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60c74d5c842e65869edb345b | 10.26434/chemrxiv.12090828.v2 | Comparison of Clinically Approved Molecules on SARS-CoV-2 Drug Target Proteins: A Molecular Docking Study | <p>The new type of coronavirus, SARS-CoV-2 has affected more than 6.3 million people worldwide. Since the first day the virus has been spotted in Wuhan, China, there are numerous drug design studies conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SASR-CoV-2, which is known to bind human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus’ replication. However, there might be a third target, human furin protease, which cleaves the virus’ S1-S2 domains taking active role in its entry into the host cell. In this study we docked five clinically used drug molecules, favipiravir, hydroxychloroquine, remdesivir, lopinavir, and ritonavir onto three target proteins, receptor binding domain of SARS-CoV-2 spike protein, SARS-CoV-2 main protease, and human furin protease. Results of molecular docking simulations revealed that human furin protease might be targeted against COVID-19. Remdesivir, a nucleic acid derivative, strongly bound to the active site of this protease, suggesting this molecule can be used as a template for designing novel furin protease inhibitorsto fight with the disease. Protein-drug interactions revealed at the molecular level in this study can pave the way for better drug design for each specific target.<br /></p> | Hasan Cubuk; Mehmet Ozbil | Bioinformatics and Computational Biology; Chemical Biology; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d5c842e65869edb345b/original/comparison-of-clinically-approved-molecules-on-sars-co-v-2-drug-target-proteins-a-molecular-docking-study.pdf |
65f7dd57e9ebbb4db9ec653d | 10.26434/chemrxiv-2024-6t79h | Coherent anti-Stokes hyper-Raman Spectroscopy | Coherent Raman scattering spectroscopies have been established as a powerful tool for investigating molecular systems with high chemical specificity. The existing coherent Raman scattering techniques detect only Raman active modes, which are a part of the whole molecular vibrations. Here, we report the first observation of coherent anti-Stokes hyper-Raman scattering (CAHRS) spectroscopy, which allows measuring hyper-Raman active vibrations at high speed. The CAHRS process relies on a fifth-order nonlinear process that combines hyper-Raman scattering with coherent Raman scattering. Observed signals are proven to come from the CAHRS process through various experiments concerning the dependences of the signals on incident laser powers, time-delay, polarizations, and selection rules of molecular vibrations. Comparisons of CAHRS signals with spontaneous hyper-Raman signals from para-nitroaniline solutions and benzene liquid manifest much higher signal-to-noise ratios of CAHRS signals than spontaneous hyper-Raman signals. This study illustrates that CAHRS spectroscopy can offer new information on molecular vibrations unobtainable from the present coherent Raman techniques at a much higher speed than spontaneous hyper-Raman spectroscopy. | Kazuki Inoue; Masanari Okuno | Physical Chemistry; Optics; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f7dd57e9ebbb4db9ec653d/original/coherent-anti-stokes-hyper-raman-spectroscopy.pdf |
60c9e3b1059ce2f8e476bb45 | 10.26434/chemrxiv.14778150.v1 | Fast Prediction of Distances Between Synthetic Routes with Deep Learning | We expand our recent work on clustering of synthesis routes and train a deep learning model to predict the distances between arbitrary routes. The model is based on an long short-term memory (LSTM) representation of a synthesis route and is trained as a twin network to reproduce the tree edit distance (TED) between two routes. The ML approach is approximately two orders of magnitude faster than the TED approach and enables clustering many more routes from a retrosynthesis route prediction. The clusters have a high degree of similarity to the clusters given by the TED-based approach and are accordingly intuitive and explainable. We provide the developed model as open-source (https://github.com/MolecularAI/route-distances). | Samuel Genheden; Ola Engkvist; Esben Jannik Bjerrum | Organic Synthesis and Reactions; Chemoinformatics; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b1059ce2f8e476bb45/original/fast-prediction-of-distances-between-synthetic-routes-with-deep-learning.pdf |
67930f56fa469535b99a0dd1 | 10.26434/chemrxiv-2025-zktwx | Autonomous Phase Mapping of Gold Nanoparticles Synthesis with Differentiable Models of Spectral Shape | Autonomous experimentation, or self-driving labs as they are popularly known, is a novel way of experimental planning and scheduling to systematically integrate automated material synthesis, characterization, and data analysis for accelerated materials design and discovery. This paper presents an autonomous experimentation workflow to conduct an iterative, on-demand synthesis, and structural characterization of colloidal gold nanoparticles to map composition information to nano-scale structure in a closed loop. We introduce a unified experimental planning framework based on differentiable models of the shape of a spectrum to solve the two categories of problems tackled using autonomous experimentation: a) quantitatively mapping compositional parameters to regions with particular behavior in structure or property i.e. phase mapping; b) inverse design of materials with a target structure or function i.e. material retrosynthesis. Using functional data analysis, we describe a data-driven computational model to map correlations between the compositions (i.e., synthesis or processing conditions) to the shape of a characterization curve (e.g.: UV-Vis spectroscopy). By integrating generative pre-training, active learning, and high-throughput experimentation, we train a surrogate model capable of predicting characterization curves across compositional spaces. The model-based approach to experimental planning provides convergence criteria for terminating iterative experimentation by measuring the model's test accuracy. We demonstrate the utility of trained differentiable models in generating phase maps of a seed-mediated growth of colloidal gold nanoparticles for extracting design rules, secondary interaction effects (between synthesis components and their impact on nanoparticle structure), and efficient navigation of different gold nanoparticle morphologies space. We then describe an application of the differentiable models to colloidal gold nanoparticle retrosynthesis using a gradient-based optimization to showcase the construction of a self-driving lab doubly capable of structure optimization and phase map generation. | Kiran Vaddi; Huat Thart Chiang; Lilo D Pozzo | Materials Science; Nanoscience; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67930f56fa469535b99a0dd1/original/autonomous-phase-mapping-of-gold-nanoparticles-synthesis-with-differentiable-models-of-spectral-shape.pdf |
650ea28eed7d0eccc30f46cc | 10.26434/chemrxiv-2023-n6475 | Functionalized oxide biosensor interfaces for in-situ, acid-modulated peptide synthesis | In this paper we report a novel acid-modulated strategy for peptide microarray production on biosensor interfaces. We have initially selected controlled pore glass (CPG) as support for solid phase peptide synthesis (SPPS) to implement a chemistry that can be efficiently performed at the interface of multiple FET sensors, eventually to generate label-free peptide microarrays for protein screening. Our chemistry uses temporary protection of the N-terminal amino function of each amino acid building block with a tert-butyloxycarbonyl (Boc) group that can be removed after each SPPS cycle, in combination with semi-permanent protection of the side chains of trifunctional amino acid residues. Such protection scheme, with a well-proven record of application in conventional, batchwise SPPS, has been fine tuned for optimal performance on CPG and, from there, translated to SPR chips that allow layer-by-layer monitoring of amino acid coupling. Our results validate this acid-modulated synthesis as a feasible approach for producing peptides in high yield and purity on flat glass surfaces such as those in bio-FETs. | Edgar Cristóbal Lecina; Janwa El-Maiss; Eduard Figueras; Aruna Chandra singh; Thomas Osterbye; César Pascual García; David Andreu | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650ea28eed7d0eccc30f46cc/original/functionalized-oxide-biosensor-interfaces-for-in-situ-acid-modulated-peptide-synthesis.pdf |
60c7544d469df46355f44f0f | 10.26434/chemrxiv.13643807.v1 | Surfactant-Free Colloidal Strategies for Highly Dispersed and Active Supported IrO2 Catalysts: Synthesis and Performance Evaluation for the Oxygen Evolution Reaction | Supported Ir oxide catalysts obtained from surfactant-free
colloidal Ir nanoparticles (NPs) synthesized in alkaline methanol (MeOH),
ethanol (EtOH), and ethylene glycol (EG) are investigated and compared. The
comparison of independent techniques such as transition electron microscopy
(TEM), small angle X-ray scattering (SAXS), and electrochemistry allows shedding
light on the parameters that affect the dispersion of the active phase as well
as the catalytic activity. The colloidal dispersions obtained are suitable to
develop supported catalysts with little NP agglomeration on a carbon support
leading to highly active catalysts with more than 400 A g<sup>-1</sup><sub>Ir</sub>
reached at 1.5 V<sub>RHE</sub> for the OER. While the more common
surfactant-free alkaline EG synthesis requires flocculation and re-dispersion
leading to Ir loss, the main difference between methanol and ethanol as solvent
is related to the dispersibility of the support material. The choice of the
suitable monoalcohol determines the maximum achieved Ir loading on the support
without detrimental particle agglomeration. This simple consideration on
catalyst design can readily lead to significantly improved catalysts. | Francesco Bizzotto; Jonathan Quinson; Johanna Schröder; Alessandro Zana; Matthias Arenz | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7544d469df46355f44f0f/original/surfactant-free-colloidal-strategies-for-highly-dispersed-and-active-supported-ir-o2-catalysts-synthesis-and-performance-evaluation-for-the-oxygen-evolution-reaction.pdf |
60c7494f337d6cc4d6e276c8 | 10.26434/chemrxiv.12049584.v1 | Isoreticular Linker Substitution in Conductive Metal–Organic Frameworks with Through-Space Transport Pathways | <p>The extension of reticular chemistry concepts to electrically conductive three-dimensional metal-organic frameworks (MOFs) has been challenging, particularly for cases in which strong interactions between electroactive linkers create the charge transport pathways. Here, we report the successful replacement of tetrathiafulvalene (TTF) with a nickel glyoximate core in a family of isostructural conductive MOFs with Mn<sup>2+</sup>, Zn<sup>2+</sup>, and Cd<sup>2+</sup>. Different coordination environments of the framework metals lead to variations in the linker stacking geometries and optical properties. Single crystal conductivity data are consistent with charge transport along the linker stacking direction, with conductivity values only slightly lower than those reported for the analogous TTF materials. These results serve as a case study demonstrating how reticular chemistry design principles can be extended to conductive frameworks with significant intermolecular contacts.</p> | Lilia S. Xie; Sarah S. Park; Michał J. Chmielewski; Hanyu Liu; Ruby A. Kharod; Luming Yang; Michael G. Campbell; Mircea Dinca | Coordination Chemistry (Inorg.); Solid State Chemistry; Supramolecular Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7494f337d6cc4d6e276c8/original/isoreticular-linker-substitution-in-conductive-metal-organic-frameworks-with-through-space-transport-pathways.pdf |
6481a504be16ad5c57a44abd | 10.26434/chemrxiv-2023-301gj | Modelling local and general quantum mechanical properties with attention-based pooling | Atom-centred neural networks represent the state-of-the-art for approximating the quantum chemical properties of molecules, such as internal energies. While the design of machine learning architectures that respect chemical principles has continued to advance, the final atom pooling operation that is necessary to convert from atomic to molecular representations in most models remains relatively undeveloped. The most common choices, sum and average pooling, compute molecular representations that are naturally a good fit for many physical properties, while satisfying properties such as permutation invariance which are desirable from a geometric deep learning perspective. However, there are growing concerns that such simplistic functions might have limited representational power, while also being suboptimal for physical properties that are highly localised or intensive. Based on recent advances in graph representation learning, we investigate the use of a learnable pooling function that leverages an attention mechanism to model interactions between atom representations. The proposed pooling operation is a drop-in replacement requiring no changes to any of the other architectural components. Using SchNet and DimeNet++ as starting models, we demonstrate consistent uplifts in performance compared to sum pooling and a recent physics-aware pooling operation designed specifically for orbital energies, on several datasets, properties, and levels of theory, with up to 85% improvements depending on the specific task. | David Buterez; Jon Paul Janet; Steven J. Kiddle; Dino Oglic; Pietro Liò | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6481a504be16ad5c57a44abd/original/modelling-local-and-general-quantum-mechanical-properties-with-attention-based-pooling.pdf |
60c73d92bb8c1ab17e3d9797 | 10.26434/chemrxiv.5928406.v1 | Development of a Protein-Ligand Extended Connectivity (PLEC) Fingerprint and Its Application for Binding Affinity Predictions. | <div>Fingerprints (FPs) are the most common small molecule representation in cheminformatics. There are a wide variety of fingerprints, and the Extended Connectivity Fingerprint (ECFP) is one of the best-suited for general applications. Despite the overall FP abundance, only a few FPs represent the 3D structure of the molecule, and hardly any encode protein-ligand interactions. Here, we present a Protein-Ligand Extended Connectivity (PLEC) fingerprint that implicitly encodes protein-ligand interactions by pairing the ECFP environments from the ligand and the protein. PLEC fingerprints were used to construct different machine learning (ML) models tailored for predicting protein-ligand affinities (pK<sub>i/d</sub>). Even the simplest linear model built on the PLEC fingerprint achieved R<sub>p</sub>=0.83 on the PDBbind v2016 "core set”, demonstrating its descriptive power. The PLEC fingerprint has been implemented in the Open Drug Discovery Toolkit (https://github.com/oddt/oddt).</div> | Maciej Wójcikowski; Michał Kukiełka; Marta Stepniewska-Dziubinska; Pawel Siedlecki | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d92bb8c1ab17e3d9797/original/development-of-a-protein-ligand-extended-connectivity-plec-fingerprint-and-its-application-for-binding-affinity-predictions.pdf |
649f28c99ea64cc1673bea11 | 10.26434/chemrxiv-2023-9ckg2 | Cu-releasing nanoparticles induce the catalytic transamination of amino acids and GSSG under tumor microenvironment conditions | Catalytic cancer therapy is emerging as a powerful tool to target cancer cells by exploiting specific characteristics of the tumor microenvironment (TME). To this end, the catalytic activity of nanoparticles, enzymes and homogeneous catalysts is recruited to induce reactions that are damaging to cancer cells. Thus, the pro-drug activation approach uses chemical constructs that become toxic species inside the tumor, typically following removal of a protecting group. In contrast, TME-based catalytic strategies do not rely on the introduction of foreign species and instead use molecules that are already present in the TME. So far, only four processes have been explored in relation to cancer therapy, two oxidation reactions (glucose and glutathione), generation of reactive oxygen species (ROS) and production of oxygen to alleviate tumor hypoxia. This is surprising, since the rich chemical environment in tumor cells could in principle provide many other therapeutic opportunities. In particular, amino groups seem a suitable target, given the abundance of proteins and peptides in biological environments. Here we show that catalytic CuFe nanoparticles are able to foster transamination reactions between different amino acids and pyruvate, another key molecule that abounds in the TME. Transamination would then reduce the available aminoacid pool, which is likely to affect cell homeostasis and to effectively hinder tumor proliferation. After internalization of Cu-containing nanoparticles in U251-MG cells, we observed a significant decrease in glutamine and alanine levels up to 48 hours after treatment. In addition, we have found that not only simple amino acids, but also di- and tri-peptides undergo catalytic transamination when exposed to the Cu cations released by our nanoparticles, thus extending the range of the effects to other molecules such as GSSG. Mechanistic calculations for GSSG transamination revealed the formation of an imine between the oxo-group of pyruvate and the free -NH2 group of GSSG, followed by the coordination of the imine to Cu(II). Our results demonstrate that transamination reactions can be catalyzed in cellulo by Cu-releasing nanoparticles, adding a new reaction to the existing toolbox of catalytic therapies. | Javier Bonet-Aleta; Juan V Alegre-Requena; Javier Martin-Martin; Miguel Encinas-Gimenez; Ana Martin-Pardillos; Pilar Martin-Duque; Jose L Hueso; Jesus Santamaria | Biological and Medicinal Chemistry; Catalysis; Nanoscience; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649f28c99ea64cc1673bea11/original/cu-releasing-nanoparticles-induce-the-catalytic-transamination-of-amino-acids-and-gssg-under-tumor-microenvironment-conditions.pdf |
63adc929dadddc10809f28e2 | 10.26434/chemrxiv-2022-nsd13 | Amplifying Reactivity of Metal Hydrides: A Heterotrimetallic NiAl2(μ2-H)2 Catalyst for the Facile Dearomatization of N-Heterocycles | Identifying methods to modulate the reactivity of metal-hydrides are lacking yet highly desirable given the role they play in a plethora of catalytic applications. Herein we report novel methodology to amplify reactivity of metal hydrides through the design of well-defined heterometallic bridged hydride species. Catalytic hydroboration of quinolines was dramatically altered by the addition of a secondary metal to bridge the Al-hydride species LAlH. Specifically, the addition of Ni(COD)2 led to the formation of novel heterotrimetallic species 1 which features Ni participating in 3-center- bonding with sterically accessible Al-H species and exhibits catalytic hydroboration of sterically encumbered quinolines and approximately a 400 times enhancement in catalytic reactivity in comparison to LAlH. | Edgardo De Leon; Fernando Gonzalez; Preetika Bauskar; Sergio Gonzalez-Eymard; David De Los Santos; Manar Shoshani | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Transition Metal Complexes (Inorg.); Base Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63adc929dadddc10809f28e2/original/amplifying-reactivity-of-metal-hydrides-a-heterotrimetallic-ni-al2-2-h-2-catalyst-for-the-facile-dearomatization-of-n-heterocycles.pdf |
60c74802337d6c8335e27453 | 10.26434/chemrxiv.11825679.v1 | Combining Cloud-Based Free Energy Calculations, Synthetically Aware Enumerations and Goal-Directed Generative Machine Learning for Rapid Large-Scale Chemical Exploration and Optimization | The hit identification process usually involves the profiling of millions to more recently billions of compounds either via traditional experimental high throughput screens (HTS) or computational virtual high throughput screens (vHTS). We have previously demonstrated that by coupling reaction-based enumeration, active learning and free energy calculations, a similarly large-scale exploration of chemical space can be extended to the hit-to-lead process. In this work, we augment that approach by coupling large scale enumeration and cloud-based FEP profiling with goal-directed generative machine learning, which results in a higher enrichment of potent ideas compared to large scale enumeration alone, while simultaneously staying within the bounds of a predefined drug-like property space. We are able to achieve this by building the molecular distribution for generative machine learning from the PathFinder rules-based enumeration and optimizing for a weighted sum QSAR based multi-parameter optimization function. We examine the utility of this combined approach by designing potent inhibitors of cyclin-dependent kinase 2 (CDK2) and demonstrate a coupled workflow that can: (1) provide a 6.4 fold enrichment improvement in identifying < 10nM compounds over random selection, and a 1.5 fold enrichment in identifying < 10nM compounds over our previous method (2) rapidly explore relevant chemical space outside the bounds of commercial reagents, (3) use generative ML approaches to “learn” the SAR from large scale in silico enumerations and generate novel idea molecules for a flexible receptor site that are both potent and within relevant physicochemical space and (4) produce over 3,000,000 idea molecules and run 2153 FEP simulations, identifying 69 ideas with a predicted IC<sub>50</sub> < 10nM and 358 ideas with a predicted IC<sub>50</sub> <100 nM. The reported data suggest combining both reaction-based and generative machine learning for ideation results in a higher enrichment of potent compounds over previously described approaches, and can rapidly accelerate the discovery of novel chemical matter within a predefined potency and property space.<br /> | Phani Ghanakota; Pieter Bos; Kyle Konze; Joshua Staker; Gabriel Marques; Kyle Marshall; Karl Leswing; Robert Abel; SATHESH BHAT | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74802337d6c8335e27453/original/combining-cloud-based-free-energy-calculations-synthetically-aware-enumerations-and-goal-directed-generative-machine-learning-for-rapid-large-scale-chemical-exploration-and-optimization.pdf |
