id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
65211d3ebda59ceb9a0b5d64 | 10.26434/chemrxiv-2023-5x59s | Identification of Acidic and Basic Dyes in Different Candies | Synthetic food colors are added in different food items. These colors directly affect consumer food selection and acceptance. Synthetic colors on the basis of solubility are categorized into acidic (permitted) and basic (non-permitted). The present study was conducted to check the synthetic color present in branded and unbranded candies it is either acidic or basic. For this purpose, 15 samples were collected and analyzed in Food Science and Technology Laboratory of the University of Haripur. It was observed that all tested samples contain acidic colors when 20 grams of grinded sample and 5 ml of acetic acidic were taken. The present of acidic synthetic colors may lead to the conclusion that these tested candies can be used at permissible concentrations of dye without any risk to human health. The use of basic colors may cause human health affect from mild to severe whereas permitted acidic colors are safe to use if use within permitted range. | Nosheen Khalid; Nosheen Khalid; Muhammad Jahangir; Saira Imdad; Khurshid Anwar; Nida Arif; Adnan Khan; Naqqash Aslam | Agriculture and Food Chemistry; Food | CC BY 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65211d3ebda59ceb9a0b5d64/original/identification-of-acidic-and-basic-dyes-in-different-candies.pdf |
60c74b5cf96a0080e62875c1 | 10.26434/chemrxiv.12318926.v1 | Dynamic Range Expansion by Gas-Phase Ion Fractionation and Enrichment for Imaging Mass Spectrometry | In the analysis of biological tissue by imaging mass spectrometry (IMS), the limit of detection and dynamic range are of paramount importance in obtaining experimental results that provide insight into underlying biological processes. Many important biomolecules are present in the tissue milieu in low concentrations and in complex mixtures with other compounds of widely ranging abundances, challenging the limits of analytical technologies. In many IMS experiments, the ion signal can be dominated by a few highly abundant ion species. On trap-based instrument platforms that accumulate ions prior to mass analysis, these high abundance ions can diminish the detection and dynamic range of lower abundance ions. Herein, we characterize two strategies for combating these challenges during IMS experiments on a hybrid QqFT-ICR MS. In one iteration, the mass resolving capabilities of a quadrupole mass filter are used to selectively enrich for ions of interest via a technique previously termed continuous accumulation of selected ions (CASI). Secondly, we have introduced a supplemental dipolar AC waveform to the quadrupole mass filter of a commercial QqFT-ICR mass spectrometer to perform selected ion ejection prior to the ion accumulation region. This setup allows the selective ejection of the most abundant ion species prior to ion accumulation, thereby greatly improving the molecular depth with which IMS can probe tissue samples.<br /> | Boone Prentice; Daniel Ryan; Kerri Grove; D. Shannon Cornett; Richard Caprioli; Jeffrey Spraggins | Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b5cf96a0080e62875c1/original/dynamic-range-expansion-by-gas-phase-ion-fractionation-and-enrichment-for-imaging-mass-spectrometry.pdf |
6352ab85ca86b834efbd8c14 | 10.26434/chemrxiv-2022-c1bt4 | Transition Metal-Free Difunctionalization of Sulfur Nucleophiles | Efficient protocols for accessing iodo-implanted diaryl and aryl(vinyl) thioethers have been developed using iodonium salts as reactive electrophilic arylation and vinylation reagents. The reactions take place under transition metal-free, thiol-free, and external base-free conditions. A wide variety of functional groups are tolerated in the S-diarylation, leading to the regioselective late-stage application of several heterocycles and drug molecules under mild reaction conditions. A novel S-difunctionalization pathway was discovered using vinyliodonium salts, which proceeds under additive-free reaction conditions and grants excellent stereoselectivity in the synthesis of (aryl)vinyl thioethers. A one-pot strategy combining transition metal-free diarylation and subsequent reduction provided facile access to electron-rich thioanilines and direct synthesis of a potential drug candidate derivative. The retained iodo group allows a wide array of further synthetic transformations. Mechanistic insights were elucidated by isolating the key intermediate, and the relevant energy profile was substantiated by DFT calculations. | Shobhan Mondal; Ester Maria Di Tommaso; Berit Olofsson | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6352ab85ca86b834efbd8c14/original/transition-metal-free-difunctionalization-of-sulfur-nucleophiles.pdf |
675c38cd7be152b1d0dc3680 | 10.26434/chemrxiv-2024-3pt2b | A printed gate controlled electrochemical capacitor-diode (G-CAPode) for AC filtering applications | For the first time a printable, miniaturized and gate-controlled electrochemical capacitor-diode (G-CAPode) is presented. The heart of the device consists of a recently developed asymmetric electrical double-layer capacitor system based on selective, size-depended ion adsorption. Due to the introduction of a sieving carbon with ultramicroporous pores (d = 0.69 nm) as one electrode material an effective blocking of ions with sizes below the pore size of the carbon can be achieved, leading to a unidirectional charging comparable to a diode (CAPode). This “working capacitor” (W-Cap) was further expanded by introducing a third (“gate”) electrode enabling a control of current and voltage output of the W-Cap depending on the applied gate bias between gate electrode and counter electrode of the W-Cap resembling transistor features. By varying the gate bias voltage, the potentials and therefore the working window of the W-Cap electrodes are shifted to more positive or negative potentials, leading to an increase or decrease of the G-CAPode capacitance. The printed G-CAPode was tested as switchable device analogous to an I-MOS varactor for the adjustable filtering of AC signals in a high-pass filter and band-pass filter application. This investigation opens the possibility to couple capacitive (energy storage), diodic (current rectification) and transistor (voltage-controlled switching) characteristics in one device and also addresses its process integration via 3D printing. | Christin Gellrich; Przemyslaw Galek; Leonid Shupletsov; Nick Niese; Ahmed Bahrawi; Julia Grothe; Stefan Kaskel | Inorganic Chemistry; Nanoscience; Energy; Nanodevices; Electrochemistry; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c38cd7be152b1d0dc3680/original/a-printed-gate-controlled-electrochemical-capacitor-diode-g-ca-pode-for-ac-filtering-applications.pdf |
631cce9d0429d6839199ca6c | 10.26434/chemrxiv-2022-m1wp6 | New insight to the catechol photochemistry: The role of different monomer and dimer configurations in radiationless decay of S1 electronic excited state | The equilibrium geometries of the ground and first electronic excited states as well as the radiationless deactivation channels of catechol in its monomer and dimer configuration have been investigated using the standard linear-response and the spin-flipped TDDFT methods as well as by the similarity transformed equation-of-motion coupled cluster built with the domain-based local pair natural orbitals (DLPNO-STEOM-CCSD). For the monomer, it was found that there is a new conical intersection geometry that can explain why catechol exhibits different photochemical behavior. This deactivation pathway involves almost simultaneously, an excited state intramolecular proton transfer between the two O atoms and an O–H bond breaks at the proton that is not between the two O atoms. From
the energy balance point of view, these geometries are not associated with high potential barriers, so radiationless relaxation can be achieved through these geometries. For cyclohexane solvent, the lowest CI geometry shows a potential barrier with about 4 kcal/mol lower than that found for acetonitrile, making even more easier the
relaxation. In the case of catechol dimer structures, it was
found several so-called dimer-type CI geometries where both monomers exhibit substantial geometric distortions together with the formation of a weaker C–C bond between the two catechol monomers. These CI geometries are energetically more favorable and, in the case of aggregation processes, more likely to decay the excited states of the catechol through these radiationless deactivation channels. | Attila Bende; Alex-Adrian Farcas; Alexandra Falamas; Anca Petran | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631cce9d0429d6839199ca6c/original/new-insight-to-the-catechol-photochemistry-the-role-of-different-monomer-and-dimer-configurations-in-radiationless-decay-of-s1-electronic-excited-state.pdf |
60f69c9a8f6bf67fde6fb5bc | 10.26434/chemrxiv-2021-8sd68-v2 | Modified desolvation method enables simple one-step synthesis of gelatin nanoparticles from different gelatin types with any bloom values | Gelatin nanoparticles found numerous applications in drug delivery, bioimaging, immunotherapy, and vaccine development as well as in biotechnology and food science. Synthesis of gelatin nanoparticles is usually made by a two-step desolvation method, which, despite providing stable and homogeneous nanoparticles, has many limitations, namely complex procedure, low yields, and poor reproducibility of the first desolvation step. Herein, we present a modified one-step desolvation method, which enables the quick, simple, and reproducible synthesis of gelatin nanoparticles. Using the proposed method one can prepare gelatin nanoparticles from any type of gelatin with any bloom number, even with the lowest ones, which remains unattainable for the traditional two-step technique. The method relies on quick one-time addition of poor solvent (preferably isopropyl alcohol) to gelatin solution in the absence of stirring. We applied the modified desolvation method to synthesize nanoparticles from porcine, bovine, and fish with bloom values from 62 to 225 on the hundreds-of-milligram scale. Synthesized nanoparticles had average diameters between 130 and 190 nm and narrow size distribution. Yields of synthesis were 62-82% and can be further increased. Gelatin nanoparticles have good colloidal stability and withstand autoclaving. Moreover, they were non-toxic to human immune cells. | Pavel Khramtsov; Oksana Burdina; Sergey Lazarev; Anastasia Novokshonova; Maria Bochkova; Valeria Timganova; Dmitriy Kiselkov; Svetlana Zamorina; Mikhail Rayev | Biological and Medicinal Chemistry; Polymer Science; Nanoscience; Biopolymers; Drug delivery systems; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f69c9a8f6bf67fde6fb5bc/original/modified-desolvation-method-enables-simple-one-step-synthesis-of-gelatin-nanoparticles-from-different-gelatin-types-with-any-bloom-values.pdf |
64678e8afb40f6b3eed9696b | 10.26434/chemrxiv-2023-tn92w-v2 | Regioselective Direct C−H Bond (Hetero)arylation of Thiazoles Enabled by a Novel Iminopyridine-Based α‐Diimine Nickel(II) Complex Evaluated by DFT Studies. | Direct C−H bond arylation is a highly effective method for synthesizing arylated heteroaromatics. This method reduces synthetic steps and minimizes the formation of impurities. We report an air and moisture-stable iminopyridine-based α-diimine nickel (II) complex for direct C5-H bond arylation of thiazole derivatives. Under low catalyst loading and performing the reactions at lower temperatures (80 °C) under aerobic conditions, we produced mono- and diarylated thiazole units. Competition experiments and density functional theory calculations (DFT) revealed that the mechanism of C−H activation in 4-methylthiazole involves electrophilic aromatic substitution. | Phillip Damien E. Arche; Shubham Chatterjee; Md Muktadir Talukder; Justin T. Miller; John Michael O. Cue; Chinthaka M. Udamulle Gedara; Richard Lord; Michael C. Biewer; G. Andrés Cisneros; Mihaela C. Stefan | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64678e8afb40f6b3eed9696b/original/regioselective-direct-c-h-bond-hetero-arylation-of-thiazoles-enabled-by-a-novel-iminopyridine-based-diimine-nickel-ii-complex-evaluated-by-dft-studies.pdf |
62be69a5e60d982250f3c8a8 | 10.26434/chemrxiv-2022-lb0dt | Novel dual-motor nanorotator assembled by cyclo[18]carbon and figure-eight carbon hoop | Two unique nanorings recently generated, namely cyclo[18]carbon (C18) and oligoparaphenylene (OPP), were theoretically designed to assemble an extraordinary dual-motor supramolecular rotator (2C18@OPP) with large included angle. The size adaptability and shape complementarity of guest C18 to host OPP as well as the thermodynamic analysis of 2C18@OPP showed that the complex can form easily and exist stably below 404 K. Energy decomposition and various real-space function analyses of host-guest interaction revealed the characteristic and nature of the non-covalent interaction in this supramolecule. The scanning results of the potential energy surface (PES) showed that the rotational barrier of C18 in OPP is extremely small, implying the possibility of the supramolecular complex as an ultrafast molecular rotator. Molecular dynamics (MD) simulations confirmed that C18 and OPP can spontaneously assemble into up to 1:2 ring-in-ring host-guest complexes, and C18 can rotate at an ultrahigh speed in OPP at ambient temperature. The thermodynamic parameters of the nanorotator at different temperatures were also investigated to determine the thermal stability of 2C18@OPP. Such assemble is the first example of two C18 molecules being encapsulated simultaneously to realize a dual-motor nanorotator and promises to open new avenues for the construction of complicated molecular machines as well as the controllable storage of C18. | Zeyu Liu; Xia Wang; Tian Lu; Jiaojiao Wang; Mengdi Zhao; Xiufen Yan | Theoretical and Computational Chemistry; Physical Chemistry; Physical and Chemical Processes; Physical and Chemical Properties; Self-Assembly; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62be69a5e60d982250f3c8a8/original/novel-dual-motor-nanorotator-assembled-by-cyclo-18-carbon-and-figure-eight-carbon-hoop.pdf |
66be62f3a4e53c48767dc4fe | 10.26434/chemrxiv-2024-mmj9z | Towards a Circular Nitrogen Bioeconomy: Integrating Nitrogen Bioconcentration, Separations, and High-Value Products for Nitrogen Recovery | Recovering nitrogen (N) from wastewater is a potential avenue to reduce reliance on energy-intensive synthetic nitrogen fixation via Haber-Bosch and subsequent treatment of N-laden wastewaters through nitrification-denitrification. However, many technical and economic factors hinder widespread application of N recovery, particularly low N concentrations in municipal wastewater, paucity of high-efficiency separations technologies compatible with biological treatment, and suitable products and markets for recovered N. In this perspective, we contextualize the challenges of N recovery today, propose integrated biological and physicochemical technologies to improve selective and tunable N recovery, and propose an expanded product portfolio for recovered N products beyond fertilizers. We highlight cyanophycin, an N-rich biopolymer produced by a diverse range of bacteria, as a potential target for N bioconcentration and downstream recovery from municipal wastewater. This perspective emphasizes the equal importance of integrated biological systems, physicochemical separations, and market assessment in advancing nitrogen recovery from wastewater. | Edward Apraku; McKenna Farmer; Chayse Lavallais; Danna Soriano; Justin Notestein; Keith Tyo; Jennifer Dunn; William Tarpeh; George Wells | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Agriculture and Food Chemistry; Wastes; Natural Resource Recovery; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66be62f3a4e53c48767dc4fe/original/towards-a-circular-nitrogen-bioeconomy-integrating-nitrogen-bioconcentration-separations-and-high-value-products-for-nitrogen-recovery.pdf |
63fd0c5d937392db3d25b507 | 10.26434/chemrxiv-2023-2tfdv | Designing Chemical Reaction Arrays using phactor and ChatGPT | High throughput experimentation (HTE) is a common practice in the pharmaceutical industry. Medicinal chemists design reaction arrays to optimize the yield of couplings between building blocks and/or pharmacophores. Popular reactions attempted by medicinal chemists include the amide coupling, Suzuki coupling, and Buchwald-Hartwig coupling. We show how the artificial intelligence (AI) language model ChatGPT can automatically formulate reaction arrays for these common reactions based on the literature corpus it was trained on. Furthermore, we showcase how ChatGPT results can be directly translated into inputs for the HTE management software phactor, which enables automated execution and analysis of assays. This workflow is experimentally demonstrated. | Babak Mahjour; Jillian Hoffstadt; Tim Cernak | Organic Chemistry; Chemical Education; Organic Synthesis and Reactions; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fd0c5d937392db3d25b507/original/designing-chemical-reaction-arrays-using-phactor-and-chat-gpt.pdf |
60c7555a4c89194bf6ad468b | 10.26434/chemrxiv.14045072.v1 | A Bag of Tricks for Automated De Novo Design of Molecules with the Desired Properties: Application to EGFR Inhibitor Discovery | <p>Deep generative neural networks have been used increasingly
in computational chemistry for <i>de novo</i> design of molecules with desired
properties. Many deep learning approaches employ reinforcement
learning for optimizing the target properties of the generated molecules. However,
the success of this approach is often hampered by the problem of sparse rewards as the majority of
the generated molecules are expectedly predicted as inactives. We propose several
technical innovations to address this problem and improve the balance between
exploration and exploitation modes in reinforcement learning. In a
proof-of-concept study, we demonstrate the application of the deep generative
recurrent neural network enhanced by several novel technical tricks to designing
experimentally validated potent inhibitors of the epidermal growth factor
(EGFR). The proposed technical solutions are expected to substantially improve
the success rate of finding novel bioactive compounds for specific biological targets
using generative and reinforcement learning approaches.</p> | Maria Korshunova; Niles Huang; Stephen Capuzzi; Dmytro S. Radchenko; Olena Savych; Yuriy S. Moroz; Carrow Wells; Timothy M. Willson; Alexander Tropsha; Olexandr Isayev | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7555a4c89194bf6ad468b/original/a-bag-of-tricks-for-automated-de-novo-design-of-molecules-with-the-desired-properties-application-to-egfr-inhibitor-discovery.pdf |
658cd0609138d23161a614cc | 10.26434/chemrxiv-2023-p0nwc-v2 | Biomimetic Vesicles with Designer Phospholipids Can Sense Environmental Redox Cues | Cell-like materials that sense environmental cues can serve as new-generation biosensors and help advance the understanding of intercellular communication. While top-down approaches typically require genetic engineering or complex logic circuits, bottom-up assembly of chemical building blocks to form protocell models remains to be a major challenge. Herein we describe giant unilamellar vesicles (GUVs) with biomimetic lipid membranes capable of sensing environmental redox cues. The GUVs employ activity-based sensing through designer phospholipids that are fluorescently activated under a specific reductive (hydrogen sulfide) or oxidative (hydrogen peroxide) condition. These synthetic phospholipids, derived from 1,2-dipalmitoyl-rac-glycero-3-phosphocholine, possess a head group with heterocyclic aromatic motifs and, thus, deviate significantly from the natural phosphocholine. Despite structural deviation in the head group, designer phospholipids (0.5–1.0 mol%) mixed with natural lipids can vesiculate, and the resulting GUVs (7–20 µm in diameter) remain intact after redox sensing. All-atom molecular dynamics simulations gave insight into how these lipids are positioned within the hydrophobic core of the membrane bilayer and at the membrane-water interface. This work provides a purely chemical method to investigate potential redox signaling and opens up new design opportunities for soft materials that mimic protocells. | Huseyin Erguven; Liming Wang; Bryan Gutierrez; Andrew Beaven; Alexander Sodt; Enver Izgu | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Supramolecular Chemistry (Org.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658cd0609138d23161a614cc/original/biomimetic-vesicles-with-designer-phospholipids-can-sense-environmental-redox-cues.pdf |
