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66b50a2c01103d79c53fed30 | 10.26434/chemrxiv-2024-0g4sz | A multi-robot-multi-task scheduling system for autonomous chemistry laboratories | We present a multi-robot-multi-task scheduling system designed for autonomous chemistry laboratories to enhance the efficiency of executing complex chemical experiments. Building on the herein formulated and developed scheduling algorithms and employing a constraint programming approach, the scheduling system optimizes task allocation across three robots and 18 experimental stations, facilitating the coordinated and concurrent execution of experiments. The system allows for dynamic task insertion during ongoing operations without significant disruption, enhancing laboratory efficiency and flexibility while providing a scalable solution for high-throughput experimentation. In real-world applications involving four diverse chemical experiments with varied step counts, step durations, and sample throughputs, the system demonstrated its ability to reduce total execution time by nearly 40% compared to sequential execution of individual experiments, where in-experiment tasks were already optimized for concurrency. Our multi-robot-multi-task system represents a timely and significant advancement in autonomous chemistry, enabling automated laboratories to conduct experiments with greater efficiency and versatility. By reducing the time and resources required for experimentation, it accelerates the pace of scientific discovery and offers a robust framework for developing more sophisticated autonomous laboratories capable of handling increasingly complex and diverse scientific tasks. | Junyi Zhou; Man Luo; Linjiang Chen; Qing Zhu; Shan Jiang; Fei Zhang; Weiwei Shang; Jun Jiang | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b50a2c01103d79c53fed30/original/a-multi-robot-multi-task-scheduling-system-for-autonomous-chemistry-laboratories.pdf |
65b91d119138d231610e4867 | 10.26434/chemrxiv-2023-09mdd-v2 | Engineering Frustrated Lewis Pair Active Sites in Porous Organic Scaffolds for Catalytic CO2 Hydrogenation | Frustrated Lewis pairs (FLPs), featuring reactive combinations of Lewis acids and Lewis bases, have been utilized for myriad homogeneous catalytic processes. Immobilizing the active Lewis sites to a solid support, especially to porous scaffolds, has shown great potential to ameliorate FLP catalysis by circumventing some of its inherent drawbacks, such as product separation and catalyst recyclability. Nevertheless, designing immobilized Lewis pair active sites (LPASs) is challenging due to the requirement of placing the donor and acceptor centers in appropriate geometric arrangements while maintaining the necessary chemical environment to perform catalysis, and clear design rules have not yet been established. In this work, we formulate simple guidelines to build highly active LPASs for direct catalytic hydrogenation of CO2 through a large-scale screening of a diverse library of 25,000 immobilized FLPs. The library is built by introducing boron-containing acidic sites in the vicinity of the existing basic nitrogen sites of the organic linkers of metal-organic frameworks collected in a ``top-down" fashion from an experimental database. The chemical and geometrical appropriateness of these LPASs for CO2 hydrogenation is determined by evaluating a series of simple descriptors representing the intrinsic strength (acidity and basicity) of the components and their spatial arrangement in the active sites. Analysis of the leading candidates enables the formulation of pragmatic and experimentally-relevant design principles and the leading candidates constitute the starting point for further exploration of FLP-based catalysts for the reduction of CO2. | Shubhajit Das; Ruben Laplaza; J. Terence Blaskovits; Clémence Corminboeuf | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b91d119138d231610e4867/original/engineering-frustrated-lewis-pair-active-sites-in-porous-organic-scaffolds-for-catalytic-co2-hydrogenation.pdf |
6367c3b4ecdad5b292fd2f94 | 10.26434/chemrxiv-2022-kspbc | Binding of exogenous cyanide reveals new active-site states in [FeFe] hydrogenases | [FeFe] hydrogenases are highly efficient metalloenyzmes for hydrogen conversion. Their active site cofactor (the H-cluster) is composed of a canonical [4Fe-4S] cluster ([4Fe-4S]H) linked to a unique organometallic di-iron subcluster ([2Fe]H). In [2Fe]H the two Fe ions are coordinated by a bridging 2-azapropane-1,3-dithiolate (ADT) ligand, three CO and two CN- ligands, leaving an open coordination site on one Fe where substrates (H2 and H+) as well as inhibitors (e.g. O2, CO, H2S) may bind. Here, we investigate two new active site states that accumulate in [FeFe] hydrogenase variants where the cysteine (Cys) in the proton transfer pathway is mutated to alanine (Ala). Our experimental data, including atomic resolution (≈1 Å) crystal structures and supported by calculations, suggest that in these two states a third CN- ligand is bound to the apical position of [2Fe]H. These states can be generated both by “cannibalization” of CN- from damaged [2Fe]H subclusters as well as by addition of exogenous CN-. This is the first reported interaction of exogenous CN- with [FeFe] hydrogenases. Similar CN--bound states can also be generated in wild-type hydrogenases, but do not form as readily as with the Cys to Ala variants. These results highlight how the interaction between the first amino acid in the proton transfer pathway and the active site tunes ligand binding to the open coordination site and affects the electronic structure of the H-cluster. | Maria Alessandra Martini; Konstantin Bikbaev; Yunjie Pang; Christian Lorent; Charlotte Wiemann; Nina Breuer; Ingo Zebger; Serena DeBeer; Ingrid Span; Ragnar Bjornsson; James A. Birrell; Patricia Rodriguez Macia | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Spectroscopy (Inorg.); Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6367c3b4ecdad5b292fd2f94/original/binding-of-exogenous-cyanide-reveals-new-active-site-states-in-fe-fe-hydrogenases.pdf |
60c75069bb8c1a7c083dbafb | 10.26434/chemrxiv.13038236.v1 | Anticancer Mechanism of Withania Somnifera and Its Bioactive Compounds : A Short Review Along with Computational Molecular Docking Study | <p>Withania somnifera, known as Aswogondha in Bangladesh and some part
of India, is a shrub of Solanceae family. Parts of this plant is used as
alternative medicine in this region to cure diseases from bronchitis to
insomnia. Although such use of the plant is not supported by clinical
research, recent studies have found anticancer activity of some proteins
derived from w. somnifera. The purpose of this study is to summarize
the anticancer activity of medicinal plant Withania somnifera and its
bioactive compounds as well as to predict the interaction between
phytochemicals (Withanolide, Withaferin-A) and macromolecules that are
responsible for cancer cell proliferation. Studies suggested that
Withanolide and Withaferin-A from W. somnifera can be used as a cancer
chemotherapeutic agent for cancerous cell lines in mice models through
modulating various signaling pathway including inhibition, autophagy,
apoptosis, radiopreventive pathway and reactive oxygen species pathway.
Molecular docking of Withanolide and Withaferin-A against 9 types of
vital protein mediators concluded that 3A8X (Protein kinase C iota type)
and 1A9U (MAP KINASE P38) are the most active receptor for binding and
interacting with Withanolide and Withaferin-A for the prevention and
treatment of cancer. On the basis of this review and docking study, it
can be concluded that Withania somnifera as well as its derivatives
Withanolide and Withaferin-A may be considered as a promising anticancer
agent. </p> | Mita Shikder; Tasnin Al Hasib; Md. Lutful Kabir | Drug Discovery and Drug Delivery Systems; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75069bb8c1a7c083dbafb/original/anticancer-mechanism-of-withania-somnifera-and-its-bioactive-compounds-a-short-review-along-with-computational-molecular-docking-study.pdf |
61727d7d4c04e877c18bee11 | 10.26434/chemrxiv-2021-9xwlh | Sustainable polyesters via direct functionalization of lignocellulosic sugars | The development of sustainable plastics from abundant renewable feedstocks has been limited by the complexity and efficiency of their production as well as their lack of competitive material properties. Here, we demonstrate the direct transformation of the hemicellulosic fraction of non-edible biomass into a diester plastic precursor at 83% yield (95% from commercial xylose) during integrated plant fractionation with glyoxylic acid. Melt polycondensation of the resulting xylose-based diester with a range of aliphatic diols led to high-molecular weight amorphous polyesters with combined high glass transition temperatures, tough mechanical properties, and strong gas barriers, which could be processed by injection-molding, thermoforming, and 3D-printing. These polyesters could then be chemically recycled from mixed plastic waste streams or digested under biologically relevant conditions. The transformation’s simplicity led to projected costs that were competitive with fossil alternatives and significantly reduced associated greenhouse gas emissions, especially if glyoxylic acid was sourced from CO2. | Lorenz Manker; Graham Dick; Adrien Demongeot; Maxime Hédou; Christèle Rayroud; Thibault Rambert; Marie Jones; Irina Sulaeva; Yves Leterrier; Antje Potthast; Francois Maréchal; Véronique Michaud; Harm-Anton Klok; Jeremy Luterbacher | Polymer Science; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61727d7d4c04e877c18bee11/original/sustainable-polyesters-via-direct-functionalization-of-lignocellulosic-sugars.pdf |
635c30942e0c6371e44076e5 | 10.26434/chemrxiv-2022-01jhn | The hydrothiolation of TIPS-CΞC-SF5 – Charting the chemical space of beta-SF5 vinyl sulfides | The pentafluorosulfanyl group is suggested to be a promising candidate adding to the toolbox of emerging fluorinated motifs. While the synthesis of non-aromatic SF5 bulding blocks generally requires on-site fluorination or pentafluorosulfanylation steps employing toxic and/or gaseous reagents, downstream processing of commercially available prefunctionalized molecules is proposed as an alternative strategy to allow access to this motif by less specialized laboratories. Herein, we report a benign bench-top protocol for the synthesis of Z-configured beta-pentafluorosulfanylated vinyl sulfides in good to excellent yields with excellent Z-diasteroselectivity and broad functional group tolerance. This general method exploits an in-situ protodesilylation-hydrothiolation sequence of commercially available liquid and high-boiling TIPS-CΞC-SF5 (TASP). This so far uncharted class of compounds was analyzed by means of NMR-spectroscopy as well as SC-XRD. Furthermore, we suggest the reaction to proceed via a kinetically controlled closed-shell reaction pathway corroborated by in-silico experiments. | Hannes Kucher; Jonas Oliver Wenzel; David Rombach | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635c30942e0c6371e44076e5/original/the-hydrothiolation-of-tips-c-c-sf5-charting-the-chemical-space-of-beta-sf5-vinyl-sulfides.pdf |
632ada48fee74e1c4244a730 | 10.26434/chemrxiv-2022-l8rf6 | Fate and Reactivity of Peroxides formed over BiVO4 Anodes in Bicarbonate Electrolytes | For the electrochemical and photoelectrochemical synthesis of hydrogen peroxide, aqueous bicarbonate electrolytes have been reported with much higher efficiency compared to other alternatives. It was proposed that this is due to efficient oxidation of the bicarbonate to peroxymonocarbonate (PMC) with subsequently hydrolyzes to hydrogen peroxide. However, as we show herein, PMC forms stable concentrations and does not hydrolyze completely. Due to its much better oxidation kinetics this may influence the sensitivity of the employed peroxide quantification methods. Particularly commercial test strips are susceptible to this, giving rise to uncertainty about the validity of the high peroxide formation efficiency in bicarbonate electrolytes. On the other side, PMC’s superior oxidation kinetics may mean that the resulting solutions are even more potent oxidants than previously suspected. | Tobias Schanz; Bastien O. Burek; Jonathan Z. Bloh | Physical Chemistry; Inorganic Chemistry; Analytical Chemistry; Analytical Chemistry - General; Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632ada48fee74e1c4244a730/original/fate-and-reactivity-of-peroxides-formed-over-bi-vo4-anodes-in-bicarbonate-electrolytes.pdf |
60c74da94c8919a91cad3843 | 10.26434/chemrxiv.12052512.v11 | Tripartite combination of potential pandemic mitigation agents: Vitamin D, Quercetin, and Estradiol manifest properties of candidate medicinal agents for mitigation of the severity of pandemic COVID-19 defined by genomics-guided tracing of SARS-CoV-2 targets in human cells. | <p>
</p><p>
</p><p>
</p><p>
</p><p>
</p><p>
</p><p>
</p><p>
</p><p>
</p><p>
</p><p>Genes
required for SARS-CoV-2 entry into human cells, <i>ACE2</i> and <i>FURIN</i>, were
employed as baits to build genomics-guided molecular maps of up-stream
regulatory elements, their expression and functions in human body, including
pathophysiologically-relevant cell types. Repressors and activators of the <i>ACE2</i> and <i>FURIN</i> genes were identified based on the analyses of gene silencing
and overexpression experiments as well as relevant transgenic mouse models.
Panels of repressors (<i>VDR; GATA5; SFTPC;
HIF1a</i>) and activators (<i>HMGA2; INSIG1</i>)
were then employed to identify existing drugs manifesting gene expression
signatures of the potential coronavirus infection mitigation agents. Using this
strategy, Vitamin D and Quercetin have been identified as putative COVID-19
mitigation agents. Quercetin has been identified as one of top-scoring
candidate therapeutics in the supercomputer SUMMIT drug-docking screen and Gene
Set Enrichment Analyses (GSEA) of expression profiling experiments (EPEs), indicating
that highly similar structurally Quercetin, Luteolin, and Eriodictyol could
serve as scaffolds for development of efficient inhibitors of the SARS-CoV-2
infection. In agreement with this notion, Quercetin alters expression of 98 of
332 (30%) of human genes encoding protein targets of SARS-CoV-2, thus
potentially interfering with functions of 23 of 27 (85%) of the SARS-CoV-2 viral
proteins in human cells. Similarly, Vitamin D may interfere with functions of
19 of 27 (70%) of the SARS-CoV-2 proteins by altering expression of 84 of 332
(25%) of human genes encoding protein targets of SARS-CoV-2. Considering the
potential effects of both Quercetin and Vitamin D, the inference could be made
that functions of 25 of 27 (93%) of SARS-CoV-2 proteins in human cells may be
altered. GSEA and EPEs identify multiple drugs, smoking, and many disease
conditions that appear to act as putative coronavirus infection-promoting
agents. Discordant patterns of Testosterone versus Estradiol impacts on SARS-CoV-2
targets suggest a plausible molecular explanation of the apparently higher male
mortality during coronavirus pandemic. Estradiol, in contrast with
Testosterone, affects expression of a majority of human genes (203 of 332; 61%)
encoding SARS-CoV-2 targets, thus potentially interfering with functions of 26
of 27 SARS-CoV-2 viral proteins. A hypothetical tripartite combination
consisting of Quercetin/Vitamin D/Estradiol may affect expression of 244 of 332
(73%) human genes encoding SARS-CoV-2 targets. Of major concern is the ACE2 and
FURIN expression in many human cells and tissues, including immune cells,
suggesting that SARS-CoV-2 coronavirus may infect a broad range of cellular
targets in the human body. Infection of immune cells may cause
immunosuppression, long-term persistence of the virus, and spread of the virus
to secondary targets. Present analyses and numerous observational studies
indicate that age-associated Vitamin D deficiency may contribute to high
mortality of older adults and elderly. Immediate availability for targeted
experimental and clinical interrogations of potential COVID-19 pandemic
mitigation agents, namely Vitamin D and Quercetin, as well as of the highly
selective (K<sub>i, </sub>600 pm) intrinsically-specific FURIN inhibitor (a1-antitrypsin
Portland (a1-PDX), is considered an encouraging factor. Observations reported
in this contribution are intended to facilitate follow-up targeted experimental
studies and, if warranted, randomized clinical trials to identify and validate
therapeutically-viable interventions to combat the COVID-19 pandemic. Specifically,
gene expression profiles of Vitamin D and Quercetin activities and their
established safety records as over-the-counter medicinal substances strongly
argue that they may represent viable candidates for further considerations of
their potential utility as COVID-19 pandemic mitigation agents. In line with results
of present analyses, a randomized interventional clinical trial entitled “Phase
II Clinical Trial of Estradiol to Reduce Severity of COVID19 Infection in COVID19+
and Presumptive COVID19+ Patients” has been posted on ClinicalTrials.gov website
(<a href="https://clinicaltrials.gov/ct2/show/NCT04359329">https://clinicaltrials.gov/ct2/show/NCT04359329</a> )
and two interventional randomized clinical trials evaluating effects of Vitamin
D on prevention and treatment of COVID-19 were listed on ClinicalTrials.gov
website (<a href="https://www.clinicaltrials.gov/ct2/show/NCT04334005">https://www.clinicaltrials.gov/ct2/show/NCT04334005</a>
and <a href="https://clinicaltrials.gov/ct2/show/NCT04344041">https://clinicaltrials.gov/ct2/show/NCT04344041</a>
).</p><p>
<b></b><i></i><u></u><sub></sub><sup></sup><br /></p> | Gennadi Glinsky | Biochemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74da94c8919a91cad3843/original/tripartite-combination-of-potential-pandemic-mitigation-agents-vitamin-d-quercetin-and-estradiol-manifest-properties-of-candidate-medicinal-agents-for-mitigation-of-the-severity-of-pandemic-covid-19-defined-by-genomics-guided-tracing-of-sars-co-v-2-target.pdf |
66077722e9ebbb4db9f56ce0 | 10.26434/chemrxiv-2023-4tshv-v2 | Cavity Controlled Upconversion in CdSe
Nanoplatelet Polaritons | Strong coupling between electronic transitions of matter and confined electromagnetic fields inside an optical cavity creates hybrid, light-matter states known as polaritons. Polaritons provide a versatile platform for investigating quantum electrodynamics effects in chemical systems, such as polariton-altered chemical reactivity. However, using polaritons in chemical contexts will require a better understanding of the photophysical properties of polaritons, especially at ambient temperature and pressure, where chemistry is typically performed. Here, we investigated leveraging strong light-matter interactions to control the excited state dynamics of colloidal CdSe nanoplatelets (NPLs) coupled to a Fabry-Pérot optical cavity. Importantly, changes in the cavity quality (Q) factor, which is a measure of photon loss from the cavity, were used to profoundly change the polariton dynamics. As the Q-factor was increased, we observed significant population of the upper polariton (UP) state, exemplified by the rare observation of substantial UP photoluminescence (PL) at room temperature. In fact, with low energy excitation at the lower polariton (LP), which is not absorbed by uncoupled nanoplatelets, we observed upconverted PL emission from the UP branch, due to efficient exchange of population between the LP, UP and the reservoir of dark states present in collectively coupled polaritonic systems. Critical physical insight into the mechanism of PL enhancement of the UP, and PL upconversion, was provided by state-of-the-art quantum dynamics simulations that account for multiple cavity electromagnetic modes and cavity loss. In addition, by resolving lower and upper polariton PL lifetimes, we found timescales for polariton dynamics on the order of 100 picoseconds, implying great potential for NPL based polariton systems to affect photochemical reaction rates. This work provides important insight into the photophysics of nanocrystal-based exciton-polariton systems and is a significant step towards the development of practical polariton photochemistry platforms. | Mitesh Amin; Eric R Koessler ; Ovishek Morshed; Farwa Awan; Nicole MB Cogan; Robert Collison; Trevor Tumiel; William Girten; Christopher S Leiter ; A. Nickolas Vamivakas ; Pengfei Huo; Todd D Krauss | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66077722e9ebbb4db9f56ce0/original/cavity-controlled-upconversion-in-cd-se-nanoplatelet-polaritons.pdf |
