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6436794e08c86922ffd57a1c | 10.26434/chemrxiv-2023-chzq3 | Excited-state singlet-triplet inversion in hexagonal aromatic and heteroaromatic compounds | The inversion of the energies of the lowest singlet (S1) and triplet (T1) excited states in violation of Hund’s multiplicity rule is a rare phenomenon in stable organic molecules. S1-T1 inversion has significant consequences for the photophysics and photochemistry of organic chromophores. In this work, ab initio computational methods were employed to explore the possibility of S1-T1 inversion in hexagonal polycyclic aromatic and heteroaromatic compounds. Although the singlet-triplet energy gap ΔST = ES1 – ET1 decreases with increasing size of hexagonal polycyclic aromatics, it remains positive up to kekulene (19 rings). However, symmetric substitution of C-C pairs by B-N groups in the interior, keeping the conjugation of the outer rim intact, results in compounds with robustly negative ΔST. The non-overlapping pattern of the densities of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) is identified as the decisive criterion for S1-T1 inversion. These findings establish the existence of a new family of boron carbon nitrides with inverted singlet-triplet gaps. | Andrzej L. Sobolewski; Wolfgang Domcke | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6436794e08c86922ffd57a1c/original/excited-state-singlet-triplet-inversion-in-hexagonal-aromatic-and-heteroaromatic-compounds.pdf |
60c9e3b1551c4f6c67c4c30a | 10.26434/chemrxiv.14774898.v1 | Engineering Dirhodium Artificial Metalloenzymes for Diazo Coupling Cascade Reactions | <p>Artificial metalloenzymes (ArMs) are now commonly used to control the stereoselectivity of catalytic reactions, but controlling ArM chemoselectivity remains challenging. In this study, we engineer a dirhodium ArM to catalyze diazo cross-coupling to form an alkene that, in a one-pot cascade reaction, is reduced to an alkane with high enantioselectivity (typically >99% e.e.) by an alkene reductase. The numerous protein and small molecule components required for the cascade reaction had minimal effect on ArM catalysis, while the dirhodium cofactor itself provided only O-H insertion products from reaction with water and glucose under the same conditions. Directed evolution of the ArM led to improved yields and E/Z selectivities for a variety of substrates, which translated well to cascade reaction yields. MD simulations of ArM variants were used to understand the structural role of the cofactor on large-scale scaffold structural dynamics. These results highlight the ability of ArMs to control both catalyst stereoselectivity and chemoselectivity to enable reactions in complex media that would otherwise lead to undesired side reactions.</p> | David M. Upp; Rui Huang; Ying Li; Maxwell J. Bultman; Benoît Roux; Jared C. Lewis | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b1551c4f6c67c4c30a/original/engineering-dirhodium-artificial-metalloenzymes-for-diazo-coupling-cascade-reactions.pdf |
60c73d91567dfeb421ec3651 | 10.26434/chemrxiv.5858538.v1 | The Influence of Nanoscale Roughness on the Electrostatic Double Layer: the Shift of the Isoelectric Point of Cluster-Assembled Nanostructured Zirconia Films | We investigated the influence of the nanoscale surface morphology on the electrostatic double layer at corrugated surfaces in aqueous electrolytes. To this purpose, we have produced cluster-assembled nanostructured zirconium dioxide (ns-ZrOx, x ≈ 2) films with controlled morphological properties by supersonic cluster beam deposition (SCBD), and measured the double layer interaction using atomic force microscopy with colloidal probes. SCBD allowed tuning the characteristic widths of the corrugated interface (the rms roughness, the correlation length) across a wide range of values, matching the width of the electrostatic double-layer (the Debye length), and the typical size of nano-colloids (proteins, enzymes, and catalytic nanoparticles). To accurately characterize the surface charge density in the high-roughness regime, we have developed a two-exponential model of the electrostatic force that explicitly includes roughness, and better accounts for the roughness-induced amplification of the interaction. We were then able to observe a marked reduction of the isoelectric point of ns-ZrOx surfaces on increasingly rough surfaces. This result is in good agreement with our previous observations on cluster-assembled nanostructured titania films, and demonstrates that the phenomenon is not limited to a specific material, but more generally depends on peculiar nanoscale morphological effects, related to the competition of the characteristic lengths of the system.<br /> | Francesca Borghi; Bianca Scaparra; Costanza Paternoster; Paolo Milani; Alessandro Podestà | Thin Films; Nanostructured Materials - Nanoscience; Interfaces; Physical and Chemical Properties; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d91567dfeb421ec3651/original/the-influence-of-nanoscale-roughness-on-the-electrostatic-double-layer-the-shift-of-the-isoelectric-point-of-cluster-assembled-nanostructured-zirconia-films.pdf |
63160d533e2e36cd462baf77 | 10.26434/chemrxiv-2022-38ws8 | Synthetic control of intrinsic defect formation in metal oxide nanocrystals using dissociated spectator metal salts | Crystallographic defects are essential to the functional properties of semiconductors, controlling everything from conductivity to optical properties and catalytic activity. In nanocrystals, too, defect engineering with extrinsic dopants has been fruitful. Although intrinsic defects like vacancies can be equally useful, synthetic strategies for controlling their generation are comparatively underdeveloped. Here we show that intrinsic defect concentration can be tuned during synthesis of colloidal metal oxide nanocrystals by the addition of metal salts. Although not incorporated in the nanocrystals, the metal salts dissociate at high temperature, promoting the dissociation of carboxylate ligands from metal precursors, leading to introduction of oxygen vacancies. For example, the concentration of oxygen vacancies can be controlled up to 9% in indium oxide nanocrystals. This method is broadly applicable as we demonstrate by generating intrinsic defects in metal oxide nanocrystals of various morphologies and compositions. | Kihoon Kim; Jiwon Yu; Jungchul Noh; Lauren Reimnitz; Matthew Chang; Daniel Gamelin; Brian Korgel; Gyeong Hwang; Delia Milliron | Inorganic Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63160d533e2e36cd462baf77/original/synthetic-control-of-intrinsic-defect-formation-in-metal-oxide-nanocrystals-using-dissociated-spectator-metal-salts.pdf |
65bcf82f66c1381729cff84a | 10.26434/chemrxiv-2024-6xndt | Encapsulation of InP/ZnS quantum dots into MOF-5 matrices for solid-state luminescence: ship in the bottle and bottle around the ship methodologies. | The utilization of InP-based quantum dots (QDs) as alternative luminescent nanoparticles to cadmium-based QDs, known for their toxicity, is actively pursued. However, leveraging their luminescent attributes for solid-state applications presents challenges due to the sensitivity of InP QDs to oxidation and aggregation-caused quenching. Hence an appealing strategy is to protect and disperse InP QDs within hybrid materials. Metal-organic frameworks (MOFs) offer a promising solution as readily available crystalline porous materials. Among these, MOF-5, composed of {Zn4O}6+ nodes and terephthalate struts, can be synthesized under mild conditions (at room temperature and basic pH), making it compatible with InP QDs. In the present work, luminescent InP QDs are successfully incorporated within MOF-5 through two distinct methods. Firstly, employing the bottle around the ship (BAS) approach, wherein the MOF was synthesized around2 the QDs. Secondly, utilizing the ship in the bottle (SIB) strategy, the QDs were embedded via capillarity into a specially engineered, more porous variant of MOF-5. Comparative analysis of the BAS and SIB approaches, evaluating factors such as operational simplicity, photoluminescence properties, and the resistance of the final materials to leaching are carried out. This comparative study provides insights into the efficacy of these strategies for the integration of InP QDs within MOF-5 for potential solid-state applications in materials chemistry. | Alexis Tran; Rodolphe Valleix; François Réveret; Lawrence Frezet; Federico Cisnetti; Damien Boyer | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bcf82f66c1381729cff84a/original/encapsulation-of-in-p-zn-s-quantum-dots-into-mof-5-matrices-for-solid-state-luminescence-ship-in-the-bottle-and-bottle-around-the-ship-methodologies.pdf |
63a9208816e9a8f0af35130c | 10.26434/chemrxiv-2022-n2xk8-v2 | Microplastics in the Nigerian Environment- A review | The use of plastics and their applications is growing by the second. Their quick production and consequent improper disposal have made plastics a concern for researchers and policymakers. Plastics less than 5 mm are called microplastics and are now found almost everywhere. Microplastics are very resistant to microbial degradation and can spend a century before being thoroughly degraded, their introduction into the environment poses a threat. In addition, microplastics are easily broken out of plastics while in contact with light or radiation, which causes them to break down. It is worth emphasising that there are just a few researchers working on this subject in Nigeria, and there is a void that needs to be addressed. Nevertheless, the persistence of microplastics in the food chain and ecology has been identified as a significant issue. For that purpose, a number of studies have been conducted in the country, quantifying microplastics from various sources, such as the air, water, and soils. This paper examines the environmental hazard posed by plastics and microplastics, including contributions from the Nigerian scientific community, research gaps, and potential solutions. | Ayodele Ifeoluwa Faleti | Polymer Science; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes | CC BY NC 4.0 | CHEMRXIV | 2022-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a9208816e9a8f0af35130c/original/microplastics-in-the-nigerian-environment-a-review.pdf |
66799359c9c6a5c07a47fc67 | 10.26434/chemrxiv-2024-19n7x | Validation of a Rapid GC-MS Method for Forensic Seized Drug and Ignitable Liquid Screening Applications | With the lack of standardized validation protocols across the forensic chemistry community, validation of instrumentation can be a challenging and time-consuming task. However, this process is crucial to understand the associated capabilities and limitations, especially for nascent technologies. Rapid GC-MS is one such emerging analytical technique being increasingly implemented in forensic laboratories due to its fast and informative screening capabilities. However, a full validation for forensic samples has yet to be published since its debut. This work presents the results of a comprehensive validation of an in-house rapid GC-MS system for seized drug and ignitable liquid analyses through the assessment of nine components: selectivity, matrix effects, precision, accuracy, range, carryover/contamination, robustness, ruggedness, and stability. Single- and/or multi-compound test solutions of commonly encountered seized drug or ignitable liquid compounds were used for each study to assess method and system performance. Results met the designated acceptance criteria for a majority of components. For example, retention time and mass spectral search score % RSDs were ≤ 10 % for precision and robustness studies. Limitations were identified for components that did not meet the acceptance criteria (e.g., inability for isomer differentiation). The study designs are part of a larger validation package developed for rapid GC-MS that includes validation plans and automated workbooks for each forensic application. The template, available for adoption by laboratories as needed, ultimately aims to reduce the barrier of implementation for rapid GC-MS technology. | Briana Capistran; Edward Sisco | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66799359c9c6a5c07a47fc67/original/validation-of-a-rapid-gc-ms-method-for-forensic-seized-drug-and-ignitable-liquid-screening-applications.pdf |
619b13642bf8a9fb5de77e6c | 10.26434/chemrxiv-2021-jnv18 | Biosynthesis-Guided Discovery of Enteropeptins, Unusual
Sactipeptides Containing an N-Methylornithine
| The combination of next-generation DNA sequencing technologies and bioinformatics have revitalized natural product discovery. Using a new bioinformatic search strategy, we recently identified ~600 gene clusters in animal microbiomes that code for ribosomal peptide natural products synthesized by radical S-adenosylmethionine enzymes. These grouped into 16 subfamilies and pointed to an unexplored microbiome biosynthetic landscape. Herein, we report the structure, biosynthesis, and function of one of these natural product groups, that we term enteropeptins, from the gut microbe Enterococcus cecorum. We elucidate three novel reactions, each catalyzed by a different family of metalloenzymes, in the biosynthesis of enteropeptins. Among these, we characterize the founding member of a widespread superfamily of Fe-S-containing methyltransferases, which, together with a di-Mn-dependent arginase, installs an N-methylornithine in the peptide sequence. Biological assays with the mature product revealed bacteriostatic activity only against the producing strain, extending an emerging theme of fratricidal or self-inhibitory metabolites in microbiome firmicutes. | Kenzie A. Clark; Brett C. Covington ; Mohammad R. Seyedsayamdost | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619b13642bf8a9fb5de77e6c/original/biosynthesis-guided-discovery-of-enteropeptins-unusual-sactipeptides-containing-an-n-methylornithine.pdf |
60c74bbf469df47dcdf43f7e | 10.26434/chemrxiv.12377693.v1 | Uncovering a copper(II) Alkynyl Complex in C−C Bond Forming Reactions | <p>Copper(II) alkynyl species are proposed as key intermediates in numerous Cu−catalysed C−C coupling reactions. Supported by a β−diketiminate ligand, the three coordinate copper(II) alkynyl [Cu<sup>II</sup>]−C≡CAr (Ar = 2,6−Cl<sub>2</sub>C<sub>6</sub>H<sub>3</sub>) forms upon reaction of the alkyne H−C≡CAr with the copper(II) <i>tert</i>−butoxide complex [Cu<sup>II</sup>]−O<i><sup>t</sup></i>Bu. In solution, this [Cu<sup>II</sup>]−C≡CAr species cleanly transforms the to the Glaser coupling product ArC≡C−C≡CAr and [Cu<sup>I</sup>](solvent). Addition of nucleophiles R′C≡CLi (R′ = aryl, silyl) and Ph–Li to [Cu<sup>II</sup>]−C≡CAr affords the corresponding C<sub>sp</sub>−C<sub>sp</sub> and C<sub>sp</sub>−C<sub>sp2</sub>coupled products RC≡C−C≡CAr and Ph–C≡CAr with concomitant generation of [Cu<sup>I</sup>](solvent) and {[Cu<sup>I</sup>]−C≡CAr}<sup>−</sup>. Supported by DFT calculations, redox disproportionation forms [Cu<sup>III</sup>](C≡CAr)(R) species that reductively eliminate R−C≡CAr products. [Cu<sup>II</sup>]−C<a>≡</a>CAr also captures the trityl radical Ph<sub>3</sub>C• to give Ph<sub>3</sub>C−C≡CAr. Radical capture represents the key C<sub>sp</sub>−C<sub>sp3</sub> bond forming step in the copper catalysed C-H functionalization of benzylic substrates R−H with alkynes H−C≡CR′ (R′ = (hetero)aryl, silyl) that provide C<sub>sp</sub>−C<sub>sp3</sub> coupled products R−C≡CR via radical relay with <i><sup>t</sup></i>BuOO<i><sup>t</sup></i>Bu as oxidant.</p> | Abolghasem (Gus) Bakhoda; Otome Okoromoba; Christine Greene; Mahdi Raghibi Boroujeni; Jeffery A. Bertke; Timothy H. Warren | Organic Synthesis and Reactions; Organometallic Compounds; Homogeneous Catalysis; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bbf469df47dcdf43f7e/original/uncovering-a-copper-ii-alkynyl-complex-in-c-c-bond-forming-reactions.pdf |
60c742ac702a9b355418a4c7 | 10.26434/chemrxiv.8343995.v1 | Prediction and Interpretable Visualization of Synthetic Reactions Using Graph Convolutional Networks | <div>Recently, many research groups have been addressing data-driven approaches for reaction prediction and retrosynthetic analysis. Although the performances of the data-driven approach have progressed due to recent advances of machine learning and deep learning techniques, problems such as improving capability of reaction prediction and the black-box problem of neural networks still persist for practical use by chemists. To expand data-driven approaches to chemists, we focused on two challenges: improvement of reaction prediction and interpretability of the prediction. In this paper, we propose an interpretable prediction framework using Graph Convolutional Networks (GCN) for reaction prediction and Integrated Gradients (IGs) for visualization of contributions to the prediction to address these challenges. As a result, our model showed better performances than the approach using Extended-Connectivity Fingerprint (ECFP). Furthermore, IGs based visualization of the GCN prediction successfully highlighted reaction-related atoms.</div> | Shoichi Ishida; Kei Terayama; ryosuke kojima; Kiyosei Takasu; Yasushi Okuno | Organic Synthesis and Reactions; Chemoinformatics; Computational Chemistry and Modeling; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ac702a9b355418a4c7/original/prediction-and-interpretable-visualization-of-synthetic-reactions-using-graph-convolutional-networks.pdf |
62f50e3569f3a58302b3e956 | 10.26434/chemrxiv-2022-45861 | The Commercial Antibiotics with Inherent Aggregation-Induced Emission Characteristics | Pharmacologists usually focus on the structure-activity relationships of drugs, such as antibiotics, to enhance their activity, but often ignore their optical properties. However, investigating their photophysical properties is of great significance because they could be used to in situ visualize their positions and help us to understand their working metabolism. In this work, we identified a class of commercialized antibiotics, such as levofloxacin, norfloxacin, and moxifloxacin (MXF) hydrochloride, featuring the unique aggregation-induced emission (AIE) characteristics. By taking advantage of their AIE feature, antibiotic metabolism in cells could be in situ visualized, which clearly shows that the luminescent aggregates accumulate in the lysosomes. Moreover, after a structure-activity relationship study, we found an ideal site of MXF to be modified with a triphenylphosphonium and an antibiotic derivative MXF-P was prepared, which is able to specifically differentiate bacterial species after only 10 min of treatment. Moreover, MXF-P shows highly effective broad-spectrum antibacterial activity, excellent therapeutic effects and biosafety for S. aureus-infected wound recovery. Thus, this work not only discovers the multifunctionalities of the antibiotics but also provides a feasible strategy to make the commercialized drugs more powerful. | Bingnan Wang; Lirong Wang; Haozhong Wu; Xiaolin Liu; Jiamiao Zhu; Rong Hu; Dan Ding; Anjun Qin; Ben Zhong Tang | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f50e3569f3a58302b3e956/original/the-commercial-antibiotics-with-inherent-aggregation-induced-emission-characteristics.pdf |
638437364b1a5f49c38f9d9b | 10.26434/chemrxiv-2022-151bv | Synthesis of polyacene: exceeding the limits of benzene rings extension | The acene series, an important class of linearly polycyclic aromatic hydrocarbons, are of significant interest owing to their unique physicochemical features. With an increase in the number of fused benzene rings, acenes display an evolution of electronic structure and properties. Thus, tremendous efforts have been devoted to the synthesis of longer acenes, reaching dodecacene being the longest acene (12-fused benzene rings) reported to date. However, the formation of polymeric acenes with numerous benzene rings, namely polyacene (PA), has yet to be realized. Herein, we present a methodology for the synthesis of PA, as a long-sought-after compound, mediated by a metal−organic framework (MOF). Nanoconfined synthesis of precursor polymers in MOF channels and the subsequent dehydro-aromatization reaction produced PA that was overwhelmingly longer than the previously reported acenes. The scalable synthesis of PA could allow us to unveil the stability and electronic properties of PA, paving the way for their widespread applications in both the scientific and industrial fields. | Takashi Kitao; Takumi Miura; Ryo Nakayama; Yusuke Tsutsui; Yee Seng Chan; Hironobu Hayashi; Hiroko Yamada; Shu Seki; Taro Hitosugi; Takashi Uemura | Materials Science; Polymer Science; Conducting polymers; Coordination polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638437364b1a5f49c38f9d9b/original/synthesis-of-polyacene-exceeding-the-limits-of-benzene-rings-extension.pdf |