6604358066c1381729f967f8 | 10.26434/chemrxiv-2024-4j2gw-v2 | Reactivity Switch of Platinum with Gallium: From Reverse Water Gas Shift to Methanol Synthesis | The development of efficient catalysts for the hydrogenation of CO2 to methanol using “green” H2 is foreseen to be a key step to close the carbon cycle. In this study, we show that small and narrowly distributed alloyed PtGa nanoparticles supported on silica, prepared via a surface organometallic chemistry (SOMC) approach, display notable activity for the hydrogenation of CO2 to methanol, reaching 7.2 mol h-1 molPt-1 methanol formation rate with a 54% intrinsic CH3OH selectivity. This reactivity sharply contrasts with what is expected for Pt, which favors the reverse water gas shift reaction, albeit with a poor activity (2.6 mol h-1 molPt-1). In situ XAS studies indicate that ca. 50% of Ga is reduced to Ga0 yielding alloyed PtGa nanoparticles, while the remaining 50% persist as isolated GaIII sites. The PtGa catalyst slightly dealloys under CO2 hydrogenation conditions and displays redox dynamics with PtGa-GaOx interfaces, responsible for promoting both CO2 hydrogenation activity and methanol selectivity. Further tailoring the catalyst interface by using a carbon support in place of silica enables to improve the methanol formation rate by a factor of ~5. | Wei Zhou; Enzo Brack; Christian Ehinger; James Paterson; Jamie Southouse; Christophe Copéret | Catalysis; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6604358066c1381729f967f8/original/reactivity-switch-of-platinum-with-gallium-from-reverse-water-gas-shift-to-methanol-synthesis.pdf |
657bb66a66c1381729352293 | 10.26434/chemrxiv-2023-lpl9s | Combining Cationic and Anionic Polymerizations using a Universal Mediator: Enabling Access to Two- and Three-Mechanism Block Copolymers | The combination of multiple polymerization mechanisms and monomer classes to make block copolymers is an ongoing challenge. In particular, the combination of cationic and anionic polymerization mechanisms commonly requires extra compatibilization steps or the use of multi-functional initiators. Herein, we report the use of thiocarbonyl thio compounds (TCTs) as universal mediators to sequentially polymerize ethyl vinyl ether via photocontrolled cationic polymerization (photo-CP) and the thiirane phenoxy propylene sulfide via thioacyl anionic group transfer polymerization (TAGT). Thermal analyses of the resulting block copolymers provide evidence of microphase separation of the blocks. The resulting diblocks can be further chain extended using photoinduced electron/energy transfer reversible addition-fragmentation chain transfer polymerization (PET-RAFT) of N-isopropylacrylamide to make a triblock terpolymer from three different monomer classes incorporated via three different mechanisms without any end group modification steps. The development of this simple, sequential synthesis using a universal mediator opens up new possibilities by providing facile access to diverse block copolymers of vinyl ethers, thiiranes, and acrylamides. | Brandon Hosford; William Ramos; Jessica Lamb | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657bb66a66c1381729352293/original/combining-cationic-and-anionic-polymerizations-using-a-universal-mediator-enabling-access-to-two-and-three-mechanism-block-copolymers.pdf |
65c64e46e9ebbb4db90001f3 | 10.26434/chemrxiv-2023-lgv9f-v2 | Insights into the Main Protease of SARS-CoV-2: Thermodynamic Analysis, Structural Characterization, and the Impact of Inhibitors | The main protease of SARS-CoV-2 (Mpro) is an essential enzyme for coronaviral maturation and is the target of Paxlovid, which is currently the standard-of-care treatment for COVID-19. There remains a need to identify new inhibitors of Mpro as viral resistance to Paxlovid emerges. Here, we report the use of native mass spectrometry coupled with 193-nm ultraviolet photodissociation (UVPD) to structurally characterize Mpro and its interactions with potential covalent inhibitors. Melting temperatures and the overall energy landscape were obtained using variable temperature nano-electrospray ionization (vT-nESI), thus providing quantitative evaluation of inhibitor binding on the stability of Mpro. The melting temperature was determined to be approximately 30°C for the dimer and 36°C for the monomer, suggesting an initial thermal dissociation pathway before subsequent unfolding of the monomer species. Thermodynamic parameters extracted from Van’t Hoff plots revealed that the dimeric complexes containing each inhibitor showed enhanced stability through increased melting temperatures as well as overall lower average charge states, giving insight into the basis for potential inhibition mechanisms. | Jamie Butalewicz; Sarah Sipe; Kyle Juetten; Virginia James; Thomas Meek; Jennifer Brodbelt | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c64e46e9ebbb4db90001f3/original/insights-into-the-main-protease-of-sars-co-v-2-thermodynamic-analysis-structural-characterization-and-the-impact-of-inhibitors.pdf |
67dc50b381d2151a023019c7 | 10.26434/chemrxiv-2025-3wl26 | Quantifying Multidimensional Effects of Physicochemical Parameters on PFAS Adsorption Using a Hybrid Response Surface Methodology-Machine Learning Approach | Per- and polyfluoroalkyl substances (PFAS) contamination has posed a significant environmental and public health challenge due to their ubiquitous nature. Adsorption has emerged as a promising remediation technique, yet optimizing adsorption efficiency remains complex due to the diverse physicochemical properties of PFAS and the wide range of adsorbent materials. Traditional modeling approaches, such as response surface methodology (RSM), struggled to capture nonlinear interactions, while standalone machine learning (ML) models required extensive datasets. This study addressed these limitations by developing hybrid RSM-ML models to improve the prediction and optimization of PFAS adsorption. A comprehensive dataset was constructed using experimental adsorption data, integrating key parameters such as pH, pHpzc, surface area, temperature, and PFAS molecular properties. RSM was employed to model adsorption behavior, while gradient boosting (GB), random forest (RF), and extreme gradient boosting (XGB) were used to enhance predictive performance. Hybrid models—linear, RMSE-based, multiplicative, and meta-learning—were developed and evaluated. The meta-learning HOP-RSM-GB model achieved near-perfect accuracy (R² = 1.00, RMSE = 10.59), outperforming all other models. Surface plots revealed that low pH and high pHpzc maximized the adsorption while increasing log Kow consistently enhanced PFAS adsorption. These findings establish hybrid RSM-ML modeling as a powerful framework for optimizing PFAS remediation strategies. The integration of statistical and machine learning approaches significantly improves predictive accuracy, reduces experimental costs, and provides deeper insights into adsorption mechanisms. This study underscores the importance of data-driven approaches in environmental engineering and highlights future opportunities for integrating ML-driven modeling with experimental adsorption research. | Harsh V. Patel; Jazmin Green; Hyo-Shin (John) Park; Stephanie Luster-Teasley Pass; Renzun Zhao | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dc50b381d2151a023019c7/original/quantifying-multidimensional-effects-of-physicochemical-parameters-on-pfas-adsorption-using-a-hybrid-response-surface-methodology-machine-learning-approach.pdf |
60c7436c702a9b165e18a5c4 | 10.26434/chemrxiv.9122009.v1 | Cofactor-Independent Pinacolase Directs Non-Diels-Alderase Biogenesis of the Brevianamides | <p>Fungal bicyclo[2.2.2]diazaoctane indole
alkaloids demonstrate intriguing structures
and a wide spectrum of biological activities. Although biomimetic total syntheses
have been completed for representative compounds of this structural family, the
details of their biogenesis have remained largely uncharacterized. Among them, Brevianamide A represents the most
basic form within this class bearing a dioxopiperazine core structure and a rare
3-<i>spiro</i>-<i>psi</i>-indoxyl skeleton. Here, we identified
the Brevianamide A biosynthetic gene cluster from <i>Penicillium brevicompacticum</i>
NRRL 864 and fully elucidated the metabolic pathway by targeted gene disruption, heterologous expression,
precursor incorporation studies, and <i>in
vitro</i> biochemical analysis. In particular, we determined that BvnE is a cofactor-independent
isomerase that is essential for selective production
of Brevianamide A. Based on a high resolution crystal structure of BvnE,
molecular modeling, mutational analysis, and computational studies provided new
mechanistic insights into the
diastereoselective formation of the 3-<i>spiro</i>-<i>psi</i>-indoxyl moiety in Brevianamide A.
This occurs through a biocatalyst controlled semi-Pinacol rearrangement and a
subsequent
spontaneous intramolecular [4+2] <i>hetero</i>-Diels-Alder
cycloaddition.</p> | Ying Ye; Lei Du; Xingwang Zhang; Sean A. Newmister; Wei Zhang; Shuai Mu; Atsushi Minami; Morgan McCauley; Juan V. Alegre-Requena; Amy E. Fraley; Maria L. Adrover-Castellano; Nolan Carney; Vikram V. Shende; Hideaki Oikawa; Hikaru Kato; Sachiko Tsukamoto; Robert S. Paton; Robert M. Williams; David H. Sherman; Shengying Li | Natural Products; Organic Synthesis and Reactions; Biochemistry; Chemical Biology; Microbiology; Computational Chemistry and Modeling; Biocatalysis; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436c702a9b165e18a5c4/original/cofactor-independent-pinacolase-directs-non-diels-alderase-biogenesis-of-the-brevianamides.pdf |
65096e01b927619fe76ab5a3 | 10.26434/chemrxiv-2023-sgbfb | Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations | Compounds containing halogens can form halogen bonds (XBs) with biological targets such as proteins and membranes due to their anisotropic electrostatic potential. To accurately describe this anisotropy, off-center point-charge (EP) models are commonly used in force field methods allowing the description of XBs at the molecular mechanics and molecular dynamics level. Various EP implementations have been documented in the literature and despite being efficient in reproducing protein-ligand geometries and sampling of XBs, it is unclear how well these EP models predict experimental properties such as hydration free energies (\dGhyd{}), which are often used to validate force field performance. In this work, we report the first assessment of three EP models using alchemical free energy calculations to predict \dGhyd{} values. We show that describing the halogen anisotropy using some EP models can lead to a slight improvement in the prediction of the \dGhyd{} when compared with the models without EP, especially for the chlorinated compounds, however, this improvement is not related to the establishment of XBs but is most likely due to the improvement of the sampling of hydrogen bonds (HBs). We also highlight the importance of the choice of the EP model, especially for the iodinated molecules since a slight tendency to improve the prediction is observed for compounds with a larger $\sigma$--hole but significantly worse results were obtained for compounds that are weaker XB donors. | Andreia Fortuna; Paulo J. Costa | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65096e01b927619fe76ab5a3/original/assessment-of-halogen-off-center-point-charge-models-using-explicit-solvent-simulations.pdf |
629d505b23bf1feefbb67acb | 10.26434/chemrxiv-2022-gqq4q-v2 | The microkinetics of ammonia synthesis: the effect of surface coverage on apparent activation energy and reaction order | We investigated the coverage effect on the experimental results using Ru and Ru+K for ammonia synthesis at 0.1 MPa and 380~460℃. Especially for Ru+K, the reaction order changed significantly with temperature, and the rate-limiting step was also affected by temperature. The apparent activation energy decreased as the gas flow rate decreased, even when the total pressure was the same. We showed through experimental techniques that even relatively small changes in experimental conditions on a laboratory scale can change the coverage and have a non-negligible effect on the reaction order and apparent activation energy. | Ryusei Morimoto; Takaya Ogawa; Keiichi Ishihara | Physical Chemistry; Chemical Kinetics | CC BY 4.0 | CHEMRXIV | 2022-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629d505b23bf1feefbb67acb/original/the-microkinetics-of-ammonia-synthesis-the-effect-of-surface-coverage-on-apparent-activation-energy-and-reaction-order.pdf |
611a78fae540bb2ce3795157 | 10.26434/chemrxiv-2021-tnngb | TD-DMRG coupled with n-mode representation potentials for the excited state radiationless decay rate: formalism and application to azulene
| We propose a method for calculating the nonradiative decay rates for polyatomic molecules including anharmonic effects of the potential energy surface (PES) in the Franck-Condon region. The method combines the n-mode representation method to construct the ab initio PES and the nearly exact time-dependent density matrix renormalization group method (TD-DMRG) to simulate quantum dynamics. In addition, in the framework of TD-DMRG, we further develop an algorithm to calculate the final-state-resolved rate coefficient which is very useful to analyze the contribution from each vibrational mode to the transition process. We use this method to study the internal conversion (IC) process of azulene after taking into account the anharmonicity of the ground state PES. The results show that even for this semi-rigid molecule the intramode anharmonicity enhances the IC rate significantly, and after considering the two-mode coupling effect, the rate increases even further. The reason is that the anharmonicity enables the C-H vibrations to receive electronic energy while C-H vibrations do not contribute on the harmonic PES as the Huang-Rhys factor is close to 0.
| Jiajun Ren; Yuanheng Wang; Weitang Li; Tong Jiang; Zhigang Shuai | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611a78fae540bb2ce3795157/original/td-dmrg-coupled-with-n-mode-representation-potentials-for-the-excited-state-radiationless-decay-rate-formalism-and-application-to-azulene.pdf |
60c747010f50dbb414396520 | 10.26434/chemrxiv.11472618.v1 | Discovery of an Unexpected Similarity in Ligand Binding Between BRD4 and PPARγ | Knowledge about interrelationships between different proteins is crucial in fundamental research for the elucidation of protein networks and pathways. Furthermore, it is especially critical in chemical biology to identify further key regulators of a disease and to take advantage of polypharmacology effects. A comprehensive scaffold-based analysis uncovered an unexpected relationship between bromodomain-containing protein 4 (BRD4) and peroxisome-proliferator activated receptor gamma (PPARγ). They are both important drug targets for cancer therapy and many more important diseases. Both proteins share binding site similarities near a common hydrophobic subpocket which should allow the design of a polypharmacology-based ligand targeting both proteins. Such a dual-BRD4-PPARγ-modulator could show synergistic effects with a higher efficacy or delayed resistance development in, for example, cancer therapy. Thereon, a complex structure of sulfasalazine was obtained that involves two bromodomains and could be a potential starting point for the design of a bivalent BRD4 inhibitor. | Lina Humbeck; Jette Pretzel; Saskia Spitzer; Oliver Koch | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747010f50dbb414396520/original/discovery-of-an-unexpected-similarity-in-ligand-binding-between-brd4-and-ppar.pdf |
61f3125e71868d6dc1c0e964 | 10.26434/chemrxiv-2022-sls20 | Trace Measurements of Ethylene Oxide using Cavity-enhanced Absorption Spectrometry near 3066 cm-1 | Ethylene oxide (EtO) is a key carcinogen that is widely used in chemical manufacturing and biotechnology industries. Recent work has suggested that permissible exposure limits for EtO be reduced from 1 – 5 ppm to sub-ppb levels. Such new standards will require new methodologies that are capable of measuring EtO with the requisite precision. In this paper, we demonstrate a new analyzer based on cavity-enhanced absorption spectrometry that utilizes a broad EtO absorption feature near 3066 cm-1. A fit function is developed that includes water, methane, and EtO absorbances and accounts for absorption both inside and outside the cavity. A methane standard is used to determine the cavity gain factor, and the EtO absorbance spectrum is empirically determined. The final system shows excellent linearity from 0 – 909 ppb EtO (R2 ~ 0.9999) with a measurement precision of better than ±1 ppb (1-sigma, 60 seconds) that improved to ±0.5 ppb (1-sigma, 15 minutes). Deliberate ambient EtO releases demonstrate the instrument’s utility in rapidly detecting hazardous conditions. Further work will include improving the measurement precision and directly comparing the system to EPA Method TO-15. | Manish Gupta; Andrew Chan; Michael Sullivan; Rupal Gupta | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f3125e71868d6dc1c0e964/original/trace-measurements-of-ethylene-oxide-using-cavity-enhanced-absorption-spectrometry-near-3066-cm-1.pdf |
64a64d5aba3e99daef99abd3 | 10.26434/chemrxiv-2023-fzk1h | Schlenk-type Equilibria of Grignard-analogous Arylberyllium Complexes: Steric Effects | The presence of complex Schlenk equilibria is a central property of synthetically invaluable Grignard reagents substantially affecting their reactivity and selectivity in chemical transformations. In this work, we systematically studied the steric effects of aryl substituents on the Schlenk-type equilibria of their lighter congeners, arylberyllium bromides. Combination of diarylberyllium complexes Ar2Be(OEt2) (1Ar, Ar = Tip, Tcpp; Tip = 2,4,6-iPr3C6H3, Tcpp = 2,4,6-Cyp3C6H3, Cyp = c-C5H9), containing sterically demanding aryl groups, and BeBr2(OEt2)2 (2) affords the Grignard-analogous arylberyllium bromides ArBeBr(OEt2) (3Ar, Ar = Tip, Tcpp). In contrast, Mes2Be(OEt2) (1Mes, Mes = 2,4,6-Me3C6H3) and 2 exist in a temperature-dependent equilibrium with MesBeBr(OEt2) (3Mes) and free OEt2. Ph2Be(OEt2) (1Ph) reacts with 2 to afford dimeric [PhBeBr(OEt2)]2 ([3Ph]2). Moreover, the influence of replacing the OEt2 donor by an N-heterocyclic carbene, IPr2Me2 (IPr2Me2 = C(iPrNCMe)2), on the redistribution reactions was investigated. The solution- and solid-state structures of the diarylberyllium and arylberyllium bromide complexes were comprehensively characterized using multinuclear (1H, 9Be, 13C) NMR spectroscopic methods and single-crystal X-ray diffraction, while DFT calculations were employed to support the experimental findings. | Christoph Helling; Cameron Jones | Inorganic Chemistry; Main Group Chemistry (Inorg.); Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a64d5aba3e99daef99abd3/original/schlenk-type-equilibria-of-grignard-analogous-arylberyllium-complexes-steric-effects.pdf |
60c744dfbdbb894e41a388e7 | 10.26434/chemrxiv.9919022.v1 | Highly Selective, Amine-Derived Cannabinoid Receptor 2 Probes | The endocannabinoid (eCB) system is implied in
various human diseases ranging from central nervous system to autoimmune
disorders. Cannabinoid receptor 2 (CB<sub>2</sub>R) is an integral component of
the eCB system. Yet, the downstream effects elicited by this G protein-coupled
receptor upon binding of endogenous or synthetic ligands are insufficiently
understood—likely due to the limited arsenal of reliable biological and
chemical tools. Herein,
we report the design and synthesis of CB<sub>2</sub>R-selective cannabinoids along with their <i>in vitro</i> pharmacological
characterization (binding and functional studies). They combine structural
features of HU-308 and AM841 to give chimeric ligands that emerge as potent CB<sub>2</sub>R agonists with high selectivity over the closely related cannabinoid
receptor 1 (CB<sub>1</sub>R). The synthesis work includes convenient preparation of
substituted resorcinols often found in cannabinoids. The utility of the
synthetic cannabinoids in this study is showcased by preparation of the most
selective high-affinity fluorescent probe for CB<sub>2</sub>R to date. | Matthias V. Westphal; Roman C. Sarott; Elisabeth A. Zirwes; Anja Osterwald; Wolfgang Guba; Christoph Ullmer; Uwe Grether; Erick M. Carreira | Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744dfbdbb894e41a388e7/original/highly-selective-amine-derived-cannabinoid-receptor-2-probes.pdf |
62097cc07d068a05e91ebf88 | 10.26434/chemrxiv-2022-g2h9s | Iterative Synthesis of 1,3-Polyboronic Esters with High Stereocontrol: Applications to Bahamaolide A and Polyfunctionalised Hydrocarbons | Polyketide natural products often contain common repeat motifs, e.g., propionate, acetate and deoxypropionate, and so can be synthesized by using iterative processes. We report a highly efficient iterative strategy for the synthesis of polyacetates based on boronic ester homologation that does not require functional group manipulation between iterations. This process involves sequential asymmetric diboration of a terminal alkene, forming a 1,2-bis(boronic ester), followed by regio- and stereoselective homologation of the primary boronic ester with a butenyl metallated carbenoid to generate a 1,3-bis(boronic ester). Each transformation independently controls stereochemical configuration, making the process highly versatile, and the sequence can be iterated prior to stereospecific oxidation of the 1,3-poly(boronic ester) to reveal the 1,3-polyol. The methodology was applied to a 14-step synthesis of the oxopolyene macrolide bahamaolide A, and the versatility of the 1,3-polyboronic esters was demonstrated in various stereospecific transformations, leading to poly-alkenes, -alkynes, -ketones, and -aromatics with full stereocontrol. | Sheenagh Aiken; Joe Bateman; Hsuan-Hung Liao; Alex Fawcett; Teerawut Bootwicha; Paolo Vincetti; Eddie Myers; Adam Noble; Varinder Aggarwal | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62097cc07d068a05e91ebf88/original/iterative-synthesis-of-1-3-polyboronic-esters-with-high-stereocontrol-applications-to-bahamaolide-a-and-polyfunctionalised-hydrocarbons.pdf |