66f98ca451558a15ef84353d | 10.26434/chemrxiv-2024-9r9gn-v2 | Current Status of the MB-pol Data-Driven Many-Body Potential for Predictive Simulations of Water Across Different Phases | Developing a molecular-level understanding of the properties of water is central to numerous scientific and technological applications. However, accurately modeling water through computer simulations has been a significant challenge due to the complex nature of the hydrogen- bonding network that water molecules form under different thermodynamic conditions. This complexity has led to over five decades of research and many modeling attempts. The introduction of the MB-pol data-driven many-body potential energy function marked a significant advancement toward a universal molecular model capable of predicting the structural, thermo- dynamic, dynamical, and spectroscopic properties of water across all phases. By integrating physics-based and data-driven (i.e., machine-learned) components, which correctly capture the delicate balance among different many-body interactions, MB-pol achieves chemical and spectroscopic accuracy, enabling realistic molecular simulations of water, from gas-phase clusters to liquid water and ice. In this review, we present a comprehensive overview of the data- driven many-body formalism adopted by MB-pol, highlight the main results and predictions made from computer simulations with MB-pol to date, and discuss the prospects for future extensions to data-driven many-body potentials of generic and reactive molecular systems. | Etienne Palos; Ethan F. Bull-Vulpe; Xuanyu Zhu; Henry Agnew; Shreya Gupta; Suman Saha; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Quantum Mechanics; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f98ca451558a15ef84353d/original/current-status-of-the-mb-pol-data-driven-many-body-potential-for-predictive-simulations-of-water-across-different-phases.pdf |
666ad5545101a2ffa87ed760 | 10.26434/chemrxiv-2024-3xz4v | Inversion of Circularly Polarized Luminescence in Phenylethynyl-substituted Binaphthol Derivatives | An inversion in the sign of circularly polarized luminescence (CPL) was achieved by strategically varying the substitution positions of phenylethynyl (PE) groups on the binaphthyl backbone while maintaining consistent axial chirality. Theoretical investigations indicated that the substitution position of PE groups on binaphthyl significantly influence the orientation of the transition dipole moments in the excited state, resulting in the sign inversion of CPL in 7-PEn compared with other substrates. | Ayumi Imayoshi; Shinya Fujio; Yuuki Nagaya; Misato Sakai; Atsushi Terazawa; Misa Sakura; Keita Okada; Takahiro Kimoto; Tadashi Mori; Yoshitane Imai; Masahiko Hada; Kazunori Tsubaki | Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666ad5545101a2ffa87ed760/original/inversion-of-circularly-polarized-luminescence-in-phenylethynyl-substituted-binaphthol-derivatives.pdf |
61e6f07cf2bef73f2aa5c1ec | 10.26434/chemrxiv-2022-lv85f | Organocatalytic Enantioselective Synthesis of Bicy-clo[2.2.2]octenones via Oxaziridinium Catalysed ortho-Hydroxylative Phenol Dearomatization | Hydroxylative dearomatization reactions of phenols (HPD) offer an efficient way to assemble complex, biologically relevant scaffolds. Despite this, enantioselective hydroxylative phenol dearomatizations for the construction of bicy-clo[2.2.2]octenones are classically limited to stoichiometric chiral reagents, and a practical, enantioselective catalytic method has remained elusive. Herein, we describe a highly enantioselective, organocatalytic tandem o-HPD-[4+2] reaction. Our methodology utilizes a chiral oxaziridinium organocatalyst that affords high enantioselectivity for a wide range of phenol substitution patterns, and was applied in the synthesis of (+)-biscarvacrol and bis(2,6-xylenol). The practicality of our conditions were demonstrated at gram-scale, using an amine precatalyst that can be accessed in a single synthetic step. | Tom D'Arcy; Benjamin Buckley | Organic Chemistry; Catalysis; Natural Products; Organic Synthesis and Reactions; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e6f07cf2bef73f2aa5c1ec/original/organocatalytic-enantioselective-synthesis-of-bicy-clo-2-2-2-octenones-via-oxaziridinium-catalysed-ortho-hydroxylative-phenol-dearomatization.pdf |
650edc6ab927619fe7ac0922 | 10.26434/chemrxiv-2023-l9zmx | A Convergent Click Ligation Approach to the Synthesis of Triazole-incorporated PMOs and Evaluation of Hybridization Properties | The synthesis of Phosphorodiamidate Morpholino Oligonucleotides (PMOs) incorporating single triazole rings in the backbone has been achieved via Cu(I) catalyzed Azide-Alkyne cycloaddition reaction (CuAAC). The synthetic approach implemented, is convergent, involving the ligation of a 5'-azide PMO fragment to 3'-alkyne fragment both in solution and on solid support. To access the 3'-alkyne PMO fragment, we synthesized 3'-N-propargyl chlorophosphoramidate morpholino monomers for all four nucleobases. The resulting triazole-incorporated PMOs (TL-PMOs) have exhibited comparable or improved binding affinity towards complementary DNA/RNA strands compared to its regular analogs. | Arpan Banerjee; Arnab Das; Atanu Ghosh; Abhishek Gupta; SURAJIT SINHA | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650edc6ab927619fe7ac0922/original/a-convergent-click-ligation-approach-to-the-synthesis-of-triazole-incorporated-pm-os-and-evaluation-of-hybridization-properties.pdf |
6622753b418a5379b03160a8 | 10.26434/chemrxiv-2024-3fxcj | Adaptive Lambda Scheduling: A method for computational efficiency in Free Energy Perturbation simulations | Despite growing accessibility due to advances in computing power, ligand-protein Relative Binding Free Energy (RBFE) calculation remains a resource-intensive activity, which limits its practical application. Improved computational efficiency via bespoke sampling of the alchemical transformation coordinate, λ, is under-explored. We show here that a simple approach for on-the-fly bespoke λ scheduling, named Adaptive Lambda Scheduling (ALS), yields significant reduction in computational cost whilst retaining predictive performance. | Scott Midgley; Sofia Bariami; Matthew Habgood; Mark Mackey | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6622753b418a5379b03160a8/original/adaptive-lambda-scheduling-a-method-for-computational-efficiency-in-free-energy-perturbation-simulations.pdf |
60c743d60f50dbc821395fce | 10.26434/chemrxiv.9534920.v1 | Solvent Effect on Dipeptide Bond Formation: Glycine as a Case Study | Peptide bond formation is a crucial chemical process that dominates most biological mechanisms and is claimed to be a governing factor in the origin of life. Dipeptides made from glycine are studied computationally via Density Functional Theory (DFT) using two different basis sets. This reaction was investigated from both a thermodynamic and kinetic point of view. The effect of explicit solvation via the introduction of discreet solvent molecules was investigated. Water, methanol, and cyclohexane were all employed as solvent media in addition to gas to investigate their effects on the mechanism of peptide bond formation. This computational investigation revealed that methanol is slightly better than water to leverage peptide bond formation both kinetically and thermodynamically, while cyclohexane, a non-polar and non-protic solvent, is the least effective after gas as a medium of solvation. Energetic results in the gas environment are very close to those obtained in polar and protic solvents, suggesting that peptide bonds can be formed under interstellar conditions. | Sofiene Achour; Zied Hosni; Sarra Darghouth; Christopher Syme | Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743d60f50dbc821395fce/original/solvent-effect-on-dipeptide-bond-formation-glycine-as-a-case-study.pdf |
60c74966842e6568a9db2d2e | 10.26434/chemrxiv.12024738.v2 | Dipole Field Interactions Determine the CO2 Reduction Activity of 2D FeNC Single Atom Catalysts | <p>Electrochemical CO2 Reduction (CO2R) can potentially allow for the sustainable production of valuable fuels and chemicals. Recently, single atom catalysts on a 2D support have been shown to be a promising catalyst candidate. Using state-of-the-art methods, we develop a model for Fe doped graphene which rationalises several critical experimental observations: the contentious origin of the pH dependence of reactivity and the dependence of current-potential relationships on active site. We show that single atom catalysts have the unique ability to stabilise different dipoles associated with critical reaction intermediates, which translates to significant shifts in activity. This provides a new rational design principle and paves the way for rigorous computation-guided catalyst design of new single atom catalysts for CO2R.</p> | Sudarshan Vijay; Joseph Gauthier; Hendrik Heenen; Vanessa Jane Bukas; Henrik Høgh Kristoffersen; Karen Chan | Catalysts; Theory - Computational; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74966842e6568a9db2d2e/original/dipole-field-interactions-determine-the-co2-reduction-activity-of-2d-fe-nc-single-atom-catalysts.pdf |
65578db46e0ec7777f249c21 | 10.26434/chemrxiv-2022-nz7rz-v2 | Studying the adsorption of emerging organic contaminants in zeolites with dispersion-corrected density functional theory calculations: From numbers to recommendations | It has been established that adsorption energies obtained from dispersion-corrected density functional theory (DFT) calculations show a considerable dependence on the choice of exchange-correlation functional and dispersion correction. A number of investigations have employed different approaches to compute adsorption energies of small molecules like methane, ethane, or carbon dioxide in different types of zeolites (all-silica, protonated, cation-exchanged), using reference values from high-level calculations and/or experiments. Such comparative studies are lacking for the adsorption of larger functional organic molecules such as pharmaceuticals or personal care products, despite the potential relevance for applications, e.g., in contaminant removal or drug delivery. The present study aims to fill this gap by comparing adsorption energies and, for selected cases, equilibrium structures of emerging organic contaminants adsorbed in all-silica zeolites, employing a total of 13 dispersion-corrected DFT approaches. Methods using a pairwise (D3) dispersion correction as well as non-local van der Waals density functionals were included. A comparison of adsorption energies obtained for a variety of contaminants in MOR- and FAU-type zeolites showed that absolute values vary widely, whereas qualitative trends across the set of zeolite-guest combinations are not strongly dependent on the choice of functional. For selected cluster models, DFT adsorption energies were compared to reference values obtained with coupled cluster (DLPNO-CCSD(T)) calculations. Although all DFT approaches delivered systematically more negative adsorption energies than the coupled cluster reference, the rev-vdW-DF2 functional emerged as functional for which this tendency is least pronounced. | Michael Fischer; Jakob Brauer | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Interfaces; Structure; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65578db46e0ec7777f249c21/original/studying-the-adsorption-of-emerging-organic-contaminants-in-zeolites-with-dispersion-corrected-density-functional-theory-calculations-from-numbers-to-recommendations.pdf |
63da581a89c04b6693c85747 | 10.26434/chemrxiv-2023-5ks97 | Intrinsically switchable electroactive fluorophores based on lambda-5-phosphinine dimers | We report the synthesis and full characterization of a family of stable lambda- 5-phosphinine dimers connected through a variety of pi-conjugated bridges. The impact of the pi-bridge on the optical (absorption/emission) and redox properties is investigated using a joint experimental/theoretical approach. In contrast to the pi-extended ones, the dimers directly connected through a C-C bond display two easily accessible and reversible oxidations highlighting their multi-stage redox character. The in situ formed radical cations are studied by spectro-electrochemistry and electron paramagnetic resonance. Finally, electrochemical modulation of fluorescence (electrofluorochromism) was performed and revealed the potential of these intrinsically switchable electroactive fluorophores for further applications as switchable materials. | Thitiporn Sangchai; Nicolas Ledos; Antoine Vacher; Marie Cordier; Boris Le Guennic; Muriel Hissler; Denis Jacquemin; Pierre-Antoine Bouit | Organic Chemistry; Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da581a89c04b6693c85747/original/intrinsically-switchable-electroactive-fluorophores-based-on-lambda-5-phosphinine-dimers.pdf |
64deddbe01042bc1cc3e7ccc | 10.26434/chemrxiv-2023-kbltp | Mechanically-Sensitive Fluorochromism by Molecular Domino Transformation in a Schiff Base Crystal | The ability to make large changes in properties against small external stimuli is one of key factors in sensing materials. Molecular domino transformation, i.e. polymorphic transformation starting at a stimulated point and extending to the whole crystal, is an attractive phenomenon from this viewpoint. We recently found such a transformation in a crystal of 4-nitro-N-salicylideneaniline as one of Schiff bases. In this study, quantitative evaluations were conducted on a mechanical stimulus and emission properties in the transformation of the crystal. Our results demonstrate the potential applicability of the crystal to detection of even less than a few μN mechanical stimuli as an emission color change. A molecular level transformation mechanism revealed by microcrystal electron diffraction also contributes to future development of the transformation-based materials. | Toshiyuki Sasaki; Takanori Nakane; Akihiro Kawamoto; Yakai Zhao; Yushi Fujimoto; Tomohiro Nishizawa; Fuyuki Ito; Upadrasta Ramamurty; Ranjit Thakuria; Genji Kurisu | Physical Chemistry; Materials Science; Photochemistry (Physical Chem.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64deddbe01042bc1cc3e7ccc/original/mechanically-sensitive-fluorochromism-by-molecular-domino-transformation-in-a-schiff-base-crystal.pdf |
6682466a5101a2ffa8fabd16 | 10.26434/chemrxiv-2024-7q438-v3 | When Do Quantum Mechanical Descriptors Help Graph Neural Networks Predict Chemical Properties? | Deep graph neural networks are extensively utilized to predict chemical reactivity and molecular properties. However, because of the complexity of chemical space, such models often have difficulty extrapolating beyond the chemistry contained in the training set. Augmented model with quantum mechanical (QM) descriptors is anticipated to improve its generalizability. However, obtaining QM descriptors often requires CPU-intensive computational chemistry calculations. To identify when QM descriptors help graph neural networks predict chemical properties, we conduct a systematic investigation of the impact of atom, bond, and molecular QM descriptors on the performance of directed message passing neural networks (D-MPNNs) for predicting 16 molecular properties. The analysis surveys computational and experimental targets, classification and regression tasks, and varied dataset sizes from several hundred to hundreds of thousands of datapoints. Our results indicate that QM descriptors are mostly beneficial for D-MPNN performance on small datasets, provided that the descriptors correlate well with the targets and can be readily computed with high accuracy. Otherwise, using QM descriptors can add cost without benefit or even introduce unwanted noise that can degrade model performance. Strategic integration of QM descriptors with D-MPNN unlocks potential for physics-informed, data-efficient modeling with some interpretability that can streamline de novo drug and material designs. To facilitate the use of QM descriptors in machine learning workflows for chemistry, we provide a set of guidelines regarding when and how to best leverage QM descriptors, a high-throughput workflow to compute them, and an enhancement to Chemprop, a widely adopted open-source D-MPNN implementation for chemical property prediction. | Shih-Cheng Li; Haoyang Wu; Angiras Menon; Kevin Spiekermann; Yi-Pei Li; William Green | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6682466a5101a2ffa8fabd16/original/when-do-quantum-mechanical-descriptors-help-graph-neural-networks-predict-chemical-properties.pdf |
6261159ced4d883e141343ff | 10.26434/chemrxiv-2022-h1860 | Unified Synthesis of Multiply Arylated Alkanes by Catalytic Deoxygenative Transformation of Diarylketones | A deoxygenative transformation of diarylketones leading to multiply arylated alkanes was developed. Diarylketones were reacted with di-phenylphosphine oxide resulting in a phospha-Brook rearrangement, followed by palladium-catalyzed cross-couplings or a Friedel–Crafts type alkylation to afford the corresponding multiply arylated alkanes. A variety of diarylketones can be converted to multiply arylated alkanes such as diarylmethanes, tetraarylethanes, and triarylmethanes by reduction, dimerization, and arylation in one pot. Furthermore, a one-pot conversion from arylcarboxylic acids to diarylmethanes and tetraarylethanes, and a synthesis of tetraarylmethane and tri-phenylethane using sequential coupling reactions are also presented. | Miki B Kurosawa; Kenta Kato; Kei Muto; Junichiro Yamaguchi | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6261159ced4d883e141343ff/original/unified-synthesis-of-multiply-arylated-alkanes-by-catalytic-deoxygenative-transformation-of-diarylketones.pdf |
63e0e239a8f79476ca6e7d9f | 10.26434/chemrxiv-2023-jbb0r | Unexpected Discovery of Saturated Pyridine Mimetics | A general approach to 3-azabicyclo[3.1.1]heptanes was unexpectedly discovered. The mechanism, scope, and scalability of this method were studied. The core was incorporated into the structure of the antihistamine drug Rupatidine instead of the pyridine ring, which led to a dramatic improvement in physicochemical properties. | Dmitry Dibchak; Mariya Snisarenko; Artem Mishuk; Oleg Shablykin; Lina Bortnichuk; Oleksii Klymenko-Ulianov; Yurii Kheylik; Iryna Sadkova; Henry Rzepa; Pavel Mykhailiuk | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e0e239a8f79476ca6e7d9f/original/unexpected-discovery-of-saturated-pyridine-mimetics.pdf |
60c756bc567dfe21e1ec6539 | 10.26434/chemrxiv.14299631.v1 | The Environmental and Economic Viability of Chitosan Production in Guayas-Ecuador: A Robust Investment and Life Cycle Analysis | Ecuador is a country where shrimp production is one of its primary industries. It generates annually about 72 thousand tons of wastes in the form of shrimp shells. Therefore, using this waste as a raw material resource to produce chitosan, a biopolymer, is established. An environmental and economic performance study is carried out as a possible investment report; where a conceptual design of the process is defined, a financial viability report is obtained. An environmental impact report establishes the degree of harm to the environment. The economic viability study considered costs related to capital and operation for the processing of 5000 tons of shrimp shells each year. On the other hand, a life cycle assessment was performed to obtain the environmental impact for 1 kg of chitosan produce, where a cradle-to-gate approach was established. Results showed that this new industry has a net present value of 10.38 million USD, a rate of return of 67.31%, and a payback period of 0.7 years. Additionally, it was calculated that the environmental impact with a higher normalized value was the human non-carcinogenic toxicity. It is concluded that the production of chitosan in Guayas-Ecuador is economically viable, cost-competitive in the market, and it represents an industrial activity with no considerable environmental impacts. | Ariel Riofrio; Tania Alcivar; Haci Baykara | Industrial Manufacturing; Natural Resource Recovery | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756bc567dfe21e1ec6539/original/the-environmental-and-economic-viability-of-chitosan-production-in-guayas-ecuador-a-robust-investment-and-life-cycle-analysis.pdf |
60c751bc702a9b42e418bff5 | 10.26434/chemrxiv.13138349.v1 | NMR Metabolomics and Metabolic Pathways Analysis of Cassava Genotypes at Different Harvesting Times and Cooking Characteristics | Cassava is an important staple food for low income countries. However, its cooking characteristics are especially affected by genotype. In this study, two groups of genotypes, namely hard to cook (HTC) and easy to cook (ETC), harvested at different times (9 and 15 months) were evaluated by <sup>1</sup>H NMR and chemometrics. Additionally, the lignin of these materials was studied by <sup>1</sup>H-<sup>13</sup>C HSQC. The carbohydrates were the most important class of compounds to differentiate the cassava genotypes. The correlation of NMR with cooking time and starch content showed that the higher content of primary metabolites, mostly glucose, can be associated to longer cooking times and reduction of starch corroborating the metabolic pathways analysis. Furthermore, it was observed that the lignin from cell wall did not differentiate the cooking performance of the genotypes. | Elenilson Godoy Alves Filho; Lorena Mara Alexandre Silva; Robson M. Martins; Willyane J.D.J. Oliveira; Cristine Soares Vidal; Luciana Alves de Oliveira; Edy Brito | Food | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751bc702a9b42e418bff5/original/nmr-metabolomics-and-metabolic-pathways-analysis-of-cassava-genotypes-at-different-harvesting-times-and-cooking-characteristics.pdf |