61a0ee44a9c8d50e945e955f | 10.26434/chemrxiv-2021-39frr | Synthesis of hybrid polyphenol/hydroxyapatite nanomaterials: adsorption vs. in situ incorporation | Plant-derived natural bioactive molecules are of great therapeutic potential but their application in nanomedicine has been so far scarcely studied. This work aimed at comparing two methodologies, i.e. adsorption and in situ incorporation, to prepare hybrid polyphenol/hydroxyapatite nanoparticles. Two flavonoids, baicalin and its aglycone derivative baicalein, and two phenolic acids derived from caffeic acid, rosmarinic and chlorogenic acids, were studied. Adsorption of these polyphenols on pre-formed hydroxyapatite nanoparticles did not modify particles size or shape and loading was less than 10 % (w/w). In contrast, presence of polyphenols during the synthesis of nanoparticles significantly impacted, and sometimes fully inhibited, hydroxyapatite formation, but recovered particles could exhibit higher loadings. Antioxidant properties of the polyphenols were preserved after adsorption but not when incorporated in situ. These results provide fruitful clues for the valorization of natural bioactive molecules in nanomedicine | Estelle Palierse; Sylvie Masse; Guillaume Laurent; Patrick Le Griel; Gervaise Mosser; Thibaud Coradin; Claude Jolivalt | Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a0ee44a9c8d50e945e955f/original/synthesis-of-hybrid-polyphenol-hydroxyapatite-nanomaterials-adsorption-vs-in-situ-incorporation.pdf |
672493a0f9980725cfc45050 | 10.26434/chemrxiv-2024-dpn21 | Efficient nickel precatalysts for Suzuki-Miyaura cross-coupling of aryl chlorides and arylboronic acids under mild conditions | The synthesis and catalytic properties of Ni(II) complexes, with the general formula Ni(NHC)[P(OR)3](Ar)Cl is described. These complexes are air-stable and extremely effective precatalysts in the Suzuki-Miyaura cross-coupling reaction. The reaction protocols described allow for the cross-coupling of aryl chlorides and arylboronic acids, employing low catalyt-ic loading, to deliver a large variety of functionalized biaryl compounds. For the coupling of aryl chlorides with N-heterocyclic boronic acids, TBAF was used as an additive to afford aryl-N-heterocyclic products. Overall, these cross-coupling protocols operate at room or mild temperatures and can be applied to a variety of electronically and sterically differentiated coupling partners. Fundamental insights into the mechanism of this reaction, including the proposed for-mation of the catalytically active Ni(NHC)[P(Oi-Pr)3] and resting state species are also reported. | Scott Stewart; Morgan John; Michael Nutt; Josephine Offer; Jeremy Duczynski; Ken Yamazaki; Tomoya Miura; Stephen Moggach; George Koutsantonis; Reto Dorta | Organic Chemistry; Catalysis; Organometallic Chemistry; Combinatorial Chemistry; Organic Synthesis and Reactions; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672493a0f9980725cfc45050/original/efficient-nickel-precatalysts-for-suzuki-miyaura-cross-coupling-of-aryl-chlorides-and-arylboronic-acids-under-mild-conditions.pdf |
66c0a5f9f3f4b05290304232 | 10.26434/chemrxiv-2024-r17m0 | Induced Chirality in QDs Using Thermoresponsive Elastin-Like Polypeptides | Circular dichroism (CD) spectroscopy has emerged as a potent tool for probing chiral small molecule ligand exchange on natively achiral quantum dots (QDs). In this study, we report a novel approach to identifying QD-biomolecule interactions by inducing chirality in CdS QDs using thermoresponsive elastin-like polypeptides (ELPs) engineered with C-terminal cysteine residues. Our method is based on a versatile two-step ligand exchange process starting from monodisperse oleate-capped QDs in non-polar media and proceeding through an easily accessed achiral glycine-capped QD intermediate. Successful conjugation of the ELPs onto the QDs is confirmed by the diagnostic CD response corresponding to the QD electronic transitions in the visible range. The resulting ELP:CdS conjugates demonstrate thermally reversible coacervation, as observed through dynamic light scattering, small-angle X-ray scattering, and electron microscopy. This research provides a foundation for using induced chirality in QD electronic transitions to probe QD conjugation to complex peptides and proteins, opening pathways for designing dynamic, stimuli-responsive hybrid nanomaterials. | Christopher Lowe; Helen Larson; Yifeng Cai; Huat Thart Chiang; Lilo Pozzo; Francois Baneyx; Brandi Cossairt | Materials Science; Nanoscience; Aggregates and Assemblies; Biological Materials; Hybrid Organic-Inorganic Materials; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c0a5f9f3f4b05290304232/original/induced-chirality-in-q-ds-using-thermoresponsive-elastin-like-polypeptides.pdf |
63dd446f068fd759791d9f56 | 10.26434/chemrxiv-2022-rkqw8-v2 | Plasmonic response of complex nanoparticle assemblies | Optical properties of nanoparticle assemblies reflect the distinctive characteristics of their building blocks and their spatial organization, giving rise to emergent phenomena. Integrated experimental and computational studies have established design principles connecting structure to properties for assembled clusters and superlattices. However, conventional electromagnetic simulations are too computationally expensive to treat more complex assemblies. Here we establish a fast, materials agnostic method to simulate the optical response of large nanoparticle assemblies incorporating both structural and compositional complexity. This many-bodied, mutual polarization method resolves limitations of established approaches, achieving rapid, accurate convergence for configurations including thousands of nanoparticles, some overlapping. We demonstrate these capabilities by reproducing experimental trends and uncovering far- and near-field mechanisms governing the optical response of plasmonic semiconductor nanocrystal assemblies, including structurally complex gel networks and compositionally complex mixed binary superlattices. This broadly applicable framework will facilitate design of complex, hierarchically structured, and dynamic assemblies for desired optical characteristics. | Zachary M. Sherman; Kihoon Kim; Jiho Kang; Benjamin J. Roman; Hannah S. N. Crory; Diana L. Conrad; Stephanie A. Valenzuela; Emily Y. Lin; Manuel N. Dominguez; Stephen L. Gibbs; Eric V. Anslyn; Delia J. Milliron; Thomas M. Truskett | Materials Science; Optical Materials | CC BY 4.0 | CHEMRXIV | 2023-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dd446f068fd759791d9f56/original/plasmonic-response-of-complex-nanoparticle-assemblies.pdf |
60c74972469df49f1ff43bd6 | 10.26434/chemrxiv.12061200.v1 | Ultrafast Exciton Dynamics in Two Dimensional Covalent Organic Frameworks Reveals Size Dependence to Exciton Diffusion | <p>Large singlet exciton diffusion lengths are a hallmark of high performance in organic based devices such as photovoltaics, chemical sensors, and photodetectors. In this study, exciton dynamics of a two-dimensional covalent organic framework, COF- 5, is investigated using ultrafast spectroscopic techniques. Following photoexcitation, the COF-5 exciton decays via three pathways: 1) excimer formation (4 ± 2 ps), 2) excimer relaxation (160 ± 40 ps), and 3) excimer decay (>3 ns). Excitation fluence-dependent transient absorption studies suggest that COF-5 has a relatively large diffusion coefficient (0.08 cm2/s). Furthermore, exciton-exciton annihilation processes are characterized as a function of COF-5 crystallite domain size in four different samples, which reveal domain- size dependent exciton diffusion kinetics. These results reveal that exciton diffusion in COF-5 is constrained by its crystalline domain size. These insights indicate the outstanding promise of delocalized excitonic processes available in 2D COFs, which motivate their continued design and implementation into optoelectronic devices. </p> | Nathan C. Flanders; Matthew S. Kirschner; Pyosang Kim; Thomas Fauvell; Austin Evans; Waleed Helweh; Austin
P. Spencer; Richard D. Schaller; William Dichtel; Lin X. Chen | Nanostructured Materials - Materials; Conducting polymers; Organic Polymers; Polymer scaffolds; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74972469df49f1ff43bd6/original/ultrafast-exciton-dynamics-in-two-dimensional-covalent-organic-frameworks-reveals-size-dependence-to-exciton-diffusion.pdf |
60c74b59702a9b718718b409 | 10.26434/chemrxiv.12323726.v1 | Metal and Ligand Effects on Coordinated Methane pKa. Direct Correlation with the Methane Activation Barrier | <p>DFT and coupled cluster methods were used to investigate the impact of 3d metals and ligands upon the acidity and activation of coordinated methane C–H bonds. A strong, direct relationship was established between the p<i>K<sub>a</sub></i> of coordinated methane and the subsequent free energy barriers to H<sub>3</sub>C–H activation. The few outliers to this relationship indicated other factors– such as thermodynamic stability of the product and ligand-metal coordination type – also impacted the methane activation barrier (dG<sup>‡</sup>). High variations in the activation barriers and p<i>K<sub>a</sub> </i>values were found with a range of 34.8 kcal/mol for the former and 28.6 p<i>K<sub>a</sub></i> units for the latter. Clear trends among specific metals and ligands were also derived; specific metals, such as Co<sup>I</sup>, as well as Lewis and p-acids consistently yielded higher acidity for the ligated methane and hence lower dG<sup>‡</sup>.<sup></sup></p> | Amy Guan; Ivy Liang; Christopher Zhou; Thomas Cundari | Organometallic Compounds; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b59702a9b718718b409/original/metal-and-ligand-effects-on-coordinated-methane-p-ka-direct-correlation-with-the-methane-activation-barrier.pdf |
61baecff9efae791011c4235 | 10.26434/chemrxiv-2021-h0cwv-v2 | A Polymer Prodrug Strategy to Switch from Intravenous to Subcutaneous Cancer Therapy for Irritant/Vesicant Drugs | Chemotherapy is almost exclusively administered via the intravenous (IV) route, which has serious limitations (e.g., patient discomfort, long hospital stays, need for trained staff, high cost, catheter failures, infections). Therefore, the development of effective and less costly chemotherapy that is more comfortable for the patient would revolutionize cancer therapy. While subcutaneous (SC) administration has the potential to meet these criteria, it is extremely restrictive as it cannot be applied to most anticancer drugs, such as irritant or vesicant ones, for local toxicity reasons. Herein, we report a facile, general and scalable approach for the SC administration of anticancer drugs through the design of well-defined hydrophilic polymer prodrugs. This was applied to the anticancer drug paclitaxel (Ptx) as a worst-case scenario due to its high hydrophobicity and vesicant properties (two factors promoting necrosis at the injection site), whereas polyacrylamide (PAAm) was chosen as a hydrophilic polymer for its biocompatibility and stealth properties. A small library of Ptx-based polymer prodrugs was designed by adjusting the nature of the linker (ester, diglycolate and carbonate), and then evaluated in terms of rheological/viscosity properties in aqueous solutions, drug release kinetics in PBS and in murine plasma, cytotoxicity on two different cancer cell lines, acute local and systemic toxicity, pharmacokinetics and biodistribution, and finally their anticancer efficacy. We demonstrated that Ptx-PAAm polymer prodrugs could be safely injected subcutaneously without inducing local toxicity while outperforming Taxol, the commercial formulation of Ptx, thus opening the door to the safe transposition from IV to SC chemotherapy. | Alexandre Bordat; Tanguy Boissenot; Nada Ibrahim; Marianne Ferrere; Manon Levêque; Stéphanie Denis; Sébastien Garcia-Argote; Olivia Carvalho; Jérôme Abadie; Catherine Cailleau; Gregory Pieters; Nicolas Tsapis; Julien Nicolas | Polymer Science; Drug delivery systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61baecff9efae791011c4235/original/a-polymer-prodrug-strategy-to-switch-from-intravenous-to-subcutaneous-cancer-therapy-for-irritant-vesicant-drugs.pdf |
60c73dbd567dfe20a5ec36c6 | 10.26434/chemrxiv.6070925.v1 | The Discrete Existence of Singlet Nitrenium Ions Revisited: Computational Studies of Non-Aryl Nitrenium Ions and Their Rearrangements | Nitrenium ion species are examined using computational methods (DFT, MP2, coupled-cluster, and a composite method, CBS-APNO) with a particular emphasis on non-aromatic species (i.e. those lacking an aromatic or heteroaromatic ring in direct conjugation with the formal nitrenium ion center.) Substitution of the N+ center with alkyl, alkoxy, vinyl, acyl, sulfonyl, among others, were evaluated. For these species, three properties are considered. (1) the stability of the nitrenium ions to unimolecular isomerizations such as 1,2 alkyl or H shifts. And, to the extent the singlet states could be characterized as discrete minima on the PES, (2) the effect of the substituents on singlet-triplet energy splitting as well as (3) the relative stabilities of the nitrenium ions as defined by N-hydration enthalpies (RR’N+ + H¬2O -> RR’NOH¬2+). Nearly all simple alkyl and di-alkyl nitrenium ion singlet states are predicted to rearrange without detectable barriers, largely through 1,2 H or alkyl shifts. Methyl and N-N-dimethylnitrenium ion singlet states could be characterized as formal minima on the PES. However these species show small or insignificant barriers to isomerization. Disubstituted nitrenium ions that include an alkyl group and a conjugating substituent such as alkoxyl, vinyl or phenyl, show meaningful barriers to isomerization and are thus predicted to possess non-trivial lifetimes in solution. Alkyl groups substantially stabilize the singlet state relative to the situation in the parent nitrenium ion NH¬2+ To the point where the two states are nearly degenerate. Other groups that interact with the nitrenium ion center decrease DEst in the order formoyl< vinyl < phenyl < alkoxy ~sulfonyl < cyclopropyl ~ cyclobutyl. The latter two substituents interact strongly with the (singlet) nitrenium ion center through the formation of non-classical bonding reminiscent of the bisected cyclopropylcarbinyl ion case for carbocations. When singlet state stability is evaluated in the context of N-hydration enthalpies, it is found that the ordering is acyl<br /> | Daniel Falvey | Organic Synthesis and Reactions; Reaction (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dbd567dfe20a5ec36c6/original/the-discrete-existence-of-singlet-nitrenium-ions-revisited-computational-studies-of-non-aryl-nitrenium-ions-and-their-rearrangements.pdf |
619f81c9c481c31387f852e6 | 10.26434/chemrxiv-2021-qwxbh | Development of a First-in-Class Small Molecule Inhibitor of the C-terminal Hsp90 Dimerization | Heat shock protein 90 (Hsp90) is a promising therapeutic target due to its involvement in stabilizing several aberrantly expressed oncoproteins. In cancerous cells, Hsp90 expression is elevated, thereby contributing in exerting anti-apoptotic effects, which is essential for the malignant transformation and progression of several tumor types. Most of the Hsp90 inhibitors (Hsp90i) under investigation target the ATP binding site in the N-terminal domain (NTD) of Hsp90. However, adverse effects, including induction of the pro-survival resistance mechanism (heat shock response or HSR) and associated dose-limiting toxicity, have so far precluded clinical approval of these Hsp90i. In contrast, modulators that interfere with the C-terminal domain (CTD) of Hsp90 do not inflict HSR and, thus, emerge as a promising alternative approach to target Hsp90. Since the CTD dimerization of Hsp90 is essential for its chaperone activity, interfering with this essential dimerization process by small-molecule protein-protein interaction (PPI) inhibitors is a promising strategy for anticancer drug research. We have developed the first-in-class small molecule inhibitor (5b) targeting the Hsp90 CTD dimerization interface, based on a tripyrimidonamide scaffold through structure-based molecular design, chemical synthesis, binding mode model prediction, assessment of the biochemical affinity and efficacy against therapy-resistant leukemia cells. 5b reduces xenotransplantation of leukemia cells in zebrafish models and induces apoptosis in BCR-ABL1+ (T315I) tyrosine kinase inhibitors (TKIs) resistant leukemia cells, without inducing HSR. | Sanil Bhatia; Lukas Spanier; David Bickel; Niklas Dienstbier; Vitalij Woloschin; Melina Vogt; Henrik Pols; Beate Lungerich; Jens Reiners; Narges Aghaallaei; Daniela Diedrich; Benedikt Frieg; Julian Schliehe-Diecks; Bertan Boop; Franziska Lang; Mohanraj Gopalswamy; Jennifer Loschwitz; Baubak Bajohgli; Julia Skokowa; Arndt Borkhardt; Julia Hauer; Finn K. Hansen; Sander H.J. Smits; Joachim Jose; Holger Gohlke; Thomas Kurz | Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2021-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619f81c9c481c31387f852e6/original/development-of-a-first-in-class-small-molecule-inhibitor-of-the-c-terminal-hsp90-dimerization.pdf |
60c74bf9702a9b609a18b588 | 10.26434/chemrxiv.12408083.v1 | An Ion Mobility-Mass Spectrometry Imaging Workflow | <p>Mass spectrometry imaging
(MSI) is a powerful technique for the label-free spatially-resolved analysis of
biological tissues. Coupling ion mobility (IM) separation with MSI allows
separation of isobars in the mobility dimension and increases confidence of peak
assignments. Recently, imaging
experiments have been implemented on the Agilent 6560 Ion Mobility Quadrupole
Time of Flight Mass Spectrometer, making MSI experiments more broadly
accessible to the MS community. However, the absence of data analysis software
for this system presents a bottleneck. Herein, we present a vendor-specific imaging
workflow to visualize IM-MSI data produced on the Agilent IM-MS system. Specifically,
we have developed a Python script, the ion mobility-mass spectrometry image creation
script (IM-MSIC), which interfaces Agilent’s Mass Hunter Mass Profiler software
with the MacCoss lab’s Skyline software and generates drift time and
mass-to-charge selected ion images. In the workflow, Mass Profiler is used for
an untargeted feature detection. The IM-MSIC script mediates user input of data
and extracts ion chronograms utilizing Skyline’s command-line interface, then proceeds
towards ion image generation within a single user interface. Ion image
post-processing is subsequently performed using different tools implemented in accompanying
scripts.</p> | Daniela Mesa Sanchez; Steve Creger; Veerupaksh Singla; Ruwan T. Kurulugama; John Fjeldsted; Julia Laskin | Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf9702a9b609a18b588/original/an-ion-mobility-mass-spectrometry-imaging-workflow.pdf |
60c756b1ee301c689dc7b3de | 10.26434/chemrxiv.14307839.v1 | Unprecedented Coumarin-Pyronin Hybrid Dyes: Synthesis, Fluorescence Properties and Theoretical Calculations | A novel class of rosamine dyes bearing a 7-substituted 4-hydroxycoumarin unit as <i>meso</i>-heteroaryl ring is presented. The latent <i>C</i>-nucleophilic character of 4-hydroxycoumarin derivatives (<i>i.e.</i>, their C-3 position as nucleophilic center) has been drawn on in the designing of two unprecedented synthetic routes towards these atypical xanthene dyes. They are based on an effective formal Knoevenagel condensation with either pyronin derivatives or a mixed bis-aryl ether bearing both an aldehyde and a masked phenylogous amine, possibly applicable to a wide range of latent cyclic <i>C</i>-nucleophiles. We also report experimental and theoretical photophysical investigations of these unique coumarin-pyronin hybrid structures and particularly their form low-lying quenching states, some of dark twisted intramolecular charge transfer (TICT) nature, depending on the medium (CHCl<sub>3</sub> and water). Furthermore, two fluorophore compounds <b>9</b> and <b>11</b> have been applied for imaging in paraformaldehyde-fixed A549 cells to gain insights into their permeation and localization. | Kevin Renault; Arnaud Chevalier; Jérôme Bignon; Denis Jacquemin; Jean-Alexandre Richard; Anthony ROMIEU | Organic Compounds and Functional Groups | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756b1ee301c689dc7b3de/original/unprecedented-coumarin-pyronin-hybrid-dyes-synthesis-fluorescence-properties-and-theoretical-calculations.pdf |
674042655a82cea2fa5a585a | 10.26434/chemrxiv-2024-bnj6p-v2 | Autonomous Optimization of Discrete Reaction Parameters: Mono-Functionalization of a Bifunctional Substrate via a Suzuki-Miyaura Reaction | The autonomous optimization of discrete reaction parameters in organic synthesis remains unexplored, offering the potential to revolutionize synthetic methodology and expand the scope and efficiency of reaction development. Here, we introduce a fully integrated system that combines an automated synthesis robot, supercritical fluid chromatography, and Bayesian optimization to achieve the selective mono-functionalization of a bifunctional substrate via a Suzuki–Miyaura reaction. By leveraging variations in the ligand, base, and solvent, our approach enables precise tuning of the reaction parameters to achieve the targeted selectivity. Preliminary trials spanning 68 conditions identified eight critical descriptors, providing a framework for the systematic parameter characterization. This framework supported autonomous experimentation across 192 reaction conditions, comprising the initial four conditions and 47 iterative cycles, which ultimately enhanced the product yield to 49%. The generated mono-functionalized products serve as promising building blocks for organic photoelectronic applications, highlighting the far-reaching impact of autonomous, data-driven methodologies in synthetic and materials chemistry. | Seiji Akiyama; Hayaka Akitsu; Ryo Tamura; Wataru Matsuoka; Satoshi Maeda; Koji Tsuda; Yuuya Nagata | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674042655a82cea2fa5a585a/original/autonomous-optimization-of-discrete-reaction-parameters-mono-functionalization-of-a-bifunctional-substrate-via-a-suzuki-miyaura-reaction.pdf |
