperonin-at-pase-and-client-protein-folding-functions.pdf |
60c73e51ee301cec6ac786e1 | 10.26434/chemrxiv.6789326.v1 | Chemical Accuracy in Modeling Halide Ion Hydration from Many-Body Representations | <div>
<div>
<div>
<p>Despite the key role that ionic solutions play in several natural and industrial processes,
a unified, molecular-level understanding of how ions affect the structure and dynamics
of water across different phases remains elusive. In this context, computer simulations
can provide new insights that are difficult, if not impossible, to obtain by other means.
However, the predictive power of a computer simulation directly depends on the level
of “realism” that is used to represent the underlying molecular interactions. Here, we
report a systematic analysis of many-body effects in halide-water clusters and
demonstrate that the recently developed MB-nrg full-dimensional many-body potential
energy functions achieve high accuracy by quantitatively reproducing the individual
terms of the many-body expansion of the interaction energy, thus opening the door to
realistic computer simulations of ionic solutions.
</p>
</div>
</div>
</div> | Paesani Lab; Pushp Bajaj; Marc Riera | Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Quantum Mechanics; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e51ee301cec6ac786e1/original/chemical-accuracy-in-modeling-halide-ion-hydration-from-many-body-representations.pdf |
6397800c7b7c91617eeedeed | 10.26434/chemrxiv-2022-mhlff | Li+ Conduction in Glass-forming Single-ion Conducting Polymers with and without Ion Clusters Studied in the Impedance Frequency Regime | Single-ion conducting polymer electrolytes have been studied for their advantages such as high transference number, lower interfacial resistance with electrodes, and ability to accommodate low-cost manufacturing for battery applications. However, amorphous poly(ethylene oxide) (PEO) and related electrolytes are limited by their ion transport rate that is coupled with -EO- segmental motion. Polymer electrolytes with ion-clusters can potentially provide fast transport in ion-channels, because the ion cluster phase is ionophilic and its energy landscape is continuous. In this contribution, we report on single-ion conducting polymers with varying polymer backbone types that contain delocalized tethered anions (-sulfonyl(trifluoromethylsulfonyl)imide (-TFSI-)) prepared from side-chain monomers capable of free-radical polymerization. The polymer backbone type is found to have strong implications for ion aggregation and nanoscale morphology. The new side-chain ionic polymer with non-polar backbone (polystyrene derivative) is found to self-assemble with lamellar ordering of nanoscale ion clusters. Meanwhile, side-chain ionic polymers with polar backbones (polyacrylate and polymethacylate derivatives) were found to be less ordered and were compared to the former to generate insight on ion transport mechanisms. We show that, in the impedance frequency regime, regardless of the ion aggregation morphology that the ionic conductivity is related to α relaxation which is similar to glass-forming liquids, though with certain degrees of decoupling. Nonetheless, these results do not preclude that fast cation dynamics exist locally in the ion cluster phase. | Jiacheng Liu; Jennifer Schaefer | Materials Science; Polymer Science; Energy; Liquid Crystals; Polymer morphology; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6397800c7b7c91617eeedeed/original/li-conduction-in-glass-forming-single-ion-conducting-polymers-with-and-without-ion-clusters-studied-in-the-impedance-frequency-regime.pdf |
60c73e18702a9b30da189ce4 | 10.26434/chemrxiv.6667496.v1 | Solar Electrochemical Thermal Process (STEP) Ammonia: Optimization of the Electrolysis Conditions | In the solar thermal electrochemical process (STEP), sunlight is split
into visible (for photovoltaic electricity) and thermal (unused, sub-bandgap)
radiation using the full solar spectrum to efficiently drive high temperature
electrolyzes. Electrolysis conditions for STEP ammonia are investigated. A
mixed molten carbonate/hydroxide electrolyte with iron oxide catalyzes ammonia
formation from water (steam) and air (nitrogen) via an iron intermediate. The higher temperature required for
effective iron formation needs to be balanced by the lower temperature for
effective hydration of the electrolyte. STEP ammonia is illustrated at a nickel
anode and steel cathode at 650 °C in Li<sub>1.6</sub>Ba<sub>0.3</sub>Ca<sub>0.1</sub>CO<sub>3</sub>
with 6m LiOH and 1.5m Fe<sub>2</sub>O<sub>3</sub>. | Fang-Fang Li; Richa Singhal; Jiawen Ren; Marcus Johnson; Matthew Lefler; Stuart Licht | Environmental Science; Electrocatalysis; Power | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e18702a9b30da189ce4/original/solar-electrochemical-thermal-process-step-ammonia-optimization-of-the-electrolysis-conditions.pdf |
620431b3a6fb4d0a2950892f | 10.26434/chemrxiv-2021-g0ktd-v2 | Multi-electron excitation contributions towards primary
and satellite states in the photoelectron spectrum | The computation of Dyson orbitals and corresponding ionization energies has been implemented
within the Equation of Motion Coupled Cluster Singles, Doubles and Perturbative Triples (EOMCC3)
method. Coupled to an accurate description of the electronic continuum via a time-dependent
density functional approach using a multicentric B-spline basis, this yields highly accurate photoionization
dynamical parameters (cross-sections, branching ratios, asymmetry parameters and dichroic
coefficients) for primary states (1h) as well as satellite states of (2h1p) character. Illustrative results
are presented for the molecular systems H2O, H2S, CS, CS2 and (S)-propylene oxide (a.k.a.
methyloxirane). | Torsha Moitra; Alexander C. Paul; Piero Decleva; Henrik Koch; Sonia Coriani | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620431b3a6fb4d0a2950892f/original/multi-electron-excitation-contributions-towards-primary-and-satellite-states-in-the-photoelectron-spectrum.pdf |
64270728db1a20696e4fc30b | 10.26434/chemrxiv-2023-v3vl0 | Enantioselective C–P Bond Formation through C(sp3)–H Functionalization | An unprecedented enantioselective C–P bond formation has been developed through a C(sp3)–H activation in an oxidation step followed by an organocatalyzed hydrophosphonylation protocol. The asymmetric organocatalytic Pudovik reaction has been successfully achieved following a one-pot strategy, starting from different benzylic alcohols and dibenzylphosphite, using MnO2 as the oxidant and a chiral squaramide as organocatalyst. The scope of the reaction provides enantiomerically enriched α-hydroxy phosphonates in good to excellent yields (up to >95%) and high enantioselectivities (up to >99%). Furthermore, the use of this methodology has been successfully demonstrated to form a quaternary centre, generating an acetophenone derivative in situ, using diphenyl phosphite. Therefore, this approach represents a highly effective strategy for constructing chiral C–P bonds, which are of significant interest to the pharmaceutical industry. This proof of concept represents a significant breakthrough in the field of chemistry. | Sandra Ardevines; Devan Horn; Juan V. Alegre-Requena; Marta González-Jiménez; M. Concepción Gimeno; Eugenia Marqués-López; Raquel P. Herrera | Organic Chemistry; Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64270728db1a20696e4fc30b/original/enantioselective-c-p-bond-formation-through-c-sp3-h-functionalization.pdf |
62829a4a59f0d6285e92b33e | 10.26434/chemrxiv-2021-v0d1j-v2 | Metal Halide Perovskite and Perovskite−like Materials Through the Lens of Ultra−wideline 35/37Cl NMR Spectroscopy | With their exceptional optoelectronic features, metal halide perovskites (MHPs) are pushing the next wave of energy−related materials research. Heretofore, most solid–state nuclear magnetic resonance (NMR) investigations have focused on readily accessible nuclei. In contrast, the halogen environments have been avoided due to their challenging quadrupolar nature. Here, we report a rapid 35/37Cl NMR strategy for MHPs, halide double perovskites (HDPs) and perovskite−inspired (PI) materials embracing ultra−wideline acquisition approaches at moderate and ultrahigh magnetic fields. The observed quadrupolar NMR parameters (CQ and η), supported by GIPAW−DFT computations, provide an analytical fingerprint revealing distinct features for chemically unique Cl environments sensitive to ion mixing, dimensionality, cell volume and Cl coordinating polyhedra. Moreover, we report resolution between two nearly identical and two distinct Cl environments of 3D and 2D Cs–based lead halide perovskites, respectively. These results reveal a strategy for a routine and robust spectroscopic approach to analyze local Cl chemical environments in metal halide perovskites that can be extended broadly to other halogen containing semiconductors. | Diganta Sarkar; Riley Hooper; Abhoy Karmakar; Amit Bhattacharya; Arkadii Pominov; Victor Terskikh; Vladimir Michaelis | Physical Chemistry; Analytical Chemistry; Spectroscopy (Physical Chem.); Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62829a4a59f0d6285e92b33e/original/metal-halide-perovskite-and-perovskite-like-materials-through-the-lens-of-ultra-wideline-35-37cl-nmr-spectroscopy.pdf |
61065c31537d10740980da3b | 10.26434/chemrxiv-2021-fr7t7 | Porphyrin based metal-organic frameworks with record sensitivity in optical oxygen sensing | The optical oxygen sensing capabilities of the porphyrin-based metal-organic frameworks, PCN-224, Pt(II)PCN-224 and Pd(II)PCN-224 were investigated. The bimolecular quenching constants (kq) of 37000 (PCN-224), 6700 (Pd(II)PCN-224) and 3900 Pa-1s-1 (Pt(II)PCN-224) were found and reveal an exceptionally high oxygen-permeability for these materials. A fast gas transport within the network, large pore sizes, electronic and spatial isolation of the porphyrin indicator in the framework are held responsible for the unprecedentedly high kq values. PCN-224 shows 6.7 ns fluorescence lifetime and the fluorescence in air is quenched by 4.2-fold. The metal-organic frameworks based on phosphorescent Pt(II) and Pd(II) porphyrins possess significantly longer decay times of 18.6 and 390 µs, respectively, and are suited to detect oxygen in trace and ultra-trace ranges with limits of detection of 1 and 0.015 Pa, respectively.
