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65b21dd766c13817293976e5 | 10.26434/chemrxiv-2024-1s52z | Subcellular Concurrent Delivery of Hydrogen Sulfide
and A Payload with Near-Infrared Light
| Hydrogen sulfide (H2S) is a gaseous signaling molecule, exerting crucial regulatory functions in organelles and cellular environments. H2S exhibits high therapeutic potential, synergistic effects with other drugs, and its potency is notably enhanced through organelle-specific targeting. Yet navigation of light-activated H2S donors to specific organelles remains absent. Here we report a cyanine-based dual-action photocage operated by tissue-penetrating near-infrared light. The system simultaneously delivers H2S and a fluorogenic payload, displaying a self-reporting behavior of the uncaging. We demonstrate that H2S and an amine payload are concurrently uncaged in the mitochondria of live human cells using fluorescence microscopy and confirm the localization of their delivery using mitochondria-specific fluorescent probes. Anticipating that these photocages will permit the future delivery of H2S–drug pairs with high spatiotemporal control, we envision these photocages to drive harnessing synergistic effects and opening the way to innovative therapeutic avenues. | Katarzyna Hanc; Hana Janeková; Peter Stacko | Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b21dd766c13817293976e5/original/subcellular-concurrent-delivery-of-hydrogen-sulfide-and-a-payload-with-near-infrared-light.pdf |
60c74191ee301c1fabc78cb7 | 10.26434/chemrxiv.8067020.v1 | Palladium/ Zeolite Low Temperature Passive NOx Adsorbers (PNA): Structure-Adsorption Property Relationships for Hydrothermally Aged PNA Materials | <p>Zeolites with
different framework structures (SSZ-13, ZSM-5, BEA) but similar Si/Al ratios and
Pd loading (~1 wt%) were synthesized and evaluated as low temperature passive
NOx adsorbers (PNA). These materials exhibit high NOx adsorption efficiency with
atomically dispersed Pd the active adsorption site. Hydrothermal aging at 750
ºC for 16 hours in the presence of 10% water vapor in air resulted in the
formation of PdO nanoparticles in all three samples as evidenced by high energy
XRD. Hydrothermal aging of the small-pore Pd/SSZ-13 (Si/Al = 6), which contain
~100-90% atomically dispersed palladium ions, decreases its PNA performance only
by ~10-20%, indicating agglomeration of only ~10-20% of all atomically
dispersed Pd into PdO. High-field solid state <sup>27</sup>Al NMR studies on the
fresh and aged samples substantiate dealumination and significant changes in the
distribution of Al (and thus, Brönsted acid) sites after hydrothermal aging.
FTIR measurements with NO probe molecule and titration of Brönsted acid sites
with nitrosyl (NO<sup>+</sup>)<sup> </sup>ions further corroborate the <sup>27</sup>Al
NMR data. Because framework aluminum atoms are the anchoring sites for
atomically dispersed Pd ions, their elution from the framework causes the loss
of active atomically dispersed Pd species. With the aid of HAADF-STEM imaging
and synchrotron XRD studies, we further confirm and visualize the fate of these
Pd species – they agglomerate into PdO nanoparticles on the external surface of
zeolite. Consequently, these changes lead to the decrease in PNA performance of
these materials after hydrothermal aging. The thus formed agglomerates cannot
be re-dispersed back to their ionic state due to the loss of framework Al
T-sites and/or inherent stability of such large PdO particles.</p>
<p>Our study
demonstrates that, unlike in previous studies that found increased PNA
performance upon HTA, high temperatures hydrothermal aging of PNA materials,
that contain atomically dispersed Pd initially, results in a decrease in NOx
storage efficiency due to the formation of PdO agglomerates. However, we also highlight
the high hydrothermal stability of predominantly atomically dispersed 1-3 wt%
Pd/SSZ-13 (Si/Al = 6), whose performance decreases only marginally after
prolonged hydrothermal aging at 750 ºC. This study shows that hydrothermally
stable passive NOx materials can be prepared using small-pore SSZ-13 zeolite. </p> | Konstantin Khivantsev; Nicholas
R. Jaegers; Libor Kovarik; Jian Zhi Hu; Yong Wang; Feng Gao; János Szanyi | Catalysts; Environmental Science; Industrial Manufacturing | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74191ee301c1fabc78cb7/original/palladium-zeolite-low-temperature-passive-n-ox-adsorbers-pna-structure-adsorption-property-relationships-for-hydrothermally-aged-pna-materials.pdf |
6369079afbfd381ff1d23dab | 10.26434/chemrxiv-2022-3j39v | Structural Evidence for Aromatic Heterocycle N–O Bond Activation via Oxidative Addition | Many methods report the scission of the N–O bonds of aromatic heterocycles and their subsequent functionalization. Oxidative addition is one of the presumed pathways through which aromatic N–O bond activation with transition metals is achieved. We report the first well-defined pathway of (benz)isoxazole’s aromatic N–O bond activation through oxidative addition. We also provide control experiments which show that aromatic N–O bonds may be broken by strong inorganic reductants. These results highlight that N–O bonds are susceptible to both reduction and oxidative addition, which has important implications for catalysis. Exploring the reactivity of one of these complexes towards a series or electrophiles led to the discovery of a Staudingertype β-lactam synthesis upon reaction with a ketene. Finally, we demonstrate that choice of different metal/ligand combinations allows for selective oxidative addition into either C–I bonds or N–O bonds in the presence of the other. | Michael Bogdos; Patrick Müller; Bill Morandi | Organometallic Chemistry; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6369079afbfd381ff1d23dab/original/structural-evidence-for-aromatic-heterocycle-n-o-bond-activation-via-oxidative-addition.pdf |
60c752cd4c89190bd5ad41ac | 10.26434/chemrxiv.13341209.v1 | Metallophilicity-Induced Clusterization: Single-Component White-Light Clusteroluminescence with Stimuli Responses | <p>The single-component
white-light-emitting materials play an essential role in the next-generation
solid-state lighting technology. Herein, linear gold(I) complex TPPGPA with conglobate
trimer configuration trigged by aurophilic interactions in crystalline state was
prepared to emit dual phosphorescent white-light emission, which also exhibited
multi-stimuli responsive luminescent properties including thermochromism and mechanochromism.
Specifically, the molecular packing mode and aurophilic interactions regulation
were subtly taken as a functional relationship of the experimental
correlation with emission. The results showed that the regulated aurophilic
interactions and restriction of molecular motion were determined to be the
precipitating factor and as a function of the wavelength and intensity, which
is significant for the design guide about intelligent stimuli-responsive
white-light emissive luminescent materials. Furthermore, their application in temperature-responsive
white-light illumination was successfully demonstrated. </p> | Xueqian ZHAO; Parvej Alam; Jianyu Zhang; Shiyun Lin; Qian Peng; Jun Zhang; Guodong Liang; Jing Zhang; Herman H.-Y. Sung; Jacky W. Y. Lam; ian duncan williams; Zheng Zhao; Xinggui Gu; Ben Zhong Tang | Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752cd4c89190bd5ad41ac/original/metallophilicity-induced-clusterization-single-component-white-light-clusteroluminescence-with-stimuli-responses.pdf |
60c745f6567dfe5d10ec4535 | 10.26434/chemrxiv.10301735.v1 | Covalently Tethered Rhodamine Voltage Reporters for High Speed Functional Imaging in Brain Tissue | Voltage-sensitive fluorophores enable the direct
visualization of membrane potential changes in living systems. To pair the
speed and sensitivity of chemical synthesized fluorescent indicators with
cell-type specific genetic methods, we here develop Rhodamine-based Voltage
Reporters (RhoVR) that can be covalently tethered to genetically-encoded,
self-labeling enzymes. These chemical-genetic hybrids feature a photoinduced
electron transfer (PeT) triggered RhoVR voltage-sensitive indicator coupled to
a chloroalkane HaloTag ligand through a long, water-soluble polyethyleneglycol
(PEG) linker (RhoVR-Halos). When applied to cells, RhoVR-Halos selectively and
covalently bind to surface-expressed HaloTag enzyme on genetically modified
cells. RhoVR-Halos maintain high voltage sensitivities—up to 34% ΔF/F per 100
mV—and fast response times typical of untargeted RhoVRs, while gaining the
selectivity typical of genetically encodable voltage indicators. We show that
RhoVR-Halos can record action potentials in single trials from cultured rat
hippocampal neurons and can be used in concert with green-fluorescent Ca<sup>2+</sup>
indicators like GCaMP to provide simultaneous voltage and Ca<sup>2+</sup>
imaging. In brain slice, RhoVR-Halos provide exquisite labeling of defined
cells and can be imaged using epifluorescence, confocal, or two-photon
microscopy. Using high-speed epifluorescence microscopy, RhoVR-Halos provide a
read out of action potentials from labeled cortical neurons in rat brain slice,
without the need for trial averaging. These results demonstrate the potential
of hybrid chemical-genetic voltage indicators to combine the optical
performance of small-molecule chromophores with the inherent selectivity of
genetically-encodable systems, permitting imaging modalities inaccessible to
either technique individually. | Parker Deal; Pei Liu; Sarah Al-Abdullatif; Vikram Muller; Kiarash Shamardani; Hillel Adesnik; Evan Miller | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745f6567dfe5d10ec4535/original/covalently-tethered-rhodamine-voltage-reporters-for-high-speed-functional-imaging-in-brain-tissue.pdf |
66aa1ad85101a2ffa8afff61 | 10.26434/chemrxiv-2024-10h93-v2 | Precise estimation of activation energies in gas-phase chemical reactions via artificial neural network | Various machine learning (ML) models are presented in this study, aiming to forecast the barrier heights (BHs) of gas-phase chemical reactions. The input features utilized in six distinct models were obtained from the structural and thermodynamic attributes of molecules, encompassing enthalpy, topological indices, and Morgan fingerprints derived from SMILES, using a dataset consisting of 5040 decomposition reaction records sourced from the Gas Phase Organic Chemistry database. Evaluating the effectiveness of the models included the application of essential metrics such as coefficient of determination, mean absolute error, and root mean square error. It is worth noting that artificial neural networks outperform the other models in this regard. Then we utilized Morgan fingerprints of different dimensions as inputs for the neural network models and conducted training with varying numbers of hidden layers. This endeavor led to slight improvements in the performance of gas-phase decomposition reactions, resulting in an average determination coefficient of 0.965 and a mean absolute error of 0.079 eV. Subsequently, the model was subjected to retraining using a comprehensive dataset comprising a wide range of chemical reactions. The results indicate that the artificial neural network approach has the capacity to generalize and adjust to a wider range of chemical reactions. | Guo-Jin Cao; Sheng-Jie Lu | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aa1ad85101a2ffa8afff61/original/precise-estimation-of-activation-energies-in-gas-phase-chemical-reactions-via-artificial-neural-network.pdf |
66e87171cec5d6c14241a420 | 10.26434/chemrxiv-2024-93b2q | The generalisation challenge: assessment of the efficacy of
acoustic signals for state estimation of lithium-ion batteries via machine learning | Acoustic measurements of batteries are known to be correlated to their state-of-charge, creating opportunities for state estimation that do not rely on electrical signals. State estimators are typically parametric models fitted from data, often from the broad toolbox of machine learning. Such models can be easily designed to have millions of tuneable parameters, which endows them with tremendous but often misinterpreted fitting ability. The real performance metric, commonly omitted in the battery literature, is a model’s generalisation performance with respect to a population, which requires successful predictions to be made on data from one or more ‘held out’ cells. This study demonstrates that regression models based on neural networks can perform highly accurate state estimation on multiple cells; however, this is shown to be conditional on all cells being represented in the training dataset. Generalisation to the wider population is shown to be more challenging than other studies claim; a conclusion which follows from tests on multiple feature configurations and multiple model variants. It is hypothesized that success on multi-cell data in the absence of wider generalisation is due to the ability of models to learn cell-specific patterns implicitly, which is a type of 'overfitting'. This hypothesis is tested in two ways. First, classifiers performing a matching operation between acoustic waveforms and their respective cells are used to show that cell-specific characteristics are present in the waveforms. Next, unsupervised learning methods are used to perform a projection of all acoustic signals to two-dimensional latent space. In the latent space it is found that datapoints cluster according to the cell identity, indicating that the distinctiveness of cells dominates over any state-related commonalities in the acoustic dataset. The study highlights the need for caution in how the generalisation of machine learning models (of any kind) is evaluated in battery research. | Elias Galiounas; Rhodri E. Owen; James B. Robinson; Rhodri Jervis | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Quality Control; Energy Storage; Power | CC BY 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e87171cec5d6c14241a420/original/the-generalisation-challenge-assessment-of-the-efficacy-of-acoustic-signals-for-state-estimation-of-lithium-ion-batteries-via-machine-learning.pdf |
6450fdde1ca6101a45a8f688 | 10.26434/chemrxiv-2023-hfcl7-v2 | Exploring the Chemical Space of C3H2NO Isomers and Bimolecular Reactions with Hydrogen Cyanide and Formaldehyde: Insights into the Emergence of Life | The emergence of life remains one of the most intriguing scientific questions, and understanding the chemical processes that led to it is essential. Recent discoveries of C3H2NO isomers in the interstellar medium have motivated further exploration of this molecular formula. Here, we use density functional theory to explore the potential energy surface of C3H2NO isomers, including acyclic and cyclic structures, and identify twelve low-lying isomers. We then investigate bimolecular reaction with HCN and H2CO using an artificial force-induced automated search and transition state search for the minimal energy routes. Our results predict the formation of Oxiran- 2-ylazanide and (Z)2-aminoacetaldehyde as the kinetically and thermodynamically controlled products, respectively. These results provide insights into the potential formation of biomarkers such as N-methyleneformamide in the interstellar medium, which have been found in recent years. Our study contributes to prebiotic chemistry and offers a critical step toward understanding the chemical processes that led to the emergence of life in the universe. | Sunanda Panda; Ayusman Chiranjibi; Devesh Awasthi; Anakuthil Anoop | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Space Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6450fdde1ca6101a45a8f688/original/exploring-the-chemical-space-of-c3h2no-isomers-and-bimolecular-reactions-with-hydrogen-cyanide-and-formaldehyde-insights-into-the-emergence-of-life.pdf |
67dd28cb81d2151a024c433b | 10.26434/chemrxiv-2025-gdx2s | From Polyanions to Infinite Chains: Chemical Bonding Evolution in AX3 Polyhalides under Pressure | Polyhalides are molecular systems that defy conventional views of chemical bonding, being infinite linear halide chains the most challenging systems. By studying CsI3 under compression, we show how I3‒ polyanions, with electron-rich multicenter bonds, polymerize giving rise to infinite linear iodine chains, I∞, and demonstrate that these chains, and, by extension, infinite linear halide chains, feature electron-deficient multicenter bonds. This result is in sharp contrast with previous assumptions that considered this type of bond to be impossible in valence electron-rich elements as halogens. Importantly, the process of formation of electron-deficient multicenter bonds in CsI3 at high pressure agrees with the recently proposed unified theory of multicenter bonding. | Enrico Bandiello; Álvaro Lobato; Fernando Izquierdo; Hussien Helmy Osman; Alfonso Muñoz; Plácida Rodríguez-Hernández; Francisco Javier Manjón | Physical Chemistry; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd28cb81d2151a024c433b/original/from-polyanions-to-infinite-chains-chemical-bonding-evolution-in-ax3-polyhalides-under-pressure.pdf |
60c74265bb8c1a16533da0fc | 10.26434/chemrxiv.8263415.v1 | Concise Synthesis of GB22 by Endo-Selective Siloxycyclopropane Arylation | <div><div><div><p>The first synthesis of GB22 was accomplished by a con- cise, modular route. Two building blocks converged in a novel sp3-sp2 attached-ring coupling that used Ir/Ni dual-catalysis to reverse the regioselectivity of siloxycy- clopropane arylation. This cross-coupling proved general to access β-substituted tetralones via ring-expansion of indanone-derived siloxycyclopropanes. The congested, bridging rings of the GB alkaloids were completed using an aluminum-HFIP complex that effected intramolecular cyclization of an acid-labile substrate.</p></div></div></div> | Hannah E. Burdge; Takuya Oguma; Takahiro Kawajiri; Ryan Shenvi | Natural Products; Organic Synthesis and Reactions; Photochemistry (Org.); Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74265bb8c1a16533da0fc/original/concise-synthesis-of-gb22-by-endo-selective-siloxycyclopropane-arylation.pdf |
6790a3f3fa469535b92ef3fa | 10.26434/chemrxiv-2025-t9ns0 | A Proof of Concept of Zn- mediated RDRP of Alanine for dye encapsulation | A pH-responsive synthetic biohybride module poly(L-alanine acrylamide)-block-poly( methylmethacrylate (PAAla-b-PMMA) diblock biohybrids, based on hydrophilic PAAla and hydrophobic PMAA segments, is developed via direct switching from Zinc (Zn) catalyst polymerization. EbiB was used as an initiator to Zn-mediate Reversible Deactivation Radical Polymerization (RDRP) of alanine-derived monomer, Alanine acrylamide (AAla), yielding a series of (PAAla-b-PMAA)-The copolymer's stimuli response has been assessed against pH. The aim of this investigation was to translate this structure into a synthetic polymer. The copolymer is capable of removal of toxic dye from wastewater. This approach not only enhances the effectiveness of dye removal but also contributes to the development of eco-friendly and recyclable materials for water purification applications. | Subrata Dolui | Materials Science; Polymer Science | CC BY 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6790a3f3fa469535b92ef3fa/original/a-proof-of-concept-of-zn-mediated-rdrp-of-alanine-for-dye-encapsulation.pdf |
652d6bd745aaa5fdbb234cc4 | 10.26434/chemrxiv-2023-s60n5-v3 | Durable Light-Driven pH Switch for CO2 Capture/Release Enabled by Tuning Solvation Environment of Photoacids | Photoacids are organic molecules that release protons under illumination, providing spatiotemporal control of pH. Such light-driven pH switches offer the ability to cyclically alter the pH of the medium and are highly attractive for a wide variety of applications, including CO2 capture. Although photoacids such as protonated merocyanine can enable fully reversible pH cycling in water, they have a limited chemical stability against hydrolysis (<24 hours). Moreover, these photoacids have low solubility and provide only a small pH-jump. In this work we introduce a simple pathway to dramatically increase stability and solubility of photoacids by tuning their solvation environment in binary solvent mixtures. We show that a preferential solvation of merocyanine by aprotic solvent molecules results in a 60% increase in pH modulation magnitude when compared to the behavior in pure water and can withstand stable cycling for > 350 hours. Our results suggest that a very high stability of merocyanine photoacids can be achieved in the right solvent mixtures, offering a way to bypass complex structural modifications of photoacid molecules and serving as the key milestone towards their application in a photo-driven CO2 capture process. | Anna de Vries; Kateryna Goloviznina; Manuel Reiter; Mathieu Salanne; Maria R. Lukatskaya | Physical Chemistry; Energy; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652d6bd745aaa5fdbb234cc4/original/durable-light-driven-p-h-switch-for-co2-capture-release-enabled-by-tuning-solvation-environment-of-photoacids.pdf |
65e0b8c49138d23161569889 | 10.26434/chemrxiv-2024-qg66r | Identification of Novel Smyd1 Inhibitors for Cardiovascular Disease Treatment through Molecular Modelling | Smyd1 (SET And MYND Domain Containing 1) plays a crucial role in cardiomyocyte differentiation and cardiac morphogenesis, offering promising potential for the treatment of cardiovascular disease. However, the lack of human crystal structures and published inhibitors for Smyd1 has hindered progress in developing effective therapeutics. To address this gap, our study employs computational methods to identify novel Smyd1 inhibitors.