66f6e09e12ff75c3a1b10863 | 10.26434/chemrxiv-2024-x08ph | Chemo-Click: Receptor-Controlled and Bioorthogonal Chemokine Ligation for Real-time Imaging of Drug-Resistant Leukemic B Cells | Drug resistance in B cell leukemia is characterized by the co-expression of CXCR5 and CXCR3 chemokine receptors, making it a valuable biomarker for patient stratification. Herein we report a novel platform of activatable chemokines to selectively image drug-resistant leukemic B cells for the first time. The C-terminal derivatization of the human chemokines CXCL13 and CXCL10 with bioorthogonal tetrazine-BODIPY and BCN groups retained binding and internalization via their cognate CXCR5 and CXCR3 receptors and enabled rapid fluorescence labeling of CXCR5+ CXCR3+ resistant B cells -but not drug-susceptible leukemic cells- via intracellular chemokine ligation. This modular chemical approach offers a versatile strategy for real-time immunophenotyping of cell populations with distinct chemokine profiles and will accelerate the design of new precision medicine tools to advance personalized therapies in blood tumors. | Marco Bertolini; Lorena Mendive-Tapia; Utsa Karmakar; Marc Vendrell | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f6e09e12ff75c3a1b10863/original/chemo-click-receptor-controlled-and-bioorthogonal-chemokine-ligation-for-real-time-imaging-of-drug-resistant-leukemic-b-cells.pdf |
6594647d9138d231610aa6a3 | 10.26434/chemrxiv-2023-ff18g-v2 | Design & Synthesis of Novel Nitrofuranyl Indole Carboxylates as Potential Antibacterial Drug Conjugates | Mankind has immensely benefited from the first marketed antibacterial drug i.e. Salvarsan® in 1910 to the recently released Vaborem®, and the discovery of penicillin gave birth to the modern age of antibacterial treatment. Since the ‘golden age’ of antibacterial discovery (from the ‘40s to the ‘60s), in which most common antibacterial agents were discovered, antibacterial discovery has slowed dramatically with no new antibacterial scaffolds being introduced from 1962 until 2000. Recent developments in Oxford have led to identification of non-β-lactam indole carboxylates as potent metallo-β-lactamase inhibitors; as a result, and in extension of the aforementioned endeavours in combating antibacterial resistance, herein this work reports a set of novel nitrofuranyl indole carboxylates (NInCs) which are thought to have potential to be developed into antibacterial drug conjugates. Inasmuch as stable ester prodrugs of the aforementioned NInCs may be biologically inactive, this work also presents various methods for ester hydrolysis of these potential antibacterial drug conjugates together with some modification to their cleavable linkers. | Ashley L. Dey | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6594647d9138d231610aa6a3/original/design-synthesis-of-novel-nitrofuranyl-indole-carboxylates-as-potential-antibacterial-drug-conjugates.pdf |
620bb761cbb4f44f5ec1b02c | 10.26434/chemrxiv-2022-ttm2s | Zwitterionic Osmolytes Employ Dual Mechanisms for Resurrection of Surface Charge under Salt-stress | Salt imbalance in cells is a major detrimental abiotic stress which causes ionic toxicity and disrupts important cellular functions. To counter this saline stress, cell often produces low molecular weight cosolutes, known as osmolytes, which have the ability to resuscitate homeostasis. Here we combine atomistic computer simulation, contact angle measurements and Raman spectroscopic analysis to identify the mechanistic role of multiple osmolytes (glycine, TMAO and betaine) in modulating the electrostatic interaction under salt stress, a slowly emerging aspect of osmoprotection. By utilising a pair of negatively charged silica surfaces in a ternary mixture of osmolyte and KCl solution as a proxy of charged surface of biomacromolecule, our investigation reveals that all three osmolytes are able to resurrect the electrostatic interaction between the two surfaces, which had been otherwise charge-screened by excess salt. The joint venture of experiment and simulation discover dual and mutually exclusive mechanisms of recovering charge interaction by zwitter-ionic osmolytes. However, the relative ability and the underlying mechanism of revival of electrostatic interactions are found to be strongly dependent of chemical nature of osmolyte. Specifically, glycine was found to competitively desorb the salt-ions from the surface via its direct interaction with the surface. On the other hand, TMAO and betaine counter-act salt stress by retaining adsorbed cations but partially neutralising their charge-density via ion-mediated interaction. We believe that the access to dual and mutually alternative modes of osmolytic actions, as elucidated here, would provide the cell the required adaptability in combating salt-stress. | Susmita Sarkar; Anku Guha; T. N. Narayanan; Jagannath Mondal | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Theory - Computational; Biophysical Chemistry; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620bb761cbb4f44f5ec1b02c/original/zwitterionic-osmolytes-employ-dual-mechanisms-for-resurrection-of-surface-charge-under-salt-stress.pdf |
674337c37be152b1d09b87dd | 10.26434/chemrxiv-2024-ft8zt | Material sustainability evaluation of electrocatalysts in early-stage development | Sustainable energy materials for energy storage applications are crucial for a reliable energy transition. However, evaluating material sustainability in early stages of energy material research is a big challenge, as it is difficult to predict the final industrial process and supply chain of the investigated material. In this work we showcase that a sustainability evaluation can already be conducted in the early stage of electrocatalyst research. We provide a case study of two highly active alkaline oxygen evolution catalysts La0.6Sr0.4CoO3-δ and La0.6Ca0.4FeO3-δ with a thin film model catalyst approach. For the sustainability evaluation, we consider the material criticality, compare precursor prices, conduct an environmental impact analysis of the precursors based on life cycle assessment and provide a qualitative discourse for social impacts of raw material extraction. We find that La0.6Ca0.4FeO3-δ has a reduced environmental footprint, smaller precursor supply risk and 10 times lower precursor price compared to La0.6Sr0.4CoO3-δ. However, for both perovskites the high environmental impact and high supply risk of lanthanum is of immediate concern towards larger scale application purposes. Sustainability evaluation in the early stages of energy material research can be a great chance to develop new material selection strategies leveraging sustainability in later stages of materials research for the energy transition. | Lisa Heymann; Andrea Schreiber; Christian Pithan; Christoph Baeumer; Felix Gunkel | Catalysis; Energy; Earth, Space, and Environmental Chemistry; Environmental Science; Electrocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674337c37be152b1d09b87dd/original/material-sustainability-evaluation-of-electrocatalysts-in-early-stage-development.pdf |
64228c1291074bccd0697e44 | 10.26434/chemrxiv-2023-lgjq6 | Solid-Phase Synthesis of Iterative RAFT Single Unit Monomer Insertion Adducts | In this communication, we disclose the use of a solid-phase methodology to synthesize iterative RAFT single unit mono-mer insertion (SUMI) adducts. This methodology features a reversible thiocarbonylthio protecting group and radical chain growth of vinyl monomers, with minimal purification required during the synthesis. To achieve this, a RAFT chain transfer agent was immobilized on a common peptide synthesis resin via the “R-group” in the first instance. Using an ox-ygen-tolerant PET-RAFT methodology, we then extended the iterative synthesis of sequence-defined indene-maleimide alternating co-oligomers to 18 units with minimal dispersity, completely unprecedented in SUMI chemistry. Furthermore, as we demonstrate, this solid-phase methodology can be generalized to other maleimide derivatives and other solid-phase resins. | Karen Hakobyan; Benjamin Noble; Jiangtao Xu | Polymer Science; Organic Polymers; Polymerization (Polymers); Polymerization kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64228c1291074bccd0697e44/original/solid-phase-synthesis-of-iterative-raft-single-unit-monomer-insertion-adducts.pdf |
60c75168bdbb892b6aa3a0d2 | 10.26434/chemrxiv.13160717.v1 | UEMtomaton: A Source-Available Platform to Aid in Start-up of Ultrafast Electron Microscopy Labs | We provide here a description of a basic, entry-level method and user interface for automating ultrafast electron microscopy (UEM) experiments. We provide access to the source code and scripts via a GitHub site for ease of implementation or as a starting reference point for those entering or seeking to enter the field. Core instrumentation and physical connections in the UEM lab at Minnesota are described. An application designed and programmed with C++/CLI as Windows Forms in Microsoft Visual Studio - dubbed UEMtomaton - is also presented. It is our hope that this note provides useful insight for current and future UEM researchers.<br /> | Daniel Du; Spencer Reisbick; David Flannigan | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75168bdbb892b6aa3a0d2/original/ue-mtomaton-a-source-available-platform-to-aid-in-start-up-of-ultrafast-electron-microscopy-labs.pdf |
60c747980f50db1a2339662f | 10.26434/chemrxiv.8268197.v4 | Identifying and Tracking Defects in Dynamic Supramolecular Polymers | A central paradigm of self-assembly is to create ordered structures starting from molecular<br />monomers that spontaneously recognize and interact with each other via noncovalent interactions.<br />In the recent years, great efforts have been directed toward reaching the perfection in the<br />design of a variety of supramolecular polymers and materials with different architectures. The<br />resulting structures are often thought of as ideally perfect, defect-free supramolecular fibers,<br />micelles, vesicles, etc., having an intrinsic dynamic character, which are typically studied at the<br />level of statistical ensembles to assess their average properties. However, molecular simulations<br />recently demonstrated that local defects that may be present or may form in these assemblies, and which are poorly captured by conventional approaches, are key to controlling their dynamic<br />behavior and properties. The study of these defects poses considerable challenges, as the<br />flexible/dynamic nature of these soft systems makes it difficult to identify what effectively constitutes<br />a defect, and to characterize its stability and evolution. Here, we demonstrate the power<br />of unsupervised machine learning techniques to systematically identify and compare defects in<br />supramolecular polymer variants in different conditions, using as a benchmark 5°A-resolution<br />coarse-grained molecular simulations of a family of supramolecular polymers. We shot that this<br />approach allows a complete data-driven characterization of the internal structure and dynamics<br />of these complex assemblies and of the dynamic pathways for defects formation and resorption.<br />This provides a useful, generally applicable approach to unambiguously identify defects in<br />these dynamic self-assembled materials and to classify them based on their structure, stability<br />and dynamics.<br /> | Piero Gasparotto; Davide Bochicchio; Michele Ceriotti; Giovanni M. Pavan | Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747980f50db1a2339662f/original/identifying-and-tracking-defects-in-dynamic-supramolecular-polymers.pdf |
65d1a121e9ebbb4db99ce2d6 | 10.26434/chemrxiv-2024-vqbk9 | Through-space conjugation-dominated luminescence mechanism | The influence of through-space conjugation (TSC) on the optical properties of molecules was consistently neglected in past research. Recently, TSC-related luminescence phenomena were reported sporadically, but a general lack of in-depth understanding of the TSC luminescence mechanism exists. The TSC factors, TSC intensity, and the impact of TSC on material properties remained theoretical blind spots. This work selected cyclooctatetrathiophene (COTh) as a research model and comprehensively analyzed the nature of TSC at the experimental and theoretical levels. The COTh molecule exhibited an anomalous luminescence that did not match the degree of through-bond conjugation. Instead, it was determined to be a luminescence phenomenon dominated by TSC. A unique overpass-shaped TSC channel was the key to achieving TSC-dominated luminescence. Orbital phase, angle, and spatial distance were essential factors in forming an effective TSC channel. Moreover, both COTh isomers and aryl-substituted COTh derivatives were shown to possess TSC-dominated luminescence properties, which provided sufficient evidence for the TSC-dominated luminescence mechanism. In addition, a practical TSC analysis tool was developed that could quickly analyze the TSC path, action location, and action intensity for any molecular system. This work will provide helpful guidance and inspiration for TSC research and promote the development of TSC-related research. | Bo Wu; Guoqing Zhang; Zheng Zhao; Ben Zhong Tang | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Optics | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d1a121e9ebbb4db99ce2d6/original/through-space-conjugation-dominated-luminescence-mechanism.pdf |
63b47d73a2da4b571919f480 | 10.26434/chemrxiv-2023-2xfjs | Deuterodehalogenation Under Net Reductive or Redox-Neutral Conditions Enabled by Paired Electrolysis | Interest in deuterated de novo active pharmaceutical ingredients (APIs) is increasing due to the release of
the first FDA approved deuterated drug, deutetrabenazine. Deuteration also holds promise for kinetic
isotope effect (KIE) regulated fine-tuning of active pharmaceutical ingredient performance. As such,
methods for highly selective deuteration of organic molecules—particularly at positions that are prone to
undergoing biochemical reactions—are highly desirable. Herein, we present an electrochemical method
for the selective deuterodehalogenation of benzylic halides via a radical-polar crossover mechanism, using
inexpensive deuterium oxide (D2O) as the deuterium source. We demonstrate broad functional group
compatibility across a range of aryl and heteroaryl benzylic halides. Furthermore, we uncover a sequential
paired electrolysis regime, which permits switching between net reductive and overall redox-neutral
reactions of sulfur-containing substrates simply by changing the identity of the sacrificial reductant
employed. | Devin Wood; Song Lin | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b47d73a2da4b571919f480/original/deuterodehalogenation-under-net-reductive-or-redox-neutral-conditions-enabled-by-paired-electrolysis.pdf |
60c74fd7469df4ef90f4476e | 10.26434/chemrxiv.12949697.v1 | Understanding the Solid-State Assembly of Pharmaceutically-Relevant N,N-Dimethyl-O-Thiocarbamates in the Absence of Labile Hydrogen Bonds | There are many pharmaceutical compounds that do not contain N-H, O-H, and S-H hydrogen-bond donor functional groups. Some of these compounds are N,N-disubstituted O-thiocarbamates which exhibit desirable medicinal properties, yet the study of these important molecules in the solid-state has been relatively unexplored. Herein, we report the synthesis and analysis of a series of N,N-dimethyl-O-thiocarbamates, and use X-ray diffraction techniques to gain insight into how these molecules self-assemble in the solid-state and discern certain packing patterns. It was observed that the aryl-thiocarbamate C-O bonds are twisted such that the planar aryl and carbamate moieties are orthogonal. Such a non-planar molecular geometry affects the way the molecules pack and crystal structure analyses revealed four general modes in which the molecules can associate in the solid-state, with some members of the series displaying isostructural relationships. The crystal structure of a well-known yet unreported O-thiocarbamate drug, Tolnaftate, is also reported. Additionally, Hirshfeld surface analysis was also performed on these compounds as well as several related O-thiocarbamates in the literature.<br /> | Davin Tan; Zi xuan Ng; Rakesh Ganguly; yongxin Li; Han Sen Soo; Felipe Garcia | Supramolecular Chemistry (Org.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fd7469df4ef90f4476e/original/understanding-the-solid-state-assembly-of-pharmaceutically-relevant-n-n-dimethyl-o-thiocarbamates-in-the-absence-of-labile-hydrogen-bonds.pdf |
66b53f9d5101a2ffa8a0042e | 10.26434/chemrxiv-2024-0gssb | Replica Exchange with Solute Tempering for Protein Conformational Sampling | Molecular dynamics (MD) simulations have become indispensable in numerous biological studies, facilitated by advances in algorithms and high-performance computing. These simulations have played a pivotal role in uncovering both the structural and functional characteristics of biomolecules, particularly proteins, through sophisticated molecular modeling techniques. However, the comprehensive understanding of molecular functions hinges on the ability to thoroughly explore their conformational space. Despite the power of MD simulations, complex systems such as proteins often present challenges, as they can become trapped in local energy minima within the rugged free energy landscape. While recent advancements in hardware and distributed computing platforms have enabled longer simulations and the study of protein folding in explicit solvents, conventional MD simulations still face difficulties in adequately sampling protein configuration space due to this trapping phenomenon. To address this issue, generalized ensemble (GE) sampling algorithms like the replica exchange method (REM) and simulated tempering (ST) have been developed. These algorithms facilitate the exploration of conformational space by inducing a random walk in temperature space within an expanded ensemble. By enabling the exchange of conformations between different temperature replicas, these algorithms can help facilitate the escape from local energy minima, particularly at higher temperatures where thermal fluctuations are more pronounced. These temperature-based GE algorithms are widely employed in simulating proteins and other biological macromolecules. In this chapter, we provide an overview of replica exchange methods, followed by a detailed discussion of Hamiltonian-based replica exchange methods, with a particular focus on replica exchange with solute tempering (REST), REST2 and their variants, including generalized REST (gREST) and replica exchange with hybrid tempering (REHT). Finally, we explore several applications of these enhanced sampling methods in elucidating biological conformational changes. | Yichong Lao; Michael O’Connor; Xuhui Huang | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b53f9d5101a2ffa8a0042e/original/replica-exchange-with-solute-tempering-for-protein-conformational-sampling.pdf |
60c755e0f96a007ef3288990 | 10.26434/chemrxiv.14176577.v1 | Electrical Promotion-Assisted Automotive Exhaust Catalyst: Highly Active and Selective NO Reduction to N2 at Low-Temperatures | Pd catalyst (Pd/Ce<sub>0.7</sub>Zr<sub>0.3</sub>O<sub>2</sub>)
in an electric field exhibits extremely high three-way catalytic activity (TWC:
NO-C<sub>3</sub>H<sub>6</sub>-CO-O<sub>2</sub>-H<sub>2</sub>O). By applying an
electric field to the semiconductor catalyst, low-temperature operation of TWC can be achieved even at 473 K by virtue of the activated surface-lattice
oxygen. | Yuki Omori; Ayaka Shigemoto; Kohei Sugihara; Takuma Higo; Toru Uenishi; Yasushi Sekine | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e0f96a007ef3288990/original/electrical-promotion-assisted-automotive-exhaust-catalyst-highly-active-and-selective-no-reduction-to-n2-at-low-temperatures.pdf |
6617eac591aefa6ce159d492 | 10.26434/chemrxiv-2024-rsc2n | NEQUIM Contact System (NCS): A tool for generation and analysis of protein-ligand interaction fingerprint | NEQUIM Contact System (NCS) is a system to generate and analyze interaction vectors of protein-ligand complexes. Core features include multiple views of vectors, multiple selection options, cluster analysis and the generation of interaction vector models. The input could be from a PDB format or from files generated by automatic docking softwares AutoDock/Vina or Surflex.