63569fc0ca86b8001cc14b67 | 10.26434/chemrxiv-2022-rk82h-v2 | MemCross: Accelerated Weight Histogram method to assess membrane permeability | Passive permeation events across biological membranes are determining steps in the pharmacokinetics of xenobiotics. To reach an accurate and rapid prediction of membrane permeation coefficients of drugs is a complex challenge, which can efficiently support drug discovery. Such predictions are indeed highly valuable as they may guide the selection of potential leads with optimum bioavailabilities prior to synthesis. Theoretical models exist to predict these coefficients. Many of them are based on molecular dynamics (MD) simulations, which allow calculation of permeation coefficients through the evaluation of both the potential of mean force (PMF) and the diffusivity profiles. However, these simulations still require intensive computational efforts, and novel methodologies should be developed and benchmarked. Free energy perturbation (FEP) method was recently shown to estimate PMF with a significantly reduced computational cost compared to the adaptive biasing force method. This benchmarking was achieved with small molecules, namely short-chain alcohols. Here, we show that to estimate the PMF of bulkier, drug-like xenobiotics, conformational sampling is a critical issue. To reach a sufficient sampling with FEP calculations requires a relatively long time-scale, which can lower the benefits related to the computational gain. In the present work, the Accelerated Weight Histogram (AWH) method was employed for the first time in all-atom membrane models. The AWH-based protocol, named MemCross, appears affordable to estimate PMF profiles of a series of drug-like xenobiotics, compared to other enhanced sampling methods. The continuous exploration of the crossing pathway by MemCross also allows modelling subdiffusion by computing fractional diffusivity profiles. The method is also versatile as its input parameters are largely insensitive to the molecule properties. It also ensures a detailed description of the molecule orientations along the permeation pathway, picturing all intermolecular interactions at an atomic resolution. Here, MemCross was applied on a series of 12 xenobiotics, including four weak acids, and a coherent structure-activity relationship was established. | Mehdi Benmameri; Benjamin Chantemargue; Antoine Humeau; Patrick Trouillas; Gabin Fabre | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63569fc0ca86b8001cc14b67/original/mem-cross-accelerated-weight-histogram-method-to-assess-membrane-permeability.pdf |
61c4aa2df52bc4d26acaf9aa | 10.26434/chemrxiv-2021-l9gq4 | Optimization of N-piperidinyl-benzimidazolone derivatives as potent and selective inhibitors of 8-Oxo Guanine DNA Glycosylase 1 | 8-oxo Guanine DNA Glycosylase 1 is the initiating enzyme within base excision repair and removes oxidized guanines from damaged DNA. Since unrepaired 8-oxoG could lead to G:C→T:A transversion, base removal is of the utmost importance for cells to ensure genomic integrity. For cells with elevat-ed levels of reactive oxygen species this dependency is further increased. In the past we and others have validated OGG1 as a target for inhibitors to treat cancer and inflammation. Here, we present the optimization campaign that led to the broadly used tool compound TH5487. Based on a high-throughput screen, we performed hit to lead expansion and arrived at potent and selective substituted N-piperidinyl-benzimidazolones. Using X-ray crystallography data, we describe the surprising bind-ing mode of the most potent member of the class, TH8535. Here, the N-Piperidinyl-linker adopts a chair instead of a boat conformation which was found for weaker analogues. We further demonstrate cellular target engagement and efficacy of TH8535 against a number of cancer cell lines. | Olov Wallner; Armando Cázares-Körner; Emma Rose Scaletti; Geoffrey Masuyer; Tove Bekkhus; Torkild Visnes; Kirill Mamonov; Florian Ortis; Thomas Lundbäck; Maria Volkova; Tobias Koolmeister; Elisée Wiita; Olga Loseva; Monica Pandey; Evert Homan; Carlos Benítez-Buelga; Jonathan Davies; Martin Scobie; Ulrika Warpman Berglund; Christina Kalderén; Pål Stenmark; Thomas Helleday; Maurice Michel | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c4aa2df52bc4d26acaf9aa/original/optimization-of-n-piperidinyl-benzimidazolone-derivatives-as-potent-and-selective-inhibitors-of-8-oxo-guanine-dna-glycosylase-1.pdf |
631e3e801856841fc5125346 | 10.26434/chemrxiv-2022-57cht | Transition metal dissolution mechanisms and impacts on electronic conductivity in composite LiNi0.5Mn1.5O4 cathode films | The high-voltage LiNi0.5Mn1.5O4 (LNMO) spinel cathode material offers high energy density storage capabilities without the use of costly Co that is prevalent in other Li ion battery chemistries (e.g., LiNixMnyCozO2 (NMC)). Unfortunately, LNMO-containing batteries suffer from poor cycling performance due the intrinsically coupled processes of electrolyte oxidation and transition metal dissolution that occurs at high voltage. In this work, we use operando electron paramagnetic resonance (EPR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy to demonstrate that transition metal dissolution in LNMO is tightly coupled to HF formation (and thus, electrolyte oxidation reactions as detected with operando and in situ solution NMR), indicative of an acid-driven disproportionation reaction that occurs during delithiation (i.e., battery charging). X-ray photoelectron emission microscopy (XPEEM) provided surface sensitive and localized X-ray absorption spectroscopy (XAS) measurements that indicate that disproportionation is enabled by surface reconstruction that occurs upon charging that leads to surface Mn3+ sites on the LNMO particle surface that can disproportionate into Mn2+(dissolved) and Mn4+(s). During discharge of the battery, we observe high quantities of metal fluorides (particularly rich in MnF2) deposit in the CEI layer on the LNMO particles as well as the conductive carbon additives on the composite surface. Electronic conductivity measurements indicate that the MnF2 decreases film conductivity by 3-fold compared to LiF, suggesting that this CEI may impede both the ionic and electronic properties of the cathode. Our data indicate that in order to prevent transition metal dissolution and the associated side reactions in spinel-type cathodes (particularly those that operate at high voltage like LNMO), the use of electrolytes that offer improved anodic stability and prevent acid byproducts will be necessary. | Julia Hestenes; Jerzy Sadowski; Richard May; Lauren Marbella | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631e3e801856841fc5125346/original/transition-metal-dissolution-mechanisms-and-impacts-on-electronic-conductivity-in-composite-li-ni0-5mn1-5o4-cathode-films.pdf |
610bb047d800add5fe400b77 | 10.26434/chemrxiv-2021-w3j0f | Luminol Anchors Improve the Electrochemical-Tyrosine-Click Labelling of Proteins | New methodologies for the chemo-selective modifications of peptides and native proteins are of great importance in chemical biology and for the developm ent of therapeutic conjugates. Less abundant and uncharged amino-acid residues are interesting targets to form less heterogeneous conjugates and preserve biological functions. Phenylurazole (PhUr), N-methylphenylurazole (NMePhUr) and N-methylluminol (NMeLum) derivatives were described as tyrosine (Y) anchors after chemical or enzymatic oxydations. Recently, we developed the first electrochemical Y-bioconjugation method coined eY-click to activate PhUr in biocompatible media. In this work, we assessed the limitations, benefits and relative efficiencies of eY-click conjugations performed with a set of PhUr, NMePhUr and NMeLum derivatives. Results evidenced a high efficiency of NMeLum that showed a complete Y-chemoselectivity on polypeptides and biologically relevant proteins after soft electrochemical activation. Side reactions on nucleophilic or heteroaromatic amino-acids such as lysine or tryptophan were never observed during mass spectrometry analysis. Myoglobine, bovine serum albumin, a plant mannosidase, glucose oxidase and the therapeutically relevant antibody trastuzumab were efficiently labelled with a fluorescent probe in a two-step approach combining eY-click and strain-promoted azide-alkyne cyclization (SPAAC). The proteins conserved their structural integrity as observed by circular dichroism and the trastuzumab conjugate showed a similar binding affinity for the natural HER2 ligand as shown by bio-layer interferometry. Compared to our previously described protocol with PhUr, eY-click with NMeLum species showed faster reaction kinetics, higher (complete) Y-chemoselectivity and reactivity, and offer the interesting possibility for the double tagging of solvent-exposed Y. | Sébastien Depienne; Dimitri Alvarez-Dorta; Mikael Croyal; Ranil Temgoua; Cathy Charlier; david deniaud; Mohammed Boujtita; sebastien gouin | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2021-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610bb047d800add5fe400b77/original/luminol-anchors-improve-the-electrochemical-tyrosine-click-labelling-of-proteins.pdf |
60c7498a469df44acdf43bf1 | 10.26434/chemrxiv.12078138.v1 | Synthesis and Spectral Properties of 6'-Triazolyl-Dihydroxanthene-Hemicyanine Fused Near-Infrared Dyes | We describe the synthesis of a range of 6’-triazolyl-dihydroxanthene-hemicyanine (DHX-hemicyanine) fused dyes through an effective copper-catalyzed azide-alkyne cycloaddition (CuAAC) "click" reaction, with the dual aim of providing molecular diversity and fine tuning spectral properties of these near-infrared (NIR)-active materials. This was implemented by reacting 16 different aliphatic and aromatic azides with a terminal alkynyl-based-DHX-hemicyanine hybrid scaffold prepared in four steps and 35% overall yield from 4-bromosalicylaldehyde. The resulting triazole derivatives have been fully characterized and their optical properties determined both in organic solvents and simulated physiological conditions (phosphate buffered saline containing 5% of bovine serum albumin protein). This systematic study is a first important step towards the development of NIR-I fluorogenic "click-on" dyes or related photoactive agents for light-based diagnostic and/or therapeutic applications. | Gu Lingyue; Kévin RENAULT; Anthony ROMIEU; Jean-Alexandre RICHARD; Rajavel Srinivasan | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7498a469df44acdf43bf1/original/synthesis-and-spectral-properties-of-6-triazolyl-dihydroxanthene-hemicyanine-fused-near-infrared-dyes.pdf |
63cbf3021fe142256354800a | 10.26434/chemrxiv-2023-zj3tv | Comparative Analyses of Data Driven Machine Learning Models for TADF Emitters | Thermally activated delayed fluorescence (TADF) chromophores have attracted significant attention because they can harvest singlets and triplets in organic light-emitting diodes (OLEDs), resulting in high external quantum efficiency (EQE). This work aims to use a data-driven machine-learning model to predict the relationship between EQE and essential features of TADF-based OLEDs. The study uses a set of experimental data and applies various machine-learning models to analyze the relationship between EQE and the features of the device. The Random Forest model is found to have the highest accuracy for predicting EQE for non-doped TADF emitters. The importance of feature selection and its correlation with EQE is also analyzed, providing insight into how to select the best machine-learning model for rapid material screening and device optimization for non-doped TADF materials. | Kalishankar Bhattacharyya | Physical Chemistry; Energy; Energy Storage; Photovoltaics; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cbf3021fe142256354800a/original/comparative-analyses-of-data-driven-machine-learning-models-for-tadf-emitters.pdf |
60c745c6469df44a20f43571 | 10.26434/chemrxiv.10099058.v1 | Sterically Controlled C‒H Olefination of Heteroarenes | We report a sterically controlled C–H olefination using heteroarenes as the limiting reagent. The method enables the highly C5-selective olefination of a wide range of heteroarenes and is shown to be useful in the context of late-stage functionalization.<br /> | Hao Chen; Mirxan Farizyan; Francesca Ghiringhelli; Manuel van Gemmeren | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c6469df44a20f43571/original/sterically-controlled-c-h-olefination-of-heteroarenes.pdf |
623c9a988ab373d5f8703b6f | 10.26434/chemrxiv-2022-h70dk | Benchmarking the dynamic luminescent properties and UV
stability of B18H22-based materials | The dynamic photoluminescent properties, and potential quenching mechanisms, of anti-B18H22, 4,4’-Br2-anti-B18H20, and 4,4’-I2-anti-B18H20 are investigated in solution and polymer films. UV stability studies of the neat powders show no decomposition occurring after intense 7 day light soaking. In contrast, clusters incorporated into polymer films are found to degrade into smaller borane fragments under the same irradiation conditions. To highlight the utility of these compounds, we leverage their favorable optical properties in a prototype UV imaging setup. | Kierstyn Anderson; Ash Hua; John Plumley; Austin Ready; Arnold Rheingold; Thomas Peng; Peter Djurovic; Christopher Kerestes; Neil Snyder; Andrew Andrews; Justin Caram; Alexander Spokoyny | Inorganic Chemistry; Main Group Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623c9a988ab373d5f8703b6f/original/benchmarking-the-dynamic-luminescent-properties-and-uv-stability-of-b18h22-based-materials.pdf |
60c74643702a9b9aec18ab7b | 10.26434/chemrxiv.11288573.v1 | DFT Study of Unstrained Ketone C-C Bond Activation via Rhodium(I)-Catalyzed Suzuki-Miyaura Cross-Coupling Reactions | Unstrained cyclic ketones can participate in cooperative Suzuki-Miyaura cross-coupling type reaction using rhodium(I)-based catalyst via C-C bond activation. The regioselectivity indicates a trend where the most substituted side is activated and it is controlled by the beta-substituents. In this work, Density Functional Theory (DFT) calculations have been carried out to disclose the underlying mechanism in the reaction of a ketone series and arylboronate using ylidene as ancillary ligand and pyridine as co-catalysts. The computed energies suggest the reductive elimination step with the highest energy while the reductive elimination has the highest energy barrier. By the means of the Activation Strain Model (ASM) of chemical reactivity, it is found that the ketone strain energy released on the oxidative addition does not control the relativity of the OA reactivity, but indeed is the interaction energy between Rh(I) and C-C bond the ruling effect. The effect of the beta-substituents on regioselectivity has been additionally studied. | Dengmengfei Xiao; Lili Zhao; Diego Andrada | Bond Activation; Catalysis; Coordination Chemistry (Organomet.); Theory - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74643702a9b9aec18ab7b/original/dft-study-of-unstrained-ketone-c-c-bond-activation-via-rhodium-i-catalyzed-suzuki-miyaura-cross-coupling-reactions.pdf |
60c74f389abda29c2bf8d7fe | 10.26434/chemrxiv.12416042.v3 | Simultaneous Suppression of pi- and sigma- Transmission in pi-Conjugated Molecules | <div><div><div><p>Molecular dielectric materials require ostensibly conflicting requirements of high polarizability and low conductivity. As previous efforts towards molecular insulators focused on saturated molecules, it remains an open question whether pi- and sigma-transport can be simultaneously suppressed in conjugated systems. Here, we demonstrate that there are conjugated molecules where the sigma-transmission is suppressed by destructive sigma-interference, while the pi-transmission can be suppressed by a localized disruption of conjugation. Using density functional theory, we study the Landauer transmission and ballistic current density, which allow us to determine how the transmission is affected by various structural changes in the molecule. We find that in para-linked oligophenyl rings the sigma-transmission can be suppressed by changing the remaining hydrogens to methyl groups due to the inherent gauche-like structure of the carbon backbone within a benzene ring, similar to what was previously seen in saturated systems. At the same time, the methyl groups fulfil a dual purpose as they modulate the twist angle between neighboring phenyl rings. When neighboring rings are orthogonal to each other, the transmission through both pi- and sigma-systems is effectively suppressed. Alternatively, breaking conjugation in a single phenyl ring by saturating two carbons atoms with two methyl substituents on each carbon, results in suppressed pi- and sigma-transport independent of dihedral angle. These two strategies demonstrate that methyl-substituted oligophenyls are promising candidates for the development of molecular dielectric materials.</p></div></div></div> | Marc Hamilton Garner; Gemma C. Solomon | Nanodevices; Computational Chemistry and Modeling; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f389abda29c2bf8d7fe/original/simultaneous-suppression-of-pi-and-sigma-transmission-in-pi-conjugated-molecules.pdf |
61f424a5e59d87d6734cc716 | 10.26434/chemrxiv-2022-hw0sn | Exploring aspartic protease inhibitor binding to design selective antimalarials | Selectivity is a major issue in the development of drugs targeting pathogen aspartic proteases. Here we explore the selectivity determining factors by studying specifically designed malaria aspartic protease (plasmepsin) open-flap inhibitors. Metadynamics simulations are used to uncover the complex binding/unbinding pathways of these inhibitors, and describe the critical transition states in atomistic resolution. The simulation results are compared to experimentally determined enzymatic activities. Our findings demonstrate that plasmepsin inhibitor selectivity can be achieved by targeting the flap loop with hydrophobic substituents that enable ligand binding under the flap loop, as such behaviour is not observed for several other aspartic proteases. The ability to estimate compound selectivity before they are synthesized is of great importance in drug design, therefore, we expect that our approach will be useful in selective inhibitor design not only against aspartic proteases, but other enzyme classes as well. | Raitis Bobrovs; Emils Basens; Laura Drunka; Iveta Kanepe; Sofija Matisone; Karlis Velins; Victor Andrianov; Gundars Leitis; Diana Zelencova-Gopejenko; Dace Rasina; Aigars Jirgensons; Kristaps Jaudzems | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f424a5e59d87d6734cc716/original/exploring-aspartic-protease-inhibitor-binding-to-design-selective-antimalarials.pdf |
66b203d5c9c6a5c07a2615cf | 10.26434/chemrxiv-2024-6l7w3 | Embedded machine-readable molecular representation
for more resource-efficient deep learning applications | The practical implementation of Deep Learning methods for chemistry applications relies on encoding chemical structures into machine-readable formats that can be efficiently processed by computational tools. To this end, One Hot Encoding (OHE) is an established representation of alphanumeric categorical data into expanded numerical matrices. We have developed an embedded alternative to OHE that encodes discrete alphanumeric tokens of an N-sized alphabet into a few real numbers that constitute a simpler matrix representation of chemical structures. The implementation of this embedded One Hot Encoding (eOHE) in training machine learning models achieves comparable results to OHE in model accuracy and robustness, while significantly reducing the use of computational resources. Our benchmarks across three molecular representations (SMILES, DeepSMILES, and SELFIES) and three different molecular databases (ZINC, QM9, and GDB-13) for Variational Autoencoders (VAE) and Recurrent Neural Networks (RNN) show that using eOHE reduces RAM memory usage by up to 50%, while increasing disk Memory Reduction Efficiency (MRE) to 80% average. This encoding method opens new avenues for data representation into embedded formats that promote energy efficiency, and scalable computing in resource-constrained devices, or in scenarios with limited computing resources. The application of eOHE impacts not only the chemistry field, but other disciplines that rely on the use of OHE. | Emilio Nuñez-Andrade; Isaac Vidal-Daza; James Ryan; Rafael Gomez-Bombarelli; Francisco J. Martin-Martinez | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b203d5c9c6a5c07a2615cf/original/embedded-machine-readable-molecular-representation-for-more-resource-efficient-deep-learning-applications.pdf |
