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60c74c15f96a000af3287707 | 10.26434/chemrxiv.12420860.v1 | Consensus Virtual Screening of Dark Chemical Matter and Food Chemicals Uncover Potential Inhibitors of SARS-CoV-2 Main Protease | The COVID-19 pandemic
caused by SARS-CoV-2 has claimed more than 380,000 lives Worldwide and more
than 6.5 million people are infected. Unfortunately, there is no drug or
vaccine for the treatment of COVID-19. The increasing information available of
key molecular targets of SARS-CoV-2 and active compounds against related
coronavirus facilitates computational tools to rapidly suggest drug candidates
for the treatment of COVID-19. As part of a global effort to fight the COVID-19
pandemic, herein we report a consensus virtual screening of large collections
of food chemicals and compounds classified as Dark Chemical Matter. The rationale
is to complement global efforts and explore regions of the chemical space
currently underexplored. The consensus approach included combining similarity
searching with various queries and fingerprints, molecular docking with two
docking programs, and ADMETox profiling. We propose three compounds
commercially available that were sent to experimental testing. We disclose the
full list of virtual screening hits that can be subject to additional selection
for acquisition or synthesis and experimental testing. This manuscript will be
updated when the experimental testing of the selected compounds becomes
available. | Marisa G. Santibáñez-Morán; Edgar López-López; Fernando D. Prieto-Martínez; Norberto Sánchez-Cruz; Jose L. Medina-Franco | Chemical Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c15f96a000af3287707/original/consensus-virtual-screening-of-dark-chemical-matter-and-food-chemicals-uncover-potential-inhibitors-of-sars-co-v-2-main-protease.pdf |
65105761b927619fe7bc2617 | 10.26434/chemrxiv-2023-v0q44 | Photochemical Stability of 5-Methylcytidine Relative
to Cytidine: Photophysical Insight for mRNA
Therapeutic Applications | 5-Methylcytidine (5mCyd) has recently been investigated with renewed interest for utilization in mRNA therapeutics. However, its photostability following exposure to electromagnetic radiation has been overlooked. This Letter compares the photostability and excited state dynamics of 5mCyd with those of the canonical RNA nucleoside, cytidine (Cyd) using steady-state and femtosecond transient absorption spectroscopy under physiologic conditions. 5mCyd is shown to have a 5-fold higher fluorescence yield and a 5-fold longer 1ππ* excited state decay lifetime. Importantly, however, the excited state population in 5mCyd decays primarily by internal conversion, with a photodegradation rate 3 times smaller than in Cyd. In Cyd, the population of a 1nπ* state with a lifetime of ca. 45 ps is implicated in the formation 6-hydroxycytidine and other photoproducts. | Sean J. Hoehn; Sarah E. Krul; Michael M. Pogharian; Erqian Mao; Carlos Crespo-Hernández | Physical Chemistry; Biological and Medicinal Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65105761b927619fe7bc2617/original/photochemical-stability-of-5-methylcytidine-relative-to-cytidine-photophysical-insight-for-m-rna-therapeutic-applications.pdf |
625eafcf11b1466b59286d8d | 10.26434/chemrxiv-2022-9qmlh | Thiol catalysis of selenosulfide bond cleavage by a triarylphosphine | The arylthiol 4-mercaptophenylacetic acid (MPAA) is a powerful catalyst of selenosulfide bond reduction by the triarylphosphine 3,3′,3′′-phosphanetriyltris(benzenesulfonic acid) trisodium salt (TPPTS). Both reagents are water-soluble at neutral pH and are particularly adapted for working with unprotected peptidic substrates. Contrary to trialkylphosphines such as tris(2-carboxyethyl)phosphine hydrochloride (TCEP), TPPTS has the advantage of not inducing deselenization reactions. We believe that the work reported here will be of value for those manipulating selenosulfide bonds in peptidic or protein molecules. | Olga Firstova; Oleg Melnyk; Vincent Diemer | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625eafcf11b1466b59286d8d/original/thiol-catalysis-of-selenosulfide-bond-cleavage-by-a-triarylphosphine.pdf |
