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60c74e7a0f50db72a339722d | 10.26434/chemrxiv.12762314.v1 | Rapid, Ambient Temperature Synthesis of Imine Covalent Organic Frameworks Catalyzed by Transition Metal Nitrates | <div>
<p>Covalent Organic Frameworks (COFs) are crystalline, porous
organic materials with promise for applications including catalysis, energy
storage, electronics, gas storage, water treatment, and drug delivery. Conventional
solvothermal synthesis approaches to COFs require elevated temperatures, inert
reaction environments, and long reaction times. Here, we report that transition
metal nitrates can catalyze the rapid synthesis of imine COFs. We tested a
series of transition metal nitrates as catalysts for the synthesis of a model
COF and found that all transition metal nitrates produced crystalline COF
products for reactions conducted at ambient temperatures. The reactions were
insensitive to the presence of oxygen. Fe(NO<sub>3</sub>)<sub>3</sub>·9H<sub>2</sub>O
was found to produce the most crystalline product, and by optimizing the
catalyst loading we found that crystalline COF could be produced within 10
minutes. We further tested Fe(NO<sub>3</sub>)<sub>3</sub>·9H<sub>2</sub>O as a
catalyst for 6 different COF targets varying in linker lengths, substituents,
and stabilities, and found that Fe(NO<sub>3</sub>)<sub>3</sub>·9H<sub>2</sub>O
effectively catalyzed the synthesis of all imine COFs tested. This work
demonstrates a simple, low-cost approach for the synthesis of imine COFs and
will significantly lower the barrier for the development of imine COFs for
various applications. </p>
</div> | Dongyang Zhu; Zhuqing Zhang; Muhammad M. Rahman; Yilin Li; Morgan Barnes; Safiya Khalil; Pulickel
M. Ajayan; Rafael Verduzco | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e7a0f50db72a339722d/original/rapid-ambient-temperature-synthesis-of-imine-covalent-organic-frameworks-catalyzed-by-transition-metal-nitrates.pdf |
6397622bcfb5ffdc27687942 | 10.26434/chemrxiv-2022-l60b2 | Rationalizing aggregate structures with orbital
contributions to the exchange-repulsion energy | It is shown that repulsive interactions have a crucial influence on the structure of prototypical non-covalently bonded systems. To explain this, we propose a molecular orbital based model for the exchange-repulsion contribution to the total interaction energy. As a central result, our model
shows that energetically preferred aggregate structures exhibit reduced exchange repulsion, which can be deduced
from the nodal structure of certain occupied orbitals. In
this way, the directionality of halogen bonds and the preferred arrangements in pi-aggregates are explained using the Cl2-He, benzene-benzene, and benzene-hexafluorobenzene systems as examples, where commonly applied electrostatic models fail. | Johannes Henrichsmeyer; Michael Thelen; Marc Bröckel; Mariam Fadel; Stefan Behnle; Majda Sekkal Rahal; Reinhold Fink | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Mechanics; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6397622bcfb5ffdc27687942/original/rationalizing-aggregate-structures-with-orbital-contributions-to-the-exchange-repulsion-energy.pdf |
60c73ec1469df414c8f42911 | 10.26434/chemrxiv.7092263.v1 | Xenon Trioxide Adducts of O-Donor Ligands; [(CH3)2CO]3XeO3, [(CH3)2SO]3(XeO3)2, (C5H5NO)3(XeO3)2, and [(C6H5)3PO]2XeO3 | Oxygen coordination to
the Xe(VI) atom of XeO<sub>3</sub> was observed in its adducts with
triphenylphosphine oxide, dimethylsulfoxide, pyridine-N-oxide, and acetone. The
crystalline adducts were characterized by low-temperature, single-crystal X-ray
diffraction and Raman spectroscopy. Unlike solid XeO<sub>3</sub>, which
detonates when mechanically or thermally shocked, the solid [(C<sub>6</sub>H<sub>5</sub>)<sub>3</sub>PO]<sub>2</sub>XeO<sub>3</sub>,
[(CH<sub>3</sub>)<sub>2</sub>SO]<sub>3</sub>(XeO<sub>3</sub>)<sub>2</sub>,<sub>
</sub>and (C<sub>5</sub>H<sub>5</sub>NO)<sub>3</sub>(XeO<sub>3</sub>)<sub>2</sub>
adducts are insensitive to mechanical shock, but undergo rapid deflagration
when ignited by a flame. Both [(C<sub>6</sub>H<sub>5</sub>)<sub>3</sub>PO]<sub>2</sub>XeO<sub>3
</sub>and (C<sub>5</sub>H<sub>5</sub>NO)<sub>3</sub>(XeO<sub>3</sub>)<sub>2</sub>
are air-stable whereas [(CH<sub>3</sub>)<sub>2</sub>SO]<sub>3</sub>(XeO<sub>3</sub>)<sub>2</sub>
slowly decomposes over several days and [(CH<sub>3</sub>)<sub>2</sub>CO]<sub>3</sub>XeO<sub>3</sub>
undergoes adduct dissociation at room temperature. The xenon coordination
sphere of [(C<sub>6</sub>H<sub>5</sub>)<sub>3</sub>PO]<sub>2</sub>XeO<sub>3</sub>
is a distorted square pyramid which provides the first example of a
five-coordinate XeO<sub>3</sub> adduct. The xenon coordination spheres of the
remaining adducts are distorted octahedra comprised of three Xe---O secondary
contacts that are approximately trans to the primary Xe–O bonds of XeO<sub>3</sub>. Quantum-chemical
calculations were used to assess the Xe---O adduct bonds, which are
predominantly electrostatic σ-hole
bonds between
the nucleophilic oxygen atoms of the bases and the σ-holes
of the xenon atoms. | Katherine Marczenko; James Goettel; Gary Schrobilgen | Bonding; Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry; Ligands (Inorg.); Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ec1469df414c8f42911/original/xenon-trioxide-adducts-of-o-donor-ligands-ch3-2co-3xe-o3-ch3-2so-3-xe-o3-2-c5h5no-3-xe-o3-2-and-c6h5-3po-2xe-o3.pdf |
664f7d1b418a5379b01c326a | 10.26434/chemrxiv-2024-kxjpb | Creating a Catalog of the Crystal Structures of Monolayer-Protected Clusters | Over the decades, numerous crystal structures of the monolayer-protected clusters (MPCs) have been reported and the number of discoveries is rapidly increasing. Via crystallography, it is possible to construct the atomic structures with atom level precision. This enables computational and theoretical studies, which can shed light to the origin of experimentally observed properties and help discoveries of new materials. However, the reported MPC crystal structures are commonly deposited into large crystallographical databases or dispersed in supplementary information files of the publications, and in order to find all of them one is required go through an immense amount of literature. Hence, it is of interest to establish an editable catalog for the community to keep track of discoveries. The catalog is hosted in Wikipedia and this paper works as an initialization document and a citable source for the catalog. | Antti Pihlajamäki; Sami Malola ; Hannu Häkkinen | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664f7d1b418a5379b01c326a/original/creating-a-catalog-of-the-crystal-structures-of-monolayer-protected-clusters.pdf |
60c7471d0f50db84ea39654e | 10.26434/chemrxiv.11523117.v1 | Deep Protein-Ligand Binding Prediction Using Unsupervised Learned Representations | In-silico protein-ligand binding prediction is an ongoing area of research in computational chemistry and machine learning based drug discovery, as an accurate predictive model could greatly reduce the time and resources necessary for the detection and prioritization of possible drug candidates. Proteochemometric modeling (PCM) attempts to make an accurate model of the protein-ligand interaction space by combining explicit protein and ligand descriptors. This requires the creation of information-rich, uniform and computer interpretable representations of proteins and ligands. Previous work in PCM modeling relies on pre-defined, handcrafted feature extraction methods, and many methods use protein descriptors that require alignment or are otherwise specific to a particular group of related proteins. However, recent advances in representation learning have shown that unsupervised machine learning can be used to generate embeddings which outperform complex, human-engineered representations. We apply this reasoning to propose a novel proteochemometric modeling methodology which, for the first time, uses embeddings generated via unsupervised representation learning for both the protein and ligand descriptors. We evaluate performance on various splits of a benchmark dataset, including a challenging split that tests the model’s ability to generalize to proteins for which bioactivity data is greatly limited, and we find that our method consistently outperforms state-of-the-art methods. | Paul Kim; Robin Winter; Djork-Arné Clevert | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7471d0f50db84ea39654e/original/deep-protein-ligand-binding-prediction-using-unsupervised-learned-representations.pdf |
63999cc314d92d63fbae7300 | 10.26434/chemrxiv-2022-24xg3 | Neuroprotective and antibacterial effects of phlorotannins isolated from the cell walls of brown algae Fucus vesiculosus and Pelvetia canaliculata | The Phaeophyceae (brown algae) essentially contribute to biotopes of cold and temperate seas. Their thalli are rich in biologically active natural products which are strongly and universally dominated with phlorotannins – polyphenols of complex and diverse structure based on multiple differently arranged phloroglucinol units. These electron-rich compounds are strong antioxidants with antimicrobial, anti-inflammatory and neuroprotective activities. In the algal cells phlorotannins can either accumulate in cytoplasm or can be secreted into the cell wall (CW) with subsequent covalent binding to the alginate network. The biological activities of easily extractable intracellular phlorotannins were comprehensively characterized, whereas the properties of the CW-bound polyphenol fraction are still mostly unknown. Recently, we identified dibenzodioxin bonding as the principal structural feature of the CW-bound phlorotannins of fucoid algae, whereas soluble intracellular phlorotannins relied on aryl- and ether bonds. However, profiles of biological activity associated with these structural differences are still unknown. Therefore, here, to the best of our knowledge, for the first time, we address the antioxidant, cytotoxic, neuroprotective, and antibacterial properties of the CW-bound phlorotannin fractions isolated from two representatives of the order Fucales - Fucus vesiculosus and Pelvetia canaliculata. The CW-bound phlorotannins appeared to be softer antioxidants, stronger antibacterial agents and were featured with essentially less cytotoxicity in comparison to the intracellular fraction. However, the neuroprotective effects of both sub-cellular phlorotannin fractions of F. vesiculosus and P. canaliculata were essentially similar. Thus, due to their lower cytotoxicity, CW-bound phlorotannins can be considered as promising antioxidants and neuroprotectors. | Darya Meshalkina; Elena Tsvetkova; Anastasia Orlova; Renata Islamova; Elana Kysil; Maria Grashina; Daria Gorbach; Vladimir Babakov; Antonio Francioso; Luciana Mosca; Elena Tarakhovskaya; Andrej Frolov | Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63999cc314d92d63fbae7300/original/neuroprotective-and-antibacterial-effects-of-phlorotannins-isolated-from-the-cell-walls-of-brown-algae-fucus-vesiculosus-and-pelvetia-canaliculata.pdf |
65816d1066c138172990436e | 10.26434/chemrxiv-2023-jh1kk | A new protein-ligand docking software with an improved method of molecular conformation optimization | We study methods of non-linear global optimization in the problem of molecular docking and present a new implementation of protein-ligand docking and preparation of molecules for docking in a new open source software Hess. It uses BFGS for local optimization and two different forms of Monte Carlo method for global optimization. We compare Hess to another open-source package, Smina, and find that the chosen methods give better results in both performance and binding energy (using the same Vinardo scoring function). Also, during preparation of some molecules Hess provides a more accurate computation of implicit hydrogens thanks to the dearomatization algorithm provided by the Indigo cheminformatics package. | Rafael Temirgaliev; Dmitry Pavlov | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65816d1066c138172990436e/original/a-new-protein-ligand-docking-software-with-an-improved-method-of-molecular-conformation-optimization.pdf |
60c74683702a9b7efe18abfa | 10.26434/chemrxiv.9255446.v2 | The Limited Predictive Power of the Pauling Rules | The Pauling rules have been used for decades to rationalise the crystal structures of ionic compounds. Despite their importance, there has been so far no statistical assessment of the performances of these five empirical rules. Here, we test rigorously and automatically all five Pauling rules for a large data set of around 5000 known oxides. We discuss each Pauling rule separately stressing their limits and range of application in terms of chemistries and structures. We conclude that only 13% of the oxides simultaneously satisfy the last four rules, indicating their much lower predictive power than expected.<br /> | Janine George; David Waroquiers; Davide Di Stefano; Guido Petretto; Gian-Marco Rignanese; Geoffroy Hautier | Solid State Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74683702a9b7efe18abfa/original/the-limited-predictive-power-of-the-pauling-rules.pdf |
61acb409bc299c44248a2b12 | 10.26434/chemrxiv-2021-n23f5 | The effect of the multiple mutations in Omicron RBD on its binding to human ACE2 receptor and immune evasion: an investigation of molecular dynamics simulations | SARS-coronavirus-2 (SARS-CoV2) Omicron variant (B.1.1.529) is of great concern to the world due to multiple mutations that may have an impact on transmissibility and immune evasion. Compared to the wild type (WT), there are 15 mutations in the Omicron receptor-binding domain (RBD), 10 of which are in the receptor-binding motif (RBM), where the host angiotensin-converting enzyme 2 (ACE2) interacts directly with. As a comparison, the currently dominant variant Delta (B.1.617.2) only has 2 mutations (L452R and T478K) or an additional E484K mutation in the RBM. As many as 15 mutations in Omicron RBD make it very hard to predict whether the mutations would increase the binding affinity to ACE2, particularly considering that 10 mutations crowded in the RBM. To understand the combinatorial mutation effect on Omicron RBD binding to ACE2 and potential immune evasion, we calculated the binding affinities of the WT/Delta/Omicron RBDs to ACE2 and antibodies with 600 ns molecular dynamics simulations for each system. We found that Omicron RBD has slightly weaker ACE2 affinities than WT RBD (-29.39 ± 2.96 Kcal/mol vs. -33.13 ± 3.26 Kcal/mol), and much lower affinities than Delta RBD (-42.76 ± 2.38 Kcal/mol). Further analysis revealed that Omicron N501Y increase ACE2 binding but Q493K and Q498R decrease ACE2 binding. In addition, Omicron RBD might escape the launched monoclonal antibodies (mAbs) Etesevimab and clinical BD-368-2 but may still sensitive to the launched mAbs Bebtelovimab. | Leyun Wu; Liping Zhou; Mengxia Mo; Yishui Li; Jiaxin Han; Jintian Li; Yanqing Yang; Xinben Zhang; Chunye Gong; Kai Lu; Likun Gong; Chengkun Wu; Weiliang Zhu; Zhijian Xu | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61acb409bc299c44248a2b12/original/the-effect-of-the-multiple-mutations-in-omicron-rbd-on-its-binding-to-human-ace2-receptor-and-immune-evasion-an-investigation-of-molecular-dynamics-simulations.pdf |
675b762ef9980725cfe31213 | 10.26434/chemrxiv-2024-8lcx6 | Polymorphic ROYalty: The 14th ROY Polymorph Discovered via High-Throughput Crystallization | Polymorphism, when a substance can exist in more than one crystalline form yet return to the same liquid or solution phase, is characterized by differences in packing or molecular conformation. Polymorphs often exhibit differing physical properties, and they are therefore particularly important in the development of materials and pharmaceuticals. However, gaining a thorough understanding of the solid-state landscape of a molecule requires exhaustive experimental screening of crystallization conditions, a particular challenge when using classical crystallization methods. We show that high-throughput Encapsulated Nanodroplet Crystallization (ENaCt) can enable the rapid and efficient exploration of the solid-state landscape of highly polymorphic molecules, through an in-depth study of 5-methyl-2-((2-nitrophenyl)amino)thiophene-3-carbonitrile (ROY), the most polymorphic small molecule known. An ENaCt screen encompassing 1,536 individual crystallization experiments, spanning 320 unique conditions, resulted in direct access to single crystals, suitable for X-ray diffraction analysis, for all six of the known polymorphs accessible from solution (Y, R, YN, ON, ORP and R18). In addition, two polymorphs (Y04 and Y19) previously accessed only via melt and heteroseeded melt experiments, and a new polymorph of ROY (O22), the fourteenth to be discovered, were obtained. Furthermore, ENaCt screening resulted in the identification of the first ROY solvate (ROY•methyl anthranilate) and the first example of a ROY dimer, formed via in situ oxidation. ENaCt is thus shown to be an impactful tool for the experimental mapping of the solid-state landscape of highly polymorphic molecules and, through the discovery of a new polymorph O22, has ensured that tetradecamorphic ROY retains the world record for most polymorphic small molecule. | Jake Weatherston; Michael Probert; Michael John Hall | Materials Science; Inorganic Chemistry; Analytical Chemistry; Analytical Chemistry - General; Solid State Chemistry; Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675b762ef9980725cfe31213/original/polymorphic-ro-yalty-the-14th-roy-polymorph-discovered-via-high-throughput-crystallization.pdf |
640cdd12b5d5dbe9e81b77f9 | 10.26434/chemrxiv-2023-b2hnk | Machine learning quantum-chemical bond scission in thermosets under extreme deformation | Despite growing interest in polymers under extreme conditions, most atomistic molecular dynamics simulations cannot describe the bond scission events underlying failure modes in polymer networks undergoing large strains. In this work, we propose a physics-based machine learning approach that can detect and perform bond breaking with near quantum-chemical accuracy on-the-fly in atomistic simulations. Particularly, we demonstrate that by coarse-graining highly correlated neighboring bonds, the prediction accuracy can be dramatically improved. Compared to existing quantum mechanics/molecular mechanics (QM/MM) methods, our approach is approximately two orders of magnitude more efficient and exhibits improved sensitivity towards rare bond breaking events at low strain. The proposed bond breaking molecular dynamics scheme enables fast and accurate modeling of strain hardening and material failure in polymer networks, and can accelerate the design of polymeric materials under extreme conditions. | Zheng Yu; Nicholas Jackson | Theoretical and Computational Chemistry; Polymer Science; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640cdd12b5d5dbe9e81b77f9/original/machine-learning-quantum-chemical-bond-scission-in-thermosets-under-extreme-deformation.pdf |
6448655be4bbbe4bbf4021b8 | 10.26434/chemrxiv-2023-wpff0 | Inferring the nominal molecular mass of an analyte from its electron ionization mass spectrum | The performance of three algorithms for predicting nominal molecular mass from an analyte’s electron ionization mass spectrum are presented. The Peak Interpretation Method (PIM) attempts to quantify the likelihood that a molecular ion peak is contained in the mass spectrum, whereas the Simple Search Hitlist Method (SS-HM) and iterative Hybrid Search Hitlist Method (iHS-HM) leverage results from mass spectral library searching. These predictions can be employed in combination (recommended) or independently. The methods were tested on two sets of query mass spectra searched against libraries that did not contain reference mass spectra of the same compounds: 19,074 spectra of various organic molecules searched against NIST17 mass spectral library, and 162 spectra of small molecule drugs searched against SWGDRUG version 3.3. Individually, each molecular mass prediction method had computed precisions (the fraction of positive predictions that were correct) of 91 %, 89 % and 74 %, respectively. The methods become more valuable when predictions are taken together as an ensemble. When all three predictions were identical, which occurred in 33% of the test cases, the predicted molecular mass was almost always correct (> 99 %). | Arun Moorthy; Anthony Kearsley; William Mallard; William Wallace; Stephen Stein | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6448655be4bbbe4bbf4021b8/original/inferring-the-nominal-molecular-mass-of-an-analyte-from-its-electron-ionization-mass-spectrum.pdf |