Apart from free-standing crystals, also metal-organic frameworks supported on different fibrous substrates (poly(acrylonitrile) nanofibers, glass fibres), and flat substrates (TLC silica-gel, poly(amide) filter) were prepared in order to provide oxygen sensor materials of practical use. Electrospun and thermally treated poly(acrylonitrile) nanofibers were proven to be particularly favourable and the resulting composite material exhibited the same sensitivity as the free crystals. All sensing materials show reversible cross-talk to humidity at levels up to 53 % relative humidity but demonstrate a drastic decrease of oxygen sensitivity at high humidity levels and when exposed to water.
| Tobias Burger; Christian Winkler; Irene Dalfen; Christian Slugovc; Sergey Borisov | Inorganic Chemistry; Analytical Chemistry; Sensors; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61065c31537d10740980da3b/original/porphyrin-based-metal-organic-frameworks-with-record-sensitivity-in-optical-oxygen-sensing.pdf |
67d92d8181d2151a02cf1d15 | 10.26434/chemrxiv-2025-cf5pg | Automated Reaction Exploration of Ozonation Processes for Model Olefins in Water | Comprehensive evaluation of pollutant abatement in chemical oxidation processes and identification of potentially hazardous transformation products is a fundamental challenge in water and wastewater treatment. Here, we demonstrate how high-throughput computational chemistry enables the elucidation of reaction pathways via automated, quantum chemistry-based chemical reaction network (CRN) explorations. We evaluated the predictive capabilities of this computational approach using the Software for Chemical Interaction Networks (SCINE) for studying the reactions of ozone with two model olefins, ethene and tetramethylethene, in aqueous solution. Following a benchmarking of quantum chemical methodology for structure optimization and energy calculations, we generated CRNs containing hundreds of compounds and thousands of reactions, identified reaction mechanisms, and evaluated product formation kinetics through microkinetic modeling. These CRN explorations led to the correct reproduction of experimental evidence for mechanisms and products of olefin ozonolyis for reactions of ozone and ethene based solely on defining the reactants and their initial concentrations. The study of reactions of ozone and tetramethylethene also matched experimental data for the main products, but revealed consequences of limited exploration depth and shortcomings of the implicit solvation model. Our work illustrates that automated CRN explorations offer novel means for predicting transformation pathways of organic compounds in chemical oxidation processes and can support chemical analysis, assess of environmental risks, and design of environmentally benign chemicals. | Enric Petrus; Livia A. Hunkeler; Markus Reiher; Urs von Gunten; Thomas B. Hofstetter | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d92d8181d2151a02cf1d15/original/automated-reaction-exploration-of-ozonation-processes-for-model-olefins-in-water.pdf |
654aebf1a8b423585a2d73f3 | 10.26434/chemrxiv-2022-h9gjq-v3 | Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences | We have performed exhaustive torsion sampling on more than 3 million compounds using the GFN2 method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that must be stable, synthetically accessible, and able to be crystallized. In this work, we evaluate the differences in torsional preferences of experimental crystallographic geometries and gas-phase computed conformers from a broad selection of compounds to determine whether torsional angle distributions obtained from semi-empirical methods are suitable for conformer sampling. We find that differences in torsion preferences can be mostly attributed to a lack of available experimental crystallographic data, with some deviations derived from gas-phase geometry differences. GFN2 demonstrates the ability to provide accurate and reliable torsional preferences that can provide a basis for new methods free from limitations of experimental data collection. We provide Gaussian-based fits and sampling distributions suitable for torsion sampling, and propose an alternative to ETKDG using quantum-torsion derived distance geometry methods (QTDG). | Dakota Folmsbee; David Koes; Geoffrey Hutchison | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654aebf1a8b423585a2d73f3/original/systematic-comparison-of-experimental-crystallographic-geometries-and-gas-phase-computed-conformers-for-torsion-preferences.pdf |
669e714001103d79c53bd506 | 10.26434/chemrxiv-2024-z8mhr | Machine Learning-Driven Optimization of Gas Diffusion Layer Microstructure for PEM Fuel Cells | The gas diffusion layer (GDL) is a vital component within PEMFCs, playing a crucial role in mass and heat transport. Enhancing the microstructure of the GDL directly improves transport properties, thereby leading to more efficient and durable PEMFCs. In this study, we developed a novel machine learning methodology to optimize the microstructure and properties of the GDL. The developed optimization framework, to the best of our knowledge, is the first of its kind and demonstrated high efficacy, with an R2 score ~95 % in 6 out of 7 properties and a R2 score ~90 % for the contact resistance, in identifying optimal manufacturing parameters to stochastically generate GDL microstructures and their associated properties. We validated our machine learning approach by comparing the predicted GDL properties to those calculated through digital characterization using physics-based methods from the stochastically reconstructed GDL, using the optimal manufacturing parameters identified by the optimizer. Our machine learning model was able to accurately predict 7 GDL properties with a significant decrease on the computational cost (~3 seconds wall time) compared to the physics-based calculations which takes ~3 - 4 hours wall time. In addition, the developed optimizer framework presented low fiber concentration accompanied by low compression ratio to achieve maximum diffusivity and minimum GDL-MPL contact resistance. Furthermore, prioritizing maximum electrical and/or thermal conductivities while minimizing GDL-MPL contact resistance require high fiber concentration with high compression ratio. This optimization strategy shows significant potential for improving gas transport, water management, efficient current collection, and thermal regulation within PEMFCs. | Rashen Lou Omongos; Diego Galvez-Aranda; Franco Zanotto; Andras Vernes; Alejandro A. Franco | Theoretical and Computational Chemistry; Materials Science; Energy; Carbon-based Materials; Artificial Intelligence; Fuel Cells | CC BY 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e714001103d79c53bd506/original/machine-learning-driven-optimization-of-gas-diffusion-layer-microstructure-for-pem-fuel-cells.pdf |
673f636cf9980725cf549552 | 10.26434/chemrxiv-2024-3p7wb | New Insights into the Catalytic Mechanism of the Fe(II)/2OG-Dependent Ethylene Forming Enzyme | Ethylene-forming enzyme (EFE) has economic importance due to its ability to catalyze the formation of ethylene and 3-hydroxypropionate (3HP). Understanding the catalytic mechanism of EFE is essential for optimizing the biological production of these important industrial chemicals. In this study, we implemented molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) to elucidate the pathways leading to ethylene and 3HP formation. Our results suggest that ethylene formation occurs from the propion-3-yl radical intermediate rather than the (2-carboxyethyl)carbonato-Fe(II) intermediate (EFIV), which conclusively acts as a precursor for 3HP formation. The results also explain the role of the hydrophobic environment surrounding the 2OG binding site in stabilizing the propion-3-yl radical, which defines their conversion to either ethylene or 3HP. Our simulations on the A198L EFE variant, which produces more 3HP than wild-type (WT) EFE based on experimental observations, predict that the formation of EFIV intermediate is more favored than WT. Also, MD simulations on EFIV intermediate in both WT and A198L EFE predicted that the water molecules approach the Fe center, which suggests a role of water molecules in the breakdown of EFIV intermediate. QM/MM simulations on the EFIV intermediate of WT and A198L EFE predicted that the Fe-bound water molecule could provide a proton for the 3HP formation from EFIV. The study underscores the critical influence of the enzyme’s hydrophobic environment and second coordination sphere residues in determining product distribution between ethylene and 3HP. These mechanistic insights lay a foundation for targeted enzyme engineering, aiming to improve the selectivity and catalytic efficiency of EFE in biological ethylene and 3HP production. | Simahudeen Bathir Jaber Sathik Rifayee; Midhun George Thomas; Christo Christov | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673f636cf9980725cf549552/original/new-insights-into-the-catalytic-mechanism-of-the-fe-ii-2og-dependent-ethylene-forming-enzyme.pdf |
60c742af9abda214b5f8c087 | 10.26434/chemrxiv.8396855.v1 | Assessing the Accuracy of Simplified Coupled Cluster Methods for Electronic Excited States in F0 Actinide Compounds | <p>We present a benchmark study of the performance of various recently presented EOM-pCCD-based methods to model ground and excited state properties of a set of f0 actinide species that feature different types of electronic excitations, like local excitations or charge transfer. Our data suggests that the recently developed EOM-pCCD-LCCSD method outperforms conventional approaches like EOM-CCSD reducing the standard error by a factor of 2 (to 0.25 eV). Thus, EOM-pCCD-LCCSD can be considered as an alternative to model excited states in challenging systems, especially those who feature a double electron transfer for which EOM-CCSD typically fails.</p> | Artur Nowak; Paweł Tecmer; Katharina Boguslawski | Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742af9abda214b5f8c087/original/assessing-the-accuracy-of-simplified-coupled-cluster-methods-for-electronic-excited-states-in-f0-actinide-compounds.pdf |
65eeac0a66c1381729b9206e | 10.26434/chemrxiv-2024-l2dk7 | Prediction of Inhibitory Activity Against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models | Renal secretion plays an important role in drug excretion from the kidney. Two major transporters known to be highly involved in renal secretion are MATE1/2-K and OCT2, the former of which is highly related to drug-drug interactions. Among published in silico models for MATE inhibitors, a previous model obtained a ROC-AUC value of 0.78 using high throughput percentage inhibition data [J Med Chem. 2013;56(3): 781–795] which we aimed to improve upon here using a combined fingerprint and physics-based approach. To this end, we collected 225 publicly available compounds with pIC50 values against MATE1. Subsequently, on the one hand we performed a physics-based approach using an Alpha-Fold protein structure, from which we obtained MM-GB/SA scores for those compounds. On the other hand, we built Random Forest (RF) and Message Passing Neural Network (MPNN) models using Extended-Connectivity Fingerprints with radius 4 (ECFP4) and chemical structures as graphs, respectively, which also included MM-GB/SA scores as input variables. In a five-fold cross-validation with a separate test set we found that the best predictivity for the hold-out test was observed in the RF model (including ECFP4 and MM-GB/SA data) with an ROC-AUC of 0.833±0.036; while that of the MM-GB/SA regression model was 0.742. However, the MM-GB/SA model was able to extrapolate to novel chemical space better. Additionally, via Structural Interaction Fingerprint analysis, we identified interacting residues with inhibitor as identical for those with non-inhibitors, including substrates, such as Gln49, Trp274, Tyr277, Tyr299, Ile303, Tyr306. The similar binding modes are consistent with the observed similar IC50 values inhibitor when using different substrates experimentally, and practically this can release the experimental scientists from bothering of selecting substrates for MATE1. Hence, we were able to build a highly predictive classification models for MATE1 inhibitory activity with both ECFP4 and MM-GB/SA score as input features, which is fit-for-purpose for use in the drug discovery process. | Koichi Handa; Shunta Sasaki; Satoshi Asano; Michiharu Kageyama; Takeshi Iijima; Andreas Bender | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eeac0a66c1381729b9206e/original/prediction-of-inhibitory-activity-against-the-mate1-transporter-via-combined-fingerprint-and-physics-based-machine-learning-models.pdf |