Availability: The NCS is available free of charge from SourceForge web site https://sourceforge.net/projects/nequimcontacts
| Andrelly Martins-José; Julio Lopes | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6617eac591aefa6ce159d492/original/nequim-contact-system-ncs-a-tool-for-generation-and-analysis-of-protein-ligand-interaction-fingerprint.pdf |
6560aaf65bc9fcb5c947c90d | 10.26434/chemrxiv-2023-cfpdp | Ultra-clean pure shift NMR with optimal water suppression for analysis of aqueous pharmaceutical samples | Pure shift NMR experiments greatly enhance spectral resolution by collapsing multiplet structures into singlets and, with water suppression, can be used for aqueous samples. Here, we combine ultra-clean pure-shift NMR (SAPPHIRE) with two different internally encoded water suppression schemes to achieve optimal performance for small molecule and macrocyclic peptide pharmaceuticals in water and acetonitrile-water mixtures. | Guilherme Dal Poggetto; Adam DiCaprio; Mikhail Reibarkh; Ryan D. Cohen | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.); Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6560aaf65bc9fcb5c947c90d/original/ultra-clean-pure-shift-nmr-with-optimal-water-suppression-for-analysis-of-aqueous-pharmaceutical-samples.pdf |
60c741a9f96a005588286491 | 10.26434/chemrxiv.8082506.v1 | Localizing Electron Density Errors in Density Functional Theory | This work attempts to provide a clear picture on the relative quality of different Density Functional Approximations through the use of Quantum Chemical Topology on molecular electronic densities. In particular, two simple yet ever-important systems are studied, the N2 and CO molecules. Our results exemplify how real-space descriptors can clearly assess the calculated electronic density of a molecular system, avoiding unwanted error compensation present in simplified statistical metrics. Errors in ``well'' built functionals are shown to be concentrated in chemically meaningful regions of space, and hence they are predictable. Conversely, strongly parametrized functionals show isotropic errors that cannot be traced back to chemical transferable units. Moreover, we will show that energetic corrections are mapped back into improvements in the density in chemically meaningful regions. These results point at the relevance of real-space perspectives when parametrizing or assessing energy and density errors.<br /> | Rubén Laplaza; Victor Polo; Julia Contreras-García | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a9f96a005588286491/original/localizing-electron-density-errors-in-density-functional-theory.pdf |
64368a771d262d40ea4eb331 | 10.26434/chemrxiv-2023-nf7v3 | Facet-Dependent Formation and Adhesion of Au Oxide and Nanoporous Au on Poly-Oriented Au Single Crystals | Nanoporous Au has different properties compared to bulk Au, making it an interesting material for numerous applications. Depending on the preparation procedure, the porosity, thickness, and homogeneity of the NPG films can be tuned. To modify the structure of NPG films in a targeted manner and thus adapt them to specific applications, a fundamental understanding of the structure formation is essential. In this work, we focus on NPG prepared from Au oxide formed during high voltage electrolysis in an alkaline electrolyte on a poly-oriented Au single crystal electrode. These poly-oriented single crystals consist of a single crystalline metal bead, with faces with different crystallographic orientations. Consequently, these POSCs allow screening of the influence of the crystallographic orientation on the structure formation of the Au oxide formed during high voltage electrolysis and the NPG film formed via electrochemical reduction of the Au oxide for different facets in a single experiment. The high voltage electrolysis is performed at current densities between 2.70 and 3.76 A / cm² (300 V) and between 0.24 and 6.39 A / cm² (540 V) with electrolysis times ranging from 100 ms to 30 s. The amount of Au oxide formed is determined by electrochemical measurements and the structural properties are investigated by scanning electron microscopy and optical microscopy. We show that the Au oxide formation is mostly independent of the crystallographic orientation except for thick Au oxide layers. In turn, the macroscopic structure of the NPG films depend on the experimental parameters, the thickness of the Au oxide precursor thickness, and the crystallographic orientation of the substrate. Possible reasons for the frequently observed exfoliation of the NPG films are discussed. | Evelyn Artmann; Tobias Schmider; Timo Jacob; Albert K. Engstfeld | Physical Chemistry; Materials Science; Nanoscience | CC BY 4.0 | CHEMRXIV | 2023-04-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64368a771d262d40ea4eb331/original/facet-dependent-formation-and-adhesion-of-au-oxide-and-nanoporous-au-on-poly-oriented-au-single-crystals.pdf |
65f2d1d366c1381729f8c7d4 | 10.26434/chemrxiv-2023-l391z-v2 | Anion-Responsive Colorimetric and Fluorometric Red-Shift in Triarylborane Derivatives: Dual Role of Phenazaborine as Lewis Acid and Electron Donor | Photophysical modulation of triarylboranes (TABs) through Lewis acid-base interactions is a fundamental approach in sensing anions. Yet, design principles for anion-responsive TABs displaying significant red-shift in absorption and photoluminescence (PL) have remained elusive. Herein, a new strategy for modulating photophysics of TABs in red-shift mode has been presented, endowing a nitrogen-bridged triarylborane (phenazaborine: PAzB) with contradictory dual role as a Lewis acid and an electron donor. Following the strategy, a PAzB derivative connected with an electron-deficient azaaromatic has been developed, and it displays distinct red-shift in absorption and PL in response to an anion. Spectroscopic analyses and quantum chemical calculations have revealed the formation of tetracoordinated borate upon addition of fluoride, narrowing the HOMO-LUMO gap and enhancing charge transfer character in the excited state. This approach has also been demonstrated in solid-state films. | Nae Aota; Riku Nakagawa; Leonardo Evaristo de Sousa; Norimitsu Tohnai; Satoshi Minakata; Piotr de Silva; Youhei Takeda | Physical Chemistry; Organic Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f2d1d366c1381729f8c7d4/original/anion-responsive-colorimetric-and-fluorometric-red-shift-in-triarylborane-derivatives-dual-role-of-phenazaborine-as-lewis-acid-and-electron-donor.pdf |
654889ffc573f893f1e64546 | 10.26434/chemrxiv-2023-dj4hz | Understanding the initial events of the oxidative damage and protection mechanisms of the AA9 lytic polysaccharide monooxygenase family | Lytic polysaccharide monooxygenase (LPMO) is a new class of oxidoreductases that boosts polysaccharide degradation employing a copper active site. This boost may facilitate the cost-efficient production of biofuels and high-value chemicals from polysaccharides such as lignocellulose. Unfortunately, self-oxidation of the active site inactivates LPMOs. Other oxidoreductases employ hole-hopping mechanisms as pro- tection against oxidative damage, but little is generally known about the details of these mechanisms. Herein, we employ highly accurate theoretical models based on density functional theory (DFT) molecular mechanics (MM) hybrids to understand the initial steps in LPMOs’ protective measures against self-oxidation; we identify several intermediates recently proposed from experiment, and quantify which are important for protective hole-hopping pathways, and which lead to oxidative damage. Investigations on two different LPMOs show consistently that a tyrosine residue close to copper is crucial for protection: This explains recent experiments, showing that LPMOs without this tyrosine are more susceptible to self-oxidation. | Marlisa M. Hagemann; Erna K Wieduwilt; Erik Donovan Hedegård | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Theory - Inorganic | CC BY 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654889ffc573f893f1e64546/original/understanding-the-initial-events-of-the-oxidative-damage-and-protection-mechanisms-of-the-aa9-lytic-polysaccharide-monooxygenase-family.pdf |
66ea8317cec5d6c1426992f6 | 10.26434/chemrxiv-2024-ng3ws | All-in-one foundational models learning across quantum chemical levels | Machine learning (ML) potentials typically target a single quantum chemical (QC) level while the ML models developed for multi-fidelity learning have not been shown to provide scalable solutions for foundational models. Here we introduce the all-in-one (AIO) ANI model architecture based on multimodal learning which can learn an arbitrary number of QC levels. Our all-in-one learning approach offers a more general and easier-to-use alternative to transfer learning. We use it to train the AIO-ANI-UIP foundational model with the generalization capability comparable to semi-empirical GFN2-xTB and DFT with a double-zeta basis set for organic molecules. We show that the AIO-ANI model can learn across different QC levels ranging from semi-empirical to density functional theory to coupled cluster. We also use AIO models to design the foundational model Δ-AIO-ANI based on Δ-learning with increased accuracy and robustness compared to AIO-ANI-UIP. The code and the foundational models are available at https://github.com/dralgroup/aio-ani; they will be integrated into the universal and updatable AI-enhanced QM (UAIQM) library and made available in the MLatom package so that they can be used online at the XACS cloud computing platform (see https://github.com/dralgroup/mlatom for updates). | Yuxinxin Chen; Pavlo O. Dral | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ea8317cec5d6c1426992f6/original/all-in-one-foundational-models-learning-across-quantum-chemical-levels.pdf |
63573008cf6de9bcaa20cea6 | 10.26434/chemrxiv-2022-scww8 | Synthesis of 3-alkyl oxazolidines, derived from 2-hydroxymethyl piperidine, as analytical standards for the analysis of volatile aldehydes in the workplace | Hexahydro-3-alkyl-3H-oxazolo[3,4-a]pyridines 4-15 for the quantitative analysis of various aldehydes were obtained in good yield via the condensation reaction of 2-hydroxymethylpiperidine (2-HMP) with aldehydes under mild conditions. When acrolein is used, the bicyclic 17 was obtained. This novel compound has suitable physical characteristic for an analytical standard. The hexahydro-3-vinyl-3H-oxazolo[3,4-a]pyridine 16 can be achieve at higher temperature. Using specific conditions, a diastereomeric mixture of 18/19 and pure 18, which are both bisadducts of 2-HMP with acrolein, can be obtained. Mechanistically, a thorough 1H-NMR study did not show any evidence that the condensation reaction proceeded via an enamine. The reaction probably proceeds through an elusive hemiaminal and fleeting iminium ion, which underwent subsequent cyclisation to gave hexahydro-3-alkyl-3H-oxazolo[3,4-a]pyridines 4-16. The reaction pathways for the preparation of 4-18 are described. | Amadou R. Yaya; Martin Girard; Karima Belkhadem; Rémi Piard; Andreas Decken; Catherine Choinière; Pierre-Luc Cloutier; Jacques Lesage; Livain Breau | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63573008cf6de9bcaa20cea6/original/synthesis-of-3-alkyl-oxazolidines-derived-from-2-hydroxymethyl-piperidine-as-analytical-standards-for-the-analysis-of-volatile-aldehydes-in-the-workplace.pdf |
6628345121291e5d1d859a94 | 10.26434/chemrxiv-2024-24xcv | Computational Large-Scale Screening of Bioorthogonal 1,2,4,5-Tetrazine/trans-Cyclooctene Cycloadditions | Bioorthogonal reactions between 1,2,4,5-tetrazines and trans-cyclooctenes have emerged as valuable chemical tools in the fields of chemical biology and material science, and they hold significant potential for medical applications. The most critical attribute of such reactions is their rate. Experimental investigations into the reactivity of 1,2,4,5-tetrazines are time-consuming and costly. In contrast, computational screenings can rapidly identify reactants that exhibit desired reactivity. In this study, we introduce a tool for automated computational screening that assesses the reactivity of a large pool of tetrazines. This effort has produced an initial dataset of 1,288 reaction barriers, which can be utilized to develop machine learning models. | Dennis Svatunek | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6628345121291e5d1d859a94/original/computational-large-scale-screening-of-bioorthogonal-1-2-4-5-tetrazine-trans-cyclooctene-cycloadditions.pdf |
63452eacfee74eb7c15ed1ec | 10.26434/chemrxiv-2022-qmhlj-v2 | Evidence for water antibonding orbital mixing in the hydrated electron from its oxygen 1s X-ray absorption spectrum | The X-ray absorption spectrum (XAS) of the hydrated electron (e−(aq)) has been simulated using time- dependent density functional theory with a quantum mechanics/molecular mechanics description. A unique XAS peak at 533 eV is observed with an energy and intensity in quantitative agreement with recent time-resolved experiments, allowing its definitive assignment as arising from water O1s transitions to the singly occupied molecular orbital (SOMO) in which the excess electron resides. The transitions acquire oscillator strength due to the SOMO comprising an admixture of a cavity-localized orbital and water 4a1 and 2b2 antibonding orbitals. The mixing of antibonding orbitals has implications for the strength of couplings between e−(aq) and intramolecular modes of water. | Xingpin Li; Xiangyu Jia; Amiel Paz; Yuquan Cao; William Glover | Theoretical and Computational Chemistry; Physical Chemistry; Quasiparticles and Excitations; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63452eacfee74eb7c15ed1ec/original/evidence-for-water-antibonding-orbital-mixing-in-the-hydrated-electron-from-its-oxygen-1s-x-ray-absorption-spectrum.pdf |
60c753c9bdbb89552da3a502 | 10.26434/chemrxiv.13551383.v1 | A Frustrated [Mn18] Wheel-of-Wheels | <p>A [Mn<sub>18</sub>] wheel of
wheels is obtained from the reaction of MnBr<sub>2</sub> and LH<sub>3</sub> in
MeOH. The metallic skeleton reveals two asymmetric [Mn<sup>III</sup><sub>6</sub>Mn<sup>II</sup><sub>2</sub>]
squares connected into a wheel via two apical Mn<sup>II</sup> ions. Magnetic
susceptibility and magnetisation data reveal competing exchange interactions,
supported by computational studies revealing spin frustration. </p> | Marco Coletta; Thomais Tziotzi; Mark Gray; Gary Nichol; Mukesh Singh; Constantinos J. Milios; Euan Brechin | Coordination Chemistry (Inorg.); Ligands (Inorg.); Magnetism; Reaction (Inorg.); Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753c9bdbb89552da3a502/original/a-frustrated-mn18-wheel-of-wheels.pdf |
678ff6176dde43c90897fb18 | 10.26434/chemrxiv-2025-ttl38 | A Photoactivatable Free Mycolic Acid Probe to Investigate Mycobacteria–Host Interactions | Mycolic acids are long-chain, α-branched, β-hydroxylated fatty acid lipids that populate the outer mycomembrane of mycobacteria, including the pathogen Mycobacterium tuberculosis. Mycolic acids predominantly occur in the form of glycolipids, but non-glycosylated free mycolic acids (fMA), which are generated during mycomembrane remodeling, are major constituents of the M. tuberculosis biofilm extracellular matrix and promote host immune evasion during M. tuberculosis infection. However, our understanding of these processes is nascent, and there is limited information about the fMA–protein interactions involved. To facilitate such studies, we synthesized a fMA analogue probe (x-Alk-MA) containing a photo-crosslinking diazirine and a clickable alkyne to enable live-cell capture and analysis of protein interactors. The synthetic strategy featured asymmetric hydrogenation to establish the β-hydroxy group, diastereoselective alkylation to establish the α-branch, and late-stage modification to install the functional tags. In macrophages, x-Alk-MA recapitulated the cytokine response of native MA and selectively photo-labeled TREM2, a host cell receptor for fMAs that suppresses macrophage activation and has been implicated in M. tuberculosis immune evasion. The synthetic strategy, chemical probes, and photo-labeling methods disclosed herein should facilitate future studies aimed at understanding the roles of fMA in mycobacterial physiology and pathogenesis. | Kingsley Agu; Nicholas Banahene; Carolina Santamaria; Christi Kim; Jessica Cabral; Kyle Biegas; Casey Papson; Andrew Kruskamp; M. Sloan Siegrist; Benjamin Swarts | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Microbiology | CC BY NC 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ff6176dde43c90897fb18/original/a-photoactivatable-free-mycolic-acid-probe-to-investigate-mycobacteria-host-interactions.pdf |
60c74209bb8c1a01393da052 | 10.26434/chemrxiv.8192345.v1 | The Effect of Gamma Irradiation on the Physiochemical Properties of Caesium-Selective Ammonium Phosphomolybdate-Polyacrylonitrile (AMP-PAN) Composites | Managing certain by-products of the
nuclear fuel cycle, such as the radioactive isotopes of caesium: Cs-134, Cs-135
and Cs-137 is challenging due to their environmental mobility and
radioactivity. While a great many materials can isolate Cs<sup>+</sup> ions
from neutral or basic aqueous solutions via ion exchange, few of these, with
the exception of ammonium phosphomolybdate (AMP), function effectively in
acidic media. The use of AMP, and its porous composite in polyacrylonitrile
(PAN) for management of Cs radioisotopes in various nuclear wastes have been
known for decades and are well studied, yet the effects of radiation on the
physiochemical properties of such composites have only received limited
attention to date. In a previous publication, we demonstrated that a 100 kGy
gamma irradiation dose has negligible effect on the ion exchange performance of
AMP and AMP-PAN with respect to capacity or kinetics under the Cs<sup>+</sup>
concentrations and acidity found in spent fuel recycling. As a continuation of
this prior study, in this publication we explore the effects of gamma
irradiation on the physiochemical properties of AMP and AMP-PAN using a range
of characterisation methods. The effects of the same gamma dose on the
oxidation state of Mo in AMP and AMP-PAN, the thermal degradation of both AMP
and AMP-PAN, combined with a first study into the high-temperature degradation
AMP, are reported. The implications of irradiation, its possible mechanism, the
conditions present in SNF recycling, and for the end-of-life disposal or
recycling of these materials are also discussed. | Alistair Holdsworth; Harry Eccles; daniel rowbotham; Adam Brookfield; David Collison; Gary Bond; Parthiv Kavi; Ruth Edge | Organic Polymers; Nuclear Chemistry; Polymers; Transition Metal Complexes (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2019-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74209bb8c1a01393da052/original/the-effect-of-gamma-irradiation-on-the-physiochemical-properties-of-caesium-selective-ammonium-phosphomolybdate-polyacrylonitrile-amp-pan-composites.pdf |
668b9aaf01103d79c55e9fab | 10.26434/chemrxiv-2024-tnx83 | A roadmap towards the synthesis of Life | The synthesis of life from non-living matter has captivated scientists for centuries. It is a grand challenge aimed at unraveling the fundamental principles of life and leveraging its unique features, such as resilience, sustainability, and the ability to evolve. Synthetic life holds immense potential in biotechnology, medicine, and materials science. Advancements in synthetic biology, systems chemistry, and biophysics have brought us closer to achieving this ambitious goal. Researchers have successfully assembled cellular components and synthesized biomimetic hardware for synthetic cells, while chemical reaction networks have demonstrated potential for Darwinian evolution. However, numerous challenges persist, including defining terminology and objectives, interdisciplinary collaboration, and addressing ethical aspects and public concerns. Our perspective offers a roadmap toward the engineering of life based on discussions during a two-week workshop with scientists from around the globe. | Christine Kriebisch; Olga Bantysh; Lorena Baranda; Andrea Belluati; Eva Bertosin; Kun Dai; Maria de Roy; Hailin Fu; Nicola Galvanetto; Julianne Gibbs; Samuel Santhosh Gomez; Gaetano Granatelli; Alessandra Griffo; Maria Guix; Cenk Onur Gurdap; Johannes Harth-Kitzerow; Ivar Haugerud; Gregor Häfner; Pranay Jaiswal; Sadaf Javed; Ashkan Karimi; Shuzo Kato; Brigitte Kriebisch; Sudarshana Laha; Pao-Wan Lee; Wojciech Lipinski; Thomas Matreux; Thomas Michaels; Erik Poppleton; Alexander Ruf; Annemiek Slootbeek; Iris Smokers; Héctor Soria-Carrera; Alessandro Sorrenti; Michele Stasi; Alisdair Stevenson; Advait Thatte; Mai Tran; Merlijn van Haren; Hidde Vuijk; Shelley Wickham; Pablo Zambrano; Katarzyna Adamala; Karen Alim; Ebbe Sloth Andersen; Claudia Bonfio; Dieter Braun; Erwin Frey; Ulrich Gerland; Wilhelm Huck; Frank Jülicher; Nadanai Laohakunakorn; L. Mahadevan; Sijbren Otto; James Saenz; Petra Schwille; Kerstin Göpfrich; Christoph Weber; Job Boekhoven | Biological and Medicinal Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.); Biophysics; Cell and Molecular Biology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668b9aaf01103d79c55e9fab/original/a-roadmap-towards-the-synthesis-of-life.pdf |
6238c3e613d4787b9196e912 | 10.26434/chemrxiv-2022-lq7jn | Role of Electronic Passivation in Stabilizing Solid Electrolyte Interphases | The solid-electrolyte interphase (SEI) is crucial to the electrochemical performance of all-solid-state batteries (ASSBs). Theoretical characterization of SEI properties will help understand the origin of interfacial stability (and instability) between solid electrolytes and electrodes. Among solid electrolytes for Lithium(Li)-ion ASSBs, the lithium phosphorus oxynitride LixPOyNz (LiPON) is one of the most stable against Li metal anode. However, it has been shown that LiPON reacts with Li metal and forms SEIs. The SEI formation stops after a thin layer is formed, but the mechanism that enables this apparent stabilization is unclear. Thermodynamics underpins the defect formation in materials and in turn, creation of electronic charge. Materials for energy storage, including solid electrolytes, are no exception to this fundamental process.