669f9689c9c6a5c07a9f0f2b | 10.26434/chemrxiv-2024-2t8hw | Photocages Made to Order: Late-Stage Caging Protocol Enables Anti-Cancer Control with Near-Infrared Light | Nature has perfected the reversible control over the activity of molecules and biomolecules in the human body. Photocages aim to mimic this control in space and time using light as a trigger, and the field has witnessed many excellent contributions that extend their use to the tissue-penetrating region. Yet little attention has been paid to developing simple caging strategies which are crucial to translate photocages into a widely accepted tool beyond chemical space. Here, we report a robust and user-friendly protocol that enables installation of amine, thiol and phenol payloads in a single step under mild conditions and using bench-stable intermediates. The protocol displays excellent compatibility with payloads, manifested by caging hormones, neurotransmitters, a tripeptide and many highly complex FDA-approved drugs, including antibiotics or anti-cancer agents. In a proof-of-concept study, we utilize this strategy to cage the clinically used CDK4/6 inhibitor palbociclib and control the activity of the tumor suppressing retinoblastoma protein in human breast cancer cells by near-infrared (NIR) light. We anticipate that normalizing the access to NIR-absorbing photocages through this protocol will empower research across various scientific disciplines. | Marina Russo; Dominika Zielinska; Katarzyna Hanc; Andrea Ramundo; Delia Meier; Attila Szabo; Peter Stacko | Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Cell and Molecular Biology | CC BY NC 4.0 | CHEMRXIV | 2024-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669f9689c9c6a5c07a9f0f2b/original/photocages-made-to-order-late-stage-caging-protocol-enables-anti-cancer-control-with-near-infrared-light.pdf |
6287b99e6cae1c6d9210d3f1 | 10.26434/chemrxiv-2022-fhd7b | Synthesis and styrene copolymerization of novel dichloro and difluoro ring-substituted octyl phenylcyanoacrylates | Novel ring-substituted octyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2(CH2)6CH3 (where R is 2,3-dichloro, 2,4-dichloro, 2,5-dichloro, 2,6-dichloro, 3,4-dichloro, 2,3-difluoro, 2,4-difluoro, 2,5-difluoro, 2,6-difluoro, 3,4-difluoro, 3,5-difluoro) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and octyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Christian Ibarra; Andy N. La; Victoria Orban; Taha Raziuddin; Amir Sedighzadeh; Amina Torlo; Ania Tyrawa; Peter A. Wild Crea; Jessica E. Youngs; Stephanie Block; David C. Dainko; Sara M. Rocus; William S. Schjerven; Gregory B Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6287b99e6cae1c6d9210d3f1/original/synthesis-and-styrene-copolymerization-of-novel-dichloro-and-difluoro-ring-substituted-octyl-phenylcyanoacrylates.pdf |
6571c03bcf8b3c3cd704b282 | 10.26434/chemrxiv-2023-8bmjg-v3 | Experimental design of blending samples to increase precision of 1H NMR urine metabolomics | Urine is an equally attractive biofluid for metabolomics analysis as it is a challenging matrix analytically. Accurate urine metabolite concentration estimates by Nuclear Magnetic Resonance are hampered by pH and ionic strength differences between samples resulting in large peak shift variability. Here we show that calculating spectra of original samples from mixtures of samples using linear algebra reduces the shift problems and makes various error estimates possible. Since the use of 2D NMR to confirm metabolite annotations is effectively impossible to employ on every sample of large sample sets, stabilization of metabolite peak positions increases the confidence in identifying metabolites, avoiding the pitfall of oranges-to-apples comparisons. | Anders Bay Nord; Helen Lindqvist; Millie Rådjursöga; Anna Winkvist; Göran Karlsson; Daniel Malmodin | Analytical Chemistry; Chemoinformatics; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6571c03bcf8b3c3cd704b282/original/experimental-design-of-blending-samples-to-increase-precision-of-1h-nmr-urine-metabolomics.pdf |
64f14341dd1a73847febfe0e | 10.26434/chemrxiv-2023-09l28 | A “Neat” Synthesis of Substituted 2-Hydroxy-pyrido[1,2-a]pyrimidin-4-ones | We report the synthesis of a series of substituted 2-hydroxy-pyrido[1,2-a]pyrimidin-4-ones through solvent-free condensation of of 2-aminopyridines and diethyl malonate. This method is contrasted with three reported general procedures for the preparation of these compounds, revealing the simple, “neat” synthesis conditions are suitable for a number of derivatives. Environmental, safety, and economic factors were considered in exploring this effective and robust synthetic method. | Gregory Gaube; James Mutter; David Leitch | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f14341dd1a73847febfe0e/original/a-neat-synthesis-of-substituted-2-hydroxy-pyrido-1-2-a-pyrimidin-4-ones.pdf |
62acef3dc573466753310aed | 10.26434/chemrxiv-2022-6xnsn | Multifunctional Amine Modifiers for Selective Dehydration of Methyl Lactate to Acrylates | Dehydration of methyl lactate to acrylic acid and methyl acrylate was experimentally evaluated over Na-FAU zeolite catalyst impregnated with multifunctional diamines. 1,2-bis(4-pyridyl)ethane (12BPE) and 4,4-trimethylenedipyridine (44TMDP), at a nominal loading of 40 wt% or two molecules per Na-FAU supercage, afforded a dehydration selectivity of 96+3% over 2000 min time on stream, exceeding the selectivity target of 90% for commercial viability. During continuous reaction at 300 °C, the amine loadings in Na-FAU remained constant for 12BPE but decreased as much as 83% for 44TMDP. Although 12BPE and 44TMDP have van der Waals diameters approximately 90% of the Na-FAU window opening diameter, both flexible diamines interact with internal active sites of Na-FAU as characterized by infrared spectroscopy. Tuning the weighted hourly space velocity (WHSV) from 0.9 to 0.2 h-1 afforded a yield as high as 92% at a selectivity of 96% with 44TMDP impregnated Na-FAU, resulting in the highest yield reported to date. | Yutong Pang; ChoongSze Lee; Bess Vlaisavljevich; Christopher Nicholas; Paul Dauenhauer | Catalysis; Acid Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62acef3dc573466753310aed/original/multifunctional-amine-modifiers-for-selective-dehydration-of-methyl-lactate-to-acrylates.pdf |
60c750df9abda255eff8dae7 | 10.26434/chemrxiv.12366623.v4 | Saturation Profile Based Conformality Analysis for Atomic Layer Deposition: Aluminum Oxide in Lateral High-Aspect-Ratio Channels | <p>ABSTRACT: Atomic layer deposition (ALD) raises global interest
through its unparalleled conformality. This work describes new microscopic
lateral high-aspect-ratio (LHAR) test structures for conformality analysis of
ALD. The LHAR structures are made of silicon and consist of rectangular
channels supported by pillars. Extreme aspect ratios even beyond 10 000:1
enable investigations where the adsorption front does not penetrate to the end of
the channel, thus exposing the saturation profile for detailed analysis. We use
the archetypical trimethylaluminum (TMA)-water ALD process to grow alumina as a
test vehicle to demonstrate the applicability, repeatability and
reproducibility of the saturation profile measurement and to provide a
benchmark for future saturation profile studies. Through varying the TMA
reaction and purge times, we obtained new information on the surface chemistry
characteristics and the chemisorption kinetics of this widely studied ALD process.
We propose new saturation profile related classifications and terminology. </p> | Jihong Yim; Oili Ylivaara; Markku Ylilammi; Virpi Korpelainen; Eero Haimi; Emma Verkama; Mikko Utriainen; Riikka Puurunen | Thin Films; Nanostructured Materials - Nanoscience; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750df9abda255eff8dae7/original/saturation-profile-based-conformality-analysis-for-atomic-layer-deposition-aluminum-oxide-in-lateral-high-aspect-ratio-channels.pdf |
60c75885842e650835db4880 | 10.26434/chemrxiv.14555796.v1 | Evaluation of Virucidal Activity of Residual Quaternary Ammonium-treated Surfaces on SARS-CoV-2 | A commercially available and EPA/PMRA registered
quaternary ammonium antimicrobial formulation was applied to stainless steel
carrier disks and sent to two virology research institutes to independently
determine whether samples treated with SiQAC-C18 antimicrobial material could
deactivate deposited SARS-CoV-2 virions on contaminated surfaces. The results independently
support a sustained antiviral effect imparted from these treated surfaces by
both SARS-CoV-2 virion destruction and degradation of viral RNA. These
preliminary results indicate the SiQAC-18 treated surfaces could play an
important role in mitigating the communicability and fomite transmission of
SARS-CoV-2. | Alexander Caschera; JULIE MCAULEY; Youry Kim; DAMIAN PURCELL; Jasper Rymenants; Daniel Foucher | Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75885842e650835db4880/original/evaluation-of-virucidal-activity-of-residual-quaternary-ammonium-treated-surfaces-on-sars-co-v-2.pdf |
60c74062842e65863cdb1ca6 | 10.26434/chemrxiv.7725209.v1 | Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold-hopping capability | This study aims at improving upon existing
activity predictions methods by augmenting chemical structure fingerprints with
bio-activity based fingerprints derived from high-throughput screening (HTS)
data (HTSFPs). The HTSFPs were generated from HTS data obtained from PubChem
and combined with an ECFP4 structural fingerprint. The combined experimental
and structural fingerprint (CESFP) was benchmarked against the individual ECFP4
and HTSFP fingerprints. Results showed that the CESFP has improved predictive performance
as well as scaffold hopping capability. The CESFP identified unique compounds compared
to both the ECFP4 and the HTSFP fingerprint indicating synergistic effects
between the two fingerprints. A feature importance analysis showed that a small
subset of the HTSFP features contribute most to the overall performance of the
CESFP. This combined approach allows for activity prediction of compounds with
only sparse HTSFPs due to the supporting effect from the structural fingerprint. | Oliver Laufkötter; Noé Sturm; Jürgen Bajorath; Ola Engkvist; Hongming Chen | Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74062842e65863cdb1ca6/original/combining-structural-and-bioactivity-based-fingerprints-improves-prediction-performance-and-scaffold-hopping-capability.pdf |
60c73f9e842e65ec28db1b38 | 10.26434/chemrxiv.7447397.v1 | Thermal Chemical Vapor Deposition of Epitaxial Rhombohedral Boron Nitride from Trimethylboron and Ammonia | Epitaxial rhombohedral boron nitride films were deposited on α-Al2O3(001) substrates by chemical vapor deposition, using trimethylboron, ammonia, and with a low concentration of silane in the growth flux. The depositions were performed at temperatures from 1200 to 1485 °C, pressures from 30 to 90 mbar and N/B ratios from 321 to 1286. The most favorable conditions for epitaxy were: a temperature of 1400 °C, N/B around 964, and pressures below 40 mbar. Analysis by thin film X-ray diffraction showed that most deposited films were polytype-pure epitaxial r-BN with an out-of-plane epitaxial relationship of r-BN[001]∥ w-AlN[001]∥ α-Al2O3[001] and with two in-plane relationships of r-BN[110]∥ w-AlN[110]∥ α-Al2O3[100] and r-BN[110]∥ w-AlN[110]∥ α-Al2O3[1̅00] due to twinning. | Laurent Souqui; Henrik Pedersen; Hans Högberg | Ceramics; Coating Materials; Thin Films; Main Group Chemistry (Inorg.); Solid State Chemistry; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9e842e65ec28db1b38/original/thermal-chemical-vapor-deposition-of-epitaxial-rhombohedral-boron-nitride-from-trimethylboron-and-ammonia.pdf |
670136c651558a15ef2c07f0 | 10.26434/chemrxiv-2024-k9mr8 | Raman Spectroscopic Observation of Electrolyte-Dependent Oxygen Evolution Reaction Intermediates in Nickel-Based Electrodes | Oxygen evolution reaction (OER) is the counterpart in the hydrogen production by the water electrolysis. Further challenges have been required to bypass the energy consumption processes in OER. It is still important to unveil the OER intermediates toward the effective green hydrogen production. In this study, we conducted the in-situ Raman observation of the OER intermediates over Ni nanohole-array electrodes in the various electrolyte conditions. Ni nanohole-array electrodes were prepared with the interference exposure methods. Intense Raman peaks were observed from the Ni-OH, Ni-OOH, and active oxygen species as OER intermediates. The OER behavior can be classified with the reactants, such as OH− and H2O. The presented study demonstrates the importance of the electrolyte for the designing active OER catalysis for the next generation energy society. | Tomohiro Fukushima; Kenko Tsuchimoto; Nobuaki Oyamada; Daiki Sato; Hiro Minamimoto; Kei Murakoshi | Physical Chemistry; Catalysis; Energy; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670136c651558a15ef2c07f0/original/raman-spectroscopic-observation-of-electrolyte-dependent-oxygen-evolution-reaction-intermediates-in-nickel-based-electrodes.pdf |
6454576c1ca6101a45cbf7d3 | 10.26434/chemrxiv-2023-cdpqb | A Lewis Acid-Controlled Enantiodivergent Epoxidation | Two epoxidation catalysts one of which consists of two VANOL ligands and an aluminum and the other of two VANOL ligands and a boron were compared. Both catalysts are highly effective in the catalytic asymmetric epoxidation of a variety of aromatic and aliphatic aldehydes with diazoacetamides giving high yields and excellent asymmetric inductions. The aluminum catalyst is effective at 0 °C and the boron catalyst at –40 °C. Although both the aluminum and boron catalysts of (R)-VANOL give very high asymmetric inductions (up to 99% ee), they give opposite enantiomers of the epoxide. The mechanism, rate- and enantioselectivity-determining step, and origin of enantiodivergence is evaluated using DFT calculations. | Aliakbar Mohammadlou; Chetan Joshi; Brendyn Smith; Li Zheng; Virginia Canestraight; Saeedeh Torabikohlbouni; Maryamdokht Taimoory ; Stephanie Corio; Babak Borhan; Richard Staples; Mathew Vetticatt; William Wulff | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry | CC BY 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6454576c1ca6101a45cbf7d3/original/a-lewis-acid-controlled-enantiodivergent-epoxidation.pdf |
66c897b2f3f4b05290da9427 | 10.26434/chemrxiv-2024-s0kr4 | Non-toxic and rapid chemical bath deposition for SnO2 electron transporting layers in perovskite solar cells | Perovskite solar cells are a promising new solar technology with efficiencies surpassing polycrystalline silicon solar cell technology. For the n-i-p perovskite solar cells, tin oxide is typically used as the electron transport layer. One typical deposition method is chemical bath deposition. However, the drawbacks are toxic precursors and the slow reaction driven by dissolved oxygen forming SnO2 x. Here, we present a tin oxide chemical bath deposition starting from non-toxic sodium stannate solutions. Within 6 minutes of reaction time, a 9 nm thick amorphous Sn(IV)-oxide film is grown yielding solar cells with power conversion efficiencies of at least 23.2%. Surprisingly, the sole use of Sn(IV) precursors contradicts the previous Sn(II) doping assumption required for n-doping & high electric conductivity, and, unexpectedly, amorphous tin oxide films are as suitable for charge transport layers as their crystalline counterparts. The synthesis method is transferrable to other substrates (ITO, glass) and other thin-film metal oxide coatings (MoOx, SiO2) and beneficial for devices such as solar cells, photodetectors, light emitting diodes, and heterogeneous catalysis. | Matthias J. Grotevent; Linda Kothe; Yongli Lu; Chantalle Krajewska; Meng-Chen Shih; Shaun Tan; Michael Tiemann; Moungi G. Bawendi | Materials Science; Inorganic Chemistry; Energy; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c897b2f3f4b05290da9427/original/non-toxic-and-rapid-chemical-bath-deposition-for-sn-o2-electron-transporting-layers-in-perovskite-solar-cells.pdf |
6392f2087b7c91402ae9d983 | 10.26434/chemrxiv-2022-s8nnj | Efficient circularly polarized electroluminescence from achiral luminescent materials | Circularly polarized electroluminescence (CP-EL) with a defined color is generally produced in organic light-emitting diodes (OLEDs) based on CP luminescent (CPL) materials with similar colors. Such kind of many-to-many relationship requires numerous new CPL materials to fabricate CP-OLEDs because the well-developed achiral luminescent materials are rarely considered to be capable of directly producing CP-EL. Herein, the one-to-many strategy is proposed for CP-EL by employing high-performance near ultraviolet CPL materials to sensitize achiral luminescent materials. These newly developed near ultraviolet CPL materials have excellent photoluminescence (PL) quantum yields and good CPL dissymmetry factors, and can induce efficient blue to red CP-PL for achiral fluorescence, phosphorescence, thermally activated delayed fluorescence (TADF) and multi-resonance (MR) TADF materials. Efficient near ultraviolet CP-EL with the best external quantum efficiencies (ηexts) of 9.0% at 404 nm and extremely small efficiency roll-offs are achieved by using them as emitters for CP-OLEDs. By adopting them as hosts or sensitizers, commercially available yellow-orange achiral phosphorescence, TADF and MR-TADF materials can generate strong CP-EL, with absolute dissymmetry factors and outstanding ηexts of up to 2.87 × 10−3 and 30.8%, respectively, which are the state-of-the-art CP-EL performances reported so far, demonstrating a simple and universal avenue towards efficient CP-EL. | Letian Xu; Hao Liu; Xiaoluo Peng; Pingchuan Shen; Ben Zhong Tang; Zujin Zhao | Physical Chemistry; Optics; Photochemistry (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6392f2087b7c91402ae9d983/original/efficient-circularly-polarized-electroluminescence-from-achiral-luminescent-materials.pdf |
667c145e5101a2ffa88e7b20 | 10.26434/chemrxiv-2024-j4dsz | Dissecting Transmetalation Reactions at the Molecular Level: Aryl Transfer in Copper-Tetraarylborate Complexes | Boron-copper transmetalation reactions are practically important, but their detailed mechanisms remain elusive. To im-prove our understanding of these transformations, we have analyzed the systems Cu+/(BArX4)− (ArX = p-X−C6H4 with X = OMe, Me, H, F, Cl, CF3) by a combination of NMR spectroscopy, ESI-mass spectrometry, gas-phase experiments, and quantum chemical calculations. By probing the gas-phase fragmentation of mass-selected adducts of the type [Cu(BArX4)(BPh4)]− and [(MeCN)2Cu2(BArX4)]+, we obtain intimate insight into the microscopic reactivity of these model complexes. In all cases, transmetalation reactions occur, the relative efficiency of which depends on the electronic prop-erties of the aryl groups, the charge of the complex, and the number of solvent molecules bound to the latter. Specifically, electron-rich aryl groups show a higher tendency toward being transferred to copper than their electron-poor counter-parts, whereas the addition of individual MeCN molecules diminishes the propensity toward transmetalation. The quan-tum chemical calculations are essential for the interpretation of the experimental results by providing structural and thermochemical information. The trends derived from the present gas-phase models promise to help in the mechanistic analysis of boron-copper transmetalation in solution. | Finn Kraft; Marcel Sommer; Alexandr Y. Pereverzev; Jana Roithová; Thomas Auth; Konrad Koszinowski | Theoretical and Computational Chemistry; Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Reaction (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c145e5101a2ffa88e7b20/original/dissecting-transmetalation-reactions-at-the-molecular-level-aryl-transfer-in-copper-tetraarylborate-complexes.pdf |
60c750864c89199267ad3db9 | 10.26434/chemrxiv.12320486.v2 | Binding of Divalent Cations to Aqueous Acetate: Molecular Simulations Guided by Raman Spectroscopy | <div>
<div>
<div>
<p>In spite of the biological importance of the binding of Zn2+, Ca2+, and Mg2+ to the carboxylate
group, cation-acetate binding affinities and binding modes remain actively debated. Here, we
report the first use of Raman multivariate curve resolution (Raman-MCR) vibrational spectroscopy
to obtain self-consistent free and bound metal acetate spectra and one-to-one binding constants,
without the need to invoke any a priori assumptions regarding the shapes of the corresponding
vibrational bands. The experimental results, combined with classical molecular dynamics
simulations with a force field effectively accounting for electronic polarization via charge scaling
and ab initio simulations, indicate that the measured binding constants pertain to direct (as opposed
to water separated) ion pairing. The resulting binding constants do not scale with cation size, as
</p><div>
<div>
<div>
<p>the binding constant to Zn2+ is significantly larger than that to either Mg2+ or Ca2+, although Zn2+
and Mg2+ have similar radii that are about 25% smaller than Ca2+. Remaining uncertainties in the
metal acetate binding free energies are linked to fundamental ambiguities associated with
identifying the range of structures pertaining to non-covalently bound species.