64b6b1ceb053dad33a773187 | 10.26434/chemrxiv-2023-smwj6 | Aging Hallmarks and Anti-aging Strategies: A Landscape of Research Advancement | Aging is a dynamic, time-dependent process characterized by a gradual accumulation of cell damage. Continual functional decline in the intrinsic ability of living organisms to accurately regulate homeostasis leads to increased susceptibility and vulnerability to diseases. Anti-aging research has a long history throughout civilization, with many efforts put forth to understand and prevent the effects of aging. Thus, the major cellular and molecular hallmarks of aging have been identified and multiple strategies aiming to promoting healthy aging and extending the lifespan including lifestyle adjustments, medical treatments, and social programs, have been developed. Here, we use data from the CAS Content Collection to analyze the publication landscape of recent research. We review the advances in knowledge and delineate trends in research advancement on aging factors and attributes, as well as the anti-aging strategies across time, geography, and development pipelines. We also review the current concepts related to the major aging hallmarks on the molecular, cellular, and organismic level, the age-associated diseases, with attention to brain aging and brain health support, as well as the major biochemical processes associated with aging. We further assess the state-of-the-art anti-aging strategies and explore their correlations with age-related diseases. Well-recognized and novel, currently evaluated anti-aging agents have been summarized. Finally, we review clinical applications of anti-aging products with their development pipelines. We hope this review will be helpful for apprehending the current knowledge in the field of aging progression and prevention, in effort to further solve the remaining challenges and fulfil its potential. | Rumiana Tenchov; Janet Sasso; Xinmei Wang; Qiongqiong Angela Zhou | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b6b1ceb053dad33a773187/original/aging-hallmarks-and-anti-aging-strategies-a-landscape-of-research-advancement.pdf |
6788fb4d81d2151a0263a351 | 10.26434/chemrxiv-2025-fdnnq | Going beyond SMILES enumeration for generative deep learning in low data regimes | Data augmentation can alleviate the limitations of small molecular datasets for generative deep learning, by ‘artificially inflating’ the number of instances available for training. SMILES enumeration – whereby multiple valid SMILES strings are used to represent the same molecules – has resulted particularly beneficial to improve the quality of de novo molecule design. Here, we investigate whether rethinking SMILES augmentation techniques could further enhance the quality of de novo design. To this end, we introduce four approaches for SMILES augmentation in de novo design, drawing inspiration from natural language processing and chemistry insights: (a) token deletion, (b) atom masking, (c) bioisosteric substitution, and (d) self-training. Via a systematic analysis, our results show the promise of considering additional strategies for SMILES augmentation. Every strategy showed distinct advantages, with atom masking resulting particularly promising to learn desirable physico-chemical properties in very low-data regimes. This new repertoire of SMILES augmentation strategies expands the available toolkit to design molecules with bespoke properties in low-data scenarios. | Helena Brinkmann; Antoine Argante; Hugo ter Steege; Francesca Grisoni | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6788fb4d81d2151a0263a351/original/going-beyond-smiles-enumeration-for-generative-deep-learning-in-low-data-regimes.pdf |
6606c4d3e9ebbb4db9e7be56 | 10.26434/chemrxiv-2024-j68gq | Regioselective Preparation of Hetero-2,3-Diarylpropionic Acids | A stepwise copper-catalyzed boracarboxylation then palladium-catalyzed Suzuki-Miyaura cross-coupling methodology was developed to access 2,3-diarylpropionic acid derivatives regioselectively by pre-setting the position of the carboxylic acid in the first catalytic reaction. This method provides a single regioisomer compared to the traditional hydrocarboxylation strategies that afford both regioisomers. Pharmaceutical potential was demonstrated in synthesizing a glucagon receptor antagonist drug in 3-steps (31% overall yield) from the commercially available 4-tert-butylstyrene. | Mason Hamilton; Trina Perrone; Brian Popp | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6606c4d3e9ebbb4db9e7be56/original/regioselective-preparation-of-hetero-2-3-diarylpropionic-acids.pdf |