60c75543ee301c2176c7b149 | 10.26434/chemrxiv.14060936.v1 | Synergic Topological- and Size-Control on Phosphazane Chemistry: First Unfolded Hybrid Tetrameric Macrocycle | Herein, we report an unprecedented combination of pre-arranged building blocks and a multi-step synthetic route to rationally and simultaneously enable access to an unfolded tetrameric macrocycle, which is not accessible using conventional synthetic strategies. The obtained macrocycle, cis-[μ-P(μ-NtBu)]2(μ-p-OC6H4C(O)O)]4[μ-P(μ-NtBu)]2 (4), is the first unfolded open-face hybrid cyclodiphosphazane macrocycle reported and displays a cavity area of 110.1 Å2 - the largest of its kind.<br /> | Ying Sim; felix leon; Rakesh Ganguly; jesus diaz; Jack K. Clegg; Felipe Garcia | Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75543ee301c2176c7b149/original/synergic-topological-and-size-control-on-phosphazane-chemistry-first-unfolded-hybrid-tetrameric-macrocycle.pdf |
64ae35339ea64cc167dccf4b | 10.26434/chemrxiv-2023-0xqkw | Effectiveness and limitation of the performance prediction of perovskite solar cells by process informatics | Perovskite solar cells have garnered significant interest owing to their low fabrication costs and comparatively high power conversion efficiency (PCE). The performance of these cells is influenced not solely by material composition but also by experimental processes, rendering PCE prediction a challenging endeavor. It is also crucial to quantitatively assess the impact of process conditions on performance. In this work, we developed machine learning regression incorporating process information derived from an open-access perovskite database. Our analysis showed that the split of process information influenced the prediction accuracy and clarified the relative contribution of each process condition. The limitation of performance prediction was also prone to data degeneracy. The insights gained from this work may facilitate the data-driven design of innovative perovskite solar cells. | Ryo Fukasawa; Toru Asahi; Takuya Taniguchi | Materials Science; Energy; Hybrid Organic-Inorganic Materials; Photovoltaics | CC BY 4.0 | CHEMRXIV | 2023-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ae35339ea64cc167dccf4b/original/effectiveness-and-limitation-of-the-performance-prediction-of-perovskite-solar-cells-by-process-informatics.pdf |
60c74d3c469df46eb1f44256 | 10.26434/chemrxiv.12601538.v1 | Geometric Analysis and Formability of the Cubic A2BX6 Vacancy Ordered Double Perovskite Structure | <p>A geometric analysis of the cubic A<sub>2</sub>BX<sub>6</sub>
structure commonly formed by metal halides is presented. Using the ‘hard sphere’
approximation, where the ions are represented by spheres of a fixed radius, we
derive four limiting models that each constrain the distances between
constituent ions in different ways. We compare the lattice parameters predicted
by these four models with experimental data from the Inorganic Crystal
Structure Database (ICSD). For the fluorides, the maintenance of the AX bond
length at the sum of the A and X radii gives the best approximation of the
lattice parameter, leading to structures with widely separated BX<sub>6</sub>
octahedra. For the heavier halides, a balance between forming an A site cavity
of the correct size, and maintaining suitable anion-anion distances determines
the lattice parameter. It is found that in many A<sub>2</sub>BX<sub>6</sub>
compounds of heavier halides, the neighbouring octahedra show very significant
anion-anion overlap, meaning that the commonly used description of these
materials of having isolated BX<sub>6</sub> octahedra is misleading. We use the
geometric models to derive formability criteria for vacancy ordered double
perovskites. </p> | Anjie Cheng; Chenyang Lyu; Tianyi Shi; Ziheng Wang; Robert Palgrave | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d3c469df46eb1f44256/original/geometric-analysis-and-formability-of-the-cubic-a2bx6-vacancy-ordered-double-perovskite-structure.pdf |
63c15b5d553889fa677f9671 | 10.26434/chemrxiv-2023-x466x | Synthesis of Phosphorene Quantum Dots from Red Phosphorus | Phosphorene quantum dots (PQDs) are most commonly derived from high-cost black phosphorus, while previous syntheses from the low-cost red phosphorus (Pred) allotrope are highly oxidised. Herein, we present an intrinsically scalable method to producing high quality PQDs, by first ball-milling Pred to create nanocrystalline Pblack and subsequent reductive etching using lithium electride solvated in liquid ammonia. The resultant PQDs are spontaneously soluble as monolayers in tertiary amide solvents, laterally confined to < 100 nm dimension, photoluminescent, and crystalline with low oxygen content. This new method presents a scalable route to producing quantities of high quality PQDs for academic and industrial applications. | Rebecca Shutt; Thrinathreddy Ramireddy; Evgenios Stylianidis; Camilla Di Mino; Rebecca Ingle; Ary Wibowo; Hieu Nguyen; Christopher Howard; Alexey Glushenkov; Andrew Stewart; Adam Clancy | Materials Science; Nanoscience; Materials Processing; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c15b5d553889fa677f9671/original/synthesis-of-phosphorene-quantum-dots-from-red-phosphorus.pdf |
61ef814e537af8b454a49777 | 10.26434/chemrxiv-2022-1tv13 | Visible-light enabled C(sp3)–C(sp2) cross-electrophile coupling via synergistic nickel and halogen-atom transfer (XAT) catalysis | We herein report the first visible-light-mediated cross-coupling of unactivated alkyl iodides with aryl bromides through synergistic nickel and halogen atom transfer (XAT) catalysis. This simple protocol operates under mild reaction conditions and tolerates variety of functional groups affording C(sp3)–C(sp2) cross-coupling products in good to moderate yields. | Girish Suresh Yedase; Avishek Kumar Jha ; Veera Reddy Yatham | Catalysis; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ef814e537af8b454a49777/original/visible-light-enabled-c-sp3-c-sp2-cross-electrophile-coupling-via-synergistic-nickel-and-halogen-atom-transfer-xat-catalysis.pdf |
64140074aad2a62ca1e56625 | 10.26434/chemrxiv-2023-wl8rn | SLI-GNN: A Self-Learning-Input Graph Neural Network for Predicting Crystal and Molecular Properties | Since the structures of crystals/molecules are often non-Euclidean data in real space, graph neural networks (GNNs) are regarded as the most prospective approach for their capacity of representing materials by graph-based inputs and emerged as an efficient and powerful tool in accelerating the discovery of new materials. Here, we proposed a self-learning-input GNN framework, named SLI-GNN, to uniformly predict the properties for both crystals and molecules, in which, for the first time, we design a dynamic embedding layer to self-update the input features along with the iteration of the neural network and introduce the Infomax mechanism to maximize the average mutual information between the local features and the global features. It is found that our SLI-GNN can reach ideal prediction accuracy with less inputs and more MPNN layers. The model evaluation on the Materials Project Dataset and QM9 dataset verify that the overall performance of our GNN is comparable to that of other previously reported GNNs. Thus, our GNN framework presents excellent performance in material property prediction, thereby being promising for accelerating the discovery of new materials. | Zhihao Dong; Jie Feng; Yujin Ji; Youyong Li | Theoretical and Computational Chemistry; Machine Learning; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64140074aad2a62ca1e56625/original/sli-gnn-a-self-learning-input-graph-neural-network-for-predicting-crystal-and-molecular-properties.pdf |
642137df647e3dca99917c3e | 10.26434/chemrxiv-2023-h9wwx | Self-hydrogen Supplied Catalytic Fractionation of Raw Biomass into Lignin-derived Phenolic Monomers and Cellulose-rich Pulps | Lignocellulosic biomass is one of the most well-studied and promising green carbon sources. Fullest utilization of lignocellulosic biomass in hydrogen-free and mild conditions to produce phenolic monomers while preserving cellulose-rich pulps is challenging and has far-reaching significance. Here, we report an innovative strategy to convert lignocellulosic biomass into lignin oils and cellulose-rich pulps without exogenous hydrogen under mild conditions over Pt/NiAl2O4 catalyst. In this process, the structural hydrogens in hemicellulose are acted as hydrogen source to realize the fractionation and depolymerization of lignin into phenolic monomers while keeping cellulose intact, which is named self-hydrogen supplied catalytic fractionation (SCF). By using water as solvent, theoretical yield of phenolic monomers (46.6 wt%, with propyl(ethyl) end-chained syringol and guaiacol as main products) is achieved at 140 oC for 24 h, with 90 % cellulose intact in birch sawdust. This H2-free process can be extended to other biomass (hardwood, softwood and grass) and can be scaled up. The Pt/NiAl2O4 catalyst also shows good stability in recycling as well as a regeneration treatment. This work provides a new strategy to achieve high utilization of lignocellulosic biomass for sustainable biorefinery by using water as solvent without exogenous hydrogen under mild conditions. | Hao Zhou; Xiaohui Liu; Yong Guo; Yanqin Wang | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642137df647e3dca99917c3e/original/self-hydrogen-supplied-catalytic-fractionation-of-raw-biomass-into-lignin-derived-phenolic-monomers-and-cellulose-rich-pulps.pdf |
60c73f5a0f50dbb276395765 | 10.26434/chemrxiv.6820229.v3 | Lignin-Containing Photoactive Resins for 3D Printing by Stereolithography | Generating compatible and competitive materials that are environmentally sustainable and economically viable is paramount for the success of additive manufacturing using renewable materials. We report the successful application of renewable, modified lignin-containing photopolymer resins in a commercial stereolithography system. Resins were fabricated within operable ranges for viscosity and cure properties, using up to 15% modified lignin by weight with the potential for higher amounts. A four-fold increase in ductility in cured parts with higher lignin concentration is noted as compared to commercial SLA resins. Excellent print quality was seen in modified lignin resins, with good layer fusion, high surface definition, and visual clarity. These materials can be used to generate new products for additive manufacturing applications and help fill vacant material property spaces, where ductility, sustainability, and application costs are critical. | Jordan T. Sutton; Kalavathy Rajan; David Harper; Stephen Chmely | Biopolymers; Cellulosic materials; Polymer blends; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5a0f50dbb276395765/original/lignin-containing-photoactive-resins-for-3d-printing-by-stereolithography.pdf |
678e856e81d2151a02f46b0a | 10.26434/chemrxiv-2025-1b0jp | Decoding Regioselectivity in Cu(I)-Catalyzed Borylation of Al-kynes: Insights from Machine Learning and Artificial Intelligence | Vinyl boronates are highly valuable intermediates in chemical synthesis, extensively used in C‒C bond-forming reactions such as catalytic cross-coupling. Transition metal-catalyzed hydroboration of alkynes has emerged as a key method for synthesizing these building blocks. While classical approaches rely on noble metals like rhodium and iridium, copper-catalyzed hydroboration offers a sustainable and cost-effective alternative. This strategy utilizes bench-stable reagents under mild conditions, delivering highly stereoselective trans-vinylboronates. However, predicting regioselectivity re-mains a challenge due to the complex interplay of ligand structures, alkyne substitution patterns, and reaction conditions. To address this, we employed a combination of experimental data, high-throughput computational calculations, and ma-chine learning (ML) to develop predictive models for regioselectivity. Ligand and catalyst descriptors were derived from DFT calculations and literature databases, forming a robust dataset used to train ML algorithms. Further optimization proved effective in guiding experimental efforts by identifying promising ligands and improving hydroboration yields. This workflow integrates experimental and computational tools to achieve a stereocontrolled synthesis of substituted alkenyl boronates from alkynes. As a case study, we demonstrate the successful application of ML-guided optimization, reducing copper catalyst loading while improving yields and regioselectivity. | Guillermo Marcos-Ayuso; David Quesada; Sara Fernandez Moyano; Carlos Lendinez Sanchez; Pablo Mauleon Perez; Ramón Gómez Arrayás | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Machine Learning; Chemoinformatics - Computational Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678e856e81d2151a02f46b0a/original/decoding-regioselectivity-in-cu-i-catalyzed-borylation-of-al-kynes-insights-from-machine-learning-and-artificial-intelligence.pdf |