</p>
</div>
</div>
</div>
</div>
</div>
</div> | Denilson Mendes de Oliveira; Samual
R. Zukowski; Vladimir Palivec; Jérôme Hénin; Hector Martinez-Seara; Dor Ben-Amotz; Pavel Jungwirth; Elise Duboué-Dijon | Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750864c89199267ad3db9/original/binding-of-divalent-cations-to-aqueous-acetate-molecular-simulations-guided-by-raman-spectroscopy.pdf |
6357d11faca1987753e47739 | 10.26434/chemrxiv-2022-9t28v | Metal-free construction of aminated isoquinoline frameworks from 2-(2-oxo-2-arylethyl) benzonitrile in an aqueous medium | Herein, we report a metal-free protocol for the activation of nitrile towards the nucleophilic addition and subsequent annulation under an aqueous medium for the first time. The protocol divulges an efficient route for the construction of diversified aminated isoquinolines. Differently substituted primary as well as secondary amines underwent the reaction in a highly regioselective manner. The reaction is operationally simple, shows high functional group tolerance, easier modification of well-known drugs, and successfully extended to gram-scale synthesis. | Himanshi Sharma; Manoj Kumar; Aaftaab Sethi; Brijesh Rathi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6357d11faca1987753e47739/original/metal-free-construction-of-aminated-isoquinoline-frameworks-from-2-2-oxo-2-arylethyl-benzonitrile-in-an-aqueous-medium.pdf |
66543d98418a5379b0619cad | 10.26434/chemrxiv-2024-321x5 | Entropy of liquid water as predicted by the two-phase thermodynamic model and data-driven many-body potentials | We investigate the entropy of liquid water at ambient conditions using the two-phase thermodynamic (2PT) model, applied to both common pairwise-additive water models and the MB-pol and MB-pol(2023) data-driven many-body potentials. Our simulations demonstrate that the 2PT model yields entropy values in semiquantitative agreement with experimental data when using MB-pol and MB-pol(2023). Additionally, our anal- yses indicate that the entropy values predicted by pairwise-additive water models may benefit from error compensation between the inherent approximations of the 2PT model and the known limitations of these water models in describing many-body interactions. Despite its approximate nature, the simplicity of the 2PT model makes it a valuable tool for estimating relative entropy changes of liquid water across various environments, especially when combined with water models that provide a consistently robust representation of the structural, thermodynamic, and dynamical properties of liquid water. | Ching-Hwa Ho; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Physical and Chemical Properties; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66543d98418a5379b0619cad/original/entropy-of-liquid-water-as-predicted-by-the-two-phase-thermodynamic-model-and-data-driven-many-body-potentials.pdf |
6720a585f9980725cf3eb87a | 10.26434/chemrxiv-2024-tqcg9 | Raman Marker Bands for In-situ Quality Control During Synthesis Of Two-Dimensional Conjugated Metal-Organic Frameworks | Two-dimensional conjugated metal-organic frameworks (2D c-MOFs) are a subclass of MOFs that are of particular interest for electrocatalysis due to their good intrinsic conductivity. The electrochemical properties of such 2D frameworks are strongly related to their structure, which in turn is influenced by the synthesis conditions. However, even under formally identical conditions, MOF crystals with different structural properties are obtained, and to date there is no easy-to-apply method to predict the quality of MOF crystals already during synthesis. In the present work, we monitored the formation of phthalocyanine-based 2D MOFs at the air-water interface using in-situ Raman spectroscopy and identified Raman marker bands that characterise the degree of linker aggregation, the reaction progress, and the yield of MOFs formed during the reaction. Using transmission electron microscopy (TEM) measurements on the MOF crystals after synthesis, a correlation between the Raman marker bands and the resulting crystalline domain size distribution of the MOF could be derived. Thus, a method for a non-invasive, fast and simple in-situ quality assessment of the synthesised MOFs was established. These results are an important step towards the automation of MOF synthesis. | Fanny Reichmayr; Daniel Wolf; Geping Zhang; Mingchao Wang; Max Herzog; Renhao Dong; Xinliang Feng; Axel Lubk; Inez Weidinger | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720a585f9980725cf3eb87a/original/raman-marker-bands-for-in-situ-quality-control-during-synthesis-of-two-dimensional-conjugated-metal-organic-frameworks.pdf |
60c741e7842e655163db1f9b | 10.26434/chemrxiv.8156561.v1 | Differentiation and Functionalization of Adjacent, Remote C–H Bonds | <p>Site-selective
functionalizations of C–H bonds will ultimately afford chemists transformative
tools for editing and constructing complex molecular architectures<sup>1-4</sup>.
Towards this goal, developing strategies to activate C–H bonds that are distal
from a functional group is essential<sup>4-6</sup>. In this context, distinguishing
remote C–H bonds on adjacent carbon atoms is an extraordinary challenge due to
the lack of electronic or steric bias between the two positions. Herein, we
report the design of a catalytic system leveraging a remote directing template
and a transient norbornene mediator to selectively activate a previously
inaccessible remote C–H bond that is one bond further away. The generality of
this approach has been demonstrated with a range of heterocycles, including a
complex anti-leukemia agent, and hydrocinnamic acid substrates.</p> | Hang Shi; Lu Yi; Jiang Weng; Katherine Bay; Xiangyang Chen; Keita Tanaka; pritha verma; Kendall N. Houk; jin-quan yu | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e7842e655163db1f9b/original/differentiation-and-functionalization-of-adjacent-remote-c-h-bonds.pdf |
60c757c90f50db028e39831b | 10.26434/chemrxiv.11418978.v3 | Substituent Effects on the Thermal Decomposition of Phosphate Esters on Ferrous Surfaces | <p></p><p>Phosphate esters have a wide range of industrial applications, for example in tribology where they are used as vapour phase lubricants and antiwear additives. An atomic-level understanding of phosphate ester tribofilm formation mechanisms is required to improve their tribological performance. A process of particular interest is the thermal decomposition of phosphate esters on steel surfaces, since this initiates polyphosphate film formation. In this study, reactive force field (ReaxFF) molecular dynamics (MD) simulations are used to study the thermal decomposition of phosphate esters with different substituents on several ferrous surfaces. The ReaxFF parameterisation was validated for a representative system using density functional theory (DFT) calculations. During the MD simulations on Fe 3 O 4 (001) and α-Fe(110), chemisorption interactions between the phosphate esters and the surfaces occur even at room temperature, and the number of molecule-surface bonds increases as the temperature increases from 300 to 1000 K. Conversely, on hydroxylated, amorphous Fe 3 O 4 , most of the molecules are physisorbed and some desorption occurs at high temperature. Thermal decomposition rates were much higher on Fe 3 O 4 (001) and particularly α-Fe(110) compared to hydroxylated, amorphous Fe 3 O 4. This suggests that water passivates ferrous surfaces and inhibits phosphate ester chemisorption, decomposition, and ultimately polyphosphate film formation. For the alkyl phosphates, thermal decomposition proceeds mainly through CO and C-H cleavage on Fe 3 O 4 (001). Aryl phosphates show much higher thermal stability, and decomposition on Fe 3 O 4 (001) only occurs through P-O and C-H cleavage, which require very high temperature. The onset temperature for CO cleavage on Fe 3 O 4 (001) increases as: tertiary alkyl < secondary alkyl < primary linear alkyl ≈ primary branched alkyl < aryl. This order is consistent with experimental observations for the thermal stability of antiwear additives with similar substituents. The simulation results clarify a range of surface and substituent effects on the thermal decomposition of phosphate esters on steel that should be helpful for the design of new molecules with improved tribological performance.<br /></p><p></p> | James Ewen; Carlos Ayestaran Latorre; Chiara Gattinoni; Arash Khajeh; Joshua Moore; Joseph Remias; Ashlie Martini; Daniele Dini | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757c90f50db028e39831b/original/substituent-effects-on-the-thermal-decomposition-of-phosphate-esters-on-ferrous-surfaces.pdf |
6312184c5351a34510ec98a9 | 10.26434/chemrxiv-2022-gfp1k | An efficient implementation of the GOSTSHYP pressure model by
applying shell-bounding gaussian 1-electron-3-center integral screening | We implemented a screening algorithm for one-electron-three-center (1e3c) overlap
integrals over contracted gaussian-type orbitals (CGTOs) into the Q-Chem program
package. The respective bounds were derived using shell-bounding gaussians (SBGs)
and the Obara-Saika recurrence relations. Using integral screening, we reduced the
computational scaling of the Gaussians On Surface Tesserae Simulate HYdrostatic
Pressure (GOSTSHYP) model in terms of calculation time and memory usage to a
linear relationship with the tesserae used to discretize the surface area. Further code improvements allowed for additional performance boosts. To demonstrate the better
performance, we calculated the compressebility of fullerenes up to C180, where we were
originally limited to C40 due to the high RAM usage of GOSTSHYP. | Felix Zeller; Eric Berquist; Evgeny Epifanovsky; Tim Neudecker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6312184c5351a34510ec98a9/original/an-efficient-implementation-of-the-gostshyp-pressure-model-by-applying-shell-bounding-gaussian-1-electron-3-center-integral-screening.pdf |
678f746681d2151a02150eeb | 10.26434/chemrxiv-2025-s9mms | Circularly Polarized Luminescence Control through Molecular Rotation in Crystalline Chiral Binuclear N-Heterocyclic Carbene Au(I) Complexes | The rotational motion within molecular crystals can affect not only their internal structure and symmetry, but also often results in the alteration of bulk properties such as thermal expansion, macroscopic motion, change in electromagnetic, optical, and photophysical properties. In this work, we demonstrate how the thermally activated molecular rotation within the crystals of chiral binuclear N-Heterocyclic carbene (NHC) Au(I) complexes can modulate their circularly polarized luminescence (CPL). The enantiomeric pair of chiral binuclear NHC Au(I) complexes, 1-R and 1-S, exhibit a distinct C2-symmetric conformation, derived from non-equivalent orientations of phenyl moieties at the chiral NHC ligands. The variable-temperature solid-state 2H NMR studies revealed that these non-equivalent phenyl moieties undergo fast rotational motion above 273K, potentially promoting symmetrization of molecular structures in the crystal. The latter, in combination with the inherent chirality of 1-R and 1-S complexes, results in the emergence of the temperature-dependent CPL behavior in the crystalline state with a noticeable increase of luminescence intensity and dissymmetry factors upon cooling from 333K to 213K (|ΔICPL|: + ~300%; |glum|: + ~50%). Such thermo-responsive behavior can be attributed not only to thermal rotation-induced luminescence quenching but also to the potential effect of phenyls rotation on the symmetry of the complexes. | Pingyu Jiang; Alexander Mikherdov; Hajime Ito; Mingoo Jin | Physical Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Inorg.); Photochemistry (Physical Chem.); Materials Chemistry; Crystallography | CC BY 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678f746681d2151a02150eeb/original/circularly-polarized-luminescence-control-through-molecular-rotation-in-crystalline-chiral-binuclear-n-heterocyclic-carbene-au-i-complexes.pdf |
617fc20f7a00214b2b422dae | 10.26434/chemrxiv-2021-cxs25 | Control and Monitoring of Temperature in 3D-Printed Circular Disk Reactors for Continuous Flow Photochemistry using Raspberry Pi Based Software | In this communication we report our investigations into the control and monitoring of temperature in a 3D printed circular disk reactor (CDR) for continuous flow photochemistry using datalogging via a Raspberry Pi microprocessor. A lamp base and holder were designed and realised using 3D printing to enable efficient monitoring of temperature using a temperature probe and the photo-CDR was cooled using a constant controlled flow of compressed air. We demonstrated that temperature gains under commercial LED light sources are significant and that the design of our suitably designed low-cost air-cooled holder could control and stabilise the temperature of the photo-CDR over sustained time-periods. | Lee Walmsley; Stephen Hilton; Emilie Sellier; Matthew Penny; Daniel Maddox | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2021-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617fc20f7a00214b2b422dae/original/control-and-monitoring-of-temperature-in-3d-printed-circular-disk-reactors-for-continuous-flow-photochemistry-using-raspberry-pi-based-software.pdf |
60c744c2bdbb8962c9a388c3 | 10.26434/chemrxiv.9916235.v1 | Autocatalytic Models for the Origin of Biological Homochirality | Mechanistic studies of the Soai autocatalytic reaction in the context of biological homochirality. | Donna Blackmond | Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2019-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744c2bdbb8962c9a388c3/original/autocatalytic-models-for-the-origin-of-biological-homochirality.pdf |
669a719f01103d79c5958d02 | 10.26434/chemrxiv-2024-4fq4v | External Acidity as Performance Descriptor in Polyolefin Cracking using Zeolite-Based Materials | Thermal pyrolysis is gaining industrial adoption to convert large volumes of plastic waste into hydrocarbon feedstock. However, it suffers from a high reaction temperature and relatively low selectivity. Utilizing a catalyst in the process, moving from thermal pyrolysis to catalytic cracking could help overcome both challenges. In order to develop efficient catalyst materials for this process, understanding structure-composition-performance relationships is critical. In this work, we show that in contrast to cracking of small molecules, plastic cracking activity using ultrastable zeolite Y materials does not depend on the bulk Brønsted acid site content, but rather on the concentration of acid sites located on the outer surface and in mesopores. This external acidity, however, fails to capture all the observed performance trends. Detailed kinetic experiments revealed that the scaling of the reaction rate with the catalyst loading differs drastically between highly similar catalyst materials. More specifically, doubling the catalyst loading leads to doubling of the reaction rate for one material, while for another it leads to more than fivefold increase. When very bulky reactants, such as polyolefins, are converted over microporous catalysts, structure-composition-performance relationships established for smaller molecules need to be revisited. | Sebastian Rejman; Zoé M. Reverdy; Zeynep Bör; Jaap N. Louwen; Carolin Rieg; Joren M. Dorresteijn; Jan-Kees van der Waal; Eelco T. C. Vogt; Ina Vollmer; Bert M. Weckhuysen | Catalysis; Polymer Science; Chemical Engineering and Industrial Chemistry; Petrochemicals; Acid Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a719f01103d79c5958d02/original/external-acidity-as-performance-descriptor-in-polyolefin-cracking-using-zeolite-based-materials.pdf |
60c757389abda21cddf8e68c | 10.26434/chemrxiv.14381540.v1 | Degradation Kinetics and Solvent Effects of Various Long-Chain Quaternary Ammonium Salts | <div>Surfactants such as quaternary ammonium salts (QAS) have been in increasing demand, for emerging new applications. Recent attempts at process intensification of</div><div>their production, have disclosed the need for a better understanding of QAS thermal stability. This work aims to determine degradation kinetics of various QASs, and the</div><div>associated solvent effects. Degradation kinetics of four methyl carbonate QASs were determined in various</div><div>polar solvents in stainless steel batch autoclaves. <sup>1</sup>H NMR spectrometry was employed for online analysis of the reaction mixtures. The kinetic parameters were then used</div><div>to compare the thermal stability of the four compounds in the polar solvents. Water showed not degradation, and methanol (MeOH) was the solvent that provided the</div><div>second-best stability. Water-MeOH mixtures may provide an overall optimum. More, and longer long-chain substituents increased the degradation rate. Thermogravimetric Analysis was used to obtain the thermal stability in a solid-</div><div>state, i.e. solventless environment. Isoconversional analysis showed that no reliable kinetic parameters could be determined. Nevertheless, the data did allow for a compar-</div><div>ison of the thermal stability of 14 different QASs. Furthermore, the relative instability of the compounds in solid-state demonstrated the challenges of solventless QAS production.</div> | Roel Kleijwegt; Wyatt Winkenwerder; Wim Baan; John van der Schaaf | Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757389abda21cddf8e68c/original/degradation-kinetics-and-solvent-effects-of-various-long-chain-quaternary-ammonium-salts.pdf |
60c73ee14c8919e8b8ad1ea2 | 10.26434/chemrxiv.7177892.v1 | Photochemical and Electrochemical Reduction of Carbon Dioxide Catalyzed by a Polyoxometalate-Organic Photosensitizer Complex | <p>A manganese substituted Anderson type polyoxometalate, [MnMo<sub>6</sub>O<sub>24</sub>]<sup>9-</sup>, tethered with an anthracene photosensitizer was prepared and used as catalyst for CO<sub>2</sub> reduction. The polyoxometalate-photosensitizer hybrid complex, obtained by covalent attachment of the sensitizer to only one face of the planar polyoxometalate, was characterized by NMR, IR and mass spectroscopy. Cyclic voltammetry measurements show a catalytic response for the reduction of carbon dioxide, thereby suggesting catalysis at the manganese site on the open face of the polyoxometalate. Controlled potentiometric electrolysis showed the reduction of CO<sub>2</sub> to CO with a TOF of ~15 sec<sup>-1</sup>. Further photochemical reactions showed that the polyoxometalate-anthracene hybrid complex was active for the reduction of CO<sub>2</sub> to yield formic acid and/or CO in varying amounts dependent on the reducing agent used. Control experiments showed that the attachment of the photosensitizer to [MnMo<sub>6</sub>O<sub>24</sub>]<sup>9-</sup> is necessary for photocatalysis.</p><div><br /></div> | Chandan Dey; Ronny Neumann | Electrocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ee14c8919e8b8ad1ea2/original/photochemical-and-electrochemical-reduction-of-carbon-dioxide-catalyzed-by-a-polyoxometalate-organic-photosensitizer-complex.pdf |
60f7635b8f6bf6827b6fde55 | 10.26434/chemrxiv-2021-84b7p-v2 | Shallow and deep trap states of solvated electrons in methanol and their formation, electronic excitation, and relaxation dynamics | We present condensed-phase first-principles molecular dynamics simulations to elucidate the presence of different electron trapping sites in liquid methanol and their roles in the formation, electronic transitions, and relaxation of solvated electrons (e−met) in methanol. Excess electrons injected into liquid methanol are most likely trapped by methyl groups, but rapidly diffuse to more stable trapping sites with dangling OH bonds. After localization at the sites with one free OH bond (1OH trapping sites), reorientation of other methanol molecules increases the OH coordination number and the trap depth, and ultimately four OH bonds become coordinated with the excess electrons under thermal conditions. The simulation identified four distinct trapping states with different OH coordination numbers. The simulation results also revealed that electronic transitions of e−met are primarily due to charge transfer between electron trapping sites (cavities) formed by OH and methyl groups and that these transitions differ from hydrogenic electronic transitions involving aqueous solvated electrons (e−aq). Such charge transfer also explains the alkyl-chain-length dependence of the photoabsorption peak wavelength and the excited-state lifetime of solvated electrons in primary alcohols.