We first generated a reliable human Smyd1 homology model and conducted an in-depth analysis of the compound binding modes within the Smyd family. Subsequently, we developed and executed a virtual screening pipeline, integrating pharmacophore screening, molecular docking, and molecular dynamics simulations, to search for potential hit compounds with inhibitory activity against Smyd1. Experimental testing of the 15 most promising compounds identified three novel compounds with promising inhibitor activity, comparable or even higher to that of Sinefungin, a ligand known to bind to the Smyd1 cofactor pocket. These findings provide valuable insights into the binding mode of Smyd1 hit compounds, suggesting their potential as lead candidates. In conclusion, we present a rational approach for the discovery of potential therapeutic agents, laying the foundation for future investigations into optimizing novel Smyd1 inhibitors. | Yonghui Chen; David Schaller; Janine Berkholz; Andrea Volkamer | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Cell and Molecular Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e0b8c49138d23161569889/original/identification-of-novel-smyd1-inhibitors-for-cardiovascular-disease-treatment-through-molecular-modelling.pdf |
67c04a21fa469535b9270b47 | 10.26434/chemrxiv-2025-3gxw6 | Impact of the Long Cationic Chain in CTAB Surfactant on Solvated Electron Dynamics | This study investigates the generation of hydrated electrons by the well-known surfactant cetyltrimethylammonium chloride (CTAB) using short UV pulses and probing in the visible region. To assess the observed dynamics, we benchmark our findings against sodium iodide (NaI), a commonly used model for studying hydrated electrons due to its simple structure. The results indicate that while CTAB exhibits similar behavior to NaI, the formation of the compact pair state in CTAB is significantly less active compared to NaI. This reduced formation leads to a noticeable delay in the generation of separated species, a process that occurs more efficiently in the NaI system. Our findings provide valuable insights into utilizing CTAB as an internal probe to understand electron transfer processes at water-oil interfaces better. | Ahmed M. El-Zohry | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c04a21fa469535b9270b47/original/impact-of-the-long-cationic-chain-in-ctab-surfactant-on-solvated-electron-dynamics.pdf |
60c74c049abda23640f8d1c5 | 10.26434/chemrxiv.12413459.v1 | Positive/Negative Phototropism: Controllable Molecular Actuators with Different Bending Behavior | <div>Herein, a series of molecular actuators based on the crystals of (E)‐2‐(4‐fluorostyryl)benzo[d]oxazole (BOAF4),</div><div>(E)‐2‐(2,4‐difluorostyryl)benzo[d]oxazole (BOAF24), (E)‐2‐(4‐fluorostyryl)benzo[d]thiazole (BTAF4) and (E)‐2‐</div><div>(2,4‐difluorostyryl)benzo[d]thiazole (BTAF24) showed unprecedented different bending behavior under UV</div><div>irradiation. BOAF4 and BTAF4 bent towards light, whereas BOAF24 and BTAF24 bent away from light.</div><div>Although the chemical structures of these compounds are similar, we found out the F‒H‒C interaction was</div><div>the main driving force for the different molecular packing in the crystals, which led to the positive/negative</div><div>phototropism of the actuators. Moreover, the theoretical calculation was carried out to reveal the mechanical</div><div>properties of the crystals. Taking advantage of the photo responsive property, we achieved the potential</div><div>application in pushing objects, as well as enriching and removing pollutants. This system not only achieved a</div><div>class of molecular actuators with different bending behavior through introducing different number of F atom,</div><div>but also realized pushing and catching behavior within one molecule, which opens a novel gate for crystal</div><div>engineering</div> | Haoran Wang; Jiapeng Liu; Qiyao Li; Jianyu Zhang; Hao Xing; Peifa Wei; Jingbo Sun; Francesco Ciucci; Jacky W. Y. Lam; Ran Lu; Ben Zhong Tang | Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c049abda23640f8d1c5/original/positive-negative-phototropism-controllable-molecular-actuators-with-different-bending-behavior.pdf |
60c744839abda25327f8c3b2 | 10.26434/chemrxiv.9853445.v1 | Isotopically Labeled Desthiobiotin Azide (isoDTB) Tags Enable Global Profiling of the Bacterial Cysteinome | Rapid development of bacterial resistance has led to an urgent need to find new druggable targets for antibiotics. In this context, residue-specific chemoproteomic approaches enable proteome-wide identification of binding sites for covalent inhibitors. Here, we describe isotopically labeled desthiobiotin azide (isoDTB) tags that are easily synthesized, shorten the chemoproteomic workflow and allow an increased coverage of cysteines in bacterial systems. We quantify 59% of all cysteines in essential proteins in <i>Staphylococcus aureus</i> and discover 88 cysteines with high reactivity, which correlates with functional importance. Furthermore, we identify 268 cysteines that are engaged by covalent ligands. We verify inhibition of HMG-CoA synthase, which will allow addressing the bacterial mevalonate pathway through a new target. Overall, a comprehensive map of the bacterial cysteinome is obtained, which will facilitate the development of antibiotics with novel modes-of-action. | Patrick R. A. Zanon; Lisa Lewald; Stephan M. Hacker | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744839abda25327f8c3b2/original/isotopically-labeled-desthiobiotin-azide-iso-dtb-tags-enable-global-profiling-of-the-bacterial-cysteinome.pdf |
61f80ed571868d1293c4d5fd | 10.26434/chemrxiv-2022-99ww3-v2 | All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System | Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of Type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiates a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study these biological pathways’ structural and dynamical responses. Here, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed and ligand-unbound open forms of each STING in the membrane system by comparing conformational and dynamical differences among them. Our research provides clues for understanding the mechanism of the STING signaling pathway by uncovering some detailed insights for the examined systems: the residues from each chain in the binding pocket are strongly correlated to one another in the open STING structure compared with those in the closed STING structure. Ligand-bound closed STING displays approximately 170° rotation of the ligand-binding domain (LBD) relative to the open-STING structure. The detailed dynamical analysis of residue Cys148 in the linker region of hSTING does not support the earlier hypothesis that Cys148 can form disulfide bonds between adjacent STING dimers. We also reveal that using the full-length proteins is critical as the MD simulations of the LBD portion only cannot properly describe the global conformational properties of multiple domain proteins, such as STING. | Rachel Payne; Silvia Crivelli; Masakatsu Watanabe | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f80ed571868d1293c4d5fd/original/all-atom-simulations-uncover-structural-and-dynamical-properties-of-sting-proteins-in-the-membrane-system.pdf |
63c51dfc5ad3ef559f9aee43 | 10.26434/chemrxiv-2022-mzqhz-v3 | Combining first-principles kinetics and experimental data to establish guidelines for product selectivity in electrochemical CO(2) reduction | The electrochemical reduction of CO(2) is envisioned as one of the most promising ways to close the industrial carbon cycle by producing high value chemicals and fuels
using renewable electricity. Although the performance of CO2 electrolyzers has im proved substantially in the last decade, they still suffer from poor selectivity towards
the most desired products, ethylene and ethanol. This is in part due to the fact that a detailed mechanistic understanding of the selectivity towards various products is still lacking, although such an understanding is essential for process optimization. Herein, we perform microkinetic simulations based on constant potential density functional theory to elucidate the reaction pathways for CO(2) electroreduction on Cu towards the major multi-carbon products. We find that ethylene is the first product that bifurcates from the oxygenates, followed by acetate. Acetaldehyde is a direct intermediate in the production of ethanol. We provide atomistic level insights on the major role played by the electrode potential and electrolyte pH in determining the selectivity towards ethylene, oxygenates and methane, and relate the origin of the selectivity to general trends in electrochemical reaction energetics. We verify the results of our microkinetic simulations to an experimental database of previously reported measurements. Finally, we suggest guidelines for improving the selectivity towards the specific products. Our study paves the way for the design of efficient CO2 electrolyzers for the production of targeted multi-carbon products, thereby moving a step closer towards their widespread adaptation. | Georg Kastlunger; Hendrik Heenen; Nitish Govindarajan | Theoretical and Computational Chemistry; Materials Science; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c51dfc5ad3ef559f9aee43/original/combining-first-principles-kinetics-and-experimental-data-to-establish-guidelines-for-product-selectivity-in-electrochemical-co-2-reduction.pdf |
64c4fe019ed5166e93ad8b76 | 10.26434/chemrxiv-2023-5l4p2 | Copper Catalyzed Regio- and Stereoselective Hydroarylation of Ynamide | Presented herein is a copper-catalyzed trans-hydroarylation of ynamides. The reaction showcases the assembly of boronic acids across the carbon-carbon triple bond of ynamides. The reaction proceeds under mild conditions, offering a complementary approach for the versatile synthesis of multifunctional (E)-α,β-disubstituted enamides. Moreover, the hydroarylation process is highly regio- and stereoselective. The transformation shows broad scope (30 examples) and tolerates wide range of labile functional groups. Control experiments provide substantive evidence supporting the mechanistic cycle and the observed selectivity. | Avijit Maity; Akhila K. Sahoo | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c4fe019ed5166e93ad8b76/original/copper-catalyzed-regio-and-stereoselective-hydroarylation-of-ynamide.pdf |
652caaea8bab5d20556f1b97 | 10.26434/chemrxiv-2023-hwgll | Optofluidic Force Induction meets Raman Spectroscopy and Inductively Coupled Plasma – Mass Spectrometry: A new hyphenated technique for comprehensive and complementary characterisations of single particles | Nanoparticles are produced at accelerating rates, are increasingly integrated in scientific and industrial applications, and are widely discharged into the environment. Analytical techniques are required to characterise parameters such as particle number concentrations, mass and size distributions, molecular and elemental compositions as well as particle stability. This is not only relevant to investigate their utility for various industrial or medical applications and for controlling the manufacturing processes, but also to assess toxicity and environmental fate. Different analytical strategies aim to characterise certain facets of particles but are difficult to combine to provide a more comprehensive picture.
In this work, we suggest the on-line hyphenation of optofluidic force induction (OF2i) with Raman spectroscopy and inductively coupled plasma-time-of-flight-mass spectrometry (ICP-ToF-MS) to harness their complementary technology-specific advantages and to promote comprehensive particle characterisations. We optically trapped individual particles on a weakly focussed vortex laser beam by aligning a microfluidic flow antiparallelly to the laser propagation direction. The position of particles in this optical trap depended on the hydrodynamic diameter and therefore enabled size calibration. Additionally, laser light scattered on particles was analysed in a single particle (SP) Raman spectroscopy set-up for the identification of particulate species and phases. Finally, particles were characterised regarding elemental composition and their distributions in mass and size using SP ICP-ToF-MS. In a proof of concept, we analysed polystyrene-based plastic and TiO2 particles, and demonstrated the opportunities provided through OF2i-Raman-SP ICP-ToF-MS as new hyphenated technique.