632b4b4d114b7e8f75182f97 | 10.26434/chemrxiv-2022-1xxjh-v2 | A dual-metal catalyzed sequential cascade reaction in an engineered protein cage | In this study, we describe the creation of an artificial protein cage housing a dual metal-tagged guest protein that catalyzes a linear, two-step sequential cascade reaction. The guest protein consists of a fusion protein of HaloTag and monomeric rhizavidin. Inside the protein capsid, we establish a ruthenium-catalyzed alloc-deprotection followed by a gold-catalyzed ring-closing hydroamination reaction that leads to indoles and phenanthridines with an overall yield of up to 67% in aqueous solutions. Furthermore, we show that the encapsulation stabilizes the metal catalysts against deactivation by air, proteins and cell lysate. | Paul Ebensperger; Mariia Zmyslia; Philipp Lohner; Judith Braunreuther; Benedikt Deuringer; Anita Becherer; Regine Suess; Anna Fischer; Claudia Jessen-Trefzer | Biological and Medicinal Chemistry; Catalysis; Nanoscience | CC BY NC 4.0 | CHEMRXIV | 2022-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632b4b4d114b7e8f75182f97/original/a-dual-metal-catalyzed-sequential-cascade-reaction-in-an-engineered-protein-cage.pdf |
65f4f42866c138172915b1ef | 10.26434/chemrxiv-2024-9mbrm | The Big Problem in Surface Catalysis Modelling | The existence of native point defects in crystalline solids are inevitable during synthesis. Such native defects will usually strongly impact the device performance of materials in catalysis applications. In recent years, the ability of first-principles approaches to accurately predict defect behavior has seen major progress. The underlying issue, as one would have guessed, is that these predictions of defect behavior and catalytic efficiency are extremely sensitive to the atomic structure of defect. Therefore, the proper identification of possible defect sites, their ground-state and metastable structures, and the correction scheme is crucial to resolving our understanding and control of defects’ role on catalytic performance. In this Comment, we aim to highlight recent advances of first-principles prediction for defect behavior while proposing a protocol for rigorous computational modelling. | Chen-Chen Er; Yee Wen Teh; Xin Ying Kong; Soungmin Bae; Yu Kumagai; Siang-Piao Chai; Yee Sin Ang | Theoretical and Computational Chemistry; Materials Science; Catalysis; Catalysts; Theory - Computational; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f4f42866c138172915b1ef/original/the-big-problem-in-surface-catalysis-modelling.pdf |
60c747b1567dfe1ae2ec488f | 10.26434/chemrxiv.11770092.v1 | Stereoselective Access to Highly Substituted Vinyl Ethers via Trans-Difunctionalization of Alkynes with Alcohols and Iodine(III) Electrophile | A method for the regio- and stereoselective synthesis of highly substituted vinyl ethers via trans-1,2-difunctionalization of alkynes with a cyclic λ<sup>3</sup>-iodane electrophile (benziodoxole triflate) and alcohols is reported. The reaction tolerates a variety of internal and terminal alkynes as well as various alcohols, affording β-λ<sup>3</sup>-iodanyl vinyl ethers in good yields with high regio- and stereoselectivities. The benziodoxole moiety of the products can be used as a versatile linchpin for the synthesis of structurally diverse vinyl ethers that are difficult to access by other means. | Wei Ding; Jinkui Chai; Junliang Wu; Naohiko Yoshikai | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747b1567dfe1ae2ec488f/original/stereoselective-access-to-highly-substituted-vinyl-ethers-via-trans-difunctionalization-of-alkynes-with-alcohols-and-iodine-iii-electrophile.pdf |
616d233735b406858f17b4ea | 10.26434/chemrxiv-2021-zslwl-v2 | Delivering anion transporters to lipid bilayers in water | CYCLODEXTRINS HAVE BEEN EMPLOYED AS DELIVERY AGENTS FOR LIPOPHILIC ANION TRANSPORTERS, WHICH ALLOW THEIR INCORPORATION INTO LIPID BILAYERS WITHOUT USING AN ORGANIC SOLVENT OR PRE-INCORPORATION. | Daniel A. McNaughton; Tsz Ying (Teresa) To; Bryson A. Hawkins; David E. Hibbs; Philip Alan Gale | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616d233735b406858f17b4ea/original/delivering-anion-transporters-to-lipid-bilayers-in-water.pdf |
677ef1f7fa469535b939e014 | 10.26434/chemrxiv-2025-7k7x3 | Which modern AI methods provide accurate predictions of toxicological endpoints? Analysis of Tox24 challenge results.
| The Tox24 challenge was designed to evaluate the progress that has been made in computational method development for the prediction of in vitro activity since the Tox21 challenge. In this challenge, participants were tasked with developing models to predict chemical binding to transthyretin (TTR), a serum binding protein, based on chemical structure. The analyzed dataset included chemicals that were screened in a competitive binding assay designed to measure the reduction in fluorescence due to displacement of 8-anilino-1-naphthalenesulfonic acid ammonium salt (ANSA) from TTR. The data were randomly split into a training set of 1012 compounds, a leaderboard set of 200, and a blind set of 300. This article provides an overview of the Tox24 Challenge and some of the models developed by the participating teams. Some of the approaches taken by winning teams included use of mixtures, enumerating tautomers, data cleaning. Many of the teams used consensus models. Overall, there has been significant progress in the development of machine learning tools since the Tox21 Challenge. | Stephanie A. Eytcheson; Igor V. Tetko | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677ef1f7fa469535b939e014/original/which-modern-ai-methods-provide-accurate-predictions-of-toxicological-endpoints-analysis-of-tox24-challenge-results.pdf |
67379f26f9980725cf4e2266 | 10.26434/chemrxiv-2024-jsrc2 | A Metastable State Facilitates Low Temperature CO Oxidation over Pt Nanoparticles | The dynamic response of heterogeneous catalytic materials to their environment opens a wide variety of possible surface states which may have increased catalytic activity. In this work, we find that it is possible to facilitate the oxidation of CO over metallic 2nm Pt nanoparticles at room temperature after performing a thermal treatment of a CO*-covered Pt catalyst. By combining pressure pulse experiments with in situ spectroscopy, we find that thermal treatment in the presence of adsorbed CO* is necessary to access this metastable state and that the state collapses after elevated thermal treatment or by further readsorption of CO at room temperature. The exact nature of this surface change remains open to speculation, but it is hypothesised that this metastable high-activity state is formed after desorption of weakly bound CO* molecules from well-coordinated Pt sites. | Samantha Le; Christopher R O'Connor; Taek-Seung Kim; Christian Reece | Materials Science; Catalysis; Nanoscience; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67379f26f9980725cf4e2266/original/a-metastable-state-facilitates-low-temperature-co-oxidation-over-pt-nanoparticles.pdf |
6319172c185684dd170df8b8 | 10.26434/chemrxiv-2022-8w268 | The molecular effect of wearing silver-threaded clothing on the human skin | With growing awareness that what we put in and on our bodies affects our health and wellbeing, little is still known about the impact of textiles on the human skin. Athletic wear often uses silver threading to improve hygiene, but little is known about its effect on the body’s largest organ. In this study we investigated the impact of such clothing on the skin’s chemistry and microbiome. Samples were collected from different body sites of a dozen volunteers over the course of twelve weeks. The changes induced by the antibacterial clothing were specific for individuals, but more so defined by gender and body site. Unexpectedly, the microbial biomass on skin increased in the majority of the volunteers when wearing silver threaded t-shirts. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. Both effects were mainly observed for women. The hallmark of the induced changes was an increase in the abundance of various monounsaturated fatty acids (MUFAs), especially in the upper back. Several microbes-to-metabolites associations were uncovered including Cutibacterium, detected in the upper back area, that was correlated with the distribution of MUFAs; and Anaerococcus spp. found in the underarms, which were associated with a series of different bile acids. Overall these findings point to a notable impact of the silver threaded material on the skin microbiome and chemistry. We observed that relatively subtle changes in the microbiome result in pronounced shifts in molecular composition. | Alexey Melnik; Chris Callewaert; Kathleen Dorrestein; Rosie Broadhead; Jeremiah J. Minich; Madeleine Ernst; Greg Humphrey; Gail Ackermann; Rob Gathercole; Alexander A. Aksenov; Rob Knight; Pieter C. Dorrestein | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Biochemistry; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6319172c185684dd170df8b8/original/the-molecular-effect-of-wearing-silver-threaded-clothing-on-the-human-skin.pdf |
655728cc2c3c11ed71929939 | 10.26434/chemrxiv-2023-6d61w | OLIVES: A Go-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field | Coarse-grained molecular dynamics simulations enable the modeling of increasingly complex systems at millisecond timescales. The transferable coarse-grained force field Martini 3 has shown great promise in modeling a wide range of biochemical processes, yet folded proteins in Martini 3 are not stable without the application of external bias potentials like elastic networks or Go-like models. We herein develop an algorithm, called OLIVES, which identifies native contacts with hydrogen bond capabilities in coarse-grained proteins and use it to implement a novel Go-like model for Martini 3. We show that the protein structure instability originates, in part, from the lack of hydrogen bond energy in the coarse-grained force field representation. By using realistic hydrogen bond energies obtained from literature ab initio calculations, it is demonstrated that protein stability can be recovered by the reintroduction of a coarse-grained hydrogen bond network and that OLIVES removes the need for secondary structure restraints. OLIVES is validated against known protein complexes, and at the same time addresses the open question of whether there is a need for protein quaternary structure bias in Martini 3 simulations. It is shown that OLIVES can reduce the number of bias terms, hereby speeding up Martini 3 simulations of proteins by up to ≈ 30 % on GPU architecture compared to the established GoMARTINI Go-like model. | Kasper B. Pedersen; Luís Borges-Araújo; Amanda D. Stange; Paulo C. T. Souza; Siewert-Jan Marrink; Birgit Schiøtt | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655728cc2c3c11ed71929939/original/olives-a-go-like-model-for-stabilizing-protein-structure-via-hydrogen-bonding-native-contacts-in-the-martini-3-coarse-grained-force-field.pdf |
673b6c1b5a82cea2fa8c5ecc | 10.26434/chemrxiv-2024-d8ssv | Addressing Standardization and Semantics in an Electronic Lab Notebook for Multidisciplinary Use: LabIMotion | This work presents the LabIMotion extension for the Chemotion Electronic Lab Notebook (ELN), expanding its capabilities from organic chemistry to support interdisciplinary research and enabling the description of workflows. LabIMotion enhances documentation by introducing customizable components structured across three levels—Elements, Segments, and Datasets—enabling flexible, hierarchical organization and reuse of data. Through the integration of links to ontologies, the extension ensures precise, machine-readable data, promoting interoperability and adherence to FAIR principles. The extension features a user-friendly interface that allows users to generate new ELN content by the application of generic methods, ensuring that the platform can be quickly adapted to meet specific research needs. The LabIMotion Hub plays a crucial role in distributing and updating components, fostering standardization, and enabling collaborative development within scientific communities. These advancements significantly improve the ELN's adaptability, usability, and relevance across various research disciplines. | Chia-Lin Lin; Pei-Chi Huang; Christof Wöll; Patrick Theato; Christian Kübel; Nicole Jung; Stefan Bräse | Catalysis; Chemical Education; Electrocatalysis; Photocatalysis; Redox Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673b6c1b5a82cea2fa8c5ecc/original/addressing-standardization-and-semantics-in-an-electronic-lab-notebook-for-multidisciplinary-use-lab-i-motion.pdf |
60c740a3bb8c1add2a3d9e33 | 10.26434/chemrxiv.7791464.v1 | Development of Pyridine-Based Inhibitors for the Human Vaccinia-Related Kinases 1 and 2 | <div>
<p>Vaccinia-related kinases 1 and 2 (VRK1 and VRK2) are human
Ser/Thr protein kinases associated with increased cell division and
neurological disorders. Nevertheless, the cellular functions of these proteins
are not fully understood. Despite their therapeutic potential, there are no
inhibitors available for VRK1 or VRK2. We report here the discovery and
elaboration of an aminopyridine scaffold as a basis for VRK1 and VRK2
inhibitors. The most potent compounds displayed <i>K</i><sub>D</sub> values of 190 nM and 401 nM for VRK1 and VRK2,
respectively. Differences in compound binding mode and substituent preferences
between the two VRKs were identified by the series structure-activity
relationship combined with the crystallographic analysis of key compounds. We
expect that our results will serve as a starting point for the design of
specific and potent inhibitors against each of the two VRKs based on a pyridine
scaffold.</p>
</div> | Ricardo Serafim; Fernando de Souza Gama; Caio dos Reis; Stanley Vasconcelos; André Santiago; Jessica Takarada; Luiz Dutra; Fulvia Di Pillo; Hatylas Azevedo; Alessandra Mascarello; Jonathan Elkins; Katlin Massirer; Opher Gileadi; Cristiano Guimarães; Rafael Counago | Bioorganic Chemistry; Biochemistry; Biophysics | CC BY 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a3bb8c1add2a3d9e33/original/development-of-pyridine-based-inhibitors-for-the-human-vaccinia-related-kinases-1-and-2.pdf |
60c757b10f50db27cb3982f6 | 10.26434/chemrxiv.14447940.v1 | Highly Site-Selective Direct C−H Bond Functionalization of Unactivated Arenes with Propargyl α‑Aryl-α-diazoacetates via Scandium Catalysis | <p>Highly chemo- and regio-selective C–H bond functionalization of unactivated arenes with propargyl <i>α</i>-aryl-<i>α</i>-diazoacetates is developed using scandium catalysis. Variety of unactivated, mildly deactivated and electronically activated arenes are functionalized using this protocol. We have explored the novel combination of scandium triflate and propargyl <i>α</i>-aryl-<i>α</i>-diazoacetate as catalyst-reagent system for the effective C–H bond functionalization. The protocol avoids the use of expensive catalysts and practicality of the protocol has been demonstrated by the gram scale synthesis of very useful <i>α</i>-diarylacetates including antispasmodic drug-adephenine.</p> | Balu S. Navale; Debasish Laha; Subhrashis Banerjee; Kumar Vanka; Prof. Dr. Ramakrishna G. Bhat | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757b10f50db27cb3982f6/original/highly-site-selective-direct-c-h-bond-functionalization-of-unactivated-arenes-with-propargyl-aryl-diazoacetates-via-scandium-catalysis.pdf |
62491abd9f61cae04dff5daf | 10.26434/chemrxiv-2022-0zg7j | Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semi-empirical QM/MM Hamiltonian | Molecular dynamics (MD) simulations employing ab initio quantum mechanical and molecular mechanical (ai-QM/MM) potentials are considered to be the state of the art, but the high computational cost associated with the ai-QM calculations remains a theoretical challenge for their routine application. Here, we present a modified protocol of Multiple Time Step (MTS) method to accelerate ai-QM/MM MD simulations of condensed-phase reactions. Within a previous MTS protocol [Nam, J. Chem. Theory Comput., 2014, 10, 2175], reference forces are evaluated using a low-level (semi-empirical QM/MM) Hamiltonian and employed at inner time steps to propagate the nuclear motions. Correction forces, which arise from the force differences
between high-level (ai-QM/MM) and low-level Hamiltonians, are applied at outer time steps, where the MTS algorithm allows the time-reversible integration of the correction forces. To increase the outer step size, which is bound by the highest-frequency component in the correction forces, the semi-empirical QM Hamiltonian is re-calibrated in this work to minimize the magnitude of the correction forces. The remaining high frequency modes, which are mainly bond stretches involving hydrogen atoms, are then removed from the correction forces. When combined with Langevin or SIN(R) thermostat, the modified MTS-QM/MM scheme remains robust with an up to 8 fs (with Langevin) or 10 fs (with SIN(R)) outer time step (with 1 fs inner time steps) for the chorismate mutase system. This leads to an over 5-fold speedup over standard ai-QM/MM simulations, without sacrificing the accuracy in the predicted free energy profile of the reaction. | Xiaoliang Pan; Richard Van; Evgeny Epifanovsky; Jian Liu; Jingzhi Pu; Kwangho Nam; Yihan Shao | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62491abd9f61cae04dff5daf/original/accelerating-ab-initio-qm-mm-molecular-dynamics-simulations-with-multiple-time-step-integration-and-a-recalibrated-semi-empirical-qm-mm-hamiltonian.pdf |
65c577f1e9ebbb4db9f4432e | 10.26434/chemrxiv-2024-k6fhf | The Purported Synthesis of "Holey Graphyne" Fails Replication | A recent article by Ryu, Lee and coworkers claims synthesis of "holey graphyne," a strained sp2/sp1 carbon lattice featuring a repeating dibenzo-1,5-cyclooctadiene-3,7-diyne motif. Here, we describe the replication of the key experiments from this Article. We did not observe the formation of "holey graphyne" under the reported conditions. Furthermore, we show that the claimed copper-mediated sp2/sp1 cross-coupling chemistry fails even for undemanding model substrates. | Victor Desyatkin; Claire Bolding; Valentin Rodionov | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Homogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c577f1e9ebbb4db9f4432e/original/the-purported-synthesis-of-holey-graphyne-fails-replication.pdf |
60c73f5dbb8c1a50e03d9ac6 | 10.26434/chemrxiv.7355069.v1 | Mechanistic Study and Development of Catalytic Reactions of Sm(II) | Despite the broad utility and application of SmI<sub>2</sub>in synthesis, the reagent is used in stoichiometric amounts and has a high molecular weight, resulting in a large amount of material being used for reactions requiring one or more equivalents of electrons. We report mechanistic studies on catalytic reactions of Sm(II) employing a terminal magnesium reductant and trimethyl silyl chloride in concert with a non-coordinating proton donor source. Reactions using this approach permitted reductions with as little as 1 mol% Sm. The mechanistic approach enabled catalysis employing HMPA as a ligand, facilitating the development of catalytic Sm(II) 5-<i>exo</i>-<i>trig </i>ketyl olefin cyclization reactions. | Sandepan Maity; Robert Flowers | Physical Organic Chemistry; Catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5dbb8c1a50e03d9ac6/original/mechanistic-study-and-development-of-catalytic-reactions-of-sm-ii.pdf |
615aa7fa700ea65f3b77beb5 | 10.26434/chemrxiv-2021-c6lrq-v3 | Disruption of water networks is the cause of human/mouse species selectivity in urokinase plasminogen activator (uPA) inhibitors derived from hexamethylene amiloride (HMA) | The urokinase plasminogen activator (uPA) plays a critical role in tumor cell invasion and migration and is a promising anti-metastasis target. 6-Substituted analogs of 5-N,N-(hexamethylene)amiloride (HMA) are potent and selective uPA inhibitors that lack the diuretic and anti-kaliuretic properties of the parent drug amiloride. However, the compounds display pronounced selectivity for human over mouse uPA, thus confounding interpretation of data from human xenografted mouse models of cancer. Here, computational and experimental findings reveal that residue 99 is a key contributor to the observed species selectivity, whereby enthalpically unfavorable expulsion of a water molecule by the 5-N,N-hexamethylene ring occurs when residue 99 is Tyr (as in mouse uPA). Analog 7 lacking the 5-N,N-hexamethylene ring maintained similar water networks when bound to human and mouse uPA and displayed reduced selectivity, thus supporting this conclusion. The study will guide further optimization of dual-potent human/mouse uPA inhibitors from the amiloride class as anti-metastasis drugs. | Nehad El Salamouni; Benjamin Buckley; Longguang Jiang; Mingdong Huang; Marie Ranson; Michael Kelso; Haibo Yu | 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 | 2021-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615aa7fa700ea65f3b77beb5/original/disruption-of-water-networks-is-the-cause-of-human-mouse-species-selectivity-in-urokinase-plasminogen-activator-u-pa-inhibitors-derived-from-hexamethylene-amiloride-hma.pdf |