62e785385be041833da47763 | 10.26434/chemrxiv-2022-m1r64-v2 | Charged small molecule binding to membranes in MD simulations evaluated against NMR experiments | Interactions of charged molecules with biomembranes regulate many of their biological activities, but their binding affinities to lipid bilayers are difficult to measure experimentally and model theoretically. Classical molecular dynamics (MD) simulations have the potential to capture the complex interactions determining how charged biomolecules interact with membranes, but systematic overbinding of sodium and calcium cations in standard MD simulations raises the question of how accurately force fields capture the interactions between lipid membranes and charged biomolecules. Here, we evaluate the binding of positively charged small molecules, etidocaine and tetraphenylphosphonium (TPP), to a POPC lipid bilayer using the changes in lipid headgroup order parameters. We observed that these molecules behave oppositely to calcium and sodium ions when binding to membranes: (i) their binding affinities are not overestimated by standard force field parameters, (ii) implicit inclusion of electronic polarizability increases their binding affinity, and (iii) they penetrate into the hydrophobic membrane core. Our results can be explained by distinct binding mechanisms of charged small molecules with hydrophobic moieties and monoatomic ions. The binding of the former is driven by hydrophobic effects, while the latter has direct electrostatic interactions with lipids. In addition to elucidating how different kinds of charged biomolecules bind to membranes, we deliver tools for further development of MD simulation parameters and methodology. | Ricky Nencini; Samuli Ollila | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2022-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e785385be041833da47763/original/charged-small-molecule-binding-to-membranes-in-md-simulations-evaluated-against-nmr-experiments.pdf |
6331fc48cf38292610b34284 | 10.26434/chemrxiv-2022-b97x0-v2 | OpenPCA and Raman mapping to decipher complex spectral datasets from multi-component samples: application to cannabis trichomes | The development of analytical techniques that decode chemical information in complex biochemical samples to discriminate different structural components may open the way for several new findings. In this study, principal component analysis (PCA) is carried out using an ad hoc Matlab coding that provides a transparent access to multivariate analysis of Raman mapping datasets. Here, we illustrated the efficacy of this method to extract meaningful results from Raman images of Cannabis sativa trichomes. A large dataset of Cannabis trichome comprising of 441 Raman spectra was examined for the first time using our OpenPCA. By mapping the chemical distribution in the trichome, we could locate the secretary vesicles in the PC score maps generated from the mapped Raman spectra. Black-box PCA solutions available in commercial software can be limited by rigid input interfaces which may prevent obtaining information by tuning the PCA analysis on selected wavenumber ranges. Hence, the OpenPCA scripts facilitate the task of obtaining key information from widely distributed range of wavenumbers that are characteristic to a specific cannabinoid, namely Δ9-THC and CBD. Overall, the PCA-coding algorithm shows advantages in decoding Raman spectra that could be extended to handle all kinds of datasets with simultaneous spatial and chemical details. | Janani Balasubramanian; Elisa Crocioni; Mattia Frattini; Scott Hill; Darryen Sands; Chiara Zanchi; Matteo Tommasini; Nisha Rani Agarwal | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6331fc48cf38292610b34284/original/open-pca-and-raman-mapping-to-decipher-complex-spectral-datasets-from-multi-component-samples-application-to-cannabis-trichomes.pdf |
60c74002ee301c4de9c789d0 | 10.26434/chemrxiv.7384868.v2 | Electronic Spectroscopy of Isolated DNA Polyanions | In solution, UV-vis spectroscopy is often used to investigate structural changes in biomolecules (i.e., nucleic acids), owing to changes in the environment of their chromophores (i.e., the nucleobases). Here we address whether action spectroscopy could achieve the same for gas-phase ions, while taking the advantage of additional spectrometric separation of complex mixtures. We therefore systematically studied the action spectroscopy of homo-base 6-mer DNA strands (dG6, dA6, dC6, dT6) and discuss the results in light of gas-phase structures validated by ion mobility spectrometry and infrared ion spectroscopy, of electron binding energies measured by photoelectron spectroscopy, and of calculated electronic photo-absorption spectra. When UV photons interact with oligonucleotide polyanions, two main actions may take place: (1) fragmentation and (2) electron detachment. The action spectra reconstructed from fragmentation follow the absorption spectra well, and result from multiple cycles of absorption and internal conversion. The action spectra reconstructed from the electron photodetachment (ePD) efficiency reveal interesting phenomena: ePD depends on the charge state because it depends on electron binding energies. We illustrate with the G-quadruplex [dTG4T]4 that the ePD action spectrum shifts with the charge state, pointing to possible caveats when comparing the spectra of systems having different charge densities to deduce structural parameters. Moreover, ePD is particularly efficient for purines but not pyrimidines. ePD thus reflects not only absorption, but also particular relaxation pathways of the electronic excited states. As these pathways lead to photo-oxidation, their investigation on model gas-phase systems may prove useful to elucidate mechanisms of photo-oxidative damages, which are linked to mutations and cancers. | Steven Daly; Massimiliano Porrini; Frédéric Rosu; Valerie Gabelica | Mass Spectrometry; Biophysical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74002ee301c4de9c789d0/original/electronic-spectroscopy-of-isolated-dna-polyanions.pdf |
61551803d1fc335b7cf8fd45 | 10.26434/chemrxiv-2021-nlwvs | MegaSyn: Integrating Generative Molecule Design, Automated Analog Designer and Synthetic Viability Prediction | Drug discovery is a multi-stage process, often beginning with the identification of active molecules from a high-throughput screen or machine learning model. Once structure activity relationship trends become well established, identifying new analogs with better properties is important. Synthesizing these new compounds is a logical next step, and is key to research groups that have a synthetic chemistry team or external collaborators. Generative machine learning models have become widely adopted to generate new molecules and explore molecular space, with the goal of discovering novel compounds with desires properties. These generative models have been composed from recurrent neural networks (RNNs), Variational Autoencoders (VAEs), and Generative Adversarial Networks (GANs) and are often combined with transfer learning or scoring of physicochemical properties to steer generative design. While these generative models have proven useful in generating new molecular libraries, often they are not capable of addressing a wide variety of potential problems, and often converge into similar molecular space when combined with a scoring function for desired properties. In addition, generated compounds are often not synthetically feasible, reducing their capabilities outside of virtual composition and limiting their usefulness in real-world scenarios. Here we introduce a suite of automated tools called MegaSyn representing 3 components: a new hill-climb algorithm which makes use of SMILES-based RNN generative models, analog generation software, and retrosynthetic analysis coupled with fragment analysis to score molecules for their synthetic feasibility. We now describe the development and testing of this suite of tools and propose how they might be used to optimize molecules or prioritize promising lead compounds using test case examples. | Fabio Urbina; Christopher Lowden; Christopher Culberson; Sean Ekins | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61551803d1fc335b7cf8fd45/original/mega-syn-integrating-generative-molecule-design-automated-analog-designer-and-synthetic-viability-prediction.pdf |
6788f15d81d2151a0262bb43 | 10.26434/chemrxiv-2025-qblz5-v2 | Mechanically and photoelectrochemically stable WO3 | BiVO4 | NiFeOOH photoanodes synthesised by a scalable chemical vapour deposition method
| The development of scalable, stable and high performance photoelectrodes remains the major bottleneck in up-scaling photoelectrochemical (PEC) water splitting systems. A photoanode structure of particular promise is WO3 | BiVO4, where the formation of staggered heterojunction between nanostructured WO3 and a thin layer of BiVO4 mitigates charge carrier mobility limitations present for BiVO4 alone and suppresses recombination. Although these electrodes remain prone to photo-corrosion, this effect can be mitigated through the application of water oxidation surface co-catalysts. An additional challenge that has rarely been addressed in the literature to date is the need for strong adhesion to the substrate and mechanical stability of these photoelectrodes, so that they can withstand flow-induced shear stress exerted by the electrolyte in continuous flow under operational conditions. Herein, we propose a scalable route to synthesising WO3 | BiVO4 | NiFeOOH photoanodes entirely by aerosol-assisted chemical vapour deposition (AA-CVD). The mechanical stability of the WO3 | BiVO4 heterojunction was optimised by tuning the morphology of the WO3 underlayer and improving its adhesion to the FTO transparent substrate. To address BiVO4 dissolution at the electrode | electrolyte interface, we fabricated a NiFeOOH co-catalyst by a novel AA-CVD method. This suppressed BiVO4 dissolution and enhanced the water oxidation performance of the photoanode, characterised by linear sweep voltammetry (LSV), photoelectrochemical impedance spectroscopy (PEIS) and chopped chronoamperometry. The photoanode materials were physically characterised by X-ray diffraction (XRD), UV-vis spectroscopy, scanning electron microscopy (SEM), high resolution transmission electron microscopy (HR-TEM), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Our optimised photoanodes with 1 cm2 photoactive area delivered a stable photocurrent density of 1.75 mA cm-2 (at 1 simulated sun irradiance and 1.23 VRHE) during 24-hour testing in a continuous PEC flow reactor (operated at 0.5 cm s-1). Our method for growing WO3 | BiVO4 | NiFeOOH photoanodes is up-scalable, and therefore suitable for producing large-area demonstration devices, providing a pathway to commercial photoelectrochemical hydrogen production. | George Creasey; Tristan McCallum; Guangrui Ai; Brian Tam; John Wilman Rodriguez Acosta; Alvia Mohammad Yousuf; Sarah Fearn; Andreas Kafizas; Anna Hankin | Catalysis; Energy; Photocatalysis; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6788f15d81d2151a0262bb43/original/mechanically-and-photoelectrochemically-stable-wo3-bi-vo4-ni-fe-ooh-photoanodes-synthesised-by-a-scalable-chemical-vapour-deposition-method.pdf |
63b6cedd1699ca02e3e48190 | 10.26434/chemrxiv-2023-hd3r9 | Controllable Secondary through-Space Interaction and Clusteroluminescence of Multiaryl-Substituted Alkanes | Nonconjugated clusteroluminogens (CLgens) become increasingly important in photophysics and advanced bioelectronic applications. Most CLgens show ultraviolet emission, and it remains an enormous challenge to change the electronic structures of CLgens to improve their photophysical properties by precisely regulating the intramolecular through-space interactions (TSI). Herein we propose a general strategy to construct a higher-level intramolecular TSI in multiaryl-substituted alkanes, namely the secondary through-space interaction (2nd TSI), which is constructed by the primary through-space interaction (1st TSI) and TSI linker. By introducing methyl and phenyl into 1,1,3,3-tetraphenylpropane (TPP) respectively, butane-1,1,3,3-tetrayltetrabenzene (Me-TPP) and propane-1,1,1,3,3-pentaylpentabenzene (Ph-TPP) both show bright visible clusteroluminescence (CL), whose fluorescence quantum yield is up to ~40% and the emission wavelength extends to 530 nm. Advanced theoretical studies relating to their emission mechanism are quantitatively performed to analyze the photophysical properties of these CLgens in different states. It is found that molecular rigidity and proper conformation both play pivotal roles in improving the 1st TSI, enhancing the TSI linker and constructing 2nd TSI. Experimental and calculation results prove that the hierarchical TSIs and CL have been successfully regulated in these multiaryl-substituted alkanes (MAAs). This work not only provides a feasible strategy to achieve controllable manipulation of TSI and CL but also paves the way to the in-depth mechanistic understanding of CL. | Zuping Xiong; Jianyu Zhang; Lei Wang; Yuan Xie; Yipu Wang; Zujin Zhao; Haoke Zhang; Jing Zhi Sun; Feihe Huang; Ben Zhong Tang | Theoretical and Computational Chemistry; Materials Science; Aggregates and Assemblies; Dyes and Chromophores; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b6cedd1699ca02e3e48190/original/controllable-secondary-through-space-interaction-and-clusteroluminescence-of-multiaryl-substituted-alkanes.pdf |
6616d7ec91aefa6ce146e2da | 10.26434/chemrxiv-2024-m8v9m | Employing Metadynamics to Predict the Membrane Partitioning of Carboxy-2H-Azirine Natural Products | Natural products have diverse chemical structures and biological activities which often serve as sources of new therapeutic agents. Those containing a carboxy-2H-azirine moiety are an exciting target for investigation due in part to the broad-spectrum antimicrobial activity these compounds have and the significant chemical space for novel therapeutic development offered by this unique scaffold. The carboxy-2H-azirine moiety, including those appended to well-characterized chemical scaffolds, is understudied, which creates a challenge for understanding potential modes of inhibition. In particular, some known natural product carboxy-2H-azirines have long hydrophobic tails, which might lead to amphipathicity and implicate them in membrane associated processes. Metadynamics is an effective method for calculating the free energy changes associated with membrane embedding processes. In this study, we examined a small set of carboxy-2H-azirine natural products, including analogs with long alkyl chains, geometric isomers, and one comprising the simple carboxy-2H-azirine core. We compared the physiochemical properties of these compounds to those of established membrane embedders with similar chemical scaffolds. This was intended to isolate the physiochemical properties of the carboxy-2H-azirine group and understand molecular influences of this moiety on membrane partitioning. To accomplish this, we developed a force field for the 2H-azirine functional group and performed metadynamics simulations of the partitioning into a model membrane (75 % POPE, 25 % POPG) from aqueous solution. We determine that the carboxy-2H-azirine functional group is likely hydrophilic, imbuing the long chain analogs with amphipathicity similar to the known membrane binding molecules to which they were compared. For the long chain analogs, the carboxy-2H-azirine headgroup stays within 1 nm of the phosphate layer, while the carboxy-2H-azirines lacking the long alkyl chain partitions completely into aqueous solution. | Clyde Daly; Leah Seebald; Emma Wolk | Theoretical and Computational Chemistry; Physical Chemistry; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6616d7ec91aefa6ce146e2da/original/employing-metadynamics-to-predict-the-membrane-partitioning-of-carboxy-2h-azirine-natural-products.pdf |
60c74605bb8c1a8e4d3da7df | 10.26434/chemrxiv.10321946.v1 | Reversible Oxidative-Addition and Reductive-Elimination of Thiophene from a Titanium Complex and Its Thermally-Induced Hydrodesulfurization Chemistry | <p>The masked Ti(II) synthon (<sup>Ket</sup>guan)(<i>η</i><sup>6</sup>-Im<sup>Dipp</sup>N)Ti (<b>1</b>) oxidatively adds across thiophene to give ring-opened (<sup>Ket</sup>guan)(Im<sup>Dipp</sup>N)Ti[<i>κ</i><sup>2</sup>-<i>S</i>(CH)<sub>3</sub><i>C</i>H] (<b>2</b>). Complex <b>2</b> is photosensitive, and upon exposure to light, reductively eliminates thiophene to regenerate <b>1</b> – a rare example of early-metal mediated oxidative-addition/reductive-elimination chemistry. DFT calculations indicate strong titanium π-backdonation to the thiophene π*-orbitals leads to the observed thiophene ring opening across titanium, while a proposed photoinduced LMCT promotes the reverse thiophene elimination from <b>2</b>. Finally, pressurizing solutions of <b>2 </b>with H<sub>2</sub> (150 psi) at 80 °C leads to the hydrodesulfurization of thiophene to give the Ti(IV) sulfide (<sup>Ket</sup>guan)(Im<sup>Dipp</sup>N)Ti(S) (<b>3</b>) and butane. </p> | Alejandra Gomez-Torres; J. Rolando Aguilar-Calderón; Carlos Saucedo; Aldo Jordan; Alejandro
J. Metta-Magaña; Balazs Pinter; Skye Fortier | Coordination Chemistry (Organomet.); Kinetics and Mechanism - Organometallic Reactions; Reaction (Organomet.); Small Molecule Activation (Organomet.); Theory - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74605bb8c1a8e4d3da7df/original/reversible-oxidative-addition-and-reductive-elimination-of-thiophene-from-a-titanium-complex-and-its-thermally-induced-hydrodesulfurization-chemistry.pdf |
6440026b7be842788de8ab29 | 10.26434/chemrxiv-2023-096lm-v2 | Deciphering Complexity in Pd–Catalyzed Cross-Couplings | Understanding complex reaction systems and networks is critical in chemistry. While synthetic methods for the selective formation of products are highly sought after, oftentimes it is the full signature of a specific reaction, i.e. the complete profile of products/side-products, that informs mechanistic rationale and acceler-ates discovery chemistry. Moreover, understanding the triggers and sensitivities, under different reaction conditions, that can lead to different products assists with enhanced robustness and safety understanding. In this study we report a methodology using high-throughput experimentation methods and multivariate data analysis that can be used to take the full signature of a chemical reaction, to accelerate an understand-ing of the most complex reaction chemistries. To exemplify our approach, we selected a model Pd-catalyzed reaction system which forms many products – the reaction of two molecules of 2-bromo-N-phenylbenzamide, which affords primarily N-phenyl phenanthridinone. The reaction is a standout bench-mark model for gaining insight on a plethora of side-products. Principal component analysis, correspond-ence analysis and heatmaps with hierarchical clustering have allowed us to examine the factors contrib-uting to the variance in product distributions and show associations between solvents and reaction prod-ucts. Using robust data from experiments performed with eight solvents for four different reaction times at five different temperatures, we have been able to correlate side-products to the major dominant N-phenyl phenanthridinone product, and the post-chemical modification of other side products. Complementary stoichiometric organopalladium studies allowed examination of the Pd precatalyst activation pathway, gaining insight into likely Pd reaction intermediates, particularly an oxidative addition intermediate and downstream PdII intermediates. Automated reaction screening and advanced data analysis tools are transforming the way we examine cata-lytic and synthetic processes. Our study offers a unique and complementary approach to revealing im-portant reaction data on what is arguably one of the most complicated Pd catalyzed transformations known in the chemical literature. | George Clarke; Lyndsay Ledingham; James Firth; Christopher Horbaczewskyj; Richard Bourne; Joshua Bray; Poppy Martin; Rebecca Campbell; Alex Pagett; Duncan MacQuarrie; John Slattery; Jason Lynam; Adrian Whitwood; Jessica Milani; Sam Hart; Julie Wilson; Ian James Stewart Fairlamb | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6440026b7be842788de8ab29/original/deciphering-complexity-in-pd-catalyzed-cross-couplings.pdf |