| Christian Neuper; Marko Šimić; Thomas Lockwood; Raquel Gonzalez de Vega; Ulrich Hohenester; Harald Fitzek; Lukas Schlatt; Christian Hill; David Clases | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652caaea8bab5d20556f1b97/original/optofluidic-force-induction-meets-raman-spectroscopy-and-inductively-coupled-plasma-mass-spectrometry-a-new-hyphenated-technique-for-comprehensive-and-complementary-characterisations-of-single-particles.pdf |
60c75593702a9b327018c720 | 10.26434/chemrxiv.14129984.v1 | Peripheral Decoration of Multi-Resonance Molecules as a Versatile Approach for Simultaneous Long-Wavelength and Narrowband Emission | <p>High device
efficiency and color-purity are the two essentials for high-quality organic light emitting diodes
(OLEDs). Multi-resonance (MR) molecules show great potentials for high
color-purity OLEDs due to their sharp emission bands. However, most MR molecules
exhibit emission limited from deep-blue to green spectral region. Herein,
through peripherally decorating MR emitter with electron donors, we
demonstrated a new approach enabling the emission spectra of MR emitters red-shift
while retaining narrowband emission. By manipulating the numbers and
electron-donating abilities of the peripheries, the first narrowband yellow emitter
with emission maxima of 562 nm and a full-width at half-maximum (FWHM) of 30 nm
is realized. Highly efficient OLEDs with external quantum efficiency of over
24% and excellent color purity are fabricated by employing these newly
developed MR molecules as emitters.</p> | Yanyu Qi; Weimin Ning; Yang Zou; Xiaosong Cao; Shaolong Gong; Chuluo Yang | Dyes and Chromophores; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75593702a9b327018c720/original/peripheral-decoration-of-multi-resonance-molecules-as-a-versatile-approach-for-simultaneous-long-wavelength-and-narrowband-emission.pdf |
65e8834f66c1381729584a7d | 10.26434/chemrxiv-2024-j9f96 | Molecular copper(I)-sensitized photoanodes for alcohol oxidation under ambient conditions | Dye-sensitized photoelectrochemical cells can enable the production of molecules currently accessible through energetically demanding syntheses. Copper(I)-based dyes represent electronically tunable charge transfer and separation systems. Herein, we report a Cu(I)-bisdiimine donor-chromophore-acceptor dye with an absorbance in the visible part of the solar spectrum composed of a phenothiazine electron donor, and dipyrido[3,2-a:2′,3′-c]phenazine electron acceptor. This complex is incorporated onto a zinc oxide nanowire semiconductor surface effectively forming a photoanode that is characterized spectroscopically and electrochemically. We investigate the photo-oxidation of hydroquinone, and the photosensitization of 2,2,6,6-tetramethylpiperidine-1-oxyl and N-hydroxyphthalimide for the oxidation of furfuryl alcohol to furfuraldehyde, resulting in near quantitative conversions, with poor selectivity to the alcohol. | Joseph Ricardo-Noordberg; Saeid Kamal; Marek Majewski | Inorganic Chemistry; Coordination Chemistry (Inorg.); Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e8834f66c1381729584a7d/original/molecular-copper-i-sensitized-photoanodes-for-alcohol-oxidation-under-ambient-conditions.pdf |
60c73f40842e654c71db1a70 | 10.26434/chemrxiv.7291079.v1 | Synthesis of Cationic Gold(Iii) Complexes Using Iodine(Iii) | It is shown that halides are important in inducing scrambling in Au(III) coordination complexes, and that monodentate phosphines are less compatible than carbenes with Au(III)<br /> | Mohammad Albayer; Jason Dutton | Organic Synthesis and Reactions; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f40842e654c71db1a70/original/synthesis-of-cationic-gold-iii-complexes-using-iodine-iii.pdf |
60c746bf469df4c7e3f436cf | 10.26434/chemrxiv.11387091.v1 | Phase-Segregation and Photothermal Remixing of Mixed-Halide Lead Perovskites | <p>Mixed-halide lead
perovskites (MHPs) are promising materials for photovoltaics and
optoelectronics due to their highly tunable bandgaps. However, they phase-segregate
under continuous illumination and/or electric field, whose mechanism is still
under debate. Herein, we systematically measure the phase-segregation behavior
of CH<sub>3</sub>NH<sub>3</sub>Pb(Br<i><sub>x</sub></i>I<sub>1-<i>x</i></sub>)<sub>3</sub> MHPs as a function
of excitation intensity and nominal halide ratio by <i>in situ</i> photoluminescence micro-spectroscopy. We encapsulate the
MHPs with a layer of polystyrene polymer film to isolate them from the effects
of the immediate atmosphere. Under this passivated condition, the phase
segregation of the MHPs is very different from those without polymer
passivation reported in the literature. The initial phase segregation to I-rich
and Br-rich phase is observed followed by the formation of a new mixed-halide phase
within several seconds that has not been reported before. We observe that the
photothermal effect is amplified at the small-size I-rich domains which
significantly changes the local phase segregation in the otherwise uniform film
as early as milliseconds after illumination.</p> | Juvinch R. Vicente; Jixin Chen | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746bf469df4c7e3f436cf/original/phase-segregation-and-photothermal-remixing-of-mixed-halide-lead-perovskites.pdf |
65b2751b9138d23161ba47e3 | 10.26434/chemrxiv-2024-4krgj | Endergonic synthesis of Diels-Alder adducts enables non-equilibrium adaptive behaviors in chemical reaction networks | The overwhelming majority of artificial chemical reaction networks respond to stimuli relaxing towards an equilibrium state. The opposite response – moving away from equilibrium – can afford the endergonic synthesis of molecules, of which only rare examples have been reported. Here, we report six examples of Diels-Alder adducts accumulated in an endergonic process and use this strategy to realize adaptive phenomena. Indeed, systems respond to repeated occurrences of the same stimulus by increasing the amount of adduct formed, with the final network distribution depending on the number and frequency of stimuli received. Our findings indicate how endergonic processes can contribute to the transition from responsive to adaptive systems. | Shaymaa Al Shehimy; Hai-Dang Le; Simone Di Noja; Shuntaro Amano; Luca Monari; Giulio Ragazzon | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b2751b9138d23161ba47e3/original/endergonic-synthesis-of-diels-alder-adducts-enables-non-equilibrium-adaptive-behaviors-in-chemical-reaction-networks.pdf |
65567ce56e0ec7777f17b138 | 10.26434/chemrxiv-2023-fxlxg | iSIM: Instant Similarity | The quantification of molecular similarity has been present since the beginning of cheminformatics. Although several similarity indices and molecular representations have been reported, all of them ultimately reduce to the calculation of molecular similarities of only two objects at a time. Hence, to get the average similarity of a set of molecules, all the pairwise comparisons need to be computed, which demands a quadratic scaling in the number of computational resources. Here we propose an exact alternative to this problem: iSIM (Instant Similarity). iSIM performs comparisons of multiple molecules at the same time and yields the same value as the average pairwise comparisons of molecules represented with binary fingerprints and real-value descriptors. In this work, we introduce the mathematical framework and several applications of iSIM in chemical sampling, visualization, diversity selection, and clustering. | Kenneth Lopez Perez; Taewon Kim; Ramon Miranda-Quintana | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65567ce56e0ec7777f17b138/original/i-sim-instant-similarity.pdf |
66699c1d12188379d8ef5264 | 10.26434/chemrxiv-2024-2rjqz | StreaMD: the toolkit for high-throughput molecular dynamics simulations | Molecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein-ligand complexes. Due to its versatility and speed, GROMACS stands out as a commonly utilized software platform for executing molecular dynamics simulations. However, its effective utilization requires substantial expertise in configuring, executing, and interpreting molecular dynamics trajectories. Existing automation tools are constrained in their capability to conduct simulations for large sets of compounds with minimal user intervention, or in their ability to distribute simulations across multiple servers. To address these challenges, we developed a Python module that streamlines all phases of molecular dynamics simulations, encompassing preparation, execution, and analysis. This module minimizes the required knowledge for users engaging in molecular dynamics simulations and can efficiently operate across multiple servers within a network or a cluster. Notably, the tool not only automates trajectory simulation but also facilitates the computation of free binding energies for protein-ligand complexes and generates interaction fingerprints across the trajectory. Our study demonstrated the applicability of this tool on several benchmark datasets. Additionally, we provided recommendations for end-users to effectively utilize the tool. | Aleksandra Ivanova; Olena Mokshyna; Pavel Polishchuk | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66699c1d12188379d8ef5264/original/strea-md-the-toolkit-for-high-throughput-molecular-dynamics-simulations.pdf |
6629162321291e5d1d976594 | 10.26434/chemrxiv-2023-k1r08-v2 | Triptycene-like naphthopleiadene as a readily accessible scaffold for supramolecular and materials chemistry | Triptycene derivatives are used extensively in supramolecular and materials chemistry, however, most are prepared using multi-step synthesis involving the generation of a benzyne intermediate, which hinders production on a large scale. Inspired by the ease of the synthesis of resorcinarenes, we report the rapid and efficient preparation of triptycene-like 1,6,2’,7’-tetrahydroxynaphthopleiadene directly from 2,7-dihydroxynaphthalene and phthalaldehyde. Structural characterisation confirms the novel bridged bicyclic framework, within which the planes of the single benzene ring and two naphthalene units are fixed at an angle of ~120° relative to each other. Other diverse aromatic 1,2-dialdehydes and 2,7-disubstituted naphthalenes also provided similar triptycene-like products. The low cost of the precursors and undemanding reaction conditions allows for rapid multigram synthesis of 1,6,2’,7’-tetrahydroxynaphthopleiadene with product isolation achieved by simple filtration. The great potential for the use of the naphthopleiadene scaffold in supramolecular and polymer chemistry is demonstrated by the preparation of a very rigid novel cavitand, a microporous network polymer, and a solution-processable polymer of Intrinsic microporosity. | Md Khairul Amin; Chunchun Ye; Shuhua Pang; Yuancheng Liu; Gary Nichol; Neil McKeown | Organic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6629162321291e5d1d976594/original/triptycene-like-naphthopleiadene-as-a-readily-accessible-scaffold-for-supramolecular-and-materials-chemistry.pdf |
667d04bfc9c6a5c07a811b26 | 10.26434/chemrxiv-2024-xcs1m | On the prospects of high-entropy organic A-site halide perovskites | High-entropy is a hot topic in materials research but has not fully entered the halide perovskites (HPs) field. Aiming to achieve this goal, we synthesized and characterized penta-organic A-site cation HP solid solutions. Preliminary results on the structure and stability demonstrate the potential for future developments. | Fernando Brondani Minussi; Eudes Borges Araújo | Materials Science; Hybrid Organic-Inorganic Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667d04bfc9c6a5c07a811b26/original/on-the-prospects-of-high-entropy-organic-a-site-halide-perovskites.pdf |
645bc06aa32ceeff2d6b6424 | 10.26434/chemrxiv-2023-mlqb2 | Cu(III) Trifluoromethyl Complexes with 1,3-Diketonate Ligands and Their Versatile Reactivity in C-H Trifluoromethylation | High-valent Cu(III) trifluoromethyl complexes with 1,3-diketonates as bidentate oxygen donor ligands LCuIII(CF3)2 were prepared for the first time and fully characterized, including X-ray crystallography. These complexes are soluble in most organic solvents and were found to be more reactive than known N-donor Cu(III) trifluoromethyl complexes. They exhibit a promising reactivity in radical and radical-polar crossover trifluoromethylation reactions. Direct C-H trifluoromethylation of electron-rich arenes and indoles using Cu(III) trifluoromethyl diketonates under blue light irradiation in mild conditions is described. Azolo- and oxy-trifluoromethylation of terminal alkynes using Cu(III) trifluoromethyl diketonate complex and S-trifluoromethylation of thiophenol were demonstrated as applications. | Vladimir Motornov; Blanka Klepetarova; Petr Beier | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Organometallic Compounds; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645bc06aa32ceeff2d6b6424/original/cu-iii-trifluoromethyl-complexes-with-1-3-diketonate-ligands-and-their-versatile-reactivity-in-c-h-trifluoromethylation.pdf |
652878348bab5d20553bc8f9 | 10.26434/chemrxiv-2023-bf7wr | The Surface of Colloidal Nanoparticles Revealed by Vibrational Sum Frequency Scattering Spectroscopy | Solvation shells strongly influence the interfacial chemistry of colloidal systems, from the activity of proteins to the colloidal stability and catalysis of nanoparticles. Despite their fundamental and practical importance, solvation shells remain largely undetected by spectroscopy. Here, we apply for the first-time vibrational sum frequency scattering spectroscopy (VSFSS)—an interface-specific technique—to colloidal nanocrystals, with porous metal–organic frameworks (MOFs) as a case study. Due to the porous nature of the solvent-particle boundary, MOF particles challenge conventional models of colloidal and interfacial chemistry. Spectra indicate the presence of ordered solvation shells and spontaneous ordering within the MOF. VSFSS also applies to colloidal TiO2 and other common nanoparticles, revealing solvation shells with distinct spectral features that arise from the specific surface chemistry of each material. These findings explain the unexpected colloidal stability of MOF colloids, while providing a roadmap for applying VSFSS to wide-ranging colloidal nanocrystals in general. | Ashley Mapile; Michael LeRoy; Kevin Fabrizio; Lawrence Scatena; Carl Brozek | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Interfaces; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652878348bab5d20553bc8f9/original/the-surface-of-colloidal-nanoparticles-revealed-by-vibrational-sum-frequency-scattering-spectroscopy.pdf |
60c7453e842e657624db25d0 | 10.26434/chemrxiv.9996155.v1 | Linear Correlation Models for the Redox Potential of Organic Molecules in Aqueous Solutions | <p>In this study we use the molecular orbital energy approximation (MOEA) and the energy difference approximation (EDA) to build linear correlation models for the redox potentials of 53 organic compounds in aqueous solutions. The molecules evaluated include nitroxides, phenols and amines. Both the MOEA and EDA methods yield similar correlation models, however the MOEA method is less computationally expensive. Correlation coefficients (R2) below 0.3 and mean absolute errors above 0.25 V were found for correlation models built without solvent effects. When explicit water molecules and a continuum solvent model are added to the calculations, correlation coefficients close to 0.8 are reached and mean absolute errors below 0.18 V are obtained. The incorporation of solvent effects is necessary for good correlation models, particularly for redox processes of charged molecules in aqueous solutions. A comparison of the correlation models from different methodologies is provided.<br /></p> | Jessica C. Ortiz-Rodríguez; Juan A. Santana; Dalvin D Méndez-Hernández | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453e842e657624db25d0/original/linear-correlation-models-for-the-redox-potential-of-organic-molecules-in-aqueous-solutions.pdf |
6503a073b338ec988a7e4c36 | 10.26434/chemrxiv-2023-84kwb | Cross-linked DNA with carbazole pseudo-nucleoside enables potent inhibition of the cancer DNA- and RNA-mutating enzyme APOBEC3A | The human antiviral enzyme APOBEC3A has mutagenic activity in many human cancers, where it is used to fuel tumour evolution. Its single-stranded DNA and RNA C-to-U editing activities contribute to undesirable mutagenic outcomes in cancers. Inhibitors of APOBEC3A may therefore block mutagenesis and prevent tumour evolution and thus reduce detrimental outcomes such as drug resistance and metastasis. Here we demonstrate that use of a carbazole pseudo-nucleoside as a part of a covalent cross-link between distant nucleotides in DNA leads to a faster deaminating substrate and upon changing of dC to 2'-deoxy-5-fluorozebularine to a more potent inhibitor of APOBEC3A (Ki = 29 ± 5 nM) in comparison with a DNA hairpin and previously described cross-linked DNAs. Truncation of the DNA sequence led to the first 4-mer cross-linked DNA inhibitor of APOBEC3A with nanomolar potency that is also stable against digestion by a phosphodiesterase. This provides a platform for a rational design of competitive inhibitors of APOBEC3 with properties of small-molecule drugs. | Harikrishnan Kurup; Stefan Harjes; Yongdong Su; Thomas Hall; Geoffrey Jameson; Elena Harjes; Vyacheslav Filichev | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6503a073b338ec988a7e4c36/original/cross-linked-dna-with-carbazole-pseudo-nucleoside-enables-potent-inhibition-of-the-cancer-dna-and-rna-mutating-enzyme-apobec3a.pdf |
667c32d5c9c6a5c07a725aba | 10.26434/chemrxiv-2024-xwklk | Why are some pnictogen(III) pincer complexes planar and others pyramidal? | Geometrically-constrained pnictogen pincer complexes have emerged in recent years as platforms for unique stoichiometric and catalytic chemical transformations. These complexes feature dynamic conformations ranging from fully planar at the pnictogen centre to distorted-pyramidal geometries, as well as variation between phases. Although the valued reactivity of pnictogen pincer complexes is ascribed to their geometries, there is no unified model to explain the observed conformational outcomes across different ligands and pnictogen centres. Here we propose such a model through computational analysis of more than 1300 structures across 64 complexes (16 ligands and 4 heavy pnictogens), explaining the experimental observations and making new predictions. By looking at signatures of bond stability (bond lengths, Wiberg bond indices) and delocalization (NPA charges, Hirshfeld charges), our framework posits a pnictogen-based σ-bonding effect that favours pyramidalization and exists in competition with a ligand-based π-bonding effect that favours planarity. Variations in structure as a function of pnictogen identity, ligand tethering, electronics, and aromaticity can be reconciled with reference to a balance between these two opposing forces. Careful consideration of the σ/π-bonding effects may aid in the rational design of future pnictogen pincer complexes with predictable geometries and reactivities. | Tyler Hannah; Tamina Kirsch; Saurabh Chitnis | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Inorg.); Main Group Chemistry (Organomet.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c32d5c9c6a5c07a725aba/original/why-are-some-pnictogen-iii-pincer-complexes-planar-and-others-pyramidal.pdf |
6543ae0c48dad23120ef1bc7 | 10.26434/chemrxiv-2023-g84vw | LinChemIn: Route Arithmetic — Operations on Digital Synthetic Routes | Computational tools are revolutionizing our understanding and prediction of chemical reactivity by combining traditional data analysis techniques with new predictive models. These tools extract additional value from the reaction data corpus, but to effectively convert this value into actionable knowledge, domain specialists need to interact easily with the computer-generated output. In this application note, we demonstrate the capabilities of the open-source Python toolkit LinChemIn, which simplifies the
manipulation of reaction networks and provides advanced functionality for working with synthetic routes. LinChemIn ensures chemical consistency when merging, editing,
mining, and analyzing reaction networks. Its flexible input interface can process routes from various sources, including predictive models and expert input. The toolkit
also efficiently extracts individual routes from the combined synthetic tree, identifying alternative paths and reaction combinations. By reducing the operational barrier to
accessing and analyzing synthetic routes from multiple sources, LinChemIn facilitates a constructive interplay between Artificial Intelligence and human expertise. | Marta Pasquini; Marco Stenta | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6543ae0c48dad23120ef1bc7/original/lin-chem-in-route-arithmetic-operations-on-digital-synthetic-routes.pdf |
64070568cc600523a3cb7904 | 10.26434/chemrxiv-2023-tp5n9 | Computer Vision as a New Paradigm for Monitoring of Solution and Solid Phase Peptide Synthesis | We report a strategy for the direct, non-contact colorimetric reaction monitoring of amide bond formation, mediated by coupling reagents, from video footage. For amide bond formation in solution phase, investigation of reactions mediated by HATU, PyAOP, and DIC/Oxyma revealed correlations between color parameters extracted from video data and the extent of conversion to amide product measured by off-line HPLC analysis of concentration. These correlations, supported by mutual information analysis, were further investigated using video recordings of solid phase peptide synthesis (SPPS), co-analyzed by off-line HPLC to track remaining unreacted substrate in solution. An optimization method of coupling time in SPPS was derived from E (a measurement of color contrast), giving comparable isolated peptide quality at 65 – 95% reduced overall reaction time. The same color data enabled data-rich monitoring of reaction rate attenuation, consisted with computationally-derived measures of amino acid steric bulk. These findings evidence the promise of camera technologies towards a fully automated and online mechanistic profiling of SPPS. | Chunhui Yan; Calum Fyfe; Craig Jamieson; Marc Reid | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Analytical Chemistry - General; Imaging; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64070568cc600523a3cb7904/original/computer-vision-as-a-new-paradigm-for-monitoring-of-solution-and-solid-phase-peptide-synthesis.pdf |
66191385418a5379b0b02fae | 10.26434/chemrxiv-2024-6b7nz | ARTIFICIAL TITANIUM BASED IMPLANTS IN CERVICAL SPINE FIXATION FOR C5-C6 EPIDURAL SOL WITH QUADRIPARESIS | Artificial implants in C5-C6 cervical spine were used to treat osteolytic lesions, typically a bone tumor. The condition was caused by Mycobacterium Tuberculosis inhaled into the lungs and getting spread to the spin. A Titanium cage was used for the purpose which involved solid osteoporotic fusions for fats post operative recovery. Titanium, tantalum, magnesium, and zinc are non-toxic elements used in making nanocrystalline biomedical alloys. The variation of TaN in TiAl caused elemental dissolution and re growth of many phases affecting the mechanical complexion of the alloy | ARNAB BHATTACHARYYA | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66191385418a5379b0b02fae/original/artificial-titanium-based-implants-in-cervical-spine-fixation-for-c5-c6-epidural-sol-with-quadriparesis.pdf |
61e7ead1eab6ef81b6e65dfa | 10.26434/chemrxiv-2022-tz4mz | Spatially patterned neutralizing icosahedral DNA nanocage for efficient SARS-CoV-2 blocking | New neutralizing strategies against SARS-CoV-2 and associated variants are urgently needed for the treatment of COVID-19. Targeting the SARS-CoV-2 multi-spike trimers, an icosahedral DNA framework was assembled to spatially arrange up to thirty neutralizing aptamers (IDNA-30) with nanometer precision to inhibit viral infection. Each triangular plane of IDNA-30 is composed of three precisely positioned aptamers topologically matching SARS-CoV-2 spike trimer, thus forming a multivalent spatially patterned binding. Additionally, due to its multiple binding sites and moderate size, multifaced IDNA induces aggregation of viruses. Moreover, the rigid icosahedron framework afforded by four-helixes not only forms a steric barrier to prevent the virus from binding to host, but also limits the conformational transformation of SARS-CoV-2 spike trimer. Combining multivalent topologically patterned aptamers with structurally well-defined nano-formulations, IDNA-30 exhibits excellent neutralization against SARS-CoV-2 and a broad neutralizing activity against several mutant strains. Overall, this spatially matched neutralizing strategy provides a new direction for the assembly of neutralizing reagents to enhance the inhibitory effect of SARS-CoV-2 infection and combat other disease-causing viruses. | Jialu Zhang; Yunyun Xu; Miao Sun; Siwen Liu; Shuang Wan; Honglin Chen; Chaoyong Yang; Yang Yang; Yanling Song | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Nanoscience; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e7ead1eab6ef81b6e65dfa/original/spatially-patterned-neutralizing-icosahedral-dna-nanocage-for-efficient-sars-co-v-2-blocking.pdf |
61151439d800ad76b144bf44 | 10.26434/chemrxiv-2021-b1rdn | Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation | We describe a model for spectral tuning in red fluorescent proteins (RFPs) based on the relation between an electronic structure descriptor, the dipole moment variation upon excitation (DMV), and the excitation energy of a protein. This approach aims to overcome a problem of accurate prediction of excitation energies in RFPs, which span a very narrow window of band maxima. The latter roughly corresponds to an energy gap of 0.1 eV, which is comparable with typical errors in calculations of the excitation energy by conventional quantum chemistry methods. In this work, we demonstrate a strong quantitative correlation between DMV values, obtained computationally with modest efforts, and excitation energies ΔEex at the experimental excitation band maxima for a series of RFPs with the bands between 570 and 605 nm. Protein models are constructed by motifs of the relevant crystal structures, and atomic coordinates are optimized in quantum mechanics/molecular mechanics (QM/MM) calculations with QM-subsystems composed of large chromophore-containing regions. DMV values are evaluated with the electron density computed at the TDDFT level using several functionals and basis sets. We demonstrate that the results obtained with the CAM-B3LYP, BHHLYP and M06-2X functionals demonstrate favorable correlations between DMV and ΔEex with the mean absolute error less than 0.01 eV. Taking into account the solid theoretical grounds of the relation between the DMV and the excitation energy in fluorescent proteins, the described modeling strategy presents a rational tool for spectral tuning in these efficient markers for in vivo imaging. | Maria Khrenova; Fedor Mulashkin; Alexander Nemukhin | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2021-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61151439d800ad76b144bf44/original/modeling-spectral-tuning-in-red-fluorescent-proteins-using-the-dipole-moment-variation-upon-excitation.pdf |
60c75076842e65a745db3a0d | 10.26434/chemrxiv.13048028.v1 | Zeolitic Imidazolate Framework Antibody Conjugates in Bioanalytical Applications | <p>Improvements
in bioanalytical technologies are driven by evolving threats and challenges to
the global community. These challenges include emerging diseases, the need for
substance screening and increasing environmental pollution. Here, we present a
new bioanalytical concept that employs nanosized Metal-Organic Framework (MOF)
particles as labels for antibody-based analytical methods, including
enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay (LFIA).