60c74bbf469df4f59cf43f7f | 10.26434/chemrxiv.12377690.v1 | Preferential Orientation of Photochromic Gadolinium Oxyhydrides | <p>We report preferential orientation control
in photochromic gadolinium oxyhydride (GdHO) thin films deposited by a two-step
process. Gadolinium hydride (GdH<sub>2-x</sub>) films were grown by reactive magnetron
sputtering, followed by oxidation in air. The preferential orientation, grain
size, anion concentrations, and photochromic response of the films are strongly
dependent on the deposition pressure. GdHO films show preferential orientation
along the [100] direction and exhibit photochromism when synthesized at
deposition pressures up to 5.8 Pa and. The photochromic contrast is larger than
20 % when the films are deposited below 2.8 Pa with 0.22 H<sub>2</sub>/Ar flow
ratio. We argue that the degree of preferential orientation defines the oxygen
concentration which is known to be a key parameter for photochromism in rare-earth
oxyhydride thin films. The experimental observations described above are
explained by the oxidation-induced decrease of the grain size as a result of
the increase of the deposition pressure of the sputtering gas. </p> | Elbruz Murat Baba; Jose Montero; Dmitrii Moldarev; Marcos V. Moro; Max Wolff; Daniel Primetzhofer; Sabrina Sartori; Esra Zayim; Smagul Zh. Karazhanov | Optical Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bbf469df4f59cf43f7f/original/preferential-orientation-of-photochromic-gadolinium-oxyhydrides.pdf |
6166e9398b620d14b44e0c13 | 10.26434/chemrxiv-2021-z5720 | Mechanochemical solid state synthesis of a bifunctional copper(I)/N-heterocyclic carbene complex and its catalytic activity in hydrogenative transformations | A sophisticated bifunctional catalyst bearing a copper(I)/N-heterocyclic carbene and a guanidine organocatalyst has been prepared by a mechanochemical synthesis in a ball mill. This approach circumvents commonly employed silver(I) complexes which are associated with significant and undesired waste formation. Due to the bifunctional nature of the desired complex, earlier mechanochemical conditions were not applicable and a new protocol based on cheap and readily available K3PO4 as base has been developed. The resulting complex has been shown to be active in a variety of reduction/hydrogenation transformations employing dihydrogen as terminal reducing agent. | Ina Remy-Speckmann; Birte Zimmermann; Mahadeb Gorai; Teichert Johannes; Martin Lerch | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6166e9398b620d14b44e0c13/original/mechanochemical-solid-state-synthesis-of-a-bifunctional-copper-i-n-heterocyclic-carbene-complex-and-its-catalytic-activity-in-hydrogenative-transformations.pdf |
6721b78c5a82cea2fa493f23 | 10.26434/chemrxiv-2024-4lqf9 | Unveiling JP-10 Fuel: A DFT and NMR Study of
Exo-TCD Chair and Boat Conformers
| The rational design of high-energy-density (HED) sustainable aviation fuels (SAFs) relies on understanding the electronic structures of fuel hydrocarbons. This study uses density functional theory (DFT) to investigate the exo-chair and exo-boat isomers of Jet Propellant 10 (JP-10). The exo-chair isomer is found to be more stable by 1.83 kcal/mol, with an energy barrier of 3.65 kcal/mol separating the two using the B3LYP/cc-pVTZ method. Despite small geometric differences, significant changes in the shape, dipole moments (0.0156 Debye for the exo-chair and 0.0426 Debye for the exo-boat) and NMR chemical shifts at the flag carbon (C5), the boat tip carbon (C10) and the hydrogens bonding with them. The B3PW91/cc-pVTZ method produces more accurate carbon NMR chemical shifts than the B3LYP/cc-pVTZ method, RMSD (C) =1.48 ppm and 3.21 ppm, respectively, whereas the reverse holds for the proton-NMR chemical shifts, RMSD (H) =0.33 ppm and 0.31 ppm, in agreement with early studies. The NMR trajectories during the chair and boat transition reveal the most significant changes at the transition state (TS). In addition, the carbon atoms engaging larger strain (eg junction carbons and the flag carbon) exhibit apparent deshielding. Excess orbital energy spectrum (EOES) analysis further identifies key inner valence orbital changes during isomerization, indicating the role of bonding interactions in stabilizing the exo-chair isomer. These findings offer valuable insights into the electronic structural factors that influence the stability of multicyclic hydrocarbons, aiding the future design of more efficient SAFs. | Feng Wang; Vladislav Vasilyev | Energy | CC BY 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6721b78c5a82cea2fa493f23/original/unveiling-jp-10-fuel-a-dft-and-nmr-study-of-exo-tcd-chair-and-boat-conformers.pdf |
60c74d5e567dfecd9bec5322 | 10.26434/chemrxiv.12582761.v2 | Using High-Throughput Virtual Screening to Explore the Optoelectronic Property Space of Organic Dyes; Finding Diketopyrrolopyrrole Dyes for Dye-Sensitized Watersplitting and Solar Cells | Organic dyes based on conjugated chromophores such as diketopyrrolopyrrole (DPP) have a large range of uses beyond providing colour to other materials, such as in dye-sensitized solar cells, dye-sensitized photoelectrochemical cells, dye-sensitized colloidal photocatalysts and organic photovoltaics. We perform a high-throughput virtual screening using the xTB family of density functional tight-binding methods to map the optoelectronic property space of ~45,000 DPP dyes. The large volume of data at our disposal allows us to probe the difference between symmetric and asymmetric dyes and to identify the apparent boundaries of the optoelectronic property space for these dyes, as well as which substituents give access to particular combinations of properties. Finally, we use our dataset to screen for DPP dyes that can drive the reduction of protons to molecular hydrogen when illuminated as part of dye-sensitized photoelectrochemical cells or dye-sensitized colloidal photocatalysts, or as dyes for TiO<sub>2-</sub>based dye-sensitized solar cells. | Isabelle Heath-Apostolopoulos; Diego Vargas-Ortiz; Liam Wilbraham; Kim Jelfs; Martijn Zwijnenburg | Photosensitizers; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Photocatalysis; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d5e567dfecd9bec5322/original/using-high-throughput-virtual-screening-to-explore-the-optoelectronic-property-space-of-organic-dyes-finding-diketopyrrolopyrrole-dyes-for-dye-sensitized-watersplitting-and-solar-cells.pdf |
60c75658bb8c1a8ad63dc5e4 | 10.26434/chemrxiv.14229875.v1 | On Stereocontrol in Organocatalytic α-Chlorinations of Aldehydes | A comprehensive analysis of the organocatalytic α‐chlorination of aldehydes with N‐chloroimides and differ‐
ent catalysts is presented. For this reaction, alternate mechanisms were proposed that differ in the role of resting state
intermediates and the rationalization of the observed enantioselectivity. This manuscript aims at resolving these funda‐
mental questions on the basis of rigorous structural characterization of intermediates (configuration and conformation),
NMR studies, ion mobility‐mass spectrometry, concentration profiles, isotope studies, and DFT calculations.
<br /> | Sebastian Ponath; Chetan Joshi; Amy T. Merrill; Volker Schmidts; Kim Greis; Maike Lettow; Manuela Weber; Simon Steinhauer; Kevin Pagel; Christina Thiele; Dean Tantillo; Mathew Vetticatt; Mathias Christmann | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75658bb8c1a8ad63dc5e4/original/on-stereocontrol-in-organocatalytic-chlorinations-of-aldehydes.pdf |
64a25f5eba3e99daef6dbd99 | 10.26434/chemrxiv-2023-xl49v-v3 | Why Deep Models Often Cannot Beat Non-deep Counterparts on Molecular Property Prediction? | Molecular property prediction (MPP) is a crucial task in the drug discovery pipeline, which has recently gained considerable attention thanks to advances in deep neural networks. However, recent research has revealed that deep models struggle to beat traditional non-deep ones on MPP. In this study, we benchmark 12 representative models (3 non-deep models and 9 deep models) on 14 molecule datasets. Through the most comprehensive study to date, we make the following key observations: \textbf{(\romannumeral 1)} Deep models are generally unable to outperform non-deep ones; \textbf{(\romannumeral 2)} The failure of deep models on MPP cannot be solely attributed to the small size of molecular datasets. What matters is the irregular molecule data pattern; \textbf{(\romannumeral 3)} In particular, tree models using molecular fingerprints as inputs tend to perform better than other competitors. Furthermore, we conduct extensive empirical investigations into the unique patterns of molecule data and inductive biases of various models underlying these phenomena. | Jun Xia; Lecheng Zhang; Xiao Zhu; Stan Z. Li | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a25f5eba3e99daef6dbd99/original/why-deep-models-often-cannot-beat-non-deep-counterparts-on-molecular-property-prediction.pdf |
60c744304c89190482ad2759 | 10.26434/chemrxiv.9755951.v1 | Toward Prediction of Nonradiative Decay Pathways in Organic Compounds II: Two Internal Conversion Channels in BODIPYs | <div>Boron-dipyrromethene (BODIPY) molecules are widely used as laser dyes and have therefore become a popular research topic within recent decades. Numerous studies have been reported for the rational design of BODIPY derivatives based on their spectroscopic and photophysical properties, including absorption and fluorescence wavelengths (<i>λ</i><sub>abs</sub> and <i>λ</i><sub>fl</sub>), oscillator strength (<i>f</i>), nonradiative pathways, and quantum yield (<i>ϕ</i>). In the present work, we illustrate a theoretical, semi-empirical model that accurately predicts <i>ϕ</i> for various BODIPY compounds based on inexpensive electronic structure calculations, following the data-driven algorithm proposed and tested on the naphthalene family by us [Kohn, Lin, and Van Voorhis, <i>J. Phys. Chem. C.</i> <b>2019</b>, <i>123</i>, 15394]. The model allows us to identify the dominant nonradiative channel of any BODIPY molecule using its structure exclusively and to establish a correlation between the activation energy (<i>E</i><sub>a</sub>) and the fluorescence quantum yield (<i>ϕ</i><sub>fl</sub>). Based on our calculations, either the S<sub>1</sub> → S<sub>0</sub> or <i>L<sub>a</sub></i> → <i>L<sub>b</sub></i> internal conversion (IC) mechanism dominates in the majority of BODIPY derivatives, depending on the structural and electronic properties of the substituents. In both cases, the nonradiative rate (<i>k</i><sub>nr</sub>) exhibits a straightforward Arrhenius-like relation with the associated <i>E</i><sub>a</sub>. More interestingly, the S<sub>1</sub> → S<sub>0</sub> mechanism proceeds via a highly distorted intermediate structure in which the core BODIPY plane and the substituent at the 1-position are forced to bend, while the internal rotation of the very same substituent induces the <i>La </i>→<i> Lb</i> transition. Our model reproduces <i>k</i><sub>fl</sub>, <i>k</i><sub>nr</sub>, and <i>ϕ</i><sub>fl</sub> to mean absolute errors (MAE) of 0.16 decades, 0.87 decades, and 0.26, when all outliers are considered. These results allow us to validate the predictive power of the proposed data-driven algorithm in <i>ϕ</i><sub>fl</sub>. They also indicate that the model has a great potential to facilitate and accelerate the machine learning aided design of BODIPY dyes for imaging and sensing applications, given sufficient experimental data and appropriate molecular descriptors.</div> | Zhou Lin; Alexander Kohn; Troy Van Voorhis | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744304c89190482ad2759/original/toward-prediction-of-nonradiative-decay-pathways-in-organic-compounds-ii-two-internal-conversion-channels-in-bodip-ys.pdf |
668c3885c9c6a5c07aaca81e | 10.26434/chemrxiv-2023-1hxxc-v2 | Interpreting Graph Neural Networks with Myerson Values for Cheminformatics Approaches | Graph neural networks (GNNs) are a natural choice to represent chemical data, due to their inherent ability to handle arbitrary input topologies. They avoid the need to convert molecules into molecular fingerprints with a fixed vector length. However, like most deep learning models, GNNs are not interpretable and common explainability methods fail because of the variable input size. We introduce a novel method to interpret the predictions of GNNs based on Myerson values from cooperative game theory. Myerson values are closely related to Shapley values , which have been adapted to explain a wide variety of machine learning model predictions. Applying these approaches to GNNs have, however, proven to be challenging because of their varying graph size. Our approach treats a GNN as a coalition game and the nodes of an input layer graph as players. The Myerson value of a node then determines the contribution to the prediction of the model, with only connected nodes contributing to coalitions. All Myerson values add up to the predicted value of the model allowing for a simple and intuitive interpretation of the prediction. Because calculating Myerson values becomes computationally infeasible for large graphs, we have also implemented a scalable approximation technique using Monte Carlo sampling. We developed the technique for applications in cheminformatics and drug discovery, but it can also be used in any application that uses GNNs. The effectiveness of our approach is validated through successful applications to two proof-of-concept datasets (logP and molecular weight) as well as a real-world dataset featuring kinase inhibitors, highlighting its broad applicability and promise in explaining graph-based cheminformatic models. | Samuel K. R. Homberg; Malte L. Modlich; Janosch Menke; Garrett M. Morris; Benjamin Risse; Oliver Koch | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668c3885c9c6a5c07aaca81e/original/interpreting-graph-neural-networks-with-myerson-values-for-cheminformatics-approaches.pdf |
6560c5e629a13c4d47e66013 | 10.26434/chemrxiv-2023-l44cm | Reproducible MS/MS library cleaning pipeline in matchms | Mass spectral libraries have proven to be essential for mass spectrum annotation, both for library matching and training new machine learning algorithms. A key step in training machine learning models is having high-quality training data. Public libraries of mass spectrometry data that are open to user submission often suffer from limited metadata curation and harmonization. The resulting variability in data quality makes training of machine learning models challenging. Here we present a library cleaning pipeline designed for cleaning tandem mass spectrometry library data. The pipeline is designed with ease of use, flexibility and reproducibility as leading principles. | Niek F. de Jonge; Helge Hecht; Justin J. J. van der Hooft; Florian Huber | Theoretical and Computational Chemistry; Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6560c5e629a13c4d47e66013/original/reproducible-ms-ms-library-cleaning-pipeline-in-matchms.pdf |
640765c46642bf8c8f20eca2 | 10.26434/chemrxiv-2023-mkwmh | Prediction of Redox Power for Photocatalysts: Synergistic Combination of DFT and Machine Learning | The accurate prediction of excited state properties is a key element of rational photocatalyst design. This involves the prediction of ground and excited state redox potentials, for which an accurate description of electronic structures is needed. Even with highly sophisticated computational approaches, however, a number of difficulties arise from the complexity of excited state redox potentials as they require the calculation of the corresponding ground state redox potentials and the estimation of the 0-0 transition energies (E0,0). In this study we have systematically evaluated the performance of DFT methods for these quantities on a set of 37 organic photocatalysts representing nine different chromophore scaffolds. We have found that the ground state redox potentials can be predicted with reasonable accuracy that can be further improved by rationally minimizing the systematic underestimations. The challenging part is to obtain E0,0 as calculating it directly is highly demanding and its accuracy depends strongly on the DFT functional employed. We have found that approximating E0,0 with appropriately scaled vertical absorption energies offers the best compromise between accuracy and computational effort. An even more accurate and cost-effective approach, however, is to predict E0,0 with machine learning and avoid the use of DFT for excited state calculations. Indeed, the best excited state redox potential predictions are achieved with the combination of M062X for ground state redox potentials and ML for E0,0. With this protocol the excited state redox potential windows of the photocatalyst frameworks could be adequately predicted. This shows the potential of combining DFT with ML in the computational design of photocatalysts with preferred photochemical properties. | Péter Pál Fehér; Ádám Madarász; András Stirling | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Photocatalysis; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640765c46642bf8c8f20eca2/original/prediction-of-redox-power-for-photocatalysts-synergistic-combination-of-dft-and-machine-learning.pdf |
60c74165bdbb892b1ba38304 | 10.26434/chemrxiv.7078205.v2 | Computationally Driven Discovery of Layered Quinary Oxychalcogenides: Potential p-Type Transparent Conductors? | <p><i>n</i>-Type transparent conductors (TCs) are key materials in the modern optoelectronics industry. Despite years of research, the development of a high performance <i>p</i>-type TC has lagged far behind that of its <i>n</i>-type counterparts delaying the advent of “transparent electronics” based on fully transparent p-n junctions. Here, we propose the layered oxysulfide [Cu<sub>2</sub>S<sub>2</sub>][Sr<sub>3</sub>Sc<sub>2</sub>O<sub>5</sub>] as a structural motif for discovering novel p-type TCs. We have used density functional theory to screen the thermodynamic and dynamical stability and electronic structure of 24 compositions based on this motif, predicting 2 new p-type TCs and 8 other stable systems with semiconductor properties. Following our predictions, we have successfully synthesized our best candidate <i>p</i>-type TC, [Cu<sub>2</sub>S<sub>2</sub>][Ba<sub>3</sub>Sc<sub>2</sub>O<sub>5</sub>], which displays structural and optical properties that validate our computational models. It is expected that the design principles emanating from this analysis will move the field closer to the realization of a high figure-of-merit <i>p</i>-type TC.</p> | Benjamin Williamson; Gregory Limburn; Graeme W. Watson; Geoffrey Hyett; David Scanlon | Solid State Chemistry; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74165bdbb892b1ba38304/original/computationally-driven-discovery-of-layered-quinary-oxychalcogenides-potential-p-type-transparent-conductors.pdf |
664c827391aefa6ce195533d | 10.26434/chemrxiv-2024-jrp41 | Transfer learning of hyperparameters for fast construction of anisotropic GPR models: design and application to the machine‐learned force field FFLUX | The polarisable machine-learned force field FFLUX requires pre-trained anisotropic Gaussian process regression (GPR) models of atomic energies and multipole moments to propagate unbiased molecular dynamics simulations. The outcome of FFLUX simulations is highly dependent on the predictive accuracy of the underlying models whose training entails determining the optimal set of model hyperparameters. Unfortunately, traditional direct learning (DL) procedures do not scale well on this task, especially when the hyperparameter search is initiated from a (set of) random guess solution(s). Additionally, the complexity of the hyperparameter space (HS) increases with the number of geometrical input features, at least for anisotropic kernels, making the optimization of hyperparameters even more challenging. In this study, we propose a transfer learning (TL) protocol that accelerates the training process of anisotropic GPR models by facilitating access to promising regions of the HS. The protocol is based on a seeding-relaxation mechanism in which an excellent guess solution is identified by rapidly building one or several small source models over a subset of the target training set before readjusting the previous guess over the entire set. We demonstrate the performance of this protocol by building and assessing the performance of DL and TL models of atomic energies and charges in various conformations of benzene, ethanol, formic acid dimer and the drug fomepizole. Our experiments suggest that TL models can be built one order of magnitude faster while preserving the quality of their DL analogs. Most importantly, when deployed in FFLUX simulations, TL models compete or even outperform their DL analogs when it comes to performing FFLUX geometry optimization and computing harmonic vibrational modes. | Bienfait Isamura; Paul Popelier | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664c827391aefa6ce195533d/original/transfer-learning-of-hyperparameters-for-fast-construction-of-anisotropic-gpr-models-design-and-application-to-the-machine-learned-force-field-fflux.pdf |