62a806f6bb7519929b4d9708 | 10.26434/chemrxiv-2022-53r4m | Direct synthesis of cyanate anion from dinitrogen catalysed by molybdenum complexes bearing pincer-type ligand | Molybdenum–carbamate complex bearing a pyridine-based 2,6-bis(di-tert-butylphosphinomethyl)pyridine (PNP)-pincer ligand is synthesised from the reaction of a molybdenum–nitride complex with phenyl chloroformate. The conversion between the molybdenum–carbamate complex and the molybdenum–nitride complex under ambient reaction conditions is achieved. The use of samarium diiodide (SmI2) as a reductant promotes the formation of cyanate anion (NCO−) from the molybdenum–carbamate complex as a key step. Based on the stoichiometric reactions, we have demonstrated a synthetic cycle for NCO− from dinitrogen mediated by the molybdenum–PNP complexes in two steps. Based on this synthetic cycle, we have achieved the catalytic synthesis of NCO− from dinitrogen under ambient reaction conditions. We believe that these results described in this manuscript provide valuable information to achieve the catalytic transformations of dinitrogen into valuable organonitrogen compounds under ambient reaction conditions. | Takayuki Itabashi; Kazuya Arashiba; Akihito Egi; Hiromasa Tanaka; Shogo Kuriyama; Kazunari Yoshizawa; Yoshiaki Nishibayashi | Organometallic Chemistry; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a806f6bb7519929b4d9708/original/direct-synthesis-of-cyanate-anion-from-dinitrogen-catalysed-by-molybdenum-complexes-bearing-pincer-type-ligand.pdf |
60c74999337d6c8ee3e2773f | 10.26434/chemrxiv.12085875.v1 | Photocatalytic N-Heteroarylation of Aldehydes via Formyl C‒ H Activation | A formal C‒H addition of N-heteroaromatics to aldehydes<br />was achieved using a binary hybrid catalyst system comprising an acridinium photoredox catalyst and a thiophosphoric acid organocatalyst. The reaction proceeded through the following sequence: 1) photoredox-catalyzed single-electron oxidation of a thiophosphoric acid catalyst to generate a thiyl radical, 2) cleavage of the formyl C‒H bond of the aldehyde substrates by a thiyl radical acting as a hydrogen atom transfer catalyst to generate acyl radicals, 3) Minisci-type addition of the resulting acyl radicals to N-heteroaromatics, and 4) a spin-center shift, photoredox-catalyzed single-electron reduction, and protonation to produce secondary alcohol products. This metal-free hybrid catalysis proceeded under mild conditions for a wide range of substrates, including isoquinolines, quinolines, and pyridines as N-heteroaromatics, as well as both aromatic and aliphatic aldehydes, and tolerated various functional groups. The reaction was applicable to late-stage derivatization of drugs and their leads. | Hiromu Fuse; Harunobu Mitsunuma; Motomu Kanai | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74999337d6c8ee3e2773f/original/photocatalytic-n-heteroarylation-of-aldehydes-via-formyl-c-h-activation.pdf |
649c8ef4ba3e99daef332e62 | 10.26434/chemrxiv-2023-w2r84 | Morpholine-mediated defluorinative cycloaddition of gem-difluoroalkenes and organic azides | Here, we report the first transition-metal free defluorinative cycloaddition of gem-difluoroalkenes with organic azides in morpholine as a solvent to construct fully decorated morpholine substituted-1,2,3-triazoles. Mechanistic studies revealed the formation of an addition-elimination intermediate containing a morpholine adduct of gem-difluoroalkenes prior to triazolization reaction via two plausible pathways. Attractive elements include regioselective and straightforward direct synthesis of fully substituted 1,2,3-triazoles, which are difficult to access, from readily available starting materials. | Tzu-Yu Huang; Mario Djugovski; Sweta Adhikari; Destinee Manning; Sudeshna Roy | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649c8ef4ba3e99daef332e62/original/morpholine-mediated-defluorinative-cycloaddition-of-gem-difluoroalkenes-and-organic-azides.pdf |
64dbde9c4a3f7d0c0d3b11c5 | 10.26434/chemrxiv-2023-jzwm3 | Navigating the Potential Energy Surface of CdSe Magic-Sized Clusters: Synthesis and Interconversion of Atomically Precise Nanocrystal Polymorphs | Magic-sized clusters (MSCs) are kinetically stable, atomically precise intermediates along the quantum dot (QD) reaction potential energy surface. Literature precedent establishes two classes of cadmium selenide MSCs with QD-like inorganic cores: one class is proposed to be cation-rich with a zincblende crystal structure, while the other is proposed to be stoichiometric with a “wurtzite-like” core. However, the wide range of synthetic protocols used to access MSCs has made direct comparison of their structure and surface chemistry difficult. Furthermore, the physical and chemical relationship between MSC polymorphs has yet to be established. Here, we demonstrate that both cation-rich and stoichiometric CdSe MSCs can be synthesized from identical reagents and can be interconverted through the addition of either excess cadmium or selenium precursor. The structural and compositional differences between these two polymorphs can be contrasted using a combination of 1H-NMR spectroscopy, x-ray diffraction, pair distribution function (PDF) analysis, inductively coupled plasma optical emission spectroscopy, and UV-vis transient absorption spectroscopy. The subsequent polymorph interconversion reactions are monitored by UV-vis spectroscopy, with evidence for an altered cluster atomic structure observed by powder x-ray diffraction and PDF analysis. This work helps simplify the complex picture of the CdSe nanocrystal landscape and provides a method to explore structure-property relationships in colloidal semiconductors through atomically precise synthesis. | Hunter Ripberger; Kyle Schnitzenbaumer; Lily Nguyen; Dylan Ladd; Kelsey Levine; Damara Dayton; Michael Toney; Brandi Cossairt | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Bonding; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dbde9c4a3f7d0c0d3b11c5/original/navigating-the-potential-energy-surface-of-cd-se-magic-sized-clusters-synthesis-and-interconversion-of-atomically-precise-nanocrystal-polymorphs.pdf |
660e49c191aefa6ce1bffbb5 | 10.26434/chemrxiv-2024-pq2kg | Water clustering modulates activity and enables hydrogenated product formation during carbon monoxide electroreduction in aprotic media | Water solvation plays a critical role in a wide range of electrochemical transformations, but its role is often convoluted since it is typically used as both solvent and proton source. Here, we experimentally control water speciation and activity using aprotic solvent media during carbon monoxide reduction reaction (CORR). Remarkably, we show that aprotic solvents that support microheterogeneous water-water clusters leads to significant amounts of CORR products (methane and ethylene) with a maximum ethylene Faradaic efficiency of 22% in acetonitrile (χH2O = 0.2); the first report of heterogeneous CORR to C2+ products using water as a proton source in an aprotic solvent. In contrast, microhomogeneous systems – where water integrates into the solvents’ intermolecular binding network and has lower activity – primarily support undesired hydrogen evolution reaction (HER). Insights gained expand our understanding of water activity and nonaqueous electrolyte design for other important transformations reactions beyond CO reduction such as CO2RR and HER. | Hannah Fejzic; Ritesh Kumar; Reginaldo Gomes; Lilin He; Theodore Houser; Jaemin Kim; Nora Molten; Chibueze Amanchukwu | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e49c191aefa6ce1bffbb5/original/water-clustering-modulates-activity-and-enables-hydrogenated-product-formation-during-carbon-monoxide-electroreduction-in-aprotic-media.pdf |
66c89f4c20ac769e5f9535a9 | 10.26434/chemrxiv-2024-cwnf8-v2 | Digestion-Free Middle-down Mass Spectrometry Method for Absolute Quantification of Conjugated Payload from ADCs | Antibody-drug conjugate (ADC) is a therapeutic modality that aims to improve payload delivery specificity and reduce systemic toxicity. Considering the complex structure of ADCs, various bioanalytical methods by liquid chromatography coupled with mass spectrometry (LC-MS) and ligand binding assay (LBA) as well as hybrid LBA-LC-MS approaches have been established for ADC characterization and quantification. LCMS-based assays enable Drug-Antibody Ratio (DAR) sensitive quantification of conjugated payload. For quantitative DAR-sensitive assessment by LC-MS/MS, typically the conjugated payload is enzymatically liberated and quantified. Despite recent advances in ADC bioanalytical methods, the DAR-sensitive quantification of non-cleavable linker ADCs by LC-MS/MS remains challenging. Thus, we developed a novel digestion-free middle-down mass spectrometry (DF-MDMS) using collision-induced dissociation approach for absolute quantification of conjugated payload for four different ADCs in biological matrix with minimum sample preparation. These results demonstrate that ADCs with different linker-payload structures can be quantified, including a non-cleavable linker ADC trastuzumab emtansine. It also shows that the assay sensitivity is comparable to conventional ADC quantification method by linker-payload cleavage using enzyme, while assay dynamic range depends on factors including payload ionization and dissociation efficiency, DAR and its distribution, and species abundance. By demonstrating absolute quantification of both cleavable and non-cleavable linker ADCs, this novel middle-down ADC approach demonstrates its potential application in bioanalysis and analytical characterization, especially for early discovery where high-throughput screening is required as the new approach saves time and resources by not requiring enzymatic digestion for cleavable ADCs or development of anti-payload antibodies for non-cleavable linker ADCs. | Jiaqi Yuan; Hui Yin Tan; Yue Huang; Anton Rosenbaum | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c89f4c20ac769e5f9535a9/original/digestion-free-middle-down-mass-spectrometry-method-for-absolute-quantification-of-conjugated-payload-from-ad-cs.pdf |
62aba001e00d4e67fc2d4f2f | 10.26434/chemrxiv-2022-wzj0g | Mild and scalable synthesis of phosphonorhodamines | Since its discovery in 1887, rhodamines have become indispensable fluorophores for biological imaging. Recent studies have extensively explored heteroatom substitution at the 10' and a variety of substitution patterns on the 3', 6' nitrogens. Although 3-carboxy-substituted rhodamines were first reported in 1887 and their 3-sulfonated derivatives in 1896, the 3-phosphono analogues have never been reported. We recently reported the synthesis of 3-phosphono fluoresceins, which possessed nearly identical spectral properties to the parent carboxy dyes, but showed enhanced water solubility. However, synthesis and purification were difficult, and yields were low (<17%). Here, we report a mild, generalizable, and scalable synthetic route to 3-phosphonorhodamines. We explore the substrate scope and investigate mechanistic details of the acid-free condensation. Tetramethyl-3-phosphonorhodamine (pTMR) derivatives can be accessed on the 1.5 mmol scale in up to 98% yield (2 steps). Phosphonorhodmines show a 12- to 500-fold increase in water solubility over 3-carboxy and 3-sulfonorhodamine derivatives and have excellent chemical stability. Phosphonates allow for derivatization, and esterification of pTMR allows intracellular delivery with localization profiles that differ from 3-carboxyrhodamines. The free phosphonate can be incorporated into a molecular wire scaffold to create a phosphonated rhodamine voltage reporter, phosphonoRhoVR. PhosRhoVR 1 can be synthesized in just 6 steps, with an overall yield of 37% to provide >400 mg of material, compared to a 6-step, ~2% yield for the previously reported RhoVR 1. PhosRhoVR 1 possesses excellent voltage sensitivity (37% ΔF/F) and a 2-fold increase in cellular brightness compared to RhoVR 1. | Joshua Turnbull; Ryan Golden; Brittany Benlian; Evan Miller | Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62aba001e00d4e67fc2d4f2f/original/mild-and-scalable-synthesis-of-phosphonorhodamines.pdf |
60c7548e0f50dba5b9397d43 | 10.26434/chemrxiv.13656665.v1 | Using Python and Google Colab to Teach Physical Chemistry During Pandemic | <div> The present manuscript intends to propose using the
Google Colab platform to teach and solve physical chemistry problems using
Python computational language. Seven Jupyter notebooks were written and made
available for the students via Google Colab supplementary material of the
physical chemistry course of the chemical engineering course of the Technological
Faculty of the Rio de Janeiro State University. These notebooks include several
problems extracted from the course bibliography and solved with the use of
Python language. The scripts show how the students can perform linear and
polynomial regressions, fit math models to given data, perform numerical
integration and plot creation using Python and its standards libraries. The
Colab platform was chosen because it is free to use, does not require the
installation, setup, and configuration of Python packages and their libraries
in the students’ personal computers. It is a multiuser and collaborative
environment, ideal for remote classes. The notebooks can be shared between
instructor and students or between the students, which easy the communication
and track of students’ progress. Indeed, this resource can be useful even after
the end of the pandemic. This manuscript describes the platform, its
advantages, how it was applied in our physical chemistry course, and the
students’ feedback at the end of the term. All notebooks are available as
Supplementary Material of the manuscript, translated from Portuguese to English
since our course is entirely in Portuguese. I hope the material and experience
shared in this manuscript can be helpful to chemistry instructors who intend to
abroad their pedagogical methods to engage more students in the undergraduate
courses. </div> | Leonardo Baptista | Chemical Education - General; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7548e0f50dba5b9397d43/original/using-python-and-google-colab-to-teach-physical-chemistry-during-pandemic.pdf |
653e9fa248dad23120a74dd1 | 10.26434/chemrxiv-2023-8p6j4 | Conformational Energy Landscapes of Amphiphiles Are Modulated by Polar Co-solutes – a Markov Analysis | Microemulsions are increasingly employed within industrial processes in the pharmaceutical, food, cosmetics and petroleum industries, as well as in fundamental technologies like chemical separations. Molecular level details of microemulsion structure is a growing area of interest, as more evidence is demonstrating that intermolecular interactions between the assembled amphiphiles tune the size, shape and inter-micelle interactions within the solution. A number of features influence intermolecular interactions, including the molecular conformation of amphiphiles (through modulation of the dipole moment and molecular packing). The conformational potential energy landscape (PEL) for amphiphiles has a topology that is dictated not only by intramolecular degrees of freedom and interactions (e.g., internal hydrogen bonds) but also by how different conformations are influenced by direct solvent-solute interactions. Atomistic molecular simulations can sample the conformational ensemble, yet when monomeric units have high degrees of freedom they generate a huge amount of high-dimensional complex data. Under these circumstances, Markov state models (MSMs) are an as yet under-utilized tool to analyze simulation trajectories and provide a way to understand the conformational free energy landscape and its dependence upon solution conditions. Here, polar solute...amphiphile interactions are hypothesized to collectively control the amphiphile conformational distribution and modulate the underlying PEL. A workflow is developed for Markov state modelling that investigates the large pool of conformations that arise from the breadth of amphiphiles present in MD simulation; the MSM is used to explain the important changes to the topology of the PEL that results from solute-solvent interactions. | Biswajit Sadhu; Aurora Clark | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653e9fa248dad23120a74dd1/original/conformational-energy-landscapes-of-amphiphiles-are-modulated-by-polar-co-solutes-a-markov-analysis.pdf |
655d90195bc9fcb5c9143ff0 | 10.26434/chemrxiv-2023-w82kh | Anomalous Diffusive and Electric-field-driven Ion
Transport in Boron-Nitride Nanotubes | We report on anomalous transport of ions in solution through macroscopic arrays of vertically aligned, surface-charged boron-nitride nanotubes (BNNTs). The 3- and 12nm-diameter BNNTs revealed two atypical transport phenomena: (i) ultra-fast cation-selective diffusion under concentration gradients that exceeded Fickian diffusion by up to 31-fold and (ii) anomalous relative diffusion rates and ionic conductances for alkali-metal ions (K+, Na+, and Li+) that were opposite to the ordering of their bulk mobilities in solution, and also different from that observed in carbon nanotubes and 2D boron-nitride (BN) nanochannels. The enhanced diffusive transport is shown to result from diffusio-osmosis at the charged BN walls, with the enhancement scaling inversely with pore diameter. The anomalous relative diffusivities for different cations is seen to arise from ion-specific interactions with the charged surface of the BNNTs. These unusual transport phenomena, as well as the flexible and scalable membrane-fabrication process, may enable ion-selective membranes optimized for “blue” energy conversion, lithium recovery, and other molecular separations. As an example, macroscopic arrays of aligned BNNTs in a salt-concentration gradient produced per-pore osmotic-power densities up 15,300 W/m2, with energy-conversion efficiencies approaching the theoretical maximum of 50%. | Semih Cetindag; Aaditya Pendse; Richard J. Castellano; Pavel Rehak; Matthew Howard; Ku Wang; Joshua Yi; Robert F. Praino; Petr Kral; Liping Liu; Sangil Kim; Jerry W. Shan | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanofluidics; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655d90195bc9fcb5c9143ff0/original/anomalous-diffusive-and-electric-field-driven-ion-transport-in-boron-nitride-nanotubes.pdf |
64f21ad679853bbd78e1d6c7 | 10.26434/chemrxiv-2023-b9x37 | Modulation of the photochromic properties of TPE and other tetrasubstituted olefins by the “amino conjugation effect”: a quantitative study | Tetraphenylethylene (TPE) derivatives have been a key building block in the development of solid-state fluorophores with tunable emission wavelength and large quantum efficiencies. Recent literature has brought an array of evidence that rotation around the central C=C bond constitutes main route of deexcitation in solution, and that its restriction in solid-state leads to aggregation-induced emission (AIE) in this family of derivatives. However, the influence of substitution on the dynamics of TPEs in solution has so far received little attention, probably because of the difficulty in efficiently separating (E) and (Z) isomers. Here we report the photophysical properties in solution of extended stereopure TPE derivatives. The introduction of triphenylamine (TPA) substituent results in differences in the spectral properties between the (E) and (Z) isomers, thereby allowing modulation of the photostationary state (PSS) and thus switching in the equilibrium between these two forms depending on the irradiation wavelength. Importantly, we show that this photochromism is observed with a very marked decrease in the photoisomerization quantum yields (Φiso) of TPE-TPA, compared to non-extended TPE derivatives, which we attribute to the so called “amino conjugation effect” already reported for several stilbene derivatives. As a generalization of this mechanism, we show that TPA substitution provides similar effect on other stilbenoid derivatives. These results provide important new insight into the photophysics of electron donor substituted TPEs, and their possible use as photochromic materials. | Jean Rouillon; Chantal Andraud; Cyrille Monnereau | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f21ad679853bbd78e1d6c7/original/modulation-of-the-photochromic-properties-of-tpe-and-other-tetrasubstituted-olefins-by-the-amino-conjugation-effect-a-quantitative-study.pdf |
63558e5a1db0bd512b3676e0 | 10.26434/chemrxiv-2022-gxmvh | Enhanced photocatalytic activity of Cs4PbBr6/WS2 hybrid nanocomposite | Photocatalytic processes are among the prime means for mitigating the pollution caused by toxic effluents. In this context, photocatalysis presents a promising path and undergoing rapid evolution. Halide perovskites (HPs) are excellent candidates due to their negative conduction band minimum and the low work function that are essential for photocatalysis. Interestingly, HPs performance significantly improves by introducing transitional-metal dichalcogenides as a co-catalyst, which enables suppressed charge recombination. Here we investigate the photocatalytic performance of Cs4PbBr6/WS2 nanocomposites towards organic dye degradation under visible light illumination. We found that the Cs4PbBr6/WS2 nanostructures significantly increase the degradation rate of methylene blue compared to pristine Cs4PbBr6 nanocrystals. The transient absorption measurements reveal charge transfer from Cs4PbBr6 to WS2. The results of our study imply that the boosted photocatalytic performance of the nanocomposites is due to the reduced carrier recombination. Our findings pave the way for the implementation of Cs4PbBr6/WS2 nanocomposites as superior photocatalysts. | Philip Nathaniel Immanuel; Song-Jeng Huang; Pravrati Taank; Achiad Goldreich; Jonathan Prilusky; Archana Byregowda; Raanan Carmieli; Alla Zak; Naresh Aggarwal; K. V. Adarsh; Lena Yadgarov | Materials Science; Catalysis; Nanoscience; Dyes and Chromophores; Nanocatalysis - Catalysts & Materials; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63558e5a1db0bd512b3676e0/original/enhanced-photocatalytic-activity-of-cs4pb-br6-ws2-hybrid-nanocomposite.pdf |
60c7526e469df498f2f44b65 | 10.26434/chemrxiv.13296869.v1 | Can Halogen Clusters be Emissive? | Halogen-halogen short contacts, especially halogen bonds (XBs) have been widely utilized
in multifarious fields, owing to its bridging function among luminophores as well as well-known heavy
atom effect. However, little attention has been paid to the luminescent ability of halogen clusters. It
remains unknown whether they are emissive. Herein, inspirited by the clustering-triggered emission of
nonconventional luminophores, we report the first examples of emissive halogen clusters with
fluorescence-phosphorescence dual emission in aggregated state and even under ambient conditions.