A strategy for covalently linking antibodies to form stable, colloidal Zeolitic
Imidazolate Frameworks (ZIFs) conjugates is described. The proof of principle
for their use in LFIA is presented. In particular, ZIF-antibody conjugates
displayed excellent behaviour in dispersion and good mobility via lateral flow
on a solid substrate while retaining full selectivity of the antibody.
Moreover, protein aggregation of the antibodies was prevented, suggesting
protection against degradation in an exoskeleton-like manner. Our study could
inspire future work to address global bioanalytical and diagnostic challenges.</p> | Ander Chapartegui Arias; Anna Raysyan; Ana Belenguer; Carsten Jaeger; Teodor Tchipilov; Carsten Prinz; Carlos E. Abad Andrade; Sebastian Beyer; Rudolf. J. Schneider; Franziska Emmerling | Organic Synthesis and Reactions; Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75076842e65a745db3a0d/original/zeolitic-imidazolate-framework-antibody-conjugates-in-bioanalytical-applications.pdf |
6362832b2e0c63d735467b3a | 10.26434/chemrxiv-2022-0zg7r-v3 | Frenkel Excitons in Vacancy-ordered Titanium Halide Perovskites (Cs₂TiX₆) | Low-cost, non-toxic and earth-abundant photovoltaic materials are a long-sought target in the solar cell research community. Perovskite-inspired materials have emerged as promising candidates for this goal, with researchers employing materials design strategies including structural, dimensional and compositional transformations to avoid the use of rare and toxic elemental constituents, while attempting to maintain high optoelectronic performance. These strategies have recently been invoked to propose Ti-based vacancy-ordered halide perovskites (A₂TiX₆; A = CH₃NH₃, Cs, Rb, K; X = I, Br, Cl) for photovoltaic operation, following the initial promise of Cs₂SnX₆ compounds. Theoretical investigations of these materials, however, consistently overestimate their band gaps – a fundamental property for photovoltaic applications. Here, we reveal strong excitonic effects as the origin of this discrepancy between theory and experiment; a consequence of both low structural dimensionality and band localization. These findings have vital implications for the optoelectronic application of these compounds, while also highlighting the importance of frontier-orbital character for chemical substitution in materials design strategies. | Seán R. Kavanagh; Christopher N. Savory; Shanti M. Liga; Gerasimos Konstantatos; Aron Walsh; David O. Scanlon | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Quasiparticles and Excitations; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6362832b2e0c63d735467b3a/original/frenkel-excitons-in-vacancy-ordered-titanium-halide-perovskites-cs2ti-x6.pdf |
6391e03fb103afba0f102880 | 10.26434/chemrxiv-2022-hj8k0-v2 | Experimental and computational investigation of benperidol and droperidol solid solutions in different crystal structures | We present an experimental and computational study of solid solution formation between structurally highly similar active pharmaceutical ingredients droperidol and benperidol in nonsolvates, dihydrates, and several solvates formed by these compounds. We demonstrate that the formation of solid solutions strongly depends on the crystal structure of the phase. In part of the structures almost complete replacement of benperidol with droperidol can be achieved, whereas in other structures the replacement is possible only up to a limited molar ratio. However, only limited replacement of droperidol with benperidol can be achieved and only in part of the structures. The solid solution formation is primarily determined by the change of intermolecular interaction energy resulted by the molecule replacement. Experimentally only structures where molecule replacement allows formation of efficient intermolecular interactions can be obtained. The results indicate that energetic requirements of intermolecular interaction changes to obtain solid solutions in nonsolvated phase are less strict than that for solvates. | Kristaps Saršūns; Agris Bērziņš | Physical Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6391e03fb103afba0f102880/original/experimental-and-computational-investigation-of-benperidol-and-droperidol-solid-solutions-in-different-crystal-structures.pdf |
60c74d35469df482c5f4423f | 10.26434/chemrxiv.11811660.v4 | Evolution of Metastable Structures at Bimetallic Surfaces from Microscopy and Machine-Learning Molecular Dynamics | Restructuring of interfaces plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. By developing and performing accelerated machine-learning molecular dynamics followed by an automated analysis method, we discover and characterize previously unidentified surface restructuring mechanisms in an unbiased fashion, including Pd-Ag place exchange and Ag pop-out, as well as step ascent and descent. Remarkably, layer-by-layer dissolution of Pd into Ag is always preceded by an encapsulation of Pd islands by Ag, resulting in a significant migration of Ag out of the surface and a formation of extensive vacancy pits within a period of microseconds. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. Our approach is broadly applicable to complex multimetallic systems and enables the previously intractable mechanistic investigation of restructuring dynamics at atomic resolution. | Jin Soo Lim; Jonathan Vandermause; Matthijs A. van Spronsen; Albert Musaelian; Yu Xie; Lixin Sun; Christopher R. O’Connor; Tobias Egle; Nicola Molinari; Jacob Florian; Kaining Duanmu; Robert J. Madix; Philippe Sautet; Cynthia M. Friend; Boris Kozinsky | Alloys; Catalysts; Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence; Heterogeneous Catalysis; Interfaces; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d35469df482c5f4423f/original/evolution-of-metastable-structures-at-bimetallic-surfaces-from-microscopy-and-machine-learning-molecular-dynamics.pdf |
677e0540fa469535b926b9a1 | 10.26434/chemrxiv-2025-3lrwh | Transferable predictions of energetic and structural properties for refractory solid solution alloys across chemical compositions | We present a data-efficient approach to train graph neural networks (GNNs) on density functional theory (DFT) data for accurate and transferable predictions of energetic and structural properties of refractory solid solution alloys in the niobium-tantalum-vanadium (Nb-Ta-V) chemical space. We start by training the GNN model only on DFT data that describes refractory binary alloys niobium-tantalum (Nb-Ta), niobium-vanadium (Nb-V), and tantalum-vanadium (Ta-V) to predict formation enthalpy and root mean squared displacement. Once trained, the GNN predictions are tested on DFT data describing refractory ternary alloys Nb-Ta-V. While, unsurprisingly, direct transferability from binary to ternary is not sufficiently accurate, augmenting the training with only 1% of the available ternary data (uniformly distributed across the entire range of chemical compositions) improves significantly the quality of the GNN predictions. For comparison, we assess the transferability in the opposite direction by training GNN models on ternary Nb-Ta-V data and making predictions on binaries Nb-Ta, Nb-V, and Ta-V, which exhibits notably higher predictive errors. The proposed methodology, which favors transferability from lower-component to higher-component alloys, offers an efficient path towards avoiding the curse of dimensionality incurred when collecting DFT data for discovery and design of multi-component disordered alloys. | Massimiliano Lupo Pasini; Pei Zhang; Jong Youl Choi; German Samolyuk; Markus Eisenbach; Ying Yang | Materials Science; Alloys | CC BY NC 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677e0540fa469535b926b9a1/original/transferable-predictions-of-energetic-and-structural-properties-for-refractory-solid-solution-alloys-across-chemical-compositions.pdf |
61afd94ed10aa56cb106f086 | 10.26434/chemrxiv-2021-ph8tz | Characterization of DNA nanostructure stability by size exclusion chromatography | DNA-based nanostructures (DNs) are advantageous for the design of functional materials for biology and medicine due to the nanoscale control provided by their predictable self-assembly. However, the use of DNs in vivo has been limited due to structural instability in biofluids. As the stability of a particular DN sets the scope of its potential biological applications, efficient methods to characterize stability are required. Here, we apply size exclusion chromatography (SEC) to study the stability of a tetrahedron DNA nanostructure (TDN) and demonstrate the analytical capabilities of our method in characterizing degradation by enzymes and a diluted human serum matrix. We show that SEC analysis can reliably assay TDN degradation by a nuclease through direct injection and peak integration. Furthermore, data analysis using a ratio chromatogram technique enables TDN peak deconvolution from the matrix of serum proteins. Using our method, we found that TDNs exhibit half-lives of 23.9 hours and 10.1 hours in 20% and 50% diluted human serum, respectively, which is consistent with reported stability studies in 10% fetal bovine serum. We anticipate that this method could be broadly applicable to characterize a variety of DNs and serve as an efficient technique toward analysis of the stability of new DN designs in complex biological matrixes. | Nicole Langlois; Heather Clark | Materials Science; Analytical Chemistry; Nanoscience; Analytical Chemistry - General; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61afd94ed10aa56cb106f086/original/characterization-of-dna-nanostructure-stability-by-size-exclusion-chromatography.pdf |
668909685101a2ffa88bf5b4 | 10.26434/chemrxiv-2024-6mx5c | Effect of Weak Intermolecular Interactions on the Ionization of Benzene Derivatives Dimers | The interactions between π-systems in dimers of aromatic molecules lead to particularly stable conformations within relative orientations of the monomers. Extensive research has been conducted on the properties of these complexes in the neutral state. However, in recent decades, there has been a significant surge in applications harnessing these structures for electrical purposes. Thus, this study places particular emphasis on a deeper understanding of the redox properties of these compounds and how to modify them. To achieve this, we have focused on modeling the effect of a wide range of functional groups on the redox properties of benzene derivatives, observing a correlation between these properties and the change in the molecular dipole moment. Then, we have investigated the effect of π-stacking interactions on these properties in dimers formed by either identical or different monomers. In both cases, there is an enhancement of the reducing character of the systems due to these interactions. Upon oxidation, the charge is distributed proportionally to the redox potential of each monomer. Thus, if there is heterogeneity in these potentials, the properties of the complete cationic system will be influenced by the monomer with the greater tendency to undergo oxidation. The considered models serve as an excellent example for studying the behavior of nucleobases in DNA or aromatic amino acids, among others. | Jesús Lucia-Tamudo; Rubén López-Sánchez; Sergio Díaz-Tendero; Juan J. Nogueira | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668909685101a2ffa88bf5b4/original/effect-of-weak-intermolecular-interactions-on-the-ionization-of-benzene-derivatives-dimers.pdf |
60e89fd6b9b60109ee22dce2 | 10.26434/chemrxiv-2021-c12b9-v2 | Ten Essential Delocalization Learning Outcomes: How Well Are They Achieved? | OBJECTIVE: Delocalization (resonance) is a concept in organic chemistry that influences the chemical reactivity, activity, structure, and physical properties of molecules. However, the concept has proven challenging for students. The goal of the present study was to investigate to what extent ten essential delocalization learning outcomes (LOs) were achieved by students, how students use and reason about delocalization as well as the connections between the LOs. The goal is to discover where and how students may be struggling when answering delocalization-related exam questions and uncover potential barriers to learning delocalization.
METHODS: We analyzed students’ responses (N = 3787) on twelve exam questions related to seven of the ten LOs for the degree of achievement, common errors, and scientific reasoning.
RESULTS: The achievement on the LOs was variable. We report types of errors and strategies used, the errors are primarily related to drawing resonance structures or the resonance. Six key findings emerged from the analysis: (1) the majority of answers had few (<10%) representational errors (2) in an implicit question where delocalization or inductive effect concepts could be used to justify a response, half the students used delocalization concepts, (3) delocalization was used in 10–20% of answers when relevant but not prompted or required, (4) strategies that helped students reason with the representations (i.e., drawing out electrons or expanding a structure) were correlated with higher achievement of the LOs, (5) students’ reasoning aligned with course expectations, and (6) students who achieved later LOs typically (60–95%) also achieved LO1 and LO2 (Identify that electron delocalization is relevant, Draw resonance structures).
CONCLUSIONS: The findings have implications on how students achieve the LOs and suggest ways educators can better support learners with the tools to achieve the LOs.
IMPLICATIONS: The findings from this work could be used to design and evaluate new teaching techniques or materials, including scaffolding concepts. Further investigations could lead to a deeper understanding of students’ mental models and thought processes related to delocalization concepts.