67a9281c6dde43c908369a22 | 10.26434/chemrxiv-2025-6mxw9-v2 | De novo designed β-hairpin peptides mimicking the LPMO copper-binding histidine brace motif | Lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes that play a crucial role in lignocellulosic biomass degradation for use in biofuel production. These enzymes carry out the selective oxidation of C-H bonds in the sugar units, leading to the cleavage of the glycosidic bond. Creating LPMO mimics facilitates the study of the mechanism of action, the characterisation of the reactive species responsible for the C-H bond activation and the potential scale up for industrial application. Here we report the synthesis, characterisation and activity assays of two novel Cu-binding peptides that mimic the active site of LPMOs. CD, ATR-FTIR and EPR spectroscopic studies of the peptides and their corresponding copper complexes show that the sequences fold in a β-hairpin conformation and produce complexes with a single Cu ion bound in an LPMO-like environment, confirmed by computational studies. Activity assays were conducted with p-nitrophenyl-β-D-glucopyranoside (PNPG) and demonstrate that the Cu-complexes show LPMO-like activity on the model substrate. Furthermore, the Cu-hairpins can also perform light-driven oxidation of phosphoric acid swollen cellulose (PASC) in the presence of melanin, similarly to some LPMO enzymes, an activity that is unreported for any LPMO mimic characterised so far. This work is the first example of a β-hairpin LPMO mimic and paves the way to further exploration of small peptide mimics of this key class of metalloenzymes. | Enrico Falcone; Rosemary Tomey; Emma Turley; David Cannella; David Robinson; Luisa Ciano | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Chemical Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a9281c6dde43c908369a22/original/de-novo-designed-hairpin-peptides-mimicking-the-lpmo-copper-binding-histidine-brace-motif.pdf |
60c74e120f50db849f397161 | 10.26434/chemrxiv.12696545.v1 | Modelling-Guided Design of Paper Microfluidic Networks – A Case Study of Sequential Fluid Delivery | <p>Paper-based microfluidic devices are popular for their ability to automate multi-step assays for chemical or biological sensing at a low cost, but the design of paper microfluidic networks has largely relied on experimental trial and error. A few mathematical models of flow through paper microfluidic devices have been developed and have succeeded in explaining experimental flow behaviour. However, the reverse engineering problem of designing complex paper networks guided by appropriate mathematical models is largely unsolved. In this article, we demonstrate that a two-dimensional paper network (2DPN) designed to sequentially deliver three fluids to a test zone on the device can be computationally designed and experimentally implemented without trial and error. This was accomplished by three new developments in modelling flow through paper networks: i) coupling of the Richards equation of flow through porous media to the species transport equation, ii) modelling flow through assemblies of multiple paper materials (test membrane and wicking pad), and iii) incorporating limited-volume fluid sources. We demonstrate the application of this model in the optimal design of a paper-based signal-enhanced immunoassay for a malaria protein, P<i>f</i>HRP2. This work lays the foundation for the development of a computational design toolbox to aid in the design of paper microfluidic networks.</p> | Dharitri Rath; Bhushan Toley | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e120f50db849f397161/original/modelling-guided-design-of-paper-microfluidic-networks-a-case-study-of-sequential-fluid-delivery.pdf |
6225ddcb5f1d9aefb2b3884a | 10.26434/chemrxiv-2022-2pt95 | Computational Prediction of Speciation Diagrams and Nucleation Mechanisms: Molecular Vanadium, Niobium and Tantalum Oxide Nanoclusters in Solution | Understanding the aqueous speciation of molecular metal-oxo clusters plays a key role in different fields such as catalysis, electrochemistry, nuclear waste recycling, and biochemistry. To accurately describe the speciation, it is essential to elucidate the underlying self-assembly processes. Herein, we apply a computational method to predict the speciation and formation mechanisms of polyoxovanadates, -niobates and -tantalates. While polyoxovanadates have been widely studied, polyoxoniobates and -tantalates lack the same level of understanding. In the first place, we proposed a pentavanadate cluster ([V5O14]3-) as a key intermediate for the formation of the decavanadate. Our computed phase speciation diagram is in particularly good agreement with the experiments. Secondly, we report the formation constants of the heptaniobate, [Nb7O22]9-, decaniobate, [Nb10O28]6-, and tetracosaniobate [H9Nb24O72]9-. Additionally, we have computed the speciation and phase diagram of niobium, which so far was restricted to Lindqvist derivates. Finally, we have predicted the formation constant of the decatantalate ([Ta10O26]6-) in water, even though it had only been synthetized in toluene. Furthermore, the corresponding speciation and phase diagrams for polyoxotantalates have been also calculated. Overall, we show that our method can be successfully applied to different families of molecular metal oxides without any need for readjustments; therefore, it can be regarded as a trustworthy tool for exploring polyoxometalates’ chemistry. | Enric Petrus; Mireia Segado-Centellas; Carles Bo | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Inorganic Acid/Base Chemistry; Computational Chemistry and Modeling; Self-Assembly | CC BY NC 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6225ddcb5f1d9aefb2b3884a/original/computational-prediction-of-speciation-diagrams-and-nucleation-mechanisms-molecular-vanadium-niobium-and-tantalum-oxide-nanoclusters-in-solution.pdf |
636e5f9aafea7f25bfa0c4d5 | 10.26434/chemrxiv-2022-qrf1h | Bio-based poly(hydroxy urethane)s for efficient organic high-power energy storage | Fast, low-cost and efficient energy storage technologies are urgently needed to balance the intermittence of sustainable energy sources. High-power capacitors using organic polymers offer a green and scalable answer. They require dielectrics with high permittivity (εr) and breakdown strength (EB), which bio-based poly(hydroxy urethane)s (PHUs) can provide. PHUs combine high concentrations of hydroxyl and carbamate groups, thus enhancing their εr, and a highly tuneable glass transition (Tg), which dictates the regions of low dielectric losses. By reacting erythritol dicarbonate with bio-based diamines, fully bio-based PHUs were synthesised with Tg ~ 50 °C, εr > 8, EB > 400 MV·m-1 and low losses (tan δ < 0.03). This results in energy storage performance comparable with the flagship petrochemical materials (discharge energy density, Ue > 6 J·cm-3) combined with a remarkably high discharge efficiency (η = 85%). These bio-based PHUs thus represent a highly promising route to green and sustainable energy-storage. | Florian Le Goupil; Victor Salavado; Valère Rothan; Thomas Vidil; Guillaume Fleury; Henri Cramail; Etienne Grau | Materials Science; Polymer Science; Energy; Carbon-based Materials; Biopolymers; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636e5f9aafea7f25bfa0c4d5/original/bio-based-poly-hydroxy-urethane-s-for-efficient-organic-high-power-energy-storage.pdf |
60c75499469df4be77f44f82 | 10.26434/chemrxiv.13685917.v1 | Local, Single-Molecule Oxidative Cleaving of DNA Origami by C60 on an AFM Tip | Spatially controlled single-molecule oxidation of DNA was performed by photocatalytic generation of singlet oxygen on chemically functionalized AFM tips. A waffle-type DNA origami deposited on a mica surface is site-specifically destroyed by generation of reactive oxygen species at the AFM tip, which was modified with C<sub>60</sub>-tripod photocatalyst. Upon AFM scanning under photoirradiation, DNA morphology changes, corresponding to oxidative damage were clearly observed at the single-molecule level. The DNA cleavage occurred with strict dependence on photoirradiation and the presence of C<sub>60 </sub>on the AFM tip. | Ankita Ray; Cristiana Passiu; S.N Ramakrishna; Antonella Rossi; Akinori Kuzuya; Nicholas D. Spencer; Yoko Yamakoshi | Nanocatalysis - Catalysts & Materials; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75499469df4be77f44f82/original/local-single-molecule-oxidative-cleaving-of-dna-origami-by-c60-on-an-afm-tip.pdf |
61512d0b87a02d737b4a01d6 | 10.26434/chemrxiv-2021-dhwz4-v2 | Emissive Organogel Mediated Construction of Flexible Covalent Organic Polymer for the Separation of Aniline for Water Purification | A flexible covalent organic polymer (COP) has been successfully synthesized via dynamic covalent gel (DCG) formation through imine condensation reaction between 6-hydrazinonicotinic hydrazide hydrate and benzene-1,3,5-tricarboxaldehyde within 7 min under ambient condition. An emissive organogel mediated protocol has been developed for the construction of amorphous polymer (COP), selectively in N,N-dimethyl acetamide (DMA). Interestingly, two non-emissive building block units without large π-conjugated structures have been engaged for the construction of green emissive COP-gel. The green emission of COP-gel is generated by the intermolecular H-bonding assisted aggregation induced emission phenomenon. The dried COP efficiently adsorbs aniline molecules into its cavities and separate them from binary mixtures of aniline/nitrobenzene and aniline/water, respectively. | Apurba K. Das; Sayan Maiti; Tapas Ghosh; Arati Samal | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61512d0b87a02d737b4a01d6/original/emissive-organogel-mediated-construction-of-flexible-covalent-organic-polymer-for-the-separation-of-aniline-for-water-purification.pdf |
639b9bcc16e9a8ba8429ab4d | 10.26434/chemrxiv-2022-hwzmg | A simplified Bixon-Jortner-Plotnikov method for fast calculation of radiationless transfer rates in symmetric molecules | A simplified form of the Bixon-Jortner-Plotnikov (BJP) method is derived for calculation of internal conversion (IC) rate in a symmetrical molecule. The rate is a sum of contributions from individual transitions between vibronic states. For each transition, vibrational modes are divided into two groups, the promoting (one or two modes per electronic transition) and the surrounding ones. In the case of the non-totally symmetric transition in a symmetric molecule, the overwhelming majority of transitions do not contribute to the overall rate. Moreover, the promoting and surrounding modes belong to different symmetry representations and can be separated. It is proposed to deal with the promoting modes directly, while approximating the effect of the surrounding modes by a Pekarian function. The method was tested on polyacenes and it was shown that the calculated IC rates are in agreement with the experimental ones. The simplified method can be applied for calculating the rates of non-totally symmetric transition in a symmetric molecule, if its point symmetry group does not change after transition. | Arthur I. Martynov; Aleksandr S. Belov; Vladimir K. Nevolin | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b9bcc16e9a8ba8429ab4d/original/a-simplified-bixon-jortner-plotnikov-method-for-fast-calculation-of-radiationless-transfer-rates-in-symmetric-molecules.pdf |