Here, we computationally evaluate the electronic passivation of SEIs and its role in stabilizing the Li-LiPON interface. Specifically, we determine the defect and charge carrier concentrations in Li-LiPON SEIs, including Li2O, Li3N, Li3P, and Li3PO4. The defect and charge carrier concentrations were calculated from defect thermodynamics. We then predicted the electronic conductivity of the SEIs under different electrochemical conditions, which correspond to varying potentials to the Li metal anode. Our results reveal that the stoichiometrically abundant and uniformly distributed Li2O has expectedly negligible electronic conductivity, while the electronically conducting components, such as Li3N and Li3P, show preferential distribution in the SEI. We posit that the overall electronically insulating nature of the SEI is responsible for the stability of the Li-LiPON interface. The computational approach adopted here can be extended to reveal the origin of the interfacial stability in other ASSBs. | Yuheng Li; Pieremanuele Canepa; Prashun Gorai | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6238c3e613d4787b9196e912/original/role-of-electronic-passivation-in-stabilizing-solid-electrolyte-interphases.pdf |
663f55a5418a5379b002a1a5 | 10.26434/chemrxiv-2024-dldzf | Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment | Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here we present a systematic analysis of fifteen RNA stem-loop sequences simulated with molecular dynamics simulations in an implicit solvent environment. Analysis of RNA cluster ensembles showed that the stem-loop structures can generally adopt A-form RNA in the stem region. Loop structures are more sensitive and experimental structures could only be reproduced with modification of CH---O interactions in the force field, combined with an implicit solvent nonpolar correction to better model base stacking interactions. Accurately modeling RNA with current atomistic physics-based models remains challenging but the RNA systems studied herein may provide a useful benchmark set for testing other RNA modeling methods in the future. | Jason Linzer; Ethan Aminov; Aalim Abdullah; Colleen Kirkup; Rebeca Ventura Diaz; Vinay Bijoor; Jiyun Jung; Sophie Huang; Chi Gee Tse; Emily Alvarez-Toucet; Hugo Onghai; Arghya Ghosh; Alex Grodzki; Emilee Haines; Aditya Iyer; Mark Khalil; Alexander Leong; Michael Neuhaus; Joseph Park; Asir Shahid; Matthew Xie; Jan Ziembicki; Carlos Simmerling; Maria Nagan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663f55a5418a5379b002a1a5/original/accurately-modeling-rna-stem-loops-in-an-implicit-solvent-environment.pdf |
663a2e1891aefa6ce161e045 | 10.26434/chemrxiv-2024-xfdn8 | Catalysing (organo-) catalysis: Trends in the application of machine learning to enantioselective organocatalysis | Organocatalysis has established itself as a third pillar of homogeneous catalysis, besides transition metal catalysis and biocatalysis, as its use for enantioselective reactions has gathered significant interest over the last decades. Concurrent to this development, machine learning (ML) has been increasingly applied in the chemical domain to efficiently uncover hidden patterns in data and accelerate scientific discovery. While the uptake of ML in organocatalysis has been comparably slow, recent years have shown an increased interest in the community. This review gives an overview of the work in the field of ML in organocatalysis. The review starts by giving a short primer on ML for experimental chemists, before discussing its application for predicting the selectivity of organocatalytic transformations. Subsequently, we review ML employed for privileged catalysts, before focusing on its application for catalyst and reaction design. Concluding, we give our view on current challenges and future directions for this field, drawing inspiration from the application of ML to other scientific domains. | Stefan P. Schmid; Leon Schlosser; Frank Glorius; Kjell Jorner | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Machine Learning; Artificial Intelligence; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2024-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663a2e1891aefa6ce161e045/original/catalysing-organo-catalysis-trends-in-the-application-of-machine-learning-to-enantioselective-organocatalysis.pdf |
62e2e439a8e4dc7eac21263d | 10.26434/chemrxiv-2022-lhwmb | What X-ray absorption spectroscopy can tell us about the active state of earth-abundant electrocatalysts for the oxygen evolution reaction | Chemical energy storage is an attractive solution to secure a sustainable energy supply. It requires an electrocatalyst to be implemented efficiently. In order to rationally improve the electrocatalyst materials and thereby the reaction efficiency, one must reveal the nature of the electrocatalyst under reaction conditions, i.e., its active state. For a better understanding of earth-abundant metal oxides as electrocatalysts for the oxygen evolution reaction (OER), the combination of electrochemical (EC) methods and X-ray absorption spectroscopy (XAS) has been very insightful and still holds untapped potential. Herein, we concisely introduce the basics of EC and XAS and provide the necessary framework to discuss changes that electrocatalytic materials undergo, presenting manganese oxides as examples. Such changes may occur during preparation and storage, during immersion in an electrolyte, as well as during application of potentials without or with catalytic reactions. We conclude with a concise summary of how EC and XAS are currently combined to elucidate the active state as well as an outlook on future opportunities to understand the mechanisms of electrocatalysis using combined operando EC-XAS experiments. | Marcel Risch; Dulce M. Morales; Javier Villalobos; Denis Antipin | Physical Chemistry; Materials Science; Catalysis; Fuels - Materials; Electrocatalysis; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e2e439a8e4dc7eac21263d/original/what-x-ray-absorption-spectroscopy-can-tell-us-about-the-active-state-of-earth-abundant-electrocatalysts-for-the-oxygen-evolution-reaction.pdf |
62cf5ce44e76bf679d8cdff7 | 10.26434/chemrxiv-2022-hwb33 | Solid-State Synthesis of UV-Plasmonic Cr2N Nanoparticles | Materials that exhibit plasmonic response in the UV region can be advantageous for many applications such as biological photodegradation, photocatalysis, disinfection, and bioimaging. Transition metal nitrides have recently emerged as chemically and thermally stable alternatives to metal-based plasmonics materials. However, most free-standing nitride nanostructures explored so far have plasmonic response in the visible and near-IR region. Herein, we report the synthesis of UV-plasmonic Cr2N nanoparticles using a solid-state nitridation reaction. The nanoparticles had an average diameter of 9 ± 5 nm and a positively charged surface that yields stable colloidal suspension. The particles were composed of a crystalline nitride core and an amorphous oxide/oxynitride shell whose thickness varied between 1 - 7 nm. Calculations performed using finite element method predicted the localized surface plasmon resonance (LSPR) for these nanoparticles to be in the UV-C region (100 - 280 nm). While a distinctive LSPR peak could not be observed using absorbance measurements, low-loss electron energy loss spectroscopy showed the presence of surface plasmons between 80 - 250 nm and bulk plasmons centered around 50 - 60 nm. Plasmonic coupling was also observed between the nanoparticles resulting in resonances between 250 - 400 nm. | Reem Karaballi; Yashar Esfahani Monfared; Isobel Bicket ; Robert Coridan; Mita Dasog | Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cf5ce44e76bf679d8cdff7/original/solid-state-synthesis-of-uv-plasmonic-cr2n-nanoparticles.pdf |
60c744389abda205abf8c349 | 10.26434/chemrxiv.9763094.v1 | BAND NN: A Deep Learning Framework For Energy Prediction and Geometry Optimization of Organic Small Molecules | Recent advances in artificial intelligence along with development of large datasets of energies calculated using quantum mechanical (QM)/density functional theory (DFT) methods have enabled prediction of accurate molecular energies at reasonably low computational cost. However, machine learning models that have been reported so far requires the atomic positions obtained from geometry optimizations using high level QM/DFT methods as input in order to predict the energies, and do not allow for geometry optimization. In this paper, a transferable and molecule-size independent machine learning model (BAND NN) based on a chemically intuitive representation inspired by molecular mechanics force fields is presented. The model predicts the atomization energies of equilibrium and non-equilibrium structures as sum of energy contributions from bonds (B), angles (A), nonbonds (N) and dihedrals (D) at remarkable accuracy. The robustness of the proposed model is further validated by calculations that span over the conformational, configurational and reaction space. The transferability of this model on systems larger than the ones in the dataset is demonstrated by performing calculations on select large molecules. Importantly, employing the BAND NN model, it is possible to perform geometry optimizations starting from non-equilibrium structures along with predicting their energies. | Siddhartha Laghuvarapu; Yashaswi Pathak; U. Deva Priyakumar | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744389abda205abf8c349/original/band-nn-a-deep-learning-framework-for-energy-prediction-and-geometry-optimization-of-organic-small-molecules.pdf |
65b0a349e9ebbb4db9d9ef5c | 10.26434/chemrxiv-2024-8sxpx | Catalytic Resonance of Methane Steam Reforming by Dynamically Applied Charges | Catalyst design has traditionally focused on tuning active site properties to optimally bind reaction intermediates and balance the kinetic requirements of multiple, often sequential chemical processes, as necessitated by the Sabatier principle. It has recently been proposed that for reactions following certain potential energy landscapes the activity limit imposed by the Sabatier principle may be overcome by using programmed oscillations of surface electron density at the time scales of surface reactions (i.e., ‘catalytic resonance’). Here, we use a combination of density-functional theory (DFT) simulations and transient kinetic models (TKMs) to simulate the kinetics of steam reforming of methane (SRM) on Ru(211) surfaces under static and dynamic applied charges. DFT-calculated binding energies of SRM intermediates and transition states exhibit strong sensitivity to positive applied charges and follow scaling relationships unique from periodic trends across transition metals. Our simulations demonstrate that applying a small positive charge to Ru dramatically enhances the steady-state turnover frequency (TOF) of SRM by up to five orders of magnitude above the TOF observed over neutral Ru. Thus, statically charging Ru catalysts may be an effective strategy to lower the temperature requirements for SRM. Dynamic square wave oscillations in charge resulted in SRM catalytic resonance over a broad range of frequencies (f ~ 106 Hz – 1011 Hz), with the corresponding average TOFs exceeding the statically charged Ru surface by an additional 15%. Based on sensitivity analyses performed for the two endpoints of oscillation, we propose that dynamic TOF improvement beyond the Sabatier maximum can be expected when the system is oscillated between two kinetic regimes that are uniquely controlled by distinct elementary steps. | Veera Venkata Ramprajwal Vempatti; Shengguang Wang; Omar A. Abdelrahman; Paul J. Dauenhauer; Lars C. Grabow | Theoretical and Computational Chemistry; Catalysis; Energy; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b0a349e9ebbb4db9d9ef5c/original/catalytic-resonance-of-methane-steam-reforming-by-dynamically-applied-charges.pdf |
66e6a21f12ff75c3a1632f57 | 10.26434/chemrxiv-2024-mc54v | Understanding Catalytic Enantioselective C-H Bond Oxidation at Nonactivated Methylenes Through Predictive Statistical Modeling Analysis | Enantioselective C(sp3)‒H bond oxidation is a powerful strategy for installing functionality in C(sp3)‒H rich molecules. Site- and enantioselective oxidation of strong C‒H bonds in monosubstituted cyclohexanes with hydrogen peroxide catalyzed by aminopyridine manganese catalysts in combination with alkanoic acids has been recently described. Mechanistic uncertainties and nonobvious enantioselectivity trends challenge development of the full potential of this reaction as a powerful synthetic tool. Herein, we apply predictive statistical analysis to identify mechanistically informative correlations that provide valuable reaction understanding and will guide the development and optimization of new enantioselective C‒H oxidation reactions. | Arnau Call; Andrea Palone; Jordan P. Liles; Natalie P. Romer; Jacquelyne A. Read; Josep Maria Luis; Matthew S. Sigman; Massimo Bietti; Miquel Costas | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e6a21f12ff75c3a1632f57/original/understanding-catalytic-enantioselective-c-h-bond-oxidation-at-nonactivated-methylenes-through-predictive-statistical-modeling-analysis.pdf |
60c74a7c9abda2856df8ce66 | 10.26434/chemrxiv.12213215.v1 | Role of Ion-Selective Membranes in the Carbon Balance for CO2 Electroreduction via Gas Diffusion Electrode Reactor Designs | <p></p><p></p><p>In this work, the
effect of ion-selective membranes on the detailed carbon balance was systematically
analyzed for high-rate CO<sub>2</sub> reduction in flow electrolyzers. By using
different ion-selective membranes, we show nearly identical catalytic
selectivity for CO<sub>2</sub> reduction, which is primarily due to a similar
local reaction environment created at the cathode/electrolyte interface via the
introduction of a catholyte layer. In addition, based on a systematic exploration of gases released from electrolytes
and the dynamical change of electrolyte speciation, we demonstrate the explicit
discrepancy in carbon balance paths for the captured CO<sub>2</sub> at the
cathode/catholyte interface via reaction with OH<sup>-</sup> when using different
ion-selective membranes: (i) the captured CO<sub>2</sub> could transport
through an anion exchange membrane in the form of CO<sub>3</sub><sup>2-</sup>,
subsequently releasing CO<sub>2</sub> along with O<sub>2</sub> in<sub> </sub>the
anolyte, (ii) with a cation exchange membrane, the captured CO<sub>2</sub>
would be accumulated in the catholyte in the forms of CO<sub>3</sub><sup>2-</sup>,
(iii) whereas under the operation of a BPM, the captured CO<sub>2</sub> could
be released at the catholyte/membrane interface in the form of gaseous CO<sub>2</sub>.