| Myriam S. Carle; Romeo Junior El Issa; Nicolas Pilote; Alison B. Flynn | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e89fd6b9b60109ee22dce2/original/ten-essential-delocalization-learning-outcomes-how-well-are-they-achieved.pdf |
64a524489ea64cc167784a89 | 10.26434/chemrxiv-2023-4zjpd | Copper-Catalyzed Sulfimidations of Benzylic C(sp3)-H Bonds | In this study, we elucidate a novel strategy for benzylic C(sp3)-H activation, enabling the construction of C-S bonds through a copper-catalyzed sulfimidation process. Leveraging readily available methylarenes as substrates, our methodology offers an economically efficient and highly viable approach. The scalability of the reaction, its applicability to a broad range of substrates, and significant application value underscore its potential and transformative impact in the realm of synthetic organic chemistry. | Xunbo Lu; Guoling Huang | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a524489ea64cc167784a89/original/copper-catalyzed-sulfimidations-of-benzylic-c-sp3-h-bonds.pdf |
642d3e19db1a20696e8c57dd | 10.26434/chemrxiv-2023-cz438 | Complex formation of Cucurbit[6]uril with DABCO and DABCO derivatives: An experimental and DFT study | The complex formation of Cucurbit[6]uril with DABCO and DABCO derivatives in solution has been studied using calorimetric titrations. For a better understanding of factors influencing the complex formation, several DABCO derivatives have been synthesized. All compounds have been characterized. Inclusion complex formation could not be observed. Even with dumbbell derivatives of DABCO threading through the Cucurbit[6]uril cavity does not occur. As a result, no rotaxanes have been formed in solution. These results are in accordance with DFT calculations. | Andreas Wego; Achim Zielesny | Organic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2023-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642d3e19db1a20696e8c57dd/original/complex-formation-of-cucurbit-6-uril-with-dabco-and-dabco-derivatives-an-experimental-and-dft-study.pdf |
60c75048bb8c1a85623dbab7 | 10.26434/chemrxiv.13012907.v1 | Mechanosynthesis of a Coamorphous Formulation of Creatine with Citric Acid and Humidity–Mediated Transformation into a Cocrystal | We report a simple, efficient, and scalable mechanochemical method of
preparation of new creatine fitness supplement with increased solubility (compared to the creatine monohydrate) and
decreased acidity (compared to creatine hydrochloride). | Kyle B Pekar; Jonathan B Lefton; Christina McConville; Jewel Burleson; Daniel Sethio; Elfi Kraka; Tomce Runcevski | Food; Pharmaceutical Industry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75048bb8c1a85623dbab7/original/mechanosynthesis-of-a-coamorphous-formulation-of-creatine-with-citric-acid-and-humidity-mediated-transformation-into-a-cocrystal.pdf |
62fdd361f8cdca1ce7fd1444 | 10.26434/chemrxiv-2022-kmmbk-v2 | DNA-Assisted Selective Electrofusion (DASE) of Escherichia coli and Giant Lipid Vesicles | Synthetic biology and cellular engineering require chemical and physical alterations, which are typically achieved by fusing target cells with each other or with payload-carrying vectors. On one hand, electrofusion can efficiently induce the merging of biological cells and/or synthetic analogues via the application of intense DC pulses, but it lacks selectivity and often leads to uncontrolled fusion. On the other hand, synthetic DNA-based constructs, inspired by natural fusogenic proteins, have been shown to induce a selective fusion between membranes, albeit with low efficiency. Here we introduce DNA-assisted selective electrofusion (DASE) which relies on membrane-anchored DNA constructs to bring together the objects one seeks to merge, and applying an electric impulse to trigger their fusion. The DASE process combines the efficiency of standard electrofusion and the selectivity of fusogenic nanostructures, as we demonstrate by inducing and characterizing the fusion of spheroplasts derived from Escherichia coli bacteria with cargo-carrying giant lipid vesicles. | Sho Takamori; Pietro Cicuta; Shoji Takeuchi; Lorenzo Di Michele | Biological and Medicinal Chemistry; Nanoscience; Nanodevices; Bioengineering and Biotechnology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fdd361f8cdca1ce7fd1444/original/dna-assisted-selective-electrofusion-dase-of-escherichia-coli-and-giant-lipid-vesicles.pdf |
633b26f5975e9477b1924891 | 10.26434/chemrxiv-2021-mxrxw-v3 | Machine Learning Models to Accelerate the Design of Polymeric Long-Acting Injectables | Long-acting injectables are considered one of the most promising therapeutic strategies for the treatment of chronic diseases as they can afford improved therapeutic efficacy, safety, and patient compliance. The use of polymer materials in such a drug formulation strategy can offer unparalleled diversity owing to the ability to synthesize materials with a wide range of properties. However, the interplay between multiple parameters, including the physicochemical properties of the drug and polymer, make it very difficult to intuitively predict the performance of these systems. This necessitates the development and characterization of a wide array of formulation candidates through extensive and time-consuming in vitro experimentation. Machine learning is enabling leap-step advances in a number of fields including drug discovery and materials science. The current study takes a critical step towards data-driven drug formulation development with an emphasis on long-acting injectables. A series of machine learning algorithms were trained and refined for accurate prediction of experimental drug release profiles. Analysis of the best performing model uncovered the properties of the drug and polymer that were identified to be key determinants of drug release. This information can be used to identify promising drug-polymer combinations that result in long-acting injectables with specific drug release behaviour. The implementation of this data-driven approach has the potential to reduce the time and cost associated with formulation development. Datasets and relevant codes used to train the machine learning models have been made openly available to encourage usage in future drug formulation efforts. | Pauric Bannigan; Zeqing Bao; Riley Hickman; Matteo Aldeghi; Florian Häse; Alán Aspuru-Guzik; Christine Allen | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Controlled-Release Systems; Drug delivery systems; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633b26f5975e9477b1924891/original/machine-learning-models-to-accelerate-the-design-of-polymeric-long-acting-injectables.pdf |
65ca57679138d23161f3a65a | 10.26434/chemrxiv-2024-n7j2r | LigandDiff: 3D Transition Metal Complex Generation with Diffusion Models | Transition metal complexes are a class of compounds with varied and versatile properties making them of great technological importance. Their applications cover a wide range of fields, either as metallodrugs in medicine or as materials, catalysts, batteries, solar cells, etc. The demand for the novel design of transition metal complexes with new properties remains of great interest . However, the traditional high-throughput screening approach is inherently expensive and laborious since it depends on human expertise. Here, we present LigandDiff, a generative model to design novel transition metal complexes. Unlike the existing methods which simply extracts and combine ligands to the metal to get new complexes, LigandDiff aims at designing novel ligands from scratch, which opens new pathways for the discovery of organometallic complexes. Moreover, it overcomes the limitations of current methods where the diversity of new complexes highly relies on the diversity of available ligands while LigandDiff can enumerate novel ligands without human intervention. Our results indicate that LigandDiff designs unique and novel ligands under different contexts that are synthetically accessible. Moreover, LigandDiff shows good transferability by generating successful ligands for any transition metal complex. | Hongni Jin; Kenneth M. Merz, Jr | Theoretical and Computational Chemistry; Physical Chemistry; Organometallic Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Bioorganometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ca57679138d23161f3a65a/original/ligand-diff-3d-transition-metal-complex-generation-with-diffusion-models.pdf |
677c3647fa469535b9fecebd | 10.26434/chemrxiv-2025-6mxw9 | De novo designed β-hairpin peptides mimicking the LPMO copper-binding histidine brace motif | Lytic polysaccharide monooxygenases (LPMOs) are Cu-based enzymes that play a crucial role in lignocellulosic biomass degradation for use in biofuel production. These enzymes carry out the selective oxidation of C-H bonds in the sugar units, leading to the cleavage of the glycosidic bond. Creating LPMO mimics facilitates the study of the mechanism of action, the characterisation of the reactive species responsible for the C-H bond activation and the potential scale up for industrial application. Here we report the synthesis, characterisation and activity assays of two novel Cu-peptides complexes that mimic the LPMO active site. We carried out CD, ATR-FTIR and EPR spectroscopic studies of the peptides and their corresponding copper complexes, showing that the sequences fold in a β-hairpin conformation and produce complexes with a single copper ion bound in an LPMO-like environment, confirmed by computational studies. Activity assays were conducted with p-nitrophenyl-β-D-glucopyranoside (PNPG) and demonstrated that the Cu-complexes can perform LPMO-like activity on the model substrate. Furthermore, the Cu-hairpins were also able to perform light-driven oxidation of phosphoric acid swollen cellulose (PASC) in the presence of melanin, similarly to some LPMO enzymes, an activity that is unreported for any LPMO mimic characterised so far. This work is the first example of a β-hairpin LPMO mimic and paves the way to further exploration of small peptide mimics of this key class of metalloenzymes. | Enrico Falcone; Rosemary Tomey; Emma Turley; David Cannella; David Robinson; Luisa Ciano | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Chemical Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677c3647fa469535b9fecebd/original/de-novo-designed-hairpin-peptides-mimicking-the-lpmo-copper-binding-histidine-brace-motif.pdf |
60c74a07bdbb898b2ea392d6 | 10.26434/chemrxiv.12137817.v1 | Voltage Relaxation to Detect the Onset of Lithium Plating on Graphite for Fast Charging | Li-ion battery fast charging is critical to reduce
electric vehicle ‘range anxiety’ and enable emerging technologies such as aerial
drones and high-performance portable electronics. Fast charging is primarily limited by lithium
plating on graphite, which can cause capacity fade and catastrophic cell
shorting. The ability to detect the
initial onset of lithium plating using easily accessible battery management
system parameters (current, voltage, and capacity) would dramatically improve
the safety of fast charging protocols. In
this work, we highlight the application of a differential open-circuit voltage
analysis (dOCV) to detect when Li plating first begins during room temperature
fast charging. We quantify the Li detection
limit of the technique to be approximately 4 mAh plated Li per gram graphite,
showing that this method has high sensitivity and significant commercial
promise. | Zachary M. Konz; Eric J. McShane; Bryan D. McCloskey | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a07bdbb898b2ea392d6/original/voltage-relaxation-to-detect-the-onset-of-lithium-plating-on-graphite-for-fast-charging.pdf |
640f07467290f69f8ee96670 | 10.26434/chemrxiv-2023-fw96z-v2 | QBithm: towards the coherent control of robust spin qubits in quantum algorithms | Many efforts have succeeded over the last decade at lengthening the timescale in which spin qubits loss quantum information under free evolution. With these design principles, it is now timely to zoom out and take the whole picture: concerning applications that require user-driven evolutions, qubits should be assessed within the desired algorithm. This means to test qubits under external control while relaxation is active, and to maximize the algorithm fidelity as the actual figure of merit. Herein, we pose and analytically solve a master equation devised to run one-spin-qubit algorithms subject to relaxation. It is handled via a code, QBithm, which inputs gate sequences and relaxation rates thus connecting with the longstanding work devoted to their ab initio computation. We calculate fidelities against relaxation and imperfections, and implement well-known pulse sequences quantitatively agreeing with experimental data. Hopefully, this work will stimulate the study of many-qubit systems driven under relaxation and imperfections in quantum algorithms. | Luis Escalera-Moreno | Materials Science; Nanoscience; Magnetic Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640f07467290f69f8ee96670/original/q-bithm-towards-the-coherent-control-of-robust-spin-qubits-in-quantum-algorithms.pdf |
6304892c58843b62709a0863 | 10.26434/chemrxiv-2022-fg6j8 | Selectivity and stability of N-terminal targeting protein modification chemistries | Protein N-termini provide uniquely reactive motifs for single site protein modification. Though a number of reactions have been developed to target this site, the selectivity, generality, and stability of the conjugates formed has not been studied. We have therefore undertaken a comprehensive comparative study of the most promising methods for N-terminal protein modification, and find that there is no ‘one size fits all’ approach, necessitating reagent screening for a particular protein or application. Moreover, we observed limited stability in all cases, leading to a need for continued innovation and development in the bioconjugation field. | Lydia Barber; Nicholas Yates; Martin Fascione; Alison Parkin; Glyn Hemsworth; Paul Genever; Christopher Spicer | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304892c58843b62709a0863/original/selectivity-and-stability-of-n-terminal-targeting-protein-modification-chemistries.pdf |
60c757caf96a0001d7288d20 | 10.26434/chemrxiv.14459856.v1 | Developing Machine Learning Models for Ionic Conductivity of Imidazolium-Based Ionic Liquids | In this work, we have developed machine learning models based on support vector machine (SVM) and artificial neural network (ANN) to correlate ionic conductivity of imidazolium-based ionic liquids. The data, collected from the NIST ILThermo Database, spans six orders of magnitude and ranges from 275-475 K. Both models were found to exhibit very good performance. The ANN-model was then used to predict ionic conductivity for all the possible combinations of cations and anions contained in the original dataset, which led to the identification of an ionic liquid with 30% higher ionic conductivity than the highest conductivity reported in the database at 298 K. The model was further employed to predict ionic conductivity of binary ionic liquid mixtures. A large number of ionic liquid mixtures were found to possess non-ideal behavior in that an intermediate mole fraction for such ionic liquid mixtures resulted in either a maximum or minimum in the ionic conductivity. | Pratik Dhakal; Jindal Shah | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757caf96a0001d7288d20/original/developing-machine-learning-models-for-ionic-conductivity-of-imidazolium-based-ionic-liquids.pdf |
635744b618a8cc417d4fe946 | 10.26434/chemrxiv-2022-f6wp5 | Engineering Small Molecule Switches of Protein Function in Zebrafish Embryos
| Precise temporally regulated protein function directs the highly complex processes that make up embryo development. The zebrafish embryo is an excellent model organism to study develop-ment and conditional control over enzymatic activity is desirable to target chemical intervention to specific developmental events and to investigate biological mechanisms. Surprisingly, however, few generally applicable small molecule switches of protein function exist in zebrafish. Genetic code expansion allows for site-specific incorporation of unnatural amino acids into proteins that contain caging groups that are removed through addition of small molecule triggers such as phosphines or tetrazines. This broadly applicable control of protein function was applied to acti-vate several enzymes, including a GTPase and a protease, with temporal precision in zebrafish embryos. Simple addition of the small molecule trigger to the media produces robust and tunable protein activation, which was used to gain insight into the development of a congenital heart de-fect from a RASopathy mutant of NRAS, and to control DNA and protein cleavage events cata-lyzed by a viral recombinase and a viral protease, respectively. | Wes Brown; Joshua Wesalo; Michael Tsang; Alexander Deiters | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635744b618a8cc417d4fe946/original/engineering-small-molecule-switches-of-protein-function-in-zebrafish-embryos.pdf |
66869b5101103d79c5fe5efa | 10.26434/chemrxiv-2024-rpk9q | Distortion/Interaction Analysis via Machine Learning | Machine learning (ML) models have provided a highly efficient pathway to quantum mechanical accurate reaction barrier predictions. Previous approaches have, however, stopped at prediction of these barriers instead of developing predictive capabilities in reactivity analysis tasks such as distortion/interaction-activation strain analysis. Such methods can provide insight into reactivity trends and ultimately guide rational reaction design. In this work we present the novel application of ML to the rapid and accurate prediction of distortion and interaction DFT energies across four datasets (three existing and one new dataset). We also show how our models can accurately predict on unseen, high impact literature examples where DFT-level distortion/interaction analysis has previously been used to explain reactivity trends for cycloadditions. This work thus provides support for ML to be utilised further in reactivity analysis across different reaction classes at a fraction of the cost of traditional methods such as DFT. | Samuel Espley; Samuel Allsop; David Buttar; Simone Tomasi; Matthew Grayson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66869b5101103d79c5fe5efa/original/distortion-interaction-analysis-via-machine-learning.pdf |
67c855546dde43c90898d1ab | 10.26434/chemrxiv-2025-nrzhp | Direct Observation of Triplet-Triplet Energy Transfer Between C-Nucleotides of Thioxanthone and Naphthalene in DNA | Investigating the migration of excited-state energy in DNA is crucial for a deep understanding of protection mechanisms and light-induced DNA damage. While numerous reports focused on single electron transfer and Förster-type energy transfer in DNA, studies on the Dexter-type triplet-triplet energy transfer are scarce, in particular those with direct detection of photoexcited triplet states. Herein, we present direct measurements of the distance-dependent triplet-triplet energy transfer rates through DNA by using transient absorption spectroscopy. This was achieved through the synthetic incorporation of thioxanthone as energy donor and naphthalene as energy acceptor into a DNA double strand at defined positions. The energy transfer rates strongly depend on the number of A-T base pairs (up to four) separating the energy donor from the energy acceptor. We observed a fast energy transfer rate with a time constant of 17 ns for the DNA sample in which the donor and acceptor are directly adjacent in the DNA. By analyzing two additional donor-acceptor distances, a steep exponential distance dependence with an attenuation factor of 1.15 Å^−1 could be obtained. Our results demonstrate that DNA acts as a poor conductor of triplet energy when energy donors with triplet energies below 2.7 eV are used, complementing more indirect studies on sensitized DNA damage. | Sebastian Häcker; Till J. B. Zähringer; Hans-Achim Wagenknecht; Christoph Kerzig | Physical Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c855546dde43c90898d1ab/original/direct-observation-of-triplet-triplet-energy-transfer-between-c-nucleotides-of-thioxanthone-and-naphthalene-in-dna.pdf |