66d4eacaa4e53c487657a107 | 10.26434/chemrxiv-2024-4w0jh | Applying the principles of green chemistry to achieve a more sustainable polymer life cycle | This mini-review highlights how many of the principles of green chemistry can be used to make polymers more sustainable. The use of renewable feedstocks has grown enormously in recent years including use of bio-derived monomers and modifications of natural polymers such as carbohydrates. Polymers are also being designed to allow entry into the circular economy especially where triggered depolymerization (e.g. catalytic recycling to monomer) can occur, which can allow easy separation from other plastics in a mixed waste stream. Computational studies and reaction monitoring are useful in identifying and understanding reactivity trends for polymer synthesis and degradation. Solvent-free reactions, including mechanochemistry, can be employed to reduce process mass intensity and environmental impacts. Use of standard polymer degradation conditions (e.g. ISO standards) and life cycle assessments, in particular hot spot analyses, should be encouraged in order to accelerate progress in this important field. | Francesca Kerton | Polymer Science; Earth, Space, and Environmental Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d4eacaa4e53c487657a107/original/applying-the-principles-of-green-chemistry-to-achieve-a-more-sustainable-polymer-life-cycle.pdf |
631080ad11986c10ce4e2761 | 10.26434/chemrxiv-2022-f8z56-v2 | Merging dual photoredox/cobalt catalysis and boronic acid (derivatives) activation for the Minisci reaction | The merger of open-shell and closed-shell organometallic chemistry steps has enabled multiple effective cross-coupling pathways. Here we report a visible-light promoted photoredox-cobalt catalyzed Minisci reaction of N-heteroarenes under mild and sustainable conditions, employing various boronic acids and derivatives as alkyl radical precursors. This study demonstrates the prominent ability of the Co co-catalyst to promote the oxidation step of the photocatalytic cycle following a reductive quenching pathway, thus avoiding the use of stoichiometric (inorganic) oxidants. This feature enables the straightforward application of photo-flow conditions, particularly attractive for an easy scale-up and to enhance the efficiency of the reaction (throughput: 0.78 mmol/h in flow vs 0.02 mmol/h in batch) Furthermore, the process is predominantly selective towards the C2-alkylation of quinolines, and a mechanistic rationale has been provided with both experimental and DFT calculation support. The developed protocol demonstrates broad applicability for the alkylation of different N-heteroarenes under suitable homogeneous conditions for a flow-compatible Minisci reaction. | Serena Pillitteri; Prabhat Ranjan; Gerardo M. Ojeda-Carralero; Laura Y. Vázquez Amaya; Javier E. Alfonso-Ramos; Erik V. Van der Eycken; Upendra K. Sharma | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631080ad11986c10ce4e2761/original/merging-dual-photoredox-cobalt-catalysis-and-boronic-acid-derivatives-activation-for-the-minisci-reaction.pdf |
65c0d5bee9ebbb4db9b6a53d | 10.26434/chemrxiv-2024-msbqm | AlN interlayer-induced reduction of dislocation density in the AlGaN epilayer | The emerging ultrawide-bandgap AlGaN alloy system holds promise for the development of advanced materials in the next generation of power semiconductor and UV optoelectronic devices. Within this context, heterostructures based on III-nitrides are very popular in view of their applications as electronics and optoelectronics components. AlGaN-based deep UV emitters are gaining visibility for their disinfection capabilities. Likewise, high electron mobility transistors are attracting increasing attention owing to their superior electron transport which yields high-speed and high-power applications. Those devices are conventionally made of AlGaN/GaN heterostructures grown on foreign substrate. However, structural defects, including stress induced by a mismatch in unit cell parameters and the presence of dislocations, can not only decrease the efficiency of the light emitters (by facilitating the non-radiative recombination of electron-hole pairs), but also impede electron mobility within the two-dimensional electron gas at the AlGaN/GaN interface. Therefore, the significance of obtaining high-quality AlGaN layers becomes evident. Including a thin AlN interlayer between the GaN buffer layer and AlGaN is a possible answer to address these drawbacks. Not only we show that a thin AlN layer, approximately ≤ 3 nm in thickness, between the GaN buffer and AlGaN layers, is effective in decreasing the dislocation densities in the AlGaN layer. Still, this is responsible of an increase in the electron mobility of the resulting heterostructure compared to a classical AlGaN/GaN heterostructure. | David Maria Tobaldi; Luc Lajaunie; Arianna Cretì; Massimo Cuscunà; Iolena Tarantini; Marco Esposito; Gianluca Balestra; Mauro Lomascolo; Adriana Passaseo; Vittorianna Tasco | Physical Chemistry; Materials Science; Energy; Alloys; Physical and Chemical Properties; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c0d5bee9ebbb4db9b6a53d/original/al-n-interlayer-induced-reduction-of-dislocation-density-in-the-al-ga-n-epilayer.pdf |