The unique carbon balance path for each type of membrane is linked to ion
species transported through membranes.</p><p></p><p></p> | Ming Ma; Sangkuk Kim; Ib Chorkendorff; Brian Seger | Electrocatalysis; Energy Storage; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a7c9abda2856df8ce66/original/role-of-ion-selective-membranes-in-the-carbon-balance-for-co2-electroreduction-via-gas-diffusion-electrode-reactor-designs.pdf |
60c75016842e65d1acdb3978 | 10.26434/chemrxiv.12988883.v1 | Ultrathin Single-crystalline MgO (111) Nanosheets | Synthesizing high-quality
two-dimensional nanomaterials of non-layered metal oxide is a grand challenge because
it requires long range single-crystallinity and clean high-energy surfaces. Here,
we report the synthesis of single-crystalline MgO(111) nanosheets via a
two-step process involving the formation of ultrathin Mg(OH)<sub>2</sub>
nanosheets as precursor and their selective topotactic conversion upon heating under
dynamic vacuum. The defect-rich surface displays terminal -OH groups, 3-coordinated
O<sup>2-</sup> sites, low-coordinated Mg<sup>2+</sup> sites as well as single
electrons trapped at oxygen vacancies, that render MgO nanosheets highly reactive
as evidenced by the activation of CO molecules at low temperatures and
pressures, with formation of strongly adsorbed red-shifted CO and coupling of CO
molecules into C<sub>2</sub> species. | Pengxin Liu; Paula
M. Abdala; Guillaume Goubert; Marc Willinger; Christophe Copéret | Nanostructured Materials - Nanoscience; Solid State Chemistry; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75016842e65d1acdb3978/original/ultrathin-single-crystalline-mg-o-111-nanosheets.pdf |
625ea3a35b90090c47146272 | 10.26434/chemrxiv-2022-krbwv-v2 | Direct Synthesis of Mesoionic Carbene (MIC) Stabilized Gold Nanoparticles from 1,2,3-Triazolium Salts | Significant achievements have been reported in the last few years regarding the stabilization and functionalisation of gold nanoparticles (AuNPs), mainly through the use of thiols and imidazolylidene N-heterocyclic carbenes capping ligands. Herein, we report that mesoionic carbenes (MICs) ligands, based on the 1,2,3-triazol-5-ylidene scaffold, allow the expeditive preparation of AuNPs of exceptional stability through a simple and straightforward one-pot protocol directly from triazolium salts and discrete Au(III) sources. Control over the size of the AuNPs has been achieved by varying the Au/ligand ratio as well as the nature of the triazolium salts, the latter being facilitated by the ease of synthesis of the MIC precursors through click chemistry. Characterisation of these MIC-AuNPs by X-ray photoelectron spectroscopy (XPS) hints at the exclusive presence of MICs on the nanoparticle surface. | Alexandre Porcheron ; Omar Sadek; Salem Ba Sowid; Nathalie Bridonneau; Laura Hippolyte; Dimitri Mercier; Philippe Marcus; Clément Chauvier; Corinne Chanéac; Louis Fensterbank; François Ribot | Organic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625ea3a35b90090c47146272/original/direct-synthesis-of-mesoionic-carbene-mic-stabilized-gold-nanoparticles-from-1-2-3-triazolium-salts.pdf |
65dcae3fe9ebbb4db94cff0f | 10.26434/chemrxiv-2024-qdmfh | Cation dependence of enniatin B/membrane-interactions assessed using surface-enhanced infrared absorption spectroscopy | Enniatins are mycotoxins with well-known antibacterial, antifungal, antihelmintic and antiviral activity, which have recently come to attention as potential mitochondriotoxic anticancer agents. The cytotoxicity of enniatins is traced back to their ionophoric properties, in which the cyclodepsipeptidic structure results in enniatin:cation-complexes of various stoichiometries proposed as membrane-active species. In this work, we employed a combination of surface-enhanced infrared absorption (SEIRA) spectroscopy, tethered bilayer lipid membranes (tBLMs) and density functional theory (DFT)-based computational spectroscopy to monitor the cation-dependence (Mz+ = Na+, K+, Cs+, Li+, Mg2+, Ca2+) on the mechanism of enniatin B (EB) incorporation into membranes and identify the functionally relevant EBn:Mz+ complexes formed. We find that Na+ promotes a cooperative incorporation, modelled via an autocatalytic mechanism and mediated by a distorted 2:1-EB2:Na+ complex. K+ (and Cs+) leads to a direct but less efficient insertion into membranes due to the adoption of “ideal” EB2:K+ sandwich complexes. In contrast, the presence of Li+, Mg2+, and Ca2+ causes a (partial) extraction of EB from the membrane via the formation of “belted” 1:1-EB:Mz+ complexes, which screen the cationic charge less efficiently. Our results point to a relevance of the cation dependence for the transport into the malignant cells where the mitochondriotoxic anticancer activity is exerted. | Barbara Daiana Gonzalez; Enrico Forbrig; Guiyang Yao; Patrycja Kielb; Maria Andrea Mroginski; Peter Hildebrandt; Jacek Kozuch | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dcae3fe9ebbb4db94cff0f/original/cation-dependence-of-enniatin-b-membrane-interactions-assessed-using-surface-enhanced-infrared-absorption-spectroscopy.pdf |
66f6889551558a15ef4e4204 | 10.26434/chemrxiv-2024-dxdr9 | High-Resolution Multicolor Shortwave Infrared In Vivo Imaging with Chromenylium Nonamethine Dyes | Imaging in the shortwave infrared (SWIR) region offers high-resolution visualization of in vivo targets in a multiplexed manner. These methods require bright, bathochromically-shifted fluorescent dyes with sufficient emission at SWIR wavelengths–ideally above 1400 nm for high resolution images. Polymethine dyes are a privileged class of contrast agents due to their excellent absorption and high degree of modularity. In this work, we push flavylium and chromenylium dyes further into the SWIR region through polymethine chain extension. This panel of nonamethine dyes boasts absorbances as red as 1149 nm and tail emission beyond 1500 nm. These dyes are the brightest fluorophores at their respective bandgaps to date, with εmax ~105 M-1 cm-1 and ΦF up to 0.5%. We showcased two nonamethine dyes for multiplexed imaging with all SWIR excitation (1060, 1150 nm) and detection at the preferred SWIR wavelengths of 1500–1700 nm, enhancing the depths and resolutions able to be obtained in multicolor SWIR imaging with small molecule contrast agents. | Anthony Spearman; Eric Lin; Emily Mobley; Andriy Chmyrov; Daniel Turner; Cesar Garcia; Kyle Bui; Christopher Rowlands; Oliver Bruns; Ellen Sletten | Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f6889551558a15ef4e4204/original/high-resolution-multicolor-shortwave-infrared-in-vivo-imaging-with-chromenylium-nonamethine-dyes.pdf |
60c744b90f50dbeda639613d | 10.26434/chemrxiv.9894104.v1 | Harnessing Direct(Hetero)Arylation in Pursuit of a Saddle-Shaped Perylene Diimide Tetramer | <p>This contribution explores the direct(hetero)
arylation (DHA) cross-coupling of a saddle-like, π-conjugated cyclooctatetrathiophene
(Th<sub>4</sub>) core with the N-annulated perylene diimide (PDI)
chromophore. Replacing the bulky pivalic acid with acetic acid enabled a facile
cross-coupling, selectively forming a PDI tetramer (Th<sub>4</sub>PDI<sub>4</sub>) in a 70% overall yield. The optoelectronic
properties of Th<sub>4</sub>PDI<sub>4</sub> were characterized and density functional theory (DFT)
was used to calculate the optimized molecular geometry and molecular orbitals
(MOs). MOs determined by cyclic voltammetry corresponded well with those calculated
using DFT. The molecular geometry calculated by DFT showed Th<sub>4</sub>PDI<sub>4</sub> adopts two separate PDI-PDI conformations (propeller
and double-decker). Organic photovoltaic (OPV) devices were fabricated using a
blend of PTB7-Th:Th<sub>4</sub>PDI<sub>4</sub>, where an initial power conversion efficiency (PCE)
of 1.89 % was improved by testing a series of solvent additives and thermal
annealing techniques. Through use of 3 % (v/v) 1-chloronaphthalene additive, a
combination of higher short circuit current (J<sub>sc</sub> = 10.2 mA/cm<sup>2</sup>)
and fill factor (FF = 42 %) led to an overall increase in PCE to 4.26 %. </p> | Joshua Koenig; Audrey Laventure; Gregory Welch | Oligomers | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b90f50dbeda639613d/original/harnessing-direct-hetero-arylation-in-pursuit-of-a-saddle-shaped-perylene-diimide-tetramer.pdf |
60c74a99842e651b18db2f73 | 10.26434/chemrxiv.12227255.v1 | Advantageous Antibody Microarray Fabrication Through DNA-Directed Immobilization: A Step Toward Use of Extracellular Vesicles in Diagnostics | An optimized general
protocol for DNA-protein ligation is provided and the conjugates are used to
convert DNA arrays into antibody microarrays. Arrays obtained through DDI were
used to capture and characterize extracellular vesicles (EVs), an emerging
class of biomarkers. The proposed platform was tested against commercially
available antibody microarrays, showing good performance combined with ease of fabrication. | Dario Brambilla; Laura Sola; Marcella Chiari | Organic Polymers; Biochemical Analysis; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a99842e651b18db2f73/original/advantageous-antibody-microarray-fabrication-through-dna-directed-immobilization-a-step-toward-use-of-extracellular-vesicles-in-diagnostics.pdf |
6739fde35a82cea2fa6c10c2 | 10.26434/chemrxiv-2024-1dr10 | Rules Describing CO2 Activation on Single-Atom Alloys from DFT-meta-GGA Calculations and Artificial Intelligence | Single-atom alloys (SAAs) arise as a promising concept for the design of improved CO2 hydrogenation catalysts. However, from the immense number of possible SAA compositions and structures, only a few might display the properties required to be useful catalysts. Thus, the direct, high-throughput screening of materials is inefficient. Here, we use artificial intelligence to derive rules describing surface sites of SAAs that provide an effective CO2 activation, a crucial initial step to convert the molecule into valuable products. We start by modeling the CO2 interaction with 780 sites of flat and stepped surfaces of SAAs composed by Cu, Zn, and Pd hosts via high-quality DFT-mBEEF calculations. Then, we apply subgroup discovery to determine constraints on key physical parameters, out of 24 offered candidate descriptive parameters, characterizing subgroups (SGs) of surface sites where chemisorbed CO2 displays large elongations of its C-O bonds. The key identified parameters are free-atom properties of the elements constituting the surface sites, such as their electron affinity, electronegativity, and radii of the $d$-orbitals. Additionally, the generalized coordination number is selected as a key geometrical parameter. The SG rules are used to identify promising alloys among more than 1,500 possible single-atom and dual-atom alloys. Some of the promising alloys predicted by the SG rules were explicitly evaluated by additional DFT-mBEEF calculations and confirmed to provide a significant CO2 activation. | Herzain I. Rivera-Arrieta; Lucas Foppa | Theoretical and Computational Chemistry; Materials Science; Catalysis; Theory - Computational; Artificial Intelligence; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6739fde35a82cea2fa6c10c2/original/rules-describing-co2-activation-on-single-atom-alloys-from-dft-meta-gga-calculations-and-artificial-intelligence.pdf |
616d6f650ad1ff264b999215 | 10.26434/chemrxiv-2021-3n07b | Understanding the reaction mechanism of Kolbe electrolysis on Pt anodes | Kolbe electrolysis has been proposed an efficient electrooxidation process to synthesize (un)symmetrical dimers from biomass-based carboxylic acids. However, the reaction mechanism of Kolbe electrolysis remains controversial. In this work, we develop a DFT- based microkinetic model to study the reaction mechanism of Kolbe electrolysis of acetic acid (CH3COOH) on both pristine and partially oxidized Pt anodes. We show that the shift in the rate-determining step of oxygen evolution reaction (OER) on Pt(111)@α-PtO2 surface from OH* formation to H2O adsorption gives rise to the large Tafel slopes, i.e., the inflection zones, observed at high anodic potentials in experiments on Pt anodes. The activity passivation as a result of the inflection zone is further exacerbated in the presence of Kolbe species (i.e., CH3COO* and CH3*). Our simulations find the CH3COO* decarboxylation and CH3* dimerization steps determine the activity of Kolbe reaction during inflection zone. In contrast to the Pt(111)@α-PtO2 surface, Pt(111) shows no activity towards Kolbe products as the CH3COO* decarboxylation step is limiting throughout the considered potential range. This work resolves major controversies in the mechanistic analyses of Kolbe electrolysis on Pt anodes: the origin of the inflection zone, and the identity of the rate limiting step. | Sihang Liu; Nitish Govindarajan; Hector Prats; Karen Chan | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616d6f650ad1ff264b999215/original/understanding-the-reaction-mechanism-of-kolbe-electrolysis-on-pt-anodes.pdf |
67cb473581d2151a0288b508 | 10.26434/chemrxiv-2025-tpfff | Engineering Shootable Mycelium-Based Composites (MBCs) as Living Building Materials by Modification and Application of Psyllium Husk Gel | Conventional building materials, such as concrete, steel, and brick, are energy-intensive to produce, contribute to significant carbon emissions, and deplete finite natural resources. In response to critical environmental issues caused by these non-renewable materials, mycelium-based composites (MBCs) have attracted widespread attention. MBCs provide a renewable alternative where mycelium grows on lignocellulosic fibers forming a lightweight, low energy cost, and an effective insulating material. However, the bottleneck of large-scale architectural applications of MBCs lies in conventional mold-based manual manufacturing processes. Even though 3D-printable mycelium composites facilitate automated production and greater design freedom, the size is still limited at the centimeter scale due to the extended time required for layers to fuse from hyphal growth. The development of shootable MBCs, which can potentially overcome these constraints for flexible forms and automated large-scale construction, has not yet been explored. This study investigates biopolymer modification methods for psyllium husk gels to engineer shootable MBCs with high cohesive and adhesive properties that enable deposition on vertical surfaces. Engineered formulations demonstrated consistent shootability over a span of 50 minutes with minimal material loss (<10%), and robust mycelium growth at both the surface and throughout the cross section. The resulting composition exhibits circular building lifecycle principles as all ingredients are biodegradable and compostable at the end of building life. Additionally, a shootable composite broadens the fabrication methods and applications of MBCs, showing promise for use with shotcrete-like spraying techniques in the building industry. | Xue Brenda Bai; Ellen W. van Wijngaarden; Meredith N. Silberstein; Marta H. Wisniewska | Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Biodegradable Materials; Composites; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cb473581d2151a0288b508/original/engineering-shootable-mycelium-based-composites-mb-cs-as-living-building-materials-by-modification-and-application-of-psyllium-husk-gel.pdf |
65772b427acf130c32ff2a53 | 10.26434/chemrxiv-2023-bkgd3 | Production of Methane by Catalytic Decarboxylation of Methyl Formate as a Liquid Surrogate | Methane is a widely utilized molecule, primarily sourced from fossil fuels and it finds numerous applications in the energy sector. More sustainable sources of methane include the conversion of organic wastes or gaseous CO2. An alternative would be to use a sustainable C1 intermediate able to form methane. To this end, this work demonstrates the utilization of methyl formate as a liquid surrogate for methane, and its selective decomposition by catalytic decarboxylation. This reaction exhibited excellent yields, exceeding 90%, and the method can be expanded to produce several alkanes from alkyl formates. | Nathan De Riggi; Arnaud Imberdis; Emmanuel Nicolas; Thibault Cantat | Catalysis; Energy; Homogeneous Catalysis; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65772b427acf130c32ff2a53/original/production-of-methane-by-catalytic-decarboxylation-of-methyl-formate-as-a-liquid-surrogate.pdf |
636c736eb588501b1d45f486 | 10.26434/chemrxiv-2022-0h2ll | Electrochemical Transformation of Limestone into Portlandite and Valuable Carbonaceous Products | The cement industry is one of the largest contributors to global CO2 emissions, and it is extremely challenging to decarbonize the cement industry, as most CO2 emissions results from the calcination of limestone (CaCO3) into CaO and CO2. In this work, we demonstrate a novel electrochemical process that transforms CaCO3 into portlandite (Ca(OH)2, a key Portland cement precursor) and valuable carbonaceous products, which integrates electrochemical water splitting and CO2 reduction reaction with the chemical decomposition of CaCO3. With different metal catalyst electrodes, we have achieved Ca(OH)2 and various valuable carbonaceous products, such as CO, formate, methane, and ethylene. Our work revolutionizes cement production and provides a green and sustainable path toward carbon neutrality for the cement industry. | Qixian Xie; Lili Wan; Zhuang Zhang; Jingshan Luo | Physical Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636c736eb588501b1d45f486/original/electrochemical-transformation-of-limestone-into-portlandite-and-valuable-carbonaceous-products.pdf |
67461de47be152b1d0f1e441 | 10.26434/chemrxiv-2024-fsb28 | Atomic layer restructuring of gold surfaces by N-heterocyclic carbenes over large surface areas | Even highly planar, polished metal surfaces display varying levels of roughness that can affect their optical and electronic properties, impacting performance in state-of-the-art microelectronics. Current methods for smoothing rough metallic surfaces require either the removal or addition of substantial amounts of material using complex processes that are incompatible with 3-dimensional nano-scale features needed for state-of-the-art applications. We present a vapor-phase process that results in up to a 60% smoothing of nanometer scale rough gold surfaces through a single exposure to a new class of ligand called N-heterocyclic carbenes (NHCs). This process does not require removal or addition of metal from the surface and provides smoothing at the Ångström scale. Smoothing occurs in a single deposition, giving quantifiable differences in the adsorption behavior of the resulting surfaces. The process takes place through an adatom–extraction-driven destabilization and restructuring of the surface in a self-limiting manner. This novel process is achieved without the use of harsh chemical etchants or mechanical intervention, takes only minutes, and can easily be integrated with vapor phase processing in situ. It offers a promising avenue for subnanometer smoothing in microfabrication workflows. Our observations pave the way for atomic layer restructuring (ALR), a technique that compliments atomic layer deposition (ALD) and atomic layer etching (ALE) in the fabrication and processing high precision materials. | Eden Goodwin; Matt Davies; Maram Bakiro; Emmett Desroche; Francesco Tumino; Mark Aloisio; Cathleen M. Crudden; Paul J. Ragogna; Mikko Karttunen; Seán T. Barry | Materials Science; Coating Materials; Surfactants; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67461de47be152b1d0f1e441/original/atomic-layer-restructuring-of-gold-surfaces-by-n-heterocyclic-carbenes-over-large-surface-areas.pdf |
67a1a4a46dde43c9088721d0 | 10.26434/chemrxiv-2025-fkfwh | Vibronic Trimer Design Enhancing Intramolecular Triplet-Exciton Hopping to Accelerate Triplet-Triplet Annihilation for Photon Upconversion | Photon upconversion via triplet-triplet annihilation (TTA-UC) is well-known as a photophysical process that converts low-energy light into higher-energy light. This process has drawn attention for its potential in various fields including light-emitting device, power genera-tion, and medical applications. To promote these societal applications, it is desirable to develop TTA-UC materials that exhibit high ener-gy conversion efficiency. For this, TTA emitters with large TTA rate constants (kTTA) are required. However, molecular design for accel-erating the bimolecular rate constant of kTTA has not been considered. We present a strategy to increase kTTA by assembling multiple chromophores linked with a boron in a rotationally symmetric manner causing a symmetry breaking charge-transfer type triplet-exciton in the TTA emitter. We examined tri(9-anthryl)borane, which consists of three anthracenes linked via boron as the TTA emitter. Time-resolved luminescence measurements confirmed that kTTA is improved compared to the conventional TTA-UC system employing DPA, an anthracene-based monomer. Time-resolved electron paramagnetic resonance measurements demonstrated that the improvement in kTTA is due to fast intramolecular triplet exciton hopping coupled with vibrational motions in the trimer molecule, expanding reactivity at collision distance between the excitons through the pseudo-rotational motions. The present TTA emitter molecular designs which im-prove the TTA reactivity is expected to contribute to the future development of TTA-UC materials. | Yasuhiro Kobori; Kousuke Higashi; Tsubasa Okamoto; Nanami Iwaya; Eri Sakuda; Christopher Kay; Tadaaki Ikoma | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a1a4a46dde43c9088721d0/original/vibronic-trimer-design-enhancing-intramolecular-triplet-exciton-hopping-to-accelerate-triplet-triplet-annihilation-for-photon-upconversion.pdf |
63be90225ad3ef0e5394f125 | 10.26434/chemrxiv-2023-7cg46 | Towards controlled partial desolvation of guest-responsive Metal-Organic Frameworks for precise porosity control | Desolvation of guest responsive metal-organic frameworks (MOFs) under dynamic vacuum often leads to the collapse of the pores whereas supercritical CO2 (SC-CO2) drying was found to be the best alternative way to overcome the challenge of MOF desolvation. Nevertheless, some of the MOFs collapse during desolvation by SC-CO2 drying method. SC-CO2 drying always leads to complete desolvation of the MOFs except the metal-coordinated solvent molecules. However, controlled and partial desolvation of the MOFs can be a possible way to restrict the pore collapse of the frameworks. The importance of nuanced desolvation is demonstrated for two iso-structural newly designed tetra-carboxylic acid-based Cu-MOFs (DUT-202, DUT-203). These MOFs switch to a contracted pore phase upon complete desolvation of the solvent molecules either by vacuum treatment or SC-CO2 drying method. Therefore, a controlled desolvation technique has been followed to activate DUT-202, 203 while the closely trapped DMF remains coordinated which is essential to retain the microporous nature of the framework. Acetone-exchanged Cu-MOFs were treated under argon flow to replace the weakly connected solvent molecules inside the pores but not the strongly trapped guest molecules and the activated phases were found to have open pore phase with microporous nature. Interestingly the contracted pore phase can be reopened by heating in DMF for several hours. | Kartik Maity; Volodymyr Bon; Stefan Kaskel | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Physical and Chemical Properties; Surface; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63be90225ad3ef0e5394f125/original/towards-controlled-partial-desolvation-of-guest-responsive-metal-organic-frameworks-for-precise-porosity-control.pdf |
652712ca45aaa5fdbbcc6934 | 10.26434/chemrxiv-2023-9j9ht | Evaluating development of empirical estimates using two top-down methods at midstream natural gas facilities | To align with climate initiatives, multiple reporting programs are transitioning from generic activity-based emission factors to site-specific measured emissions data to estimate greenhouse gas emissions at oil and gas facilities. This study contemporaneously deployed two top-down (TD) aerial methods across 14 midstream facilities, extending work done in Brown et al.1. Methods produced multiple whole-facility estimates at each facility, resulting in 773 individual paired estimates (same facility, same day), and robust mean estimates for each facility. Mean estimates for each facility, aggregated across all facilities, differed by nearly 2:1 (49% [32% to 68%]). At 6 of 14 facilities, the methods produced mean estimates that differed by more than a factor of two. These data suggest that one or both methods did not produce accurate facility-level estimates, at a majority of facilities and in aggregate across all facilities.