| Jinggang Lan; Yo-ichi Yamamoto; Toshinori Suzuki; Vladimir Rybkin | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f7635b8f6bf6827b6fde55/original/shallow-and-deep-trap-states-of-solvated-electrons-in-methanol-and-their-formation-electronic-excitation-and-relaxation-dynamics.pdf |
66ea8c48cec5d6c1426a0b67 | 10.26434/chemrxiv-2024-1727n | The Role of Phosphorous in the Solid Electrolyte Interphase of Argyrodite Solid Electrolytes | The solid electrolyte interphase that forms on Li6PS5Cl argyrodite solid electrolytes has been reported to continually grow through a diffusion-controlled process, yet this process is not fully understood. Here, we use a combination of electrochemical and X-ray photoelectron spectroscopy techniques to elucidate the role of phosphorus in this growth mechanism. We uncover how Li6PS5Cl can decompose at a potential well above the full reduction to Li3P, forming partially lithiated phosphorus species LixP. We provide evidence of a gradient of LixP species throughout the SEI thickness, leading to a diffusion-limited growth. We predict continuous SEI growth as long as lithium metal is present. | Matthew Burton; Yi Liang; Jack Aspinall; Ben Jagger; Mauro Pasta | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ea8c48cec5d6c1426a0b67/original/the-role-of-phosphorous-in-the-solid-electrolyte-interphase-of-argyrodite-solid-electrolytes.pdf |
60c74928ee301c3c41c79a03 | 10.26434/chemrxiv.12038604.v1 | Treatment of COVID-19 patients: Justicia adhatoda leaves extract is a strong remedy for COVID-19 – Case report analysis and docking based study | <div>To find immediately applicable drug for the treatment of COVID-19 positive patients, a plausible life cycle of this virus is proposed from the analysis of few case reports. On the basis of this proposal and symptomatic similarities few common drug-molecules are tested as protease inhibitor and replicase inhibitor of COVID-19 virus using COVID-19 Docking Server. It is observed that<b> anisotine</b> and<b> vasicoline</b> of <i>Justicia adhatoda</i> and <b>Pemirolast</b> are very good inhibitors. As all these three compounds are market available drugs, immediate clinical trial is plausible which may lead to the golden success against the present pandemic. We prescribed different drugs for different purpose and stages of viral infection. </div><div><br /></div><div><b>Key words:</b> COVID-19, Structure of COVID-19, Infection mechanism of COVID-19, Model drugs for COVID-19, Docking study. </div> | Abhrajit Bag; Arijit Bag | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74928ee301c3c41c79a03/original/treatment-of-covid-19-patients-justicia-adhatoda-leaves-extract-is-a-strong-remedy-for-covid-19-case-report-analysis-and-docking-based-study.pdf |
64d5e4ccdfabaf06ff1763ef | 10.26434/chemrxiv-2023-8wxcz | Learning the Language of NMR: Structure Elucidation from NMR spectra using Transformer Models | The application of machine learning models in chemistry has made remarkable strides in recent years. Even though there is considerable interest in automating common proce- dure in analytical chemistry using machine learning, very few models have been adopted into everyday use. Among the analytical instruments available to chemists, Nuclear Mag- netic Resonance (NMR) spectroscopy is one of the most important, offering insights into molecular structure unobtainable with other methods. However, most processing and analysis of NMR spectra is still performed manually, making the task tedious and time consuming especially for larger quantities of spectra. We present a transformer-based machine learning model capable of predicting the molecular structure directly from the NMR spectrum. Our model is pretrained on synthetic NMR spectra, achieving a top–1 accuracy of 67.0% when predicting the structure from both the 1H and 13C spectrum. Additionally, we train a model which, given a spectrum and a set of likely compounds, selects the one corresponding to the spectrum. This model achieves a top–1 accuracy of 96.0% when trained on 1H spectra. | Marvin Alberts; Federico Zipoli; Alain C. Vaucher | Theoretical and Computational Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d5e4ccdfabaf06ff1763ef/original/learning-the-language-of-nmr-structure-elucidation-from-nmr-spectra-using-transformer-models.pdf |
65ebdbce9138d231610ebf6d | 10.26434/chemrxiv-2023-9dvlm-v3 | An Electrochemical Series for Materials | The electrochemical series is a useful tool in electrochemistry, but its effectiveness in materials chemistry is limited by the fact that the standard electrochemical series is based on a relatively small set of reactions, many of which are measured in aqueous solutions. To address this problem, we have used machine learning to create an electrochemical series for inorganic materials from tens of thousands of entries in the Inorganic Crystal Structure Database. We demonstrate that this series is generally more consistent with oxidation states in solid-state materials than the series based on aqueous ions. The electrochemical series was constructed by developing and parameterizing a physical, human-interpretable model of oxidation states in materials. We show that this model enables the prediction of oxidation states from composition in a way that is more accurate than a state-of-the-art transformer-based neural network model. We present applications of our approach to structure prediction, materials discovery, and materials electrochemistry, and we discuss possible additional applications and areas for improvement. To facilitate the use of our approach, we introduce a freely available web site and API. | Tim Mueller; Joseph Montoya; Weike Ye; Xiangyun Lei; Linda Hung; Jens Hummelshøj; Michael Puzon; Daniel Martinez; Chris Fajardo; Rachel Abela | Materials Science; Inorganic Chemistry; Electrochemistry; Theory - Inorganic; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ebdbce9138d231610ebf6d/original/an-electrochemical-series-for-materials.pdf |
628e566d6b12b655a67ec157 | 10.26434/chemrxiv-2022-zzfqs | 2,6-Bis[[bis(1,1-dimethylethyl)phosphino-κP]methyl]phenyl-κC]chlorohydro(phenylphosphine)iridium | The molecular structure of an iridium complex featuring a phenylphosphine ligand is described. Reaction of (POCOP)IrHCl (1, POCOP = 2,6-(tBu2PO)2C6H3–) with phenylphosphine gives (POC-OP)IrHCl(PH2Ph) (2) under mild conditions. Structural features are consistent with a classic pseudo-octahedral iridium compound with three neutral phosphine donors. Compound 1 is un-reactive at elevated temperature and unreactive toward excess phenylphosphine under condi-tions sampled. | Neil Mucha; Rory Waterman | Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e566d6b12b655a67ec157/original/2-6-bis-bis-1-1-dimethylethyl-phosphino-p-methyl-phenyl-c-chlorohydro-phenylphosphine-iridium.pdf |
63bde50b4fba70735c0074aa | 10.26434/chemrxiv-2022-7hwht-v2 | Untangling the Intertwined: Metallic to Semiconducting Phase Transition of Colloidal MoS2 Nanoplatelets and Nanosheets | 2D semiconducting transition metal dichalcogenides (TMDCs) are highly promising materials for future spin- and valleytronic applications and exhibit an ultrafast response to external (optical) stimuli which is essential for optoelectronics. Colloidal nanochemistry on the other hand is an emerging alternative for the synthesis of 2D TMDC nanosheet (NS) ensembles, allowing for the control of the reaction via tunable precursor and ligand chemistry. Up to now, wet-chemical colloidal syntheses yielded intertwined/agglomerated NSs with a large lateral size. Here, we show a synthesis method for 2D mono- and bilayer MoS2 nanoplatelets with a particularly small lateral size (NPLs, 7.4 nm ± 2.2 nm) and MoS2 NSs (22 nm ± 9 nm) as a reference by adjusting the molybdenum precursor concentration in the reaction. We find that in colloidal 2D MoS2 syntheses initially a mixture of the stable semiconducting and the metastable metallic crystal phase is formed. 2D MoS2 NPLs and NSs then both undergo a full transformation to the semiconducting crystal phase by the end of the reaction, which we quantify by X-ray photoelectron spectroscopy. Phase pure semiconducting MoS2 NPLs with a lateral size approaching the MoS2 exciton Bohr radius exhibit strong additional lateral confinement, leading to a drastically shortened decay of the B exciton which is characterized by ultrafast transient absorption spectroscopy. Our findings represent an important step for utilizing colloidal TMDCs, for example small MoS2 NPLs represent an excellent starting point for the growth of heterostructures for future colloidal photonics. | André Niebur; Aljoscha Söll; Philipp Haizmann; Onno Strolka; Dominik Rudolph; Kevin Tran; Franz Renz; André Philipp Frauendorf; Jens Hübner; Heiko Peisert; Marcus Scheele; Jannika Lauth | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bde50b4fba70735c0074aa/original/untangling-the-intertwined-metallic-to-semiconducting-phase-transition-of-colloidal-mo-s2-nanoplatelets-and-nanosheets.pdf |
654056b0c573f893f17a1d8b | 10.26434/chemrxiv-2023-q52xg | Insights into the Adsorption of Copper/Zinc Ions over Aged Polyethylene and Polyethylene Terephthalate Microplastics | Microplastics (MPs) have aroused growing environmental concerns due to their biotoxicity and vital roles in accelerating the spread of toxic elements. Illuminating the interactions between MPs and heavy metals (HMs) is crucial for understanding the transport and fate of HM-loaded MPs in specific environmentally relevant scenarios. Herein, the adsorption of copper (Cu2+) and zinc (Zn2+) ions over poly-ethylene (PE) and polyethylene terephthalate (PET) particulates before and after heat persulfate oxidation (HPO) treatment was comprehensively evaluated in simulated swine wastewater. The effects of intrinsic properties (i.e., degree of weathering, size, type) of MPs and environmental factors (i.e., pH, ionic strength, and co-occurring species) on adsorption were investigated thoroughly. It was observed that HPO treatment expedites the fragmentation of pristine MPs, and renders MPs with a variety of oxygen-rich functional groups, which are likely to act as new active sites for binding both HMs. The adsorption of both HMs is pH- and ionic strength-dependent at a pH of 4 to 6. Co-occurring species such as humic acid (HA) and tetracycline (TC) appear to enhance the affinity of both aged MPs for Cu2+ and Zn2+ ions via bridging complexation. However, co-occurring nutrient species (e.g., phosphate and ammonia) demonstrate different impacts on the adsorption, improving uptake of Cu2+ by precipitation while lowering affinity for Zn2+ owing to the formation of soluble zinc-ammonia complex. Spectroscopic analysis indicates that the dominant adsorption mechanism mainly involves electrostatic interactions and surface complexation. These findings provided fundamental insights into the interactions between aged MPs and HMs in an environmentally rele-vant scenario (i.e., simulated swine wastewater). | Mengyu Ma; Feihu Li | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654056b0c573f893f17a1d8b/original/insights-into-the-adsorption-of-copper-zinc-ions-over-aged-polyethylene-and-polyethylene-terephthalate-microplastics.pdf |
60c758d8842e6591b0db48e5 | 10.26434/chemrxiv.14317649.v2 | Optical Spectroscopy of Crystal Nucleation One Nucleus at a Time | <p>Crystallization is an
important process in a wide range of disciplines from fundamental science to
industrial application. Despite the importance of controlling the
crystallization and its morphology (<i>e.g.</i>
polymorphism), the lack of microscopic description of crystal nucleation often
limits the rational approach to its engineering and control. The biggest
challenge to experimentally track the nucleus formation is the stochastic and
heterogeneous nature of the nucleation occurring at nanometer scale. To overcome this challenge, we developed a method we
call “Single Nucleus Spectroscopy” or SNS and use it to follow the formation of
single crystal glycine nucleus by Raman spectroscopy at 46 ms time resolution. The
spectral evolution was analyzed by non-supervised spectral decomposition
algorithm which unraveled the Raman spectrum of prenucleation aggregates. In
order to gain microscopic insights into the structure of these aggregates we
have established a direct comparison between the experiments and theoretical works.