62a73908a784d12fca7d01e5 | 10.26434/chemrxiv-2022-0xhkn | Primary vs Secondary: Directionalized Guest Coordination in β-Cyclodextrin Derivatives | The cyclodextrin (CD) and its derivatives as useful drug carriers and reservoirs are widely used in pharmaceutical and chemical industries. The CD-guest (drug) and more generally host-guest coordinations are often considered prototypical cases that are much simpler than biological systems. As a result, in computational modelling even with dynamics propagation, only a single binding pose is considered. However, due to the asymmetric feature of the CD host, the guest can directionally bind to its primary 6’ or secondary 3’ face. Correct modelling of the primary-secondary equilibrium clearly poses a challenge, and any static or dynamic calculations modelling only a single binding preference would introduce systematic biases of unknown magnitude. In this work, using the β-CD host-guest set in a recent grand challenge, we present a comprehensive analysis of various aspects of fixed-charge modelling of β-CD host-guest complexes. The force field parameters (electrostatics and bonded terms) are evaluated in a detailed way, and the best parameter combination is employed in enhanced sampling simulations that accelerate the translational diffusion of the guest molecule, sample the binding/unbinding events extensively, and thus explore the space of possible binding modes. Finally, the binding affinities and the primary-secondary equilibrium (directionalized guest coordination preference) are computed and compared with the experimental reference. Possible reasons for deviations and further ways to improve the quality of calculation are discussed. | Zhaoxi Sun; Lei Zheng; Kai Wang; Zhe Huai; Zhirong Liu | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Polymer Science; Cellulosic materials; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a73908a784d12fca7d01e5/original/primary-vs-secondary-directionalized-guest-coordination-in-cyclodextrin-derivatives.pdf |
67bc1de1fa469535b9a89f0e | 10.26434/chemrxiv-2025-bts3z-v2 | The Polytope Formalism for Constitutional Isomerism and Isomerisation | The principles of the Polytope Formalism as developed for stereoisomerism can also be applied to constitutional isomerism reflecting a deep connection between the two and thereby opening the way for describing all isomerism including nuclearspin isomerism. Further, the conceptual framework and methodology can accommodate other discrete molecular-state aspects not typically considered “isomerism”, such as rovibrational and electronic states. The formalism thus provides a universal framework for the abstract description of chemical entities, their naming, and digital representation. Of greater importance, by accommodating a multidimensional implementation of transition-state theory, the results of the formalism meaningfully describe the landscape of the associated chemical space. This provides a powerful and essential tool for its exploration. Novel features of the Polytope Formalism of constitutional isomerism are that it is based upon atom connectivity and the explicit inclusion of subvalent and hypervalent species. The resulting comprehensive sets of possible species include isomers and their related interconversion intermediates (transition states, higher-order saddle points, etc.) providing a powerful tool for elucidating isomerisation mechanisms. The networks of species and interconversion pathways map onto the corresponding potential-energy surfaces and thus represent an “encoding” of these surfaces. Implementation of the formalism is demonstrated through worked examples of H-tautomerism, illuminating applications more broadly. | Peter Canfield; Maxwell Crossley | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Processes; Structure | CC BY 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc1de1fa469535b9a89f0e/original/the-polytope-formalism-for-constitutional-isomerism-and-isomerisation.pdf |
60c745390f50dbbc973961fb | 10.26434/chemrxiv.9961787.v1 | Transformer-CNN: Fast and Reliable Tool for QSAR | We present SMILES-embeddings derived from internal encoder state of a Transformer model trained to canonize SMILES as a Seq2Seq problem. Using CharNN architecture upon
the embeddings results in a higher quality QSAR/QSPR models on diverse benchmark datasets
including regression and classification tasks. The proposed Transformer-CNN method uses
SMILES augmentation for training and inference, and thus the prognosis grounds on an internal
consensus. Both the augmentation and transfer learning based on embedding allows the
method to provide good results for small datasets. We discuss the reasons for such effectiveness and draft future directions for the development of the method. The source code
and the embeddings are available on https://github.com/bigchem/transformer-cnn, whereas the
OCHEM environment (https://ochem.eu) hosts its on-line implementation. | Pavel Karpov; Guillaume Godin; Igor Tetko | Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745390f50dbbc973961fb/original/transformer-cnn-fast-and-reliable-tool-for-qsar.pdf |
64b09012b605c6803baa996f | 10.26434/chemrxiv-2023-78nb3 | A Study on the Efficient Separation of Oily Water Using Mullite Whiskers Membrane through Combined Filtration and Electrofiltration | Oily wastewaters pose significant environmental challenges, requiring effective treatment methods for sustainable development. This study investigates the potential of combining filtration, electrofiltration, and backwashing using a ceramic membrane for the treatment of oily water. A secondary mullite membrane is synthesized, demonstrating favorable characteristics such as high permeate flux (534 LMH), biaxial flexural strength (75.21 MPa), and cost-effectiveness. Experimental investigations were performed for operational parameters, resulting in the selection of a pressure of 2 bar and a cross-flow velocity of 0.727 m/s to achieve desirable permeate flux and oil removal rates. The critical electric field intensity (Ecrit) is determined experimentally and theoretically, ranging from 50 to 55 V, guiding the selection of optimal voltages for electrofiltration. Electrokinetic phenomena, including electrophoresis, electroosmosis, and bubble formation, are harnessed to mitigate fouling. The influence of feed solution conductivity is examined, revealing that higher salt concentrations increase fouling and diminish electric field effectiveness. Energy consumption analysis indicates significant potential for energy savings, with a decrease from 3.88 kWh/m³ in the no-voltage condition to 2.71 kWh/m³ at 65 V for salt-free solutions. However, at higher salt concentrations, increased fouling and reduced electric field effectiveness result in higher energy consumption. The findings underscore the suitability of low-cost ceramic membranes for oily water treatment, emphasizing the importance of optimizing operating parameters for enhanced performance and energy efficiency. | Masoumeh Naseri; Seyed Foad Mousavi; Mohammadreza Omidkhah | Chemical Engineering and Industrial Chemistry; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b09012b605c6803baa996f/original/a-study-on-the-efficient-separation-of-oily-water-using-mullite-whiskers-membrane-through-combined-filtration-and-electrofiltration.pdf |
636e417ebef5d44ffb5176d3 | 10.26434/chemrxiv-2022-rrs1r | Structural and mechanical properties of CrN thin films
deposited on Si substrate by using magnetron techniques
| Chromium Nitride thin films are known for their good mechanical properties. We present the characteristics of ultrathin Chromium Nitride films under 400 nm thickness deposited on silicon substrates by direct current and high-power impulse magnetron sputtering techniques. The methods of investigation of the CrN films were scanning electron microscopy, atomic force microscopy, and nanoindentation. Qualitative and quantitative analysis were performed using the AFM and SEM images by fractal dimension, surface roughness and gray-level co-occurrence matrix methods. Our results show that using the mag-netron techniques, ultrathin CrN films with excellent mechanical properties can be obtained. | Denis E. Tranca; Arcadie Sobetkii; Radu Hristu; Stefan Anton; Eugeniu Vasile; Stefan G. Stanciu; Cosmin K. Banica; Efstathios Fiorentis; David Constantinescu; George A. Stanciu | Materials Science; Nanoscience; Coating Materials; Thin Films | CC BY 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636e417ebef5d44ffb5176d3/original/structural-and-mechanical-properties-of-cr-n-thin-films-deposited-on-si-substrate-by-using-magnetron-techniques.pdf |
60c74f960f50db56d339741d | 10.26434/chemrxiv.12923558.v1 | Material Informatics with PoreBlazer v4.0 and CSD MOF Database | In
this article, we present an updated version of the PoreBlazer code, an open
access, open source Fortran 90 programme to calculate structural properties of
porous materials. The article describes the properties calculated by the code,
their physical meaning and their relationship to the properties that can be
measured experimentally. We reflect on the progress of the code over the years
and discuss features of the most recent version. The results of these calculations, along with the PoreBlazer code,
documentation, and case studies are available online from https://github.com/SarkisovGroup/PoreBlazer. | Lev Sarkisov; Rocio Bueno-Perez; Mythili Sutharson; David Fairen-jimenez | Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f960f50db56d339741d/original/material-informatics-with-pore-blazer-v4-0-and-csd-mof-database.pdf |
658ec226e9ebbb4db9fc48b8 | 10.26434/chemrxiv-2024-gz27t | Photoluminescent detection of lead dust in gunshot residue | Gunshot residue (GSR) analysis is essential for the forensic investigation of shooting incidents, but oftentimes still slow, cumbersome, and with limited spatial resolution. We here introduce a photoluminescent gunshot residue analysis (PL-Pb) for instant spatially resolved detection of GSR with high resolution. Lead dust in GSR reacts into a lead halide perovskite semiconductor that emits bright green light under ultraviolet irradiation. The sensitivity of PL-Pb enables straightforward detection of trace amounts of GSR from ricochet markings, bullet holes and combustion plumes. We show that GSR is transferable with high spatial resolution and preservation of fine details such as the polygonal patterns caused by the rifling of the pistol. Moreover, PL-Pb detection yields reproducible GSR patterns for shooting distance reconstruction series. We also show that the sensitivity and instant results make PL-Pb suitable for rapid presumptive testing of shooting suspects. Surprisingly, even after washing, we can still detect GSR on the hands of shooters, and we find GSR in a simple and straightforward manner on clothes, shoes, and other objects relevant to a shooting incident. Collectively, the instant results and sensitivity of PL-Pb opens unprecedented opportunities for (on-site) forensic investigations and highlights the potential of perovskite-based lead detection methods for lead containing, crime related micro-traces and lead dust in general. | Arno van der Weijden; Kendra Adelberg; Lukas Helmbrecht; Arian van Asten; Willem Noorduin | Inorganic Chemistry; Analytical Chemistry; Environmental Analysis; Imaging; Sensors; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658ec226e9ebbb4db9fc48b8/original/photoluminescent-detection-of-lead-dust-in-gunshot-residue.pdf |
644fb78480f4b75b536d4a6f | 10.26434/chemrxiv-2023-tldbh | High-Resolution Integrated Microfluidic Probe for Mass Spectrometry Imaging of Biological Tissues | Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization technique that enables molecular imaging of biological samples with high spatial resolution. We have recently developed an integrated microfluidic probe (iMFP) for nano-DESI mass spectrometry imaging (MSI) that significantly enhances the robustness of the technique. Herein, we report the design and performance of a second-generation iMFP for imaging with high spatial resolution. The new iMFP features smaller primary and spray channels and a new configuration of the sampling port that enables robust imaging of tissues with a spatial resolution of 8-10 µm. We demonstrate the spatial resolution, sensitivity, durability, and throughput of the iMFP by imaging mouse uterine and brain tissue sections. With a scan rate of 0.2 mm/s, we obtained high-resolution images of a mouse uterine tissue section (scanned area: 2.9 mm × 3.2 mm) in less than 29 minutes without sacrificing sensitivity. This corresponds to a 10-fold improvement in the experimental throughput in comparison with previously reported high-resolution nano-DESI MSI experiments. Overall, the new probe design opens opportunities for mapping biomolecules in biological samples with high throughput and cellular resolution, which is important for understanding biological systems. | Xiangtang Li; Hang Hu; Julia Laskin | Analytical Chemistry; Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644fb78480f4b75b536d4a6f/original/high-resolution-integrated-microfluidic-probe-for-mass-spectrometry-imaging-of-biological-tissues.pdf |
6695ecaf5101a2ffa87f3953 | 10.26434/chemrxiv-2024-plzrv | Automatic Generation of Chemical Mechanisms for Electrochemical Systems: Solid Electrolyte Interphase Formation in Lithium Batteries | Electrolytes in many lithium ion batteries decompose at the low potentials near the anode. The decomposition products form a layer termed the solid electrolyte interphase (SEI). The composition and growth of the SEI layer significantly affect both the capacity fade and safety of lithium ion batteries. However, SEI formation and growth kinetics are not well understood. In this work, we present an extension of the Reaction Mechanism Generator (RMG) software to automatically generate mechanisms for SEI formation. We extend RMG's solvation correction formulation to account for kinetic solvent effects and demonstrate the accuracy of this technique. We calculate thermochemical parameters for 252 species and rate coefficients for 69 reactions, most with associated solvation corrections. This and additional quantum chemistry data are used to extend RMG's thermodynamic group additivity and solute parameter estimation schemes to handle lithiated species and add 14 new reaction families to RMG. RMG is additionally extended to simulate electrocatalytic systems. Lastly we demonstrate RMG on the decomposition of acetonitrile and ethylene carbonate near a Li(110) anode. While this framework does not yet resolve individual ions, as appropriate thermochemistry estimators are not available, and thus, cannot yet resolve more complex electrochemical pathways, it is able to generate reasonable pathways for SEI formation that agree with important components and intermediates in literature. | Matthew Johnson; David Farina Jr.; Lance Kavalsky; Judit Zador; Richard West; Venkatasubramanian Viswanathan; William Green | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6695ecaf5101a2ffa87f3953/original/automatic-generation-of-chemical-mechanisms-for-electrochemical-systems-solid-electrolyte-interphase-formation-in-lithium-batteries.pdf |
643d72c41d262d40eaa641c9 | 10.26434/chemrxiv-2023-bszcb | Inhibitors of the Elastase LasB for the treatment of Pseudomonas aeruginosa lung infections | Infections caused by the Gram-negative pathogen Pseudomonas aeruginosa are emerging worldwide as a major threat to human health. Conventional antibiotic monotherapy suffers from rapid resistance development, underlining urgent need for novel treatment concepts. Here, we report on a non-traditional approach to combat P. aeruginosa-derived infections by targeting its main virulence factor, the elastase LasB. We discovered a new chemical class of phosphonates with an outstanding in vitro ADMET and PK profile, auspicious activity both in vitro and in vivo. We established the mode of action through a co-crystal structure of our lead compound with LasB and in several in vitro and ex vivo models. The proof of concept of a combination of our pathoblocker with levofloxacin in a murine neutropenic lung infection model and the reduction of LasB protein levels in blood as a proof of target engagement demonstrate the great potential for use as an adjunctive treatment of lung infections in humans. | Jelena Konstantinovic; Andreas M. Kany; Alaa Alhayek; Ahmed S. Abdelsamie; Asfandyar Sikandar; Katrin Voos; Yiwen Yao; Anastasia Andreas; Roya Shafiei; Brigitta Loretz; Esther Schönauer; Robert Bals; Hans Brandstetter; Rolf W. Hartmann; Christian Ducho; Claus-Michael Lehr; Christoph Beisswenger; Rolf Müller; Katharina Rox; Jörg Haupenthal; Anna Katharina Herta Hirsch | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d72c41d262d40eaa641c9/original/inhibitors-of-the-elastase-las-b-for-the-treatment-of-pseudomonas-aeruginosa-lung-infections.pdf |
60c74c01bb8c1aa4d23db320 | 10.26434/chemrxiv.12408650.v1 | Targeting SARS-CoV-2 Main Protease by Teicoplanin: A Mechanistic Insight by in Silico Studies | <p>First
emerged in late December 2019, the outbreak of novel severe acute respiratory syndrome corona virus-2
(SARS-CoV-2) pandemic has instigated public-health
emergency around the globe. Although available
medications can only alleviate few symptoms like difficulty in breathing, the
world is craving to identify specific antiviral agents or vaccines
against SARS-CoV-2. Teicoplanin is a glycopeptide class of antibiotic which is regularly
used for treating Gram-positive bacterial infections, has shown potential
therapeutic efficacy against SARS-CoV-2 <i>in vitro</i>. Therefore, in this
study, a mechanistic insight of intermolecular interactions between teicoplanin
and SARS-CoV-2 main protease has been scrutinized by employing molecular
modelling approaches. Molecular docking study was carried out by three
different docking programs including AutoDock4, AutoDock Vina and Dock6. The dynamic and thermodynamics constraints of docked drug in complex
with target protein under specific physiological conditions was ascertained by all-atom molecular dynamics (MD) simulation study. Root
mean square deviation of carbon α chain exhibited uniform value in the range of
1-1.7 Å while root mean square fluctuations were also recorded below 1.72 Å,
justifying the stability of the bound complex in biological environments. Key
interacting residues involved in hydrogen bonds include Thr26, His41, Asn142,
Ser144, Glu166, and Gln189. Several water bridges and hydrophobic interactions
also anchored docked teicoplanin in the inhibitor binding site. These
outcomes are supposed to be fruitful in rational design of antiviral drugs against
SARS-CoV-2.</p> | Faizul Azam | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c01bb8c1aa4d23db320/original/targeting-sars-co-v-2-main-protease-by-teicoplanin-a-mechanistic-insight-by-in-silico-studies.pdf |
67213da05a82cea2fa3de2f9 | 10.26434/chemrxiv-2024-ff160 | Bonded water is an integral component of dissolved organic matter in the ocean | Dissolved organic matter (DOM) in the ocean, as one of the largest pools of reduced carbon on Earth, plays an important role in the global carbon cycle, yet its chemical structure remains largely unknown. Here we show that high molecular weight DOM (HMW-DOM) contains approximately 10% bonded water (H2O) by weight. The bonded H2O molecules are an integral part of the DOM organic complex, likely maintained through strong intermolecular hydrogen bonds, as the H2O is not released during freeze drying and barely exchangeable with surrounding H2O in solution. When the bonded H2O was removed by mild heating (70 °C), the HMW-DOM became more bioavailable as shown by laboratory incubation experiments. These findings suggest that the bonded H2O plays a key role in regulating the stability and biogeochemical cycling of DOM in the ocean. | Kaijun Lu; Xiao You; Laodong Guo; Carlos Baiz; Zhanfei Liu | Organic Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67213da05a82cea2fa3de2f9/original/bonded-water-is-an-integral-component-of-dissolved-organic-matter-in-the-ocean.pdf |
60c744e9337d6c1490e26ea0 | 10.26434/chemrxiv.7695224.v3 | Investigations of Thermally-Controlled Mechanochemical Milling Reactions | Mechanochemical milling
reactions gained a lot of attention lately as a green and highly efficient path
towards various relevant materials. The control over the fundamental reaction
parameters in milling procedure, such as temperature and pressure of the reactor,
is still in infancy and the vast majority of milling reactions is done with
controlling just the basic parameters such as frequency and milling media
weight. We demonstrate here how the milling under controlled, prolonged and
variable heating programs accomplished in a new milling reactor introduces a new
level of mechanochemical reactivity beyond what can be achieved by conventional
mechanochemical or solution procedures, and also reduces the time and energy costs
of the milling process. The methodology is demonstrated on four varied systems:
C–C bond forming Knoevenagel condensation, selective C–N bond formation for
amide/urea synthesis, selective double-imine condensation, and solid-state
formation of an archetypal open metal-organic framework, MOF-74. The potential
of this methodology is best demonstrated on the one-pot selective synthesis of
four complex products containing combinations of amide, amine or urea
functionalities from the same and simple acyl azide and diamine reactants.