62b075f57da6ce7d6718682a | 10.26434/chemrxiv-2022-0rb4h | Photoinduced Site-Selective C-H Functionalization by Pyridine N-oxide Based HAT Catalysts | Readily available and facilely tunable pyridine N-oxides have been developed as effective photoinduced hydrogen-atom-transfer (HAT) catalyst for site-selective C-H functionalizations of a broad range of C-H substrates, including unactivated al-kanes. Pyridine N-oxide radicals, catalytically generated from N-oxides by photoredox catalyzed single-electron oxidation, are the key intermediate that enable effective HAT process for carbon radical generation to achieve alkylation, amination, azidation, and allylation. Additionally, the fine tuning of reactivity and selectivity of pyridine N-oxides through operationally simple structural modification was investigated and shown promising capability for selective functionalization of unactivat-ed secondary and primary C(sp3)–H bonds. | Yongming Deng; Ban Wang; Cristina Ascenzi Pettenuzzo; Jujhar Singh; Gavin Mccabe; Logan Clark; Ryan Young; Jingzhi Pu | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b075f57da6ce7d6718682a/original/photoinduced-site-selective-c-h-functionalization-by-pyridine-n-oxide-based-hat-catalysts.pdf |
662be608418a5379b0cf259f | 10.26434/chemrxiv-2024-tg4l3 | Expanding the repertoire of GalNAc analogues for cell-specific bioorthogonal tagging of glycoproteins | Glycosylation is a ubiquitous modification of proteins, necessitating approaches for its visualization and characterization. Bioorthogonally tagged monosaccharides have been instrumental to this end, offering a chemical view into the cell biology of glycans. Understanding the use of such monosaccharides by cellular biosynthetic pathways has expanded their applicability in cell biology, for instance through the strategy Bioorthogonal Cell-specific Tagging of Glycoproteins (BOCTAG). Here, we show that the cellular use of two azide-tagged analogues of the monosaccharide N-acetylgalactosamine can be promoted through expression of two biosynthetic enzymes. Cellular expression of the kinase NahK and the engineered pyrophosphorylase AGX1F383A led to biosynthesis of the corresponding activated nucleotide-sugars and subsequent bioorthogonal tagging of the cellular glycoproteome. We explore the use of both sugars for BOCTAG, demonstrating the visualization of cell surface glycosylation in a specific cell line in a co-culture system. Our work adds to the toolbox of glycoprotein analysis in biomedicine. | Abdul Zafar; Sandhya Sridhar; Ganka Bineva-Todd; Anna Cioce; Nadia Abdulla; Vincent Chang; Stacy Malaker; David Hewings; Benjamin Schumann | Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662be608418a5379b0cf259f/original/expanding-the-repertoire-of-gal-n-ac-analogues-for-cell-specific-bioorthogonal-tagging-of-glycoproteins.pdf |
6694dc51c9c6a5c07a53fff6 | 10.26434/chemrxiv-2024-6b2hs | Iminobispyrazole (IBP) Photoswitches: Two Pyrazole Rings Can Be Better Than One | We recently demonstrated that suitably functionalised aryliminopyrazoles can exhibit useful photoswitching properties. In this study, we investigate the photoswitching potential of iminobispyrazoles (IBPs). We find that the regiochemistry of the IBPs strongly dictates their photoswitching properties, most notably, the λmax, the photostationary state and the thermal half-life of the Z-isomer. | Jiarong Wu; Clara Li; Lasse Kreimendahl; Jake Greenfield | Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6694dc51c9c6a5c07a53fff6/original/iminobispyrazole-ibp-photoswitches-two-pyrazole-rings-can-be-better-than-one.pdf |
62c9a775332f02a995e35b89 | 10.26434/chemrxiv-2022-68sr0 | Evaluation of the reaction mechanism between 1,4-dihydropyridines and α,β-unsaturated nitriles. | Hydride transfer reactions involving 1,4-dihydropyridines play a central role in bioorganic chemistry as they represent an important share of redox metabolism. For this class of reactions, the direct hydrid transfer is the commonly accepted mechanism, however an Alder-Ene-like pathway has been proposed as a plausible alternative. The reaction between 1,4-ditrimethylsilyl-1,4-dihydropyridine, and α,β-unsaturated nitriles is a solid candidate for this latter pathway. In this work, we perform high level ab initio and density functional theory computations to characterize the mechanism of this reaction, taking into account diverse reaction paths, evaluating the effect of solvent polarity and variations in chemical structure. Our analysis explains the stereochemical aspects of the reaction, characterizing the detected but up to now unidentified predominant products. The reactions are found to proceed in a highly asynchronous, nearly stepwise way, under implicit solvent conditions, with transition states that display significant aromatic features. We show Alder-Ene and direct hydride transfer pathways as two extremes of a continuous mechanistic spectrum for this kind of reactions, with the analyzed
systems located approximately equidistant from both ends. | David Adrian Saez; Stefan Vogt-Geisse; Esteban Vöhringer-Martinez | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Stereochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c9a775332f02a995e35b89/original/evaluation-of-the-reaction-mechanism-between-1-4-dihydropyridines-and-unsaturated-nitriles.pdf |
61475b4678257bce442252d7 | 10.26434/chemrxiv-2021-w8v42 | Setting up the HyDRA blind challenge for the microhydration of organic molecules | The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates with experimentally known and published water donor vibrations is presented and a test set of 10 monohydrates with unknown or unpublished water donor vibrational wavenumbers is described together with relevant background literature. The rules for data submissions from computational chemistry groups are outlined and the planned publication procedure after the end of the blind challenge is discussed. | Taija Lena Fischer; Margarethe Bödecker; Anne Zehnacker-Rentien; Ricardo A. Mata; Martin A. Suhm | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61475b4678257bce442252d7/original/setting-up-the-hy-dra-blind-challenge-for-the-microhydration-of-organic-molecules.pdf |
6388b5f114d92d80ae9bf6db | 10.26434/chemrxiv-2022-65z24 | Effect of Polymer Composition and Morphology on Mechanochemical Activation in Nanostructured Triblock Copolymers | The effect of composition and morphology on mechanochemical activation in nanostructured block copolymers was investigated in a series of poly(methyl methacrylate)block-poly(n-butyl acrylate)-block-poly(methyl methacrylate) (PMMA-b-PnBA-b-PMMA) triblock copolymers containing a force-responsive spiropyran unit in the center of the rubbery PnBA midblock. Triblock copolymers with identical PnBA midblocks and varying lengths of PMMA end blocks were synthesized from a spiropyran-containing macroinitiatior via atom transfer radical polymerization, yielding polymers with volume fractions of PMMA ranging from 0.21 to 0.50. Characterization by transmission electron microscopy revealed that the polymers self-assembled into spherical and cylindrical nanostructures. Simultaneous tensile tests and optical measurements revealed that mechanochemical activation is strongly correlated to the chemical composition and morphologies of the triblock copolymers. As the glassy (PMMA) block content is increased, the overall activation increases, and the onset of activation occurs at lower strain but higher stress, which agrees with predictions from our previous computational work. These results suggest that the self-assembly of nanostructured morphologies can play an important role in controlling mechanochemical activation in polymeric materials, and provide insights into how polymer composition and morphology impact molecular-scale force distributions. | Zijian Huo; Swati Arora; Victoria Kong; Brandon Myrga; Antonia Statt; Jennifer Laaser | Polymer Science; Organic Polymers; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6388b5f114d92d80ae9bf6db/original/effect-of-polymer-composition-and-morphology-on-mechanochemical-activation-in-nanostructured-triblock-copolymers.pdf |
61927df047f47ddf9da2480d | 10.26434/chemrxiv-2021-jl1z2 | Mapping the Morphological Landscape of Oligomeric Di-block Peptide Polymer Amphiphiles | Peptide polymer amphiphiles (PPAs) are highly tunable hybrid materials that achieve complex, protein-like assembly landscapes by combining sequence-dependent properties of peptides with structural diversity of polymers. Despite their promise as functional biomimetic materials, determining how polymer and peptide properties simultaneously affect PPA self-assembly remains challenging. We herein present a systematic study of critical components within the PPA design space that dictate the self-assembled morphologies. PPAs containing hydrophobic oligo(ethyl acrylate) were used to interrogate the role of polymer molecular weight and dispersity in addition to peptide length and charge density on self-assembly. We observed that PPAs predominantly formed spherical particles (micelles and vesicles), with both polymer molecular weight and peptide hydrophilicity determining morphology. Additionally, peptide charge and polymer dispersity influence particle size. These key benchmarks will facilitate the rational design of PPAs that expand the scope of biomimetic and biocompatible functionality within assembled soft materials. | Benjamin Allen; Zoe Wright; Hailey Taylor; Thomas Oweida; Sabila Kader-Pinky; Emily Patteson; Kara Bucci; Caleb Cox; Yaroslava Yingling; Abigail Knight | Polymer Science; Nanoscience; Biopolymers; Polymer morphology; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61927df047f47ddf9da2480d/original/mapping-the-morphological-landscape-of-oligomeric-di-block-peptide-polymer-amphiphiles.pdf |
61256760b136d69fc20e2d8e | 10.26434/chemrxiv-2021-pcfcs | Comparing Two Seized Drug Workflows for the Analysis of Synthetic Cannabinoids, Cathinones, and Opioids | As the challenges faced by drug chemists continue to persist due to the presence of synthetic opioids, novel psychoactive substances, and other emerging drugs, laboratories are continuing to look for new analytical approaches or techniques to ease the burdens. These new solutions can range from simple changes in existing methods to better distinguish isomers to adoption and implementation of entirely new technologies for screening or confirmation. One barrier to making these transitions is lack of data to understand how, or even if, workflow changes will address the challenges. In this study, we attempt to compare, qualitatively and quantitatively, an existing analytical workflow for seized drug analysis to a new, experimental workflow to better understand the potential benefits and drawbacks. Using adjudicated and mock case samples containing synthetic cannabinoids, synthetic cathinones, and opioids, four forensic chemists were asked to analyze fifty samples using one of two workflows. The first was an existing workflow that employed color tests for screening alongside general purpose gas chromatography flame ionization detection (GC-FID) and general purpose gas chromatography mass spectrometry (GC-MS) analyses for confirmation. The second was an experimental workflow that combined direct analysis in real time mass spectrometry (DART-MS) for screening with class-specific (targeted) GC-MS methods for confirmation. At each step in the analysis scheme, chemists recorded the time required and as well as their interpretation of the results. Comparison of the workflows showed that screening by DART-MS required the same amount of time as color tests but yielded significantly more accurate, and specific, information. Confirmation using the general purpose GC-FID and GC-MS methods of the existing workflow required more than twice the amount of instrument time and data interpretation time while also presenting other analytical challenges that prevented compound confirmation in select samples. Use of targeted GC-MS methods simplified data interpretation, reduced consumption of reference materials, and addressed almost all the limitations of general purpose methods. While the experimental workflow is not yet validated for casework, this study shows how rethinking analytical workflows for seized drug analysis could greatly assist laboratories in reducing turnaround times, backlogs, and standards consumption. It also demonstrates the potential impact of being able to investigate workflow changes prior to implementation. | Edward Sisco; Amber Burns; Elizabeth Schneider; Charles R. Miller IV; Laurel Bobka | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61256760b136d69fc20e2d8e/original/comparing-two-seized-drug-workflows-for-the-analysis-of-synthetic-cannabinoids-cathinones-and-opioids.pdf |
62baed749ca5bb755ee9af5c | 10.26434/chemrxiv-2022-5bjb6 | Theoretical Investigation of Knowles Hydroamination Based on Systematic Exploration of Oxidation/Reduction Pathways for Photoredox-Catalyzed Radical Process | Systematic exploration of reaction paths based on quantum chemical calculations revealed the entire mechanism of Knowles’s light-promoted catalytic intramolecular hydroamination via radical processes. Bond formation/cleavage competes with single electron transfer (SET) from the catalyst/substrate to substrate/catalyst. All these processes were theoretically described by reactions through transition states in the same electronic state and non-radiative transitions through the seam of crossings (SX) between different electronic states. This study determined the energetically favorable reaction path by combining the reaction path searches and the SX geometry searches, and then discusses the entire reaction mechanism. Such a calculation was achieved by establishing a novel computational approach that represents SET as a non-adiabatic transition between substrate's PESs for different charge states adjusted based on the catalyst's redox potential. Finally, we uncovered the whole picture of the reaction process, in which N atom of the substrate is oxidized by photoredox catalyst via SET, the resulting aminium radical is added to alkene, and the hydroamination product is produced after SET process accompanying protonolysis with MeOH. The present calculations showed that the reduction and proton transfer proceed concertedly. Also, in the reduction process, there are SET paths leading to both the product and the reactant, and the redox potentials of the catalyst change the contribution of the SET path leading to the product. | Yu Harabuchi; Hiroki Hayashi; Hideaki Takano; Tsuyoshi Mita; Satoshi Maeda | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62baed749ca5bb755ee9af5c/original/theoretical-investigation-of-knowles-hydroamination-based-on-systematic-exploration-of-oxidation-reduction-pathways-for-photoredox-catalyzed-radical-process.pdf |
65cc27be9138d2316111b9c8 | 10.26434/chemrxiv-2024-l53kk | Halocyclization of alkynoic thioester and oxidative aromatization in one-pot | This paper reports the halocyclization of alkynoic thioesters, as S-nucleophiles, with N-halosuccinimide, followed by oxidative aromatization with the same reagent for the one-pot synthesis of thiophenes, important heterocycles exhibiting remark-able applications in different disciplines. Brief mechanistic studies were also performed to elucidate the halocyclization process. The potential diverse applications of the product, dihydrothiophene were also assessed. | Miari Kurihara; Hiroki Shigehisa | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cc27be9138d2316111b9c8/original/halocyclization-of-alkynoic-thioester-and-oxidative-aromatization-in-one-pot.pdf |
61e533bceab6efb44ae40dad | 10.26434/chemrxiv-2022-12k2f-v2 | Cyclic 5-Membered Disulfides Are Not Selective Substrates of Thioredoxin Reductase, but Are Opened Nonspecifically | The cyclic five-membered disulfide 1,2-dithiolane has been used as the key element in numerous chemical biology probes. Contradictory views of this disulfide populate the literature: some reports describe it as being nonspecifically reduced, others as a highly specific substrate for thioredoxin reductase (TrxR). We here show that 1,2-dithiolane probes are nonspecifically reduced by a broad
range of thiol reductants and redox-active proteins, and that
their cellular performance is barely affected by TrxR inhibition or knockout. We conclude that inhibitor screenings and "TRFS" probes that have used 1,2-dithiolanes as TrxRselective substrates should be treated with caution, and may need re-evaluation. Understanding 1,2-dithiolanes’ behaviour needs consideration of probe localisation and environmentdependent fluorescence, reduction-independent ring-opening polymerisation, thiol-dependent cellular uptake, and caution when applying thiophilic inhibitors. We present an approach controlling against assay misinterpretation with reducible probes, to ensure that future TrxR-targeted designs are robustly evaluated for selectivity, and to better orient future research. | Jan Felber; Lena Poczka; Karoline Scholzen; Lukas Zeisel; Martin
S. Maier; Sander Busker; Ulrike Theisen; Christina Brandstädter; Katja Becker; Elias Arnér; Julia Ahlfeld; Oliver Thorn-Seshold | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e533bceab6efb44ae40dad/original/cyclic-5-membered-disulfides-are-not-selective-substrates-of-thioredoxin-reductase-but-are-opened-nonspecifically.pdf |
645304b627fccdb3ea73c36e | 10.26434/chemrxiv-2023-8r2w6 | Metal- and Pyrolysis-Free Ionic Covalent Organic Framework Nanosheet for Efficient Oxygen Evolution Reaction | Metal-free electrocatalysts for oxygen evolution reaction (OER) are crucial to enable practical water splitting for future clean energy production. The preparation of such electrocatalysts remains a great challenge because they are difficult to obtain a high energy input due to the limitations of kinetically sluggish anodic half-cell reaction. Herein, we develop a novel metal- and pyrolysis-free ionic covalent organic framework (COF) nanosheet (termed JUC-627-NS) and explore its application as an efficient OER electrocatalyst for the first time. Remarkably, the samples combined with JUC-627-NS and graphene can obtain an ultralow overpotential (275 mV at a current density of 10 mA cm-2), which is one of the best among metal- and pyrolysis-free electrocatalysts reported so far. Combining theoretical calculations and in-situ infrared spectroscopy, it is proved that the imidazolium salt moiety is the active center of the electrocatalyst, and the strong cation-π interaction in the complex greatly promotes the reactivity. These results therefore provide a new strategy for designing ionic COF nanosheets as efficient metal-free OER electrocatalysts for energy conversion and storage devices. | Rui Wang; Ziqi Zhang; Jinquan Suo; Li Liao; Leibo Li; Zhuochen Yu; Jialong Song; Liangkui Zhu; Xinyu Guan; Yusran Yusran; Valentin Valtchev; Shilun Qiu; Qianrong Fang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645304b627fccdb3ea73c36e/original/metal-and-pyrolysis-free-ionic-covalent-organic-framework-nanosheet-for-efficient-oxygen-evolution-reaction.pdf |
66568c9a418a5379b0851b6d | 10.26434/chemrxiv-2024-fmn3w | A Pyridinium Ylide-alkylation Strategy for the Structural Diversification of N-Carbamoyl Pyridinium Salts | A pyridinium-ylide alkylation strategy has been developed for accessing N,N-disubstituted carbamoyl pyridinium salts that possess multiple nucleophilic sites. The method was shown to be tolerant towards an array of different pyridinium scaffolds and common electrophiles; enabling access to structurally diverse pyridinium salts. The potential versatility of the approach was demonstrated through the synthesis of chemically complex, heterotrifunctional pyridinium salts containing a pyridinium warhead, a click chemistry handle, and a third, high-value, payload. | Akash Sarkar; Benjamin Gossett; Michael Taylor | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66568c9a418a5379b0851b6d/original/a-pyridinium-ylide-alkylation-strategy-for-the-structural-diversification-of-n-carbamoyl-pyridinium-salts.pdf |
60c740e69abda2abfdf8bda2 | 10.26434/chemrxiv.7879343.v1 | A Triple Layer of Immiscible Solvents for NMR Sample Preparation: Enhanced Sensitivity and Reduced Deuterated Solvent for Observation of Heteronuclei | <p>Organic chemistry labs routinely
perform NMR in a standard 5 mm NMR tube. NMR sample is prepared by filling the
lowermost 4 cm length of a regular 5 mm 0.d. tube that holds approximately 0.55
ml of a deuterated solvent. This is actually a sample dilution procedure as the
signal mainly comes from the central part, i.e. 1.8 cm length sample that fits
the typical coil length of 1.8 cm in regular NMR spectrometers. The diluted top
and bottom part of the sample is away from the coil and contributes less
signal. This dilution procedure amplifies the requirement of expensive