Overall results are augmented with two case studies where TD estimates at two pre-selected facilities were coupled with comprehensive onsite measurements to understand factors driving the divergence between TD and bottom-up (BU) emissions estimates. In 3 of 4 paired comparisons between the intensive onsite estimates and one of the TD methods, the intensive onsite surveys did not conclusively diagnose the difference in estimates. In these cases, our work suggests that the TD methods mis-estimate emissions an unknown fraction of the time, for unknown reasons. While two methods were selected for this study, it is unlikely that the issues identified here are confined to these two methods; similar issues may exist for other similar whole-facility methods, on midstream and/or other facility types. These findings have important implications for the construction of voluntary and regulatory reporting programs that rely on emission estimates for reporting, fees or penalties, or for studies using whole-facility estimates to aggregate TD emissions to basin or regional estimates.
| Jenna Brown; Matthew Harrison; Tecle Rufael ; Selina Roman-White; Gregory Ross; Fiji George; Daniel Zimmerle | Energy | CC BY 4.0 | CHEMRXIV | 2023-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652712ca45aaa5fdbbcc6934/original/evaluating-development-of-empirical-estimates-using-two-top-down-methods-at-midstream-natural-gas-facilities.pdf |
60c756beee301c2c55c7b3f8 | 10.26434/chemrxiv.14061392.v2 | Mechanistic Investigations Towards a Successful PET with Breslow-Intermediates | Experimental mechanistic studies to learn about suitable conditions for a successful photocatalytic oxidation of Breslow intermediates.<div>Key findings </div><div>a) address the effect of additives (oxidative, reductive) and assembly effects on PET and the dark reaction, </div><div>b) include the experimental support of a SET + HAT sequence directly connecting the primary adduct of aldhyde and NHC and the Breslow intermediate.</div> | Jenny Phan; Julia Rehbein | Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756beee301c2c55c7b3f8/original/mechanistic-investigations-towards-a-successful-pet-with-breslow-intermediates.pdf |
6781fa8c6dde43c90812e68c | 10.26434/chemrxiv-2025-7v8kn | Formation and Evolution of Solid Electrolyte Interphase at Calcium Surfaces | Solid electrolyte interphase (SEI) plays a crucial role in the reversible metal-ion deposition at electrodes, impacting battery performance and lifespan. SEI formation results from the decomposition of salts/solvents at the electrode surface via redox reactions, with its growth governed by dynamic interactions between the electrode, electrolyte, and decomposed products. These interactions are difficult to capture experimentally. Here, using large-scale ab initio molecular dynamics simulations, we explored the formation and evolution of SEIs at calcium anode under varying solvent, salt, and temperature conditions over 100 picoseconds. Our simulations are inspired by several recent experiments, which show reversible calcium-ion deposition only with a few selected salts under specific experimental conditions. Our work not only deciphers these experiments but also provides detailed microscopic insights into (i) solvent decomposition, (ii) the order of salt/solvent decomposition in the cell, (iii) the impact of electrode passivation on salt’s stability, and (iv) the role of nuclear dynamics and coordination geometry in anion decomposition, and thereby influencing the reversible deposition of cations. These findings offer critical insights into the formation and evolution of SEIs at metal anodes and provide guidance for designing new electrolytes to enhance the performance and longevity of metal-anode batteries. | Subhadeep Banerjee; Sharma S. R. K. C. Yamijala | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6781fa8c6dde43c90812e68c/original/formation-and-evolution-of-solid-electrolyte-interphase-at-calcium-surfaces.pdf |
64f0a4ecdd1a73847fe4b0f1 | 10.26434/chemrxiv-2023-07737 | Spirostrain-Accelerated Chemiexcitation of Dioxetanes Yields Unprecedented Detection Sensitivity in Chemiluminescence Bioassays | Chemiluminescence is a fascinating phenomenon involving the generation of light through chemical reactions. The light emission from adamantyl-phenoxy-1,2-dioxetanes can glow from minutes to hours, depending on the specific substituent present on the dioxetane molecule. In order to improve the light emission properties produced by these chemiluminescent luminophores, it is necessary to induce the chemiexcitation rate to a flash mode wherein the bulk of light is emitted instantly rather than slowly over time. We report the realization of this goal through the incorporation of spirostrain release into decomposition of 1,2-dioxetane luminophores. DFT computational simulations provided support for the hypothesis that the spiro-cyclobutyl accelerates chemiexcitation as compared to the unstrained adamantyl substituent. Spiro-linking of cyclobutane and oxetane units led to greater than 100-fold and 1000-fold emission enhancement, respectively. This accelerated chemiexcitation rate increases the detection sensitivity for known chemiluminescent probes to the highest signal-to-noise ratio documented to date. A turn-ON probe, containing a spiro-cyclobutyl unit, for detecting the enzyme β-galactosidase, exhibited a Limit-of-Detection value that is 125-fold more sensitive than the previously described adamantyl analogue. This probe was also able to instantly detect and image β-gal activity with enhanced sensitivity in E. coli bacterial assays. | Rozan Tannous; Omri Shelef; Sara Gutkin; Maya David; Thomas Leirikh; Liang Ge; Qais Jaber; Qingyang Zhou; Pengchen Ma; Micha Fridman; Urs Spitz; Kendall N. Houk; Doron Shabat | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0a4ecdd1a73847fe4b0f1/original/spirostrain-accelerated-chemiexcitation-of-dioxetanes-yields-unprecedented-detection-sensitivity-in-chemiluminescence-bioassays.pdf |
62bb346bd66f680795b511af | 10.26434/chemrxiv-2022-ng6d8 | Simultaneous determination of organophosphorus and brominated flame retardants and polychlorinated biphenyls in hair by pressurized liquid extraction and gas chromatography/tandem mass spectrometry | Polybrominated diphenyl ethers (PBDEs), brominated flame retardants widely used since the 1980s, were banned or phased out in many countries during the 2000s and gradually replaced by organophosphorus flame retardants (OPFRs), substances for which few exposure data are available to date. Like phthalates, these OPFRs are used as additives in many materials without being chemically bound and can therefore easily be released into the environment by abrasion and/or volatilization. Exposure to these substances can be assessed indirectly via their measurement in different environmental matrices or directly via the measurement of the population impregnation.
In this context, a method for the determination of selected OPFRs but also PBDEs and PCBs in human hair samples was developed. The protocol includes a pulverization step of the hair sample followed by an automated pressurized liquid extraction (PLE) step, and finally by a targeted quantitative analysis by gas chromatography coupled to tandem mass spectrometry (GC/MS/MS). The proposed analytical method allows the determination of 37 substances among which 8 PBDEs, 11 PCBs and 15 OPFRs including tributyl phosphate (TBP), tris(2-chloroethyl) phosphate (TCEP), tris(1-chloro-2-propyl) phosphate (TCPP), tris(1,3-dichloro-2-propyl) phosphate (TDCPP), 2-ethylhexyl diphenyl phosphate (EHDPP) and triphenyl phosphate (TPP), with limits of quantification, for a 25-mg hair sample, ranging from 2 ng/g for triisopropyl phosphate (TiPP) to 400 ng/g for TCPP.
The performance of the method was then assessed (several operators and days of analysis) on an inert material (Celite® 545) unspiked and spiked at the LOQ level and at a level 10 times higher than the LOQ, on a non-contaminated real human hair sample unspiked and spiked at a level 10 times higher than the LOQ, and via replicate analysis of the standard reference material SRM 2585 (Organic Contaminants in House Dust), for which indicative, reference or certified concentrations are available for some PBDEs, PCBs and OPFRs. The results obtained were very satisfactory in terms of interday method precision (< 25% in most cases) and accuracy (between 70 and 130% for most substances). | Thomas Yon; Gaëlle Saramito; Aurélien Lecorgne; Quentin Goyat; Philippe Glorennec; Barbara Le Bot; Fabien Mercier | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bb346bd66f680795b511af/original/simultaneous-determination-of-organophosphorus-and-brominated-flame-retardants-and-polychlorinated-biphenyls-in-hair-by-pressurized-liquid-extraction-and-gas-chromatography-tandem-mass-spectrometry.pdf |
610d7d8f18911d2e90db3e13 | 10.26434/chemrxiv-2021-jb5m1 | Aluminium Mediated Isocyanide Insertion and Sequential Ring Opening Cyclization (SROC) Strategy: Synthesis of Azole Fused Benzimidazoquinazoline Skeletons | A first report on transition-metal-free aluminium chloride mediated isocyanide insertion between two amine nucleophiles have been presented. Also, an unusual C-N bond cleavage allow for the further development of copper mediated ring open-ing cyclization (SROC) strategy for the synthesis of azole fused benzimidazoquinazoline scaffolds. The key features of this protocol are aluminium chloride as non-transition-metal based mediator, oxidant/base/ligand free isocyanide insertion, three new C-N and one C-C bond formations and simultaneous construction of multiprivileged azole fused benzimidazoquinazo-line in good yields. | anand H. Shinde; Nagarjuna Babu Venkata ; Punith S.; D. S. Sharada | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610d7d8f18911d2e90db3e13/original/aluminium-mediated-isocyanide-insertion-and-sequential-ring-opening-cyclization-sroc-strategy-synthesis-of-azole-fused-benzimidazoquinazoline-skeletons.pdf |
60c74ff4842e65cacfdb392a | 10.26434/chemrxiv.12973217.v1 | Photoswitching, Umpolung and Reversible Self-Assembly of Gold Nanoparticles Covered With Thiolated Donor-Acceptor Stenhouse Adducts | The possibility of incorporating functional groups into molecular photoswitches is
a prerequisite for their versatility and broad-range applications. Herein we present the first
successful synthesis of DASA chromophores featuring a thiol group. The latter provides a
unique opportunity to investigate the photoswitching behavior of these visible-light operating
chromophores on the surface of metallic nanoparticles. This behavior can be modulated by
irradiation time, solvent composition, DASAs population, and the organic layer underneath
the chromophores. Moreover, the changes in polarity induced by DASAs photoisomerization
are translated onto the colloidal particles giving rise to unusual interfacial and bulk-phase
phenomena, including nonlinear solubility effects and reversible agglomeration that takes
place in a time-controllable fashion. These findings pave the way for the rational design of
new photoresponsive and smart materials. | grzegorz sobczak; Iwona Misztalewska-Turkowicz; Volodymyr Sashuk | Organic Compounds and Functional Groups; Nanostructured Materials - Nanoscience; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ff4842e65cacfdb392a/original/photoswitching-umpolung-and-reversible-self-assembly-of-gold-nanoparticles-covered-with-thiolated-donor-acceptor-stenhouse-adducts.pdf |
60c74022702a9bd1e018a058 | 10.26434/chemrxiv.7637009.v1 | A Chemical Theory of Topological Insulators | This article presents a chemical description of a simple topological insulators model in order to translate concepts such as "symmetry protected", "surface states" to the chemistry vocabulary | Angel Martín Pendás; Julia Contreras-García; Fernanda Pinilla; José Daniel Mella; Carlos Cárdenas; Francisco Muñoz | Solid State Chemistry; Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74022702a9bd1e018a058/original/a-chemical-theory-of-topological-insulators.pdf |
60c7455c337d6c9840e26f8d | 10.26434/chemrxiv.10006712.v1 | The Role of Sodium Sulfate Supporting Electrolyte in Ammonium Transport and Reduction at Interface Between Platinum Cathode and Solution | Ammonium is a potential hydrogen fuel and can be recovered from high ammonium wastewater via electrodeionization (EDI) process. Since NH<sub>4</sub><sup>+</sup> is a weak acid ion, sodium sulfate (Na<sub>2</sub>SO<sub>4</sub>) is used as a supporting electrolyte to improve electrolyte’s conductivity. This manuscript investigated the NH<sub>4</sub><sup>+</sup> behaviors in high Na<sub>2</sub>SO<sub>4</sub> solution through electrochemical analysis methods and molecular dynamics (MD) simulations. Ionic strength increased, leading to a decreased ionic activity, and thus negatively influenced NH<sub>4</sub><sup>+</sup> transportation with the increasing concentration of Na2<sub>S</sub>O<sub>4</sub> solution. Na<sup>+</sup> competitively occupied the place of electric double layer (EDL) and impeded NH<sub>4</sub><sup>+</sup> to get closer to the electrode surface. Besides, water molecules played a critical role in determining the net charge density and the potential drop. The experimental tests and theoretical simulation demonstrated that NH<sub>4</sub><sup>+</sup> reduction (<i>NH<sub>4(aq)</sub><sup>+ </sup>+ e<sup>- </sup>→ 0.5 H<sub>2(g) </sub>+ NH<sub>3(g)</sub></i>) in the cathode was strengthened in the low concentration range (0-0.25 M Na<sub>2</sub>SO<sub>4</sub>) but inhibited in the concentration range of 0.5-1.5 mol L<sup>-1</sup>. | Linji Xu; Yunsong Pang; Dezhao Huang; Huichuan Zhuang; Wenzong Liu; Tengfei Luo; Po-Heng Lee; Li Feng; Junchi Lu | Electrochemistry - Mechanisms, Theory & Study; Solution Chemistry; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7455c337d6c9840e26f8d/original/the-role-of-sodium-sulfate-supporting-electrolyte-in-ammonium-transport-and-reduction-at-interface-between-platinum-cathode-and-solution.pdf |
60c74850bdbb8918c8a38f6b | 10.26434/chemrxiv.11882838.v1 | Exploring the Active Compounds of Traditional Mongolian Medicine in Intervention of Novel Coronavirus (2019-nCoV) Based on Molecular Docking Method | <p>In this study, a research strategy combining network pharmacological analysis, protein docking and molecular docking virtual computation was adopted. It was found that phillyrin and chlorogenic acid could block the combination of 2019-nCoV S-protein and ACE2 at the molecular level. Both can be used as potential inhibitors of 2019-nCoV for further research and development. </p> | Jiuwang Yu; Lu Wang; Lidao Bao | Bioinformatics and Computational Biology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74850bdbb8918c8a38f6b/original/exploring-the-active-compounds-of-traditional-mongolian-medicine-in-intervention-of-novel-coronavirus-2019-n-co-v-based-on-molecular-docking-method.pdf |
640cb23ee53eff1af3f87b24 | 10.26434/chemrxiv-2023-wld91 | Polysubstituted Benzene Bioisosteres and Beyond: Photochemical Access to Bicyclo[2.1.1]hexanes | Bicyclo[2.1.1]hexanes are a versatile platform for the exploration of chemical space, with 10 different substituent vectors available. Disubstituted bicyclo[2.1.1]hexanes have been proposed as bioisosteres of ortho- and meta-substituted benzenes, both far less investigated than their para-benzene counterparts, but the bicyclo[2.1.1]hexane platform also provides new exciting opportunities for molecular design. Polysubstituted benzene bioisosteres and structures bearing substituent geometries that are non-existant in aromatic chemical space can be prepared using the bicyclo[2.1.1]hexane platform. We report the development of a photocatalytic intramolecular [2+2] cycloaddition approach to polysubstituted bicyclo[2.1.1]hexanes that provides access to these high-value motifs and enables the investigation of unexplored chemical space. | Marius Reinhold; Justin Steinebach; Johannes Walker | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640cb23ee53eff1af3f87b24/original/polysubstituted-benzene-bioisosteres-and-beyond-photochemical-access-to-bicyclo-2-1-1-hexanes.pdf |
60c75815469df43790f45597 | 10.26434/chemrxiv.14489121.v1 | A Different Protein Corona Cloaks “True-to-Life” Nanoplastics with Respect to Synthetic Polystyrene Nanobeads | Given
the complexity of separating nanoplastics from environmental samples, studies
have usually been conducted using synthetic polystyrene nanobeads. By
mechanical fragmentation in cryogenic conditions of daily-life plastic items, we
produced “true-to-life” nanoplastics (T2LNPs), that promises to give a true insight
into the interaction with biological systems. T2LNPs have been fully
characterized by Fourier transform Infrared spectroscopy and by Atomic Force
Microscopy. They result in populations of spheroidal nanoparticles with a broad
multimodal size distribution. The mandatory need for a representative sample to
evaluate the potential effects of nanoparticles on human health and the
environment is demonstrated by the different protein corona identified on
T2LNPs and synthetic polystyrene nanobeads upon incubation with human plasma. | Serena Ducoli; Stefania Federici; Roland Nicsanu; Andrea Zendrini; Claudio Marchesi; Lucia Paolini; Annalisa Radeghieri; Paolo Bergese; Laura Eleonora Depero | Environmental Science; Biochemical Analysis; Microscopy; Spectroscopy (Anal. Chem.); Nanostructured Materials - Nanoscience; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75815469df43790f45597/original/a-different-protein-corona-cloaks-true-to-life-nanoplastics-with-respect-to-synthetic-polystyrene-nanobeads.pdf |
65d145b19138d231615b0a74 | 10.26434/chemrxiv-2024-11sc4 | Significance of advanced porous configurations in enhancing solid oxide fuel cell performance: a comparative analysis between conventional porous anodes and state-of-the-art variants | Three different configurations of the porous anode of solid oxide fuel cell (SOFC) have been computationally synthesized and analyzed with respect to their electrochemical performance and topological properties. In addition to the conventional Ni/YSZ configuration of SOFC, which is usually fabricated using screen-printing, two novel designs (fibrous and lattice microstructures) are synthesized and tested. For each class of configurations, a numerical framework has been developed that can generate microstructures with specified topological characteristics. Finite volume method is employed to investigate transport phenomena and electrochemical reactions occurring within the active layer of porous anode cermet. Utilization of synthetically generated microstructures enables the direct study of certain microstructural and image acquisition attributes that may be inherently fixed within the confines and limits of a destructive 3D imaging. For instance, results showed how the choice of voxel size can greatly alter the measured Triple Phase Boundary (TPB) and the electrochemical performance. The investigation further demonstrated that lattice and fibrous structures produce an increased current density of 4.8 and 1.4 times, respectively, compared to the established conventional configuration. Finally, gradient microstructures have demonstrated the capacity to enhance electrochemical performance when subjected to careful fabrication methodologies. | Hamid Reza Abbasi; Masoud Babaei; Arash Rabbani; Constantinos Theodoropoulos | Catalysis; Energy; Heterogeneous Catalysis; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d145b19138d231615b0a74/original/significance-of-advanced-porous-configurations-in-enhancing-solid-oxide-fuel-cell-performance-a-comparative-analysis-between-conventional-porous-anodes-and-state-of-the-art-variants.pdf |
611d24ae51cfecc28194edb1 | 10.26434/chemrxiv-2021-0l4lq | Inhibition of (dppf)nickel-catalysed Suzuki-Miyaura cross-coupling reactions by α-halo-N-heterocycles | A nickel/dppf catalyst system was found to successfully achieve the Suzuki-Miyaura cross-coupling reactions of 3- and 4-chloropyridine but not 2-chloropyridine and other α-halo-N-heterocycles. Further investigations revealed that
chloropyridines undergo rapid oxidative addition to [Ni(COD)(dppf)] but that α-halo-N-heterocycles lead to the formation ofstable dimeric nickel species that are catalytically inactive in Suzuki-Miyaura cross-coupling reactions. However, the
corresponding Kumada-Tamao-Corriu reactions all proceed readily, which is attributed to more rapid transmetalation of
Grignard reagents. | Alasdair Cooper; Megan Greaves; William Donohoe; Paul Burton; Thomas Ronson; Alan Kennedy; David Nelson | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611d24ae51cfecc28194edb1/original/inhibition-of-dppf-nickel-catalysed-suzuki-miyaura-cross-coupling-reactions-by-halo-n-heterocycles.pdf |