The outcome of our analysis is a new hypothesis of glycine crystal nucleation
mechanism.<br /></p> | Oscar Urquidi; Johanna Brazard; Natalie LeMessurier; Lena Simine; Takuji Adachi | Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758d8842e6591b0db48e5/original/optical-spectroscopy-of-crystal-nucleation-one-nucleus-at-a-time.pdf |
60c74540842e650904db25d7 | 10.26434/chemrxiv.10002032.v1 | Chance Emergence of Catalytic Activity and Promiscuity in a Self-Replicator | This study reveal a mechanism by which self-replicating molecules can autonomously acquire the ability to catalyze further reaction, in addition to their own formation. It represents a first demonstration outside biology of replicators that have the ability to catalyze reactions that produce the molecules they need to replicate from. This equates to a protometabolism.<br /> | Jim Ottelé; Andreas S. Hussain; clemens mayer; Sijbren Otto | Combinatorial Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Base Catalysis; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74540842e650904db25d7/original/chance-emergence-of-catalytic-activity-and-promiscuity-in-a-self-replicator.pdf |
62ec9809659a3f493334a701 | 10.26434/chemrxiv-2021-7xc4w-v2 | Vibronic Coupling Effect on the Vibrationally-Resolved Electronic Spectra and Intersystem Crossing Rates of a TADF Emitter: 7-PhQAD | Assessing and improving the performance of organic light-emitting diode (OLED) materials require quantitative prediction of rate coefficients for the intersystem crossing (ISC) and reverse ISC (RISC) processes, which are determined not only by the energy gap and the direct spin-orbit coupling (SOC) between the first singlet and triplet excited states at a thermal equilibrium position of the initial electronic state but also by the non-Condon effects such as the Herzberg-Teller-like vibronic coupling (HTVC) and the spin-vibronic coupling (SVC). Here we apply the time-dependent correlation function approaches to quantitatively calculate the vibrationally-resolved absorption and fluorescence spectra and ISC/RISC rates of a newly synthesized multipleresonance-type (MR-type) thermally activated delayed fluorescence (TADF) emitter, 7-phenylquinolino[3,2,1-de]acridine-5,9-dione (7-PhQAD), with the inclusion of the FranckCondon (FC), HTVC, and Duschinsky rotation (DR) effects. The SVC effect on the
rates has also been approximately evaluated. We find that the experimentally-measured ISC rates of 7-PhQAD originate predominantly from the vibronic coupling, consistent with the previous reports on other MR-type TADF emitters. The SVC effect on ISC rates is about ten times larger than HTVC effect, and the latter increases the ISC rates by more than one order of magnitude while it slightly affects the vibrationally resolved absorption and fluorescence spectra. The discrepancy between the theoretical and experimental results is attributed to the inaccurate description of excited states calculated by the time-dependent density functional theory as well as not fully accounting for the complex experimental conditions. This work provides a demonstration of what proportion of ISC and RISC rate coefficients of a MR-type TADF emitter can be covered by the HTVC effect, and opens design routes that go beyond the FC approximation for
the future development of high-performance OLED devices. | Sirong Lin; Zheng Pei; Bin Zhang; Huili Ma; Wanzhen Liang | Theoretical and Computational Chemistry; Physical Chemistry; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2022-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ec9809659a3f493334a701/original/vibronic-coupling-effect-on-the-vibrationally-resolved-electronic-spectra-and-intersystem-crossing-rates-of-a-tadf-emitter-7-ph-qad.pdf |
670947fa12ff75c3a124832d | 10.26434/chemrxiv-2024-6jbn4 | In-situ Raman investigations of Fe-coated Ni OER electrodes | We have investigated the OER performance of Fe-coated Ni meshes via direct immersion of the samples in selected Fe-bearing solutions. In all cases, we were able to detect an enhancement of the OER performance, with the NM samples immersed in 20 mM Fe(NO3)3 and 20 mM FeCl2 solutions showing the best activity. The stability of the electrodes could be verified for 24 hours. Furthermore, our in-situ Raman spectroscopic studies have pinpointed the oxidation of Ni preceding the OER process; a direct relation between the activity and the detected Raman signal could be observed. Our results appear to pave the way for establishing Raman spectroscopy as a promising method of choice for identifying the active phase in Ni-bearing systems. | Ilias Efthimiopoulos; Sihan Zhang; Nafiseh Samisereht; SA Sharat; Petra Ebbinghaus; Caroline Mehrmann; Martin Rabe | Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670947fa12ff75c3a124832d/original/in-situ-raman-investigations-of-fe-coated-ni-oer-electrodes.pdf |
60c74874702a9bd9b418afaa | 10.26434/chemrxiv.11911296.v1 | Hilbert-Curve Assisted Structure Embedding Method | This work introduces a novel chemical space embedding method "Hilbert-Curve Assisted Structure Embedding (HCASE)" with help of pseudo-Hilbert Curves and Scaffold- Keys. The method was designed to produce an embedding that can be intuitively interpreted by medicinal chemists and data analysts. We analyzed the embedding of approved drug molecules (DrugBank) and natural products (CANVASS) into chemical spaces defined by Bemis-Murcko scaffolds extracted from ChEMBL (v24.1) database and from ChEMBL (v23) Natural Products. The implementation of HCASE algorithm and the input and results files of the analyses are available at https://github.com/ncats/hcase . | Gergely Zahoranszky-Kohalmi; Kanny K. Wan; Alexander G. Godfrey | Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74874702a9bd9b418afaa/original/hilbert-curve-assisted-structure-embedding-method.pdf |
60c75156842e65b682db3b97 | 10.26434/chemrxiv.12350879.v9 | Hypervalent Iodine-Mediated Styrene Hetero- and Homodimerization Initiation Proceeds with Two-Electron Reductive Cleavage | <p><a>A
mechanistic insight into </a>the hetero- and homodimerizations (HETD and HOMD) of styrenes
promoted by hypervalent iodine reagents (HVIRs; <b>DMP</b> and <b>PIDA</b>) and
facilitated by HFIP to yield all <i>trans</i> cyclobutanes is reported using
density functional theory (DFT) calculations. The initialization
involving direct bimolecular one-electron transfer is found to be highly
unfavored, especially for the <b>PIDA</b> system. At this point, we suggest
that the reaction is initiated with an overall two-electron reductive cleavage
of two I─O bond cleavages, affording I(III) (iodinane) and I(I) (iodobenzene)
product with DMP and PIDA as oxidant, respectively. The resulting acetate
groups are stabilized by the solvent HFIP through strong hydrogen bonding
interaction, which promotes the electron transfer process. The nature of the
electron transfer is studied in detail and found that the overall two-electron
transfer occurs within tri-molecular complex organized by π-stacking interactions and as a stepwise and concerted
mechanism for I(III) and I(V) oxidants, respectively. The reaction rate is
determined by the initialization step: for I(III), the initiation is
thermodynamically endergonic, whereas the endergonicity for I(V) is modest.
Upon initialization, the reaction proceeds through a stepwise [2+2] pathway,
involving a radical-cationic π-π stacked intermediate, either hetero- or
homodimerized. DFT results supported by quasiclassical molecular dynamics
simulations show that HOMD is dynamically competing pathway to HETD although
the latter is relatively faster, in accordance with experimental observations. </p> | Aqeel A. Hussein; Yumiao Ma; Ahmed Al-Yasari | Organic Synthesis and Reactions; Physical Organic Chemistry; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75156842e65b682db3b97/original/hypervalent-iodine-mediated-styrene-hetero-and-homodimerization-initiation-proceeds-with-two-electron-reductive-cleavage.pdf |
671f7c9e1fb27ce124d60a80 | 10.26434/chemrxiv-2024-z79r9 | Influence of Pluronic F68 on size stability and acoustic behavior of monodisperse phospholipid-coated microbubbles produced at room temperature | Ultrasound contrast agents, comprised of phospholipid-coated microbubbles, can be produced as monodisperse populations using a microfluidic flow-focusing device. However, microbubble coalescence remains a significant challenge. High production temperatures (e.g. 55° C) can be used to suppress coalescence, but it complicates the microfluidic device design and is incompatible with targeting agents and drug conjugates. This study investigates the production of monodisperse microbubbles at room temperature with the addition of the amphiphilic surfactant Pluronic F68. Two 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC)-based phospholipid formulations were investigated: F1, containing 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[carbonyl-methoxypolyethylene glycol] (DPPE-PEG5000), and F2, which included both DPPE-PEG5000 and polyoxyethylene(40) stearate (PEG40-stearate). We characterized the size stability and acoustic behavior of monodisperse microbubbles produced with various Pluronic F68 concentrations. Adding 5-10 mol% Pluronic F68 was found to effectively suppress coalescence and facilitated the production of monodisperse microbubbles that remained shelf stability for at least 7 days. Acoustic attenuation measurements revealed a shell stiffness ranging from 0.78 to 0.93 N/m for these microbubbles. The 10 mol% Pluronic F68 addition (10PF) demonstrated superior monodispersity and was selected for further experiments. Upon dilution, the size and resonance frequencies of both F1-10PF and F2-10PF decreased over time, though F2-10PF showed better stability compared to F1-10PF for both metrics. Both F1-10PF and F2-10PF exhibited a stronger subharmonic scattering intensity than SonoVue (clinical approved microbubbles), which offers potential for blood pressure sensing. Our study shows that incorporating Pluronic F68 facilitates the production of monodisperse microbubbles at room temperature that are stable long-term and have excellent acoustical properties, with the F2-10PF formulation demonstrating better stability than the F1-10PF. | Yuchen Wang; Sander Spiekhout; Ana Walgode; Gonzalo Collado-Lara; Antonius van der Steen; Nico de Jong; Johannes Bosch; Benjamin Johnson ; Klazina Kooiman | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671f7c9e1fb27ce124d60a80/original/influence-of-pluronic-f68-on-size-stability-and-acoustic-behavior-of-monodisperse-phospholipid-coated-microbubbles-produced-at-room-temperature.pdf |
612e3e7f42198e62fa68f76e | 10.26434/chemrxiv-2021-5n9xv | A ruthenium-oligonucleotide bioconjugated photosensitizing aptamer for cancer cell specific photodynamic therapy | Ruthenium complexes have emerged as a promising class of compounds for use as photosensitizers (PSs) in photodynamic therapy (PDT) due to their attractive photophysical properties and relative ease of chemical alteration. While promising, they generally are not inherently targeting to disease sites and may therefore be prone to side effects and require higher doses. Aptamers are short oligonucleotides that bind specific targets with high affinity. One such aptamer is AS1411, a nucleolin targeting, G-quadruplex forming, DNA aptamer. Here we present the first example of direct conjugation of a Ru(II) polypyridyl complex-based PS to an aptamer and an assessment of its in vitro cancer cell specific photosensitization including discussion of the challenges faced. | Luke McKenzie; Marie Flamme; Patrick Felder; Johannes Karges; Frédéric Bonhomme; Albert Gandioso; Christian Malosse; Gilles Gasser; Marcel Hollenstein | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e3e7f42198e62fa68f76e/original/a-ruthenium-oligonucleotide-bioconjugated-photosensitizing-aptamer-for-cancer-cell-specific-photodynamic-therapy.pdf |
630542e30187d91b149ea12b | 10.26434/chemrxiv-2022-qx6vw | Common Structural Features of Hydrophobic α-Helical Hot Spots: Insights for the Design of Novel α-Helix Mimetics | The binding conformations of hydrophobic α-helical hot spots are convergent into two spatial areas in protein–protein interaction (PPI) complex structures. The physical basis for convergence was disclosed, which enables the generation of pharmacophore models for i/i + 4/i + 7 or i/i + 3/i + 4 α-helical hot spots. Further investigation revealed that this convergence of binding conformations is common among all hydrophobic α-helical hot spots regardless of helical positions. This observation led to a streamlined generation of pharmacophore models for hydrophobic hot spots at any positions along the α-helix. These successfully evaluated pharmacophore models may be useful for designing novel α-helical hot spot mimetics for regulations of α-helix-mediated PPIs. | Shelby R. Kell; Zhen Wang; Haitao Ji | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630542e30187d91b149ea12b/original/common-structural-features-of-hydrophobic-helical-hot-spots-insights-for-the-design-of-novel-helix-mimetics.pdf |
6246d727739db157df201449 | 10.26434/chemrxiv-2022-l6x03 | alpha-amino ketyl radical generation via hydrogen atom transfer catalysis | The applications of a-amino ketyl radicals in the synthesis of valuable and potentially biologically-active molecules is currently limited; this is due to the need for strong (Ered > –2 V vs SCE) reductants, such as large excesses of samarium(II) iodide, to generate these versatile intermediates. Here we present an operationally-simple, straightforward approach to access -amino ketyl radicals via photoredox-mediated hydrogen atom transfer catalysis. This highly selective strategy allows for direct access to g oxo-d-amino esters, a prominent scaffold in a wide range of pharmaceuticals and biologically active molecules, from readily available and bench-stable amino alcohols and conjugated olefins. Preliminary mechanistic investigations support the key role of phenylboronic acid to enhance both the efficiency, and the selectivity of the reaction. | Kay Merkens; Adrián Gómez-Suárez | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6246d727739db157df201449/original/alpha-amino-ketyl-radical-generation-via-hydrogen-atom-transfer-catalysis.pdf |
60c74a2a0f50db4e31396a0e | 10.26434/chemrxiv.12106773.v2 | Self-Assembly of Charged Oligomeric Bilayers at the Aqueous/Organic Interface Regulated by Ion-Pair Associations | <div>
<p>Phospholipid bilayer membranes show promise as biomolecular
soft materials that mimic the ability of living systems to sense, respond and
learn but are fragile. Amphiphilic charged oligomers
(oligodimethylsiloxane-methylimidazolium cation, ODMS-MIM<sup>(+)</sup>),
assembled into bilayers at the oil-aqueous interfaces of droplet interface
bilayers (DIBs), possessed similar size and functionality as phospholipid bilayers,
but were stable. The ionic liquid headgroups (MIM<sup>(+)</sup>) of the
oligomers were covalently bound to short-chain hydrophobic tails (ODMS).
Bilayer self-assembly was influenced both by the charged headgroups,
constrained to two-dimensional diffusion at the liquid-liquid interface, which formed
electric double layers in the aqueous phase, and the tails in the organic phase.
Bilayers formed spontaneously at low ionic strength but required an external
voltage to form at higher ionicities. This switch in assembly behavior was due
to ion-pairing of the MIM<sup>(+)</sup> headgroups with chloride ions, resulting
in an increase in the density of the charged headgroups at the interface and
the ODMS hydrophobic tails in the oil phase as they were covalently grafted to
the headgroups. <a>Chain overlap led to repulsive
disjoining pressures between droplets due to osmotic stress</a>. The applied
voltage caused an attractive electrocompressive stress that overcame the
repulsion, enabling bilayer formation. <a>Bilayer assembly
at high ionic strength, while requiring a voltage to initiate, was
irreversible, and the resulting membrane was considerably more stable than
those formed at lower values of the ionic strength</a>. This switching of
assembly behavior can be exploited as an additional mechanism for short-term
synaptic plasticity in neuromorphic device applications using soft materials.</p>
</div> | Graham J. Taylor; Yingdong Luo; Kunlun Hong; Stephen A. Sarles; Robert L. Sacci; Benjamin Doughty; C. Patrick Collier | Nanostructured Materials - Nanoscience; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a2a0f50db4e31396a0e/original/self-assembly-of-charged-oligomeric-bilayers-at-the-aqueous-organic-interface-regulated-by-ion-pair-associations.pdf |
60c73ed8f96a00c023285fb7 | 10.26434/chemrxiv.6633980.v3 | Re-Evaluating the Spherical-Nucleic-Acid Technology | We re-evaluate the evidence presented for the detection of mRNA in cells and tissues with Spherical Nucleic Acids.<br /> | Maria Czarnek; David Mason; Gal Haimovich; Víctor F. Puntes; Paolo Bergese; Joanna Bereta; Raphaël Lévy | Imaging; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed8f96a00c023285fb7/original/re-evaluating-the-spherical-nucleic-acid-technology.pdf |
63c00db25ad3ef59f4969df2 | 10.26434/chemrxiv-2023-0kjqq | Simultaneous Detection of L-lactate and D-glucose Using DNA Aptamers in Human Blood Serum | L-lactate is a key metabolite indicative of physiological state, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need other substrates. In this work, DNA aptamers for L-lactate were obtained using a library-immobilization selection method and the highest affinity aptamer reached a Kd of 0.43 mM as determined using isothermal titration calorimetry. The aptamers showed up to 50-fold selectivity for L-lactate over D-lactate and had no measurable response to other closely related analogs such as pyruvate and 3-hydroxybutyrate. A fluorescent biosensor based on the strand displacement method showed a limit of detection of 0.55 mM. Simultaneous detection of L-lactate and D-glucose in the same serum solution was achieved. This work has broadened the scope of aptamers to very simple metabolites and provided a useful probe for the continuous and multiplexed monitoring. | Po-Jung Jimmy Huang; Juewen Liu | Biological and Medicinal Chemistry; Analytical Chemistry; Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c00db25ad3ef59f4969df2/original/simultaneous-detection-of-l-lactate-and-d-glucose-using-dna-aptamers-in-human-blood-serum.pdf |
60c742ab4c8919041cad24bd | 10.26434/chemrxiv.6744440.v2 | Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning | <p>Computational modeling of chemical and biological systems at atomic resolution is a crucial tool in the chemist's toolset. The use of computer simulations requires a balance between cost and accuracy: quantum-mechanical methods provide high accuracy but are computationally expensive and scale poorly to large systems, while classical force fields are cheap and scalable, but lack transferability to new systems. Machine learning can be used to achieve the best of both approaches. Here we train a general-purpose neural network potential (ANI-1ccx) that approaches CCSD(T)/CBS accuracy on benchmarks for reaction thermochemistry, isomerization, and drug-like molecular torsions. This is achieved by training a network to DFT data then using transfer learning techniques to retrain on a dataset of gold standard QM calculations (CCSD(T)/CBS) that optimally spans chemical space. The resulting potential is broadly applicable to materials science, biology and chemistry, and billions of times faster<i></i>than CCSD(T)/CBS calculations. </p> | Justin S Smith; Benjamin T. Nebgen; Roman Zubatyuk; Nicholas Lubbers; Christian Devereux; Kipton Barros; Sergei Tretiak; Olexandr Isayev; Adrian Roitberg | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ab4c8919041cad24bd/original/approaching-coupled-cluster-accuracy-with-a-general-purpose-neural-network-potential-through-transfer-learning.pdf |
60c7584ebb8c1a24b23dc9e2 | 10.26434/chemrxiv.14535282.v1 | Activating Power of the Phosphopantetheine Arm in α-Oxoamine Synthase Catalysis | <p>PLP-dependent enzymes are attractive biocatalysts due to their ability to perform complexity building transformations on amine-containing, readily available substrates from the chiral pool such as amino acids. Although many classes of PLP-dependent enzymes are routinely employed in synthesis, select families remain underutilized due to limitations in practical scalability. For example, some PLP-dependent enzymes act on prohibitively expensive substrates such as coenzyme A-bound substrates. To address this challenge, we have investigated the mechanism of action of coenzyme A in gating catalysis of one α-oxoamine synthase, SxtA AOS. Through investigation of the reactivity of SxtA AOS with panels of substrates and in the presence of various coenzyme A mimics as well as monitoring PLP absorbances and the behavior of SxtA AOS variants, we have determined that activity is gated through the binding of the eastern phosphodiester group by the residue Arg142 that is located in a tunnel that leads to the active site. To circumvent this gating mechanism, a synthetic CoA mimic additive was designed that allows for enhanced reactivity with non-CoA substrates. These findings outline a strategy for employing AOS enzymes without the need for cost-prohibitive coenzyme A substrates.</p> | Sarah Ackenhusen; Ye Wang; Stephanie W. Chun; Alison Narayan | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7584ebb8c1a24b23dc9e2/original/activating-power-of-the-phosphopantetheine-arm-in-oxoamine-synthase-catalysis.pdf |
67680f8d81d2151a0294a340 | 10.26434/chemrxiv-2024-sdssl | Removal of PFOA (perfluorooctanoic acid) from water using supercritical carbon dioxide. | In an experimental study using a multipurpose pilot plant suitable for intensively contacting water with supercritical carbon dioxide (scCO2) it has been demonstrated that scCO2 can take up perfluorooctanoic acid (PFOA) from water to levels down to the low µg/L level in the water. The water initially contained 100 µg/L of PFOA in all experiments. PFOA has been removed from 6 L of water for more than 98.5% using supercritical CO2 (323 K, 250 bars) in semi-continuous operation (24 L/hr). After 20 mins at 250 bar more than 90% of the PFOA was removed from the water. Batch operation (at 323 K) showed that the removal percentage decreased with pressure/density: 250 bar (834 kg/m3): 93%, 150 bar(700 kg/m3): 91 %, 105 bar(416 kg/m3): 69 %. The extracted PFOA was not recovered. | Andreia Farinha; Martijn Van der Kraan; Geert-Jan Witkamp | Chemical Engineering and Industrial Chemistry; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67680f8d81d2151a0294a340/original/removal-of-pfoa-perfluorooctanoic-acid-from-water-using-supercritical-carbon-dioxide.pdf |
66a9fe75c9c6a5c07a959d88 | 10.26434/chemrxiv-2024-bqs8z | Visible-Light-Induced Desulfurative Coupling of Alkyl Benzothiazolyl Sulfides with Electron-Deficient Alkenes/Alkynes: Dual Role of Base-Activated Hantzsch Ester | Hantzsch ester is a widely used organic reductant. We describe a new use of this classical reductant in visible-light-induced desulfurative coupling of alkyl benzothiazolyl sulfides with electron-deficient alkenes/alkynes through activation with base additives. The C(sp3)-S scission has been achieved in two independent ways, catalyst-free Hantzsch ester anion-mediated reaction and organo-photocatalysis. The synthetic utility is illustrated with several examples of the derivatization of natural products including monosaccharides. The mechanistic investigation has revealed that Hantzsch ester anion works as a photoreductant in the catalyst-free reaction, whereas it is included as a sacrificial reductant in the organo-photocatalysis. | Tetsuya Sengoku; Koki Matsune; Takuma Shimotori; Nagisa Kikuchi; Haruto Hijikata; Shun Nishioka; Reo Takahashi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a9fe75c9c6a5c07a959d88/original/visible-light-induced-desulfurative-coupling-of-alkyl-benzothiazolyl-sulfides-with-electron-deficient-alkenes-alkynes-dual-role-of-base-activated-hantzsch-ester.pdf |
663a0c58418a5379b0a9220c | 10.26434/chemrxiv-2024-9w7hc | A Sterol Panel for Multiple Rare Lipid Disorders: Validation and Application for Sitosterolemia, Cerebrotendinous Xanthomatosis and Smith-Lemli-Opitz Syndome | BACKGROUND.