645e11affb40f6b3ee758185 | 10.26434/chemrxiv-2023-cxsb8 | Chiral Selective Self-Replicators | Self-replicating molecules provide a simple approach for investigating fundamental processes in scenarios of the emergence of life. Although homochirality is an important aspect of life and of how it emerged, the effects of chirality on self-replicators have received only little attention so far. Here we report several self-assembled self-replicators with chiral selectivity, that emerge spontaneously and grow only from enantiopure material. These require a relatively small number of chiral units in the replicators (down to 8) and in the precursors (down to a single chiral unit), compared to the only other chiral selective replicator reported previously. One replicator was found to incorporate material of its own handedness with high fidelity when provided with a racemic mixture of precursors, thus sorting (L)- and (D)-precursors into (L)- and (D)-replicators. Systematic studies reveal that the presence or absence of chiral selectivity depends on structural features (ring size of the replicator) that appear to impose constraints on its supramolecular organization. This work reveals new aspects of the little researched interplay between chirality and self-replication and represents another step towards the de novo synthesis of life. | Shuo Yang; Yannick Geiger; Marc Geerts; Marcel J. Eleveld; Armin Kiani; Sijbren Otto | Organic Chemistry; Physical Organic Chemistry; Stereochemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645e11affb40f6b3ee758185/original/chiral-selective-self-replicators.pdf |
657129ee29a13c4d47d3afb2 | 10.26434/chemrxiv-2023-k3sth-v2 | Three-Component Friedel–Crafts Alkenylation of Arenes and Heteroarenes with Ynamides and Iodine(III) Electrophile | The three-component Friedel–Crafts type functionalization of an arene using an alkyne and an electrophile can offer a strategy for rapidly increasing the molecular complexity of aromatic compounds. While conceptually straightforward, the implementation of this reaction manifold has been largely limited to unfunctionalized alkynes and electrophiles such as iodine(I) reagents. Here, we report the development of a three-component Friedel–Crafts alkenylation that utilizes a mix of ynamides and a cationic iodine(III) electrophile (benziodoxole triflate). The reaction proceeds quickly under mild conditions across diverse arenes and heteroarenes, producing α-aryl- β-iodanyl enamides in a regio- and stereocontrolled manner. The robust trans-selectivity of this iodo(III)arylation process is attributed to the reactivity of a highly distorted keteniminium species generated from the ynamide and the iodine(III) electrophile. The iodanyl moiety in these reaction products is amenable to a variety of transition metal- mediated coupling, thus offering access to densely functionalized enamides. | Jun Kikuchi; Toya Nagata; Shingo Ito; Naohiko Yoshikai | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657129ee29a13c4d47d3afb2/original/three-component-friedel-crafts-alkenylation-of-arenes-and-heteroarenes-with-ynamides-and-iodine-iii-electrophile.pdf |
60c751379abda2480ef8db9e | 10.26434/chemrxiv.13110389.v1 | CapiPy: Python Based GUI-Application to Assist in Protein Immobilization | CapiPy is a user-friendly application for
protein model creation and subsequent analysis with special focus on
its ease of use and result interpretation to help in protein
immobilization. More information can be found in https://github.com/drou0302/CapiPy. <br /> | David Roura Padrosa; Valentina Marchini; Francesca Paradisi | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751379abda2480ef8db9e/original/capi-py-python-based-gui-application-to-assist-in-protein-immobilization.pdf |
67d0f63181d2151a021192ac | 10.26434/chemrxiv-2025-rwt00 | Enhanced Interfacial Bonding of Branched Polymers | The weak welding strength between filament layers in fused deposition modeling (FDM) products results in anisotropic mechanical properties that are also sensitive to print patterns. Furthermore, poor transverse directional alignment coupled with slow printing rates limit their applicability for industrial production. We hypothesize that interfilamentous welding strength can be enhanced by modifying the chemistry of the building blocks and the topological arrangement of the macromolecular structure. To test this, we carried out coarse-grained molecular dynamics simulations to investigate the dynamics of both linear and branched polymer across representative interfaces. We observe that the diffusion controlled interdigitation follows a power law, with the exponent decreasing from 0.34 to 0.11 as grafting density increases from 7.5% to 196% (sidechains are grafted to both sides of a monomer unit). Surprisingly, the addition of sidechains enhances welding efficiency, as dense bottlebrush polymers with high grafting density reach maximum rupture strength faster than linear polymers. However, their saturated rupture strength is lower. This observation is subsequently corroborated by experimental lap shear tests using ungrafted polyethylene and branched polyethylene grafted by octane. Our MD simulations show that while linear polymer welding relies on backbone entanglement, in bottlebrush polymers, sidechains play a dominant role in enhancing interfacial strength, surpassing the contribution of the backbone. And linear polymers require more time to diffuse into neighboring filaments to achieve desired bulk properties. Furthermore, our molecular dynamics simulations reveal a brittle rupture behavior with significant hardening in linear and comb-like (mildly grafted) polymers, while bottlebrush (densely grafted) polymers display elastomeric behavior with a pronounced stress plateau prior to fracture. By comparing the gyration radii of all topological polymers, we found that they exhibit an increase in gyration radius parallel to the stretching direction and a decrease perpendicular to the deformation. The increase becomes more pronounced with higher grafting density. These results not only provide deeper insight into the underlying welding mechanisms of topological polymers but also present a potential approach for mitigating the anisotropy that is inherent in FDM-based additive manufacturing. | Yawei Gao; Ajay Jayswal; Jan Michael Carrillo; Joshua T. Damron; Logan T. Kearney; Christopher Bowland; Zeyang Yu; Michael D. Toomey; Bobby G. Sumpter; Amit K Naskar | Polymer Science | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d0f63181d2151a021192ac/original/enhanced-interfacial-bonding-of-branched-polymers.pdf |
671b0b9f1fb27ce12487a513 | 10.26434/chemrxiv-2024-jjg4n | Strain-promoted azide-alkyne cycloaddition enhanced by the secondary interactions | Azide-alkyne cycloaddition of cyclooct-2-yn-1-ol and 2-(azidophenyl)boronic acid proceeded rapidly at room temperature with complete regioselectivity to afford a triazole having a boronate ester group. The secondary covalent interaction of the boronate ester contributed to the rate acceleration and the control of regioselectivity. The interaction of an imine was also evaluated. | Riko Yoshikawa; Shohei Hamada; Jun-ichi Matsuo | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671b0b9f1fb27ce12487a513/original/strain-promoted-azide-alkyne-cycloaddition-enhanced-by-the-secondary-interactions.pdf |
65453bfc48dad231200316e3 | 10.26434/chemrxiv-2023-d9ngz-v2 | Programmable Catalysis by Support Polarization: Elucidating and Breaking Scaling Relations | The Sabatier principle and the scaling relations have been widely used to search for and screen new catalysts in the field of catalysis. However, these powerful tools can also serve as limitations of catalyst control and breakthrough. To overcome this challenge, this work proposes an efficient method of studying catalyst control by support polarization from first-principles. The results demonstrate that the properties of catalysts are determined by support polarization, irrespective of the magnitude of spontaneous polarization of support. The approach enables elucidating the scaling relations between binding energies at various polarization values of support. Moreover, we observe the breakdown of scaling relations for the surface controlled by support polarization, without requiring ensemble modification. By studying the surface electronic structure and decomposing the induced charge into contributions from different atoms and orbitals, we identify the inherent structural property of the interface that leads to the breaking of the scaling relations. Specifically, the displacements of the underlying oxide support impose its symmetry on the catalyst, causing the scaling relations between different adsorption sites to break. | Seongjoo Jung; Cristina Pizzolitto; Pierdomenico Biasi; Paul J. Dauenhauer; Turan Birol | Materials Science; Catalysis; Catalysts; Thin Films; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65453bfc48dad231200316e3/original/programmable-catalysis-by-support-polarization-elucidating-and-breaking-scaling-relations.pdf |
64ad8d8e6e1c4c986b368d4f | 10.26434/chemrxiv-2023-x78jt | Short, Scalable Access to Pyrrovobasine | A concise, gram-scale synthesis of pyrrovobasine (1) is reported. Key transformations include a 3-step decagram-scale synthesis of the tetracyclic compound without protecting groups, Mn-mediated direct radical cyclization, and introducing a naturally rare pyrraline structure. The synthesis is designed to be applicable to gram-scale synthesis using inexpensive and readily available reagents. | Longhui Yu; Hugh Nakamura | Biological and Medicinal Chemistry; Organic Chemistry; Organometallic Chemistry; Natural Products; Process Chemistry; Reaction (Organomet.) | CC BY 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ad8d8e6e1c4c986b368d4f/original/short-scalable-access-to-pyrrovobasine.pdf |
662f390f91aefa6ce1b6dc8a | 10.26434/chemrxiv-2021-pvr0m-v4 | Development of an untargeted DNA adductomics method by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry | Background: Genotoxicants originating from inflammation, diet, and environment can covalently modify DNA, possibly initiating the process of carcinogenesis. DNA adducts have been known for long, but the old methods allowed to target only a few known DNA adducts at a time, not providing a global picture of the “DNA adductome”. DNA adductomics is a new research field, aiming to screen for unknown DNA adducts by high resolution mass spectrometry (HRMS). However, DNA adductomics presents several analytical challenges such as the need for high sensitivity and for the development of effective screening approaches to identify novel DNA adducts.
Results: In this work, a sensitive untargeted DNA adductomics method was developed by using ultra-high performance liquid chromatography (UHPLC) coupled via an ESI source to a quadrupole-time of flight mass spectrometric instrumentation. Mobile phases with ammonium bicarbonate gave the best signal enhancement. The MS capillary voltage, cone voltage, and detector voltage had most effect on the response of the DNA adducts. A low adsorption vial was selected for reducing analyte loss. Hybrid surface-coated analytical columns were tested for reducing adsorption of the DNA adducts. The optimized method was applied to analyse DNA adducts in calf thymus, cat colon, and human colon DNA by performing a MSE acquisition (all-ion fragmentation acquisition) and screening for the loss of deoxyribose and the nucleobase fragment ions. Fifty-four DNA adducts were tentatively identified, hereof 38 never reported before.
Significance: This is the first untargeted DNA adductomics study on human colon tissue, and one of the few untargeted DNA adductomics studies in the literature reporting the identification of such a high number of unknowns. This demonstrates promising results for the application of this sensitive method in future human studies for investigating novel potential cancer-causing factors.
| Giorgia La Barbera; Marshal Spenser Shuler; Søren Hammershøj Beck; Per Holger Ibsen; Lars Joachim Lindberg; John Gàsdal Karstensen; Lars Ove Dragsted | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662f390f91aefa6ce1b6dc8a/original/development-of-an-untargeted-dna-adductomics-method-by-ultra-high-performance-liquid-chromatography-coupled-to-high-resolution-mass-spectrometry.pdf |
6234a7048ab373261f690955 | 10.26434/chemrxiv-2022-7gvdx | Synthesis and styrene copolymerization of novel methoxy and halogen ring-trisubstituted isobutyl phenylcyanoacrylates | Novel methoxy and halogen ring-trisubstituted isobutyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH(CH3)2 , where R is 2,3,4-trimethoxy, 2,4,5-trimethoxy, 2,4,6-trimethoxy, 3,4,5-trimethoxy, 4-benzyloxy-3,5-dimethyl, 2-chloro-3,4-dimetoxy, 3-chloro-4,5-dimetoxy, 5-chloro-2,3-dimetoxy were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-trisubstituted benzaldehydes and isobutyl cyanoacetate and characterized by CHN analysis, IR, 1H and 13C NMR. The acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Zachary J. Compton; Carlos J. Medina; Zohaib Z. Satti; Geena S. Scariah; Victoria L. Patrone; Claire E. Polar; Stephany Valladares; Emma K. Weiland; Sara M Rocus; William Schjerven; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6234a7048ab373261f690955/original/synthesis-and-styrene-copolymerization-of-novel-methoxy-and-halogen-ring-trisubstituted-isobutyl-phenylcyanoacrylates.pdf |
64fe6bd899918fe537bad226 | 10.26434/chemrxiv-2023-8blq5 | Improved Prediction of Reaction Kinetics for Amine Absorbent-based Carbon Capture using Reactive Site-based Transition State Conformer Search Method | There is no doubt that carbon emissions are one of the greatest challenges facing humanity today. Carbon capture, utilization, and storage is an effective way to achieve carbon neutrality. However, the commonly used commercial absorbents for post-combustion captures still have some limitations such as low chemical absorption rate constants. In this paper, a universal reaction kinetic model is developed for amine-based carbon capture based on the transition state theory, density functional theory, and hybrid solvation model. The developed reaction kinetic model is applicable to a wide range of amine-solvent solutions involving primary/secondary/tertiary amines and aqueous/nonaqueous solvents. The key contribution of this work is developing a reactive site-based transition state conformer search method, which has greatly improved the prediction accuracy of the reaction kinetic model from R2=0.819 to R2=0.943 based on a dataset of 21 various amine-solvent solutions. The results highlight the critical impacts of the transition state conformational isomers on amine-based CO2 chemical absorption rate constants. | Qilei Liu; Sheng Xiang; Jian Du; Qingwei Meng; Lei Zhang | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2023-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fe6bd899918fe537bad226/original/improved-prediction-of-reaction-kinetics-for-amine-absorbent-based-carbon-capture-using-reactive-site-based-transition-state-conformer-search-method.pdf |
60c73e2f337d6cd415e262c9 | 10.26434/chemrxiv.5985187.v2 | Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer | Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure–function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if <i>ab initio </i>QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of <i>ab initio </i>QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymatic rate enhancement in methyltransferases are identified with large-scale electronic structure.<br /> | Heather Kulik | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e2f337d6cd415e262c9/original/large-scale-qm-mm-free-energy-simulations-of-enzyme-catalysis-reveal-the-influence-of-charge-transfer.pdf |
60c73e96567dfe8032ec3816 | 10.26434/chemrxiv.6825401.v2 | Sampling of Tissues with Laser Ablation for bottom-up Proteomics: Comparison of Picosecond Infrared Laser (PIRL) and Microsecond Infrared Laser (MIRL) | The analysis of proteomes directly from tissues requires the proteins to be released from the cells and their compartments and solubilized, which usually is achieved by mechanical homogenization. It was recently shown, that sampling of tissues with the novel picosecond infrared laser (PIRL) offers higher yields of proteins with respect to the total amount and total number of individual proteins in comparison to mechanical homogenization. Furthermore, proteins obtained from tissues by homogenization with PIRL are significantly less enzymatically degraded, giving improved access to the original composition of proteoforms. The effective cold vaporization of tissue with PIRL is very soft, which is responsible for the phenomenon, that even enzymatic activities of proteins in the tissue aerosol are maintained. In contrast, the energy following irradiation of tissue with microsecond infrared laser (MIRL) pulses is not thermally and acoustically confined to the ablated volume. In this study, PIRL (1 J·cm-2) and MIRL (40-60 J·cm-2) were compared for sampling different tissue types for bottom-up proteomics. We showed that PIRL at low fluence is optimal for soft tissue and desired in scenarios were enzymatic activities of proteins must be maintained as well as were no residual tissue damage is a requirement. MIRL could be well suited for scenarios were enzymatic activities must be suppressed within the intact tissue and thermal and acoustic damage is not a concern.<br /> | Andrey Krutilin; Stephanie Maier; Raphael Schuster; Sebastian Kruber; Marcel Kwiatkowski; Wesley D. Robertson; Dwayne R. J. Miller; Hartmut Schluter | Analytical Chemistry - General; Biochemical Analysis; Mass Spectrometry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e96567dfe8032ec3816/original/sampling-of-tissues-with-laser-ablation-for-bottom-up-proteomics-comparison-of-picosecond-infrared-laser-pirl-and-microsecond-infrared-laser-mirl.pdf |
60c74d454c89193558ad37b8 | 10.26434/chemrxiv.12608228.v1 | Illuminating Elite Patches of Chemical Space | In the past few years, there has been considerable activity in both academic and industrial research to develop innovative machine learning approaches to locate novel, high-performing molecules in chemical space. Here we describe a new and fundamentally different type of approach that provides a holistic overview of how high-performing molecules are distributed throughout a search space. Based on an open-source, graph-based implementation [Jensen, Chem. Sci., 2019, 12, 3567-3572] of a traditional genetic algorithm for molecular optimisation, and influenced by state-of-the-art concepts from soft robot design [Mouret et al., IEEE Trans. Evolut. Comput., 2016, 22, 623-630], we provide an algorithm that (i) produces a large diversity of high-performing, yet qualitatively different molecules, (ii) illuminates the distribution of optimal solutions, and (iii) improves search efficiency compared to both machine learning and traditional genetic algorithm approaches. | Jonas Verhellen; Jeriek Van den Abeele | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d454c89193558ad37b8/original/illuminating-elite-patches-of-chemical-space.pdf |
60c75161f96a00488d287fe6 | 10.26434/chemrxiv.12705695.v2 | Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents | We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and variable number of pi-conjugated thiophene units in the backbone, used as donor material in organic photovoltaic devices. Available intra-fragment parameterizations of the individual fragment building blocks are combined with inter-fragment bonded and non-bonded parameters explicitly derived from density-functional theory calculations. To validate the force field we perform classical molecular dynamics simulations of single polymer chains with 1, 2, and 3 thiophenes in good and bad solvents, and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass transition temperature for the polymer melts is found to be in the range of 340K to 370K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10ps associated with nearly harmonic vibrations and a slow one on the order of 100 associated with temperature activated cis-trans transitions. | Vivek Sundaram; Alexey V. Lyulin; Björn Baumeier | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75161f96a00488d287fe6/original/development-and-testing-of-an-all-atom-force-field-for-diketopyrrolopyrrole-polymers-with-conjugated-substituents.pdf |
65bfa41fe9ebbb4db9a684e9 | 10.26434/chemrxiv-2024-fc8wr | Computational Investigations of Potential Antiviral and
Immunomodulatory Drugs Targeting CD155 for Polio
Treatment | This scientific paper explores the antiviral and immunomodulatory potential of fourteen drugs,
including Upadacitinib, Osimertinib, Lopinavir, Linagliptin, Imatinib, Ibrutinib, Flavoxate,
Emtricitabine, Elbasvir, Copanlisib, Cabotegravir, Bictegravir, Baricitinib, and Acrivastine,
focusing on their interactions with the CD155 receptor—a critical component in polio treatment.