60c74a86ee301c7ee3c79c7f | 10.26434/chemrxiv.12213431.v1 | Enhanced Li-Ion Conductivity in Nanosized Li10GeP2S12 | <div>The discovery of the lithium superionic conductor Li10GeP2S12 (LGPS) has led to significant research activity on solid electrolytes for high-performance and safe solid-state batteries. LGPS exhibits a remarkably high room-temperature Li-ion conductivity of 12 mS/cm, comparable to</div><div>that of the liquid electrolytes used in current Li-ion batteries. Here, we predict that nanosizing of LGPS can be used to further enhance its already outstanding Li-ion conductivity. By utilizing state-of-the-art nanoscale molecular dynamics techniques, we are able to simulate the Li-ion conductivities of nanocrystalline LGPS systems with average grain sizes from 10 to 2 nm. Our results reveal that the Li-ion conductivity of LGPS increases with decreasing grain volume. For the smallest nanometric grain size, the Li-ion conductivity at room temperature is three times higher that of the bulk system. These findings reveal that nanosizing LGPS and related solid electrolytes could be an effective approach for enhancing their Li-ion conductivity.</div> | James Dawson; Saiful Islam | Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a86ee301c7ee3c79c7f/original/enhanced-li-ion-conductivity-in-nanosized-li10ge-p2s12.pdf |
67c9bee06dde43c908c0ef86 | 10.26434/chemrxiv-2025-g9h10 | Amplifying Interfacial Capacitance Through Underpotential Deposition in Salt-in-Ionic Liquid Electrolytes | Rapid growth of intermittent energy sources, such as wind and solar, is causing a resurgence in research on materials and devices that store electrochemical energy. Electrochemical capacitors exhibit promising device characteristics to help level grid scale power fluctuations, including fast charge-discharge kinetics and long device lifetimes. This is especially true for ionic liquids, which promise increased safety and performance, as compared to volatile organic electrolytes commonly used in batteries. However, large scale implementation of ionic liquid-based capacitors remains limited by low device energy densities, as the interfacial capacitance of ionic liquid-electrode interfaces decreases significantly under large polarization. Here, we investigate how incorporating metal cations of varying size and valence into ionic liquids modifies electric double layer formation. We find that alkali cations substantially amplify interfacial capacitance in salt-in-ionic liquid electrolytes, overcoming capacitive limitations caused by ion crowding. Remarkably, we observe capacitive enhancement exceeding 350% in lithium- and sodium-containing electrolytes at Au and Cu electrodes under large polarization, where ion crowding diminishes interfacial capacitance in neat ionic liquids. Our data indicates that metal cation underpotential deposition plays a key role in capacitive enhancement, and we observe that this process can be highly reversible under cycling. Our findings suggest that tuning metal-electrolyte interactions to enable underpotential deposition provides avenues for increasing capacitor performance. This opens the door to additional opportunities for developing devices that could play an essential role in leveling power fluctuations that are inherent to renewable energy grids. | Jack McAlpine; Hrishikesh Tupkar; Sila Alemdar; Adrian Gonzalez-Marcano; Jack Verich; Matthew A. Gebbie | Physical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c9bee06dde43c908c0ef86/original/amplifying-interfacial-capacitance-through-underpotential-deposition-in-salt-in-ionic-liquid-electrolytes.pdf |
67c92e8b6dde43c908b114fe | 10.26434/chemrxiv-2025-tdfs3 | Oxygen reduction reaction on Fe doped Cu oxide electrodes | The work presents an investigation into Fe-doped CuOx (Cu[Fe]Ox/Au) catalysts, expanding on the previous studies of transition metal-doped CuOx systems for the oxygen reduction reaction (ORR). While Cu[Fe]Ox/Au does not exhibit the same level of enhancement as Cu[Co]Ox, Cu[Ni]Ox, or Cu[Mn]Ox, it still demonstrates notable improvements over its pure-phase counterparts, particularly in enhanced ORR currents and reduced H2O2 formation. This reinforces the broader hypothesis that transition metal doping into CuOx enhances catalytic efficiency, even when the extent of improvement varies among different dopants.
A key mechanistic insight from this study is the distinct behavior of Cu[Fe]Ox/Au in H2O2 reduction. Unlike other Cu[M]Ox electrodes, where O2 and H2O2 reduction seem to occur at the same active sites, Cu[Fe]Ox/Au exhibits H2O2 reduction currents more similar to pure CuOx/Au, suggesting that O2 and H2O2 reduction might occur at separate catalytic sites.