deuterated solvent and lowers sensitivity. The present study explores a new way
of sample preparation which involves sandwiching a small amount of the
deuterated solvent (D<sub>2</sub>O) of length 1.8 cm containing the analyte
between two non-deuterated solvents (CCl<sub>4</sub> at bottom of length ≈ 1 cm
and similarly C<sub>6</sub>H<sub>6</sub> at top), which are immiscible with the
former using a regular 5 mm o.d. NMR tube in such a way that total length is
still 4 cm as demanded by the magnetic field homogeneity considerations. The
analyte now being closer to NMR coil dissolved in 1.8 cm solvent, improves
sensitivity and reduces deuterated solvent hitherto required. <sup>13</sup>C
and <sup>15</sup>N spectra from such a set-up display two to three-fold higher
signal to noise ratio and hence four to eightfold savings in experimental time
or faster data collection.</p><br /> | Bikash Baishya; Atish Chandra | Spectroscopy (Anal. Chem.) | CC BY 4.0 | CHEMRXIV | 2019-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e69abda2abfdf8bda2/original/a-triple-layer-of-immiscible-solvents-for-nmr-sample-preparation-enhanced-sensitivity-and-reduced-deuterated-solvent-for-observation-of-heteronuclei.pdf |
61fa9fdd49bd32ace24253eb | 10.26434/chemrxiv-2022-c9fp1 | Tuning the flexibility of MIL-88A(Sc) through synthetic optimisation and postsynthetic halogenation | Breathing in metal-organic frameworks (MOFs), the distinctive transformation between a porous phase and a less (or non) porous phase, often controls the uptake of guest molecules, endowing flexible MOFs with highly selective gas adsorptive properties. In highly flexible topologies, breathing behaviour can be tuned by linker modification, which is typically achieved pre-synthetically by the use of functionalised linkers. Herein, we show that MIL-88A(Sc) exhibits the characteristic flexibility of its topology, which can be tuned by (i) modifying synthetic conditions to yield a formate-buttressed analogue that is rigid and porous, and (ii) postsynthetic bromination across the alkene functionality of the fumarate ligand, generating a product that is rigid but non-porous. As well as providing different methodologies for tuning the flexibility and breathing behaviour of this archetypal MOF, we show that bromination of the formate-bridged analogue results in an identical material, representing a rare example of two different MOFs being postsynthetically converted to the same end product. | Catherine Walshe; Alexander Thom; Claire Wilson; Sanliang Ling; Ross Forgan | Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2022-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fa9fdd49bd32ace24253eb/original/tuning-the-flexibility-of-mil-88a-sc-through-synthetic-optimisation-and-postsynthetic-halogenation.pdf |
676e80896dde43c908812aa1 | 10.26434/chemrxiv-2024-hg581 | Nanotechnology and Biopolymers: A Perfect Synergy for Modern Applications | This review comprehensively explores biodegradable polymer-based nanocomposites and their diverse applications, including water purification, environmental remediation, and hydrogen production. A detailed scientometric analysis highlights key trends and developments in biopolymers such as cellulose and chitosan. These biopolymers can be functionalized or conjugated with advanced materials like metallic nanoparticles, metal oxides, zeolites, perovskites, covalent-organic frameworks (COFs), metal-organic frameworks (MOFs), zeolitic imidazolate frameworks (ZIFs), and MXenes. The resulting biopolymer/nanoparticle composites exhibit remarkable multifunctional properties, making them highly suitable for industrial-scale production and integration into modern technologies. Nanocellulose, in particular, has emerged as a promising material for enabling advanced fabrication techniques, such as integrating MOFs into commercial products via three-dimensional (3D) printing. This review highlights these materials' potential to revolutionize sustainability and green technology applications, offering innovative solutions for critical challenges in various sectors. | Hani Nasser Abdelhamid | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e80896dde43c908812aa1/original/nanotechnology-and-biopolymers-a-perfect-synergy-for-modern-applications.pdf |
646fd2fabe16ad5c57e953b8 | 10.26434/chemrxiv-2023-dq01m-v3 | Informing methane emissions inventories using facility aerial measurements at midstream natural gas facilities | Increased interest in greenhouse gas (GHG) emissions, including recent legislative action and voluntary programs, has increased attention on quantifying, and ultimately reducing, methane emissions from the natural gas supply chain. While inventories used for public or corporate GHG policies have traditionally utilized bottom-up (BU) methods to estimate emissions, the validity of such inventories has been questioned. Therefore, there is attention on utilizing full-facility measurements using airborne, satellite or drone (top-down (TD)) techniques to inform, improve, or validate inventories. This study utilized full-facility estimates from two independent TD methods at 15 midstream natural gas facilities in the U.S.A., and were compared with a contemporaneous daily inventory assembled by the facility operator, employing comprehensive inventory methods. Estimates from the two TD methods statistically agreed in 2 of 28 paired measurements. Operator inventories, which included extensions to capture sources beyond regular inventory requirements and to integrate local measurements, estimated significantly lower emissions than the TD estimates for 40 of 43 paired comparisons. Significant disagreement is observed at most facilities, both between the two TD methods and between the TD estimates and operator inventory. These findings have two implications. Firstly, improving inventory estimates will require additional on-site or ground-based diagnostic screening and measurement of all sources. Secondly, the TD full-facility measurement methods need to undergo further testing, characterization, and potential improvement specifically tailored for complex midstream facilities. | Jenna Brown; Tecle Rufael ; Matthew Harrison; Selina Roman-White; Gregory Ross ; Fiji George; Daniel Zimmerle | Energy | CC BY 4.0 | CHEMRXIV | 2023-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646fd2fabe16ad5c57e953b8/original/informing-methane-emissions-inventories-using-facility-aerial-measurements-at-midstream-natural-gas-facilities.pdf |
6601a6cd9138d2316144253d | 10.26434/chemrxiv-2024-vxxkw | Extrusion of MOF-Polymer Nanocomposites with High MOF Loadings | While metal-organic frameworks (MOFs) hold great promise for a wide range of industrial applications, the challenges of handling fine crystalline powders have limited their adoption. MOF-polymer composites are one solution to this challenge, as composites or membranes are substantially easier to handle, however most existing MOF-polymer composites have low MOF loadings and suffer MOF leaching due to the weak interactions between the MOF and the polymer. In this work, we report the continuous extrusion of MOF-polymer composites containing up to 60 wt% of commercially available MOFs and successful extrusion of small amounts composites containing 70 wt% MOF, with the composite viscosity an important factor in the success of the extrusion. The MOF is well-distributed through the composite and remains crystalline despite the high temperatures and mechanical forces involved in the extrusion process. While the composites are more brittle than the base polymer and appear largely non-porous, the suspected presence of inaccessible internal pores coupled with the increased thermal stability of the composites compared to the base polymer indicate potential for the composites to be used as fire resistant materials. | Joshua A Powell; Jazmine Aiya D Marquez; Giles A Johnson; Ray O K Ozdemir; Qingsheng Wang | Materials Science; Polymer Science; Composites; Materials Processing; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6601a6cd9138d2316144253d/original/extrusion-of-mof-polymer-nanocomposites-with-high-mof-loadings.pdf |
635c5f3aca86b8169ec7e4a2 | 10.26434/chemrxiv-2022-52cn3 | EPISOL: A Software Package with Expanded Functions to Perform 3D-RISM Calculations for the Solvation of Chemical and Biological Molecules | Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the Expanded Package for IET-based Solvation (EPISOL), that performs 3D-reference interaction site model (3D-RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D-RISM theory, including the recent hydrophobicity-induced density inhomogeneity (HI) theory for hydrophobic solutes and ion-dipole correction (IDC) theory for negatively charged solutes. To speed up the convergence and enhance the stability of the self-consistent iterations, we have introduced several numerical schemes in EPISOL, including a newly developed dynamic mixing approach. We show that these schemes have significantly reduced the failure rate of 3D-RISM calculations compared to AMBER-RISM software. EPISOL consists of both a user-friendly graphic interface and a kernel library that allows users to call its routines and adapt them to other programs. EPISOL is compatible with the force-field and coordinate files from both AMBER and GROMACS simulation packages. Moreover, EPISOL is equipped with an internal memory control to efficiently manage the use of physical memory, making it suitable for performing calculations on large biomolecules. We demonstrate that EPISOL can efficiently and accurately calculate solvation density distributions around various solute molecules (including a protein chaperone consisting of 120,715 atoms) and obtain solvent free energy for a wide range of organic compounds. We expect that EPISOL can be widely applied as a solvation model for chemical and biological systems. EPISOL is available at https://github.com/EPISOLrelease/EPISOL. | Siqin Cao; Michael Kalin; Xuhui Huang | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635c5f3aca86b8169ec7e4a2/original/episol-a-software-package-with-expanded-functions-to-perform-3d-rism-calculations-for-the-solvation-of-chemical-and-biological-molecules.pdf |
6685010fc9c6a5c07a250bac | 10.26434/chemrxiv-2024-pggps | High Entropy Boride-SiC Composite: Synthesis, Characterization and Thermo-oxidative behaviour | Silicon carbide reinforced multicomponent high entropy diboride-based particulate composites (HEB-SiC) were fabricated by spark plasma sintering at 1800°C using diboride powders prepared from boro-carbothermal reduction method to investigate the influence of the addition of SiC (SiC content = 20, 40 vol%) on the microstructural evolution, oxidation, and exposure to arc-jet behaviour was reported. SiC has been found to improve the densification of pristine diboride, with attainment of a maximum of ~ 98% relative density for SiC content of 40 vol%. A percolating network of SiC grains in the HEB matrix was observed in the case of composites with 40% volume fraction of SiC. The oxidative behavior at 1400°C in air revealed excellent improvement of oxidation resistance of 20 vol% SiC reinforced composite as compared to other sintered specimens. Arc-jet testing on 20 vol% SiC reinforced composite revealed no structural deformity with very minute-scaled formation of surface oxide layers. These results indicate that the addition of 20 vol% SiC in a diboride matrix can contribute to the optimal preparation of high entropy diboride-based ceramics with balanced mechanical properties with improved oxidation resistance.
| Rahul Mitra; Subhra Sourav Jana; Venkateswaran Thiruvenkatam ; Chanchal Ghosh; Tanmoy Maiti; Krishanu Biswas | Materials Science; Ceramics; Composites | CC BY NC 4.0 | CHEMRXIV | 2024-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6685010fc9c6a5c07a250bac/original/high-entropy-boride-si-c-composite-synthesis-characterization-and-thermo-oxidative-behaviour.pdf |
67793c286dde43c908468c2a | 10.26434/chemrxiv-2025-8dblf | Development of Ethyl Hydrazide-Based Selective Histone Deacetylase 6 (HDAC6) PROTACs | Histone deacetylases (HDACs) are promising targets for epigenetic drug discovery. Additionally, targeted degradation of HDACs has emerged as a novel approach in medicinal chemistry and chemical biology. However, most inhibitors and degraders rely on the potentially genotoxic hydroxamate as a zinc-binding group (ZBG). In this study, we present the development of HDAC6-directed proteolysis-targeting chimeras (PROTACs) featuring an ethyl hydrazide moiety as an alternative ZBG. This approach avoids the genotoxicity concerns of hydroxamates while maintaining potent HDAC6 degradation. We synthesized a series of CRBN- and VHL-recruiting PROTACs and identified several potent HDAC6 degraders (HDAC6 Dmax > 80%). Among these, 17c was the most effective, achieving an HDAC6 degradation of 91% and a DC50 value of 14 nM. Further characterization proved that 17c acts via the ubiquitin-proteasome system and chemoproteomics confirmed selective HDAC6 degradation over other HDAC isoforms. | Daniel Stopper; Irina Honin; Felix Feller; Finn Kristian Hansen | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67793c286dde43c908468c2a/original/development-of-ethyl-hydrazide-based-selective-histone-deacetylase-6-hdac6-prota-cs.pdf |
60c745cd337d6c79d5e2705f | 10.26434/chemrxiv.10272041.v1 | Ab initio Molecular Dynamics of CdSe Quantum Dots Doped Glasses | <div>
<div>
<div>
<p>We have probed the local atomic structure of the interfacial structure between
the CdSe quantum dots (QDs) and sodium silicate glass matrix. Using ab initio
molecular dynamics simulations, we determined the structural properties and bond
length, in excellent agreement with previous experimental observations. Based on
analysis of radial distribution functions, coordination environment and ring structures,
we demonstrate that huge structure reconstruction occurs at the interface between the
CdSe QDs and the glass matrix. The incorporation of the CdSe QDs disrupts the Na-O
bonds, while stronger SiO4 tetrahedra are reformed. The existence of the glass matrix
breaks the stable 4-member (4MR) and 6-member (6MR) of Cd-Se rings, and we
observe a disassociated Cd atom dissolved in the glass matrix. Besides, the formation
of Se-Na and Cd-O linkages is observed at the CdSe QDs/glass interface. These results
significantly extend our understanding of the interfacial structure of the CdSe QDs
doped glasses, and provide physical and chemical insight into the possible defect
structure origin of CdSe QDs, of interest to the fabrication of the highly luminescent
CdSe QDs doped glasses.
</p>
</div>
</div>
</div> | Wenke Li; Xiujian Zhao; Chao Liu; François-Xavier Coudert | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745cd337d6c79d5e2705f/original/ab-initio-molecular-dynamics-of-cd-se-quantum-dots-doped-glasses.pdf |
6557b089dbd7c8b54b793327 | 10.26434/chemrxiv-2023-m34cq | Maximum and Comparative Efficiency Calculations for Integrated Capture and Conversion CO2 | The integration of CO2 capture and conversion has the potential to decrease the capital and energetic cost of utilizing dilute CO2 streams. Herein we evaluate the overall energy efficiency for electrochemical conversion of dilute CO2 streams to product. Additionally, the energetic requirement for the use of intermediary sorbents for CO2 capture is described, which facilitates the comparison of catalyst efficiencies using the same sorbent in the context of initial CO2 concentration. We also introduce a parameter, ΔERCC, that evaluates the suitability of sorbents for dilute CO2 streams. These energetic considerations provide quantitative metrics for evaluating integrated CO2 capture and conversion systems. | Aaron Appel; Jenny Yang | Catalysis; Energy; Electrocatalysis; Energy Storage; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6557b089dbd7c8b54b793327/original/maximum-and-comparative-efficiency-calculations-for-integrated-capture-and-conversion-co2.pdf |
65a1a59e66c13817294fccc3 | 10.26434/chemrxiv-2024-jpwhj | Competition Between Water-Water Hydrogen bonds and Water-pi Bonds in Pyrene-Water Cluster Anions | We present infrared spectra and density functional theory calculations of hydrated pyrene anion clusters with up to four water molecules. The experimental spectra were acquired using infrared Ar messenger photodissociation spectroscopy. Water molecules form clusters on the surface of the pyrene, forming hydrogen bonds with the -system. The structures of the water clusters and their interaction with the system are encoded in the OH stretching vibrational modes. We find that the interactions between water molecules are stronger than between water molecules and the -system. While all clusters show multiple conformers, three- and four-membered rings are the lowest energy structures in the larger hydrates. | Heinrich Salzmann; Anne Rasmussen; Joel Eaves; J. Mathias WEBER | Physical Chemistry; Clusters; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a1a59e66c13817294fccc3/original/competition-between-water-water-hydrogen-bonds-and-water-pi-bonds-in-pyrene-water-cluster-anions.pdf |
60c741ccbdbb89ecfea383c4 | 10.26434/chemrxiv.8131847.v1 | Development of Inhibitors Against Mycobacterium Abscessus tRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches | Mycobacterium abscessus (Mab) is a rapidly growing species of multidrug-resistant nontuberculous mycobacteria (NTM) that has emerged as a growing threat to individuals with cystic fibrosis, and other pre-existing chronic lung diseases. Mab pulmonary infections are difficult, or sometimes impossible, to treat and result in accelerated lung function decline and premature death. There is therefore an urgent need to develop novel antibiotics with improved efficacy. tRNA (m1G37) methyltransferase (TrmD) is a promising target for novel antibiotics. It is essential in Mab and other mycobacteria, improving reading frame maintenance on the ribosome to prevent frameshift errors. In this work a fragment-based approach was employed with the merging of two fragments bound to the active site, followed by structure-guided elaboration to design potent nanomolar inhibitors against Mab TrmD. Several of these compounds exhibit promising activity against mycobacterial species, including Mycobacterium tuberculosis and Mycobacterium leprae in addition to Mab, supporting the use of TrmD as a target for the development of antimycobacterial compounds. | Andrew J. Whitehouse; Sherine E. Thomas; Karen P. Brown; Alexander Fanourakis; Daniel Chan; M. Daben J. Libardo; Vitor Mendes; Helena I. M. Boshoff; R. Andres Floto; Chris Abell; Tom. L. Blundell; Anthony Coyne | Bioorganic Chemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ccbdbb89ecfea383c4/original/development-of-inhibitors-against-mycobacterium-abscessus-t-rna-m1g37-methyltransferase-trm-d-using-fragment-based-approaches.pdf |
60c74bbebb8c1a10f23db28d | 10.26434/chemrxiv.12376469.v1 | Route Exploration and Synthesis of the Reported Pyridone-Based PDI Inhibitor STK076545 | The enzyme protein disulfide isomerase (PDI) is essential for the correct folding of proteins and the activation of certain cell surface receptors, and is a promising target for the treatment of cancer and thrombotic conditions. A previous high-throughput screen identified the commercial compound STK076545 as a promising PDI inhibitor. To confirm its activity and support further biological studies, a resynthesis was pursued of the reported b-keto-amide with an N-alkylated pyridone at the a-position. Numerous conventional approaches were complicated by undesired fragmentations or rearrangements. However, a successful 5-step synthetic route was achieved using an aldol reaction with an a-pyridone allyl ester as a key step. An X-ray crystal structure of the final compound confirmed that the reported structure of STK076545 was achieved, however its lack of PDI activity and inconsistent spectral data suggest that the commercial structure was misassigned. | Eric Greve; Sergey Lindeman; Chris Dockendorff | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bbebb8c1a10f23db28d/original/route-exploration-and-synthesis-of-the-reported-pyridone-based-pdi-inhibitor-stk076545.pdf |