60c73e14bb8c1a2e0b3d9833 | 10.26434/chemrxiv.6355802.v1 | Compositional Inhomogeneity and Tuneable Thermal Expansion in Mixed-Metal ZIF-8 Analogues | <div>We study the structural and thermomechanical effects</div><div>of cation substitution in the compositional family of</div><div>metal–organic frameworks Zn1xCdx(mIm)2 (HmIm = 2-</div><div>methylimidazole). We find complete miscibility for all</div><div>compositions x, with evidence of inhomogeneous distributions of Cd and Zn that in turn affect framework aperture characteristics. Using variable-temperature X-ray powder diffraction measurements, we show that Cd substitution drives a threefold reduction in the magnitude of thermal expansion behaviour. We interpret this effect in terms of an increased density of negative thermal expansion modes in the more flexible Cd-rich frameworks.</div> | Adam Sapnik; Harry Geddes; Emily Reynolds; Hamish Yeung; Andrew Goodwin | Organometallic Compounds; Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e14bb8c1a2e0b3d9833/original/compositional-inhomogeneity-and-tuneable-thermal-expansion-in-mixed-metal-zif-8-analogues.pdf |
6544a05ea8b423585adabe35 | 10.26434/chemrxiv-2023-f5xxd | Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography | Determining short-lived intermediate structures in chemical reactions is challenging. Although ultrafast spectroscopic methods can detect the formation of transient intermediates, real-space structures cannot be determined directly from such studies. Time-resolved serial femtosecond crystallography (TR-SFX) has recently proven to be a powerful method for capturing molecular changes in proteins on femtosecond timescales. However, the methodology has been mostly applied to natural proteins/enzymes and limited to reactions promoted by synthetic molecules due to structure determination challenges. This work demonstrates the applicability of TR-SFX for investigations of chemical reaction mechanisms of synthetic metal complexes. We fixed a light-induced CO-releasing Mn(CO)3 reaction center in porous hen egg white lysozyme (HEWL) microcrystals. By controlling light exposure and time, we succeeded in capturing the real-time formation of Mn-carbonyl intermediates during the CO release reaction. The asymmetric protein environment was found to influence the order of CO release. The experimentally-observed reaction path agrees with quantum mechanical calculations. Therefore, our demonstration offers a new approach to visualize atomic-level reactions of small molecules using TR-SFX with real-space structure determination. This advance holds the potential to facilitate design of artificial metalloenzymes with precise mechanisms, empowering design, control and development of innovative reactions. | Basudev Maity; Mitsuo Shoji; Fangjia Luo; Takanori Nakane; Satoshi Abe ; Shigeki Owada; Jungmin Kang; Kensuke Tono; Rie Tanaka; Thuc Toan Pham; Mariko Kojima; Yuki Hishikawa; Junko Tanaka; Jiaxin Tian; Hiroki Noya; Yuto Nakasuji ; Asuka Asanuma ; Xinchen Yao; So Iwata; Yasuteru Shigeta ; Eriko Nango; Takafumi Ueno | Inorganic Chemistry; Bioinorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6544a05ea8b423585adabe35/original/real-time-observation-of-a-metal-complex-driven-reaction-intermediate-using-a-porous-protein-crystal-and-serial-femtosecond-crystallography.pdf |
60c74045bdbb895176a38135 | 10.26434/chemrxiv.7687427.v1 | Interactions Between the Aryldiazonium Cations and Graphene Oxide – a DFT Study | Understanding
the grafting behavior of the aryldiazonium cations is of fundamental and also
of practical importance for the vast number of applications that involve the
use of modified Graphene oxide (from simple adsorption process to electronic
and photovoltaic applications). In this work, the mechanism of the adsorption
and grafting diazonium cations on the graphene oxide surface was investigated by the use of Density Functional
Theory. Two types of aryldiazonium cations one bearing only phenyl ring and the
other nitrophenyl were selected as adsorbates/grafted moiety. By evaluating the adsorption energies at 7
different positions onto the graphene
oxide both in the gaseous and solvent phase (using COSMO approach) the most
probable adsorption sites were
found. Moreover, the most stable
adsorption sites were used to calculate and plot NCI (Non-Covalent
Interactions). The obtained results are important as they not only give molecular insights regarding the
nature of the interaction and its
dependence on the adsorption site of graphene oxide surface but also on the
activation energy for such a grafting reaction to take place - providing a
mechanistic aspect to understand these grafting reactions. | Avni Berisha | Computational Chemistry and Modeling; Theory - Computational; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74045bdbb895176a38135/original/interactions-between-the-aryldiazonium-cations-and-graphene-oxide-a-dft-study.pdf |
678b8acf6dde43c9080989c4 | 10.26434/chemrxiv-2025-hdqz8 | Exploring reactive oxygen species dynamics in pea germination to improve variety selection in stressful environments | Non-biological stressors constitute a significant threat to crop productivity and food security, underscoring the imperative to select appropriate seeds for specific environmental conditions. However, conventional method for seed variety selection is time-consuming and labour-intensive. This study introduces an AIEgen (TBPBB) based image recognition system, which utilizes fluorescence probe imaging signals of reactive oxygen species (ROS) during the germination phase of pea (Pisum sativum L) seeds to to accelerate the selection of superior varieties under non-biological stressors. The accuracy of the system's screening is highly congruent with that of traditional manual selection methods, with an accuracy of 100% for harvest parameters, 93.8% for germination percentage and 87.5% for vigour index in distinguishing pea varieties in an alkaline cultivation environment. This seed selection strategy significantly reduces the labor intensity, achieving a substantial reduction in time from 228 days to 73 hours. The research underscores the potential of AIEgen-based fluorescence image recognition technology in enhancing crop quality under specific stressors conditions. It offers a promising avenue for innovative technological approaches that contribute to the sustainable development of agriculture. | lin kong; Wei He; Zhen Zhao; Ben Zhong Tang; Rui Zhang; Fen Zhao | Materials Science | CC BY 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678b8acf6dde43c9080989c4/original/exploring-reactive-oxygen-species-dynamics-in-pea-germination-to-improve-variety-selection-in-stressful-environments.pdf |
637cae57ebc1c72858ce248c | 10.26434/chemrxiv-2022-xnh88 | Solution-Phase Synthesis of Co-N-C Catalysts Using Alkali Metals-Induced N-C Templates with Metal Vacancy-Nx sites | Nitrogen-coordinated metal sites (MNx) in metal- and nitrogen-co-doped carbon (M-N-C) catalysts are known for their versatile and promising electrocatalytic activity. However, the synthesis of MNx moieties with desired configuration and catalytic property is still quite challenging using the conventional high-temperature treatment approach. In this study, we demonstrate the solution-phase synthesis of Co-N-C catalysts via the formation of CoNx moieties at metal vacancy-Nx (MVNx) sites on nitrogen-doped carbon (N-C) templated by alkali metals, including sodium and potassium. The formation of CoNx sites is confirmed via a combined approach of various physical characterization techniques, elemental analysis, and electrochemical analysis. For each series of Co-N-C catalysts templated by the same alkali metal (e.g., Na or K), there is a correlation between the CoNx content and the electrocatalytic activity for the oxygen reduction reaction (ORR). Moreover, the correlation of CoNx content with ORR activity also depends on the type of sacrificial alkali metals, suggesting the role of sacrificial metals in creating MVNx sites with a diverse coordination environment. These findings may further guide the future development of M-N-C electrocatalysts with abundant and versatile MNx moieties through this solution-phase coordination approach. | Mengxue Huang; Lifang Chen; Ruimin Ding; Wenwen Shi; Qianqian Qin; Jie Yang; Shufang Shi; Shanshan Liu; Xi Yin | Catalysis; Energy; Electrocatalysis; Fuel Cells; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637cae57ebc1c72858ce248c/original/solution-phase-synthesis-of-co-n-c-catalysts-using-alkali-metals-induced-n-c-templates-with-metal-vacancy-nx-sites.pdf |
60c74473567dfe2896ec429a | 10.26434/chemrxiv.9788459.v1 | Salt Mediated Self-Assembly of Poly(ethylene Glycol)-Functionalized Gold Nanorods | Although challenging, assembling and orienting non-spherical nanomaterials into two- and three-dimensional (2D and 3D) ordered arrays can facilitate versatile collective properties by virtue of their shape-dependent properties that cannot be realized with their spherical counterparts. Here, we report on the self-assembly of gold nanorods (AuNRs) into 2D films at the vapor/liquid interface facilitated by grafting them with poly(ethylene glycol) (PEG). Using surface sensitive synchrotron grazing incidence small angle X-ray scattering (GISAXS) and specular X-ray reflectivity (XRR), we show that PEG-AuNRs in aqueous suspensions migrate to the vapor/liquid interface in the presence of salt, forming a uniform monolayer with planar-to-surface orientation. Furthermore, the 2D assembled PEG functionalized AuNRs exhibit short range order into rectangular symmetry with side-by-side and tail-to-tail nearest-neighbor packing. The effect of PEG chain length and salt concentration on the 2D assembly are also reported. | Hyeong Jin Kim; Wenjie Wang; Wei Bu; Md. Mir Hossen; Alejandra Londono-Calderon; Andrew C. Hillier; Tanya Prozorov; Surya K. Mallapragada; David Vaknin | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74473567dfe2896ec429a/original/salt-mediated-self-assembly-of-poly-ethylene-glycol-functionalized-gold-nanorods.pdf |
6709461bcec5d6c142decc21 | 10.26434/chemrxiv-2024-prwm8 | Carbon-to-nitrogen atom swap enables direct access to benzimidazoles from drug-like indoles | The ability to selectively edit organic molecules at the atomic level has the potential to streamline lead discovery and optimization in the pharmaceutical and agrochemical industry. While numerous atom insertion and deletion reactions have recently been reported, examples of single atom swaps remain scarce due to the challenge of orchestrating the selective cleavage and formation of multiple chemical bonds around the same atom. We herein report a method for the carbon-to-nitrogen atom swap in N-alkyl indoles, allowing for the direct conversion of indoles to the corresponding benzimidazoles. The reaction leverages the innate reactivity of the indole scaffold to engage in an initial oxidative cleavage step, followed by oxidative amination, Hofmann-type rearrangement and cyclization. This complex sequence of steps is mediated by the simple combination of commercially available PIDA and ammonium carbamate as nitrogen atom source. The reaction tolerates a wide range of functional groups which is demonstrated by the interconversion of 15 drug-like molecules implying its immediate applicability across a wide range of discovery programs. Furthermore, it shows how leveraging the innate reactivity of a common heterocycle can unlock otherwise challenging skeletal editing reactions. | Ann-Sophie Paschke; Yannick Brägger; Bence Botlik; Erich Staudinger; Ori Green; Bill Morandi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6709461bcec5d6c142decc21/original/carbon-to-nitrogen-atom-swap-enables-direct-access-to-benzimidazoles-from-drug-like-indoles.pdf |
60c749db702a9b85aa18b1d3 | 10.26434/chemrxiv.9780596.v2 | Interaction of Hydrogen with Actinide Dioxide (011) Surfaces | <p>The
hydrogen catalysed oxidation of nuclear materials has led to containment vessel
failure. The interaction of hydrogen with actinide dioxide (AnO<sub>2</sub>, An
= U, Np, Pu) (011) surfaces has been completed by DFT+U; where, spin-orbit
interactions and noncollinear 3k antiferromagnetic behaviour have been included.