Additionally, multi-tunable PL in response to excitation wavelength, temperature, and pressure are
noticed. These results shed new lights on the underlying emission mechanism and would inspirit further
exploration of nonconventional luminophores involving halogen moieties. | Zihao Zhao; Saixing Tang; Siyu Tao; Tianjia Yang; Yueying Lai; Wang Zhang Yuan | Dyes and Chromophores; Optical Materials; Clusters; Optics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7526e469df498f2f44b65/original/can-halogen-clusters-be-emissive.pdf |
62af6df1f5524a9d9f187ce5 | 10.26434/chemrxiv-2022-ltz8p | Dynamic Electrocatalysis: Examining Resonant Catalytic Rate Enhancement Under Oscillating Electrochemical Potential | It has been shown through recent simulations that heterogeneous catalysts with dynamic properties – for example, the ability to vary adsorbate binding energy with time – could, in principle, reach higher turnover frequencies (TOFs) than an optimized catalyst operating at steady state (i.e. the “volcano curve” maximum, assuming typical scaling relations between elementary steps of the reaction). The enhancements are maximized near resonant frequencies in line with the time scales of the elementary steps. In this work, we perform a microkinetic analysis on a generalized electrochemical mechanism in order to evaluate the extent to which electrochemical potential can be used as a lever to achieve resonant catalytic rate enhancement. We illustrate that, because changing the electrochemical potential changes the free energy of reaction, the approach is conceptually distinct from oscillating binding energies of catalytic intermediates in isolation. However, benchmarks for rate and efficiency gains relative to potentiostatic operation can still be defined. We show that for faradaic reactions in series, no enhancements relative to the maximum steady-state TOF (within the potential range spanned by oscillation) can be achieved, even in cases where the dynamic potential limits favor adsorption and desorption, respectively. Enhancements relative to the average steady-state TOF (weighted by time at each potential), can be achieved at specific frequency/amplitude/duty cycle combinations, but only if the elementary reactions show disparate symmetry factors. In contrast, if a faradaically-driven parallel reaction controls the coverage of a strongly-adsorbed blocking species on a surface, significant dynamic rate enhancements over the maximum steady-state TOFs can be achieved, albeit at a significant cost of thermodynamic efficiency. We discuss how these simulations elucidate the possible sources of rate enhancements observed experimentally for dynamic electrocatalytic systems. | Adam Baz; Mason Lyons; Adam Holewinski | Physical Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Electrocatalysis; Heterogeneous Catalysis; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2022-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62af6df1f5524a9d9f187ce5/original/dynamic-electrocatalysis-examining-resonant-catalytic-rate-enhancement-under-oscillating-electrochemical-potential.pdf |
6596e465e9ebbb4db96f862d | 10.26434/chemrxiv-2024-g19r6 | Cytotoxic, Antiproliferative and Pro-apoptotic Activities of Spirobisindole Alkaloids from the Philippine Medicinal Plant Voacanga globosa | Cancer remains a public health burden which is currently exacerbated by the occurrence of chemotherapeutic resistance and adverse effects associated with present drugs. Owing to their structural diversity and well-established pharmaceutical activities, natural products have been tapped in anticancer drug discovery. Herein, we investigated the cytotoxic and antiproliferative activities of spirobisindole alkaloids from the Philippine medicinal plant Voacanga globosa, including the pro-apoptotic activity of the most potent alkaloid. Previously isolated alkaloids globospiramine (1), deoxyvobtusine (2) and vobtusine lactone (3) were subjected to in vitro MTT and CellTiter Blue assays. Alkaloids 1-3 showed cytotoxicity and antiproliferative activities against tested cell lines (L929, KB3.1, A431, MCF-7, A549, PC-3, and SKOV-3) with 1 being the most biologically active. Western blot analysis revealed 1 promoted increased expression of cleaved caspase-3 and PARP, which are indicators that the treated cancer cells underwent the caspase-dependent apoptosis. Overall, our study demonstrated the anticancer potentials of spirobisindole alkaloids, especially globospiramine (1), from Voacanga globosa. The pro-apoptotic activity of globospiramine (1) is also reported. | JOE ANTHONY MANZANO; ELIAN ANGELO ABELLANOSA; CHIA-HUNG YEN; ALLAN PATRICK MACABEO; NICANOR PIER AUSTRIACO | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6596e465e9ebbb4db96f862d/original/cytotoxic-antiproliferative-and-pro-apoptotic-activities-of-spirobisindole-alkaloids-from-the-philippine-medicinal-plant-voacanga-globosa.pdf |
62fe520858843b49089425e5 | 10.26434/chemrxiv-2022-78s83 | Backward Elimination: A Strategy for High-Entropy Alloy Catalyst Discovery | A promising opportunity and major challenge in the field of High-Entropy Alloy (HEA) catalysis is the abundance of possible compositions. The number of possible compositions makes it impossible to study all of them. Therefore, sophisticated methods are required to intelligently select interesting compositions. On one hand, adding an element to a composition space increases the dimensionality of that space and the number of compositions within it combinatorially. However, it also increases the number of sub-spaces that are part of this larger composition space. Assuming a constant sampling density, the number of experiments required to study a large, combined composition space of sufficient dimensionality can be less than studying all of its individual sub-spaces. This hypothesis is investigated using experimental work in which 200 compositions in an 8-element composition space composed of Au, Ir, Os, Pd, Pt, Re, Rh, and Ru were synthesized as nanoparticles. Each composition was experimentally tested for the electrocatalytic activity towards the oxygen reduction reaction. The model that was constructed using this data turned out to adequately predict data in three of its 5-element composition sub-spaces. This observation paves way for a backward elimination strategy in HEA discovery. According to this strategy all elements of interest are studied in a single composition space from which knowledge of all subspaces can be learnt. Subsequently, elements that do not show a positive influence towards the studied reaction can be removed from the search space. Ultimately, this backward elimination search produces an alloy space which has a high probability of containing the most active catalyst composition. | Vladislav Mints; Jack Kirk Pedersen; Gustav Karl Henrik Wiberg; Jan Rossmeisl; Matthias Arenz | Physical Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fe520858843b49089425e5/original/backward-elimination-a-strategy-for-high-entropy-alloy-catalyst-discovery.pdf |
65c1310be9ebbb4db9bcb67a | 10.26434/chemrxiv-2024-x60hm | Iodine in the Atmosphere I: Computational Benchmark and Dimer Formation of Oxy-acids and Oxides | The contribution of iodine-containing compounds to atmospheric new particle formation is still not fully understood, but iodic acid and iodous acid are thought to be significant contributors. While several quantum chemical studies have been carried out on clusters containing iodine, there is no comprehensive benchmark study quantifying the accuracy of the applied methods. Here, we present the first paper in a series that investigate the role iodine species in atmospheric cluster formation. In this work, we have studied the iodic and iodous acid monomers, the iodine tetroxide and iodine pentoxide monomers, and their dimer formation with common atmospheric precursors. We have tested the accuracy of commonly applied methods for calculating the geome- try of the monomers, thermal corrections of monomers and dimers, the contribution of spin-orbit coupling to monomers and dimers, and finally the accuracy of the electronic energy correction calculated at different levels of theory. We find that optimizing the structures either at the ωB97X-D3BJ/aug-cc-pVTZ-PP or the M06-2X/aug-cc-pVTZ-PP level achieves the best thermal contribution to the binding free energy. The electronic energy correction can then be calculated at the ZORA-DLPNO-CCSD(T0) level with the SARC-ZORA-TZVPP basis for iodine and ma-ZORA-def2-TZVPP for non-iodine atoms. This combination of methods yields results in excellent agreement with fully relativistic calculations at a comparatively low computational cost. We applied this methodology to calculate binding free energies of the iodine-containing dimer clusters, where we confirm the qualitative trends observed in previous studies. However, we identify that previous studies overestimate the stability of the clusters by several kcal/mol due to the neglect of relativistic effects. This means that their contribution to the currently studied nucleation pathways of new particle formation is likely overestimated. | Morten Engsvang; Haide Wu; Jonas Elm | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Clusters; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c1310be9ebbb4db9bcb67a/original/iodine-in-the-atmosphere-i-computational-benchmark-and-dimer-formation-of-oxy-acids-and-oxides.pdf |
657787d8bec7913d276385b8 | 10.26434/chemrxiv-2023-2jvp6 | Cross-Electrophile Coupling of Benzyl Halides and Disulfides Catalyzed by Iron | Cross-electrophile couplings are influential reactions that typically require a terminal reductant or photoredox conditions. We discovered an iron-catalyzed reaction that couples benzyl halide starting materials with disulfide building blocks to yield thioether products in the absence of a terminal reductant and photoredox conditions. The disclosed platform proceeds without sulfur-induced catalyst poisoning or the use of exogenous base, supporting a broad scope and circumventing undesired elimination pathways. We applied the developed chemistry in a new mode of disulfide bioconjugation, drug synthesis, gram-scale synthesis, and product derivatization. Lastly, we performed mechanistic experiments to better understand the stereoablative reaction between two electrophiles. Disulfides and benzylic thioethers are imperative motifs in biological and pharmaceutical applications, among other areas, that are severely understudied in comparison to their ethereal and amino counterparts. Hence, we expect this platform of iron catalysis and the downstream applications, including drug synthesis and a new form of bioconjugation, are of interest to the greater scientific community. | Julius Semenya; Yuanjie Yang; Elias Picazo | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657787d8bec7913d276385b8/original/cross-electrophile-coupling-of-benzyl-halides-and-disulfides-catalyzed-by-iron.pdf |
674420ec5a82cea2fab8e2f9 | 10.26434/chemrxiv-2024-4wfr8-v2 | Can SCF and ROKS DFT-based methods predict the inversion of the singlet-triplet gap in organic molecules? | Inverted singlet-triplet gap materials (INVEST) have emerged as an intriguing class of materials with potential applications as emitters in Organic Light Emitting Diodes (OLEDs). Indeed, this type of material exhibits a negative singlet-triplet energy gap (ΔEST), i.e., an inversion of the low-est singlet (S1) and triplet (T1) excited states, that goes against Hund’s rule. In this study, the ΔEST of a set of 15 INVEST molecules has been computed within the framework of Restricted Open-Shell Kohn-Sham (ROKS) and Delta Self-Consistent Field (ΔSCF) methods and the results benchmarked against wavefunction-based calculations performed at the EOM-CCSD, NEVPT2 and SCS-CC2 levels. We find that ROKS always (and wrongly) predicts a positive ΔEST with global hybrid, meta-GGA and long-range corrected functionals and that this is almost functional-independent. We also show that the only way to get an inverted gap was to resort to double hy-brid functionals. In contrast, using the above-mentioned functionals, ΔSCF usually gives a nega-tive ΔEST, although the results are largely functional-dependent. Overall, applying a ΔSCF meth-od based on the PBE0 functional provides the lowest MSD and MAD with respect to EOM-CCSD results. We further show that the singlet-triplet inversion is driven by different degrees of orbital relaxation in the singlet versus triplet state and that this is well captured by ΔSCF calcula-tions. As a matter of fact, this orbital relaxation in ΔSCF somehow mimics the involvement of double and higher-order excitations in EOM-CCSD, which leads to a difference in spatial locali-zation of the and spins, and accounts for spin polarization effects sourcing the negative ΔEST. However, care should be taken when using the ΔSCF method to screen materials with potential INVEST behavior in view of their limited quantitative correlation with reference EOM-CCSD results on the molecular data basis used here. | Danillo Valverde; Gaetano Ricci; Juan Carlos Sancho García; David Beljonne; Yoann Olivier | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674420ec5a82cea2fab8e2f9/original/can-scf-and-roks-dft-based-methods-predict-the-inversion-of-the-singlet-triplet-gap-in-organic-molecules.pdf |
6510b51fed7d0eccc32673b0 | 10.26434/chemrxiv-2023-kr97k | How Nanoparticle Size and Bubble Merging is Governed by Short-Range Spatially-Controlled Double-Beam Laser Ablation in Liquids | Pulsed laser ablation in liquid (LAL) is a method for synthesizing nanoparticles with controlled composition and high purity. However, current research predominantly examines isolated cavitation bubbles, overlooking real-world LAL scenarios where numerous bubbles interact simultaneously. This study addresses this gap by investigating the effects of short-range micrometric spatially controlled double-pulse laser ablation in liquids on nanoparticle size distribution. Gold and YAG are used as model materials, and a dimensionless parameter, H*, is introduced to quantify the ratio between double bubble spatial separation and their maximum height. This parameter correlates with cavitation bubble merging time, bubble volume change rate, and subsequent nanoparticle size increase. Shadowgraphs provide valuable insights into bubble contact and fusion dynamics, showcasing phase separation by a thin water film and subsequent merging into a single bubble. Notably, a two-fold increase in nanoparticle size is observed for both Au and YAG at H* = 0.25. Our research indicates a strong association between nanoparticle size trends and cavitation bubble volume rate change, particularly emphasized at H* = 0.25. Understanding the dynamics of neighboring bubbles during LAL emphasizes the relevance of lateral pulse distances in dual-beam LAL, impacting particle size distribution in a distance-dependent manner. | Farbod Riahi; Carlos Doñate-Buendía; Stephan Barcikowski; Bilal Gökce | Materials Science; Nanoscience; Materials Processing; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6510b51fed7d0eccc32673b0/original/how-nanoparticle-size-and-bubble-merging-is-governed-by-short-range-spatially-controlled-double-beam-laser-ablation-in-liquids.pdf |
60c74faa702a9b9a5718bc0d | 10.26434/chemrxiv.12927533.v1 | Structure and Formation of Soot Particles from Tribofilm Decomposition Under Real Engine Conditions | Lubrication of an internal combustion engine is critical for unwanted energy and material losses. Zinc dialkyldithiophosphate (ZDDP) is a commonly used anti-wear additive that forms by <i>in situ </i>decomposition a protecting interface between sliding surfaces. The interface consists of the tribofilm on both surfaces and oil in the contact. Soot particles from a petrol engine and gas engine were analyzed using X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) techniques: electron energy loss spectroscopy (EELS) and energy dispersive X-ray spectroscopy (EDS). These techniques revealed that the end-products in soot contain 3-5 nm ZnO-based particles with additions of phosphorus and sulfur, originating from the ZDDP anti-wear additive. Our results unravel the tribofilm decomposition under real field conditions and hint toward potentially unidentified hazards with respect to ZDDP-containing lubricants. | Thomas Thersleff; Istvan Zoltan Jenei; Serhiy Budnyk; Nicole Dörr; Adam Slabon | Environmental Science; Wastes; Analytical Chemistry - General; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74faa702a9b9a5718bc0d/original/structure-and-formation-of-soot-particles-from-tribofilm-decomposition-under-real-engine-conditions.pdf |
613e78faabeb63d5e0d09367 | 10.26434/chemrxiv-2021-j0r1x | DeltaPCA: A Statistically Robust Method for Detecting Protein Analyte Binding to Aptamer-Functionalised Nanoparticles using Surface-Enhanced Raman Spectroscopy | In this work, we introduce a novel joint experimental design and computational analysis procedure to reliably and reproducibly quantify protein analyte binding to DNA aptamer-functionalised silver nanoparticles using slippery surface-enhanced Raman spectroscopy. We employ an indirect detection approach, based upon monitoring spectral changes in the covalent bond-stretching region as intermolecular bonds are formed between the surface-immobilized probe biomolecule and its target analyte. Sample variability is minimized by preparing aptamer-only and aptamer-plus-analyte samples under the same conditions, and then analysing difference spectra. To account for technical variability, multiple spectra are recorded from the same sample. Our new DeltaPCA analysis procedure takes into account technical variability within each spectral data set while also extracting statistically robust difference spectra between data sets. Proof of principle experiments using thiolated aptamers to detect CoV-SARS-2 spike protein reveal that analyte binding is mediated through the formation of N-H...X and C-H...X hydrogen bonds between the aptamer (H-bond donor) and protein (H-bond acceptor). Our computational analysis code can be freely downloaded from https://github.com/dlc62/DeltaPCA. | Fiona Given; Tamsyn Stanborough; Mark Waterland; Deborah Crittenden | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Spectroscopy (Anal. Chem.); Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613e78faabeb63d5e0d09367/original/delta-pca-a-statistically-robust-method-for-detecting-protein-analyte-binding-to-aptamer-functionalised-nanoparticles-using-surface-enhanced-raman-spectroscopy.pdf |
653408b787198ede07f92f7e | 10.26434/chemrxiv-2023-nwxjq | A Platform for Multiple Isotope Labeling via Carbon-Sulfur Bond Exchange | Isotopes are at the foundation of applications in life science such as nuclear imaging and are essential tools for the determination of pharmacokinetic and dynamic profiles of new pharmaceuticals. However, the insertion of an isotope into an organic molecule remains challenging and current technologies are element-specific. Despite the ubiquitous presence of sulfur in many biologically active molecules, sulfur isotope labeling is an underexplored field and sulfur isotope exchange has been overlooked. In this work, we explore a nickel-catalyzed reversible carbon-sulfur (C-S) bond activation strategy to achieve selective sulfur isotope exchange. This approach enables to move beyond standardized element-specific procedures and was applied to multiple isotopes, including deuterium, carbon-13, sulfur-34 and radioactive carbon-14. These results provide a unique platform for multiple isotope labeling and are compatible with a wide range of substrates, including pharmaceuticals. In addition, this technology proved its potential as isotopic encryption device of organic molecules. | Bouchaib Mouhsine; Maylis Norlöff; Juba Ghouilem; Antoine Sallustrau; Frédéric Taran; Davide Audisio | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653408b787198ede07f92f7e/original/a-platform-for-multiple-isotope-labeling-via-carbon-sulfur-bond-exchange.pdf |