Principal control over this enhanced reactivity and selectivity stemmed from
the application of specific heating regimes to mechanochemical processing
accomplished by a new, in-house developed mechanochemical reactor. As even the
moderate increase in temperature strongly affects the selectivity and the rate
of mechanochemical reactions, the results presented are in line with recent
challenges of the accepted theories of mechanochemical reactivity. | Nikola Cindro; Martina Tireli; Tomislav Mrla; Krunoslav Uzarevic | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Hybrid Organic-Inorganic Materials; Materials Processing; Coordination Chemistry (Inorg.); Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744e9337d6c1490e26ea0/original/investigations-of-thermally-controlled-mechanochemical-milling-reactions.pdf |
60c73e574c89195c26ad1d97 | 10.26434/chemrxiv.6879671.v1 | Chemical Transformation of Fe, Air & Water to Ammonia: Variation of Reaction Rate with Temperature, Pressure, Alkalinity and Iron | The rate of ammonia production by the <u>chemical </u>oxidation of iron, N<sub>2</sub>(from air or as pure nitrogen) and water is studied as a function of (1) iron particle size, (2) iron concentration, (3) temperature, (4) pressureand (5) concentration of the alkaline reaction medium. The reaction meduium consists of an aqueous solution of equal molal concentrations of NaOH and KOH (Na<sub>0.5</sub>K<sub>0.5</sub>OH). We had previously reported on the <u>chemical </u>reaction of iron and nitrogen in alkaline medium to ammonia as an intermediate step in the <u>electrochemical </u>synthesis of ammonia by a nano-sized iron oxide electrocatlyst. Here, the intermediate <u>chemical </u>reaction step is exclusively explored. The ammonia production rate increases with temperature (from 20 to 250°C), pressure (from 1 atm to 15 atm of air or N<sub>2</sub>), and exhibits a maximum rate at an electrolyte concentration of 8 molal Na<sub>0,5</sub>K<sub>0,5</sub>OH in a sealed N<sub>2</sub>reactor. 1-3 µm particle size Fe drive the highest observed ammonia production reaction rate. The Fe mass normalized rate of ammonia production increases with decreasing added mass of the Fe reactant reaching a maximum observed rate of 2.2x10<sup>-4</sup>mole of NH<sub>3</sub>h<sup>-1</sup>g<sup>-1</sup>for the reaction of 0.1 g of 1-3 µm Fe in 200°C 8 molal Na<sub>0.5</sub>K<sub>0.5</sub>OH at 15 atm. Under these conditions 5.1 wt% of the iron reacts to form NH<sub>3</sub>via the reaction N<sub>2</sub>+ 2Fe + 3H<sub>2</sub>O ®2NH<sub>3</sub>+ Fe<sub>2</sub>O<sub>3</sub>. | Ping Peng; Fang-Fang Li; Xinye Liu; Jiawen Ren; jessica stuart; Matthew Lefler; Marcus Johnson; Juan Vicini; Stuart Licht | Kinetics and Mechanism - Inorganic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e574c89195c26ad1d97/original/chemical-transformation-of-fe-air-water-to-ammonia-variation-of-reaction-rate-with-temperature-pressure-alkalinity-and-iron.pdf |
60c746a8bdbb8978daa38c43 | 10.26434/chemrxiv.11328128.v1 | A Mountaineering Strategy to Excited States: Highly-Accurate Energies and Benchmarks for Medium Size Molecules | <div><div><div><p>Following our previous work focussing on compounds containing up to 3 non-hydrogen atoms [J. Chem. Theory Comput. 14 (2018) 4360–4379], we present here highly-accurate vertical transition energies obtained for 27 molecules encompassing 4, 5, and 6 non-hydrogen atoms: acetone, acrolein, benzene, butadiene, cyanoacetylene, cyanoformaldehyde, cyanogen, cyclopentadiene, cyclopropenone, cyclopropenethione, diacetylene, furan, glyoxal, imidazole, isobutene, methylenecyclopropene, propynal, pyrazine, pyridazine, pyridine, pyrimidine, pyrrole, tetrazine, thioacetone, thiophene, thiopropynal, and triazine. To obtain these energies, we use equation-of-motion coupled cluster theory up to the highest technically possible excitation order for these systems (CC3, EOM-CCSDT, and EOM-CCSDTQ), selected configuration interaction (SCI) calculations (with tens of millions of determinants in the reference space), as well as the multiconfigurational 𝑛-electron valence state perturbation theory (NEVPT2) method. All these approaches are applied in combination with diffuse-containing atomic basis sets. For all transitions, we report at least CC3/aug-cc-pVQZ vertical excitation energies as well as CC3/aug-cc-pVTZ oscillator strengths for each dipole-allowed transition. We show that CC3 almost systematically delivers transition energies in agreement with higher-level methods with a typical deviation of ±0.04 eV, except for transitions with a dominant double excitation character where the error is much larger. The present contribution gathers a large, diverse and accurate set of more than 200 highly-accurate transition energies for states of various natures (valence, Rydberg, singlet, triplet, 𝑛 → 𝜋★, 𝜋 → 𝜋★, . . . ). We use this series of theoretical best estimates to benchmark a series of popular methods for excited state calculations: CIS(D), ADC(2), CC2, STEOM-CCSD, EOM-CCSD, CCSDR(3), CCSDT-3, CC3, as well as NEVPT2. The results of these benchmarks are compared to the available literature data.</p></div></div></div> | Pierre-Francois Loos; Filippo Lipparini; Martial Boggio-Pasqua; Anthony Scemama; Denis Jacquemin | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746a8bdbb8978daa38c43/original/a-mountaineering-strategy-to-excited-states-highly-accurate-energies-and-benchmarks-for-medium-size-molecules.pdf |
60c7592d702a9b67d018ce59 | 10.26434/chemrxiv.14668503.v1 | Solid-State NMR of Spin-9/2 Nuclei 115In and 209Bi in Functional Inorganic Complex Oxides | Indium and bismuth are technologically important elements, in particular as oxides for optoelectronic applications. <sup>115</sup>In and <sup>209</sup>Bi are both I = 9/2 nuclei with high natural abundances and moderately high frequencies but large nuclear electric quadrupole moments. Leveraging the quadrupolar interaction as a measure of local symmetry and polyhedral distortions for these nuclei could provide powerful insights on a range of applied materials. However, the absence of reported NMR parameters on these nuclei, particularly in oxides, hinders their use by the broader materials community. In this contribution, solid-state <sup>115</sup>In and <sup>209</sup>Bi NMR of three recently discovered quaternary bismuth or indium oxides are reported, supported by density functional theory calculations, numerical simulations, diffraction, and additional multinuclear (<sup>27</sup>Al, <sup>69,71</sup>Ga, <sup>121</sup>Sb) solid-state NMR measurements. The compounds LiIn<sub>2</sub>SbO<sub>6</sub>, BiAlTeO<sub>6</sub>, and BiGaTeO<sub>6</sub> are measured without special equipment at 9.4 T, demonstrating that wideline techniques such as the QCPMG pulse sequence and frequency-stepped acquisition can enable straightforward extraction of quadrupolar tensor information in I = 9/2 <sup>115</sup>In and <sup>209</sup>Bi even in sites with large quadrupolar coupling constants. Relationships are described between the NMR observables and local site symmetry. These are amongst the first reports of the NMR parameters of <sup>115</sup>In, <sup>121</sup>Sb, and <sup>209</sup>Bi in oxides. | Kent Griffith; Fenghua Ding; Steven Flynn | Solid State Chemistry; Spectroscopy (Inorg.); Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7592d702a9b67d018ce59/original/solid-state-nmr-of-spin-9-2-nuclei-115in-and-209bi-in-functional-inorganic-complex-oxides.pdf |
635d971c2e0c630fa141b0e7 | 10.26434/chemrxiv-2022-fxx2d | Design and synthesis of orexin 1 receptor-selective agonists | Orexins are a family of neuropeptides that regulate various physiological events such as sleep/wakefulness as well as emotional and feeding behavior, and that act on two G-protein-coupled receptors, i.e., the orexin 1 (OX1R) and orexin 2 receptors (OX2R). Since the discovery that dysfunction of the orexin/OX2R system causes the sleep disorder narcolepsy, several OX2R-selective and OX1/2R dual agonists have been disclosed. However, an OX1R-selective agonist has not yet been reported, despite the importance of the biological function of OX1R. Herein, we report the discovery of a potent OX1R-selective agonist, (R,E)-3-(4-methoxy-3-(N-(8-(2-(3-methoxyphenyl)-N-methylacetamido)-5,6,7,8-tetrahydronaphthalen-2-yl)sulfamoyl)phenyl)-N-(pyridin-4-yl)acrylamide ((R)-YNT-3708; EC50 = 7.48 nM for OX1R; OX2R/OX1R EC50 ratio = 22.5). Unlike the OX2R-selective agonist, the OX1R-selective agonist (R)-YNT-3708 exhibited antinociceptive and reinforcing effects in mice more potently than the dual agonist. | Keita Iio; Kao Hashimoto; Yasuyuki Nagumo; Mao Amezawa; Taisei Hasegawa; Naoshi Yamamoto; Noriki Kutsumura; Katsuhiko Takeuchi; Yukiko Ishikawa; Masashi Yanagisawa; Hiroshi Nagase; Tsuyoshi Saitoh | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635d971c2e0c630fa141b0e7/original/design-and-synthesis-of-orexin-1-receptor-selective-agonists.pdf |
6648a1e291aefa6ce158afb3 | 10.26434/chemrxiv-2024-dh07n | Target-Directed Dynamic Combinatorial Chemistry Affords Binders of Mycobacterium Tuberculosis IspE | In the search for new antitubercular compounds, we leveraged target-directed dynamic combinatorial chemistry (tdDCC) as an efficient hit-identification method. In tdDCC, the target selects its own binders from a dynamic library generated in situ, reducing the number of compounds that require synthesis and evaluation. We combined a total of twelve hydrazides and six aldehydes to generate 72 structurally diverse N-acylhydrazones. To amplify the best binders, we employed anti-infective target 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis (Mtb). We successfully validated the use of tdDCC as hit-identification method for IspE and optimised the analysis of tdDCC hit determination. From the 72 possible N-acylhydrazones, we synthesised twelve of them revealing several new starting points for the development of IspE inhibitors as antibacterial agents. | Maria Braun-Cornejo; Camilla Ornago; Vidhisha Sonawane; Jörg Haupenthal; Andreas M. Kany; Eleonora Diamanti; Gwenaëlle Jézéquel; Norbert Reiling; Wulf Blankenfeldt; Peter Maas; Anna K. H. Hirsch | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6648a1e291aefa6ce158afb3/original/target-directed-dynamic-combinatorial-chemistry-affords-binders-of-mycobacterium-tuberculosis-isp-e.pdf |
65267a6cbda59ceb9a55eded | 10.26434/chemrxiv-2023-mxg14 | Fuel Cells - An Overview of Their Green Value and Readiness Levels | With CO2, nitrous oxides, and methane emissions data across the African continent, this review paper quantitatively describes the health, environmental, and mortality (expressed as avoidable deaths in thousands per year) effects that the combustion of fossil fuels generates. As a solution, this research study goes further to describe, with visual aids, the technology of fuel cells, their attractive green value, the types of fuel cells including low-temperature and high-temperature fuel cells (LTFC & HTFC) that enable different applications, as well as their levels of commercialization readiness. | Adedayo Adeyanju | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage; Fuels - Energy Science; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65267a6cbda59ceb9a55eded/original/fuel-cells-an-overview-of-their-green-value-and-readiness-levels.pdf |
63ef6a34fcfb27a31fef33f5 | 10.26434/chemrxiv-2023-fhnz9 | Microkinetic Modeling of the Methanol Electro-oxidation Reaction on Platinum | The development of electrocatalysts with high activity at low overpotentials for methanol electro-oxidation reaction is one of the challenges to overcome towards the wider applicability of this alcohol in energy conversion systems. Many works in the last decades have contributed with mechanistic studies on this reaction. Nevertheless, the reaction scheme is entangled which makes difficult to correlate it with the kinetic response in electrochemical experiments. In this paper we propose a microkinetic model for the methanol electro-oxidation reaction on polycrystalline platinum. The model was built on relevant mechanistic aspects available in the literature and formulated based on the mean-field approach. The kinetic parameters were determined by optimization and the validation was performed through the comparison with distinct sets of experimental data, namely cyclic voltammetry, chronoamperometry, and also oscillatory time-series recorded under galvanostatic conditions. The resulting model was able to simulate successfully the nonlinear dynamics observed in galvanostatic experiments, including chaotic behavior, as well as a reasonable voltammetric profile with the same set of electrokinetic parameters. The sensitivity analysis of the kinetic parameters showed that the electro-oxidation pathway through the formic acid intermediate is not significant under these experimental conditions and that the OHad and COad species are mainly involved in the origin of the oscillations, while species that affect the rate of formation/consumption of the latter causes the mixed-mode oscillations. The electrokinetic parameters were discussed with the data available for the electrooxidation reaction of formic acid, where the connection between the values highlights the applicability of this approach to other electrocatalytic reactions. | Enrique Paredes-Salazar; Alfredo Calderón-Cárdenas; Hamilton Varela | Physical Chemistry; Catalysis; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ef6a34fcfb27a31fef33f5/original/microkinetic-modeling-of-the-methanol-electro-oxidation-reaction-on-platinum.pdf |
6597d00b66c1381729c54ef9 | 10.26434/chemrxiv-2024-k6l9d | “Small is beautiful” – the significance of reliable determination of low- abundant therapeutic antibody glycovariants | Glycans associated with biopharmaceutical drugs play crucial roles in drug safety and efficacy, and therefore, their reliable detection and quantification is essential. Our study introduces a multi-level quantification approach for glycosylation analysis in monoclonal antibodies, focusing on minor abundant glycovariants. Mass spectrometric data is evaluated mainly employing open-source software tools. Released glycan and glycopeptide data form the basis for integrating information across different molecular and structural levels up to intact glycoproteins. A comprehensive site-specific comparison showed that indeed, variations across structural levels were observed especially for minor abundant species. Utilizing MoFi, a tool for annotating mass peaks of intact proteins, we quantify isobaric glycosylation variants at the intact protein level. Our workflow's utility is demonstrated on NISTmAb, rituximab and adalimumab, profiling their minor abundant variants for the first time across diverse structural levels. This study enhances understanding and accessibility in glycosylation analysis, emphasizing the significance of minor abundant glycovariants in therapeutic antibodies. | Katharina Böttinger; Christof Regl; Veronika Schäpertöns; Erdmann Rapp; Therese Wohlschlager; Christian G. Huber | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6597d00b66c1381729c54ef9/original/small-is-beautiful-the-significance-of-reliable-determination-of-low-abundant-therapeutic-antibody-glycovariants.pdf |
67696c7a81d2151a02aecc76 | 10.26434/chemrxiv-2025-vjjxw | Rapid photoluminescence “turn-on” sensing of tertiary amines and opioids via dual-emissive ground and excited charge-transfer states | The recognition and differentiation of organic amines are essential for applications in drug analysis, food spoilage, biomedical assays, and clinical diagnostics. Existing luminescence-based recognition methods for amines largely rely on fluorescence quenching. Here, we present a photoluminescence “turn-on” approach for rapidly distinguishing different organic amines based on their unique excited-state and ground-state interactions with naphthalimide, where the quantum yield and emission color are influenced by amine substituent groups and molecular flexibility. Specifically, primary and secondary amines and other common lone-pair donors, including alcohols, ethers, thiols, thioethers, and phosphines, exhibited no visual photoluminescence changes. For tertiary amines, however, bright green photoluminescence activation was rapidly produced for molecules containing at least one methyl group; red-shifted yellow emission was observed for ones with bulkier side groups other than methyl; and for conformationally locked bicycloamines, no emission was observed. Additionally, the “turn-on” process is influenced not only by the substituent group but also by distinct ground- and excited-state dynamics observed in time-resolved spectroscopy. This approach enables the rapid and qualitative recognition of opioids, such as heroin, fentanyl, and metonitazene, offering a simpler and faster alternative to existing methods like the Marquis reagent kit, with potential applications in on-site testing and real-time monitoring. | Aoyuan Cheng; Xuewen Gu; Chengze Yang; Mei Liu; Baicheng Zhang; Hongping Liu; Xiaoyu Chen; Airong Feng; Jun Jiang; Yi Luo; Pieter E. S. Smith; Wenhuan Huang; Guoqing Zhang | Physical Chemistry; Organic Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67696c7a81d2151a02aecc76/original/rapid-photoluminescence-turn-on-sensing-of-tertiary-amines-and-opioids-via-dual-emissive-ground-and-excited-charge-transfer-states.pdf |
60c74de9702a9b2b4c18b938 | 10.26434/chemrxiv.12673736.v1 | Structure of the Silica/Divalent Electrolyte Interface: Molecular Insight into Charge Inversion with Increasing pH | The molecular origin of overcharging at mineral oxide surfaces remains a cause of contention within the geochemistry, physics, and colloidal chemistry communities owing to competing “chemical” vs “physical” interpretations. Here, we combine vibrational sum frequency spectroscopy and streaming potential measurements to obtain molecular and macroscopic insights into the pH-dependent interactions of calcium ions with a fused silica surface. In 100 mM CaCl<sub>2</sub> electrolyte, we observe evidence of charge neutralization at pH~10.5, as deducted from a minimum in the interfacial water signal. Concurrently, adsorption of calcium hydroxide cations is inferred from the appearance of a spectral feature at ~3610 cm<sup>-1</sup>. However, the interfacial water signal increases at higher pH, while adsorbed calcium hydroxide appears to remain constant, indicating that overcharging results from hydrated Ca<sup>2+</sup> ions present within the Stern layer. These findings suggest that both specific adsorption of hydrolyzed ions and ion-ion correlations of hydrated ions govern silica overcharging with increasing pH. | Mokhtar Rashwan; Benjamin Rehl; Adrien Sthoer; Akemi Darlington; Md. Shafiul Azam; Hongbo Zeng; Qingxia Liu; Eric Tyrode; Julianne Gibbs | Interfaces; Optics; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de9702a9b2b4c18b938/original/structure-of-the-silica-divalent-electrolyte-interface-molecular-insight-into-charge-inversion-with-increasing-p-h.pdf |
60c73f9d469df4a152f42b05 | 10.26434/chemrxiv.7406618.v1 | Selective Inhibition of Histone Deacetylase 10: Hydrogen Bonding to the Gatekeeper Residue is Implicated | The discovery of isozyme-selective histone deacetylase (HDAC) inhibitors is critical for understanding the biological functions of individual HDACs and for validating HDACs as clinical drug targets. The isozyme HDAC10 contributes to chemotherapy resistance via inhibition of autophagic flux and has recently been described to be a polyamine deacetylase, but no studies directed toward selective HDAC10 inhibitors have been published. Herein, we disclose that the use of two complementary ligand-displacement assays has revealed unexpectedly potent HDAC10 binding of tubastatin A, which has been previously described as a highly selective HDAC6 inhibitor. We synthesized a targeted selection of tubastatin A derivatives and found that a basic amine in the cap group was required for strong HDAC10, but not HDAC6, binding. Only potent HDAC10 binders mimicked HDAC10 knockdown by causing dose-dependent accumulation of acidic vesicles in the BE(2)-C neuroblastoma cell line. Docking of inhibitors into human HDAC10 homology models indicated that a hydrogen-bond between a basic cap group nitrogen and the HDAC10 gatekeeper residue Glu272 was responsible for potent HDAC10 binding. Taken together, the presented assays and homology models provide an optimal platform for the development of HDAC10-selective inhibitors, as exemplified with the tubastatin A scaffold.<br /> | Magalie Géraldy; Michael Morgen; Peter Sehr; Raphael R. Steimbach; Johannes Ridinger; Ina Oehme; Olaf Witt; Mauro S. Nogueira; Oliver Koch; Nikolas Gunkel; Aubry K. Miller; Mona Malz | Biochemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2018-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9d469df4a152f42b05/original/selective-inhibition-of-histone-deacetylase-10-hydrogen-bonding-to-the-gatekeeper-residue-is-implicated.pdf |
627b47dc809e3262938b9c11 | 10.26434/chemrxiv-2022-z6shp |
Double-Lariat Caged Morpholino Oligonucleotides for Optical Gene Silencing | Caged morpholino oligonucleotides (cMOs) are synthetic tools that allow light-inducible gene silencing in live organisms. Previously reported cMOs have utilized hairpin, duplex, and cyclic structures, as well as caged nucleobases. While these optochemical technologies enable efficient optical gene silencing, they can have limited dynamic range. To address this issue, a new caging strategy was developed where the two MO termini are conjugated to an internal position through a self-immolative trifunctional linker, thereby generating a bicyclic cMO with a double lariat-like structure. The efficacy of this alternative cMO design has been demonstrated in zebrafish embryos and compared to the monocyclic constructs. | Sankha Pattanayak; Alexander Deiters; James Chen | Biological and Medicinal Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627b47dc809e3262938b9c11/original/double-lariat-caged-morpholino-oligonucleotides-for-optical-gene-silencing.pdf |
662be3ef418a5379b0cf0b33 | 10.26434/chemrxiv-2024-sp7m4 | Transpersulfidation or H2S Release? Understanding the Landscape of Persulfide Chemical Biology | Persulfides (RSSH) are biologically important reactive sulfur species that are endogenously produced, protect key cysteine residues from irreversible oxidation, and are important intermediates during different enzymatic processes. Although persul-fides are stronger nucleophiles than their thiol counterparts, persulfides can also act as electrophiles in their neutral, proto-nated form in specific environments. Moreover, persulfides are electrophilic at both sulfur atoms, and reaction with a thiolate can lead to either H2S release with disulfide formation or alternatively result in transpersulfidation. Despite the broad ac-ceptance of these reaction pathways, the specific properties that control whether persulfides react through the H2S releasing or transpersulfidation pathway remains elusive. Herein, we use a combined computational and experimental approach to directly investigate the reactivity between persulfides and thiols to answer these questions. Using DFT calculations, we demonstrate that increasing steric bulk or electron withdrawal near the persulfide can shunt persulfide reactivity through the transpersulfidation pathway. Building from these insights, we use a persulfide donor and TME-IAM trapping agent to experi-mentally monitor and measure transpersulfidation from a bulky penicillamine-based persulfide to a cysteine-based thiol, which to the best of our knowledge is the first direct observation of transpersulfidation between low molecular weight spe-cies. Taken together, these combined approaches highlight how the properties of persulfides are directly impacted by local environments, which has significant impacts in understanding the complex chemical biology of these reactive species. | Kaylin Fosnacht; Jyoti Sharma; Pier Alexandre Champagne; Michael Pluth | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Small Molecule Activation (Inorg.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662be3ef418a5379b0cf0b33/original/transpersulfidation-or-h2s-release-understanding-the-landscape-of-persulfide-chemical-biology.pdf |
60eb132b8a469b4d4e79742f | 10.26434/chemrxiv-2021-tszk1 | Bimodal Evans−Polanyi Relationships in Hydrogen Atom Transfer from C(sp3)--H Bonds
to the Cumyloxyl Radical. A Combined Time-Resolved Kinetic and Computational Study | The applicability of the Evans-Polanyi (EP) relationship to HAT reactions from C(sp3)-H bonds to the cumyloxyl radical (CumO) has been investigated. A consistent set of rate
constants kH, for HAT from the C-H bonds of 56 substrates to CumO, spanning a range of more than four orders of magnitude, has been measured under identical experimental conditions. A corresponding set of consistent gas-phase C-H BDEs spanning 26 kcal/mol has been calculated using the (RO)CBS-QB3 method. The log kH vs C-H BDE plot shows two distinct EP relationships, one for substrates bearing benzylic and allylic C-H bonds (unsaturated group) and the other one, with a steeper slope, for saturated hydrocarbons, alcohols, ethers, diols, amines and carbamates (saturated group), in line with the bimodal behavior observed previously in theoretical studies of reactions promoted by other HAT reagents. The parallel use of BDFEs instead of BDEs allows the transformation of this correlation into a linear free energy relationship, analyzed within the framework of the Marcus theory. The ΔG‡
HAT vs ΔG°HAT plot shows again distinct behaviors