The energy of atomic hydrogen adsorption for UO<sub>2</sub> (0.44 eV), NpO<sub>2</sub>
(-0.47 eV), and PuO<sub>2</sub> (-1.71 eV) has been calculated, where the subsequent
formation of an OH group is shown to distort the surface structure. The
dissociation of hydrogen on the PuO<sub>2</sub> (011) surfaces has been found;
however, UO<sub>2</sub> (011) and NpO<sub>2</sub> (011) surfaces are relatively
inert. The recombination of hydrogen ions on the UO<sub>2</sub> (011) and NpO<sub>2</sub>
(011) surfaces is highly-probable; whereas, hydroxide formation on the PuO<sub>2</sub>
(011) surface has been shown. The results have consequences for fuel storage
management.</p> | James Pegg; Ashley E. Shields; Mark T. Storr; David Scanlon; Nora De Leeuw | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749db702a9b85aa18b1d3/original/interaction-of-hydrogen-with-actinide-dioxide-011-surfaces.pdf |
61a655f7ceb7d3755101418a | 10.26434/chemrxiv-2021-0b2wc-v3 | Structure-Activity Relationship and Bioactivity Studies of
Neurotrophic trans-Banglene | Neurotrophic small molecule natural products are functional analogs of signaling proteins called neurotrophins, which cause a pro-growth, pro-survival, or pro-differentiation response in neuronal cells. While these phenotypic responses are desirable to combat neurodegenerative disease progression, the pharmacokinetic properties of neurotrophins present challenges to their administration. Therefore, neurotrophic small molecules such as the cis- and trans-banglenes offer attractive alternatives. We describe the synthesis and testing of banglene derivatives and establish a structure-activity response for the banglene family. We demonstrate that (–) trans-banglene is the primarily active enantiomer, and that select modifications on the cyclohexene ring of trans-banglene do not significantly impair its bioactivity. Finally, we demonstrate that (–) trans-banglene potentiation of NGF induced neuritogenesis is unaffected by the presence of these Erk1/2, Akt and Pkc inhibitors. Our structure-activity results also suggest that (–) trans-banglene neurotrophic activity and its potentiation of NGF activity might be distinct unassociated processes. | Khyati Gohil; M. Zain Kazmi; Florence Williams | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a655f7ceb7d3755101418a/original/structure-activity-relationship-and-bioactivity-studies-of-neurotrophic-trans-banglene.pdf |
60c75344567dfe23b9ec5e17 | 10.26434/chemrxiv.11983845.v2 | A Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding | We present a reliable and accurate solution to the induced fit docking problem for protein-ligand binding by combining ligand-based pharmacophore docking (Phase), rigid receptor docking (Glide), and protein structure prediction (Prime) with explicit solvent molecular dynamics simulations. We provide an in-depth description of our novel methodology and present results for 41 targets consisting of 415 cross-docking cases divided amongst a training and test set. For both the training and test-set, we compute binding modes with a ligand-heavy atom RMSD to within 2.5 Å or better in over 90% of cross-docking cases compared to less than 70% of cross-docking cases using our previously published induced-fit docking algorithm and less than 41% using rigid receptor docking. Applications of the predicted ligand-receptor structure in free energy perturbation calculations is demonstrated for both public data and in active drug discovery projects, both retrospectively and prospectively. | Edward Miller; Robert Murphy; Daniel Sindhikara; Ken Borrelli; Matthew Grisewood; Fabio Ranalli; Steven Dixon; Steven Jerome; Nicholas Boyles; Tyler Day; Phani Ghanakota; Sayan Mondal; Salma B. Rafi; Dawn M. Troast; Robert Abel; Richard Friesner | Computational Chemistry and Modeling; Theory - Computational; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75344567dfe23b9ec5e17/original/a-reliable-and-accurate-solution-to-the-induced-fit-docking-problem-for-protein-ligand-binding.pdf |
6234ca3f202c06e82dd88605 | 10.26434/chemrxiv-2022-q9ffh | Ab initio random structure searching and catalytic properties of copper-based nanocluster with Earth-abundant metals for the electrocatalytic CO2-to-CO conversion | Understanding the effect of nano-structuring and metal doping on the properties of copper-based clusters is crucial to developing effective catalysts for the electrochemical conversion of CO2 to value-added chemicals. We present a computational approach based on density functional and random structure searching to investigate the structures of mono- and bi-bimetallic nanoclusters, the acti-vation of CO2 on the catalyst, and the mechanism of CO2 dissociation. We have applied this approach to predict the structure and catalytic properties of Cun (n = 1–55) and (Cu-M)m (M = Fe, Sn, Zn with 1 ≤ m ≤ 27) nanoclusters. We also considered the CO2 acti-vation and conversion on the low index Cu and Cu-M (100) surfaces and high-symmetry (icosahedral) and core-shell Cu-M clusters. We found low-symmetry pure copper clusters with an amorphous character to be the most stable and have higher catalytic activity than the copper surface and high-symmetry icosahedral nanoclusters. In both pure copper and bimetallic systems, the physiosorbed state of CO2 is the most stable and energy is required to activate the molecule. Stabilization of the chemisorbed state occurs in sys-tems such as Cu-Fe where there is a delocalization of orbitals around the Fermi level, causing the large charge transfer from the cata-lyst to CO2. We have also conducted calculations of the free energy profiles of the CO2-to-CO conversion and the competitive hy-drogen evolution reaction (HER). The CO2 reduction reaction is dominant over HER on the Cu randomly generated cluster due to the lower potential limiting step. Among other considered bimetallic, the core@shell models also display good catalytic activity and selectivity towards the CO2 reduction reaction. This work identifies insightful structure-property relationships for CO2 activation, highlighting the influence of size and composition on the CO2 activation and intermediate stability in designing catalytic cupper-based mono- and bi-metallic clusters for the CO2 reduction reaction. | Azeem Ghulam Nabi; Aman ur Rehman; Akhtar Hussain; Devis Di Tommaso | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6234ca3f202c06e82dd88605/original/ab-initio-random-structure-searching-and-catalytic-properties-of-copper-based-nanocluster-with-earth-abundant-metals-for-the-electrocatalytic-co2-to-co-conversion.pdf |
6469a2fbf2112b41e9e3982e | 10.26434/chemrxiv-2023-bdvcr | Enigmatic Alternatives for Epoxides in Graphene Oxide | The structural mystery of the long-known graphene oxide (GO) unfolds as one of the formidably abstract conceptual problems among nanomaterials. Generally construed as the oxidized form of graphene, it is variously proposed to host a variety of functional groups with oxygen and hydrogen. Theoretical studies are abundant on the highly-strained epoxides, while larger cyclic ethers having one or more oxygen atoms and vinylogous carbonyls are paid scant attention even though they are predicted by several structural models. The nature of the geometric and electronic structure of these alternative functional groups, the preferred distribution on the graphene lattice, comparative stability, etc., remains unexplored. Our systematic inquiry into the impact of hexagonal and periodic constraints on these mystic functional groups unveils several surprises. Among those that retain the hexagonal carbon backbone, epoxides are surprisingly more stable than larger ethers despite the excessive strain associated with their acute triangular geometry. Epoxidation conserves the planarity of the carbon backbone that allows their optimal distribution on the lattice by reducing the repulsive interactions from oxygen lone pairs and π-electrons. These findings categorically rule out the possibility of 1,3 ethers in GO and settle the long-standing debate on its existence. They face severe steric repulsion even in low dimensional systems that tear down the σ-skeleton of graphene completely apart, reducing its dimensionality. We show that selective breaking of the σ-bonds is preferred over epoxides if backed by cyclic delocalization of electrons. Particularly, 1,6-diones in trans orientation are thermodynamically favored and justify the large holes experimentally observed through microscopic imaging. | Gaurav Jhaa; Pattath D. Pancharatna; Musiri M. Balakrishnarajan | Organic Chemistry; Materials Science; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6469a2fbf2112b41e9e3982e/original/enigmatic-alternatives-for-epoxides-in-graphene-oxide.pdf |
6540d31f48dad23120c41bdb | 10.26434/chemrxiv-2023-rsrwv | Electrochemical Analysis of Gold Nanoparticles Multifunctionalised with Cytochrome c and a Zinc Porphyrin | Cytochrome c (Cyt c), known for its functional redox capabilities, plays a pivotal role in biological processes such as the electron transport chain and apoptosis. However, understanding how different conjugation strategies impact its structural and redox characteristics is limited. To fill this gap, we investigated the effects of conjugating Cyt c and a zinc(II) porphyrin (Zn Porph) to gold nanoparticles (AuNPs). We used circular dichroism (CD) spectroscopy to detect structural conformational changes in Cyt c upon conjugation and time-of-flight secondary ion mass spectrometry (TOF-SIMS) to identify protein orientation. Cyt c was predicted to have different orientations depending on the size of AuNPs and methods used to conjugate the protein, it was hypothesised that the orientation of Cyt c may influence the redox properties of the protein. The electrochemical properties of Cyt c were assessed using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). We used DPV-based to determine the heterogeneous rate constant (k0). The results show a lower k0 for conjugated Cyt c than free Cyt c, likely due to structural changes in the protein. The spatial orientation of Cyt c had minimal influence on k0, while ligand density and AuNP size had an effect. The k0 value of Zn Porph did not decrease on conjugation. Despite these changes, Cyt c and Zn Porph maintained their electrochemical capabilities after conjugation. | Jordan Potts; Akhil Jain; David Amabilino; Lluïsa Pérez-García; Frankie Rawson | Analytical Chemistry; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6540d31f48dad23120c41bdb/original/electrochemical-analysis-of-gold-nanoparticles-multifunctionalised-with-cytochrome-c-and-a-zinc-porphyrin.pdf |