67a41328fa469535b9340493 | 10.26434/chemrxiv-2025-z7wcx | Chemodivergent Defluorinative Alkylation and Hydroalkylation of α-Trifluoromethyl Alkenes via Eosin Y Catalysis and EDA Photo-chemistry | Herein, we report a novel, visible-light-induced approach for the selective construction of both gem-difluoroalkenes and trifluoromethyl alkanes from α-trifluoromethyl olefins using alcohol-derived N-alkoxyphthalimides as alkyl radical precursors. This strategy leverages Eosin Y as a photocatalyst in a defluorinative alkylation reaction and a catalyst-free electron donor-acceptor (EDA)-mediated hydroalkyl-ation process. By modulating the reaction conditions, the desired products were selectively obtained with excellent chemo-selectivity and in high yields. The protocol accommodates a wide variety of substrates, including primary, secondary, and tertiary alcohols, as well as diverse α-trifluoromethyl styrenes, and is applicable to late-stage functionalization of natural products and bioactive molecules. | Tianshuai Zhu; Xinyu Xie; Yue Zhang; Hua-Wei Liu; Jing-Jing Zhang; Zhen Chen | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a41328fa469535b9340493/original/chemodivergent-defluorinative-alkylation-and-hydroalkylation-of-trifluoromethyl-alkenes-via-eosin-y-catalysis-and-eda-photo-chemistry.pdf |
64111991b5d5dbe9e843f857 | 10.26434/chemrxiv-2022-lrqzq-v2 | Air-stable methyldisulfide-functionalized metal bis(terpyridine) complexes | Metal bis(terpyidine) complexes comprising directly connected methyldisulfide groups are synthetically accessible and air-stable in solution for ≥7 d, in stark contrast to their thiol analogues. These compounds exhibit a rich solution electrochemistry, and provide a robust foundation for future studies of this prominent class of molecules adsorbed on metal surfaces. | Christina Trang; Thomas Saal; Michael Inkpen | Physical Chemistry; Inorganic Chemistry; Nanoscience; Coordination Chemistry (Inorg.); Electrochemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64111991b5d5dbe9e843f857/original/air-stable-methyldisulfide-functionalized-metal-bis-terpyridine-complexes.pdf |
62ef6d77a05ea1c14b963e79 | 10.26434/chemrxiv-2022-g1n35 | A Au(I)-Catalyzed Alkoxylation-Induced Double Aldol Condensation Approach to 2,2'-Spirobi[indene] Derivatives | An efficient gold(I)-catalyzed intramolecular alkoxylation/double aldol condensation cascade cyclization strategy to synthesize 2,2'-spirobi[indene] derivatives has been developed. The scope of this strategy was examined by using a batch of synthetic alkynone substrates and a possible mechanism was proposed. | Jingfu Zhang; Sen Zhang; Zhixing Ding; Anbin Hou; Jiayue Fu; Hongwei Su; Maosheng Cheng; Bin Lin; Lu Yang; Yongxiang Liu | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ef6d77a05ea1c14b963e79/original/a-au-i-catalyzed-alkoxylation-induced-double-aldol-condensation-approach-to-2-2-spirobi-indene-derivatives.pdf |
649b40f0ba3e99daef2334f4 | 10.26434/chemrxiv-2023-rfg4t | Building an ab initio solvated DNA model using Euclidean
neural networks | Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine learning electron density model based on a Euclidean neural network framework to model explicitly solvated double-stranded DNA. The neural network framework has a built-in understanding of equivariance, allowing the model to learn 3D structural information efficiently by exploiting the properties of Euclidean symmetry. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level. | Alex Lee; Joshua Rackers; Shivesh Pathak; William Bricker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649b40f0ba3e99daef2334f4/original/building-an-ab-initio-solvated-dna-model-using-euclidean-neural-networks.pdf |
65b00ffe66c13817291b8eaf | 10.26434/chemrxiv-2024-80jqw | N-propionyl thiosuccinimide linker upon hydrolysis becomes into a cleavable crosslinker by a gas phase metastable fragmentation and makes more reliable the conjugation sites identification. | Maleimide thiol chemistry is widely used for the synthesis of conjugate vaccines and antibody-drug-conjugates. Proteolysis of a conjugate vaccine mainly generates linear and type 2 peptides (cross-linked peptides) with a thiosuccinimide linker and its stabilized forms (thiazine, and/or hydrolyzed thiosuccinimide). Type 2 peptides contain valuable information on the conjugation sites. Cleavable crosslinkers could make more reliable the conjugation sites identifications, but based on a different chemistry, they are used to study protein-protein interactions and not in the synthesis of bioconjugates. Hydrolysis not only stabilizes the thiosuccinimide linker, but also turns it into a cleavable crosslinker via a gas phase metastable fragmentation observed in MALDI- and ESI-MS/MS analysis. The carboxyl group in the hydrolyzed thiosuccinimide linker provides a mobile proton that destabilizes the nearest pseudopeptide bond and, through the rearrangement of a five-membered ring intermediate, yields two intense linker fragment ions named here as P+71 and C+98. Specific 18O-labeling of the hydrolyzed thiosuccinimide linker confirms that P+71 ion, has the epsilon amino group of Lys modified by a -alanine residue while C+98 ion has the Cys residue S-alkylated by a succinic anhydride molecule. P+71 and C+98 provide information on the molecular masses of the crosslinked peptides pair, decrease the number of unassigned signals in the MS/MS spectra; and their backbone fragment ions increased the sequence coverage and make more reliable the assignment of conjugation sites. Stepped HCD is the fragmentation method of choice because in a single MS/MS spectrum several linker fragment ions and bn/yn ions were observed. | Luis Javier González; Pablo Enmanuel Ramos; Satomy Pousa; Paulo Carvalho; Rodrigo Soares Caldeira Brant; Michel Batista; Hironobu Hojo; Alina Rodríguez Mallón; Vladimir Besada; Toshifumi Takao | Analytical Chemistry; Analytical Chemistry - General | CC BY 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b00ffe66c13817291b8eaf/original/n-propionyl-thiosuccinimide-linker-upon-hydrolysis-becomes-into-a-cleavable-crosslinker-by-a-gas-phase-metastable-fragmentation-and-makes-more-reliable-the-conjugation-sites-identification.pdf |
60c758179abda26838f8e83f | 10.26434/chemrxiv.14498676.v1 | Multicomponent Stereoselective Polymerizations toward Multifunctional AIE Polymers with α,β-Unsaturated Amidines | <p>Heterochain polymers play an essential role in our daily lives due to their distinctive properties. Among various heteroatom-rich structures, amidine derivatives serve as a synthetically important and pharmacologically useful structural branch and have found wide applications in synthetic chemistry and biomedicine field. In this work, we developed a straightforward and powerful polymerization tool to access diverse heterochain polymers with <i>α</i>,<i>β</i>-unsaturated amidine units. The multicomponent electrophilic polymerizations of readily accessible diynes, disulfonyl azides, and <i>N</i>,<i>N</i>-dimethylformamide dimethyl acetal proceed efficiently at room temperature, producing amidine-containing polymers with high molecular weights (<i>M</i><sub>w</sub> up to 74500) in high yields within merely 1 h. Nuclear magnetic resonance spectra analysis revealed that all the obtained polymers are formed with excellent stereoselectiviy. The introduction of aggregation-induced emission (AIE) luminogen together with the inherent heteroatom-rich structure feature endow these polymers with multiple functionalities. The nanoaggregates of the diethylamino-substituted polymer show remarkable and reversible fluorescence response to acid and base, and the acid-fumed polymer thin film can be used as a sensitive and reusable fluorescent probe for detecting seafood spoilage. This polymer system can also be employed as a highly selective and sensitive Au<sup>3+</sup> sensor, and efficient gold recovery can be achieved based on the excellent gold enrichment capability of the polymer. In addition, the AIE polymers can also be applied in lysosome-specific cell imaging with low cytotoxicity and excellent photostability.</p> | xiang su; Niu Niu; Haoxuan Li; Ting Han; Dong Wang; Ben Zhong Tang | Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758179abda26838f8e83f/original/multicomponent-stereoselective-polymerizations-toward-multifunctional-aie-polymers-with-unsaturated-amidines.pdf |
64b19aaeb605c6803bb62705 | 10.26434/chemrxiv-2023-frr79-v2 | Nature of the amorphous-amorphous interfaces in solid-state batteries revealed using machine-learned interatomic potentials | Non-crystalline solid materials have attracted growing attention in energy storage for their desirable properties such as ionic conductivity, stability and processability. However, compared to bulk crystalline materials, fundamental understanding of these highly complex metastable systems is hindered by the scale limitations of density functional theory (DFT) calculations and resolution limitations of experimental methods. To fill the knowledge gap and guide the rational design of amorphous battery materials and interfaces, we present a molecular dynamics (MD) framework based on machine-learned interatomic potentials trained on the fly to study the amorphous solid electrolyte Li3PS4 and its protective coating, amorphous Li3B11O18. The use of machine-learned potentials allows us to simulate the materials at time and length scales that are not accessible to DFT while maintaining a near-DFT level of accuracy. This approach allows us to calculate amorphization energies, amorphous-amorphous interface energies, and the impact of the interface on lithium ion conductivity. This study demonstrates the promising role of actively-learned interatomic potentials in extending the application of ab-initio modeling to more complex and realistic systems such as amorphous materials and interfaces. | Chuhong Wang; Muratahan Aykol; Tim Mueller | Theoretical and Computational Chemistry; Materials Science; Coating Materials; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b19aaeb605c6803bb62705/original/nature-of-the-amorphous-amorphous-interfaces-in-solid-state-batteries-revealed-using-machine-learned-interatomic-potentials.pdf |
65663f825bc9fcb5c998d5a3 | 10.26434/chemrxiv-2023-nnnf2-v2 | Speciation and organic phase structure in nitric acid extraction with trioctylamine | Understanding chemical speciation and intermolecular interactions in multicomponent liquids is essential to understanding their phase behavior, which underpins chemical separation processes including solvent extraction. Here we report on the extraction of nitric acid from its aqueous solutions into organic solutions of trioctylamine (TOA) in toluene, investigated with spectroscopic, X-ray scattering, and computational tools to understand the molecular speciation in the organic phase and its relationship with the nanoscale structure of the organic phase. Trends in acid and water extraction clearly show two and three regimes, respectively, but the speciation of HNO3, water, and amine in these regimes is not apparent. 1H-NMR of the organic phase shows that there are at least two distinct acidic protons in the organic phase while ATR-FTIR results show that the organic phase with excess acid extraction is a mixture of trioctylammonium-nitrate ion pairs (TOAH.NO3), and undissociated HNO3 molecules. Comparison with DFT-computed IR spectra show that the chain-like configurations of TOAH.NO3.HNO3.H2O are favored over TOAH.NO3.H2O.HNO3, i.e., direct interaction between the two HNO3 molecules is more favored compared to a water-mediated interaction. SAXS of the organic phases were modeled as sums of Ornstein-Zernike (O-Z) scattering and a prepeak feature in the higher Q region, corresponding to features from density fluctuations and extractant packing, respectively. The extraction of undissociated HNO3 by the ion pairs leads to an increased X-ray scattering contrast in the organic phase without any significant change in the O-Z correlation length. These results show that the organic phase nanostructure is more sensitive to the concentration of TOAH.NO3 and is relatively unaffected by excess acid extraction. These findings will enable a molecular understanding of the mechanisms behind metal extractions from acidic media with basic extractants. | Srikanth Nayak; Michael J. Servis; Derrick Combs; Krystian Szeliga; Soenke Seifert | Physical Chemistry; Solution Chemistry; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65663f825bc9fcb5c998d5a3/original/speciation-and-organic-phase-structure-in-nitric-acid-extraction-with-trioctylamine.pdf |
61af206302d90d723457742a | 10.26434/chemrxiv-2021-dhk4c | In vitro/ In vivo Electrochemical Detection of Pt(II) Species | The biodistribution of chemotherapy compounds within tumor tissue is one of the main challenges in the development of antineoplastic drugs, and novel techniques for simple, non-expensive, sensitive, and selective detection of various analytes in tumors are of great importance. In this paper we propose the use of platinized carbon nanoelectrodes (PtNE) for electrochemical detection of platinum-based drugs in various biological models, including single cells and tumor spheroids in vitro, and inside solid tumors in vivo. We have demonstrated quantitative direct detection of Pt(II) in breast adenocarcinoma MCF-7 cells treated with cisplatin and cisplatin-based DNP prodrug. To realize the potential of this technique in advanced tumor models, we measured Pt(II) in 3D tumor spheroids in vitro and tumor-bearing mice in vivo. The concentration gradient of Pt (II) species correlated with the distance from the sample surface in MCF-7 tumor spheroids. We then performed detection of Pt(II) species in tumor-bearing mice treated intravenously with cisplatin and DNP. We found that there was deeper penetration of DNP in comparison to cisplatin. This research demonstrates a novel minimally invasive, real-time electrochemical technique for the study of platinum-based drugs. | Alexander Vaneev; Petr Gorelkin; Olga Krasnovskaya; Roman Akasov; Daniil Spector; Elena Lopatukhina; Roman Timoshenko; Anastasia Garanina; Yanjun Zhang; Sergey Salikhov; Christopher Edwards; Natalia Klyachko; Yasufumi Takahashi; Alexander Majouga; Yuri Korchev; Alexander Erofeev | Analytical Chemistry; Nanoscience; Analytical Chemistry - General; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61af206302d90d723457742a/original/in-vitro-in-vivo-electrochemical-detection-of-pt-ii-species.pdf |
66032ad5e9ebbb4db99b0b9a | 10.26434/chemrxiv-2024-v2kgp | Assessing the activity of benzodioxol, phenol and aniline derivatives as radical trapping antioxidants that inhibit ferroptosis | A small molecule screen has identified a benzodioxol anilide as a ferroptosis inhibitor. To determine the structure-activity relationship (SAR) of this compound class, we have synthesized a library of 35 derivatives followed by testing their ability to inhibit cell death that was induced via RSL3, an inhibitor of the main ferroptosis regulator glutathione peroxidase 4 (GPX4), in the mouse embryonic fibroblast cell line Pfa-1. Choosing 12 representative structures, rescue experiments were performed following the tamoxifen-induced deletion of GPX4 in Pfa-1 cells to complement the pharmacological induction of ferroptosis with a genetic induction and the experiments were extended to the human epithelial lung adenocarcinoma cell line HCC827. To assess if the compounds act as radical trapping antioxidants (RTAs) that scavenge peroxy radicals which drive lipid peroxidation, a hallmark of ferroptotic cell death, we have used a fluorescence-enabled inhibited autoxidation (Fenix) assay. Mitochondria were identified as the site-of-action using an alkynylated benzodioxol probe together with a copper-catalyzed alkyne-azide cycloaddition (CuAAC)-based Alexa Fluor 488 imaging kit. Our SAR study has yielded insights into the substitution-dependent activity of benzodioxol, aniline and phenol groups as RTAs that inhibit ferroptosis which led to the design of MM-12-Urea as a new broadly applicable chemical probe. Since the investigated functional groups are common motifs in small molecule ligands or natural products, we highlight that it is worth testing their ability to act as RTAs to avoid a potentially compounding factor in their bioactivities. | Helene B. E. Schricker; Mohamed M. Mouzayek; Jonas Wanninger; Hala Zahran; Kyra Lützel; Anna V. Milton; Eikan Mishima; Toshitaka Nakamura; Bettina Proneth; Marcus Conrad; David B. Konrad | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66032ad5e9ebbb4db99b0b9a/original/assessing-the-activity-of-benzodioxol-phenol-and-aniline-derivatives-as-radical-trapping-antioxidants-that-inhibit-ferroptosis.pdf |
61f8af581fd27415ef2206d7 | 10.26434/chemrxiv-2022-1q5dw-v2 | Catalytic Addition of Nitroalkanes to Unactivated Alkenes via Directed Carbopalladation | We report a redox-neutral catalytic coupling of nitroalkanes and unactivated alkenes that proceeds by a directed carbopalladation mechanism. The reaction is uniquely enabled by the combination of PdI2 as the precatalyst and HFIP solvent. Structurally complex nitroalkane products, including nitro-containing carbo- and heterocycles, are prepared under operationally convenient conditions without the need for toxic or corrosive reagents. Deuterium labeling experiments and isolation of a catalytically relevant intermediate shed light on the reaction mechanism. By taking advantage of different catalytic activation modes, we demonstrate orthogonal methods for site-selective functionalization of a polyfunctional nitroalkyl ketone. | Amit Simlandy; Warabhorn Rodphon; Hui-Qi Ni; John Gurak; Keary Engle | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f8af581fd27415ef2206d7/original/catalytic-addition-of-nitroalkanes-to-unactivated-alkenes-via-directed-carbopalladation.pdf |
61b208cf25f39abb0cd2e16d | 10.26434/chemrxiv-2021-8t2vk | Visualizing the three-step freezing process and three-phase reaction not predicted by the (NH4) 2SO4/H2O phase diagram | According to the conventional phase diagrams, aqueous solutions freeze at the liquidus and are frozen/solid below the eutectic solidus. Herein, using differential scanning calorimetry (DSC) and optical cryo-microscopy (OC-M), we demonstrate that hy-poeutectic, eutectic 40 wt% (NH4)2SO4 and hypereutectic (NH4)2SO4/H2O remain liquid well below the eutectic solidus before freezing in three steps: fast-slow-fast. The first fast freezing produces a ramified ice microstructure (IM) and freeze-concentrated solution (FCS) containing up to ~70 wt% (NH4)2SO4. As temperature decreases further, the slow freezing of FCS precedes its fast freezing, which produces a striped IM and (NH4)2SO4 microcrystals. Videos recorded upon warming of frozen (NH4)2SO4/H2O reveal a new three-phase reaction, which is the recrystallization of ice and (NH4)2SO4 microcrystals into the lamellar eutectic ice-(NH4)2SO4 superlattice. This work demonstrates limitations of the (NH4)2SO4/H2O phase diagram and pro-poses an effective strategy for studying other deeply supercooled solutions whose behavior is not predicted by the phase dia-gram. | Anatoli Bogdan | Physical Chemistry; Physical and Chemical Processes; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2021-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b208cf25f39abb0cd2e16d/original/visualizing-the-three-step-freezing-process-and-three-phase-reaction-not-predicted-by-the-nh4-2so4-h2o-phase-diagram.pdf |
641c999a647e3dca9964f2a2 | 10.26434/chemrxiv-2023-7sn7h | Direct Light-Enabled Access to α-Boryl Radicals: Application in the Stereodivergent Synthesis of Allyl Boronic Esters | Operationally simple strategies to assemble boron containing organic frameworks are highly enabling in organic synthesis. While conventional retrosynthetic logic has engendered many platforms focusing on the direct formation of C–B bonds, α-boryl radicals have recently reemerged as versatile open-shell alternatives to access organoborons via adjacent C–C bond formation. Direct light-enabled α-activation is currently contingent on photo- or transition metal-catalysis activation to efficiently generate radical species. Here, we disclose a facile activation of α-halo boronic esters using only visible light and a simple Lewis base to enable homolytic scission. Intermolecular addition to styrenes facilitates the rapid construction of highly versatile E-allylic boronic esters. The simplicity of activation permits the strategic merger of this construct with selective energy transfer catalysis to enable the complimentary stereodivergent synthesis of Z-allylic boronic esters. | Alessandro Marotta; Hao Fang; Callum E. Adams; Kailey Sun Marcus; Constantin G. Daniliuc; John James Molloy | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641c999a647e3dca9964f2a2/original/direct-light-enabled-access-to-boryl-radicals-application-in-the-stereodivergent-synthesis-of-allyl-boronic-esters.pdf |