for the two groups. A good fit to the Marcus equation is observed only for the saturated group, with lambda = 58 kcal mol-1, indicating that with the unsaturated group lambda must increase with increasing driving force. Taken together these results provide a qualitative connection between Bernasconi’s Principle of Nonperfect Synchronization and Marcus theory and suggest that the observed bimodal behavior is a general feature in the reactions of oxygen-based HAT reagents with C(sp3)-H donors. | Michela Salamone; Marco Galeotti; Eduardo Romero-Montalvo; Jeffrey van Santen; Benjamin Groff; James Mayer; Gino DiLabio; Massimo Bietti | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Chemical Kinetics; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60eb132b8a469b4d4e79742f/original/bimodal-evans-polanyi-relationships-in-hydrogen-atom-transfer-from-c-sp3-h-bonds-to-the-cumyloxyl-radical-a-combined-time-resolved-kinetic-and-computational-study.pdf |
66fac9ddcec5d6c142b0b069 | 10.26434/chemrxiv-2024-03pqd | Recent developments in modeling the electric double layer with density functional theory | Improving our fundamental understanding of charge transfer processes at the electrified double layer currently relies heavily on density functional theory (DFT) simulations, as many in situ and operando spectroscopic methods are hindered by the aqueous electrolyte. However, modeling charged states with semi-local DFT faces serious challenges, and several bifurcating strategies have been developed in an attempt to address them. In this Mini Review, we present a highly abridged overview of some of the challenges faced when modeling charge transfer processes across the electric double layer with DFT. Focusing primarily on charge transfer kinetics, we highlight polarizable continuum models (PCMs) and their use in evaluating energetics in the adiabatic limit of electron transfer, i.e. treating electrons grand canonically during a coupled proton-electron transfer (CPET) reaction. We highlight their use in understanding electrocatalytic processes, in particular the ability to localize transition states at constant potential. Finally, we present our outlook on opportunities for improvement in this critical research area, and nascent methods being developed to test the validity of PCMs and evaluating energetics in the grand canonical ensemble. | Mikael Maraschin; Mahsa Askari; Veena Chauhan; Luis Feistel; Samuel Olusegun; Jessica Ortega-Ramos; Joseph Gauthier | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fac9ddcec5d6c142b0b069/original/recent-developments-in-modeling-the-electric-double-layer-with-density-functional-theory.pdf |
65490c65a8b423585a102731 | 10.26434/chemrxiv-2023-rtsmv | Continuous Gas-to-Liquid Conversion for Carbon-Efficient Electroreduction of CO2 | Addressing climate change necessitates scalable Carbon Capture, Utilization, and Storage (CCUS) technologies including the efficient electrochemical CO2 reduction process. This study unveils a novel CO2 electrolysis system optimized for continuous gas-to-liquid electroreduction of CO2. Unlike traditional single-pass systems, the devised setup circulates CO2 gas for multiple passes through the cathode, bolstering carbon-conversion efficiencies (CCEs) and enriching product concentrations in the flowing electrolyte. Two operational modes were studied, with the “regeneration” mode activated upon byproduct accumulation, leading to an increase of CO2 concentration inside the gas loop. This mode oxidizes H2 and CO for energy and carbon recovery, eliminating the need for additional gas separation processes, thereby enhancing the practicality and economic viability of distributed carbon utilization systems. Remarkably, a 312-hour continuous operation was demonstrated with >90% carbon efficiency, underscoring the system's robustness and long-term operational stability. Continuous conversion of CO2 to formate, a versatile industrial chemical, further accentuates the potential of this system in advancing carbon-neutral or carbon-negative chemical and fuel production, marking a significant stride towards the practical deployment of CCUS technologies. | Hao Shen; Chengao Zhou; Zimin He; Canhui Wang; Jinyi Zhang; Buwei Hou; Fei Xu; Yulin Liu; Chao Wang | Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65490c65a8b423585a102731/original/continuous-gas-to-liquid-conversion-for-carbon-efficient-electroreduction-of-co2.pdf |
60c75617842e65b542db4458 | 10.26434/chemrxiv.14210963.v1 | Electrochemical Borylation of Carboxylic Acids | A simple electrochemically mediated method for the conversion of alkyl carboxylic acids to their borylated congeners is presented. This protocol features an undivided cell setup with inexpensive carbon-based electrodes and exhibits a broad substrate scope and scalability in both flow and batch reactors. The use of this method in challenging contexts is exemplified with a modular formal synthesis of jawsamycin, a natural product harboring five cyclopropane rings. | Lisa M. Barton; Longrui Chen; Donna Blackmond; Phil Baran | Natural Products; Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75617842e65b542db4458/original/electrochemical-borylation-of-carboxylic-acids.pdf |
60c7458dee301cead1c7936d | 10.26434/chemrxiv.10059809.v1 | Ligand Redox Non-Innocence in [Coᴵᴵᴵ(TAML)]0/‒ Complexes Affects Nitrene Formation | The redox non-innocence of the TAML scaffold in cobalt-TAML (Tetra-Amido Macrocyclic Ligand) complexes has been under debate since 2006. In this work we demonstrate with a variety of spectroscopic measurements that the TAML backbone in the anionic complex <b>[Co<sup>III</sup>(TAML<sup>red</sup>)]<sup>-</sup></b> is truly redox non-innocent, and that one-electron oxidation affords <b>[Co<sup>III</sup>(TAML<sup>sq</sup>)]</b>. Multi-reference (CASSCF) calculations show that the electronic structure of <b>[Co<sup>III</sup>(TAML<sup>sq</sup>)]</b> is best described as an intermediate spin (S = 1) cobalt(III) center that is antiferromagnetically coupled to a ligand-centered radical, affording an overall doublet (S = ½) ground-state. Reaction of the cobalt(III)-TAML complexes with PhINNs as a nitrene precursor leads to TAML-centered oxidation, and produces nitrene radical complexes without oxidation of the metal ion. The ligand redox state (TAML<sup>red</sup> or TAML<sup>sq</sup>) determines whether mono- or bis-nitrene radical complexes are formed. Reaction of <b>[Co<sup>III</sup>(TAML<sup>sq</sup>)]</b> or <b>[Co<sup>III</sup>(TAML<sup>red</sup>)]<sup>-</sup></b> with PhINNs results in formation of <b>[Co<sup>III</sup>(TAML<sup>q</sup>)(N<sup>•</sup>Ns)]</b> and <b>[Co<sup>III</sup>(TAML<sup>q</sup>)(N<sup>•</sup>Ns)<sub>2</sub>]<sup>-</sup></b>, respectively. Herein, ligand-to-substrate single-electron transfer results in one-electron reduced Fischer-type nitrene radicals (N<sup>•</sup>Ns<sup>-</sup>) that are intermediates in catalytic nitrene transfer to styrene. These nitrene radical species were characterized by EPR, XANES, and UV-Vis spectroscopy, high resolution mass spectrometry, magnetic moment measurements and supporting CASSCF calculations. <br /> | Nicolaas P. van Leest; Martijn A. Tepaske; Jean-Pierre H. Oudsen; Bas Venderbosch; Niels R. Rietdijk; Maxime A. Siegler; Moniek Tromp; Jarl Ivar van der Vlugt; Bas de Bruin | Bond Activation; Catalysis; Coordination Chemistry (Organomet.); Ligands (Organomet.); Reaction (Organomet.); Spectroscopy (Organomet.); Theory - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7458dee301cead1c7936d/original/ligand-redox-non-innocence-in-co-iii-taml-0-complexes-affects-nitrene-formation.pdf |
60f688a47bf0c96a135f894b | 10.26434/chemrxiv-2021-h1rb5 | [Fe15]: A Frustrated, Centred Tetrakis Hexahedron | The combination of two different FeIII salts in a solvothermal reaction with triethanolamine results in the formation of a high symmetry [FeIII15] cluster whose structure conforms to a centred, tetrakis hexahedron. | Daniel Cutler; Mukesh Singh; Gary Nichol; Marco Evangelisti; Juergen Schnack; Leroy Cronin; Euan Brechin | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Transition Metal Complexes (Inorg.) | CC BY 4.0 | CHEMRXIV | 2021-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f688a47bf0c96a135f894b/original/fe15-a-frustrated-centred-tetrakis-hexahedron.pdf |
61821f4ff9f05bfd88eacb52 | 10.26434/chemrxiv-2021-2w0jx | Metal-Free Z-Selective Allylic C-H Nitrogenation, Oxygenation, and Carbonation of Alkenes by Thianthrenation | Selective functionalization of allylic C-H bonds into other chemical bonds with Z-selectivity are among the most straightforward and attractive, yet challenging transformations. Herein, a transition-metal-free protocol for direct allylic C-H nitrogenation, oxygenation, and carbonation of alkenes by thianthrenation was developed. This operationally simple protocol allows for the unified allylic C-H amination, esterification, etherification, and arylation of vinyl thiathrenium salts. Notably, the reaction preferably provides multialkyl substituted allylic amines, esters, and ethers with Z-selectivity. The reaction proceeds under mild conditions with excellent functional group tolerance and could be applied to late-stage allylation of natural products, drug molecules and peptides with excellent chemoselectivity. | Wei Shu; Ming-Shang Liu; Hai-Wu Du | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61821f4ff9f05bfd88eacb52/original/metal-free-z-selective-allylic-c-h-nitrogenation-oxygenation-and-carbonation-of-alkenes-by-thianthrenation.pdf |
67c5991ffa469535b9bd9354 | 10.26434/chemrxiv-2025-59f1j | Triplet state reactivity and long-lived room temperature phosphorescence of chalcones enabled by micelles | Cheap SDS micelles are used to facilitate long-lived room temperature phosphorescence and [2+2] photocycloadditions of chalcone by enabling excited-state aggregate formation. Within the micellar environment chalcone aggregation is promoted leading to stabilization of a planar geometry in the triplet state, resulting in long lived (19 μs) emission λ(max) = 700 nm under blue light irradiation. This long-lived triplet state is exploited in [2+2] cycloadditions with activated alkenes. The micelles effectively isolate the reactive species from molecular oxygen, thereby preventing undesired quenching of triplet states. | Gianna Pölderl; Julian Kürschner; Fabio Rizzo; Line Dahl Næsborg | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c5991ffa469535b9bd9354/original/triplet-state-reactivity-and-long-lived-room-temperature-phosphorescence-of-chalcones-enabled-by-micelles.pdf |
67c1652981d2151a02699a06 | 10.26434/chemrxiv-2025-8nzcj | Enhancing oxidative dehydrogenation of alcohols for clean hydrogen production fromTiO2-doped photocatalysts under LED irradiation | While hydrogen global demand goes on increasing, green and efficient production of on-demand hydrogen is still needed to compete with current systems based on the use of fossil fuels. Among recent technologies, photocatalytic hydrogen production is a promising alternative, whose scale-up remains limited owing to various reactional parameters impacting the efficiency of the process. In this context, alcohols as liquid organic hydrogen carriers (LOHCs) constitute a relevant strategy for the production of clean H2 through their oxidative dehydrogenation. The aim of this study was to rationalize conditions for the preparation of TiO2-doped photocatalyst as efficient material for hydrogen production from photoreforming of alcohols in water. The impact of simple engineering parameters was also studied to enhance the catalytic activity, thus allowing to reach an unprecedented hydrogen production rate of 135 600 µmol.g-1.h-1, that could be relevant for further industrial applications. In the optimized conditions, high apparent quantum yield was also achieved. | Oriane DELAUNAY; Audrey Denicourt-Nowicki; Alain ROUCOUX | Catalysis; Energy; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Fuels - Energy Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1652981d2151a02699a06/original/enhancing-oxidative-dehydrogenation-of-alcohols-for-clean-hydrogen-production-from-ti-o2-doped-photocatalysts-under-led-irradiation.pdf |
60c74785702a9b068118adcd | 10.26434/chemrxiv.11705415.v1 | A Biocompatible Fluorescent Probe for the Selective Detection of Amyloid Fibrils | The misfolding and aggregation of proteins leading to amyloid formation has been linked to numerous diseases, necessitating the development of tools to monitor the fibrillation process. Here we report an intramolecular charge transfer (ICT) dye, DMNDC, as an alternative to Thioflavin-T (ThT), most commonly used for monitoring amyloid fibrils. Using insulin as a model protein, we show that DMNDC efficiently detects all stages of fibril formation, namely, nucleation, elongation, and saturation. An approximately 70 nm hypsochromic shift along with a large increase in emission intensity was observed upon binding of DMNDC to protein fibrils. The aggregation kinetics of insulin remained unaffected at excess DMNDC concentration, suggesting that DMNDC does not inhibit insulin aggregation. Additionally, the efficient cellular internalization and low toxicity of DMNDC make it highly suited for sensing and imaging of amyloid fibrils in the complex biological milieu.<br /> | Anirban Das; Tanoy Dutta; Laxmikant Gadhe; Apurba Koner; Ishu Saraogi | Analytical Chemistry - General; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74785702a9b068118adcd/original/a-biocompatible-fluorescent-probe-for-the-selective-detection-of-amyloid-fibrils.pdf |
651f5873bda59ceb9af360e4 | 10.26434/chemrxiv-2023-2m7jh | Understanding Ion-transfer Reactions in Silver Corrosion and Electrodeposition from First-principles Calculations and Experiments | The electrified aqueous/metal interface is critical in controlling the performance of energy conversion and storage devices, but an atomistic understanding of even basic interfacial electrochemical reactions challenges both experiment and computation. We report a combined simulation and experimental study of (reversible) ion-transfer reactions involved in anodic Ag corrosion, a model system for interfacial electrochemical processes generating or consuming ions. With the explicit modeling of the electrode potential and a hybrid implicit-explicit solvation model, the density functional theory calculations produce free-energy curves predicting thermodynamics, kinetics, partial charge profiles, and reaction trajectories. The calculated (equilibrium) free-energy barriers (0.2 eV), and their asymmetries, agree with experimental activation energies (0.4 eV) and transfer coefficients, which were extracted from temperature-dependent voltage-step experiments on Au-supported, Ag-nanocluster substrates. The use of Ag nanoclusters eliminates the convolution of the kinetics of Ag+(aq.) generation and transfer with those of nucleation or etch-pit formation. The results indicate that the barrier is controlled by the bias-dependent competition between partial solvation of the incipient ion, metal-metal bonding and electrostatic stabilization by image charge. Both the latter factors are weakened by more positive bias. We also report simulations of the bias-dependence of defect generation relevant to nucleating corrosion by removing an atom from a perfect Ag(100) surface, which is predicted to occur via a vacancy-adatom intermediate. Together, these experiments and calculations provide the first validated, accurate, molecular model of the central steps that govern the rates of important corrosion/deposition reactions of broad relevance across the energy sciences. | Richard Kang; Yang Zhao; Diptarka Hait; Joseph Gauthier; Paul Kempler; Kira Thurman; Shannon Boettcher; Martin Head-Gordon | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651f5873bda59ceb9af360e4/original/understanding-ion-transfer-reactions-in-silver-corrosion-and-electrodeposition-from-first-principles-calculations-and-experiments.pdf |
653a07bbc573f893f11bb0a4 | 10.26434/chemrxiv-2023-3ds8h | Tryptophan Molecular Moiré Superlattices with Visible Fluorescence | Moiré superlattices of molecules may give birth to a new field of chemistry. For example, when crystalline nanoscale 2D sheets of a molecule are stacked with lattice planes twisted at low angles of each other, the interactions at the interfaces - that differs from the supramolecular interactions within the crystalline nanosheet and can be termed as hypermolecular interactions - may bring about new physical and chemical properties. Herein, we report for the first time the chemical synthesis of moiré superlattices of L or D tryptophan (trp) molecules formed in situ through twisted stacking of trp crystalline nanosheets. Transmission emission microscopy (TEM) measurements supported the formation of moiré superlattices of the crystalline 2D nanosheets. The resulting films were stable under alkaline conditions and exhibited strong photoluminescence emission peak at 452 nm and an additional peak at 500 nm due to the formation of a new energy state. | Ujjala Dey; Arun Chattopadhyay | Physical Chemistry; Self-Assembly; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653a07bbc573f893f11bb0a4/original/tryptophan-molecular-moire-superlattices-with-visible-fluorescence.pdf |
63979235e6f9a198eb375bb5 | 10.26434/chemrxiv-2022-h010f | How to Quantify Electrons in Plasmonic Colloidal Metal Oxide Nanocrystals | Distinct from noble metal nanoparticles, doped metal oxide nanocrystals (NCs) exhibit localized surface plasmon resonance (LSPR) in the infrared region that can be tuned by changing the free electron concentration through both synthetic and post-synthetic doping. Redox reagents have commonly been used to post-synthetically modulate the LSPR, but to understand the relationship between the electron transfer processes and the resulting optical changes, it is imperative to quantify electrons in the NCs. Titration and LSPR peak fitting analysis are the most common methods used for quantifying electrons; however, comparison between these methods has previously revealed discrepancies up to an order of magnitude without a clear explanation. Here, we apply these electron quantification techniques concurrently to Sn-doped In2O3 NCs with varying size, doping concentration, and extent of post-synthetic reduction. We find that oxidative titration consistently overestimates the number of electrons per NC, owing to the failure of the assumed stoichiometric equivalence between moles of oxidant added and moles of free electrons extracted from the NCs. The NC characteristics we examine strongly influence the driving force for the oxidation process, affecting the relative agreement between oxidative titration and LSPR fitting; the two methods more closely agree when the electron transfer driving force is larger. Overall, these analyses inform best practices for quantifying electrons in plasmonic semiconductor NCs and reveal how accuracy is affected by NC characteristics.
| Sofia Shubert-Zuleta; Bharat Tandon; Benjamin Roman; Xing Yee Gan; Delia Milliron | Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63979235e6f9a198eb375bb5/original/how-to-quantify-electrons-in-plasmonic-colloidal-metal-oxide-nanocrystals.pdf |
637e290c94ff6071513cb018 | 10.26434/chemrxiv-2022-x0n2w | Highly Enantioselective Ni(0)-Catalyzed Cascade Reductive Syn-Arylative Cyclization for Five-membered Heterocyclics Bearing Chiral Quaternary Carbon Stereocenters of Tetrasubstituted Allylic Alcohols | Construction of chiral quaternary carbon stereocenters is a significant challenge of asymmetric synthesis. Catalytic synthesis of these structures with trisubstituted allylic alcohols is highly important. However, most of reported methodologies required precious transition-metal catalyst. Herein we reported the first highly enantioselective synthesis of five-membered heterocyclics bearing chiral quaternary carbon stereocenters of tetrasubstituted allylic alcohols by cascade reductive syn-arylative cyclization of hetereo 1,6-alkynones with aryl boronic acids catalyzed by the earth-abundant Nickel catalysis Ni(cod)2 and P-chiral monophosphine ligand (S)-BIDIME applying proton solvent tert-butanol. Various multi-substituted functionalized pyrrolidines and tetrahydrofurans were achieved in high yield (up to 98%), excellent enantioselectivity (>99:1 er) with broad substrate scope. Totally thirty-seven examples were successfully applied for this transformation. The catalytic cycle and the role of proton solvent was proposed, modified and confirmed first time by detailed density functional theory (DFT) calculations, and further clarified the ligand-control for the excellent enantioselectivity initiated by Ni(0) precursor. Ligand effects, gram scale reaction and control experiments were carried out. New reaction design was proposed for further application of this methodology. This developed methodology and mechanism study is anticipated to find wider applications in organic synthesis and chemical biology. | Guodu Liu; Wanjun Chen; Xin long Yan; Xu Guo; Rongrong Lv; Tao Zhang; Zhaozhou Li; Jian Yang; Shaofang Zhou | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Stereochemistry; Theory - Computational; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637e290c94ff6071513cb018/original/highly-enantioselective-ni-0-catalyzed-cascade-reductive-syn-arylative-cyclization-for-five-membered-heterocyclics-bearing-chiral-quaternary-carbon-stereocenters-of-tetrasubstituted-allylic-alcohols.pdf |
623c85a813d478b6079a4ba4 | 10.26434/chemrxiv-2022-chbvt-v2 | Co-design of zinc titanium nitride semiconductor towards durable photoelectrochemical applications | Photoelectrochemical fuel generation is a promising route to sustainable liquid fuels produced from water and captured carbon dioxide with sunlight as the energy input. Development of such technologies requires photoelectrode materials that are both photocatalytically active and operationally stable in harsh oxidative and/or reductive electrochemical environments. Such photocatalysts can be discovered based on co-design principles, wherein design for stability is based on the propensity for the photocatalyst to self-passivate under operating conditions and design for photoactivity is based on the ability to integrate the photocatalyst with established semiconductor substrates. Here we report on synthesis and characterization of zinc titanium nitride (ZnTiN2) that follows these design rules by having a wurtzite-derived crystal structure and showing self-passivating surface oxides created by electrochemical polarization. The sputtered ZnTiN2 thin films have optical absorption onsets below 2 eV and n-type electrical conduction of 0.1 S/cm. The band gap of this material is reduced from the 3.5 eV theoretical value by cation site disorder, and the impact of cation antisites on the band structure of ZnTiN2 is explored using density functional theory. Under electrochemical polarization, the ZnTiN2 surfaces have TiO2- or ZnO-like character, consistent with Materials Project Pourbaix calculations predicting the formation of stable solid phases under near-neutral pH. These results show that ZnTiN2 is a promising candidate for photoelectrochemical liquid fuel generation and demonstrate a new materials design approach to other photoelectrodes with self-passivating native operational surface chemistry. | Ann L. Greenaway; Sijia Ke; Theodore Culman; Kevin R. Talley; John S. Mangum; Karen N. Heinselman; Ryan S. Kingsbury; Rebecca W. Smaha; Elisa M. Miller; Kristin A. Persson; John M. Gregoire; Sage R. Bauers; Jeffrey B. Neaton; Adele C. Tamboli; Andriy Zakutayev | Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623c85a813d478b6079a4ba4/original/co-design-of-zinc-titanium-nitride-semiconductor-towards-durable-photoelectrochemical-applications.pdf |
62a983d81fdc343caa3a799f | 10.26434/chemrxiv-2022-9prf3 | Cheap turns superior: A linear regression-based correction method to reaction energy from DFT | Workflows to predict chemical reaction networks based on density functional theory (DFT) are prone to systematic errors in reaction energy due to the extensive use of cheap DFT exchange-correlation functionals to limit computational cost. Recently, machine learning-based models are increasingly applied to mitigate this problem. However, machine learning models require systems similar to trained data, and the models often perform poorly for out-of-distribution systems. Here, we present a simple bond-based correction method that improves the accuracy of DFT-derived reaction energies. It is based on linear regression, and the correction terms for each bond are derived from reactions among the QM9 dataset. We demonstrate the effectiveness of this method with three DFT functionals in three different rungs of Jacob's ladder. The simple correction method is effective for all rung but especially so for the cheapest PBE functional. Finally, we applied the correction method to a few reactions with molecules significantly different from those in the QM9 dataset that was used to fit the linear regression model. Once corrected by this method, we found that the DFT reaction energies for such out-of-distribution reactions are within 0.05eV of the G4MP2 method. | Surajit Nandi; Jonas Busk; Peter Bjørn Jørgensen; Tejs Vegge; Arghya Bhowmik | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a983d81fdc343caa3a799f/original/cheap-turns-superior-a-linear-regression-based-correction-method-to-reaction-energy-from-dft.pdf |
67aa9be76dde43c90855ad11 | 10.26434/chemrxiv-2025-fh2v7 | Structure-Based Drug Design to Discover Potential Hit Molecules for the Trim71 protein to prevent Congenital Hydrocephalus | Congenital Hydrocephalus (CH) is a neurodevelopmental disorder characterized by the excessive accumulation of cerebrospinal fluid (CSF) in the brain’s ventricles. Current treatments, such as neurological shunting, pose significant risks and fail to address the underlying molecular causes, underscoring the urgent need for targeted therapeutic solutions. Recent studies have found gain-of-function mutations in the TRIM71 gene that cause abnormal binding of the TRIM71 protein to key mRNAs like lsd1 and Ctnnb1, disrupting neural differentiation.