62557e82d048ede7bd4075d5 | 10.26434/chemrxiv-2022-xdkxs-v2 | Time-resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ion | Daptomycin (DP) is effective against multiple drug-resistant Gram-positive pathogens because of its distinct mechanism of action. An accepted mechanism includes Ca2+-triggered aggregation of the DP molecule to form oligomers. DP and its oligomers have so far defied structural analysis at a molecular level, and we studied the process by the combined use of dynamic light scattering in water and atomic-resolution cinematographic imaging of DP molecules captured on a carbon nanotube on which the DP molecule is installed as a fishhook. We found that the DP molecule aggregates weakly into dimers, trimers, and tetramers in water, and strongly in the presence of calcium ions, and that the tetramer is the largest oligomer in a homogeneous aqueous solution. The dimer remains as the major species under a variety of conditions, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer is the largest oligomer observed both in the absence and in the presence of a large excess of calcium ions. Taken together with statistical data, the microscopic structural information obtained at a single-molecule level favors a cyclic form of the dimer and the tetramer over a linear or stacked form. Such experimental structural information is new and will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording of dynamic motions of molecules for the study of self-organization processes. | Takayuki Nakamuro; Ko Kamei; Keyi Sun; Jeffrey W. Bode; Koji Harano; Eiichi Nakamura | Organic Chemistry; Nanoscience; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62557e82d048ede7bd4075d5/original/time-resolved-atomistic-imaging-and-statistical-analysis-of-daptomycin-oligomers-with-and-without-calcium-ion.pdf |
60c73f9b337d6c2fb2e26537 | 10.26434/chemrxiv.6964703.v3 | Photoactivatable Hsp47: A Tool to Control and Regulate Collagen Secretion & Assembly | Hsp47 is a chaperone protein with a fundamental
role in the folding, stability and intracellular transport of procollagen
triple helices. A light-responsive Hsp47 recombinant protein, engineered to
control in situ the production and assembly of cellular collagen is here
demonstrated. This novel light-driven tool enables unprecedented fundamental
studies of collagen biosynthesis and associated diseases. | Essak Khan; Shrikrishnan Sankaran; Julieta Paez; Christina Muth; Mitchell Han; Aránzazu del Campo | Photochemistry (Org.); Biocompatible Materials; Biological Materials; Biopolymers; Biochemistry; Bioengineering and Biotechnology; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9b337d6c2fb2e26537/original/photoactivatable-hsp47-a-tool-to-control-and-regulate-collagen-secretion-assembly.pdf |
61b3b18d689c872488de8301 | 10.26434/chemrxiv-2021-zthkp | Finding the Sweet Spot of Photocatalysis – A Case Study using Bipyridine-based CTFs | Covalent Triazine Frameworks (CTFs) are a class of Porous Organic Polymers which attracts continuously growing interest because of their outstanding chemical and physical properties. However, the control of extended porous organic frameworks’ structures at the molecular scale for a precise adjustment of their properties has hardly been achieved so far. Here, we present a series of bipyridine-based CTFs synthesized through polycondensation, in which the sequence of specific building blocks is well controlled. The reported synthetic strategy allows to tailor the physicochemical features of the CTF materials, including nitrogen content, apparent specific surface area and opto-electronic properties. Based on a comprehensive analytic investigation, we demonstrate a direct correlation of the CTF bipyridine content with the material features such as specific surface area, bandgap, charge separation and surface wettability with water. The entirety of those parameters dictates the catalytic activity as demonstrated for the photocatalytic hydrogen evolution reaction (HER). The material with the necessary balance between opto-electronic properties and highest hydrophilicity enables HER production rates of up to 7.2 mmol·h-1·g-1 under visible light irradiation and in the presence of a platinum co-catalyst. | Marcelo Alves Fávaro; Daniel Ditz; Jin Yang; Ashta C. Ghosh; Chantal Lorentz; Jérôme Roeser; Elsje Alessandra Quadrelli; Arne Thomas; Regina Palkovits; Jérôme Canivet; Florian M. Wisser | Catalysis; Heterogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b3b18d689c872488de8301/original/finding-the-sweet-spot-of-photocatalysis-a-case-study-using-bipyridine-based-ct-fs.pdf |
65e71c8ae9ebbb4db9f26283 | 10.26434/chemrxiv-2024-8sc71 | Tuning sorbent properties to reduce the cost of direct air capture | The question has shifted from whether solid sorbents can work in direct air capture (DAC) technologies to which solid sorbents are more economically advantaged. Determining this is challenging due to the influence of many different yet interconnected sorbent properties on the cost of CO2 capture. Existing DAC economic models oversimplify sorbent stability by treating it as a simple replacement rate, neglecting crucial factors such as capacity loss rate and form. To address this challenge, we have developed an economic model that accounts for sorbent degradation in DAC processes. By factoring in capacity loss over time, our model provides a more accurate estimate of the cost associated with DAC and highlights the optimum time for sorbent replacement. We then identified sorbent characteristics and process features that minimize both the carbon footprint and the cost of captured CO2. To further investigate the interplay of sorbent properties and DAC cost, we constructed a series of alkyl- and epoxy-functionalized polyamine sorbents. The sorbents’ CO2 uptake, heat of adsorption and capacity fade were adjusted via a one-step modification, varying the proportions of primary, secondary, and tertiary amines. We then integrated the experimentally-measured parameters, including the form of degradation, into our economic model to probe which combination of sorbent properties results in the lowest cost of DAC for a fixed operating condition. The results provide guidelines and priorities for sorbent performance metrics that will yield the most cost-effective DAC technologies. | Hannah E. Holmes; Sayan Banerjee; Anthony Vallace; Ryan P. Lively; Christopher W. Jones; Matthew J. Realff | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e71c8ae9ebbb4db9f26283/original/tuning-sorbent-properties-to-reduce-the-cost-of-direct-air-capture.pdf |
665026ff418a5379b025e9a7 | 10.26434/chemrxiv-2024-0q1cm | Continuous N2O capture and reduction to N2 using Ca-zeolite adsorbent and Pd/La/Al2O3 reduction catalyst | There is an urgent need to develop effective methods for converting nitrous oxide (N2O) into non-harmful N2 because N2O is a potent greenhouse gas, and its increasing concentration in the atmosphere is a major concern for global warming. In this study, we developed a two-step N2O capture and reduction system, employing CaO-incorporated zeolites (Ca-zeolites) as N2O adsorbents and Pd nanoparticles on La-containing Al2O3 (Pd/La/Al2O3) as catalysts for N2O reduction. This process is suitable for continuous operation over a temperature swing of 50–150 °C. The N2O capture capacity and subsequent reduction ability were preserved for at least 15 h (10 cycles). Notably, this system can operate at low temperatures (below 150 °C) using a simple temperature-swing process in the presence of O2. | Yuan Jing; Chenxi He; Li Wan; Jiahuan Tong; Jialei Zhang; Shinya Mine; Ningqiang Zhang; Yuuta Kageyama; Hironori Inomata; Ken-ichi Shimizu; Takashi Toyao | Catalysis; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665026ff418a5379b025e9a7/original/continuous-n2o-capture-and-reduction-to-n2-using-ca-zeolite-adsorbent-and-pd-la-al2o3-reduction-catalyst.pdf |
626ba7a6d048ed5edd55633a | 10.26434/chemrxiv-2022-t149s | Supervariate ceramics: ice-like solids, stress-induced liquefaction, and biomineralization | Unlike the malleable polymers or metals, ceramics and many other inorganic materials are harder to process, because of their brittle nature and high melting points. If these refractory materials could be liquefied at lower temperatures, their fusion, molding, casting, mixing, deformation, segmentation, carving, and polishing would be greatly facilitated. Here we report a stress-induced liquefaction mechanism that transforms “ice-like” (shrinking upon melting) materials into supercooled liquids at room temperature, opening a route for processing refractory substances. Furthermore, this discovery sheds light on key puzzles in materials science, particularly how life fuse and modify bioceramics in water under ambient conditions. | Jie Pan; Chong Wang; Jing Zhong; Hongkun Li; Zhengtao Xu; Jian Lu; Yang Yang LI | Materials Science; Ceramics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626ba7a6d048ed5edd55633a/original/supervariate-ceramics-ice-like-solids-stress-induced-liquefaction-and-biomineralization.pdf |
65ddb53c66c1381729aa7ce9 | 10.26434/chemrxiv-2024-pvzsr | Friedel-Crafts Benzylations Mediated by FeCl3-based Deep Eutectic Solvents. Access to Substituted 1,1-diarylalkanes using Activated and Deactivated Electrophiles | The development of new, more efficient Friedel-Crafts arylation methodologies that provide access to 1,1- diarylalkanes is an important objective of interest for the production of pharmaceuticals and fine chemical products. In this regard, this study introduces a novel synthetic route to 1,1-diarylalkanes conducted in the Deep Eutectic Solvent (DES) 3FeCl3 · 6H2O/Gly, which serves as both a reaction medium and promoter. Under these conditions, Friedel-Crafts benzylations of various arenes bearing activating and deactivating ortho-/para-directing groups, can be performed using diverse benzylating reagents such as styrenes, alcohols, acetates, ethers, and chlorides. Importantly, highly electronically deactivated electrophiles, including those with CF3 and NO2 groups, are suitable substrates. This methodology provides a wide range of asymmetric 1,1-diarylalkanes (up to 124 examples) with generally good yields and high regioselectivities. The efficacy of this approach was demonstrated with the multigram-scale synthesis (10 mmol) of 1-phenyl-1-xylyl ethane (PXE), a liquid with great industrial applicability. Moreover, the Fe(III)-based DES could be reused for a minimum of 20 consecutive cycles with no appreciable erosion of the yields. | Alejandro Presa Soto; Marina Ramos-Martín; Joaquín García-Álvarez | Organic Chemistry; Inorganic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ddb53c66c1381729aa7ce9/original/friedel-crafts-benzylations-mediated-by-fe-cl3-based-deep-eutectic-solvents-access-to-substituted-1-1-diarylalkanes-using-activated-and-deactivated-electrophiles.pdf |
60c7478e842e657deddb29bd | 10.26434/chemrxiv.10031789.v3 | Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On-the-Fly Approach | <div>We present a methodology using fixed charge force-fields for alchemical solvation free energy calculations which accounts for the change in polarity that the solute experiences as it transfers from the gas-phase to the condensed phase. We update partial charges using QM/MM snapshots, decoupling the electric field appropriately when updating the partial charges. We also show how to account for the cost of self-polarization. We test our methodology on 30 molecules ranging from small polar to large drug-like molecules. We use Minimum Basis Iterative Stockholder (MBIS), Restrained Electrostatic Potential (RESP) and AM1-BCC partial charge methodologies. Using our method with MP2/cc-pVTZ and MBIS partial charges yields an Average Absolute Deviation (AAD) of 6.3 kJ·mol−1 in comparison with the AM1-BCC result of 8.6 kJ·mol−1. AM1-BCC is within experimental uncertainty on 10% of the data compared to 30% with our method. We conjecture that results can be further improved by using Lennard-Jones and torsional parameters refitted to MBIS and RESP partial charge methods that use high levels of theory.</div> | Braden Kelly; William Smith | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7478e842e657deddb29bd/original/alchemical-hydration-free-energy-calculations-using-molecular-dynamics-with-explicit-polarization-and-induced-polarity-decoupling-an-on-the-fly-approach.pdf |