Disease-specific sterols accumulate in the blood of patients with several rare lipid disorders. Biochemical measurement of these sterols is important for correct diagnosis and sometimes monitoration of treatment. Existing methods to measure sterols in blood, particularly plant sterols, are often laborious and time consuming. Partly as a result, clinical access to sterol measurements are limited in many parts of the world.
METHODS.
A simple and rapid method to extract free sterols from human serum and quantitate their concentration using isotope-dilution liquid chromatography tandem mass spectrometry (LC-MS/MS) without derivatization was developed. The method was designed to be “compatible” with routine workflows (eg. 96-well format) in a clinical lab and was extensively validated. Serum from 73 controls were analyzed and used to estimate the upper reference limits for sitosterol, campesterol, stigmasterol, desmosterol, 7-dehydrocholesterol (7DHC), lathosterol and cholestanol. Serum from patients with the rare lipid disorders sitosterolemia (n=7), Smith-Lemli-Optiz syndrome (SLOS; n=1) and cerebrotendinous xanthomatosis (CTX; n=1) were analyzed.
RESULTS.
All seven sitosterolemia patients were measured to have greatly elevated levels of free plant sterols (sitosterol, campesterol and stigmasterol) compared to the controls. The SLOS serum contained massively increased concentrations of 7DHC and an unidentified compound (likely 8-dehydrocholesterol). CTX serum contained greatly increased concentrations of cholestanol, as well as 7DHC and lathosterol. Spiking experiments indicated that the method is likely also useful in the diagnosis of desmosterolosis and lathosterolosis.
CONCLUSION.
The reported method is a relatively simple and fast method capable of quantitating diagnostically important sterols and differentiating patients with several rare lipid disorders from controls.
| Alexander Bauer Westbye; Lili L Dizdarevic; Sandra R Dahl; Emil Andreas Asprusten; Yngve Thomas Bliksrud; Per M Thorsby; Kjetil Retterstøl | Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663a0c58418a5379b0a9220c/original/a-sterol-panel-for-multiple-rare-lipid-disorders-validation-and-application-for-sitosterolemia-cerebrotendinous-xanthomatosis-and-smith-lemli-opitz-syndome.pdf |
61136dd1abc9e2076f6af2b5 | 10.26434/chemrxiv-2021-4bkvh | Computational investigation on natural quinazoline alkaloids as potential inhibitors of the main protease (Mpro) of SARS_CoV_2 | Drug discovery is still behind in the race compared to vaccine discovery in fighting COVID-19. Recently, a few alkaloids from a traditional Indian medicinal plant, Vasaka (Justicia adhatoda), have been linked computationally to the main protease (Mpro) of SARS_CoV_2. To expand the knowledge and for further investigation, we have selected 41 quinazoline alkaloids from two natural product databases to create an adequate library and performed detailed computational studies against the main protease (Mpro) of SARS_CoV_2. The screening of the library was carried out through blending the rigid docking and pharmacokinetic analysis that resulted in nine alkaloids as initial leads against Mpro. These nine alkaloids were further subjected to advance flexible docking using first reference famotidine for the analysis of structure-based interactions. For further selection, a second screening was carried out based on binding energies and interaction profiles that yielded three alkaloids namely CNP0416047, 3-hydroxy anisotine and anisotine as hits. The stereo-electronic features of hit alkaloids were further investigated through additional structure-based E-pharmacophore mapping against a second reference, known X77 ligand. Additionally, the reactivity of hit alkaloids at the binding site of the protein was estimated by measuring the electron distribution on the frontier molecular orbitals and HOMO-LUMO band energies. Finally, the stabilities of complexes between hit alkaloids with the protein were accessed extensively using robust molecular dynamics simulation through RMSD, RMSF, Rg, and MM-PBSA calculation. Thus, this study identifies three natural quinazoline alkaloids as potential inhibitors of MPro through extensive computational analysis. | Deb Ranjan Banerjee; Abhisek Jana; Tarun Roy; Sarbajit Layek; Subhash Ghosal | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2021-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61136dd1abc9e2076f6af2b5/original/computational-investigation-on-natural-quinazoline-alkaloids-as-potential-inhibitors-of-the-main-protease-mpro-of-sars-co-v-2.pdf |
67db04526dde43c908721ab9 | 10.26434/chemrxiv-2023-hp0mt-v2 | Investigating Molybdenum and Tungsten Carbonyls as a Bridge Between Elemental Chalcogens and CO: Formation of COS and Selenium Complexes | Carbonyl sulfide (COS) is implicated in prebiotic chemistry, and recent work on COS/H2S donors has invigorated COS chemistry. We demonstrate that [TpM(CO)3]- (M=Mo,W) react with S8 to form COS, but form [TpW(CO)2]2Se3 not COSe upon reaction with Se. These results advance the metal-mediated interconnectivity of CO and reactive S/Se species. | Tobias Sherbow; Haley Smith; Keyan Li; Lev Zakharov; Michael Pluth | Inorganic Chemistry; Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67db04526dde43c908721ab9/original/investigating-molybdenum-and-tungsten-carbonyls-as-a-bridge-between-elemental-chalcogens-and-co-formation-of-cos-and-selenium-complexes.pdf |
60c741a3bdbb89a96aa3838c | 10.26434/chemrxiv.8068793.v1 | Assessing Many-Body Effects of Water Self-Ions. II: H3O+(H2O)n Clusters | <div>
<div>
<div>
<p>The importance of many-body effects in the hydration of the hydronium ion (H3O+) is
investigated through a systematic analysis of the many-body expansion of the interaction energy carried out at the coupled cluster level of theory for the low-lying isomers
of H3O+(H2O)n clusters with n = 1 − 5. This is accomplished by partitioning individual fragments extracted from the whole clusters into “groups” that are classified by
both the number of H3O+ and water molecules and the H-bonding connectivity within
a given fragment. Effects due to the presence of the Zundel ion, (H5O2)+, are analyzed by further partitioning fragment groups by the “context” of their parent clusters.
With the aid of the absolutely localized molecular orbital energy decomposition analysis
(ALMO EDA), this structure-based partitioning is found to largely correlate with the
character of different many-body interactions, such as cooperative and anticooperative hydrogen-bonding, within each fragment. This analysis emphasizes the importance of
a many-body representation of inductive electrostatics and charge transfer in modeling
the hydration of an excess proton in water. The comparison between the reference coupled cluster many-body interaction terms with the corresponding values obtained with
various exchange-correlation functionals demonstrates that many of these functionals
yield an unbalanced treatment of the H3O+(H2O)n configuration space. </p>
</div>
</div>
</div> | Colin K. Egan; Paesani Lab | Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a3bdbb89a96aa3838c/original/assessing-many-body-effects-of-water-self-ions-ii-h3o-h2o-n-clusters.pdf |
66a12ef5c9c6a5c07ac8372c | 10.26434/chemrxiv-2024-j10kv | Non-concerted Alkyne Insertion in Au(I) Acetylides: Influence of the Nuclearity | The reaction between NHC-supported (NHC = N-heterocyclic carbene) gold(I) trimethylsilylacetylide complexes with NHC gold(I) hydroxide species renders different symmetrical homobimetallic Au complexes. These compounds readily undergo migratory insertion of DMAD (dimethyl acetylenedicarboxylate) at 25 °C to give the corresponding bimetallic enyne products. On the contrary, monometallic analogues require much more forcing reaction conditions (excess of DMAD and temperature ≥ 110 °C) to give the same transformation. Experimental and computational studies reveal that the second metal fragment is responsible for the enhanced nucleophilicity of the reactive carbon atom of the acetylide C≡C bond, which initially leads to a more favorable interaction with DMAD in the rate-determining step of an unprecedented, non-concerted mechanism where the lability of the Au−C bonds plays an instrumental role. | Juan Cayuela-Castillo; Francisco José Fernández-de-Córdova; Israel Fernández; Pablo Rios | Inorganic Chemistry; Organometallic Chemistry; Bonding; Kinetics and Mechanism - Inorganic Reactions; Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a12ef5c9c6a5c07ac8372c/original/non-concerted-alkyne-insertion-in-au-i-acetylides-influence-of-the-nuclearity.pdf |
6674f09d01103d79c5bd4afe | 10.26434/chemrxiv-2024-0jf0s | Top-down mass spectrometry analysis of capsid proteins of recombinant adeno-associated virus using multiple ion activations and proton transfer charge reduction | Adeno-associated viruses are common vectors for emerging gene therapies due to their lack of pathogenicity in humans. Here, we present our investigation of the viral proteins (i.e., VP1, VP2, and VP3) of the capsid of adeno-associated viruses via top-down mass spectrometry. These proteins, ranging from 59 kDa to 81 kDa, were chromatographically separated using hydrophilic interaction liquid chromatography and characterized in the gas-phase by high-resolution Orbitrap Fourier transform mass spectrometry. Complementary ion dissociation methods were utilized to improve the overall sequence coverage. By reducing the overlap of product ion signals via proton transfer charge reduction on the Orbitrap Ascend BioPharma Tribrid mass spectrometer, the sequence coverage of each VP was significantly increased, reaching up to ~40% in the case of VP3. These results showcase the improvements in the sequencing of proteins >30 kDa that can be achieved by manipulating product ions via gas-phase reactions to obtain easy-to-interpret fragmentation mass spectra. | Jake Kline; Jingjing Huang; Linda Lieu; Kristina Srzentić; David Bergen; Christopher Mullen; Graeme McAlister; Kenneth Durbin; Rafael Melani; Luca Fornelli | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6674f09d01103d79c5bd4afe/original/top-down-mass-spectrometry-analysis-of-capsid-proteins-of-recombinant-adeno-associated-virus-using-multiple-ion-activations-and-proton-transfer-charge-reduction.pdf |
62756f5f809e323ec585d80f | 10.26434/chemrxiv-2022-s9gq1 | Review of Technical Criteria for High-Impact Battery Applications with Examples of Industry Performance | Six technical criteria { cell-level specific energy, cell-level specific power, cycle life, affordability, safety, and storage characteristics { are defined and discussed as applied to six high-impact battery applications: Electric vehicles, renewable energy, consumer electronics, unmanned aerial vehicles (UAV), medical, and military batteries. Sub-applications, additional criteria, and other applications are briefly discussed. Strengths and weaknesses of commercial and start-up technologies such as Panasonic nickel cobalt rechargeable (NCR), Altairnano lithium-titanate (LTO), Venom lithium-polymer (LiPo), Oxis Energy lithium-sulfur (Li-S), Polyplus lithium-oxygen (Li-O2), and Sion Power lithium-metal (Li-metal) batteries are given. | Sterling Baird | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62756f5f809e323ec585d80f/original/review-of-technical-criteria-for-high-impact-battery-applications-with-examples-of-industry-performance.pdf |
667a7e6201103d79c514256d | 10.26434/chemrxiv-2024-7c846 | Efficient and scalable H2S treated nickel foam electrocatalyst for alkaline water electrolysis under industrial conditions | Development of facile synthesis methods for efficient electrocatalysts plays a crucial role in improving the overall efficiency of alkaline water electrolysis. Here we explore a synthesis route using H2S gas to enhance the efficiency of nickel foam electrocatalysts. A uniform film consisting of distinctive nanostructures was successfully grown on the surface of nickel foam by sulfiding at 95-145 °C in 3 % H2S/Ar for 1-17 hours. Electrochemical performance tests under industrial relevant conditions with 30 wt% KOH at 85 °C tested at 200-500 mA cm-2 for up to two weeks, showed a reduction in cell voltage up to 0.4 V for modified electrodes, corresponding to 18% higher efficiency for overall water splitting, as compared to pristine nickel foam. Surface area analysis showed a 30-fold increase of the surface area following H2S treatment. Structural and compositional analyses of the modified nickel foam electrodes were conducted using X-Ray Photoelectron Spectroscopy (XPS), Scanning Electron Microscopy (SEM), Energy Dispersive X-Rays (EDX) analysis and synchrotron powder X-ray diffraction (XRD). The analysis revealed the presence of Ni3S2 with a film thickness of 1-4 μm after H2S treatment. Extended reaction times showed continuous reaction and the emergence of NiS. All analyses were performed before and after alkaline water electrolysis. Post-electrolysis characterizations indicated either the absence or minimal presence of sulfur. This suggests that the enhanced performance is likely not attributed to sulfur catalytic activity but rather to alterations in the surface morphology of the nickel foam. | Soffi Olesen; Anders W. Jensen; Magnus Kløve; Filippo Fenini; Jesper Nissen; Bo Iversen; Anders Bentien; Lars Pleth Nielsen | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667a7e6201103d79c514256d/original/efficient-and-scalable-h2s-treated-nickel-foam-electrocatalyst-for-alkaline-water-electrolysis-under-industrial-conditions.pdf |
62a46358804dbee2b041dcd6 | 10.26434/chemrxiv-2022-8v4h3 | Systematic analysis of the nitrogen adsorption-desorption isotherms recorded for a series of microporous – mesoporous amorphous aluminosilicates using classical methods | Understanding the porous structure of microporous – mesoporous materials is very important for developing useful scientific concepts and principles in materials science, surface science, heterogeneous catalysis, adsorption and related technological applications. Amorphous aluminosilicates are of particular interest in this sense because it is relatively simple to design them with diverse porous structures comprising micro, meso, and even macropores. In this work, we took advantage of the latter and developed a systematic and in-depth analysis of the results of nitrogen physisorption tests at 77 K performed over a series of microporous – mesoporous amorphous aluminosilicates and of the characterization of their texture by classical models to estimate surface area and porosity. The strategy for the analysis consisted of making a thorough description of the features showed by the recorded nitrogen isotherms, first. As a result, a proposal for considering two new types of isotherms, types I(c) and IV(c), and five new types of hysteresis loops, H1(b), H2(c), H3(b), H3(c), and H4(b), in addition to the standard IUPAC classification. These new categories stemmed from the microporous – mesoporous nature of the materials and from the presence of strong network effects. The previous analysis helped interpreting and judging the results of the calculations made with classical methods to assess the texture of the materials; namely, their BET surface area, t-plot microporosity, BJH mesopore size distribution, and fractal dimension. The performed analyses allowed establishing that the relative percentage of microporosity of the materials can be correlated to the physisorption energy as described qualitatively by the CBET constant. Concerning mesopore size distributions, it was found that the BJH method remains to be very valuable for describing the porous structure of the materials particularly if the results obtained with both branches of the isotherms are considered. Finally, it was shown that the fractal dimension can complement the analysis of the porous structure of microporous – mesoporous materials if the latter are compared considering the features of their isotherms and of their hysteresis loops. Overall, the present study can thus be said to make two contributions: (i) it proposes a systematic methodology for analyzing both the raw data and the textural properties calculated by classical methods both derived from nitrogen physisorption experiments. (ii) It presents useful new insights on the texture of microporous – mesoporous materials. | Víctor Gabriel Baldovino Medrano; Viviana Niño Celis; Rafael Isaacs Giraldo | Materials Science; Inorganic Chemistry; Catalysis; Catalysts; Nanostructured Materials - Materials; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a46358804dbee2b041dcd6/original/systematic-analysis-of-the-nitrogen-adsorption-desorption-isotherms-recorded-for-a-series-of-microporous-mesoporous-amorphous-aluminosilicates-using-classical-methods.pdf |
6166a5d22aca530c9262214d | 10.26434/chemrxiv-2021-v1w7s | Microfluidic oxygen tolerability screening of nanocarriers for triplet
fusion photon upconversion | The full potential of triplet fusion photon upconversion (TF-UC) of providing high-energy photons locally with low-energy
excitation is limited in biomedicine and life sciences by its oxygen sensitivity. This hampers the applicability of TF-UC systems in
sensors, imaging, optogenetics and drug release. Despite the advances in improving the oxygen tolerability of TF-UC systems,
the evaluation of oxygen tolerability is based on comparing the performance at completely deoxygenated (0 % oxygen) and
ambient (20–21 %) conditions, leaving the physiological oxygen levels (0.3–13.5 %) neglected. This oversight is not deliberate
and is only the result of the lack of simple and predictable methods to obtain and maintain these physiological oxygen levels in
an optical setup. Herein, we demonstrate the use of microfluidic chips made of oxygen depleting materials to study the oxygen
tolerability of four different micellar nanocarriers made of FDA-approved materials with various oxygen scavenging capabilities
by screening their TF-UC performance over physiological oxygen levels. All nanocarriers were capable of efficient TF-UC even
in ambient conditions. However, utilizing oxygen scavengers in the oil phase of the nanocarrier improves the oxygen tolerability
considerably. For example, at the mean tumour oxygen level (1.4 %), nanocarriers made of surfactants and oil phase both
capable of oxygen scavenging retained remarkably 80 % of their TF-UC emission. This microfluidic concept enables faster,
simpler and more realistic evaluation of, not only TF-UC, but any micro or nanoscale oxygen-sensitive system and facilitates
their development and implementation in biomedical and life science applications. | Jussi Isokuortti; Iiro Kiiski; Tiina Sikanen; Nikita Durandin; Timo Laaksonen | Physical Chemistry; Nanoscience; Nanodevices; Photochemistry (Physical Chem.); Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6166a5d22aca530c9262214d/original/microfluidic-oxygen-tolerability-screening-of-nanocarriers-for-triplet-fusion-photon-upconversion.pdf |
60c7418b337d6c3c35e268ef | 10.26434/chemrxiv.8063042.v1 | Phase & Morphology Engineered Surface Reducibility of MnO2 Nano-heterostructures: Implications on Catalytic Activity Towards CO Oxidation | This work addresses two vital aspects of catalytic nanohybrids viz., a chemistry-based
control of crystallographic phase/ morphology that serves as a handle for engineering
the surface reducibility and correlating the catalytic activity to the reducibility.