60c756bf9abda2c20af8e5a0 | 10.26434/chemrxiv.14317205.v1 | An Inverse Thermogelling Bioink Based on an ABA Type Poly(2-Oxazoline) Amphiphile | Hydrogels are key components in several biomedical research areas such as biofabrication. Here, a novel ABA-type triblock copolymer is introduced that undergoes a inverse thermogelation, i.e. it forms a hydrogel about cooling aqueous polymer solutions. The macroporous hydrogel was rheologically investigate in detail and used for 3D printing using an extrusion based printer. Preliminary experiment show very good cytocompatibility of NIH 3T3 cells also after printing and the possibility to combine the novel material with other hydrogel forming materials such as alginate.<br /> | Lukas Hahn; Emine Karakaya; Theresa Zorn; Benedikt Sochor; Matthias Maier; Philipp Stahlhut; Stefan Forster; Karl Fischer; Sebastian Seiffert; Ann-Christin Pöppler; Rainer Detsch; Robert Luxenhofer | Biocompatible Materials; Biological Materials; Biodegradable Materials; Composites; Materials Processing; Biopolymers; Hydrogels; Organic Polymers; Polymer scaffolds; Fluid Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756bf9abda2c20af8e5a0/original/an-inverse-thermogelling-bioink-based-on-an-aba-type-poly-2-oxazoline-amphiphile.pdf |
67aba6f081d2151a020104b0 | 10.26434/chemrxiv-2025-djf43-v2 | The Hitchhiker's Guide to Socratic Methods in Prompting Large Language Models for Chemistry Applications | The Socratic method, grounded in iterative questioning and critical dialogue, offers a compelling framework for leveraging large language models (LLMs) to advance scientific reasoning and discovery in chemistry and materials science. In this paper, we explore how Socratic principles can be integrated into prompt engineering to enhance model performance by fostering hypothesis refinement, conceptual clarity, and iterative problem-solving in computational and experimental chemistry. By aligning with chain-of-thought techniques, Socratic prompting enables systematic inquiry and deeper engagement with challenges such as defining key scientific concepts, evaluating competing theoretical models, and refining hypotheses through evidence-based reasoning. We also demonstrate how a structured approach that combines multiple Socratic principles enhances the adaptability and rigor of LLM-based scientific problem-solving. Through examples of Socratic prompting applied to chemistry and materials research, we illustrate how this method can refine hypotheses, improve model interpretability, and guide structured scientific reasoning. This work highlights the transformative potential of Socratic prompting as a structured reasoning tool for chemistry and a strategy for leveraging LLMs in scientific research. | Hassan Harb; Yunkai Sun; Rajeev Surendran Assary | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aba6f081d2151a020104b0/original/the-hitchhiker-s-guide-to-socratic-methods-in-prompting-large-language-models-for-chemistry-applications.pdf |
6306e6b7d147b260afb7c23c | 10.26434/chemrxiv-2022-0hx82 | Solvent-ligand Interactions Govern Stabilizing Repulsions between Colloidal Metal Oxide Nanocrystals | Nanocrystal interactions in solvent influence colloidal stability and dictate self-assembly outcomes. Small-angle X-ray scattering is used to study how dilute oleate-capped In2O3 nanocrystals with 7–19 nm core diameters interact when dispersed in a series of nonpolar solvents. Osmotic second virial coefficient analysis finds toluene-dispersed NCs interact like hard spheres with diameters comprising the inorganic core and a ligand-solvent corona with a core-size independent thickness. Dynamic light scattering measurements show consistent hydrodynamic and thermodynamic size scaling, further indicating hard-sphere-like behavior. By choosing solvents with stronger ligand-solvent attractions, the effective ligand-solvent corona thickness can be increased by approximately one solvent molecular diameter (0.8 nm). These results highlight the
role that solvent choice could play in designing nanocrystal contact spacing, important in the initial stages of superlattice assembly or for modulating the optical response of plasmonic or photoluminescent colloidal gel networks. | Charles Kofi Ofosu; Thomas M. Truskett; Delia J. Milliron | Physical Chemistry; Materials Science; Nanoscience; Interfaces; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6306e6b7d147b260afb7c23c/original/solvent-ligand-interactions-govern-stabilizing-repulsions-between-colloidal-metal-oxide-nanocrystals.pdf |
66c82ff0a4e53c487653b61a | 10.26434/chemrxiv-2024-34hhn | Fabrication of BaO-promoted Cobalt Catalyst Incorporated into Carbon Framework by Citric Acid Sol-gel Method for Ammonia Synthesis | Developing non-noble metal catalysts with excellent NH3 synthesis activity at mild conditions is a long-term objective. The reported best catalysts require either laborious multiple steps and controlled environments to fabricate the catalysts or high temperatures and long times to activate the catalysts. This work reports a facile one-pot method to fabricate carbon-based Ba-promoted Co catalysts via the citric acid sol-gel method using metal nitrates as precursors and water as the solvent, which allows the metal ions to be incorporated into the carbon framework homogeneously. The obtained (Ba/Co)0.3/C catalyst shows an outstanding NH3 synthesis activity of 34 mmol gcat−1 h−1 (350 oC, 1.0 MPa) with excellent stability. In-depth characterizations reveal that Ba exists as BaO, which is homogeneously distributed on the carbon framework and around the Co metal nanoparticles. We uncover that by retarding the BaCO3 formation in the fresh catalyst, the reduction temperature and time can be greatly decreased (485 oC/4 h), which is a fundamental advantage in this method. Density functional theory and molecular dynamics simulations indeed support the experimental observations. We anticipate that this facile and economical strategy will resolve the issues in a broad field of heterogeneous catalyst research. | Kanishka De Silva; Katsutoshi Sato; Takahiro Naito; Takaaki Toriyama; Tomokazu Yamamoto; Ryotaro Aso; Yasukazu Murakami; Pradeep Varadwaj; Ryoji Asahi; Koji Inazu; Katsutoshi Nagaoka | Materials Science; Catalysis; Chemical Engineering and Industrial Chemistry; Carbon-based Materials; Catalysts; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c82ff0a4e53c487653b61a/original/fabrication-of-ba-o-promoted-cobalt-catalyst-incorporated-into-carbon-framework-by-citric-acid-sol-gel-method-for-ammonia-synthesis.pdf |
61b84ac7dcbea271bba3cf51 | 10.26434/chemrxiv-2021-4jzd5 | Red Carbon: a Carbon-Oxygen-based covalent semiconductor for selective amine sensing | The requirements for organic semiconductor materials and new methods for their synthesis at low temperature have risen over the last decades, especially due to concerns of sustainability. Herein, we present an innovative method for the synthesis of a so-called “red carbon” thin film, being composed of carbon and oxygen, only. This material was already described by Kappe and Ziegler at the beginning of the 20th century, but now can complement the current research on covalent organic semiconductor materials. The herein described red carbon can be homogeneous deposited on glass substrates as thin ilms which reveal a highly ordered structure. The films are highly reactive towards amines and were employed as amine vapor sensors for a scope of analogous amines. The gas-to-solid phase reaction causes a significant change of the films optical properties in all cases, blue-shifting the bandgap and the photoluminescence spectra from the red to the near UV range. The irreversible chemical reaction between the thin film and the vapor was also exploited for the preparation of nitrogen containing thin carbon films. We expect the herein presented red carbon material is of interest not only for sensing applications, but also in optoelectronics. | Paolo Giusto; Daniel Cruz; Yael Rodriguez; Regina Rothe; Nadezda Tarakina | Materials Science; Carbon-based Materials; Optical Materials; Thin Films; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b84ac7dcbea271bba3cf51/original/red-carbon-a-carbon-oxygen-based-covalent-semiconductor-for-selective-amine-sensing.pdf |
676e183d6dde43c90877c52c | 10.26434/chemrxiv-2024-bl6f9 | Data-Driven Parametrization of All-atom force fields for Organic Semiconductors | Organic semiconductors (OSCs) composed of π conjugated molecules have gained significant interest in the study of bulk properties such as molecular arrangement and electron mobility. However, the types of torsion in the traditional force field (FF) are limited, fail to cover the chemical space of π conjugated molecules, and thus, hinder further molecular dynamics (MD) simulation to deduce these bulk properties through statistical mechanics. In this study, we introduce OSCFF, which supports various types of torsion for conjugated molecules and enables the generation of RESP charges with high accuracy through the neural network (NN). To develop the OSCFF, we construct two expansive and highly diverse molecular datasets: one consists of around 56,000 fragment geometries with torsion profiles, and another consists of around 472,000 optimized molecule geometries with RESP charges. The OSCFF demonstrates high accuracy in predicting torsional energy profiles, RESP charges, and the radial distribution function (RDF) for conjugated molecule systems. Furthermore, our OSCFF is compatible with the GAFF2 and a pipeline is provided for automatically generating the Gromacs supported topology file. We expect OSCFF will reduce the manual effort required for MD simulations of OSCs and serve as a valuable tool for multiple stages of OSCs design. | Guojiang Zhao; Taiping Hu; Hongshuai Wang ; Lirong Wu ; Shuqi Lu; FengTianCi Yang ; Shangqian Chen ; Zhifeng Gao ; Xinyan Wang ; Zheng Cheng | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e183d6dde43c90877c52c/original/data-driven-parametrization-of-all-atom-force-fields-for-organic-semiconductors.pdf |
620934bc0c0bf04afae81d3b | 10.26434/chemrxiv-2022-qkcqx | Visualization of Concentration Gradients and Colloidal Dynamics under Electrodiffusiophoresis | In this work, we present an experimental study of the dynamics of charged colloids under direct currents and gradients of chemical species (electrodiffusiophoresis). In our approach, we simultaneously visualize the development of concentration polarization and the ensuing dynamics of charged colloids near electrodes. With the aid of confocal microscopy and fluorescent probes, we show that the passage of current through water confined between electrodes, separated about a hundred microns, results in significant pH gradients. Depending on the current density and initial conditions, steep pH gradients develop, thus becoming a significant factor in the behavior of charged colloids. Furthermore, we show that steep pH gradients induce the focusing of charged colloids away from both electrodes. Our results provide the experimental basis for further development of models of electrodiffusiophoresis and the design of non-equilibrium strategies for materials fabrication. | Kun Wang; Behrouz Behdani; Carlos Silvera Batista | Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.); Interfaces; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620934bc0c0bf04afae81d3b/original/visualization-of-concentration-gradients-and-colloidal-dynamics-under-electrodiffusiophoresis.pdf |
60c753b4842e654e65db3fed | 10.26434/chemrxiv.13536767.v1 | Synthesis of an Exhaustive Library of Naturally Occurring Galf-Manp and Galp-Manp Disaccharides. Towards Fingerprinting According to the Ring Size by Advanced Mass Spectrometry-Based IM-MS and IRMPD. | Nature
offers a huge diversity of glycosidic derivatives. Amongst numerous structural
modulations, the nature of the ring size of hexosides may induce significant
differences on both biological and physicochemical properties of the
glycoconjugate of interest. On this assumption, we expect that small
disaccharides bearing either a furanosyl entity or a pyranosyl residue would
give a specific signature, even in the gas phase. On the basis of the scope of
mass spectrometry, two analytical techniques to register those signatures were
considered, i.e. the ion-mobility (IM) and the infra-red multiple photon
dissociation (IRMPD), in order to build up cross-linked databases. D-Galactose
occurs in natural products in both tautomeric forms and presents all possible
regioisomers when linked to D-mannose. Consequently, the four reducing Gal<i>f</i>-Man<i>p</i>
disaccharides as well as the four Gal<i>p</i>-Man<i>p</i> counterparts were firstly synthesized
according to a highly convergent approach, and IM-MS and IRMPD-MS data were
secondly collected. Both techniques used afforded signatures, specific to the
nature of the connectivity between the two glycosyl entities. | Bénédicte Favreau; Oznur Yeni; Simon Ollivier; Joel Boustie; françoise Le Dévéhat; Jean-Paul Guégan; Mathieu Fanuel; Hélène Rogniaux; Richard Brédy; Isabelle Compagnon; David Ropartz; Laurent Legentil; Vincent FERRIERES | Organic Synthesis and Reactions; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753b4842e654e65db3fed/original/synthesis-of-an-exhaustive-library-of-naturally-occurring-galf-manp-and-galp-manp-disaccharides-towards-fingerprinting-according-to-the-ring-size-by-advanced-mass-spectrometry-based-im-ms-and-irmpd.pdf |
6347f64abb6d8be96e572cb9 | 10.26434/chemrxiv-2022-vwm3t | Size-Dependency of Hückel’s Rule in Neutral Molecules: Alternating Behavior in Global Ring Current of Furan-Acetylene Macrocycles | Global aromaticity is commonly observed in charged macrocycles, but rarely in their neutral state. Therefore, the significance of global effects in neutral macrocycles, as well as their size dependency, remains an open question. Here we present a series of furan-acetylene macrocycles, ranging from pentamer to octamer, which display alternating contributions of the global aromatic and antiaromatic ring currents at their neutral state. Calculations and X-ray structures reveal relatively planar geometries regardless of the macrocycle size. We find that the odd-membered macrocycles display global aromatic characteristics, while the even-membered macrocycles display contributions from globally antiaromatic ring current. These factors are expressed electronically (oxidation potentials), optically (emission spectra), and magnetically (chemical shifts). DFT calculations support the experimental findings, showing HOMO and LUMO degeneracy for the odd-membered macrocycles and HOMO-1 and LUMO+1 degeneracy for antiaromatic macrocycles. The global characteristics are more pronounced for small macrocycles and are attenuated for larger members, establishes furan-acetylene macrocycles as shape-persistent models for the study of global aromaticity. | Yuval Rahav; Shinaj Rajagopalan; Or Dishi; Benny Bogoslavsky ; Ori Gidron | Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6347f64abb6d8be96e572cb9/original/size-dependency-of-huckel-s-rule-in-neutral-molecules-alternating-behavior-in-global-ring-current-of-furan-acetylene-macrocycles.pdf |
60c7455fbb8c1acdc73da698 | 10.26434/chemrxiv.10007510.v1 | Organobase-Catalyzed Hydroxyl-yne Click Polymerization | The proposition of
click chemistry has provided a quick channel for saccharides modification, which
has always been worth exploring. Click reaction of hydroxyl groups possessed by
saccharides is thus highly desirable to be developed. In this paper, we report
hydroxyl-yne click polymerization using ester activated alkynes and alcoholic hydroxyl groups. The
polymers, poly(vinyl ether ester)s (PVEEs), were obtained with high weight-average
molecular weights up to 71 000 were obtained in excellent yields up to 99%
using a commercially organic base of bicyclo[2.2.2]-1,4-diazaotane (DABCO) as
catalyst under ambient conditions. The obtained polymers possess high thermal
stability and low cytotoxicity. Both semi-crystalline and amorphous polymers were
obtained due to the different flexibility of monomers. Upon incorporating
aggregation-induced emission (AIE) moiety of tetraphenylethylene (TPE), the resultant
polymers displayed typical AIE characteristics. This work provides a potential
strategy for saccharides modification via the hydroxyl-yne click reaction. | Han Si; Kaojin Wang; Bo Song; Anjun Qin; Ben Zhong Tang | Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7455fbb8c1acdc73da698/original/organobase-catalyzed-hydroxyl-yne-click-polymerization.pdf |
66b48a9fc9c6a5c07a7191e6 | 10.26434/chemrxiv-2024-d0l0z | Competitive Heavy-Atom Tunneling Reactions Controlled Through Electronic Effects | Controlling QMT reactivity remains exceptionally challenging and largely unexplored, as it requires rationales distinct from those used for classical chemical reactivity. Herein, we investigated how QMT reactivity can be controlled using electronic substituent effects. Benzazirines, which have the exceptional feature to react via two competitive QMT pathways, were used as model compounds. Three novel derivatives with increasingly stronger electron-donating substituents at C4 [R = OH, N(CH3)2, and N(CH2)4] were generated in argon matrices at 3 K. Remarkably, different QMT selectivities were observed in all benzazirines. As the electron-donating strength of the substituent increases, the QMT ring-opening to nitrene starts to compete with the QMT ring-expansion to ketenimine, becoming the dominant process for the strongest electron-donating substituent [N(CH2)4]. A theoretical analysis of the substituent effects on the QMT reactivity of benzazirines was performed and compared with the experimental data for these and other C4 derivatives. Overall, the results compellingly demonstrate how subtle changes in electronic effects can be used to fine-tune QMT selectivity, and how the barrier widths, more than the barrier heights, are the determining factor. | José P. L. Roque; Cláudio M. Nunes; Fumito Saito; Bastian Bernhardt; Rui Fausto; Peter R. Schreiner | Physical Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b48a9fc9c6a5c07a7191e6/original/competitive-heavy-atom-tunneling-reactions-controlled-through-electronic-effects.pdf |
63daa47d89c04b6693c91a9c | 10.26434/chemrxiv-2022-dkl3m-v2 | A Double-Walled Tetrahedron with AgI4 Vertices Binds Different Guests in Distinct Sites | A double-walled tetrahedral metal-organic cage assembled in solution from silver(I), 2-formyl-1,8-naphthyridine, halide, and a threefold-symmetric triamine. The AgI4X clusters at its vertices bring together six naphthyridine-imine moieties, leading to a structure in which eight tritopic ligands bridge four clusters in an (AgI4X)4L8 arrangement. Four ligands form an inner set of tetrahedron walls that are surrounded by the outer four. The cage has significant interior volume, and was observed to bind anionic guests. The structure also possesses external binding clefts, located at the edges of the cage, which bound small aromatic guests. Halide ions bound to the silver clusters were observed to exchange in a well-defined hierarchy, allowing modulation of the cavity volume. The principles uncovered here may allow for increasingly more sophisticated cages with silver- cluster vertex architectures, with post-assembly tuning of the interior cavity volume enabling targeted binding behavior. | Samuel Clark; Andrew Heard; Charlie McTernan; Tanya Ronson; Barbara Rossi; Petr Rozhin; Silvia Marchesan; Jonathan Nitschke | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63daa47d89c04b6693c91a9c/original/a-double-walled-tetrahedron-with-ag-i4-vertices-binds-different-guests-in-distinct-sites.pdf |
640cf1bb7290f69f8ed472f9 | 10.26434/chemrxiv-2023-j0zkx | Spectroscopy of radicals, clusters, and transition states using slow electron velocity-map imaging of cryogenically cooled anions | Slow electron velocity-map imaging of cryogenically cooled anions (cryo-SEVI) is a high resolution variant of anion photoelectron spectroscopy that has been applied with considerable success over the years to the study of radicals, size-selected clusters, and transition states for unimolecular and bimolecular reactions. Cryo-SEVI retains the versatility of conventional anion photoelectron spectroscopy while offering sub-meV resolution, thereby enabling the resolution of vibrational structure in the photoelectron spectra of complex anions. This article describes recent experiments in our laboratory using cryo-SEVI, including a new research direction in which anions are vibrationally pre-excited with an infrared laser pulse prior to photodetachment. | Daniel Neumark | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640cf1bb7290f69f8ed472f9/original/spectroscopy-of-radicals-clusters-and-transition-states-using-slow-electron-velocity-map-imaging-of-cryogenically-cooled-anions.pdf |