65e98929e9ebbb4db926f474 | 10.26434/chemrxiv-2024-0h765 | Insights into energy transfer in Light-harvesting complex II through machine-learning assisted simulations | Light-Harvesting Complex II (LHCII) is the major antenna of higher plants. Energy transfer processes taking place inside its aggregate of chlorophylls have been experimentally investigated with time-resolved techniques, but a complete understanding of the most relevant energy transfer pathways and relative characteristic times remains elusive. Theoretical models to disentangle experimental data in LHCII have long been challenged by the large size and complex nature of the system. Here, we show that a fully first-principles approach combining molecular dynamics and machine learning can be successfully used to reproduce transient absorption spectra and characterize the EET pathways and the involved times. | Elena Betti; Piermarco Saraceno; Edoardo Cignoni; Lorenzo Cupellini; Benedetta Mennucci | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e98929e9ebbb4db926f474/original/insights-into-energy-transfer-in-light-harvesting-complex-ii-through-machine-learning-assisted-simulations.pdf |
670863eb51558a15efbc8ad9 | 10.26434/chemrxiv-2024-cpjgk | Engineer Reversible Nanocomposite by Programming Amorphous Polymer Conformation Under Nanoconfinement | We utilize nanoconfinements to program how polymers entangle and disentangle as chain clusters to engineer pseudo bonds with tunable strength, multivalency, and directionality. When amorphous polymers are grafted to nanoparticles that are one magnitude larger in size than individual polymer, programming grafted chain conformations can “synthesize” high performance nanocomposites with moduli of ~25GPa and a circular lifecycle without forming and/or breaking chemical bonds. These nanocomposites dissipate external stresses by disentangling and stretching grafted polymers up to ~98% of their contour length, analogous to that of folded proteins; use both polymers and nanoparticles for load bearing; and exhibit a non-linear dependence on composition throughout the microscopic, nanoscopic and single particle levels. | Tiffany Chen; Yiwen Qian; Antoine Laine; Junpyo Kwon; Luofu Liu; Subhadeep Pal; Supriya Gupta ; Emma Vargo; Gregory Su; Robert Ritchie; Sinan Keten; Rui Wang; Miquel Salmeron; Ting Xu | Materials Science; Composites | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670863eb51558a15efbc8ad9/original/engineer-reversible-nanocomposite-by-programming-amorphous-polymer-conformation-under-nanoconfinement.pdf |
60c74efef96a0075c0287ba9 | 10.26434/chemrxiv.12818780.v1 | Inexpensive Open Source Laser Cut Model Kits for the Teaching of Molecular Geometry | We recently published
an article in the <i>Journal of Chemical
Education</i> on VSEPR model kits for helping teach molecular geometry. We have used these transparent acrylic models for several years now at the
University of Victoria, but the challenges of COVID-19 meant that this year we
needed to make a faster, less expensive version that could be easily mailed out
to our students, without requiring any sorting and packaging steps. Accordingly,
we designed a version that can be cut out of 2 mm thick recycled “chipboard” cardboard,
in which all 26 parts for the 13 different models fit in one piece of card 175
× 120 mm (and 16 of these kits can be cut from one sheet in the laser cutter). The
material cost is less than $0.25 per kit and the cutting time on our machine
(Trotec Speedy360, 130 W) is 1 minute and 45 seconds per kit. These files are
made freely available for all interested users as supporting information for
this contribution, in CorelDraw, Adobe Illustrator, pdf and dxf formats.<div><div>
</div>
</div> | Sean Adams; J Scott McIndoe | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74efef96a0075c0287ba9/original/inexpensive-open-source-laser-cut-model-kits-for-the-teaching-of-molecular-geometry.pdf |
60c74d7c4c8919af59ad3816 | 10.26434/chemrxiv.11901894.v3 | Three Distinct Torsion Profiles of Electronic Transmission Through Linear Carbon Wires | <p>The one-dimensional carbon allotrope carbyne, a linear chain of <i>sp</i>-hybridized carbon atoms, is predicted to exist in a polyynic and a cumulenic structure. While molecular forms of carbyne have been extensively characterized, the structural nature is hard to determine for many linear carbon wires that are made in-situ during pulling experiments. Here, we show that cumulenes and polyynes have distinctively different low-bias conductance profiles under axial torsion. We analyze the change of the electronic structure, Landauer transmission, and ballistic current density of the three types of closed-shell molecular carbynes as a function of the torsion angle. Both polyynic, odd-carbon cumulenic,<i> </i>and even-carbon cumulenic carbon wires exhibit helical frontier molecular orbitals when the end-groups are not in a co-planar configuration. This helical conjugation effect gives rise to strong ring current patterns around the linear wires. Only the transmission of even-carbon polyynic wires follows the well-known cosine-squared law with axial torsion that is also seen in biphenyl-type systems. Notably, the transmission of even-carbon cumulenic carbon wires rises with axial torsion from co-planar towards perpendicular orientation of the end-groups. The three distinct transmission profiles of polyynes, odd-carbon cumulenes,<i> </i>and even-carbon cumulenes may allow for experimental identification of the structural nature of linear carbon wires. Their different electron transport properties under axial torsion furthermore underline that, in the molecular limit of carbyne, three different subclasses of linear carbon wires exist.</p> | Marc Hamilton Garner; William Bro-Jørgensen; Gemma C. Solomon | Nanodevices; Theory - Computational; Quantum Mechanics; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d7c4c8919af59ad3816/original/three-distinct-torsion-profiles-of-electronic-transmission-through-linear-carbon-wires.pdf |
60c741a8bdbb899dbaa383ac | 10.26434/chemrxiv.8081504.v1 | Chemical Availability of Bromide Dictates CsPbBr3 Nanocrystal Growth | Lack of detailed understanding of the growth mechanism of CsPbBr3 nanocrystals has hindered sophisticated morphological and chemical control of this important emerging optoelectronic material. Here, we have elucidated the growth mechanism by slowing the reaction kinetics. When 1-bromohexane is used as an alternative halide source, bromide is slowly released into the reaction mixture, extending the reaction time from ~3 seconds to greater than 20 minutes. This enables us to monitor the phase evolution of products over the course of reaction, revealing that CsBr is the initial species formed, followed by Cs4PbBr6, and finally CsPbBr3. Further, formation of monodisperse CsBr nanocrystals is demonstrated in a bromide-deficient and lead-abundant solution. The CsBr can only be transformed into CsPbBr3 nanocubes if additional bromide is added. Our results indicate a fundamentally different growth mechanism for CsPbBr3 in comparison with more established semiconductor nanocrystal systems and reveal the critical role of the chemical availability of bromide for the growth reactions.<br /> | Je-Ruei Wen; Benjamin Roman; Freddy Rodriguez Ortiz; Noel Mireles Villegas; Nicholas Porcellino; Matthew Sheldon | Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a8bdbb899dbaa383ac/original/chemical-availability-of-bromide-dictates-cs-pb-br3-nanocrystal-growth.pdf |
60c7483c337d6c1652e274e7 | 10.26434/chemrxiv.11687139.v1 | Coordinated Action of NRPS, Baeyer-Villiger Monooxygenase, and Methyltransferase Ensures the Economical Biosynthesis of Bohemamines in Streptomyces sp. CB02009 | <p> Bohemamines (BHMs) are bacterial alkaloids containing a pyrrolizidine core with two unprecedented methyl groups. Herein we report the activation of BHMs biosynthesis in <i>Streptomyces </i>sp. CB02009 using a ribosome engineering approach. Identification and characterization of the <i>bhm</i> gene cluster reveals a coordinated action of nonribosomal peptide synthetase BhmJ, Baeyer-villiger monooxygenase BhmK and methyltransferase BhmG for BHMs biosynthesis. BhmG is responsible for the C-methylation on C-7, while the C-9 methyl group is from a non-proteinogenic amino acid (2<i>S</i>,5<i>S</i>)-5-methylproline, required for BHMs production in three model <i>Streptomyces </i>hosts. Our study shed light on the intricate interaction of BhmJ/BhmK/BhmG for the economical biosynthesis of BHMs in their native producer, and also unraveled that BhmJ and BhmK are competent biocatalysts in <i>S</i><i>treptomyce </i><i>albus</i>.</p> | Ling Liu; Sainan Li; Runze Sun; Xiangjing Qin; Jianhua Ju; Changsheng Zhang; Yanwen Duan; Yong Huang | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7483c337d6c1652e274e7/original/coordinated-action-of-nrps-baeyer-villiger-monooxygenase-and-methyltransferase-ensures-the-economical-biosynthesis-of-bohemamines-in-streptomyces-sp-cb02009.pdf |
64ee4a7479853bbd78b21dc7 | 10.26434/chemrxiv-2023-qkjtb-v2 | ORDerly: Datasets and benchmarks for chemical reaction data | Machine learning has the potential to provide tremendous value to the life sciences by providing models that aid in the discovery of new molecules and reduce the time for new products to come to market. Chemical reactions play a significant role in these fields, but there is a lack of high-quality open-source chemical reaction datasets for training ML models. Herein, we present ORDerly, an open-source Python package for customizable and reproducible preparation of reaction data stored in accordance with the increasingly popular Open Reaction Database (ORD) schema. We use ORDerly to clean US patent data stored in ORD and generate datasets for forward prediction, retrosynthesis, as well as the first benchmark for reaction condition prediction. We train neural networks on datasets generated with ORDerly for condition prediction and show that datasets missing key cleaning steps can lead to silently overinflated performance metrics. Additionally, we train transformers for forward and retrosynthesis prediction and demonstrate how non-patent data can be used to evaluate model generalisation. By providing a customizable open-source solution for cleaning and preparing large chemical reaction data, ORDerly is poised to push forward the boundaries of machine learning applications in chemistry. | Daniel Wigh; Joe Arrowsmith; Alexander Pomberger; Kobi Felton; Alexei Lapkin | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ee4a7479853bbd78b21dc7/original/or-derly-datasets-and-benchmarks-for-chemical-reaction-data.pdf |
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