In our study, we aimed to identify potential TRIM71 inhibitors using structure-based drug design of known E3 ubiquitin ligase inhibitors. Utilizing molecular modeling tools, including Accelera’s PlayMolecule platform, DockThor, and Schrödinger’s Maestro suite, we screened and analyzed binding interactions of various compounds against the TRIM71 NHL domain (PDB: 7QRX). Our findings revealed promising candidates, with one compound exhibiting an excellent binding energy score (-30.29 kcal/mol) and favorable interactions with key residues such as Arg625, Phe766, Trp704, and Arg751.
Additionally, pharmacokinetic assessments using SwissADME confirmed that Compound 5 possesses good blood-brain barrier permeability and adheres to Lipinski’s rule of five, indicating strong drug-likeness. These results highlight the potential of TRIM71-specific inhibitors in addressing the molecular pathology of CH.
Future research should focus on experimental validation of these compounds through biochemical assays and in vivo studies to confirm their effectiveness in preventing CSF accumulation and supporting normal neural development in CH patients.
| Veer Bhatia; Divya Ramamoorthy | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aa9be76dde43c90855ad11/original/structure-based-drug-design-to-discover-potential-hit-molecules-for-the-trim71-protein-to-prevent-congenital-hydrocephalus.pdf |
60c74fe3bdbb89e021a39e39 | 10.26434/chemrxiv.12957314.v1 | Porous Shape-Persistent Rylene Imine Cages with Tunable Optoelectronic Properties and Delayed Fluorescence | A simultaneous combination of porosity and tunable optoelectronic properties, common in covalent organic
frameworks, are rare in shape-persistent organic cages. Yet, organic cages offer important molecular advantages, the solubility and modularity. Herein, we report the synthesis of a series of chiral imine organic cages with three built-in rylene
units by means of dynamic imine chemistry and we investigate their textural and optoelectronic properties. Thereby we
demonstrate that the synthesized rylene cages are porous, can be reversibly reduced at accessible potentials, and can absorb
from UV up to green light. We also show that they preferentially adsorb CO2 over N2 and CH4 with a good selectivity. In
addition, we discovered that the cage incorporating three perylene-3,4:9,10-bis(dicarboximide) units displays a delayed fluorescence, likely as a consequence of formation of a correlated triplet pair, the multiexciton state in singlet fission. Rylene
cages thus represent a unique platform to investigate the effect of electronic properties on material porosity and, at the
same time, to probe excited-state phenomena in the limit of vanishing interchromophore coupling.
<br /> | Hsin-Hua Huang; Kyung
Seob Song; Alessandro Prescimone; Rajesh Mannancherry; Ali Coskun; Tomas Solomek | Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fe3bdbb89e021a39e39/original/porous-shape-persistent-rylene-imine-cages-with-tunable-optoelectronic-properties-and-delayed-fluorescence.pdf |
62fdf21c847947acdc0b8e64 | 10.26434/chemrxiv-2022-p01z2-v2 | Electric Fields and Charge Separation for
Solid Oxide Fuel Cell Electrodes | Activation losses at solid oxide-fuel cell (SOFC) electrodes have been widely attributed to charge transfer at the electrode surface. The electrostatic nature of electrode-gas interactions allows us to study these phenomena by simulating an electric field across the electrode-gas interface, where we are able to describe the activation overpotential using Density Functional Theory (DFT). The electrostatic responses to the electric field are used to approximate the behaviour of an electrode under electrical bias, and have found a correlation with experimental data for three different reduction reactions at a mixed ionic-electronic conducting (MIEC) electrode surfaces (H_2O and CO_2 on CeO_2), and {O_2 on LaFeO_3). In this work , we demonstrate the importance of decoupled ion-electron transfer and charged adsorbates on the performance of electrodes under nonequilibrium conditions. Finally, our findings on MIEC-gas interactions have potential implications in the fields of energy storage and catalysis. | Nicholas Williams; Ieuan Seymour; Dimitrios Fraggedakis; Stephen Skinner | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fdf21c847947acdc0b8e64/original/electric-fields-and-charge-separation-for-solid-oxide-fuel-cell-electrodes.pdf |
62051a2a2168672a3b71b0ef | 10.26434/chemrxiv-2022-44s22 | 1,3,2-Diazaphospholene-Catalyzed Reductive Cyclizations of
Organohalides | 1,3,2-diazaphospholenes hydrides (DAP-Hs) are highly nucleophilic organic hydrides serving as main-group catalysts for a range of attractive transformations. DAP hydrides can act as stoichiometric hydrogen atom transfer agents in radical reactions. Herein, we report a DAP-catalyzed reductive radical cyclization of a broad range of aryl and alkyl halides under mild conditions. The pivotal DAP catalyst turnover was achieved by a DBU-assisted σ-bond metathesis between the formed DAP halide and HBpin rapidly regenerating DAP H. The transformation is significantly accelerated by irradiation with visible light. Mechanistic investigations indicate that visible light irradiation leads to the formation of DAP dimers which are in equilibrium with the DAP radicals accelerating the cyclization. The direct use of (DAP)2 enabled a catalytic protocol in the absence of light. | Nicolai Cramer; Johannes Klett; Lukasz Wozniak | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62051a2a2168672a3b71b0ef/original/1-3-2-diazaphospholene-catalyzed-reductive-cyclizations-of-organohalides.pdf |
678c4cd96dde43c9081e8765 | 10.26434/chemrxiv-2025-p234l | The Role of the Droplet Interface in Controlling the Multiphase Oxidation of Thiosulfate by Ozone | Predicting reaction kinetics in aqueous microdroplets, including aerosols and cloud droplets, is challenging due to the probability that the underlying reaction mechanism can occur both at the surface and in the interior of the droplet. Here, we use a stochastic reaction-diffusion model of thiosulfate oxidation by gas phase ozone to examine how the interface influences the multiphase reaction kinetics measured in levitated microdroplets using mass spectrometry. Building a realistic kinetic model of multiphase reactions requires both a detailed multistep reaction mechanism as well as the surface affinities of all reactants and products. Deep-UV Second Harmonic Generation spectroscopy is used to probe surface affinities of thiosulfate, sulfate, and sulfite, key species in the reaction mechanism. Thiosulfate has an appreciable surface affinity with a measured Gibbs free energy of adsorption of -7.29 ± 2.47 kJ/mol in neutral solution, while sulfate and sulfite exhibit negligible surface propensity. The Gibbs free energy is combined with data from liquid flat jet ambient pressure x-ray photoelectron spectroscopy to constrain the concentration of thiosulfate at the surface in the kinetic model. Kinetic simulations show that the primary reaction between thiosulfate and ozone occurs at the interface and in the bulk, with the contribution of the interface decreasing from ~65% at pH 5 to ~45% at pH 13. Additionally, sulfate, the major product of thiosulfate ozonation and an important species in atmospheric processes, can be produced by two different pathways at pH 5, one with a contribution from the interface of >70% and the other occurring predominantly in the bulk (>98%). Finally, we use the kinetic model to demonstrate the impact of a range of atmospherically relevant droplet sizes and reactant concentrations on product distributions and relative importance of surface and bulk chemistry. The observations in this work have implications for mining wastewater remediation and are likely applicable to other atmospherically-relevant reaction mechanisms, suggesting that future microdroplet/aerosol chemistry studies should carefully consider the role of both interfacial and bulk chemistry. | Alexandra Deal; Franky Bernal; Andreas Siebert; Alexander Prophet; Mauricio Lopez Luna; Monika Blum; Richard Saykally; Kevin Wilson | Physical Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Chemical Kinetics; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678c4cd96dde43c9081e8765/original/the-role-of-the-droplet-interface-in-controlling-the-multiphase-oxidation-of-thiosulfate-by-ozone.pdf |
65af80af9138d231618a7fdd | 10.26434/chemrxiv-2023-3l19q-v2 | Cation Effects on the Acidic Oxygen Reduction Reaction at Carbon Surfaces | Hydrogen peroxide (H2O2) is a widely used green oxidant. Until now, research focused on the development of efficient catalysts for the two-electron oxygen reduction reaction (2e– ORR). However, electrolyte effects on the 2e– ORR have remained little understood. We report a significant effect of alkali metal cations (AMCs) on carbons in acidic environments. The presence of AMCs at a glassy carbon electrode shifts the half wave potential from -0.48 to - 0.22 VRHE. This cationic induced enhancement effect exhibits a uniquely sensitive on/off switching behaviour depending on the voltammetric protocol. Voltammetric and in situ X-ray photoemission spectroscopic evidence is presented, supporting a controlling role of the potential of zero charge of the catalytic enhancement. Density functional theory calculations associate the enhancement with the stabilization of the *OOH key intermediate as a result of locally induced field effects from the AMCs. Finally, we developed a refined reaction mechanism for the H2O2 production in presence of AMCs. | Jessica Hübner; Lanna Lucchetti; Hong Nhan Nong-Reier; Dmitry I. Sharapa; Benjamin Paul; Matthias Kroschel; Jiaqi Kang; Detre Teschner; Silke Behrens; Felix Studt; Axel Knop-Gericke; Samira Siahrostami; Peter Strasser | Catalysis; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65af80af9138d231618a7fdd/original/cation-effects-on-the-acidic-oxygen-reduction-reaction-at-carbon-surfaces.pdf |
60c74cb3bb8c1a19c23db47e | 10.26434/chemrxiv.12518555.v1 | Excited-State Vibration-Polariton Transitions and Dynamics in Nitroprusside | <div>
<div>
<div>
<p>Strong cavity coupling to molecular vibrations creates vibration-polaritons capable of modifying chemical
reaction kinetics, product branching ratios, and charge transfer equilibria. However, the mechanisms
impacting these molecular processes remain elusive. Furthermore, even basic elements determining the
spectral properties of polaritons, such as selection rules, transition moments, and lifetimes, are poorly
understood. Here, we use two-dimensional infrared and filtered pump–probe spectroscopy to report clear
spectroscopic signatures and relaxation dynamics of excited vibration-polaritons formed from the cavity-
coupled NO band of nitroprusside. We apply a multi-level quantum Rabi model that predicts transition
frequencies and strengths that agree very well with our experiment. Notably, the polariton features decay
~3-4 times slower than the polariton dephasing time, indicating that they support incoherent population, a
consequence of their partial matter character. Understanding the factors determining polariton population
and dephasing lifetimes will impact polariton-modified energy transfer, photophysics, and chemistry.
</p>
</div>
</div>
</div> | Andrea B. Grafton; Adam D. Dunkelberger; Blake S. Simpkins; Johan F. Triana; Federico
J. Hernandez; Felipe Herrera; Jeff Owrutsky | Optics; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cb3bb8c1a19c23db47e/original/excited-state-vibration-polariton-transitions-and-dynamics-in-nitroprusside.pdf |
60c74b63f96a00ee7c2875d1 | 10.26434/chemrxiv.12320024.v1 | AIE Stereoisomers with Huge Differences in Luminescence Behavior and Biomedical Activity | Stereoisomers that differ only in spatial orientation of their atoms could exhibit distinctive properties and have attracted immense interest in drug development and material science. Herein, a series of AIE-featured stereoisomers with pronounced difference in luminescent and biomedical activities were efficiently synthesized and easily purified. One of the isomers in the E/Z pair is emissive with high fluorescence quantum yield at room temperature, while the other one is nearly non-emissive. As the isomers could transform between each other under UV irradiation, the light-up cell imaging was successfully demonstrated using the non-emissive isomer as a turn-on probe via isomerization process. Analysis of crystal packing patterns illustrated that the contrasts in void space possibly caused the difference in molecular motion and thus led to their distinct luminescence properties. Further, the E/Z isomers displayed remarkable difference in enzymatic conversion rates and cellular toxicities for several cancer cell lines. The distinctive luminescence properties of the isomeric pair provided a powerful tool to image those divergencies in biomedical activity, holding great potential for visualizable drug screening and development. | Xuewen He; Ryan Tsz Kin Kwok; Jacky W. Y. Lam; Ben Zhong Tang | Aggregates and Assemblies; Biological Materials; Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b63f96a00ee7c2875d1/original/aie-stereoisomers-with-huge-differences-in-luminescence-behavior-and-biomedical-activity.pdf |
60edca87b9b601e2ea24289d | 10.26434/chemrxiv-2021-zcmmb-v2 | Investigating Novel Thiazolyl-Indazole Derivatives as Scaffolds for SARS-CoV-2 MPro Inhibitors | COVID-19 is a global pandemic caused by infection with the SARS-CoV-2 virus. Remdesivir, a SARS-CoV-2 RNA polymerase inhibitor, is the only drug to have received widespread approval for treatment of COVID-19. The SARS-CoV-2 main protease enzyme (MPro), essential for viral replication and transcription, remains an active target in the search for new treatments. In this study, the ability of novel thiazolyl-indazole derivatives to inhibit MPro is evaluated. These compounds were synthesized via the heterocyclization of phenacyl bromide with (R)-carvone and (R)-pulegone thiosemicarbazones. The binding affinity and atomistic interactions of each compound were evaluated through Schrödinger Glide docking, AMBER molecular dynamics simulations, and MM-GBSA free energy estimation, and these results were compared with similar calculations of MPro binding various 5-mer substrates (VKLQA, VKLQS, VKLQG). From these simulations, we can see that binding is driven by residue specific interactions such as π-stacking with His41, and S/π interactions with Met49 and Met165. The compounds were also experimentally evaluated in a MPro biochemical assay and the most potent compound containing a phenylthiazole moiety inhibited protease activity with an IC50 of 92.9 µM. This suggests that the phenylthiazole scaffold is a promising candidate for the development of future MPro inhibitors. | Justin Airas; Catherine A. Bayas; Abdellah N'Ait Ousidi; My Youssef Ait Itto; Aziz Auhmani; Mohamed Loubidi; M'hamed Esseffar; Julie A. Pollock; Carol A. Parish | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60edca87b9b601e2ea24289d/original/investigating-novel-thiazolyl-indazole-derivatives-as-scaffolds-for-sars-co-v-2-m-pro-inhibitors.pdf |
670e7694cec5d6c1423a2f2c | 10.26434/chemrxiv-2024-lk0pg | Expanding Polycyclic Tetramate Macrolactam (PoTeM) Core Structure Diversity by Chemo-Enzymatic Synthesis and Bioengineering | Polycyclic tetramate macrolactams (PoTeMs) represent a growing class of bioactive natural products that are derived from a common tetramate polyene precursor, lysobacterene A, produced by an unusual bacterial iterative polyketide synthase (PKS) / non-ribosomal peptide synthetase (NRPS). The structural and functional diversity of PoTeMs is biosynthetically elaborated from lysobacterene A by pathway-specific cyclizing and modifying enzymes. This results in diverse core structure decoration and cyclization patterns. However, approaches to directly edit the PoTeM carbon skeleton are currently not existing. We thus set out to modify the PoTeM core structure by exchanging the natural L-ornithine-derived building block by L-lysine, hence extending macrocycle size by an additional CH2 group. We developed streamlined synthetic access to lysobacterene A and the corresponding extended analog and achieved cyclization of both precursors by the cognate PoTeM cyclases IkaBC in vitro. This chemo-enzymatic approach corroborated the catalytic competence of IkaBC to produce a larger macrolactam yielding homo-ikarugamycin. We thus engineered the adenylation domain active site of IkaA to directly accept L-lysine, which upon co-expression with IkaBC delivered a recombinant bacterial homo-ikarugamycin producer. Our work establishes an entirely new PoTeM structural framework and sets the stage for the biotechnological diversification of the PoTeM natural product class in general. | Sebastian Schuler; Manuel Einsiedler; Julia Evers; Mert Malay; Valdet Uka; Sabine Schneider; Tobias Gulder | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670e7694cec5d6c1423a2f2c/original/expanding-polycyclic-tetramate-macrolactam-po-te-m-core-structure-diversity-by-chemo-enzymatic-synthesis-and-bioengineering.pdf |
60c754dfbb8c1a41e23dc307 | 10.26434/chemrxiv.12912452.v2 | Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops | Despite their pivotal role in protein function and
antibody binding affinity, <i>β</i>-hairpins
bearing long non-canonical loops are a challenge to modern synthesis because of
the large entropic penalty associated with their folding. Little is known about
the contribution and impact of stabilizing motifs on the folding of <i>β</i>-hairpins of variable length and plasticity. Here we report a direct comparison between these <i>b</i>-straps thermodynamics and their thermal stability
behavior using several local spectroscopic probes of the folding/unfolding
landscape. The judicious cooperative interactions crafted in <i>β</i>-Strap <u>R</u>W(<u>V</u>W)•••(W<u>V</u>/<u>H</u>)W<u>E</u> (<i>strap</i> = <i>str</i>and + c<i>ap</i>) greatly stabilized hairpins with up to 10-residue loops lacking an innate nucleating-turn
locus (<i>T<sub>m</sub> </i>up to 52 <sup>o</sup>C;
88 ± 1% folded at 291 K). The present design of
novel <i>β</i>-straps aims to
provide the foundation to study new classes of long hairpins and ultimately offer
an attractive alternative to macrocyclic peptides for the mimicry of functional
loops from proteins and antibodies. | Alexis Richaud; Guangkuan zhao; Stephane Roche; Samir Hobloss | Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754dfbb8c1a41e23dc307/original/folding-in-place-design-of-strap-motifs-to-stabilize-the-folding-of-hairpins-with-long-loops.pdf |
668c80aac9c6a5c07aaff7c9 | 10.26434/chemrxiv-2024-8mxvd-v2 | High-Spin State of a Ferrocene Electron Donor Revealed by Optical and X-ray Transient Absorption Spectroscopy | Ferrocene is one of the most common electron donors, and mapping its ligand-field excited states is critical to designing donor-acceptor (D-A) molecules with long-lived charge transfer states. Although 3(d-d) states are commonly invoked in the photophysics of ferrocene complexes, mention of the high-spin 5(d-d) state is scarce. Here, we provide clear evidence of 5(d-d) formation in a bimetallic D-A molecule, ferrocenyl cobaltocenium hexafluorophosphate ([FcCc]PF6). Femtosecond optical transient absorption (OTA) spectroscopy reveals two distinct electronic excited states with 30 ps and 500 ps lifetimes. Using a combination of ultraviolet, visible, nearinfrared, and short-wave infrared probe pulses, we capture the spectral features of these states over an ultrabroadband range spanning 320 nm to 2200 nm. Time-dependent density functional theory calculations of the lowest triplet and quintet states, both primarily Fe(II) (d-d) in character, qualitatively agree with the experimental OTA spectra, allowing us to assign the 30 ps state as the 3(d-d) state and the 500 ps state as the high-spin 5(d-d) state. To confirm the ferrocene-centered high-spin character of the 500 ps state, we performed X-ray transient absorption (XTA) spectroscopy at the Fe and Co K edges. The Fe K-edge XTA spectrum at 150 ps shows signatures of bond-length expansion and a Jahn-Teller distortion, consistent with an Fe(II) high-spin state. No transient signal is detected at the Co K-edge, confirming the ferrocene-centered character of the excited state. Altogether, these results demonstrate that the high-spin state of ferrocene should be considered when designing donor-acceptor assemblies for photocatalysis and photovoltaics. | John Burke; Dae Young Bae; Rachel Wallick; Conner Dykstra; Thomas Rossi; Laura Smith; Clare Leahy; Richard Schaller; Liviu Mirica; Josh Vura-Weis; Renske van der Veen | Physical Chemistry; Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668c80aac9c6a5c07aaff7c9/original/high-spin-state-of-a-ferrocene-electron-donor-revealed-by-optical-and-x-ray-transient-absorption-spectroscopy.pdf |
61b269ac0e35ebc1be9ba877 | 10.26434/chemrxiv-2021-bd6g6 | Heterogeneous Catalysts in Grammar School | The discovery of new catalytically active materi-
als is one of the holy grails of computational chemistry as it
has the potential to accelerate the adoption of renewable energy sources and reduce the energy consumption of chemical industry. Indeed, heterogeneous catalysts are essential for the production of synthetic fuels and many commodity chemicals. Consequently, novel catalysts with higher activity and selectivity, increased sustainability and longevity, or improved prospects for rejuvenation and cyclability are needed for a diverse range of processes. Unfortunately, computational catalyst discovery is a
daunting task, among other reasons because it is often unclear whether a proposed material is stable or synthesizable. This perspective proposes a new approach to this challenge, namely the use of generative grammars. We outline how grammars can guide the search for stable catalysts in a large chemical space and sketch out several research directions that would make this technology applicable to real materials. | Johannes T. Margraf; Zachary W. Ulissi; Yousung Jung; Karsten Reuter | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b269ac0e35ebc1be9ba877/original/heterogeneous-catalysts-in-grammar-school.pdf |