63d337a41fe142a68b5b3508 | 10.26434/chemrxiv-2023-l45n1 | Synthesis of biolabile thioalkyl-protected phosphates from an easily accessible phosphotriester precursor | Phosphates are regularly incorporated into bioactive small molecules, for example in sugar-1-phosphate derivatives that are used for metabolic oligosaccharide engineering. To enable efficient cellular uptake, the phosphate groups are commonly masked with biolabile S-acyl-2-thioethyl (SATE) protecting groups that are removed once the molecule is inside the cell. Typically, SATE-protected monophosphates are synthesised through phosphoramidite chemistry, which suffers from issues with hazardous and unstable reagents and can give unreliable yields. Here, we report the development of an alternative approach that makes use of an easy to synthesise tri(2-bromoethyl)phosphotriester precursor, providing access to bis-SATE-protected mixed phosphotriesters in two steps. We demonstrate the viability of our strategy on tetrabenzylated glucose as a model monosaccharide, onto which a bis-SATE-protected phosphate is introduced at either the anomeric position or at C6. We also show compability with various protecting groups and further explore the scope and limitations of the approach on different substrates, including N-acetylhexosamines and amino acid derivatives. | Lloyd Murphy; Kathryn Huxley; Ava Wilding; Cyane Robinson; Quentin Foucart; Lianne Irene Willems | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d337a41fe142a68b5b3508/original/synthesis-of-biolabile-thioalkyl-protected-phosphates-from-an-easily-accessible-phosphotriester-precursor.pdf |
6343d923e665bd6b8c25411b | 10.26434/chemrxiv-2022-c497b-v2 | Alkyl Formates as Transfer Hydroalkylation Reagents and Their Use in the Conversion of Imines to Alkylamines | Easily accessible via a simple esterification of alcohols with
formic acid, alkyl formates are used as a novel class of transfer hydroalkylation reagents, CO2 acting as a traceless linker. As a proof-of-concept, their reactivity in the transfer hydroalkylation of imines is investigated, using a ruthenium-based catalyst and LiI as promoter to cleave the C−O σ–bond of the formate scaffold. Providing tertiary amines, the reaction displays a reverse and complementary regioselectivity compared to previously reported transfer hydroalkylation strategies. | Etienne Crochet; Lucile Anthore-Dalion; Thibault Cantat | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6343d923e665bd6b8c25411b/original/alkyl-formates-as-transfer-hydroalkylation-reagents-and-their-use-in-the-conversion-of-imines-to-alkylamines.pdf |
60c75647567dfe973fec644c | 10.26434/chemrxiv.14226065.v1 | Covalent d-Block Organometallics: Teaching Lewis Structures and sd/sd2 Hybridization Gives Students Additional Explanations and Powerful Predictive Tools | Despite tremendous efforts by instructors and textbook authors, students find it difficult to develop useful chemical intuitions about preferred structures, structural trends, and properties of even the most common d-block element organometallic species, that is d6, d8, and d10 systems. A full molecular orbital analysis of a transition metal species is not always feasible or desirable, and crystal field theory, while generally useful, is often too simplistic and limited. It would be helpful to give students of organometallic chemistry an additional toolkit that helps them to understand d-block compounds, in particular highly covalent ones. It is well known in the research literature in organometallic chemistry that hybridization arguments involving s and d orbitals (such as sd and sd2 hybridization for d8 and d6 systems, respectively) provides useful insight. However, this knowledge is much underused in undergraduate teaching and not taught in undergraduate textbooks. The purpose of this article is to make descriptions of bonding that are based on s,d-hybridized orbitals more accessible in a way that is directly useful for undergraduate teaching. Geometries of unusual low-coordinate structures can be successfully predicted. An in-depth physical explanation for the trans-influence, the weakening of a bond due to a strong bond trans to it, is provided. A clear explanation is given for why the cis isomer normally more stable than the trans isomer in square-planar d8 complexes of the type MR2L2 (R = alkyl/aryl, L = relatively weakly bonded neutral ligand). Similarly, the relative stability of fac versus mer isomers in octahedral d6 complexes of the type MR3L3 is explained. Relevant to catalysis, the method explains why strongly donating ligands do not always facilitate oxidative addition and why 12-electron and 14-electron Pd(0) species are thermodynamically much more accessible than one might expect. The method capitalizes on 1st year knowledge such as the ability to write Lewis structures and to use hybridization arguments. It also ties into the upper-year experience, including graduate school, where covalent d-block complexes may be encountered in research and where the hybridization schemes described here naturally emerge from using the NBO formalism. It is discussed where the method might fit into the inorganic curriculum.<br /> | Ulrich Fekl | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75647567dfe973fec644c/original/covalent-d-block-organometallics-teaching-lewis-structures-and-sd-sd2-hybridization-gives-students-additional-explanations-and-powerful-predictive-tools.pdf |
60c7484e702a9b485518af68 | 10.26434/chemrxiv.11887971.v1 | Facile Preparation of WO3-x Dots with Remarkably Low Toxicity and Uncompromised Activity as Coreactants for Clinic Electrochemiluminescent Diagnosis | <p></p><p>The
exceptional nature of WO<sub>3-<i>x</i></sub> dots has inspired widespread
interests (<i>Science</i>, 2017, 358, 1192; <i>Adv. Mater.</i><i>,</i> 2016, 28, 10518),
but it is still a major challenge to synthesize high-quality WO<sub>3-<i>x</i></sub>
dots without using unstable reactants, expensive equipment, and complex
synthetic processes. Chemical tailoring of nanosheets is an essential way for
the synthesis of nanodots, however it is NOT applicable to exfoliate bulk WO<sub>3
</sub>due to its covalently-bound layers. As such, most of the synthesis rely
on a bottom-up method by using WCl<sub>6</sub> as a typical precursor but
water-free conditions are usually required due to the highly hydrolytic
property of WCl<sub>6</sub> (<i>J. Am. Chem. Soc.</i> 2005, 127, 15595). In
addition, to diminish the anisotropic growth during the synthesis, the surface
of the WO<sub>3-<i>x</i></sub> dots is usually anchored with aliphatic amines
or oleic acid as surfactant/template, which leads to SLOW Faradic
electrochemistry (<i>Adv. Mater. </i>2014, 26, 4260). Along these lines, it is of
both fundamental and technical importance to overcome these deficiencies in the
synthesis of high-quality WO<sub>3-<i>x</i></sub> dots. </p>
<p>In
this work, we report the synthesis of WO<sub>3-<i>x</i></sub>
dots by
a facile exfoliation of bulk WS<sub>2</sub> instead of bulk WO<sub>3</sub> followed
by a mild chemical conversion. The WO<sub>3-<i>x</i></sub>
dots were not only ligand-FREE and highly water-dispersible but also had tunable
oxygen-vacancies, ready for a varity of high-demanding applications. As an example,
the WO<sub>3-<i>x</i> </sub>dots were emerged as a new generation of coreactants
for the electrochemiluminescence (ECL) of Ru(bpy)<sub>3</sub><sup>2+</sup> with
a tremendous enhancement factor up to 500-fold, owing
to the unique electrochemical and catalytic properties. More
importantly, compared to the commonly used tripropylamine (TPA) coreactant in the clinics, the WO<sub>3-<i>x</i></sub>
dots displayed a factor of ca. 300 less ANIMAL toxicity. Along these lines, the
enormous potential of WO<sub>3-<i>x</i></sub> dots as ECL coreactants in replacing TPA for clinic diagnosis
was further exemplified by cytosensing circulating tumor cells with a uncompromised performance.
This work would not only open a new way to synthesize WO<sub>3-<i>x</i> </sub>dots
with superior properties but also stimulate an emerging application in clinic
ECL diagnosis as coreactants with uncompromised high performance and
unprecedented low toxicity.</p><br /><p></p> | Deng Pan; Zhengzou Fang; Zhenqiang Ning; Qing Zhou; Erli Yang; Kaiyang Chen; Yongjun ZHENG; Yuanjian Zhang; Yanfei Shen | Nanostructured Materials - Materials; Analytical Chemistry - General; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7484e702a9b485518af68/original/facile-preparation-of-wo3-x-dots-with-remarkably-low-toxicity-and-uncompromised-activity-as-coreactants-for-clinic-electrochemiluminescent-diagnosis.pdf |
60c75408842e65c8bedb4085 | 10.26434/chemrxiv.13604006.v1 | Substituent Effects of Amines on Genipin Dye Formation – Insights into Dye Origins | <p>Genipin, a naturally occurring iridoid, represents
an interesting class of reactive dyes. This colorless molecule produces
brilliant blue dyes in the presence of primary aliphatic amines. The mechanism
behind this unique reaction has been suggested to proceed via an oxidative
polymerization reaction, albeit few studies have investigated this process. By utilizing
aromatic amines, we demonstrate that the dye absorption properties can be redshifted
to form green dyes as opposed to the blue that is most associated with
aliphatic amines. Characterization of the green material with gel-permeation
chromatography, mass spectrometry, and electrochemical experiments suggest an
alternate structure of the dye molecules and led us to revisit the mechanism
behind this reaction. Generation of dyes from the reaction of genipin and
methylamine or various aniline derivatives revealed the complete absence of
polymeric material and instead revealed a material that contains an open-shell
configuration as determined by EPR spectroscopy. Herein we report the first
findings that dyes formed from the reaction of genipin with amines form
persistent radicals that are likely responsible for their vibrant colors, as
opposed to the previously suggested polymer formation. </p> | Fiona Jeeva; Chris Caputo | Natural Products; Dyes and Chromophores | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75408842e65c8bedb4085/original/substituent-effects-of-amines-on-genipin-dye-formation-insights-into-dye-origins.pdf |
62ec5e8b15fdaec998229def | 10.26434/chemrxiv-2022-4677k | Multiscale modelling of phosphate…π contacts in RNA U-turns reveals AMBER force-field deficiencies | Phosphate…π, also called anion…π, contacts occur between nucleobases and phosphate OP oxygens in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). We investigated these contacts in detail by using state-of-the-art quantum chemical methods (QM) to characterize some of their physico-chemical properties and to evaluate the ability of the AMBER force field (AFF) to describe these contacts. We found that AFF interaction energies of phosphate…π contacts calculated for model dimethyl phosphate…nucleobase systems are less stabilizing in comparison with double-hybrid DFT methods and that the minimum contact distances are stretched for all nucleobase systems. This distance stretch is also observed in large-scale AFF computations on several r(gcGNRAgc) tetraloop hairpins when compared to QM/MM. Further, classical molecular dynamics (MD) simulations of these tetraloop hairpins confirm this distance stretch and reveal shifted OP2/nucleobase positions when compared to experimental data extracted from high-resolution X ray/cryo EM structures (≤ 2.5 Å) of r(GNRA) tetraloops using the WebFR3D bioinformatic tool. We propose that discrepancies between QM and AFF are caused by a combination of missing polarization, too large AFF Lennard-Jones (LJ) radii of nucleobase carbon atoms and exaggerated short-range repulsion due to an approximate r−12 LJ repulsive term. We put these results in regard with those obtained in earlier investigations on lone pair…π contacts occurring in CpG Z-steps. Charge-transfer calculations do not support any significant n->π* donation effects and hence this label is inappropriate. We also investigated thiophosphate…π contacts for which we calculated less stabilizing interaction energies than for the phosphate…π contacts. We thus challenge suggestions that the experimentally observed enhanced thermodynamic stability of phosphorothioated r(GNRA) tetraloops can be straightforwardly explained by larger London dispersion. | Klaudia Mráziková; Holger Kruse; Vojtěch Mlýnský; Pascal Auffinger; Jiří Šponer | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ec5e8b15fdaec998229def/original/multiscale-modelling-of-phosphate-contacts-in-rna-u-turns-reveals-amber-force-field-deficiencies.pdf |
61546263aef99c3b0d060901 | 10.26434/chemrxiv-2021-wrrws | Catalytic Deracemization of α-Branched Aldehydes via Visible Light Promoted E/Z Isomerization of Enamine Intermediate | Catalytic deracemization of α-branched aldehydes represents an unmet challenge with fundamental importance in carbonyl chemistry. In this work, we report a photochemical E/Z isomerization strategy for the deracemization of α-branched aldehydes by using simple aminocatalysts and readily available photosensitizers. Various racemic α-branched aldehydes could be directly transformed into their corresponding single enantiomers in high enantioselectivity. Rapid photodynamic E/Z isomerization and highly stereospecific iminium/enamine tautomerization are two key factors that underlie the highly effective enantio-enrichment. This study presents a distinctive photochemical E/Z isomerizing strategy for externally tuning enamine catalysis. | Mouxin Huang; Long Zhang; Tianrun Pan; Sanzhong Luo | Organic Chemistry; Catalysis; Stereochemistry; Organocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61546263aef99c3b0d060901/original/catalytic-deracemization-of-branched-aldehydes-via-visible-light-promoted-e-z-isomerization-of-enamine-intermediate.pdf |
67c09fdafa469535b9335ec4 | 10.26434/chemrxiv-2025-k9rtv | Two-Dimensional Electronic Spectroscopy of Betaine-30 | Betaine-30, is well established as a standard dye for solvatochromism, and has long been studied by ultrafast spectroscopy. Electronic excitation leads to rapid intramolecular electron transfer, while the decay of the resulting state corresponds to back electron transfer to the electronic ground state. Thus, Betaine-30’s photophysics offer a route to probing the role of vibrational excitation and solvent dynamics play in electron transfer reaction rates. Here we probe the excited state dynamics of Betaine-30 in two solvents (ethanol and acetonitrile) by means of two-dimensional electronic spectroscopy. Population dynamics in ethanol are measured at two pump wavelengths and global analysis reveals a wavelength dependence of the electron transfer rate. This is assigned to excitation of distinct ground state conformers, which is confirmed by quantum chemical calculations. “Beatmaps” of coherently excited vibrations are recovered and analysed in terms of the contribution of Raman active modes in ground and excited states. The contribution of modes in the excited state is a strong function of the rate of the electron transfer reaction. | Stephen Meech; James Bull; Giovanni Bressan | Physical Chemistry; Optics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c09fdafa469535b9335ec4/original/two-dimensional-electronic-spectroscopy-of-betaine-30.pdf |
66141a73418a5379b068bd0f | 10.26434/chemrxiv-2024-l50l1-v2 | Nature of Metal-Support Interaction Discovered by Interpretable Machine Learning
| Metal catalysts supported on oxides play a paramount role in numerous industrial reactions. Modulating metal-support interaction is a key strategy to boost catalytic productivity and stability; however, the nature of metal-support interaction and quantification remain major unsolved problems. By leveraging interpretable machine learning, domain knowledge, and experimental data available, we discover a physical metal-support interaction equation applicable to metal nanoparticles and adatoms on oxides, and oxide films on metals. Though metal-oxygen interaction dominates metal-support interaction and determines the metal composition effect, metal-metal interaction delineates the support effect. This ensures a principle of strong metal-metal interaction for encapsulation of suboxide over metal nanoparticles, substantiated comprehensively by molecular dynamics simulations and previous experiments. The developed theory provides valuable insights and guidance in engineering the metal-support systems. | Tairan Wang; Runhai Ouyang; Jianyu Hu; Yutao Wang; Wu Shu; Xuting Chai; Sulei Hu; Wei-Xue Li | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Theory - Computational; Machine Learning; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66141a73418a5379b068bd0f/original/nature-of-metal-support-interaction-discovered-by-interpretable-machine-learning.pdf |
64b0e413b053dad33a36d7ef | 10.26434/chemrxiv-2023-hf60w | Emerging Materials and Design Principles for Wurtzite-type Ferroelectrics | The energy demand for computing and data storage will continue to rise exponentially unless non-traditional computing architectures and innovative storage solutions are explored. Low-energy computing, including compute-in-memory architectures, has the potential to address these energy and environmental challenges and, in particular, tetrahedral (wurtzite-type) ferroelectrics are promising options for both performance and integration with existing semiconductor processes. The AlScN alloy is among the few tetrahedral materials that exhibit ferroelectric switching, but the electric field required to switch the polarization i.e., the coercive field, E_c, is on the order of MV/cm, which is about 1–2 orders of magnitude higher than more traditional oxide perovskite ferroelectrics (E_c < 100 kV/cm). Instead of further engineering AlScN and related alloys, we explore the alternative route of computationally identifying new materials with switching barriers lower than AlN while still possessing high enough intrinsic breakdown fields. Going beyond binary compounds, we explore the search space of multinary compounds with wurtzite-type structures. Through this large-scale search, we identify four promising ternary nitrides and oxides, including Mg2PN3, MgSiN2, Li2SiO3, and Li2GeO3, for future experimental realization and engineering. In > 90% of the considered multinary materials, we identify unique switching pathways and non-polar structures that are distinct from the commonly assumed switching mechanism in AlN-based materials. Our results disprove the existing design principle based on reduction of wurtzite c/a lattice parameter ratio while supporting two emerging design principles – ionicity and bond strength. | Cheng-Wei Lee; Naseem Ud Din; Keisuke Yazawa; Geoff L Brennecka; Andriy Zakutayev; Prashun Gorai | Materials Science; Energy; Ceramics; Piezoelectricity and Thermoelectricity; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b0e413b053dad33a36d7ef/original/emerging-materials-and-design-principles-for-wurtzite-type-ferroelectrics.pdf |
60f953eb171fc76257b8036c | 10.26434/chemrxiv-2021-9j7wg-v2 | DECIMER 1.0: Deep Learning for Chemical Image Recognition using Transformers | The amount of data available on chemical structures and their properties has increased steadily over the past decades. In particular, articles published before the mid-1990 are available only in printed or scanned form. The extraction and storage of data from those articles in a publicly accessible database are desirable, but doing this manually is a slow and error-prone process. In order to extract chemical structure depictions and convert them into a computer-readable format, optical chemical structure recognition (OCSR) tools were developed where the best performing OCSR tools are mostly rule-based.
The DECIMER (Deep lEarning for Chemical ImagE Recognition) project was launched to address the OCSR problem with the latest computational intelligence methods to provide an automated open-source software solution. Various current deep learning approaches were explored to seek a best-fitting solution to the problem. In a preliminary communication, we outlined the prospect of being able to predict SMILES encodings of chemical structure depictions with about 90% accuracy using a dataset of 50-100 million molecules. In this article, the new DECIMER model is presented, a transformer-based network, which can predict SMILES with above 96% accuracy from depictions of chemical structures without stereochemical information and above 89% accuracy for depictions with stereochemical information.