6539229248dad231204f3478 | 10.26434/chemrxiv-2023-5nx25-v2 | Anion-Rocking Chair Batteries with Tuneable Voltage using Viologen- and Phenothiazine Polymer-based Electrodes | Organic battery electrode materials offer the unique opportunity for full cells to operate in an anionrocking chair mode. For this configuration a pair of p-type redox-active electrode materials is required with a substantial potential gap between their redox processes. We herein investigate viologenfunctionalized polystyrenes as negative electrode paired with a phenothiazine polymer as positive electrode in all-organic full cells. The 10% crosslinked viologen polymer X10-PVBV gave better performance than the linear PVBV and was employed in a full cell as negative electrode with crosslinked poly(3-vinyl-N-methylphenothiazine) (X-PVMPT) as positive electrode. Three cell configurations regarding the voltage range were investigated, of which one with an operating potential of 0.9 V gave the highest performance. The full cell delivered a specific discharge capacity of 64 mA h g−1 (of X-PVMPT) in the first cycle and a capacity retention of 79% after 100 cycles. This is one of only few reported anion rocking chair all-organic cells and the first employing a phenothiazine-based positive electrode material. | Manik Bhosale; Caroline Schmidt; Philipp Penert; Gauthier Studer; Birgit Esser | Organic Chemistry; Polymer Science; Energy; Organic Polymers; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6539229248dad231204f3478/original/anion-rocking-chair-batteries-with-tuneable-voltage-using-viologen-and-phenothiazine-polymer-based-electrodes.pdf |
65186dd7a69febde9efdb63a | 10.26434/chemrxiv-2023-85w9x | Deep Learning Based Anticancer Drug Combination Discovery Through Natural Compounds and Pharmaceutical Drugs | Drug combination therapies have shown effective performance in treating cancer through increased efficacy and circumvention of drug resistance through drug synergy. Two avenues can be used to discover drug combinations: a novel approach that utilizes natural products compared with the textbook approach of utilizing existing chemotherapy drug combinations. Many natural products achieve efficacy due to synergistic interactions between the active ingredients. Therefore, the pharmacophore relationships in herbal compounds which synergize can potentially be applied to chemotherapy drugs to drive combination discovery. Machine learning approaches have been developed to identify drug combinations, especially deep neural networks (DNN), which have achieved state-of-the-art performance in many drug discovery tasks. Here, we developed a drug protein interaction (DPI) prediction DNN, DeepDPI, to employ DPI drug representations and achieved state-of-the-art performance. Two DNNs were also developed to predict novel drug combinations: DeepNPD, which predicts combinations in herbs, and DeepCombo, which predicts synergy in chemotherapy drugs. We used an ensemble architecture enhanced with a novel similarity based weight adjustment (SBWA) approach and both models accurately predicted drug combinations for both known and unknown drugs. Lastly, a screening was conducted using each model where DeepNPD predicted combinations where drugs had similar targets, while DeepCombo predicted combinations where one agent potentiated the other, with both models’ predicted combinations investigated through a network-based analysis and identifying as a synergistic combinations in literature. DeepNPD illustrates how natural products are a novel path where new drug combinations can be discovered. | Elton Cao | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65186dd7a69febde9efdb63a/original/deep-learning-based-anticancer-drug-combination-discovery-through-natural-compounds-and-pharmaceutical-drugs.pdf |
65f812aa66c1381729390191 | 10.26434/chemrxiv-2024-czccz | Organophotoredox Catalyzed C‒O Bond Cleavage: A Chemoselective Deprotection Strategy for Phenolic Ethers and Esters Driven by the Oxophilicity of Silicon | An organo-photocatalyzed approach for the chemoselective dealkylation and de-esterification of phenols is developed by employing trimethyl silyl chloride as the C‒O bond activator and 9-Mes-10-MeAcr+ClO4‒ as the photoredox catalyst. This method demonstrates an exceptional selectivity towards the cleavage of phenolic ethers and esters over equivalent aliphatic scaffolds, presenting a broad range of functional group sustainability. This strategy also enables selective debenzylation of phenols in the presence of reduction-sensitive functional groups. The photocatalytic efficiency was further extrapolated in the fragmentation of lignin models and synthetic modification in manufacturing a FLAP inhibitor. Mechanistic studies, photophysical experiments and computations provide evidence for the involvement of an oxonium intermediate, generated through the photo-oxidation of the arene ring, which ultimately leads to the selective disintegration of C‒O bond, facilitated by the oxophilicity of silicon. | Tanumoy Mandal; Malekul Islam; Sanat Kumar Mahapatra; Sanju Das; Aznur Azim; Lisa Roy; Suman De Sarkar | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f812aa66c1381729390191/original/organophotoredox-catalyzed-c-o-bond-cleavage-a-chemoselective-deprotection-strategy-for-phenolic-ethers-and-esters-driven-by-the-oxophilicity-of-silicon.pdf |
64705597e64f843f41cbd4f9 | 10.26434/chemrxiv-2023-2wr6j | Adaptive Supramolecular Networks: Emergent Sensing from Complex Systems | Molecular differentiation by supramolecular sensors is typically achieved through sensor arrays, relying on the pattern recognition responses of large panels of isolated sensing elements. Here we report a new one-pot systems chemistry approach to differential sensing in biological solutions. We constructed an adaptive network of three cross-assembling sensor elements with diverse analyte-binding and photophysical properties. This robust sensing approach exploits complex interconnected sensor-sensor and sensor-analyte equilibria, producing emergent supramolecular and photophysical responses unique to each analyte. We characterize the basic mechanisms by which an adaptive network responds to analytes. The inherently data-rich responses of an adaptive network discriminate among very closely related proteins without relying on designed protein recognition elements. We show that a single adaptive sensing solution provides better analyte discrimination using fewer response observations than a sensor array built from the same components. We also show the network’s ability to adapt and respond to changing biological solutions over time. | Allison Selinger; Fraser Hof | Organic Chemistry; Analytical Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64705597e64f843f41cbd4f9/original/adaptive-supramolecular-networks-emergent-sensing-from-complex-systems.pdf |
637b34fce70b0a6638a4e983 | 10.26434/chemrxiv-2022-pk670 | Azoiodazinium Salts – Synthesis and Reactivity | A systematic investigation of imidazo- and pyrazoloiodazinium salts is presented. Besides a robust synthetic protocol that allowed us to synthesize these novel cyclic iodonium salts in their mono- and dicationic forms, we gained in-depth structural information through single-crystal analysis and demonstrate the ring-opening of the heterocycle-bridged iodonium species. For an exclusive set of dicationic imidazoiodaziniums, we show highly delicate post-oxidation functionalizations retaining the hypervalent iodine center. | Thomas Kuczmera; Annalena Dietz; Andreas Boelke; Boris Nachtsheim | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637b34fce70b0a6638a4e983/original/azoiodazinium-salts-synthesis-and-reactivity.pdf |
64ed02dcdd1a73847fb7d744 | 10.26434/chemrxiv-2023-jwtdg | Tough Hydrogels for Load-Bearing Applications | Tough hydrogels have emerged as a promising class of materials to target load-bearing applications, where the material has to resist multiple cycles of extreme mechanical impact. A variety of chemical interactions and network architectures have been used to enhance the mechanical properties and fracture mechanics of hydrogels. In recent years, the mechanical properties of high-performance hydrogels are benchmarked, however this is often incomplete as important variables like water content are largely ignored. In this review, we aim to clarify the reported mechanical properties of state-of-the-art tough hydrogels by providing a comprehensive library of fracture and mechanical property data. First, we briefly discuss modes of energy dissipation at work in tough hydrogels, which we use to categorize the individual data sets. Next, we introduce common methods for mechanical characterization of high-performance hydrogels, followed by a detailed analysis of the current materials and their (fracture) mechanical properties. Finally, we consider several current applications, compare high-performance hydrogels with natural materials, and discuss promising future opportunities of tough hydrogels. | Nika Petelinsek; Stefan Mommer | Materials Science; Polymer Science; Hydrogels; Polymer scaffolds; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ed02dcdd1a73847fb7d744/original/tough-hydrogels-for-load-bearing-applications.pdf |
62671fa46c989ce6abc59102 | 10.26434/chemrxiv-2021-rtxqf-v3 | Asymmetric syntheses of (+)- and (–)-collybolide enable reevaluation of kappa-opioid receptor agonism | The fungal metabolite collybolide attracted attention as a non-nitrogenous, potent and biased agonist of the kappa-opioid receptor (KOR). Here we report a 10-step asymmetric synthesis of this complex sesquiterpene that enables facile access to either enantiomer. The synthesis relies on a diastereoselective α-benzoyloxylation to install the buried C6 benzoate and avoid irreversible translactonization of the congested, functionally dense core. Neither enantiomer, however, exhibited KOR agonism, indicating that collybolide has been mischaracterized as a KOR agonist and leaving open the basis for antipruritic effects in mice. | Sophia Shevick; Stephan Freeman; Guanghu Tong; Robin Russo; Laura Bohn; Ryan Shenvi | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62671fa46c989ce6abc59102/original/asymmetric-syntheses-of-and-collybolide-enable-reevaluation-of-kappa-opioid-receptor-agonism.pdf |
6629911521291e5d1da117fe | 10.26434/chemrxiv-2024-9rbjw | Adjusting the energy profile for CH–O interactions leads to improved stability of RNA stem-loop structures in MD simulations | The role of RNA in biology continues to grow but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, we explore the role of weak CH…O interactions, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, we demonstrate that CH…O interactions are overly repulsive in the widely-used Amber RNA force fields. We developed a simple, targeted adjustment of CH…O repulsion that leaves the remainder of the force field unchanged. We then tested the standard and modified force fields using MD simulations with explicit water and salt, amassing over 300 μsec of data for multiple RNA systems containing important features such as presence of loops, base stacking interactions as well as canonical and non-canonical base pairing. Our results demonstrate that the standard force fields lead to reproducible unfolding of the NMR-based structures, as has been reported by others. Including our CH…O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested. | Lauren Raguette; Sarah Gunasekera; Rebeca Ventura Diaz; Ethan Aminov; Jason Linzer; Diksha Parwana; Qin Wu; Carlos Simmerling; Maria Nagan | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6629911521291e5d1da117fe/original/adjusting-the-energy-profile-for-ch-o-interactions-leads-to-improved-stability-of-rna-stem-loop-structures-in-md-simulations.pdf |
6740c019f9980725cf780b19 | 10.26434/chemrxiv-2024-ndxxb | Lipophilicity Effects of Monofluorination at the Tertiary Aliphatic Carbon as a Function of alpha-Substituent | Effects of monofluorination at the tertiary aliphatic carbon on the compound’s lipophilicity were measured for a series of model 4-substituted piperidine-derived benzamides. It was found that the observed LogP values strongly depend on the nature of the alpha-substituent present at the C-4 position. In particular, the LogP difference increased with the increase in the substituent’s electronegativity (as described by the field effect). Using qualitative molecular electrostatic potential surface (MEPS) analysis, we suggested that the fluorine effect on the compound’s lipophilicity in the studied systems is defined by electronic distribution modulation at the neighboring atoms (especially Hydrogens). | Kostiantyn Melnykov; Oleksandr Liashuk; Oleh Smyrnov; Dmytro Lesyk; Yuliia Holota; Petro Borysko; Viktor Yakubovskyi; Oleksandr Grygorenko | Organic Chemistry; Organic Compounds and Functional Groups | CC BY 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6740c019f9980725cf780b19/original/lipophilicity-effects-of-monofluorination-at-the-tertiary-aliphatic-carbon-as-a-function-of-alpha-substituent.pdf |
661fe2fe418a5379b00a4f9a | 10.26434/chemrxiv-2023-jcds7-v2 | Engineering Dehalogenase Enzymes using Variational Autoencoder-Generated Latent Spaces and Microfluidics | Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among residues. Computational methodologies predominantly rely on evolutionary insights, leveraging homologous sequences to pinpoint conserved and functionally critical regions. However, despite their notable advancements, deciphering the evolutionary variability and complex dependencies among residues presents substantial hurdles. Here, we present a new machine-learning method based on variational autoencoders in combination with a simple evolutionary sampling strategy to address those limitations. We customized our method to generate novel sequences of haloalkane dehalogenases, enzymes widely used in biodegradation, biocatalysis, and biosensing. Three consecutive design-build-test cycles improved the solubility of variants from 11% to 75%. Thorough experimental validation using the state-of-the-art microfluidic device MicroPEX resulted in 20 multiple-point variants. Nine of them, sharing as little as 67% sequence similarity with the template, showed a melting temperature increase of up to 9°C and an average improvement of 3°C. The most stable variant demonstrated a 3.5-fold increase in activity compared to the template, while five variants exhibited average dehalogenase activities. High-quality experimental data collected with 20 variants represent a valuable dataset for the critical validation of novel protein design approaches and scoring functions. Python scripts and data sets are available on GitHub (https://github.com/loschmidt/vae-dehalogenases), and interactive calculations will be possible via an easy-to-use website: https://loschmidt.chemi.muni.cz/fireprotasr/. | Pavel Kohout; Michal Vasina; Marika Majerova; Veronika Novakova; Jiri Damborsky ; David Bednar; Martin Marek; Zbynek Prokop; Stanislav Mazurenko | Catalysis; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661fe2fe418a5379b00a4f9a/original/engineering-dehalogenase-enzymes-using-variational-autoencoder-generated-latent-spaces-and-microfluidics.pdf |
626ab6c0368ab6097b908423 | 10.26434/chemrxiv-2022-f0rvl | Hydrogen Bonding Effect on the Oxygen Binding and Activa-tion in Cobalt(III)-peroxo Complexes | Cobalt(III)peroxo complexes serve as model metal complexes mediating oxygen activation. We report a systematic study of the effect of the hydrogen bonding on the oxygen binding and on the O-O bond activation within the cobalt(III)-peroxo complexes. To this end, we prepared a series of tris(pyridin-2-ylmethyl)amine based cobalt(III)peroxo complexes having either none, one, two or three amino groups in the secondary coordination sphere. The hydrogen bonding between the amino group(s) and the peroxo ligand was investigated within the isolated complexes in the gas phase using helium tag-ging IR photodissociation spectroscopy, energy-resolved collision induced dissociation experiments and density func-tional theory. The results show that the hydrogen bonding stabilizes the cobalt(III)-peroxo core, but the effect is on the order of units of kcal mol-1. Introduction of the first amino group to the secondary coordination sphere has the largest stabilization effect; more amino groups do not change the results significantly. The amino group can transfer a hydrogen atom to the peroxo ligands which results in the O-O bond cleavage. This process is thermodynamically favored over the O2 elimination, but entropically disfavored. | Rob Bakker; Abhinav Bairagi; Guilherme L. Tripodi; Aleksandr Y. Pereverzev; Jana Roithova | Physical Chemistry; Inorganic Chemistry; Catalysis; Bonding; Small Molecule Activation (Inorg.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626ab6c0368ab6097b908423/original/hydrogen-bonding-effect-on-the-oxygen-binding-and-activa-tion-in-cobalt-iii-peroxo-complexes.pdf |
64fad2e699918fe5379205e3 | 10.26434/chemrxiv-2023-bsft2 | The CatMath: An Online Predictive Platform for Thermal + Electrocatalysis | The catalytic volcano activity models are the quantified and visualized tools of the Sabatier principle for heterogeneous catalysis, which can depict the intrinsic activity optima and trends of a catalytic reaction as a function of the reaction descriptors, i.e., the bonding strengths of key reaction species. These models can be derived by microkinetic modeling and/or free energy changes in combination with the scaling relations among the reaction intermediates. Herein, we introduce the CatMath - an online platform for generating a variety of common and industrially important thermal + electrocatalysis. With the CatMath, users can request the volcano models for available reactions and analyze their materials of interests as potential catalysts. Besides, the CatMath provides the function of the online generation of surface Pourbaix diagram for surface state analysis under electrocatalytic conditions, which is an essential step before analyzing the activity of an electrocatalytic surface. All the model generation and analysis processes are realized by cloud computing via a user-friendly interface. | Heng Liu; Hao Zheng; Zhenhe Jia; Binghui Zhou; Yan Liu; Xuelu Chen; Yajun Feng; Li Wei; Weijie Yang; Hao Li | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fad2e699918fe5379205e3/original/the-cat-math-an-online-predictive-platform-for-thermal-electrocatalysis.pdf |
64145c08dab08ad68f44af77 | 10.26434/chemrxiv-2023-jdn8g | G-quadruplex Hydrogel-based Stimuli-responsive High-internal-phase Emulsion Scaffold for Biocatalytic Cascades and Synergistic Antimicrobial Activity | High internal phase emulsions (HIPEs) are non-equilibrium systems with distorted liquid droplet shapes consisting of high volume of internal phase (>74% v/v), enabling high loading of pharmaceutics and useful viscoelastic properties. Stability of the HIPEs is low and requires a high volume of surfactants in the continuous phase, which is environmentally unfriendly. Utilization of hydrogel as the continuous phase to stabilize HIPEs would offer a robust method to produce stable HIPE gels displaying reconfigurable and biocompatible properties, as well as access the huge repertoire of different biocompatible hydrogels. Herein, we introduce a new gel-immobilized HIPE (HIPEG) using chiral G-quadruplex (GQ) based hydrogel with external stimuli-responsive dual-drug release behavior, which is scarce for HIPEs. The hydrophilic and hydrophobic compartments of HIPEGs allow encapsulation of different drugs in both the compartments, with stimuli-responsive diffusion mediated release. Encapsulation of natural oils and antibiotics produces synergistic antimicrobial effects on both Gram positive (MRSA) and Gram negative (P. aeruginosa) bacterial strains. Moreover, we demonstrate biocatalytic reaction networks utilizing compartmentalized enzyme dyads. Notably, the ideal viscoelastic property of HIPEGs enables 3D bioprinting into different shapes, making the scaffold potential for tissue engineering applications. Altogether, our approach offers a one-step route to stimuli-responsive HIPE microcompartments immobilized in GQ hydrogels with endogenous reactivity and high viscoelasticity, and provides a viable step towards the development of biocompatible soft materials with tailorable functionality. | Sourav Das; Manju Solra; Jagabandhu Sahoo; Abhay Srivastava; Fathima S; Mrinmoy De; Subinoy Rana | Organic Chemistry; Polymer Science; Supramolecular Chemistry (Org.); Drug delivery systems; Hydrogels; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64145c08dab08ad68f44af77/original/g-quadruplex-hydrogel-based-stimuli-responsive-high-internal-phase-emulsion-scaffold-for-biocatalytic-cascades-and-synergistic-antimicrobial-activity.pdf |
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