60c7512abb8c1a63ad3dbc33 | 10.26434/chemrxiv.13129709.v1 | Supramolecular Peptide Nanofibrils with Optimized Sequences and Molecular Structures for Efficient Retroviral Transduction | Amyloid-like peptide nanofibrils (PNFs) are abundant in nature providing rich bioactivities and playing both functional and pathological roles. The structural features responsible for their unique bioactivities are, however, still elusive. Supramolecular nanostructures are notoriously challenging to optimize, as sequence changes affect self-assembly, fibril morphologies and biorecognition. Herein, we report the first sequence optimization of PNFs for enhanced retroviral gene transduction via a multiparameter and a multiscale approach. Retroviral gene transfer is the method of choice for stable delivery of genetic information into cells offering great perspectives for the treatment of genetic disorders. Single fibril imaging, zeta potential, vibrational spectroscopy and quantitative retroviral transduction assays provided the structure parameters responsible for PNF assembly, fibril morphologies and PNF-virus-cell interactions. Optimized peptide sequences have been obtained quantitatively forming supramolecular nanofibrils with high intermolecular beta-sheet content that efficiently bound virions and attached to cellular membranes revealing efficient retroviral gene transfer | Stefanie Sieste; Thomas Mack; Edina Lump; Manuel Hayn; Desiree Schütz; Annika Röcker; Christoph Meier; Frank Kirchhoff; Tuomas Knowles; Francesco S. Ruggeri; Christopher Synatschke; Jan Münch; Tanja Weil | Biocompatible Materials; Biological Materials; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7512abb8c1a63ad3dbc33/original/supramolecular-peptide-nanofibrils-with-optimized-sequences-and-molecular-structures-for-efficient-retroviral-transduction.pdf |
6757f00c085116a133ea2fb1 | 10.26434/chemrxiv-2024-1twlf | Hydrophosphinylation of Alkynes via Neutral Magnesium Complexes: Evidence for Ligand Dependency in Structure-Activity Relationships | The pursuit of practical, straightforward, and sustainable methods for forming carbon-phosphorus bonds is crucial in both academia and industry. Traditional synthetic methods often rely on hazardous, halogenated precursors through salt-metathesis routes. In this study, we have synthesized and characterized magnesium complexes [L(Mg-nBu)2] (L = bis(diiminate); nBu = n-butyl) 1 and 2. Complex 1 effectively catalyzes the hydrophosphinylation of alkynes resulting stepwise hydrophosphinylated products namely monophosphinylated vinyledene- and 1,2-diphosphinylated alkanes. While doubly addition products with the alkynes are predominant, this catalytic reaction produces anti-Markovnikov products with inactivated alkenes, whereas activated alkenes giving rise to conjugated products. This transformation showcases an excellent atom economy, broad functional group tolerance and gram scale synthesis for organophosphorus compounds. Through controlled experiments, kinetic studies, and density functional theoretical calculations, we elucidated the reaction mechanism, identifying the active catalytic species and revealing a stepwise hydrophosphinylation process of alkynes. Although complex 1 showed its potential in the hydrophosphinylation of alkynes, complexes 2 and 3 produced a lower yield of hydrophosphinylated products, indicating the role of ligand (spacer) in this catalytic transformation. This work is the first to demonstrate that a neutral magnesium complex can independently catalyse the hydrophosphinylation of alkynes and offers opportunities for the hydrophosphinylation of other compounds catalyzed by main-group metal complexes. | Darakshan Parveen; Sneha Mittal; Radhika Shrivas; Biswarup Pathak; Dipak Kumar Roy | Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Ligand Design; Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6757f00c085116a133ea2fb1/original/hydrophosphinylation-of-alkynes-via-neutral-magnesium-complexes-evidence-for-ligand-dependency-in-structure-activity-relationships.pdf |
67a60d1981d2151a02821028 | 10.26434/chemrxiv-2025-8l8jw | Discovery and SAR Exploration of Novel Nanomolar 3,4-dihydroquinazolin-2(1H)-one Non-Nucleoside Reverse Transcriptase Inhibitors | HIV continues to affect people every day and is still considered a global pandemic. Due to the absence of a cure or a vaccine, patients are subjected to a life-long treatment that is often complicated by antiviral drug resistance, highlighting the need to develop new therapies. One of the key targets for this antiviral drug development is reverse transcriptase. In this paper, we describe the discovery, synthesis and biological evaluation of a novel chemotype of potent 3,4-dihydroquinazolin-2(1H)-one NNRTIs. Several compounds exhibit nanomolar antiviral activity against WT HIV-1 and maintain an excellent activity profile against
various clinically relevant mutations. These promising first results provide an exciting foundation for further research into this novel NNRTI scaffold. | Eline Goffin; Laurynn Torfs; David Švestka; Kristien Erven; Kris Uyttersprot; Cindy Heens; Simon Wilms; Jef Rozenski; Eveline Lescrinier; Christophe Pannecouque; Peter Verwilst | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a60d1981d2151a02821028/original/discovery-and-sar-exploration-of-novel-nanomolar-3-4-dihydroquinazolin-2-1h-one-non-nucleoside-reverse-transcriptase-inhibitors.pdf |
64b13157ae3d1a7b0dae2722 | 10.26434/chemrxiv-2023-20hd2-v3 | Real-time single-molecule monitoring and control of nanoparticle formation | Methods capable of controlling synthesis at the level of an individual nanoparticle are a key step towards improved reproducibility and scalability in engineering complex nanomaterials. To address this, we combine spatially-patterned activation of the photoreductant sodium pyruvate with interferometric scattering microscopy to achieve fast, label-free monitoring and control of hundreds of gold nanoparticles in real-time. Individual particle growth kinetics are well-described by two-step nucleation autocatalysis model, but with a distribution of individual rate constants that changes with reaction conditions. | Yujie Guo; Vivien Walter; Steven Vanuytsel; Christopher Parperis; Jason Sengel; Eve Weatherill; Mark Wallace | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b13157ae3d1a7b0dae2722/original/real-time-single-molecule-monitoring-and-control-of-nanoparticle-formation.pdf |
67a1a4c5fa469535b9fd9b37 | 10.26434/chemrxiv-2025-hfmv4-v2 | Fully-Functionalized Natural Product Probes to Expand the Chemical Tractability of the Human Proteome | Photoaffinity-based chemical proteomic (chemoproteomic) methods have emerged as a powerful means for proteome-wide mapping of ligandable proteins directly in cells as well as the concatenate discovery of small molecule chemical probes. However, due to the relatively low throughput of screening small molecule libraries by proteomics and the synthetic burden incurred in installing the requisite photoactivatable functionality on each member, great priority must be placed on library design to maximize efficient exploration of biologically-relevant chemical space and to ensure the identification of authentic binding interactions. To address this challenge, here we leverage the inherent complexity of natural products (NPs) to access structurally unique series of diastereo/regioisomeric photoaffinity probes for ligand discovery in cells. Through semi-synthesis we exploit sp3-rich NP scaffolds and employ mass spectrometry-based chemoproteomics to identify and quantify their interactions in human cells, uncovering topology, regio-, and stereoselective ligands for functionally diverse proteins that currently lack reported chemical probes. Collectively, our findings highlight the potential of NP-inspired chemoproteomic libraries to expand the boundaries of the ligandable proteome. | Christian Chaheine; Louis Conway; Christopher Parker | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a1a4c5fa469535b9fd9b37/original/fully-functionalized-natural-product-probes-to-expand-the-chemical-tractability-of-the-human-proteome.pdf |
663f0c6191aefa6ce1b3e7ce | 10.26434/chemrxiv-2024-rmvt4 | Selective oxidative coupling of methane via surface-confined methyl-radical transformation | Directly converting methane into valuable-added chemicals and fuels is a grand challenge in chemistry. Methyl radical (CH3), a highly reactive and short-lived key intermediate, is generally involved in direct-methane-conversion processes, but its reaction is difficult to control, especially at elevated temperatures in the presence of oxygen. The uncontrollable homogeneous transformation of CH3 in oxidative coupling of methane (OCM) places an inherent upper bound on single-pass C2 yield (~ 28%) independent of catalyst, which is the major obstacle for its large-scale utilization. Here we report that surface-confined CH3 coupling represents a general strategy for the design of selective oxidative coupling of methane (SOCM) to perform controllable radical reactions. We show that tungstate sub-nanoclusters, embedded within ZrO2 matrix, can efficiently capture highly reactive CH3 and selectively convert them into C2 products. Experimental results and kinetic modeling unambiguously show that combining catalysts for CH3 generation versus capture can be an effective approach for improving OCM catalyst performance and breaking away from limits imposed by gas-phase kinetics. It achieves C2 yield of >30% at 650 – 700 °C and a world-record single-pass C2 yield (46.3%) far beyond the fundamental upper C2 yield bound at 800 °C. We anticipate that selective oxidative coupling of methane (SOCM) is economically competitive with current oil-based technology for ethylene production. | Shihui Zou; Junxing Wang; Jian Liu; Qiuyue Zhou; Yang Pan; Wentao Yuan; Jingbo Hu; Yue Wang; Jiuzhong Yang; Yong Wang; Juanjuan Liu; Lu Ma; Yonghua Du; Bo Yang; Jie Fan | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663f0c6191aefa6ce1b3e7ce/original/selective-oxidative-coupling-of-methane-via-surface-confined-methyl-radical-transformation.pdf |
65e654d266c138172932dd2b | 10.26434/chemrxiv-2024-mhs6s | Data-Efficient, Chemistry-Aware Machine Learning Predictions of Diels–Alder Reaction Outcomes | The application of machine learning models to the prediction of reaction outcomes currently needs large and/or highly featurized datasets. We show that a chemistry-aware model, NERF, which mimics the bonding changes that occur during reactions, allows for highly accurate predictions of the outcomes of Diels–Alder reactions using a relatively small training set, with no pretraining and no additional features. We establish a diverse dataset of 9,537 intramolecular, hetero-, aromatic, and inverse electron demand Diels–Alder reactions. This dataset is used to train a NERF model and the performance is compared against state-of-the-art classification and generative machine learning models across low- and high-data regimes, with and without pretraining. The predictive accuracy (regio- and site selectivity in the major product) achieved by NERF exceeds 90% when as little as 40% of the dataset is used for training. Another high-performing model, Chemformer, requires a larger training dataset (>45%) and pretraining to reach 90% Top-1 accuracy. Accurate predictions of less-represented reaction subclasses, such as those involving heteroatomic or aromatic substrates, require higher percentages of training data. We also show how NERF can use small amounts of additional training data to quickly learn new systems and improve its overall understanding of reactivity. Synthetic chemists stand to benefit as this model can be rapidly expanded and tailored to areas of chemistry corresponding to the low data regime. | Angus Keto; Taicheng Guo; Morgan Underdue; Thijs Stuyver; Connor Coley; Xiangliang Zhang; Elizabeth Krenske; Olaf Wiest | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e654d266c138172932dd2b/original/data-efficient-chemistry-aware-machine-learning-predictions-of-diels-alder-reaction-outcomes.pdf |
6710126112ff75c3a1a26f39 | 10.26434/chemrxiv-2024-jwcvd-v2 | Autocatalytic Activation of a Ruthenium-PNN-Pincer Hydrogenation Catalyst | In this article, we describe a detailed experimental and computational study of the activation mechanism for a highly active PNN-pincer ruthenium(0) pre-catalyst for the hydrogenation of polar organic compounds. The pre-catalyst activates by reaction with two equivalents of hydrogen, resulting in a net oxidative addition to ruthenium and hydrogenation of an imine functional group on the
supporting ligand. The kinetics of pre-catalyst hydrogenation were measured by UV-visible spectroscopy
under catalytically relevant conditions (10-39 bar hydrogen, 298 K). The kinetic data, in combination with density functional theory calculations, support an intriguing autocatalytic mechanism, where the product ruthenium(II) complex catalyzes the hydrogenation of the ruthenium(0) pre-catalyst. | Jose Fernando Carbajal Perez; Fallyn Kirlin; Eamon Reynolds; Cole Altomare-Jarczyk; Benjamin Joseph; Jason Keith; Anthony Chianese | Catalysis; Organometallic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710126112ff75c3a1a26f39/original/autocatalytic-activation-of-a-ruthenium-pnn-pincer-hydrogenation-catalyst.pdf |
65df6debe9ebbb4db97bc992 | 10.26434/chemrxiv-2024-6g4px | A de novo metalloenzyme for cerium photoredox catalysis | Cerium photoredox catalysis has emerged as a powerful strategy to activate molecules under mild conditions. Radical intermediates are formed using visible light and simple complexes of the earth-abundant lanthanide. However, it remains a major challenge to achieve stereocontrol in these reactions. Here, we report an artificial photoenzyme enabling this chemistry inside a protein. We utilize a de novo designed protein scaffold that tightly binds lanthanide ions in its central cavity. Upon visible-light irradiation, the cerium-dependent enzyme catalyzes the radical C–C bond cleavage of 1,2-diols in aqueous solution. Protein engineering led to variants with improved photostability and initial stereoselectivity. The photoenzyme cleaves a range of aromatic and aliphatic substrates, including lignin surrogates. Surface display of the protein scaffold on E. coli facilitates whole-cell photobiocatalysis. Furthermore, we show that also natural lanthanide-binding proteins are suitable for this approach. Our study thus demonstrates a new-to-nature enzymatic photoredox activity with broad catalytic potential. | Andreas Sebastian Klein; Florian Leiss-Maier; Rahel Mühlhofer; Benedikt Boesen; Ghulam Mustafa; Hannah Kugler; Cathleen Zeymer | Catalysis; Biocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65df6debe9ebbb4db97bc992/original/a-de-novo-metalloenzyme-for-cerium-photoredox-catalysis.pdf |
64146ce72bfb3dc251ec90f6 | 10.26434/chemrxiv-2023-5btjr | On the short and long phosphorescence lifetimes of aromatic carbonyls | This work uses theoretical and computational methods to investigate the relationship between phosphorescence lifetime and the electronic character of the lowest triplet state of aromatic carbonyls. It shows that phosphorescence is due to a direct spin-orbit coupling (SOC) mechanism modulated by permanent dipoles when the T1 minimum is 3np*. If the minimum is a totally symmetric 3pp*, phosphorescence is due to an indirect SOC mechanism involving transition dipole moments with other excited states. The magnitude difference between permanent and transition dipoles leads to 3np* phosphoresce to be 100 times faster than 3pp*. A vertical approximation and the nuclear ensemble approach (NEA) were tested on benzaldehyde and three derivatives in the gas phase chosen to have both 3np* and 3pp* phosphorescence. Both simulation methods deliver good results for 3n* systems. Nevertheless, vertical simulations fail for 3pp* due to the overwhelming importance of vibronic couplings. | Saikat Mukherjee; Moumita Kar; Mansi Bhati; Xing Gao; Mario Barbatti | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64146ce72bfb3dc251ec90f6/original/on-the-short-and-long-phosphorescence-lifetimes-of-aromatic-carbonyls.pdf |
662b266591aefa6ce176ac4e | 10.26434/chemrxiv-2024-k45wj | Sulfur-Bridged Diazulenylmethyl Cations: Formation of Charge-Segregated Assembly with High Charge-Carrier Mobility | Sulfur-bridged diazulenylmethyl cations were synthesized and exhibited high stability even under basic conditions (pH 10) due to the delocalization of positive charge over the whole pai-conjugated skeleton. As a result of the effective delocalization and the absence of orthogonally oriented bulky substituents, the cationic pai-conjugated skeletons formed a pai-stacked array with short interfacial distances. A derivative with SbF6 as a counter anion formed a charge-segregated assembly in the crystalline state, rather than the generally favored charge-by-charge arrangement of oppositely charged species based on electrostatic interactions. Theoretical calculations suggested that the destabilization caused by electrostatic repulsion between two positively charged pai-conjugated skeletons is compensated by the dispersion forces. In addition, the counter anion SbF6 played a role in regulating the molecular alignment through F…H-C and F…S interactions, which resulted in the charge-segregated alignment of the cationic pai-skeletons. This characteristic assembled structure gave rise to a high charge-carrier mobility of 1.7 cm2V-1s-1 as determined using flash-photolysis time-resolved microwave conductivity and photocurrent measurements. | Satoshi Takahashi; Masahito Murai; Yusuke Hattori; Shu Seki; Takeshi Yanai; Shigehiro Yamaguchi | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662b266591aefa6ce176ac4e/original/sulfur-bridged-diazulenylmethyl-cations-formation-of-charge-segregated-assembly-with-high-charge-carrier-mobility.pdf |
674f9311f9980725cff1574d | 10.26434/chemrxiv-2024-bvdw5 | Exploring Structure-Property Relationships of Phenothiazine-based Hole As Materials for Optoelctronics and large band perovskite solar cells | This study focuses on the synthesis and characterization of three novel phenothiazine-based hole transporting materials (HTMs) with wide band gaps, specifically designed for large bandgap MAPbBr3 perovskite solar cells. The plan to investigate the relationship between device performance and the structural variations in the donor peripheral group. The presence of methoxy groups on the twisted donor unit in HTM 2k is predicted to enhance the power conversion efficiency (PEC), while the absence of methoxy groups in the twisted donor of 2c demonstrates higher open circuit voltage (Voc). Conversely, introducing a planar peripheral donor by incorporating a new chemical between the two phenyl units results in decreased PCE and Voc. | MOHAMED MAGDY HASSAN DESOKY | Organic Chemistry; Energy; Photovoltaics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674f9311f9980725cff1574d/original/exploring-structure-property-relationships-of-phenothiazine-based-hole-as-materials-for-optoelctronics-and-large-band-perovskite-solar-cells.pdf |
675bd9d57be152b1d0d4394a | 10.26434/chemrxiv-2024-btcx0 | Predicting and Explaining Yields with Machine Learning for Carboxylated Azoles and Beyond | Carbon dioxide can be transformed into valuable chemical building blocks, including C2-carboxylated 1,3-azoles, which have potential applications in pharmaceuticals, cosmetics, and pesticides. However, only a small fraction of the millions of available 1,3-azoles are carboxylated at the C2 position, highlighting significant opportunities for further research in the synthesis and application of these compounds. In this study, we utilized a supervised machine learning approach to predict reaction yields for a dataset of amide-coupled C2-carboxylated 1,3-azoles. To facilitate molecular design, we integrated an interpretable heat-mapping algorithm named PIXIE (Predictive Insights and Xplainability for Informed chemical space Exploration). PIXIE visualizes the influence of molecular substructures on predicted yields by leveraging fingerprint bit importances, providing synthetic chemists with a powerful tool for the rational design of molecules. While heat mapping is an established technique, its integration with a machine-learning model tailored to the chemical space of C2-carboxylated 1,3-azoles represents a significant advancement. This approach not only enables targeted exploration of this underrepresented chemical space, fostering the discovery of new bioactive compounds, but also demonstrates the potential of combining these methods for broader applications in other chemical domains. | Kerrin Janssen; Jonny Proppe | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675bd9d57be152b1d0d4394a/original/predicting-and-explaining-yields-with-machine-learning-for-carboxylated-azoles-and-beyond.pdf |
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