| Kohulan Rajan; Achim Zielesny; Christoph Steinbeck | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f953eb171fc76257b8036c/original/decimer-1-0-deep-learning-for-chemical-image-recognition-using-transformers.pdf |
60c753900f50dbd6da397bb1 | 10.26434/chemrxiv.13513881.v1 | Auxiliary Atomic Relay Center Facilitates Enhanced Magnetic Couplings in Blatter’s Radical | <div>The recent accomplishments in obtaining the strong ferromagnetic exchange interactions in organic diradicals have made the field quite fascinating and even more promising towards its technological applications. In this context, herein we report a unique combination of remarkably strong ferromagnetic exchange interactions coupled with the molecular rigidity utilizing super-stable Blatter’s radical as a spin source. The planar analogues of the parent Blatter’s radical obtained by annulation with a chalcogen coupled to nitronyl nitroxide (NN) are investigated using density functional theory (DFT) along with the wave function based multi-configurational self-consistent field (MCSCF) methods e.g. CASSCF/NEVPT2. The calculations reveal phenomenal modulation in exchange couplings upon annulation such that remarkably strong ferromagnetic interactions are realized especially for a certain class of the Blatter - nitronyl nitroxide diradicals. The modulation of spin spin interactions is rationalised by variation in spin density distribution and molecular torsional angles. We demonstrate that annulation in OMMs opens an additional coupling pathway via auxiliary X-atom acting as atomic relay center which strongly manipulates the magnitude of exchange couplings.</div> | Ashima Bajaj; Rishu Khurana; Md. Ehesan Ali | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753900f50dbd6da397bb1/original/auxiliary-atomic-relay-center-facilitates-enhanced-magnetic-couplings-in-blatter-s-radical.pdf |
62e0bf94adb01ef80fadaeba | 10.26434/chemrxiv-2022-xqlqc | Structural investigation of Fe(III)-salen complexes as "turn-on" fluorogenic probes for selective detection of pyrophosphate ions | In this work, we revisited the disassembly approach (also known as the Zelder's approach) recently proposed for sensing pyrophosphate (PPi) in water and based on the decomposition of metal-salen complexes. A systematic study devoted to the structural optimization of this novel class of PPi-responsive fluorogenic probes was conducted. Screening of eight different vicinal diamines (i.e., bridge of the salen ligand) combined with the use of 8-formyl-7-hydroxycoumarin (i.e., salicylaldehyde derivative) as the fluorescent reporter, has led to a set of novel and fully characterized coumarin-salen Fe(III) complexes. A series of analytical validations helped us to identify that coumarin-salen Fe(III) complexes derived from ethylenediamine and racemic 1,2-propylenediamine backbones exhibit the best and selective PPi-sensing performances (the limits of detection were estimated as 3.15 × 10-6 M and 2.81 × 10-6 M respectively). The implementation of both fluorescence time-course measurements and RP-HPLC-fluorescence analyses has enabled us to gain further insights into the disassembly-based probes' activation mechanism. This study therefore contributes to demonstrate that the disassembly approach is a valuable strategy to achieve fluorogenic activity-based sensing of anions. | Eunice Y.-L. HUI; Dillon W. P. TAY; Jean-Alexandre RICHARD; Zuzana POHANCENIKOVA; Kévin RENAULT; Anthony ROMIEU; Yee Hwee LIM | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e0bf94adb01ef80fadaeba/original/structural-investigation-of-fe-iii-salen-complexes-as-turn-on-fluorogenic-probes-for-selective-detection-of-pyrophosphate-ions.pdf |
616332fc7d3da5782ff36cb8 | 10.26434/chemrxiv-2021-5q5g5 | Fabrication of Semi-Transparent SrTaO2N Photoanodes with a GaN Underlayer Grown via Atomic Layer Deposition | Quaternary metal oxynitride-based photoanodes with a large light transmittance are promising for high solar-to-hydrogen (STH) conversion efficiency in photoelectrochemical (PEC) tandem cells. Transparent substrates to support PEC water-splitting were fabricated using atomic layer deposition (ALD) to synthesize 30 and 60 nm GaN on SiC sub-strates. A generalized approach was used to grow a quaternary metal oxynitride, i.e. SrTaO2N thin film on the GaN/SiC substrates. The transparency above 60% in the wide solar spectrum highlights its availability of transmit-ting visible light to the rear side. A photocurrent onset at ca. −0.4 V vs. reversible hydrogen electrode (RHE) was achieved by the SrTaO2N/GaN/SiC photoanodes in a 0.1 M NaOH electrolyte under simulated solar irradiation. This paves the way for construction of hierarchically nanostructured tandem PEC cells. This work demonstrates the viabil-ity of integrating ALD in constructing substrates for semi-transparent quaternary metal oxynitride photoanodes. | Can Lu; Nathan O´Brien; Polla Rouf; Richard Dronskowski; Henrik Pedersen; Adam Slabon | Materials Science; Inorganic Chemistry; Energy; Nanostructured Materials - Materials; Thin Films; Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616332fc7d3da5782ff36cb8/original/fabrication-of-semi-transparent-sr-ta-o2n-photoanodes-with-a-ga-n-underlayer-grown-via-atomic-layer-deposition.pdf |
655b3a4e2c3c11ed71c439ea | 10.26434/chemrxiv-2023-3t26g | Protodefluorinated Selectfluor® Promotes Aggregative Activation of Selectfluor® for Efficient C(sp3)−H Fluorination Reactions | We report herein a simple, yet unexpected approach to dramatically improve the efficiencies of radical fluorination reactions of C(sp3)−H bonds. H−TEDA(BF4)2 is readily generated as a byproduct during fluorination reactions with Selectfluor®, the world’s most popular organic fluorination reagent. However, H−TEDA(BF4)2 to date is overlooked and discarded as waste, despite comprising 95% of the M.W. of Selectfluor®. We demonstrate that the addition of H−TEDA(BF4)2 at the start of fluorination reactions markedly increases their rates, outcompeting side reactions to access higher overall yields of fluorinated products. Showcasing the generality of the phenomenon, the performance additive enhances both photochemical/photocatalytic and thermal radical fluorination reactions by decreasing a discovered induction period in the former and by increasing the rate in the latter. Detailed mechanistic investigations reveal the key importance of aggregation changes in Selectfluor® and H−TEDA(BF4)2 to fill gaps of understanding in how radical C(sp3)−H fluorination reactions work. This study exemplifies how an overlooked reaction waste product can be upcycled for a high value-added application. | Shahboz Yakubov; Bastian Dauth; Willibald Stockerl; Wagner M. da Silva; Ruth M. Gschwind; Joshua P. Barham | Organic Chemistry; Catalysis; Analytical Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655b3a4e2c3c11ed71c439ea/original/protodefluorinated-selectfluor-promotes-aggregative-activation-of-selectfluor-for-efficient-c-sp3-h-fluorination-reactions.pdf |
6674074501103d79c5aa414c | 10.26434/chemrxiv-2024-wmxtb | Characterization and interpretation of the reaction mechanism of a novel GH115 α-Glucuronidase from Flavobacteriaceae. | Xylan is a major component in the complex network of the plant cell wall. Xylan consists of xylose units connected by β-(1,4) glycosidic bonds, which can be heavily substituted, increasing its degradation recalcitrancy. Such substituents include α-D-glucuronic acid (glucopyranosyluronic acid, GlcAp) or 4-O-methyl GlcAp (MeGlcAp) at the O-2 position. Removal of these substituents can be catalyzed by α-glucuronidases. Here we report a novel two-domain α-glucuronidase from GH family 115, termed FAgu115A, that acts on both polymeric and oligomeric xylan. A homology model was constructed, revealing the significance of residues Asp303 and Asp177 for catalysis. These residues are conserved in all characterized proteins belonging to this family. The catalytic activity of these residues was verified by site-specific mutagenesis corroborating the hypothesis that Asp303 serves as the proton donor, while Asp177 increases the nucleophilicity of the reactive water through a hydrogen bond. Additionally, a potential CBM located at the C terminus is of importance for dimerization. Its significance was confirmed by producing a truncated variant followed by determination of the molecular mass by analytical size-exclusion chromatography. Kinetic and thermal inactivation analysis were performed resulting in a Km of 3.7 g/l on beechwood xylan and an activation energy (Eα) of 67 kJ/mol. | Savvina Leontakianakou; Anders Sundin; Eva Nordberg Karlsson | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6674074501103d79c5aa414c/original/characterization-and-interpretation-of-the-reaction-mechanism-of-a-novel-gh115-glucuronidase-from-flavobacteriaceae.pdf |
60c743f5702a9bcd1318a70a | 10.26434/chemrxiv.9710579.v1 | Think Beyond the Core: The Impact of the Hydrophilic Corona on the Drug Solubilization Using Polymer Micelles | Polymeric micelles are typically characterized as core-shell structures. The hydrophobic inner core is considered as depot for hydrophobic molecules such as drugs or catalysts and the corona forming block acts as protective, stabilizing and solubilizing interface between the hydrophobic core and the external aqueous milieu. Tremendous efforts have been made to tune the hydrophobic block to increase the drug loading and stability of the micelles, while the role of hydrophilic blocks regarding drug loading and stability of micelles is rarely studied in detail. To do so, we investigated a small library of structurally similar A-B-A type amphiphiles based on poly(2-oxazoline)s and poly(2-oxazine)s by varying the hydrophilic block A utilizing poly(2-methyl-2-oxazoline) (A) or poly(2-ethyl-2-oxazoline) (A*), both excellently water-soluble polymers that are able to provide beneficial stealth properties. Surprisingly, major differences in loading capacities from A-B-A > A*-B-A > A*-B-A* highlight the impact of the hydrophilic corona of the polymer micelles on drug loading and stability. 1H-NMR spectroscopy revealed that the hydrophilic pEtOx exhibits a stronger interaction with the cargo compared with its more hydrophilic counterpart pMeOx, reducing colloidal stability of the drug loaded micelles at lower drug loading. To gain more insights, formulations were also characterized by diffusion ordered and nuclear Overhauser effect NMR spectroscopy, dynamic light scattering and (micro) differential scanning calorimetry. Our findings suggest that the interaction between the hydrophilic block and the guest molecule should be considered an important but previously largely ignored factor for the rational design of polymeric micelles.<br /> | Malik Salman Haider; Michael M Lübtow; Sebastian Endres; Vladimir Aseyev; Ann-Christin Pöppler; Robert Luxenhofer | Aggregates and Assemblies; Biocompatible Materials; Core-Shell Materials; Surfactants; Drug delivery systems; Organic Polymers; Polymer morphology; Nanostructured Materials - Nanoscience; Self-Assembly; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f5702a9bcd1318a70a/original/think-beyond-the-core-the-impact-of-the-hydrophilic-corona-on-the-drug-solubilization-using-polymer-micelles.pdf |
6357af401db0bd846838a85a | 10.26434/chemrxiv-2022-lw5n8-v2 | Challenges in Molecular Dynamics of Amorphous ZIFs using Reactive Force Fields | While amorphous metal–organic frameworks (a-MOFs) form an emerging class of materials of growing interest, their structural characterization remains experimentally and computationally challenging challenging. Out of the many molecular simulation methods that exist to model these disordered materials, one strategy consists in simulating the phase transition from a crystalline MOF to the amorphous state using molecular dynamics. ReaxFF reactive force fields have been proposed for this purpose in several studies to generate models of zeolitic imidazolate frameworks (ZIFs) glasses by melt-quenching. In this work, we investigate in detail the accuracy and reliability of this approach by reproducing the published procedures and comparing the structure of the resulting glasses to other data, including ab initio modeling. We find that the in silico melt-quench procedure is extremely sensitive to the choice of methodology and parameters, and suggest adaptations to improve the scheme. We also show that the glass models generated with ReaxFF are markedly different from their ab initio counterparts, as well as known experimental characteristics, and feature an unphysical description of the local coordination environment, which in term affects the medium-range and bulk properties. | Nicolas Castel; François-Xavier Coudert | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6357af401db0bd846838a85a/original/challenges-in-molecular-dynamics-of-amorphous-zi-fs-using-reactive-force-fields.pdf |
646380b8fb40f6b3eeaed1e9 | 10.26434/chemrxiv-2023-00vcg-v3 | Characterizing Uncertainty in Machine Learning for Chemistry | Characterizing uncertainty in machine learning models has recently gained interest in the context of machine learning reliability, robustness, safety, and active learning. Here, we separate the total uncertainty into contributions from noise in the data (aleatoric) and shortcomings of the model (epistemic), further dividing epistemic uncertainty into model bias and variance contributions. We systematically address the influence of noise, model bias, and model variance in the context of chemical property predictions, where the diverse nature of target properties and the vast chemical chemical space give rise to many different distinct sources of prediction error. We demonstrate that different sources of error can each be significant in different contexts and must be individually addressed during model development. Through controlled experiments on datasets of molecular properties, we show important trends in model performance associated with the level of noise in the dataset, size of the dataset, model architecture, molecule representation, ensemble size, and dataset splitting. In particular, we show that 1) noise in the test set can limit a model's observed performance when the actual performance is much better, 2) using size-extensive model aggregation structures is crucial for extensive property prediction, and 3) ensembling is a reliable tool for uncertainty quantification and improvement specifically for the contribution of model variance. We develop general guidelines on how to improve an underperforming model when falling into different uncertainty contexts. | Esther Heid; Charles J. McGill; Florence H. Vermeire; William H. Green | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646380b8fb40f6b3eeaed1e9/original/characterizing-uncertainty-in-machine-learning-for-chemistry.pdf |
6350d7ca4a187663e1eb57a5 | 10.26434/chemrxiv-2022-knxwb | Photoredox-Active Colloids and Polymer Membranes of Titanium-Based MOF Nanoparticles
| Nanosizing metal-organic frameworks (MOFs) facilitates their preparation in membrane- and thin-film-based technologies, while enabling solution-state techniques to probe size-dependent properties and molecular reactivity, but few MOFs have been prepared as nanoparticles (nanoMOFs). Here, we report a rapid reflux-based nanoparticle synthesis of the photoredox-active MOF Ti8O8(OH)4(terephthalate)6 (MIL-125) to achieve sizes below 30 nm in less than 2 hours, whereas previous routes generate particles larger than 100 nm in days. The resulting nanoMOFs display BET surface areas of ~1800 m2/g, rivaling the bulk counterparts, and the sizes can be reproducibly controlled by tuning the key reaction parameters identified here. Furthermore, the smallest nanoparticles exhibit colloidal stability for weeks, permitting analysis by solution-state techniques. Optical absorption and photoluminescence measurements of free-standing colloids offer the first direct evidence of Ti3+ and charge accumulation in a MOF during photoredox processes. These data also reveal for the first time that Ti centers in MIL-125 undergo a significant Jahn-Teller distortion upon photoreduction. Solution-state potentiometry measured in situ provides insight into energetic aspects of the photochemistry, while voltammetry of the colloids reports some of the only known redox potentials of a nanoMOF. Finally, we demonstrate that MIL-125 nanocrystals can be implemented into membranes by solution-processing techniques and demonstrate retention of photoactivity even when encased in polymer matrices. Taken together, these results demonstrate the feasibility of rapid nanoMOF synthesis and membrane fabrication and the deep fundamental insights they enable into photoredox chemistry. | Kevin Fabrizio; Carl Brozek | Inorganic Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Spectroscopy (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6350d7ca4a187663e1eb57a5/original/photoredox-active-colloids-and-polymer-membranes-of-titanium-based-mof-nanoparticles.pdf |
6179d79164e2af0221177810 | 10.26434/chemrxiv-2021-msrmr-v3 | Water Capture Mechanisms at Zeolitic Imidazolate Framework Interfaces
| Water capture mechanisms of zeolitic imidazolate framework ZIF-90 are revealed by differentiating the water clustering and the center pore filling step, using vibrational sum-frequency generation spectroscopy (VSFG) at a one-micron spatial resolution and state-of-the-art molecular dynamics (MD) simulations. Through spectral lineshape comparison between VSFG and IR spectra, the relative humidity dependence of VSFG intensity, and MD simulations, based on MB-pol, we found water clustering and center pore filling happen nearly simultaneously within each pore, with water filling the other pores sequentially. The integration of nonlinear optics with MD simulations provides critical mechanistic insights into the pore filling mechanism and suggests that the relative strength of the hydrogen bonds governs the water uptake mechanisms. This molecular-level detailed mechanism can inform the rational optimization of metal-organic frameworks for water harvesting. | Jackson Wagner; Kelly Hunter; Francesco Paesani; Wei Xiong | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Interfaces; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6179d79164e2af0221177810/original/water-capture-mechanisms-at-zeolitic-imidazolate-framework-interfaces.pdf |
67dc42b56dde43c90898d591 | 10.26434/chemrxiv-2025-kgz6g | Shinyscreen: Mass Spectrometry Data Inspection and Quality Checking Utility | Shinyscreen is an R package and Shiny-based web application designed for the exploration, visualization, and quality assessment of raw data from high resolution mass spectrometry instruments. Its versatile compound or mass list-based approach supports the curation of data starting from either known or “suspected” compounds (compound-based screening), or detected masses (mass list-based screening), making it adaptable to diverse analytical needs (target, suspect or non-target screening). Shinyscreen can be operated in multiple modes, including as an R package, an interactive command-line tool, a self-documented web GUI, or a network-deployable service. Shinyscreen has been applied in environmental research, database enrichment, and educational initiatives, showcasing its broad utility. Shinyscreen is available in GitLab (https://gitlab.com/uniluxembourg/lcsb/eci/shinyscreen) under the Apache License 2.0. The repository contains detailed instructions for deployment and use. Additionally, a pre-configured Docker image, designed for seamless installation and operation is available, with instructions also provided in the main repository. | Todor Kondić; Anjana Elapavalore; Jessy Krier; Adelene Lai; Hiba Mohammed Taha; Mira Narayanan; Emma Schymanski | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dc42b56dde43c90898d591/original/shinyscreen-mass-spectrometry-data-inspection-and-quality-checking-utility.pdf |
6769375bfa469535b989827a | 10.26434/chemrxiv-2024-47mz4 | Metabolomic insights into balancing the trade-off between oxidation of endogenous organics and macronutrient recovery from human urine treated with Fenton’s reagent | The high concentrations of organic and inorganic compounds in human urine present both challenges and opportunities for its treatment using advanced oxidation processes. This study evaluates Fenton oxidation for selectively degrading endogenoous organic metabolites in urine while preserving critical nutrients such as urea. Using targeted metabolomics, over 200 organic metabolites were identified in acidified urine, with creatinine, citric acid, hippuric acid, and methylhistidine comprising half of the total organic metabolite load (ΣOMs = 3.23 g L⁻¹). Under optimised conditions (pH 4.0, 1:1 Fe²⁺: H₂O₂ molar ratio), 59% of ΣOMs were degraded in unconcentrated urine treated with 1 g H₂O₂ L⁻¹. Increasing the H2O2 dose in unconcentrated urine, or treating concentrated urine obtained through evaporative water removal, resulted in higher ΣOMs degradation but also increased urea oxidation, highlighting a trade-off between efficient COD removal and nutrient recovery. COD removal was 38% at pH 4.0 and 27% at pH 6.0, suggesting that Fenton oxidation could be applied to H₂O₂ stabilised urine without strict pH adjustment. Real urine differed significantly from synthetic urine, requiring five times more Fe²⁺ catalyst for complete H₂O₂ activation and reaching equilibrium within five minutes compared to two hours in synthetic urine. Organic compounds in urine scavenged Fe³⁺, forming iron-organic complexes that disrupted Fe²⁺ regeneration and contributed to iron precipitation at higher pH values. These findings demonstrate that Fenton oxidation can be optimised to achieve selective degradation of undesirable organics while preserving plant-essential nutrients in urine collected within resource-oriented sanitation systems. | Caitlin Courtney; Abdullah Al-Saadi; Prithvi Simha | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Natural Resource Recovery | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6769375bfa469535b989827a/original/metabolomic-insights-into-balancing-the-trade-off-between-oxidation-of-endogenous-organics-and-macronutrient-recovery-from-human-urine-treated-with-fenton-s-reagent.pdf |
67dc2e50fa469535b9f53b4b | 10.26434/chemrxiv-2025-kpc2c | Hydronium ions inhibit CO2 reduction on coinage metals | The carbon-efficient electrochemical reduction of CO2 (CO2RR) requires acidic electrolytes to mitigate irreversible electrolyte carbonation. However, CO2RR only takes place in acidic electrolytes upon addition of spectator cations and the mechanistic basis for this requirement remains unclear. Herein, we present scanning voltammetry experiments conducted in bulk acidic electrolytes in conjunction with dynamic electrochemical mass spectrometry (DEMS) analysis of CO2 consumption and product formation. By quantifying both faradaic CO2 consumption via electroreduction and non-faradaic CO2 consumption via electrolyte carbonation in real-time, we deconvolute the direct role of the added electrolyte cations from their indirect role in fostering a transient local pH swing. We find that across coinage metals and electrolyte compositions, CO2RR commences only upon substantial depletion of hydronium and coincides with non-faradaic CO2 uptake via carbonation. Doping Ag with Pt to promote hydronium consumption via efficient H2 evolution serves to lower the overpotential for CO2RR onset in scanning voltammetry experiments by ~1 V. These findings together indicate that interfacial alkalinization is a pre-requisite for, rather than merely a consequence of CO2RR, and that the primary role of the supporting electrolyte cations is to establish a non-equilibrium interfacial ionic environment depleted in hydronium ions. The findings imply a putative mechanistic model in which hydronium ions serve to inhibit CO2 activation at coinage metal surfaces. This work highlights the value of pre-steady state real-time analysis of both faradaic and non-faradaic interfacial reactions and establishes a self-consistent mechanistic picture for CO2RR in bulk acidic electrolyte. | Max J. Hülsey; Bryan Y. Tang; Sophia Weng; Yogesh Surendranath | Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dc2e50fa469535b9f53b4b/original/hydronium-ions-inhibit-co2-reduction-on-coinage-metals.pdf |
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