CD155, integral to poliovirus entry and host immune modulation, stands as a pivotal target for
therapeutic intervention. This research addresses the urgency in treating polio, given its
potential to cause severe neurological complications. Effective therapeutic strategies are
imperative, with CD155 modulation serving as a promising avenue.
Using computational methodologies, including NAMD simulations, molecular dynamics (MD),
and molecular docking, this study elucidates the stability and interactions of the aforementioned
drugs with CD155. The findings suggest stable binding configurations, indicating the potential of
these drugs as antiviral and immunomodulatory agents in polio treatment.
Furthermore, the exploration of drug combinations with dual antiviral and immunomodulatory
properties is proposed. Combining drugs exhibiting stability in CD155 interactions may offer
synergistic effects, enhancing the overall therapeutic efficacy against poliovirus.
While our computational findings lay a foundation, further in vivo and in vitro experimentation is
imperative for validating the observed interactions. This research provides a roadmap for future
experimental studies, offering a rational basis for the design and development of antiviral and
immunomodulatory strategies targeting CD155 in the pursuit of effective polio therapy. | Arslan Hameed | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bfa41fe9ebbb4db9a684e9/original/computational-investigations-of-potential-antiviral-and-immunomodulatory-drugs-targeting-cd155-for-polio-treatment.pdf |
61698eb7a3d2c9154fd79f63 | 10.26434/chemrxiv-2021-724wt | Molecular persistent luminescence imaging with porphyrin derivatives for ultrasensitive image-guided cancer surgery and drug screening | Persistent luminescence without excitation light and tissue autofluorescence interference holds great promise for in vivo imaging and sensing. However, the availability of persistence luminescence materials is largely limited by potential toxicity, instability, short-wavelength emissions, and poor clinical potential for currently available ones. Here we report a series of porphyrin derivatives with near-infrared (NIR) persistence luminescence for image-guided cancer surgery and drug screening. These porphyrin derivatives showed NIR persistence luminescence over 760 nm after cessation of excitation light or upon interaction with peroxynitrite (ONOO-), and a plausible mechanism of ordered oxidation of vinylene bond is proposed. Through molecular engineering with adaptive peptides bearing the functions of β-sheet-formatting and cancer cell targeting, the resultant Ppa-FFGYSA supermolecular probe showed enhanced photoacoustic and persistence luminescence signals, facilitating preoperative photoacoustic tumor identification and intraoperative persistence luminescence image-guided tumor resection with outperformed signal-to-background ratio. In addition, the activated persistence luminescence in recognition of ONOO- also permits the specific monitoring of neutrophil infiltration and screening of immunogenic cell death (ICD) drugs with high sensitivity and specificity. | Xingchen Duan; Guoqiang Zhang; Shenglu Ji; Yiming Zhang; Jun Li; Hanlin Ou; Zhiyuan Gao; Guangxue Feng; Dan Ding | Biological and Medicinal Chemistry; Organic Chemistry; Materials Science; Photochemistry (Org.); Dyes and Chromophores; Imaging Agents | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61698eb7a3d2c9154fd79f63/original/molecular-persistent-luminescence-imaging-with-porphyrin-derivatives-for-ultrasensitive-image-guided-cancer-surgery-and-drug-screening.pdf |
6296044a80f81c895e969c83 | 10.26434/chemrxiv-2022-qpc96-v2 | Inducing Conductive Surface Layer on Nb2O5 via Ar-ion Bombardment: Enhanced Electrochemical Performance for Li-ion Batteries | Niobium pentoxide (Nb2O5) is in the limelight as a negative electrode material for advanced electrical energy storage devices owing to its unique pseudocapacitive behavior. However, its intrinsic poor electronic conductivity restricts its electrochemical performance. In this study, argon-ion bombardment is employed to enhance the interfacial properties of the Nb2O5 negative electrode by introducing highly conductive NbOx (1 ≤ x ≤ 2) species on the electrode surface. The NbOx surface architecture fosters significant improvements in the reversible capacity and rate performance of the argon-ion bombarded electrode than pristine electrodes. Detailed analysis reveals that introducing the surface NbOx layer promotes charge transfer at the electrode surface and breaks the limitations of charge transfer resistance. The result provides a pathway to enhance intrinsic shortness of conductivity and to establish surface modification simultaneously via a simple argon-ion bombardment method, thus achieving the improved electrochemical performance of Nb2O5 and serving as an expedient strategy for augmenting electrode materials for advanced energy-storage applications. | Shaoning Zhang; Jinkwang Hwang; Yuta Sato; Kazuhiko Matsumoto; Rika Hagiwara | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6296044a80f81c895e969c83/original/inducing-conductive-surface-layer-on-nb2o5-via-ar-ion-bombardment-enhanced-electrochemical-performance-for-li-ion-batteries.pdf |
60c743b0567dfe4e0aec4147 | 10.26434/chemrxiv.9461462.v1 | Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD | 2-Oxoglutarate
(2OG)-dependent dioxygenases catalyze C-H activation while performing a wide
range of chemical transformations. In contrast to their heme analogues,
non-heme iron centers afford greater structural flexibility with important
implications for their diverse catalytic mechanisms. We characterize an <i>in situ</i> structural model of the putative
transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a
combination of spectroelectrochemical and semi-empirical computational methods,
demonstrating that the Fe (III/II) transition involves a substantial, fully reversible,
redox-linked conformational change at the
active site. This rearrangement alters the apparent redox potential of the
active site between -127 mV for reduction of the ferric state and 171 mV for
oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural
perturbations exhibit limited sensitivity to mediator concentrations and
potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD
complexes, thus attributing the reorganization to the protein moiety rather
than the cosubstrates. Redox difference infrared spectra indicate a reorganization
of the protein backbone in addition to the involvement of carboxylate and
histidine ligands. Quantitative modeling of the transient redox response using two
alternative reaction schemes across a variety of experimental conditions
strongly supports the proposal for intrinsic protein reorganization as the
origin of the experimental observations. | Christopher John; Greg M. Swain; Robert P. Hausinger; Denis A. Proshlyakov | Bioinorganic Chemistry; Electrochemistry; Kinetics and Mechanism - Inorganic Reactions; Transition Metal Complexes (Inorg.); Chemical Kinetics; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b0567dfe4e0aec4147/original/strongly-coupled-redox-linked-conformational-switching-at-the-active-site-of-the-non-heme-iron-dependent-dioxygenase-tau-d.pdf |
63d9c9be01ecc690f919ac6f | 10.26434/chemrxiv-2022-m3900-v2 | Latent Spaces for Antimicrobial Peptide Design | Current antibacterial treatments cannot overcome the rapidly growing resistance of bacteria to antibiotic drugs, and novel treatment methods are required. One option is the development of new antimicrobial peptides (AMPs), to which bacterial resistance build-up is comparatively slow. Deep generative models have recently emerged as a powerful method for generating novel therapeutic candidates from existing datasets; however, there has been less research focused on evaluating the search spaces associated with these generators from which they sample their new data-points. In this research we employ five deep learning model architectures for de novo generation of antimicrobial peptide sequences and assess the properties of their associated latent spaces. We train a RNN, RNN with attention, WAE, AAE and Transformer model and compare their abilities to construct desirable latent spaces in 32, 64, and 128 dimensions. We assess reconstruction accuracy, generative capability, and model interpretability and demonstrate that while most models are able to create a partitioning in their latent spaces into regions of low and high AMP sampling probability, they do so in different manners and by appealing to different underlying physicochemical properties. In this way we demonstrate several benchmarks that must be considered for such models and suggest that for optimization of search space properties, an ensemble methodology is most appropriate for design of new AMPs. We design an AMP discovery pipeline and present candidate sequences and properties from three models that achieved high benchmark scores. Overall, by tuning models and their accompanying latent spaces properly, targeted sampling of new anti-microbial peptides with ideal characteristics is achievable. | Samuel Renaud; Rachael Mansbach | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d9c9be01ecc690f919ac6f/original/latent-spaces-for-antimicrobial-peptide-design.pdf |
62352a50658bc05043b00e6b | 10.26434/chemrxiv-2021-5gv6w-v2 | The Composition of Oxygen Functional Groups on Graphite Surfaces | The types and compositions of oxygen functional groups on graphite surfaces are heavily subjected to the method in which the graphite is synthesized and processed in experiments, which makes the characterization difficult. The challenge even extends to the modeling of oxygenated graphite surfaces in computational studies. However, determination of both the types and composition of oxygen functional groups on graphite surfaces is of paramount importance as it plays a significantly important role in dictating the behaviors and performances of electrochemical systems. For example, the surface structure and composition of the graphitic anode used in lithium-ion batteries (LIBs) determines the quality of a solid electrolyte interphase (SEI) that forms at the electrode/electrolyte interface, which in turns substantially affects the stability and lifetime of the devices. To help predict the structure and the composition of the surface oxygen functional groups on graphite surfaces resulting from solution-based synthesis and modification processes, we analyze the adsorption of different oxygen functional groups at both edge and basal sites of graphite as a function of pH under which the solution-based processes may take place. A series of DFT calculations reveal that at room temperature and for a pH range from 0 to 14, the (112 ̅0) edge surface of graphite will be fully oxygenated, while the basal sites remain unsaturated. The oxygen functional groups at the edge sites are comprised of mostly hydroxyl and ketonic groups, with carboxyl and carbonyl groups are present only in small amounts. Furthermore, we observe transformation of carbonyl group into ketonic group in the presence of empty surface carbon sites, which further stabilize the graphite surface. Meanwhile, carboxyl groups are more stable when all surface sites within a carboxyl layer are all populated. We conclude that the population of oxygen groups that can be found at the edge surface of a graphite in the ascending order are carboxyl < carbonyl < hydroxyl < ketonic. On the contrary to the edge plane, a small amount of oxygen functional groups may be forced to adsorb on the basal surface upon application of an external potential. The adsorbed groups are found to prefer to cluster together on basal sites in a highly ordered fashion, while the edge surface does not show this preference for adsorption sites. | Nadia Intan; Jim Pfaendtner | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62352a50658bc05043b00e6b/original/the-composition-of-oxygen-functional-groups-on-graphite-surfaces.pdf |
60c7516d469df47de8f44a01 | 10.26434/chemrxiv.13167197.v1 | The Devil is in the Defects: Electronic Conductivity in Solid Electrolytes | Rechargeable solid-state batteries continue to gain prominence due to their increased safety. However, a number of outstanding challenges have prevented their adoption in mainstream technology. In this study, we reveal the origins of electronic conductivity (s<sub>e</sub>) in solid electrolytes (SEs), which is deemed responsible for solid-state battery degradation, as well as more drastic short-circuit and failure. Using first-principles defect calculations and physics-based models, we predict s<sub>e</sub> in three topical SEs: Li<sub>6</sub>PS<sub>5</sub>Cl and Li<sub>6</sub>PS<sub>5</sub>I argyrodites, and Na<sub>3</sub>PS<sub>4</sub> for post-Li batteries. We treat SEs as materials with finite band gaps and apply the defect theory of semiconductors to calculate the native defect concentrations and associated electronic conductivities. Our experimental measurements of the band gap of tetragonal Na<sub>3</sub>PS<sub>4</sub> confirm our predictions. The quantitative agreement of the predicted s<sub>e</sub> in these three materials and those measured experimentally strongly suggests that self-doping via native defects is the primary source of electronic conductivity in SEs. In particular, we find that Li<sub>6</sub>PS<sub>5</sub>X are <i>n</i>-type (electrons are majority carriers), while Na<sub>3</sub>PS<sub>4</sub> is <i>p</i>-type (holes). Importantly, the predicted values set the lower bound for s<sub>e</sub> in SEs. We suggest general defect engineering strategies pertaining to synthesis protocols to reduce s<sub>e</sub> in SEs, and thereby, curtailing the degradation of solid-state batteries. The methodology presented here can be extended to investigate s<sub>e</sub> in secondary phases that typically form at electrode-electrolyte interfaces, as well as to complex oxide-based SEs. | Prashun Gorai; Theodosios Famprikis; Baltej Singh Gill; Vladan Stevanovic; Pieremanuele Canepa | Electrochemistry; Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7516d469df47de8f44a01/original/the-devil-is-in-the-defects-electronic-conductivity-in-solid-electrolytes.pdf |
634b3281a2c790d8e148c873 | 10.26434/chemrxiv-2022-m40v2 | Modular mixing in plasmonic metal oxide nanocrystal gels with thermoreversible links | Gelation offers a powerful strategy to assemble plasmonic nanocrystal networks incorporating both distinctive optical properties of constituent building blocks and customizable collective properties. Beyond what a single-component assembly can offer, characteristics of nanocrystal networks can be tuned in a broader range when two or more components are intimately combined. Here, we demonstrate mixed nanocrystal gel networks using thermoresponsive metal-terpyridine links that enable
rapid gel assembly and disassembly with thermal cycling. Plasmonic indium oxide nanocrystals with different sizes, doping concentrations, and shapes are reliably intermixed in linked gel assemblies, exhibiting collective infrared absorption that reflects the contributions of each component while also deviating systematically from a linear combination of the spectra for single-component gels. We extend a many-bodied, mutual polarization method to simulate the optical response of mixed nanocrystal
gels, reproducing the experimental trends with no free parameters and revealing that spectral deviations originate from cross-coupling between nanocrystals with distinct
plasmonic properties. Our thermoreversible linking strategy directs the assembly of mixed nanocrystal gels with continuously tunable far- and near-field optical properties
that are distinct from those of the building blocks or mixed close-packed structures.
| Jiho Kang; Zachary M. Sherman; Hannah S. N. Crory; Diana L. Conrad; Marina W. Berry; Benjamin J. Roman; Eric V. Anslyn; Thomas M. Truskett; Delia J. Milliron | Materials Science; Aggregates and Assemblies; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634b3281a2c790d8e148c873/original/modular-mixing-in-plasmonic-metal-oxide-nanocrystal-gels-with-thermoreversible-links.pdf |
60c7422c337d6c163ae26a23 | 10.26434/chemrxiv.8231246.v1 | Spectroscopic and Kinetic Insights into the Methane Reforming over Ce-pyrochlores | <p></p><p>In the present study, we have studied the effect of
doping of noble metal ions in Ce-pyrochlores for dry reforming of methane (DRM).
Two series of noble metal (Pt and Ru) doped pyrochlores i.e. Ce<sub>2</sub>Zr<sub>2</sub>O<sub>7</sub> and Ce<sub>2</sub>Ti<sub>2</sub>O<sub>7</sub> have been studied.