64b6a57eb053dad33a76a5d5 | 10.26434/chemrxiv-2023-rvvfr | A Nanocavitation Approach to Understanding Water Capture, Water Release, and Framework Physical Stability in Hierarchically Porous MOFs | Chemically-stable metal–organic frameworks (MOFs) featuring interconnected hierarchical pores have proven promising for a remarkable variety of applications. Nevertheless, framework susceptibility to capillary-force-induced pore collapse, especially during water evacuation, has often limited practical applications. Methodologies capable of predicting the relative magnitudes of these forces as functions of pore size, chemical composition of the pore walls, and fluid loading would be valuable for resolution of the pore collapse problem. Here, we report that a molecular simulation approach centering on evacuation-induced nanocavitation within fluids occupying MOF pores can yield the desired physical-force information. The computations can spatially pinpoint evacuation elements responsible for collapse and the chemical basis for mitigation of collapse of modified pores. Experimental isotherms and difference-electron-density measurements of the MOF NU-1000 and four chemical variants validate the computational approach and corroborate predictions regarding relative stability, anomalous sequence of pore-filling, and chemical basis for mitigation of destructive forces. | Jian Liu; Jesse Prelesnik; Roshan Patel; Boris Kramar; Rui Wang; Christos Malliakas; Lin Chen; J. Ilja Siepmann; Joseph Hupp | Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Theory - Inorganic; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b6a57eb053dad33a76a5d5/original/a-nanocavitation-approach-to-understanding-water-capture-water-release-and-framework-physical-stability-in-hierarchically-porous-mo-fs.pdf |
66fc576e51558a15efbeb5ca | 10.26434/chemrxiv-2024-25k81 | Total Synthesis of LL-A03411-Beta1 | The first total synthesis of the cyclic depsipeptide antibiotic LL-A03411-beta1 (LL) is described. The configuration of the -methyltryptophan (-MeTrp) residue was established by preparing all four stereoisomers of Fmoc--MeTrp which were used for the synthesis of LL via Fmoc solid phase peptide synthesis. The most active of the four peptides was the one containing (2R,3R)--MeTrp. The activity of LL was strongly inhibited by cardiolipin (CL), but not other common phos-pholipids found in bacterial cell membranes suggesting that LL interacts with CL in the lipid membrane | Lindsey Shivers; Jeremy Goodyear; scott taylor | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc576e51558a15efbeb5ca/original/total-synthesis-of-ll-a03411-beta1.pdf |
60c74d2c0f50db274f396f98 | 10.26434/chemrxiv.12510545.v2 | Transport Mechanisms Underlying Ionic Conductivity in Nanoparticle-Based Single-Ion Electrolytes | <div>Recent studies have demonstrated the potential of nanoparticle-based single-ion conductors as battery electrolytes. In this work, we introduce a coarse-grained multiscale simulation approach to identify the mechanisms underlying the ion mobilities in such systems and to clarify the influence of key design parameters on conductivity. Our results suggest that for the experimentally studied electrolyte systems, the dominant pathway for cation transport is along the surface of nanoparticles, in the vicinity of nanoparticle-tethered anions. At low nanoparticle concentrations, connectivity of cationic surface transport pathways and conductivity increase with nanoparticle loading. However, cation mobilities are reduced when nanoparticles are in close vicinity, causing conductivity to decrease for suffciently high particle loadings. We discuss the impacts of cation and anion choice as well as solvent polarity within this picture and suggest means to enhance ionic conductivities in single-ion conducting electrolytes based on nanoparticle salts.</div> | Sanket Kadulkar; Delia Milliron; Thomas Truskett; Venkat Ganesan | Composites; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2020-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d2c0f50db274f396f98/original/transport-mechanisms-underlying-ionic-conductivity-in-nanoparticle-based-single-ion-electrolytes.pdf |
66616c4e21291e5d1d301165 | 10.26434/chemrxiv-2024-42pfg | Density Isobar of Water and Melting Temperature of Ice: Assessing Common Density Functionals | We investigate the density isobars of water and the melting temperature of ice using six different density functionals. Machine-learning potentials are employed to ensure computational affordability. Our findings reveal significant discrepancies between various base functionals. Notably, even the choice of damping can result in substantial differences. Overall, the outcomes obtained through density functional theory are not entirely satisfactory across most utilized functionals. All functionals exhibit significant deviations either in the melting temperature or equilibrium volume, with most of them even predicting an incorrect volume difference between ice and water. Our heuristic analysis indicates that a hybrid functional with 25% exact exchange and van der Waals damping averaged between zero and Becke-Johnson dampings yields the closest agreement with experimental data. This study underscores the necessity for further enhancements in the treatment of van der Waals interactions and, more broadly, density functional theory, to enable accurate quantitative predictions for molecular liquids. | Pablo Montero de Hijes; Christoph Dellago; Ryosuke Jinnouchi; Georg Kresse | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66616c4e21291e5d1d301165/original/density-isobar-of-water-and-melting-temperature-of-ice-assessing-common-density-functionals.pdf |
623a7e64d6d3ed9cfb9b7bba | 10.26434/chemrxiv-2022-s00sl | Updates to the Inverted Library Search Algorithm for Mixture Analysis | Identifying mixture components is a well-known challenge in analytical chemistry. The Inverted Library Search Algorithm (ILSA) is a recently proposed method for identifying mixture components using in-source collision induced dissociation (is-CID) mass spectra of a query mixture and a reference library of pure compound is-CID mass spectra (J. Am. Soc. Mass Spectrom. 2021, 32, 7, 1725–1734). This article presents several subtle but important advances to the algorithm, including updated compound matching strategies that improve result explainability, and spectral filtering to better handle noisy mass spectra as is often observed with real-world samples such as seized drug evidence. | Arun Moorthy; Stephen Tennyson; Edward Sisco | Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2022-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623a7e64d6d3ed9cfb9b7bba/original/updates-to-the-inverted-library-search-algorithm-for-mixture-analysis.pdf |
64ef56463fdae147fa2346d4 | 10.26434/chemrxiv-2023-jqbqt | Closed-Loop Transfer Enables AI to Yield Chemical Knowledge | AI-guided closed-loop experimentation has recently emerged as a promising method to optimize objective functions,1,2 but the substantial potential of this traditionally black-box approach to reveal new scientific knowledge has remained largely untapped. Here, we report a new AI-guided approach, dubbed Closed-Loop Transfer (CLT), that integrates closed-loop experiments with physics-based feature selection and supervised learning to yield new scientific knowledge in parallel with optimization of objective functions. CLT surprisingly revealed that high-energy regions of the triplet state manifold are paramount in dictating molecular photostability in solution across a diverse chemical library of light-harvesting donor-bridge-acceptor oligomers. Remarkably, this insight emerged after automated modular synthesis and experimental characterization of only ~1.5% of the theoretical chemical space. Supervised learning models considering millions of combinations of 100+ physics-based descriptors further showed that high energy triplet states most strongly correlate with photostability, while excluding more commonly considered predictors such as the lowest energy triplet state. The physics-informed model for photostability was even further confirmed and then strengthened using an explicit experimental test set, validating the substantial power of the CLT method. Broadly, these findings show that interfacing physics-based modeling with closed-loop discovery campaigns unimpeded by synthesis bottlenecks can rapidly illuminate fundamental chemical insights and guide more rational pursuit of frontier molecular functions. | Nicholas Angello; David Friday; Changhyun Hwang; Seungjoo Yi; Austin Cheng; Tiara Torres-Flores; Edward Jira; Wesley Wang; Alàn Aspuru-Guzik; Martin Burke; Charles Schroeder; Ying Diao; Nicholas Jackson | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ef56463fdae147fa2346d4/original/closed-loop-transfer-enables-ai-to-yield-chemical-knowledge.pdf |
66c185a6a4e53c4876be8b94 | 10.26434/chemrxiv-2024-6g37p | Thermodynamic modeling of complex solid solutions in the Lu-H-N system via graph
neural network accelerated Monte Carlo simulations | Metal hydrides are important across diverse applications such as hydrogen storage, batteries, gas sensors, nuclear reactions and high-temperature superconductivity. Previous computational studies
of metal hydrides under extreme pressures, e.g., O(10^2) GPa, usually treat them as stoichiometric
compounds without considering interstitial lattice disorder. As pressures become more moderate in
the O(10^0) GPa and below range, hydrogen disorder at interstitial lattice sites becomes prominent,
e.g. in the N-doped Lu hydride that was recently claimed superconducting near 1 GPa. Further
adding compositional complexity from alloying and/or multi-element interstitial occupation makes
elucidating pressure- and temperature-dependent observables intractable by first-principles calculations alone. We therefore propose a lattice graph neural network surrogate modeling approach
to predict configuration- and pressure-dependent equation-of-state properties. Their efficiency permits
Monte Carlo simulations to calculate Gibbs energies and pressure-dependent phase diagrams,
thereby revealing insights into the synthesis conditions required for achieving desired phase equilibria. We demonstrate this concept for the compositionally complex cubic Lu(H, N,Va)3 system where three constituents (hydrogen, nitrogen and vacancy) have disordered multi-element interstitial occupancies and insights into pressure-dependent phase equilibria are critically needed, e.g., N-doping
levels can significantly lower dehydrogenation temperatures and provide a new strategy to optimize
hydrogen-storage alloys. This work can improve the thermodynamic understanding of the Lu-H-N
system and help rational synthesis of N-doped Lu hydrides, but more generally demonstrates an
efficient approach to model pressure-dependent thermodynamics of multi-component solid solutions. | Pinwen Guan; Catalin Spataru; Vitalie Stavila; Reese Jones; Peter Sharma; Matthew Witman | Energy; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c185a6a4e53c4876be8b94/original/thermodynamic-modeling-of-complex-solid-solutions-in-the-lu-h-n-system-via-graph-neural-network-accelerated-monte-carlo-simulations.pdf |
60c74da7842e657069db34de | 10.26434/chemrxiv.12645233.v1 | Fucosylated Ubiquitin and Orthogonally Glycosylated Mutant A28C: Conceptually New Ligands for Burkholderia Ambifaria Lectin (BambL)† | Ubiquitin as <i>scaffold</i> <i>protein</i> and aryl-α-O-fucoside as determinant to achieve conceptually new ligands with high affinity for <i>Burkholderia ambifaria </i>lectin are described.<div>Ub mutant A28C which displays a Cys residue in addition to the eight Lys residues was expressed. </div><div>The resulting <i>scaffold</i> was orthogonally glycosylated </div><div>to display one thio-rhamnose and up to eight residues of aryl-α-O-fucoside. </div><div>The glycosylated Ub-based scaffolds have unprecedented immune properties.<br /></div> | Cristina Nativi; Sakonwan Kuhaudomlarp; Linda Cerofolini; Sabrina Santarsia; Emilie Gillon; Silvia Fallarini; Grazia Lombardi; Maxime Denis; Stefano Giuntini; Carolina Valori; Marco Fragai; Anne Imberty; Alessandro Dondoni | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74da7842e657069db34de/original/fucosylated-ubiquitin-and-orthogonally-glycosylated-mutant-a28c-conceptually-new-ligands-for-burkholderia-ambifaria-lectin-bamb-l.pdf |
658cccac9138d23161a5e87b | 10.26434/chemrxiv-2023-bncx1 | A Rutheno-Phosphanorcaradiene as a Masked Ambiphilic Metallo-Phosphinidene | Reaction of the ruthenium carbene complex Cp*(IPr)RuCl (1, IPr = 1,3-bis(Dipp)-imidazol-2-ylidene; Dipp = 2,6-diisopropylphenyl) with sodium phosphaethynolate (NaOCP) led to intramolecular dearomatization of one of the Dipp substituents on the Ru-bound carbene to afford a Ru-bound phosphanorcaradiene. Computations by DFT reveal a transition state characterized by a concerted process whereby CO migrates to the Ru center as the P atom adds to the -system of the aryl group. The phosphanorcaradiene possesses ambiphilic properties and reacts with both nucleophilic and electrophilic substrates, resulting in re-aromatization of the ligand aryl group with net P-atom transfer to give several unusual metal-bound, P-containing main-group moieties. These new complexes include a metallo-1-phospha-3-azaallene (Ru-P=C=NR), a metallo-iminophosphanide (Ru-P=N-R), and a metallo-phosphaformazan (Ru-P(=N-N=CPh2)2). Reaction of 1 with the carbene 2,3,4,5-tetramethylimidazol-2-ylidene (IMe4) produced the corresponding phosphaalkene DippP=IMe4. | Tyler G. Saint-Denis; T. Alex Wheeler; Qingchuan Chen; Gábor Balázs; Nick S. Settineri; Manfred Scheer; T. Don Tilley | Inorganic Chemistry; Main Group Chemistry (Inorg.); Organometallic Compounds; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658cccac9138d23161a5e87b/original/a-rutheno-phosphanorcaradiene-as-a-masked-ambiphilic-metallo-phosphinidene.pdf |
60c73f60f96a005be02860be | 10.26434/chemrxiv.7364768.v1 | ONIOM(QM:QM') Electrostatic Embedding Schemes for Photochemistry in Molecular Crystals | Understanding photoinduced processes in molecular crystals is central to the design of highly emissive materials such as organic lasers and organic light-emitting diodes. The modelling of such processes is, however, hindered by the lack of excited state methodologies tailored for these systems. Embedding approaches based on the Ewald sum can be used in conjunction with excited state electronic structure methods to model the localised excitations which characterise these materials. In this article, we describe the implementation of a two-level ONIOM(QM:QM') point charge embedding approach based on the Ewald method, the Ewald Embedded Cluster (EEC) model. An alternative self-consistent method is also considered to simulate the response of the environment to the excitation. Two molecular crystals with opposing photochemical behaviour were used to benchmark the results with single reference and multireference methods. We observed that the inclusion of an explicit ground state cluster surrounding the QM region was imperative for the exploration of the excited state potential energy surfaces. Using EEC, accurate absorption and emission energies as well as S1-S0 conical intersections were obtained for both crystals. We discuss the implications of the use of these embedding schemes considering the degree of localisation of the excitation. The methods discussed herein are implemented in an open source platform (fromage, https://github.com/Crespo-Otero-group/fromage) which acts as an interface between popular electronic structure codes (Gaussian, Turbomole and Molcas). | Miguel Rivera; Michael Dommett; Rachel Crespo Otero | Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f60f96a005be02860be/original/oniom-qm-qm-electrostatic-embedding-schemes-for-photochemistry-in-molecular-crystals.pdf |
60c743b5bdbb895521a386c4 | 10.26434/chemrxiv.9593687.v1 | Rh Methylidenes from Redox Cascade Activation of Chloroalkanes | <div><div><div><p>Oxidative addition of carbon-halogen bonds at transition metals typically follow either a two-electron pathway (concerted M-R/M-X formation) or a radical chain pathway (stepwise M-R/M-X formation). When the reactive metal species is generated slowly, however, both mechanisms can compete to yield unexpected reactivity paths. The present report highlights the synthesis of rhodium methylidenes from chloroalkanes (e.g. CH2Cl2 and CHCl3) at POP-pincer frameworks (e.g. POP = 4,6-bis(di-tert- butylphosphino)dibenzo[b,d]furan) via a cascade of halide abstraction and electron transfer steps. Experimental and computational studies are reported that support the proposed mechanism, including characterization of important reaction intermediates. The overall transformation represents a route towards reactive metal alkylidenes using milder and less-reactive carbenoid precursors than what is presently used.</p></div></div></div> | Travis J. Morrow; Jordan Gipper; William
E. Christman; Navamoney Arulsamy; Elliott Hulley | Organometallic Compounds; Electrochemistry - Organometallic; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b5bdbb895521a386c4/original/rh-methylidenes-from-redox-cascade-activation-of-chloroalkanes.pdf |
6177f00d913a7490e76b313b | 10.26434/chemrxiv-2021-2z569 | Synthesis and anticancer evaluation of 4’-thio and 4’-sulfinyl pyrimidine nucleoside analogues | Analogues of the canonical nucleosides required for nucleic acid synthesis have a longstanding presence and proven capability within antiviral and anticancer research. Despite their success, newer generations of such analogues are required, to overcome issues surrounding cellular proficiency and growing resistance profiles. The chemical synthesis of a series of nucleoside analogues that incorporate bioisosteric replacement of furanose oxygen with sulfur is presented herein. Developing access to a common 4-thioribose building block enables access to thio-ribo and thio-arabino pyrimidine nucleosides, alongside their 4’-sulfinyl derivatives. In addition, this building block methodology is templated to deliver 4’-thio and 4’-sulfinyl analogues of the established anticancer drug gemcitabine. Cytotoxic capability of these new analogues is evaluated against human pancreatic cancer and human primary glioblastoma cell lines, with observed activities ranging from low μM to >200 μM; explanation for this reduced activity, compared to established nucleoside analogues, is yet unclear. Access to these chemotypes, with thiohemiaminal linkages, will enable a wider exploration of such materials for resistance towards relevant hydrolytic enzymes within nucleotide and nucleic acid biochemistries. | Mieke Guinan; Ningwu Huang; Chris Hawes; Marcelo Lima; Gavin Miller; Mark Smith | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6177f00d913a7490e76b313b/original/synthesis-and-anticancer-evaluation-of-4-thio-and-4-sulfinyl-pyrimidine-nucleoside-analogues.pdf |
67129eb312ff75c3a1d08a0a | 10.26434/chemrxiv-2024-l2852 | Synthesis and Applications of an Electrospray-Active N-Heterocyclic Carbene for Electrospray Ionization Mass Spectrometric Analysis of Organometallic Compounds | A charge-tagged N-heterocyclic carbene (NHC) has been synthesized and its utility in allowing the dynamic behaviour of metal complexes to be monitored in real time using electrospray ionization mass spectrometry demonstrated. This compound, dubbed ESIMes, was used to prepare different metal-NHC complexes, and the kinetic behaviour of complex formation and ligand exchange was monitored in real time through the use of pressurized sample infusion electrospray mass spectrometry (PSI-ESI-MS). | Charles Killeen; Allen G. Oliver; J. Scott McIndoe | Catalysis; Analytical Chemistry; Organometallic Chemistry; Mass Spectrometry; Kinetics and Mechanism - Organometallic Reactions; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67129eb312ff75c3a1d08a0a/original/synthesis-and-applications-of-an-electrospray-active-n-heterocyclic-carbene-for-electrospray-ionization-mass-spectrometric-analysis-of-organometallic-compounds.pdf |
6516764e0065940912195d6b | 10.26434/chemrxiv-2023-jbd2z | Water and Air Stable Copper(I) Complexes of Tetracationic Catenane Ligands for Oxidative C–C Cross-Coupling | Aqueous soluble and stable Cu(I) molecular catalysts featuring a catenane ligand composed of two mechanically interlocked, cationic macrocycles are reported. The mechanical bond in the catenane ligand not only fine-tunes the coordination sphere and kinetically stabilizes the Cu(I) against air oxidation and disproportionation, but also prevents the dissociation of the otherwise electrostatically repulsive cationic macrocycles which are essential for the good water solubility and sustained reactivity of the catalyst. These catenane Cu(I) complexes are active catalysts for the oxidative C–C coupling of indoles and tetrahydroisoquinolines in water with a good substrate scope. The successful use of the catenane ligands in exploiting Cu(I) for oxidative catalysis under aqueous conditions using H2O2 as a green oxidant thus highlights the many unexplored potential of mechanical bonding as a molecular design element in developing new transition metal catalysts. | Man Pang Tang; Yulin Deng; Yixiang Shi; Samuel Kin-Man Lai; Xin-Yu Pang; Chunyu Liu; Wei Jiang; Lihui Zhu; Ho Yu Au-Yeung | Inorganic Chemistry; Catalysis; Ligands (Inorg.); Transition Metal Complexes (Inorg.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516764e0065940912195d6b/original/water-and-air-stable-copper-i-complexes-of-tetracationic-catenane-ligands-for-oxidative-c-c-cross-coupling.pdf |