We would like to emphasize that the material addressed in this paper is an
earth-abundant oxide MnO<sub>2</sub>, much favorable for practical applications
in terms of cost and availability. | Noopur Jain; ahin roy | Catalysts; Nanostructured Materials - Materials; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7418b337d6c3c35e268ef/original/phase-morphology-engineered-surface-reducibility-of-mn-o2-nano-heterostructures-implications-on-catalytic-activity-towards-co-oxidation.pdf |
62f6a05818037306a7a35c4f | 10.26434/chemrxiv-2022-l269j | Insight into ortho-boronoaldehyde conjugation via a FRET-based reporter assay | Ortho-boronoaldehydes react with amine-based nucleophiles with dramatically increased rates and product stabilities, relative to unfunctionalised benzaldehydes, leading to exciting applications across biological and material chemistry. We have developed a novel Förster resonance energy transfer (FRET)-based assay to provide key new insights into the reactivity of these boronoaldehydes, allowing us to track conjugation with unprecedented sensitivity and accuracy under standardised conditions. Our results highlight the key role played by reaction pH, buffer additives, and boronoaldehyde structure in controlling conjugation speed and stability, providing design criteria for further innovations and applications in the field. | Nicholas Rose; Eve Tipple; Anais Sanchez; Jason Lynam; Christopher Spicer | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f6a05818037306a7a35c4f/original/insight-into-ortho-boronoaldehyde-conjugation-via-a-fret-based-reporter-assay.pdf |
6656dbaf21291e5d1d8714ff | 10.26434/chemrxiv-2024-3gdw8 | Probing High-Order Transient Oligomers using Ion Mobility Mass Spectrometry coupled to Infrared Action Spectroscopy | Understanding and controlling peptide aggregation is critical due to its neurotoxic implications. However, structural information on the key intermediates, the oligomers, is obscured by a cascade of coinciding events occurring at various time and energy scales, which results in complex and heterogeneous mixtures of oligomers. To address this challenge, we have developed the Photo-Synapt, a novel, multidimensional spectrometer that integrates ion mobility mass spec-trometry with infrared (IR) action spectroscopy within a single experiment. By combining three different, orthogonal analytical dimensions, we can select and isolate individual oligomers by mass, charge, size and shape and provide a unique molecular fingerprint for each oligomer. The broad application of this technology is demonstrated by its ap-plication to oligosaccharide analysis from glycoproteins, which are challenging to analyze due to the minute differ-ences between isomers. By integrating infrared action spectroscopy with ion mobility mass spectrometry, this approach adds an analytical dimension that effectively addresses this limitation, offering a unique molecular finger-print for each isomer. | Sjors Bakels; Steven Daly; Berk Doğan; Melissa Baerenfaenger; Jan Commandeur; Anouk Rijs | Physical Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6656dbaf21291e5d1d8714ff/original/probing-high-order-transient-oligomers-using-ion-mobility-mass-spectrometry-coupled-to-infrared-action-spectroscopy.pdf |
60c74c284c8919a97cad35ba | 10.26434/chemrxiv.12440012.v1 | 1- and 2-Photon Phototherapeutic Effects of Ru(II) Polypyridine Complexes in the Hypoxic Centre of Large Multicellular Tumour Spheroids and Tumour-Bearing Mice | During
the last decades, photodynamic therapy (PDT), an approved medical
technique, has received increasing attention to treat certain types of
cancer. Despite recent improvements, the treatment of large tumors
remains a major clinical challenge due to the low ability of the
photosensitizer (PS) to penetrate a 3D cellular architecture and the low
oxygen concentrations present in the tumour centre. To mimic the
conditions found in clinical tumors, exceptionally large 3D
multicellular tumour spheroids (MCTSs) with a diameter of 800 µm were
used in this work to test a series of new Ru(II) polypyridine complexes
as 1-Photon and 2-Photon PSs. These metal complexes were found to fully
penetrate the 3D cellular architecture and to generate singlet oxygen in
the hypoxic centre upon light irradiation. While having no observed
dark toxicity, the lead compound of this study showed an impressive
phototoxicity upon clinically relevant 1-Photon (595 nm) or 2-Photon
(800 nm) excitation with a full eradication of the hypoxic centre of the
MCTSs. Importantly, this efficacy was also demonstrated on mice bearing
an adenocarcinomic human alveolar basal epithelial tumour. | Johannes Karges; Shi Kuang; Yih Ching Ong; Hui Chao; Gilles Gasser | Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c284c8919a97cad35ba/original/1-and-2-photon-phototherapeutic-effects-of-ru-ii-polypyridine-complexes-in-the-hypoxic-centre-of-large-multicellular-tumour-spheroids-and-tumour-bearing-mice.pdf |
60c753240f50db637c397b01 | 10.26434/chemrxiv.13382069.v1 | Computational Study of Inverted All-Inorganic Perovskite Solar Cells Based on CsPbIxBr3-X Absorber Layer with Band Gap of 1.78 eV | All-inorganic perovskite solar cells (PSCs) with inverted p-i-n configuration have not yet reached the high efficiency achieved in the normal n-i-p architecture. However, the inverted all-inorganic PSC are more compatible with the fabrication of tandem solar cells. In this work, a theoretical study of all-inorganic PSCs with inverted structure ITO/HTL/CsPbI<sub>x</sub>Br<sub>3</sub>−x/ETL/Ag, has been performed by means of computer simulation. Four p‐type inorganic materials (NiO, Cu<sub>2</sub>O, CuSCN and CuI) and three n-type inorganic materials (ZnO, TiO<sub>2</sub> and SnO<sub>2</sub>) were used as hole and electron transport layers (HTL and ETL), respectively. A band gap of 1.78 eV was used for the CsPbI x Br<sub>3</sub>−x perovskite layer. The simulation results allow identifying that CuI and ZnO are the most appropriate materials as HTL and ETL, respectively. Additionally, optimized values of thickness, acceptor density and defect density in the absorber layer have been obtained for the ITO/CuI/CsPbI x Br<sub>3</sub>−x /ZnO/Ag, from which, an optimum efficiency of 21.82% was achieved. These promising theoretical results aim to improve the manufacturing process of inverted all-inorganic PSCs and to enhance the performance of perovskite–perovskite tandem solar cells. <br /> | Nahuel Martínez; Carlos Pinzón; Guillermo Casas; Fernando Alvira; Marcelo Cappelletti | Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753240f50db637c397b01/original/computational-study-of-inverted-all-inorganic-perovskite-solar-cells-based-on-cs-pb-ix-br3-x-absorber-layer-with-band-gap-of-1-78-e-v.pdf |
60c7555d337d6c1096e28bf0 | 10.26434/chemrxiv.14043881.v1 | Bethe-Salpeter Study of the Optical Absorption of trans and cis Azobenzene-Functionalized Metal-Organic Frameworks using Molecular and Periodic Models | The optical absorption spectra of the azobenzene-functionalized metal-organic framework, PCN-123, are calculated in cis and trans configurations using the Bethe-Salpeter equation (BSE) formalism and the GW approximation using periodic and non-periodic models. In the visible, near-UV and mid-UV region the optical excitations in the MOF are associated with the azobenzene functionalities and this results in spectral features similar to the case of the gas phase azobenzene and the azo-functionalized ligand. The most noticeable difference is the significantly more intense S<sub>1</sub> band for cis in the MOF as compared to the free molecules which points to a faster and more complete cis→trans isomerization in the framework, with strong implications for the design of MOFs with high photoconversion efficiencies. Consistent with these findings, all the molecular models employed to represent the MOF, including the smallest, are found to yield a reasonable description of the low energy optical spectra (between 2 and 5 eV) of the periodic framework, with the exception of the stronger S<sub>1</sub> band of cis in the MOF, a feature that we attribute to a limitation of the fragment model to correctly represent the wavefunction of the extended framework. | Aseem Rajan Kshirsagar; Claudio Attaccalite; Xavier Blase; Jing Li; Roberta Poloni | Hybrid Organic-Inorganic Materials; Optical Materials; Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Physical and Chemical Properties; Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7555d337d6c1096e28bf0/original/bethe-salpeter-study-of-the-optical-absorption-of-trans-and-cis-azobenzene-functionalized-metal-organic-frameworks-using-molecular-and-periodic-models.pdf |
64af9df76e1c4c986b510a3a | 10.26434/chemrxiv-2023-bf887 | On the mechanism of the peroxide epoxidation of olefins: A bond interaction perspective | A new picture of the reaction mechanism of peracid epoxidation of olefins is proposed from the perspective of bond interaction. In contrast to the mechanism from the perspective of electronic theory, which includes the movement of an electron from the -bond to the negatively charged oxygen atom, the olefin is initially protonated and then migrates to the oxygen atom. | Yuji Naruse; Takuya Kosugi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64af9df76e1c4c986b510a3a/original/on-the-mechanism-of-the-peroxide-epoxidation-of-olefins-a-bond-interaction-perspective.pdf |
65fb21bbe9ebbb4db9200c48 | 10.26434/chemrxiv-2024-r5qsk | Physicochemical properties, equilibrium adsorption performance, manufacturability, and stability of TIFSIX-3-Ni for direct air capture | The use of adsorbents for direct air capture (DAC) is regarded as a promising and essential carbon dioxide removal technology to help meet the goals outlined by the 2015 Paris Agreement. A class of adsorbents that has gained significant attention for this application is ultramicroporous metal organic frameworks (MOFs). However, the necessary data needed to facilitate process scale evaluation of these materials is not currently available. Here, we investigate TIFSIX-3-Ni, a previously reported ultramicroporous MOF for direct air capture, and measure several physicochemical and equilibrium adsorption properties. We report its crystal structure, textural properties, thermal stability, specific heat capacity, CO2, N2, and H2O equilibrium adsorption isotherms at multiple temperatures, and Ar and O2 isotherms at a single temperature. For CO2, N2, and H2O, we also report isotherm model fitting parameters and calculate heats of adsorption. We assess the manufacturability and process stability of TIFSIX-3-Ni by investigating the impact of batch reproducibility, binderless pelletization, humidity, and adsorption-desorption cycling (50 cycles) on its crystal structure, textural properties, and CO2 adsorption. For pelletized TIFSIX-3-Ni, we also report its skeletal, pellet, and bed density, total pore volume, and pellet porosity. Overall, our data enable initial process modelling and optimization studies to evaluate TIFSIX-3-Ni for DAC at the process scale. They also highlight the possibility to pelletize TIFSIX-3-Ni and the limited stability of the MOF under humid and oxidative conditions as well as upon multiple adsorption-desorption cycles. | May-Yin (Ashlyn) Low; David Danaci; Hassan Azzan; Amanda Lim Jiayi; Gordon Wu Shun Yong; Ioanna Itskou; Camille Petit | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fb21bbe9ebbb4db9200c48/original/physicochemical-properties-equilibrium-adsorption-performance-manufacturability-and-stability-of-tifsix-3-ni-for-direct-air-capture.pdf |
60c74f71842e65ba32db3835 | 10.26434/chemrxiv.12902594.v1 | Paramagnetic 14N MAS NMR without Paramagnetic Shifts: Remarkable Lattice of LaTiO2N and CeTiO2N Oxynitride Perovskites | <sup>14</sup>N magic-angle spinning (MAS) NMR spectra of diamagnetic LaTiO<sub>2</sub>N perovskite oxynitride and its paramag-<br />netic counterpart CeTiO<sub>2</sub>N are presented. The latter, to the<br />best of our knowledge, constitutes the first high-resolution <sup>14</sup>N MAS NMR spectrum collected from paramagnetic solid material. Induced paramagnetic <sup>14</sup>N NMR shift due to unpaired 4<i>f</i> -electrons in CeTiO<sub>2</sub>N is non-existent, which is remarkable given the severe paramagnetic effects on surface proton species revealed by <sup>1</sup>H NMR, and direct Ce−N contacts in the structure. <i>Ab initio</i> molecular orbital calculations predict substantial Ce→<sup>14</sup>N contact shift interaction under these circumstances, therefore, cannot explain the unprecedented <sup>14</sup>N NMR spectrum of CeTiO<sub>2</sub>N. | Zili Ma; Richard Dronskowski; Adam Slabon; Aleksander Jaworski | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f71842e65ba32db3835/original/paramagnetic-14n-mas-nmr-without-paramagnetic-shifts-remarkable-lattice-of-la-ti-o2n-and-ce-ti-o2n-oxynitride-perovskites.pdf |
60c752409abda25801f8dda4 | 10.26434/chemrxiv.13274543.v1 | In Situ Generation of Radical Initiators: Air Stable Amine-Borane Complexes Promote Atom Transfer Radical Additions of Alkyl Halides to Alkenes | Despite their instability, carbon-centered radicals have been involved as intermediates in
many organic transformations that are essential to mankind. Radical polymerization,1-5
for
example, provides a large part of polyacrylates and polystyrenes used as commodities in our
everyday life. On a molecular level, the outcome of radical-mediated reactions is usually very
different from those obtained via classical ionic based organic reactions. This is known since
the 1930’s6
and has witnessed extensive developments such as radical cyclization or Atom
Transfer Radical Additions (ATRA)7-9
. Radical processes10 typically begin with an initiation
step in which the first radical species is created. It is eventually followed by one or several
transfer steps which ultimately conduct to the formation of the main radical intermediate
responsible for the reaction. The propagation steps of the radical chain are a succession of
radical based transformations which, combined, outline the expected transformation. | Virginie Liautard; Marine Delgado; Boris Colin; Laurent Chabaud; Guillaume Michaud; Mathieu Pucheault | Organic Synthesis and Reactions; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752409abda25801f8dda4/original/in-situ-generation-of-radical-initiators-air-stable-amine-borane-complexes-promote-atom-transfer-radical-additions-of-alkyl-halides-to-alkenes.pdf |
60c74682bdbb899d0ea38c0e | 10.26434/chemrxiv.11303606.v1 | Benchmarking the Acceleration of Materials Discovery by Sequential Learning | Sequential learning (SL) strategies, i.e. iteratively updating a ma-chine learning model to guide experiments, have been proposed to significantly accelerate materials discovery and research. Applications on computational datasets and a handful of optimization experiments have demonstrated the promise of SL, motivating a quantitative evaluation of its ability to accelerate materials discovery, specifically in the case of physical experiments. The benchmarking effort in the present work quantifies the performance of SL algorithms with respect to a breadth of research goals: discovery of any "good" material, discovery of all "good" materials, and discovery of a model that accurately predicts the performance of new materials. | Brain Rohr; Helge Stein; Dn Guevarra; Yu Wang; Joel Haber; Muratahan Aykol; Santosh Suram; John Gregoire | Catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74682bdbb899d0ea38c0e/original/benchmarking-the-acceleration-of-materials-discovery-by-sequential-learning.pdf |
637d274d9b5b807394d1d08f | 10.26434/chemrxiv-2022-w3x91-v2 | Multiconfigurational calculations and photodynamics describe norbornadiene photochemistry | Storing solar energy is a vital component of using renewable energy sources to meet the growing demands of the global energy economy. Molecular solar thermal (MOST) energy storage is a promising means to store solar energy with on-demand energy release. The light-induced isomerization reaction of norbornadiene (NBD) to quadricyclane (QC) is of great interest because of the generally high energy storage density (0.97 MJᐧkg–1) and long thermal reversion lifetime (t1/2, 300K = 8346 years). However, the mechanistic details of the ultrafast excited-state [2+2]-cycloaddition is largely unknown due to the limitations of experimental techniques in resolving accurate excited-state molecular structures. We now present a full computational study on the excited-state deactivation mechanism of NBD in the gas phase. Our multiconfigurational calculations [SA6-CASSCF(4,7)/ANO-S-VDZP] and non-adiabatic molecular dynamics simulations have enumerated the possible pathways with 600 S2 initial conditions for 300 fs. The predicted S2 and S1 lifetimes are reported (62 and 221 fs). The QC: NBD formation ratio is 1:5; the predicted quantum yield of QC is 9%, which underscores the potential of NBD for MOST materials. Our simulations also show the mechanisms of forming other possible reaction products and their quantum yields. | Federico Hernandez; Jordan Cox; Jingbai Li; Rachel Crespo-Otero; Steven Lopez | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637d274d9b5b807394d1d08f/original/multiconfigurational-calculations-and-photodynamics-describe-norbornadiene-photochemistry.pdf |
65cb8c8de9ebbb4db946808b | 10.26434/chemrxiv-2024-00cnb | Teaching the Cummins Complex Heterodimerization: Formation of Unorthodox Heteroleptic X3MoMoY3 Dimers with Ultralong Metal-Metal Triple Bonds | Attempts to stabilize mononuclear trigonal-planar Mo(+3) complexes by (tripodal) silanolates or alkoxides, which had recently been shown to synergize exceedingly well with high valent molybdenum or tungsten alkylidynes, afforded unsymmetrical dimolybdenum complexes of the general type [X3MoMoY3]; not only is this ligand pattern unprece-dented, but these dimers incorporate the intact Cummins complex [(tBu)(Ar)N]3Mo (Ar = 3,5-dimethylphenyl), which is famous for not engaging in metal-metal triple bonding otherwise. The remarkable ease of heterodimerization likely reflects a pronounced kinetic selectivity. The new complexes were characterized by crystallographic and spectroscopic means; they show highly deshielded 95Mo NMR signals and comprise unusually long yet robust MoMo bonds | Daniel Rütter; Nils Nöthling; Markus Leutzsch; Alois Fürstner | Inorganic Chemistry; Bonding; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.) | CC BY 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cb8c8de9ebbb4db946808b/original/teaching-the-cummins-complex-heterodimerization-formation-of-unorthodox-heteroleptic-x3mo-mo-y3-dimers-with-ultralong-metal-metal-triple-bonds.pdf |