Reducibility of the synthesized samples was measured to understand the
interplay between the metal and support. A detailed material characterization
was performed both pre-and post-reaction to highlight the changes on the
surface of the catalyst. Further, the nature of surface intermediates was
investigated by in situ FTIR studies. Based on these experimental insights, a
comprehensive reaction pathway was developed and kinetic model was derived.</p><br /><p></p> | Disha Jain; Shreya Saha | Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422c337d6c163ae26a23/original/spectroscopic-and-kinetic-insights-into-the-methane-reforming-over-ce-pyrochlores.pdf |
6759c17ef9980725cfbf960d | 10.26434/chemrxiv-2024-mgvvj | Asymmetric Vicinal and Remote Hydroamination of Olefins via Rhodium Hydride Relay Catalysis: Powering Olefin as an Endogenous Hydride Donor | Metal hydrides are reactive intermediates in numerous catalytic processes. In numerous catalytic processes metal hydrides are formed but their potential reactivity is often wasted by reaction with a base or an oxidant to permit catalyst turnover. In this report, hydride relay catalysis based on an endogenous hydride source is described for hydroamination of unactivated olefins between aryl boronic acid, olefin, and a nitrene precursor dioxazolone. Initiated by a Heck reaction between the olefin and arylboroic acid, a rhodium hydride intermediate is generated and is retained for hydroamination of a second olefin. Depending on the chain length of the alkyl group of the olefin, - or -amino amides were obtained in excellent regio- and enantioselectivity via direct and remote (migratory) hydroamination, respectively. The coupling system features broad scope, mild conditions, and excellent enantioselectivity, and it also represents a rare example of asymmetric olefin hydroamination using a chiral rhodium(III) cyclopentadienyl catalyst. Mechanistic studies delineated the turnover-limiting and the enantiodetermining steps of this catalytic system. | Ruijie Mi; Xuejing Yao; Youzhi Xu; Shunle Hu; Genping Huang; Xingwei Li | Catalysis; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6759c17ef9980725cfbf960d/original/asymmetric-vicinal-and-remote-hydroamination-of-olefins-via-rhodium-hydride-relay-catalysis-powering-olefin-as-an-endogenous-hydride-donor.pdf |
64f6fbd5dd1a73847f3b30dc | 10.26434/chemrxiv-2023-jm6sb | Selective N-terminal modification of peptides and proteins using acyl phosphates | Selective acylation of the N-terminus over side-chains in peptides and proteins is a highly desirable but challenging reaction in chemical biology. Here we report a biomimetic approach using enzymatic in situ activation of carboxylic acids with ATP to generate reactive acyl-adenosine phosphates, which display high selectivity for the N-termini of peptides and proteins, including pharmaceutically relevant liraglutide, insulin and glucagon. The acylation tolerates a range of unsubstituted and substituted fatty acids including di-acids, thus making it suitable for N-terminal biorthogonal labelling strategies. | Laura Rodríguez Pérez; Thomas A. King; William Finnigan; Antonio Angelastro; William R. F. Goundry; Sabine L. Flitsch | Biological and Medicinal Chemistry; Catalysis; Bioengineering and Biotechnology; Chemical Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f6fbd5dd1a73847f3b30dc/original/selective-n-terminal-modification-of-peptides-and-proteins-using-acyl-phosphates.pdf |
639a266be8047a7792e8e488 | 10.26434/chemrxiv-2022-p836x | Systematic construction of progressively larger capsules from a 5-fold linking subcomponent | Biological encapsulants, such as viral capsids and ferritin protein cages, use many identical subunits to tile the surface of a polyhedron. Inspired by these natural systems, synthetic chemists have prepared an extensive series of artificial nanocages, with well-defined shapes and cavities. Rational control over the self-assembly of discrete, nanometre-scale, hollow coordination cages composed of simple components still poses considerable challenges as a result of the entropic costs associated with binding many subunits together, difficulties in the error-correction processes associated with assembly, and increasing surface energy as their size grows. Here we demonstrate the construction of a family of nanocages of increasing size derived from a single simple pentatopic pyrrole-based subcomponent. Reasoned shifts in the preferred coordination number of the metal ions employed, along with the denticity and steric hindrance of the ligands, enabled the generation of progressively larger cages, incorporating more subunits. These structural changes of the cages through these ‘mutations’ are reminiscent of differences in the folding of proteins caused by minor variations in their amino acid sequences; understanding how they impact capsule structure and thus cavity size may help to elucidate construction principles for still larger, more complex and functional capsules, capable of binding and carrying large biomolecules as cargoes. | Kai Wu; Tanya K. Ronson ; Pingru Su ; Zhi Chen; Leonard Goh; Andrew W. Heard; Xiaopeng Li ; Fabian Klautzsch; Christoph A. Schalley; Mladen Vinković ; Jonathan R. Nitschke | Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639a266be8047a7792e8e488/original/systematic-construction-of-progressively-larger-capsules-from-a-5-fold-linking-subcomponent.pdf |
668e81cb5101a2ffa8f9ae84 | 10.26434/chemrxiv-2024-hdt4m-v2 | Powder-Diffraction-Based Structural Comparison for Crystal Structure Prediction without Prior Indexing | The objective of crystal structure prediction (CSP) is to predict computationally the thermodynamically stable crystal structure of a compound from its stoichiometry or its molecular diagram. Crystal similarity indices measure the degree of similarity between two crystal structures, and are essential in CSP because they are used to identify duplicates. In addition, powder-based indices, which are based on comparing X-ray diffraction patterns, also allow the use of experimental X-ray powder diffraction data to inform the CSP search. Powder-assisted CSP presents two unique difficulties: i) the experimental and computational structures are not entirely comparable because the former is subject to thermal expansion from lattice vibrations, and ii) experimental patterns present features (noise, background contribution, varying peak shapes, etc.) that are not easily predictable computationally. In this work, we present a powder-based similarity index (GPWDF) based on a modification of de Gelder et al.'s index using cross-correlation functions that can be calculated analytically. Based on GPWDF, we also propose a variable-cell similarity index (VC-GPWDF) that assigns a high similarity score to structures that differ only by a lattice deformation and takes advantage of the analytical derivatives of GPWDF with respect to the lattice parameters. VC-GPWDF can be used to identify similarity between: two computational structures generated using different methods, a computational and a experimental structure, and two experimental structures measured under different conditions (e.g. different temperature and pressure). In addition, VC-GPWDF can also be used to compare crystal structures with experimental patterns in combination with an automatic pre-processing step. The proposed similarity indices are simple, efficient, and fully automatic. They require no indexing of the experimental pattern or a guess of the space group, account for deformations caused by varying experimental conditions, give meaningful results even when the experimental pattern is of very poor quality, and have a cost does not increase with the flexibility of the molecular motif. | Alberto Otero de la Roza | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Crystallography | CC BY NC 4.0 | CHEMRXIV | 2024-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668e81cb5101a2ffa8f9ae84/original/powder-diffraction-based-structural-comparison-for-crystal-structure-prediction-without-prior-indexing.pdf |
6168515135b406c78a1397d1 | 10.26434/chemrxiv-2021-hj3c1 | Radical Ring-Opening of Oxetanes Enabled by Co-Catalysis | Oxetanes are valuable building blocks due to their well-explored propensity to undergo ring-opening reactions with diverse nucleophiles. However, their application as precursors of radical species remains unexplored. Herein, we present a cobalt catalysis-based strategy to access various modes of radical reactivity via oxetane ring opening. The developed method involves formation of an alkylated Co-complex intermediate from vitamin B12 and oxetane. Homolytic cleavage of the Co-C bond generates nucleophilic radicals that engage in reactions with SOMOphiles and low-valent transition metals. The scope of the developed reactions is broad with various functional groups being well tolerated. Importantly, the regioselectivity of these processes complements known methodologies. | Aleksandra Potrząsaj; Michał Ociepa; Wojciech Chaładaj; Dorota Gryko | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6168515135b406c78a1397d1/original/radical-ring-opening-of-oxetanes-enabled-by-co-catalysis.pdf |
66ed2dfbcec5d6c142a2401a | 10.26434/chemrxiv-2024-6j11k-v2 | Hydrogen diffusion on Ni(100): A Combined Machine-Learning, Ring Polymer Molecular Dynamics, and Kinetic Monte Carlo Study | We introduce a methodological framework coupling machine-learning potentials, kinetic Monte Carlo (kMC), and ring polymer molecular dynamics (RPMD) to draw a comprehensive physical picture of the collective diffusion of hydrogen atoms on metal surfaces. For the benchmark case of hydrogen diffusion on a Ni(100) surface, the hydrogen adsorption and diffusion energetics and its dependence on the local coverage is described via a neural-network potential, where the training data is computed via periodic DFT and include all relevant optimized diffusion and desorption paths, sampled by nudged elastic band optimizations and molecular dynamics simulations. Nuclear quantum effects, being crucial for processes involving hydrogen at low temperatures, are treated by RPMD. The diffusion rate constants are calculated with a combination of umbrella samplings employed to map the free energy profile and separate samplings of recrossing trajectories to obtain the transmission coefficient. The calculated diffusion rates for different temperatures and local environments are then combined and fitted into a kMC model allowing to access larger time and length scales. Our results demonstrate an outstanding performance for the trained neural network potential in reproducing reference DFT energies and forces. We report the effective diffusion rates for different temperatures and hydrogen surface coverages obtained via this recipe in good agreement with the experimental results. The method combination proposed in this study can be instrumental for a wide range of applications in materials science. | Julien Steffen; Amin Alibakhshi | Theoretical and Computational Chemistry; Materials Science; Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ed2dfbcec5d6c142a2401a/original/hydrogen-diffusion-on-ni-100-a-combined-machine-learning-ring-polymer-molecular-dynamics-and-kinetic-monte-carlo-study.pdf |
643b989f73c6563f14f5c8ef | 10.26434/chemrxiv-2023-sdj66 | High-performing All-solid-state Sodium-ion Batteries Enabled by the Presodiation of Hard Carbon | All-solid-state sodium ion batteries (AS3iBs) are highly sought after for stationary energy storage systems due to their suitable safety and stability over a wide temperature range. Hard carbon (HC), which is low cost, exhibits a low redox potential, and a high capacity, is integral to achieve a practical large-scale sodium-ion battery. However, the energy density of the battery utilizing this anode material is hampered by its low initial Coulombic efficiency (ICE). Herein, two strategies, namely (i) thermal treatment and (ii) presodiation by thermal decomposition of NaBH4, are explored to improve the ICE of pristine HC. Raman spectroscopy, X-ray photoelectron spectroscopy and electrochemical characterizations elucidate that the thermal treatment increases the Csp2 content in the HC structure, while the presodiation supplies the sodium to occupy the intrinsic irreversible sites. Consequently, presodiated HC exhibits an outstanding ICE (>99%) compared to the thermally treated (90%) or pristine HC (83%) in half-cell configurations. More importantly, AS3iB using presodiated HC and NaCrO2 as the anode and cathode, respectively, exhibits a high ICE of 92% and an initial discharge energy density of 294 Wh kg_cathode^(-1) | Jin An Sam Oh; Grayson Deysher; Phillip Ridley; Yu-Ting Chen; Diyi Cheng; Ashley Cronk; So-Yeon Ham; Darren H. S. Tan; Jihyun Jang; Long Hoang Bao Nguyen; Shirley Y. Meng | Materials Science; Energy; Carbon-based Materials; Materials Processing; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643b989f73c6563f14f5c8ef/original/high-performing-all-solid-state-sodium-ion-batteries-enabled-by-the-presodiation-of-hard-carbon.pdf |
671a27fe98c8527d9e32302a | 10.26434/chemrxiv-2024-k505r-v3 | A protocol for the investigation of the IVR
problem: The isomerization of HONO as a case
of study | The conformational isomerization of nitrous acid (HONO) promoted by excitation of the $\nu_{OH}$ or $\nu_{N=O}$ stretching normal coordinates is the first observed case of an infrared-induced photochemical reaction. The energy captured by the excited normal modes is redistributed into a highly excited vibrational level of the $\tau_{OH}$ torsion normal coordinate, which is the isomerization reaction coordinate. Herein, we present simple numerical methods to qualitatively investigate the coupling between the normal coordinates and the possible gateways for vibrational energy redistribution leading to the isomerization process. Our methodology involves the generation of the relevant 2D Potential Energy Surface (PES), by spanning the reaction coordinate and one of the $3N-7$ projected normal coordinates along the Intrinsic Reaction Coordinate (IRC). Once the PES has been obtained, the time-independent wavefunctions are calculated using the standard Discrete Variable Representation (DVR) approach. The reaction barrier is investigated using the Interacting Quantum Atoms (IQA) decomposition scheme, evidencing an important contribution from the exchange-correlation energy to the isomerization. Coupling between normal coordinates indicates preferential normal modes to redistribute the vibrational energy. Thermal activated 1D tunneling rates were found to be negligible. | Leonardo José Duarte; Claudio M. Nunes; Rui Fausto; Ataualpa A. C. Braga | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a27fe98c8527d9e32302a/original/a-protocol-for-the-investigation-of-the-ivr-problem-the-isomerization-of-hono-as-a-case-of-study.pdf |
66f2036112ff75c3a1460231 | 10.26434/chemrxiv-2024-pn8m6 | Mechanistic analysis of N-arylation with diaryliodonium salts | Diaryliodonium salts are novel reagents for organic synthesis, especially for the arylation of heteroatom nucleophiles which generates pharmaceutically relevant products. The generally accepted mechanism for these reactions is based on kinetic studies that are three quarters of a century old and do not reflect the modern reaction conditions that have been developed over the past two decades-long boom in diaryliodonium salts chemistry. Here, we provide a detailed kinetic analysis of the phenylation of a tertiary amine nucleophile using modern tools of kinetic analysis, variable time normalisation analysis (VTNA), as well as temperature dependent analysis of dynamics (van’t Hoff and Arrhenius analysis). We quantify the kinetic relevance of both counter anions and aryl “dummy” ligands, and Density Functional Theory (DFT) and Natural Bond Orbital (NBO) theory provide new insight into the role that frontier orbitals on iodine play in the ligand coupling step. | Soocheta Jha; Nicole Javaly; Souradeep Basu; Theresa McCormick; David Stuart | Organic Chemistry; Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f2036112ff75c3a1460231/original/mechanistic-analysis-of-n-arylation-with-diaryliodonium-salts.pdf |
6740af82f9980725cf7615eb | 10.26434/chemrxiv-2024-v430f | Surface chemistry in Atomic Layer Deposition of Gallium Nitride
from Triethylgallium and Ammonia studied by mass spectroscopy
| Gallium nitride (GaN) is a commonly used semiconductor owing to its high chemical and thermal stability, which makes it suitable for various applications in modern electronics. GaN film deposition is favored by atomic layer deposition (ALD) with triethylgallium (TEG) and ammonia (NH3) plasma as precursors. However, the surface reaction pathways of TEG under ALD conditions have not been experimentally evaluated. In this study, the surface chemistry of GaN films deposited on Si (100) during ALD with TEG and NH3 with and without plasma activation as precursors was investigated using mass spectrometry. The results suggest that the surface chemistry of the deposition process mainly consists of ethyl ligand elimination upon the TEG pulse, followed by ligand exchange during NH3 pulsing to form ethane (C2H6) as a reaction by-product on an NH2-terminated surface. | Houyem Hafdi; Pamburayi Mpofu; Alex Moberg Byam; Henrik Pedersen | Physical Chemistry; Materials Science; Inorganic Chemistry; Materials Processing; Thin Films; Surface | CC BY 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6740af82f9980725cf7615eb/original/surface-chemistry-in-atomic-layer-deposition-of-gallium-nitride-from-triethylgallium-and-ammonia-studied-by-mass-spectroscopy.pdf |
60c74b1bee301c05a8c79d8c | 10.26434/chemrxiv.12205571.v1 | Low-frequency (gigahertz to terahertz) depolarized Raman scattering off n-alkanes, cycloalkanes, and six-membered rings: a physical interpretation | Molecular liquids have long been known to undergo various distinct and simple intermolecular motions, from fast librations and cage rattling oscillations to slow orientational and translational diffusion. However, their resultant gigahertz to terahertz spectra are far from simple, appearing as broad shapeless bands that span many orders of magnitude of frequency making meaningful interpretation troublesome. <i>Ad hoc</i> spectral lineshape fitting has become a notoriously fine art in the field; a unified approach to handling such spectra is long overdue. Here we apply ultrafast optical Kerr-effect (OKE) spectroscopy to study the intermolecular dynamics of room temperature <i>n</i>-alkanes, cycloalkanes, and six-carbon rings, as well as liquid methane and propane. This work provides stress-tests and converges upon an experimentally robust model across simple molecular series and temperatures, providing a blueprint for the interpretation of the dynamics of van der Waals liquids. This will enable the interpretation of low frequency spectra of more complex liquids. | Andrew J. Farrell; Mario González Jiménez; Gopakumar Ramakrishnan; Klaas Wynne | Physical and Chemical Processes; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b1bee301c05a8c79d8c/original/low-frequency-gigahertz-to-terahertz-depolarized-raman-scattering-off-n-alkanes-cycloalkanes-and-six-membered-rings-a-physical-interpretation.pdf |
67c1853d81d2151a026c72b2 | 10.26434/chemrxiv-2025-m4lm9 | Unveiling selectivity trends for CO2 reduction reaction over Ti3C2Tx MXene: The key role of less-stable intermediate states and coadsorbates | The electrochemical conversion of carbon dioxide via the CO2 reduction reaction (CO2RR) is an attractive strategy for the production of value-added chemicals. However, the CO2RR suffers from a selectivity problem due to the large number of carbon-based products that can be obtained and the competing hydrogen evolution reaction (HER). It has been experimentally shown that the ratio and chemical nature of terminal groups, Tx, present on the Ti3C2Tx (Tx = O, OH or F) surface under electrochemical conditions affect selectivity and activity trends of the MXene electrocatalyst. In the present manuscript, we use electronic structure theory calculations to comprehend the selectivity trends in the CO2RR over Ti3C2Tx with different terminal groups, including *OH and *F adsorbates. We show that the traditional modeling approach used in calculations to derive activity and selectivity trends, which only includes the most stable intermediate state in the analysis, is not consistent with experimental observations. Rather, it is necessary to include energetically less favorable intermediate states and coadsorbates in the analysis of mechanistic pathways. Remarkably, the inclusion of less stable intermediates and coadsorbates opens up new reaction channels that are energetically more favorable, and only by considering these extensions are we able to map our results to the experimental data. We believe that the reported finding is not only limited to the CO2RR or MXene systems, but likely also plays an important role in other catalytic transformations under applied bias. | Pablo Lozano-Reis; Kai S. Exner | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1853d81d2151a026c72b2/original/unveiling-selectivity-trends-for-co2-reduction-reaction-over-ti3c2tx-m-xene-the-key-role-of-less-stable-intermediate-states-and-coadsorbates.pdf |
60c749e20f50db8bde3969a9 | 10.26434/chemrxiv.12043989.v1 | Optimized Synthesis of 7-Aza-Indazoles by Diels–Alder Cascade and Associated Process Safety | Although pyrimidines are not among the most reac-tive partners in intramolecular inverse-electron de-mand [4πs+2πs] reactions with alkynes, they could be activated under mild and practical conditions, leading to fused nitrogen-containing heterocycles. We report an optimized synthesis of a 5-iodo-7-aza-indazole by a one-pot Diels–Alder cascade that starts from a pyrimidine substituted in the 2-position by an (alkynyl)hydrazone. The safety of the process was carefully studied by DSC studies. Eventually, a selection of cross-coupling reactions of 17 was studied and allowed the introduction of carbon- and nitrogen-based nucleophiles at the C5-position in good to excellent yields. | Nicolas Brach; Vincent Le Fouler; Vincent Bizet; Marian Lanz; Pascale Hoehn; Fabrice Gallou; Corinne Bailly; Michael Parmentier; Nicolas Blanchard | Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749e20f50db8bde3969a9/original/optimized-synthesis-of-7-aza-indazoles-by-diels-alder-cascade-and-associated-process-safety.pdf |
Subsets and Splits
No saved queries yet
Save your SQL queries to embed, download, and access them later. Queries will appear here once saved.