61c1b3d0f52bc4dfb2c84fa3 | 10.26434/chemrxiv-2021-l17v4 | Accelerating Net Zero from the perspective of Optimizing a Carbon Capture and Utilization System | Net zero requires an accelerated transition from fossil fuels to renewables. Carbon capture and utilization (CCU) can be an effective intermediate solution for the decarbonization of fossil fuels. However, many research works contain renewables in the design of CCU systems, which may mislead stakeholders regarding the hotspots of CCU systems. In this work we build a model of a CCU system with no renewables involved, and evaluate its greenhouse (GHG) emissions based on the life cycle assessment with a cradle-to-gate boundary. To pursue the best system performance, an optimization framework is established to digitalize and optimize the CCU system regarding GHG emissions reduction. The optimized CCU can reduce GHG emissions by 13% compared with the conventional process. Heating is identified as the most significant contributor to GHG emissions, accounting for 60%. Electrifying heating fully by low-carbon electricity can further reduce GHG emissions by 47%, but such extreme conditions will significantly sacrifice the economic benefit. By contrast, the multi-objective optimization can show how the decisions can affect the balance between GHG emissions and profit. Further, this work discusses the dual effect of carbon pricing on the CCU system – raising the cost of raw materials and utilities, but also gaining credits when emissions are reduced in producing valued products. | Zhimian Hao; Magda Barecka; Alexei Lapkin | Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2021-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c1b3d0f52bc4dfb2c84fa3/original/accelerating-net-zero-from-the-perspective-of-optimizing-a-carbon-capture-and-utilization-system.pdf |
6399f5ab963bf319949964da | 10.26434/chemrxiv-2022-t8r01 | Direct C-H arylation of dithiophene-tetrathiafulvalene: tuneable electronic structure and 2D self-assembled molecular networks at the solid/liquid interface | Tetrathiafulvalene is among the most well-known building block in molecular electronics due to its outstanding electron-donating and redox properties. Among its derivatives, dithiophene-tetrathiafulvalene (DT-TTF) received a lot of interest for organic electronics due to its high charge mobility. Herein we report the direct C-H arylation of DT-TTF (1) to synthesise mono- (2, 3) and tetraarylated (4, 5) derivatives bearing different functional groups. The incorporation of electron-donor or electron-withdrawing groups into the DT-TTF core allows the fine-tuning of its electronic structure as demonstrated by cyclic voltammetry, UV-vis spectroscopy and DFT calculations. The self-assembly of DT-TTF-tetrabenzoic acid (5) derivative was studied using scanning tunneling microscopy which revealed the formation of ordered, densely packed 2D hydrogen-bonded networks at the graphite/liquid interface. Importantly, molecule 5 can reach a planar geometry on the graphite surface due to van der Waals interactions with the surface and H-bonding with neighbouring molecules. This work demonstrates a simple method for synthesising arylated DT-TTF derivatives with tuneable molecular orbital energy levels and the formation of 2D networks on the surface, allowing the construction of extended electroactive frameworks based on DT-TTF building blocks. | Catarina Ribeiro; Gonçalo Valente; Miguel Espinosa; Rafaela A. L. Silva; Dulce Belo; Sara Gil-Guerrero; Nicolás Arisnabarreta; Kunal Mali; Steven De Feyter; Manuel Melle-Franco; Manuel Souto | Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6399f5ab963bf319949964da/original/direct-c-h-arylation-of-dithiophene-tetrathiafulvalene-tuneable-electronic-structure-and-2d-self-assembled-molecular-networks-at-the-solid-liquid-interface.pdf |
66b0534201103d79c5c39db4 | 10.26434/chemrxiv-2024-gchks | Oxytocin analogues for the oral treatment of abdominal pain | Abdominal pain presents an onerous day-to-day reality for millions of people affected by chronic gastrointestinal disorders such as irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD). The oxytocin receptor (OTR) has emerged as a potential novel analgesic drug target as OTR expression is upregulated on colon-innervating nociceptors, which are accessible via luminal delivery in chronic visceral hypersensitivity states. However, the low gastrointestinal stability of the endogenous OTR peptide ligand oxytocin (OT) is a crucial bottleneck for therapeutic development. Here, we report the rational development of the first series of fully gut-stable and potent OT analogues, laying the foundation for a new area of oral and gut-specific peptide therapeutics. Compound optimisation guided by systematic structure-gut-stability-activity relationship analysis yielded highly stable analogues (t1/2 >24 h, compared to t1/2 <10 min of OT in intestinal fluid) equipotent to native OT (~3 nM) and with enhanced selectivity for OTR. Colon-targeted local luminal administration of the lead compound significantly reduced colonic mechanical hypersensitivity in a concentration-dependent manner in an in vivo mouse model of chronic abdominal pain. Moreover, oral administration of the lead compound also significantly reduced colonic mechanical hypersensitivity in this abdominal pain model. The employed strategies and generated compounds could pave the way to a new class of gut-specific oral peptide probes and therapeutics to study and combat chronic gastrointestinal disorders, an area with substantial unmet medical needs. | Thomas Kremsmayr; Gudrun Schober; Matthias Kaltenböck; Bradley Hoare; Stuart Brierley; Markus Muttenthaler | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b0534201103d79c5c39db4/original/oxytocin-analogues-for-the-oral-treatment-of-abdominal-pain.pdf |
67ab38b66dde43c908632ebe | 10.26434/chemrxiv-2025-cfz52 | A Closer Look at the Substituent Effects on the Copolymerization of Thionolactones by Radical Ring-Opening Polymerization | The negative impact of plastic waste on the environment is a serious issue for the future. Adding cleavable bonds in the polymer backbone can help to impart degradability properties. To this end, radical ring opening polymerization (rROP) of-fers a very attractive way through radical copolymerization with vinyl monomers. Thionolactones, one of the various cyclic monomers that can be used in rROP, are promising structures due to the efficiency of the C=S bond in acting as a radical acceptor. In this work, we used DFT calculations to better understand the effects of different substituents on the radical reac-tivity of thionolactones (dibenzo[c,e]oxepane-5-thione DOT derivatives) already described as more or less effective for copol-ymerization with vinyl monomers in order to adjust the reactivity of these thionolactones. To carry out these calculations, we focused on the value of the transfer constant ktr and its relationship to the propagation constant kp of the vinyl monomer. The calculations performed subsequently on 7-phenyloxepane-2-thione (POT) derivatives highlighted that electron-donating groups inserted in para-position on the phenyl ring should improve the copolymerization efficiency with acrylate derivatives and in contrary electron-withdrawing groups should lead to more important compositional drift during styrene and acrylate copolymerization. Although POT derivatives bearing electro-donating groups could not be prepared, the preparation of those with CF3 and NO2 groups was successfully achieved. Experimental copolymerization of these two thionolactones with sty-rene and isobornyl acrylate are in good agreement with the calculations. This result confirmed the versatility and relevance of our calculation approach to account for the reactivity of thionolactones. | Bastien Luzel; Lucas Raggio; Eytan Benharrous; Julien Monot; Didier Bourissou; Didier Siri; Didier Gigmes; Catherine Lefay; Blanca Martin-Vaca; Yohann Guillaneuf | Materials Science; Polymer Science; Organic Polymers; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab38b66dde43c908632ebe/original/a-closer-look-at-the-substituent-effects-on-the-copolymerization-of-thionolactones-by-radical-ring-opening-polymerization.pdf |
647760c8be16ad5c573bd56c | 10.26434/chemrxiv-2023-cb75z | Distinguishing Competing Mechanistic Manifolds for C(acyl)–N Functionalization by a Ni/N-Heterocyclic Carbene Catalyst System | Carboxylic acid derivatives are appealing alternatives to organohalides as cross-coupling electrophiles for fine chemical synthesis due to their prevalence in biomass and bioactive small molecules as well as their ease of preparation and handling. Within this family, carboxamides comprise a versatile electrophile class for nickel-catalyzed coupling with carbon and heteroatom nucleophiles. However, even state-of-the-art C(acyl)–N functionalization and cross-coupling reactions typically require high catalyst loadings and specific substitution patterns. These challenges have proven difficult to overcome, in large part due to limited experimental mechanistic insight. In this work, we describe a detailed mechanistic case study of acylative coupling reactions catalyzed by the commonly employed Ni/SIPr catalyst system (SIPr = 1,3-Bis(2,6-di-isopropylphenyl)-4,5-dihydroimidazol-2-ylidine). Stoichiometric organometallic studies, in situ spectroscopic measurements, and crossover experiments demonstrate accessibility of Ni(0), Ni(I), and Ni(II) resting states. Although in situ precatalyst activation limits reaction efficiency, the low concentrations of active, SIPr-supported Ni(0) select for electrophile-first (closed-shell) over competing nucleophile-first (open-shell) mechanistic manifolds. We anticipate that the experimental insights into the nature and controlling features of these distinct pathways are likely to accelerate rational improvements to cross-coupling methodologies involving pervasive carboxamide substrate motifs. | Kaycie Malyk; Vivek G. Pillai; William Brennessel; Roberto Leon Baxin; Elliot Silk; Daniel Nakamura; C. Rose Kennedy | Organic Chemistry; Catalysis; Organometallic Chemistry; Bond Activation; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647760c8be16ad5c573bd56c/original/distinguishing-competing-mechanistic-manifolds-for-c-acyl-n-functionalization-by-a-ni-n-heterocyclic-carbene-catalyst-system.pdf |
64794e8f4f8b1884b7b10ce9 | 10.26434/chemrxiv-2023-bm7mt-v2 | Numerical study of particle retention in water-saturated porous media and the effect of particle concentration | The transport and retention of particles in slurry passing through porous media causes particle clogging, which is affected primarily by the ratio of the particle diameter to pore-throat size of the porous media. A previous study reported that the particle retention is affected by both the Stokes number and particle concentration. Therefore, this study investigates the effect of the diameter and concentration of particles on particle clogging in porous media. Furthermore, the effect of fluid velocity on particle clogging and permeability of the porous media is also investigated to study particle transport and retention in homogeneous porous media. Fluid-particle two-phase flow in porous media is numerically simulated using the computational fluid dynamics-discrete element method. Particle clogging can be directly precited via the interaction between the particles and surface of the porous media by tracing the exact location of each particle. The simulation reveals that an increase of the particle concentration increases the possibility of the particles being retained in the porous media. Additionally, particles are accumulated at the entrance region of the porous media when the particle concentration is high in the dense region. | Dan Sun | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.); Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64794e8f4f8b1884b7b10ce9/original/numerical-study-of-particle-retention-in-water-saturated-porous-media-and-the-effect-of-particle-concentration.pdf |
65cedcfce9ebbb4db97813c7 | 10.26434/chemrxiv-2024-gmrj6 | De novo designed short peptide tags for synthetic protein condensates in mammalian cells | In mammalian cells, protein condensates underlie diverse cell functions. Intensive synthetic biological research has been devoted to fabricating liquid droplets using de novo peptides/proteins designed from scratch in test tubes or bacterial cells. However, the development of de novo sequences for synthetic droplets forming in eukaryotes is challenging. Here, we report YK peptides, comprising 9–15 residues of alternating repeats of tyrosine and lysine, which form reversible amyloid-like fibrils accompanied by binding with poly-anion species such as ATP. By genetically tagging the YK peptide, superfolder GFPs assemble into artificial liquid-like droplets in living cells. Rational design of the YK system allows fine-tuning of the fluidity and construction of multi-component droplets. Furthermore, the YK system not only facilitates intracellular reconstitution of simplified models for natural protein condensates, but it also provides a toolbox for the systematic creation of droplets with different dynamicity and composition for in situ evaluation. | Takayuki Miki; Masahiro Hashimoto; Hiroki Takahashi; Masatoshi Shimizu; Sae Nakayama; Tadaomi Furuta; Hisakazu Mihara | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cedcfce9ebbb4db97813c7/original/de-novo-designed-short-peptide-tags-for-synthetic-protein-condensates-in-mammalian-cells.pdf |
637b401577ffe797aaf65b3f | 10.26434/chemrxiv-2022-prgfw-v2 | Resorcinol-based hemiindigoid derivatives as human tyrosinase inhibitors and melanogenesis suppressors in human melanoma cells | Human tyrosinase (hsTYR) catalyzes the key steps of melanogenesis, making it a privileged target for reducing melanin production in vivo. However, very few hsTYR inhibitors have been reported so far in the literature, whereas thousands of mushroom tyrosinase (abTYR) inhibitors are known. Yet, as these enzymes are actually very different, including at their active sites, there is an urgent need for new true hsTYR inhibitors in order to enable human-directed pharmacological and dermocosmetic applications without encountering the inefficiency and toxicity issues currently triggered by kojic acid or hydroquinone. Starting from the two most active compounds reported to date, i.e. a 2-hydroxypyridine-embedded aurone and thiamidol, we combined herein key structural elements and developed new nanomolar hsTYR inhibitors with cell-based activity. From a complete series of thirty-eight synthesized derivatives, excellent inhibition values were obtained for two compounds in both human melanoma cell lysates and purified hsTYR assays, and a promising improvement was observed in whole cell experiments. | Brayan Roulier; Inbal Rush; Leticia M. Lazinski; Basile Pérès; Hamza Olleik; Guy Royal; Ayelet Fishman; Marc Maresca; Romain Haudecoeur | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637b401577ffe797aaf65b3f/original/resorcinol-based-hemiindigoid-derivatives-as-human-tyrosinase-inhibitors-and-melanogenesis-suppressors-in-human-melanoma-cells.pdf |
6113f8b303182f833a1e00fe | 10.26434/chemrxiv-2021-mczbs | Selective degradation of styrene-contained plastics catalyzed by iron under visible light | Efficient degradation of plastics, the vital challenge for a sustainable future, stands in need of better chemical recycling procedures that help produce commercially valuable small molecules and redefine plastic waste as a rich source of chemical feedstock. However, the corresponding chemical recycling methods, while being generally restricted to polar polymers, need improvement. Particularly, degradation of chemical inert nonpolar polymers, the major constitutes of plastics, are reported to have suffered from low selectivity and very harsh transformation conditions. Herein, we report an efficient method for the selective degradation of styrene-contained plastics under gentle conditions through oxidative multiple sp3 C-C bond cleavage. The unpresented procedure is catalyzed with inexpensive iron salts under visible light, using oxygen as the green oxidant. Furthermore, simple iron salts can be used to degrade plastics in the absence of solvent under natural conditions, highlighting the potential application of iron salts as additives for degradable plastics. | Miao Wang; Jinglan Wen; Yahao Huang; Peng Hu | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6113f8b303182f833a1e00fe/original/selective-degradation-of-styrene-contained-plastics-catalyzed-by-iron-under-visible-light.pdf |
63bc35e7553889fcea79c385 | 10.26434/chemrxiv-2023-d7ss7 | Selection of Optimised Ligands by Fluorescence-Activated Bead Sorting | The chemistry of aptamers is largely limited to natural nucleotides, and although modifications of nucleic acids can enhance target aptamer affinity, there has not been a technology for selecting the right modifications in the right locations because enzymatic amplification does not transmit sequence-specific modification information. Here we show the first method for the selection of specific nucleoside modifications that increase aptamer binding efficacy, using the oncoprotein EGFR as a model target. Using fluorescent-activated bead sorting (FABS), we have successfully selected optimized aptamers from a library of >65,000 variations. Hits were identified by tandem mass spectrometry and validated by using an EGFR binding assay and computational docking studies. Our results provide proof of concept for this novel strategy for the selection of chemically optimised aptamers and offer a new method for rapidly synthesising and screening large aptamer libraries to accelerate diagnostic and drug discovery. | Alexandra Paul; Mario Falsaperna; Helen Lavender; Michelle Garrett; Christopher Serpell | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bc35e7553889fcea79c385/original/selection-of-optimised-ligands-by-fluorescence-activated-bead-sorting.pdf |
60c74891bb8c1a43d63daccd | 10.26434/chemrxiv.11935281.v1 | A Formulation Protocol with Pyridine to Enable DNP-SENS on Reactive Surface Sites: Case Study with Olefin Polymerization and Metathesis Catalysts | <div>Dynamic nuclear polarization surface-enhanced NMR spectroscopy (DNP-SENS) has emerged as a powerful characterization tool in material chemistry and heterogeneous catalysis by dramatically increasing, by up to two orders of magnitude, the NMR signals associated with surface sites. DNP-SENS mostly relies on using exogenous polarizing agents (PAs) – typically di-nitroxyl radicals, to boost the NMR signals, that may interact with the surface or even react with highly reactive surface sites, thus leading to loss/quenching of DNP enhancements. Herein, we describe the development of a DNP-SENS formulation that allows us to broaden the application of DNP-SENS to samples containing highly reactive surface sites, namely a Ziegler-Natta propylene polymerization catalyst, a sulfated zirconia-supported metallocene and a silica-supported cationic Mo alkylidene. The protocol consists of adsorbing pyridine prior to the impregnation of the DNP formulation (TEKPol/TCE). The addition of pyridine does not only preserve the PAs and thereby restore the DNP enhancement, but it also allows probing the presence of Lewis acid and Brønsted acid surface sites that are often present on these catalysts.</div> | Alexander Yakimov; D Mance; Keith Searles; Christophe Copéret | Heterogeneous Catalysis; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74891bb8c1a43d63daccd/original/a-formulation-protocol-with-pyridine-to-enable-dnp-sens-on-reactive-surface-sites-case-study-with-olefin-polymerization-and-metathesis-catalysts.pdf |
60c75533bdbb899471a3a7aa | 10.26434/chemrxiv.13124993.v2 | Imputation of Missing Gas Permeability Data for Polymer Membranes using Machine Learning | <p><a>Polymer-based membranes can be used for energy efficient gas separations. Successful exploitation of new materials requires accurate knowledge of the transport properties of all gases of interest. An open source database of such data is of significant benefit to the research community. The Membrane Society of Australasia (https://membrane-australasia.org/) hosts a database for experimentally measured and reported polymer gas permeabilities. However, the database is incomplete, limiting its potential use as a research tool. Here, missing values in the database were filled using machine learning (ML). The ML model was validated against gas permeability measurements that were not recorded in the database. Through imputing the missing data, it is possible to re-analyse historical polymers and look for potential “missed” candidates with promising gas selectivity. In addition, for systems with limited experimental data, ML using sparse features was performed, and we suggest that once the permeability of CO<sub>2</sub> and/or O<sub>2</sub> for a polymer has been measured, most other gas permeabilities and selectivities, including those for CO<sub>2</sub>/CH<sub>4</sub> and CO<sub>2</sub>/N<sub>2</sub>, can be quantitatively estimated. This early insight into the gas permeability of a new system can be used at an initial stage of experimental measurements to rapidly identify polymer membranes worth further investigation.</a></p> | Qi Yuan; Mariagiulia Longo; Aaron Thornton; Neil
B. McKeown; Bibiana Comesana-Gandara; Johannes
C. Jansen; Kim Jelfs | Polymerization (Polymers); Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75533bdbb899471a3a7aa/original/imputation-of-missing-gas-permeability-data-for-polymer-membranes-using-machine-learning.pdf |
662a0e1721291e5d1da93847 | 10.26434/chemrxiv-2024-9j8n7 | MatchMass: A Web-Based Tool for Efficient Mass Spectrometry Data Analysis | MatchMass is a user-friendly web-based application designed to streamline the analysis of mass spectrometry (MS) data for researchers studying complex mixtures of molecules. Users upload experimental data (m/z and abundance) and a list of theoretical monoisotopic masses. MatchMass then identifies matching molecules within the sample based on user-defined parameters (mass accuracy, abundance threshold, and ions of interest). The tool generates a visual comparison of experimental and theoretical m/z values, facilitates result exploration, and allows download of comprehensive reports. MatchMass eliminates the need for manual data processing, improving efficiency and accuracy in MS data analysis, particularly for researchers working with complicated mixtures. | Lukas Ustrnul; Tatsiana Jarg; Martin Jantson; Irina Osadchuk; Lauri Anton; Riina Aav | Analytical Chemistry; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a0e1721291e5d1da93847/original/match-mass-a-web-based-tool-for-efficient-mass-spectrometry-data-analysis.pdf |
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