668660bcc9c6a5c07a3d6879 | 10.26434/chemrxiv-2024-9tcs2 | Water splitting at imine-linked covalent organic frameworks | Covalent organic frameworks (COFs) are a promising class of metal- free catalysts, offering a high structural and functional variety. Here, we systematically study imine-linked COFs with donor (D) and ac- ceptor (A) groups using density functional theory (DFT). Using water splitting as a model reaction, we analyze the effects of protonation of the catalyst, the orientation of the imine linkage leading to differ- ent constitutional isomers, and solvation. In agreement with experi- mental results, we show that protonation decreases the band gap. In addition, COFs in which the donor is closer to the nitrogen atom of the imine group (DNCA) have lower band gaps than those in which the donor is closer to the carbon atom (DCNA). Three different D/A COFs are compared in this work, for which energies for the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) and corresponding electrochemical overpotentials are computed. We show that reaction energies are very similar for DCNA and DNCA COFs. The differences in hydrogen evolution rates between the constitutional isomers observed experimentally in (photocatalytic) HER (Yang et al., Nature Commun. 13, 6317 (2022)), are proposed to be at least in part a consequence of differences in charge distribution. | Felizitas Gottwald; Christopher Penschke; Peter Saalfrank | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Electrocatalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668660bcc9c6a5c07a3d6879/original/water-splitting-at-imine-linked-covalent-organic-frameworks.pdf |
624e2fe0f6c486533913f3ac | 10.26434/chemrxiv-2022-0w3lp | Room Temperature Electrochemical Fluoride (De)Insertion
into the Defect Pyrochlore CsMnFeF6 | We report on the reversible, electrochemical (de)fluorination of the defect fluoride pyrochlore
CsMnFeF6 at room temperature using a liquid electrolyte. CsMnFeF6 was synthesized via three
different methods (hydrothermal, ceramic, and mechanochemical), each of which yield products of
varying particle size and phase purity. Using galvanostatic cycling, we found that after three oxidative/
reductive cycles, approximately one fluoride ion can be reversibly inserted and removed from
mechanochemically synthesized CsMnFeF6 for multiple cycles. Ex-situ X-ray absorption spectroscopy
confirmed that both the Mn2+ and Fe3+ in this composition are redox active during cycling. Electrochemical
impedance spectroscopy and ex-situ synchrotron powder diffraction were utilized to investigate
the delayed onset of significant fluoride (de)insertion. We observed decreased impedance after one
full cycle and subtle expansion and contraction of the CsMnFeF6 cubic lattice on oxidation (insertion)
and reduction (removal), respectively, over the first two cycles. Our results suggest the formation of fluoride
vacancies in early cycles generates mixed-valent Fe that enhances the conductivity and improves
the reversibility in later cycles. | Jessica Andrews; Eric McClure ; Kenneth Jew; Molleigh Preefer ; Ahamed Irshad ; Matthew Lertola ; Daniel Robertson ; Charlene Salamat ; Michael Brady ; Louis Piper ; Sarah Tolbert ; Johanna Nelson Weker ; Brad Chmelka ; Bruce Dunn; Sri Narayan ; William West ; Brent Melot | Materials Science; Inorganic Chemistry; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624e2fe0f6c486533913f3ac/original/room-temperature-electrochemical-fluoride-de-insertion-into-the-defect-pyrochlore-cs-mn-fe-f6.pdf |
63320e98ba8a6d29bb5e201b | 10.26434/chemrxiv-2021-ssfpt-v2 | Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides | Many renewable energy technologies, such as hydrogen gas synthesis and carbon dioxide reduction, rely on chemical reactions involving hydride anions (H-). When selecting molecules to be used in such applications, an important quantity to consider is the thermodynamic hydricity, which is the free energy required for a species to donate a hydride anion. Theoretical calculations of thermodynamic hydricity depend on several parameters, mainly the density functional, basis set, and solvent model. In order to assess the effects of the above three parameters, we carry out hydricity calculations with different combinations of density functionals, basis sets, and solvent models for a set of organic molecules with known experimental hydricity values. The data are analyzed by comparing the R^2 and root-mean-squared error (RMSE) of linear fits with a fixed slope of 1 and using the Akaike Information Criterion (AIC) to determine statistical significance of the RMSE rank ordering. Based on these results, we quantified the accuracy of theoretical predictions of hydricity and found that the best compromise between accuracy and computational cost was obtained by using the B3LYP-D3 density functional for the geometry optimization and free energy corrections, either wB97X-D3 or M06-2X-D3 for single point energy corrections, combined with a basis set no larger than def-TZVP and the C-PCM ISWIG solvation model. At this level of theory, the RMSE of hydricity calculations for organic molecules in acetonitrile and DMSO were found to be <4 kcal/mol and <10 kcal/mol respectively for an experimental data set with a dynamic range of 20-150 kcal/mol. | Christina Yeo; Minh Nguyen; Lee-Ping Wang | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63320e98ba8a6d29bb5e201b/original/benchmarking-density-functionals-basis-sets-and-solvent-models-in-predicting-thermodynamic-hydricities-of-organic-hydrides.pdf |
60c9b9951fd53323cc56ac23 | 10.26434/chemrxiv.11984427.v3 | An Octanol Hinge Opens the Door to Water Transport | Despite prevalent use as a surrogate for partitioning of pharmacologically active and natural products across lipid membranes, the mechanism of solute transport across water/octanol phase boundaries remains unexplored. Using classical molecular dynamics with uniquely benchmarked forcefields, graph theoretical and cluster analysis, and Langevin dynamics, we reveal an elegant mechanism for the transport of the simplest solute, water. At equilibrium, small groups of octanol at the instantaneous interface bind water and swing like hinge of a door to bring water into a semi-organized second interfacial layer (octanol ``bilayer islands"), where water can then diffuse into bulk octanol or be returned to the aqueous phase. The fundamental forces, collective, and reversible behavior, is well-described by a double well potential energy function, satisfying the basic principles of a simple molecular machine for solute transport. Unlike other transporting machines, this example leverages the interfacial surface fluctuations rather than circumventing them, imparting new design principles for hierarchically organized structures that transport solutes across liquid/liquid phase boundaries. | Zhu Liu; Aurora Clark | Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9b9951fd53323cc56ac23/original/an-octanol-hinge-opens-the-door-to-water-transport.pdf |
672d4f867be152b1d0632ca3 | 10.26434/chemrxiv-2024-87xr8 | Computing Ligand Binding Free Energy in a Large Flexible Pocket of a Large Protein | Protein-ligand standard binding free energy (SBFE) calculations based on molecular dynamics simulations have recently emerged as an efficient tool for computer-aided drug design. However, the majority of studies have focused on well-defined ligand binding pockets in small proteins, while computing SBFE of a small molecule ligand to a large, flexible binding site remains problematic. Numerous proteins with large flexible binding pockets play an important role in biological processes and are of pharmaceutical importance. Therefore, the calculation of the ligand SBFE with such proteins is an important challenge. In this work, we developed a hierarchical approach to compute SBFE of a flexible multi-conformational system as an ensemble average of individual local SBFEs to specific conformational states of the protein-ligand complex. This approach allows us to simulate a truncated portion of a large protein, which brings an intractable system within the reach of modern computational tools. Our approach also accounts for the differences in conformational preferences between a ligand-bound and an apo states of the protein. The approach is validated using the T4 lysozyme mutant in complex with a small molecule inhibitor. Binding energies of a non-competitive antagonist (GYKI) with the GluA2 glutamate receptor of AMPA type (AMPAR) are computed for several poses of GYKI in the binding pocket to help facilitate structure validation at relatively low resolution. | Evgeny Gutkin; Chamali Narangoda; Maria Kurnikova | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672d4f867be152b1d0632ca3/original/computing-ligand-binding-free-energy-in-a-large-flexible-pocket-of-a-large-protein.pdf |
671787acd433919392d53da7 | 10.26434/chemrxiv-2024-5tsv7 | Controlled Chain-Growth Polymerization via Propargyl/Allenyl Palladium Intermediates | In contrast to allyl palladium complexes, propargylic/allenylic palladium speicies display complex reactivities that limit their implementation in polymer chemistry, especially for chain-growth polymerizations. Here we report the the first example of controlled chain-growth polymerization via propargyl/allenyl palladium intermediates. Vinylidenecyclopropane 1,1-dicarboxylate (VDCP), a unique allenylic electrophile, selectively reacts via the sigma-allenyl palladium complex rather than the more common pi-propargyl pathway, thereby unlocking a chain-growth process. Based on this concept, precise synthesis of alkyne-backbone polymers is realized, featuring fast rate, high molecular weight, narrow dispersity, high chemoselectivity, and excellent end-group fidelity. We demonstrate preparation of unsaturated macromolecules with advanced sequences and architectures using this method, including block, gradient, and graft copolymers. | Zheng-Lin Wang; Rong Zhu | Organometallic Chemistry; Polymer Science; Polymerization (Polymers); Polymerization (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671787acd433919392d53da7/original/controlled-chain-growth-polymerization-via-propargyl-allenyl-palladium-intermediates.pdf |
62037d5c2168670599706b56 | 10.26434/chemrxiv-2022-4dbqm | Synthesis of alpha,gamma-Chiral Trifluoromethylated Amines through the Stereospecific Isomerization of alpha-Chiral Allylic Amines | Chiral gamma-branched aliphatic amines are present in a large number of pharmaceuticals and natural products. However, enanti-oselective methods to access these compounds are scarce, and rely on the use of designed chiral transition-metal complexes. Herein, we have combined an organocatalytic method for the stereospecific isomerization of chiral allylic amines with a dia-stereoselective reduction of the chiral imine/enamine intermediates, leading to gamma-trifluoromethylated aliphatic amines with two noncontiguous stereogenic centers, in excellent yields and with high diastereo- and enantioselectivities. This approach has been used with primary amine substrates. Additionally, a gram-scale reaction demonstrates the applicability of this syn-thetic procedure. | Victor García-Vázquez; Pablo Martínez-Pardo; Alexandru Postole; A. Ken Inge; Belén Martín-Matute | Catalysis; Base Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2022-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62037d5c2168670599706b56/original/synthesis-of-alpha-gamma-chiral-trifluoromethylated-amines-through-the-stereospecific-isomerization-of-alpha-chiral-allylic-amines.pdf |
669e64b75101a2ffa894951f | 10.26434/chemrxiv-2024-qv3n6 | A water playground for re-assembly from fibrils to plates | Short-peptide amyloid assembly and disassembly play crucial roles in various research fields, which range from addressing pathologies that lack therapeutic solutions to the development of innovative soft (bio)materials. Hydrogels from short peptides typically show thermo-reversible gel-to-sol transition, whereby fibrils disassemble upon heating, and re-assemble upon cooling down to room temperature (rt). Despite ongoing intense research studies in this area, the majority focus on peptide-peptide interaction and neglect the structuring role of water in peptide supramolecular behavior. This study describes an unprotected tetrapeptide gelator that forms highly stable fibrils which, upon heating, re-organize into plates that persist upon cooling to rt. All-atom molecular dynamics (MD) simulations and experimental methods reveal water as a key player in the thermodynamics that accompany this irreversible morphological transition, and advance our understanding of supramolecular structures. | Simone Adorinni; Marina Kurbasic; Ana Maria Garcia; Slavko Kralj; Ottavia Bellotto; Erica Scarel; Paolo Pengo; Rita De Zorzi; Michele Melchionna; Attilio Vargiu; Silvia Marchesan | Materials Science; Nanoscience; Aggregates and Assemblies; Biocompatible Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e64b75101a2ffa894951f/original/a-water-playground-for-re-assembly-from-fibrils-to-plates.pdf |
60c740c7f96a005b0128632b | 10.26434/chemrxiv.7832177.v1 | Ultrafast Relaxation Dynamics of the S1 (nπ*) State and the 3p and 3d Rydberg States in Cyclohexanone by Femtosecond Photoelectron Imaging | <div>The radiationless decay dynamics of the S1 (nπ*) state and the 3p and 3d Rydberg states of cyclohexanone are investigated using femtosecond time-resolved time-of- flight mass spectrometry and photoelectron imaging spectroscopy. After two-photon excitation of the 3p and 3d states, an ultrafast population transfer to the 3s state is observed within < 120 fs. We ascribe this behavior to strong vibronic interactions of the excited Rydberg states with the <sup>1</sup>ππ* valence state that enable an ultrafast population transfer via an avoided crossing and the subsequent passage of a conical intersection between the respective electronic states. Eventually, the 3s state deactivates by internal conversion to the S<sub>1</sub> (nπ*) state, which in turn is found to be long-lived with a decay time of ~ 300 - 800 ps.</div> | Ole Hüter; Niklas Helle; Friedrich Temps | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740c7f96a005b0128632b/original/ultrafast-relaxation-dynamics-of-the-s1-n-state-and-the-3p-and-3d-rydberg-states-in-cyclohexanone-by-femtosecond-photoelectron-imaging.pdf |
60c74be9702a9b15a318b56e | 10.26434/chemrxiv.12278360.v2 | Exhibitive Nano-to-Micron Scale Sedimentation Dynamics of Colloidal Formulations Through Direct Visualization | The study of sedimentation behavior of nanoparticle dispersions
is important for revealing particle size and colloidal stability characteristics.
Quantitative appraisal of real-world colloidal systems in their native state,
is key for replacing prevailing empiricism in formulation science by
knowledge-based design. Herein, we choose fuel cell inks as one case-example
amongst many other possibilities to present a new visualization technique,
called <i>Transmittogram</i>. This technique readily depicts the time-resolved settling
behavior of solid-liquid dispersions, measured by analytical centrifugation
(AC). Although AC enables the causal examination of agglomeration, settling, and
creaming behavior of dispersions, along with its consequent effect on structure
formation and product properties, the understanding of the main transmission
readout is often non-intuitive and complex. Transmittograms are, therefore, the
missing link for straightforward data interpretation. First, we illustrate the
utility of transmittogram analysis using model silica nanoparticle systems and
further validate it against known characteristics of the system. Then, we demonstrate
the application of transmittograms to characterize fuel cell inks, showing the
strength of the approach in deconvoluting and distilling information to the
reader. Finally, we discuss the
potential of the technique for routine analysis using analytical centrifugation.<br /> | Shalmali Bapat; Doris Segets | Aggregates and Assemblies; Carbon-based Materials; Catalysts; Nanostructured Materials - Materials; Separation Science; Energy Storage; Fuels - Energy Science; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74be9702a9b15a318b56e/original/exhibitive-nano-to-micron-scale-sedimentation-dynamics-of-colloidal-formulations-through-direct-visualization.pdf |
62b4b7a67da6cec47e1d8016 | 10.26434/chemrxiv-2022-0v832-v2 | Enhanced Expansion and Reduced Kiss-and-Run Events in Fusion Pores Steered by Synaptotagmin-1 C2B Domains | The fusion pore controls the release of exocytotic vesicles contents through a precise orchestration of lipids from the fusing membranes and proteins. There is a major lipid reorganization during the different stages in life of the fusion pore: membrane fusion, nucleation and expansion, that can be scrutinized thermodynamically. In this work, using umbrella sampling simulations we describe the expansion of the fusion pore. We have calculated free energy profiles to drive a nascent, just nucleated, fusion pore to its expanded configuration. We have quantified the effects on the free energy of one and two Synaptotagmin-1 C2B domains in the cytosolic space. We show that C2B domains cumulatively reduce the cost for expansion, favoring the system to evolve towards full fusion. Finally, by conducting thousands of unbiased molecular dynamics simulations, we show that C2B domains significantly decrease the probability of kiss-and-run events. | Ary Lautaro Di Bartolo; Claudia Nora Tomes; Luis Segundo Mayorga; Diego Masone | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b4b7a67da6cec47e1d8016/original/enhanced-expansion-and-reduced-kiss-and-run-events-in-fusion-pores-steered-by-synaptotagmin-1-c2b-domains.pdf |
661a5d7421291e5d1dc06dd3 | 10.26434/chemrxiv-2024-689f3 | In Vivo Optogenetics Based on Heavy Metal-Free Photon Upconversion Nanoparticles | Photon upconversion (UC) from red or near-infrared (NIR) light to blue light is promising for in vivo optogenetics. However, the examples of in vivo optogenetics have been limited to lanthanide inorganic UC nanoparticles, and there have been no examples of optogenetics without using heavy metals. Here we show the first example of in vivo optogenetics using biocompatible heavy metal-free TTA-UC nanoemulsions. A new organic TADF sensitizer, a borondifluoride curcuminoid derivative modified with a bromo group, can promote intersystem crossing to the excited triplet state, significantly improving TTA-UC efficiency. The TTA-UC nanoparticles formed from biocompatible surfactants and methyl oleate acquire water dispersibility and remarkable oxygen tolerance. By combining with genome engineering technology using the blue light-responding photoactivatable Cre-recombinase (PA-Cre), TTA-UC nanoparticles promote Cre-reporter EGFP expression in neurons in vivo. Our results open new opportunities towards deep-tissue control of neural activities based on heavy metal-free fully organic UC systems. | Masanori Uji; Jumpei Kondo; Chikako Hara-Miyauchi; Saori Akimoto; Rena Haruki; Yoichi Sasaki; Nobuo Kimizuka; Itsuki Ajioka; Nobuhiro Yanai | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661a5d7421291e5d1dc06dd3/original/in-vivo-optogenetics-based-on-heavy-metal-free-photon-upconversion-nanoparticles.pdf |
60c74d5d469df463cff4427f | 10.26434/chemrxiv.12609815.v1 | Radiation Reduction of Carbon Dioxide: A New Chemical Industry? | A novel approach to use waste radiation from spent fuel rods to reduce carbon dioxide to produce various feedstock chemicals for the chemical industry.<div>The basic radiochemistry has been known for at least four decades. The novel element is how this all can be accomplished safely using spent-fuel assembly radiation. The latter is carbon footprint-free and the product materials are also very pure. There is no residual contamination requiring expensive 'clean-up' unlike chemical industry feedstocks produced by the petrochemical industry.</div> | Peter Livingston | Atmospheric Chemistry; Environmental Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d5d469df463cff4427f/original/radiation-reduction-of-carbon-dioxide-a-new-chemical-industry.pdf |
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