| Sekhar Biswal; Chinmoy Ranjan | Physical Chemistry; Catalysis; Electrocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c92e8b6dde43c908b114fe/original/oxygen-reduction-reaction-on-fe-doped-cu-oxide-electrodes.pdf |
60c742fc469df4de93f430b6 | 10.26434/chemrxiv.8869328.v1 | Ligand-Enabled β-C(sp3)–H Lactonization: A Stepping Stone for General and Practical β-C–H Functionalizations | β-C–H
functionalization of aliphatic acids is emerging as a valuable synthetic
disconnection that complements a wide range of conjugate addition reactions. Despite
two decades of effort on β-C–H functionalizations, reported reactions bear numerous
challenges, especially for industrial-scale applications due to the use of
expensive oxidants and poor scope. For example, arylation reactions are only compatible
with aryl iodides but not the more practical aryl bromides and chlorides,
alkylations are limited to primary alkyl coupling partners; fluorination and
amination reactions have not been possible using free carboxylic acids as
directing groups. The unselective formation of mono- and di-functionalized
products is another major drawback. Herein, we report an unprecedented palladium-catalyzed
β-C(sp<sup>3</sup>)–H lactonization of aliphatic acids enabled by a mono-<i>N</i>-protected β-amino acid ligand. The highly
strained and reactive β-lactone products are versatile linchpins for the mono-selective
installation of diverse alkyl, alkenyl, aryl, alkynyl, fluoro, hydroxyl, and
amino groups at the β position of the parent acid, thus providing a one-for-all
strategy to synthesize a myriad of carboxylic acids. The use of inexpensive <i>tert</i>-butyl
hydrogen peroxide (TBHP) as the oxidant, as well as the ease of product
purification without column chromatography renders this reaction amenable to
ton-scale manufacturing. | Zhe Zhuang; jin-quan yu | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742fc469df4de93f430b6/original/ligand-enabled-c-sp3-h-lactonization-a-stepping-stone-for-general-and-practical-c-h-functionalizations.pdf |
60c74bbeee301c25d8c79f19 | 10.26434/chemrxiv.12376679.v1 | Microsecond Simulation Analysis of Carbonic Anhydrase – II in Complex with (+)- Cathechin Revealed Molecular Interactions Responsible for Its Amelioration Effect on Fluoride Toxicity | Fluorosis is a chronic condition caused by overexposure to fluoride, marked by impaired dental, skeletal, and non-skeletal health. In presence of excess fluoride ions, in severe cases calcification of the ligaments observed. Earlier studies have suggested that the disruption of carbonic anhydrase activity via ionic homeostasis change was associated with F toxicity. In a recent study, it was demonstrated that Tamarind fruit extract was effective in increasing the urinary F excretion in male Wistar rats via studying the mRNA expression of carbonic anhydrase II (CA II) in kidney homogenates using western blotting, immunohistochemistry and quantitative Realtime PCR based studies. We have carried out this study to understand the detailed molecular level interactions responsible for this tamarind extract based (+)-cathechin compound towards lowering the F toxicity via targeting CA-II. From our study, it was revealed that due to the ability of (+)-cathechin compound to bind tightly filling complete available space at the catalytically important site forming metal coordinated ionic bonds with His94, His96 and His119 residues helps in restricting F ions to interact with Zn ion located at the core of catalytic site responsible for its functionality. On the other hand, interaction of (+)-cathechin compound with Gln92 was observed to be critically important towards inducing conformational changes in CA-II, thus allowing (+)-cathechin compound to burry even deeply inside the catalytic site. | Pulala Raghuveer Yadav; Hussain Syed; Sadam DV Satyanarayana; Pavan Kumar Pindi | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bbeee301c25d8c79f19/original/microsecond-simulation-analysis-of-carbonic-anhydrase-ii-in-complex-with-cathechin-revealed-molecular-interactions-responsible-for-its-amelioration-effect-on-fluoride-toxicity.pdf |
63a3e82a81e4bab6d9563265 | 10.26434/chemrxiv-2022-hrn32 | Modeling the Effects of Salt Concentration on Aqueous and Organic Electrolytes | Understanding the thermodynamic properties of electrolyte solutions is of vital importance for a myriad of physiological and technological applications. The activity coefficient γ± is associated with the deviation of an electrolyte solution from its ideal behavior and may be obtained by combining the Debye-Hu ̈ckel (DH) and Born (B) equations. However, the DH and B equations depend on the concentration and temperature-dependent static permittivity of the solution εr (c, T ) and size of the solvated ions ri, whose experimental data is often not available. In this work, we use a combination of molecular dynamics and density functional theory to predict εr (c, T ) and ri, which enables us to apply the DH and B equations to any technologically relevant electrolyte at any concentration and temperature of interest. | Stephanie van der Lubbe; Pieremanuele Canepa | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a3e82a81e4bab6d9563265/original/modeling-the-effects-of-salt-concentration-on-aqueous-and-organic-electrolytes.pdf |
62353091202c0621f9d8f02b | 10.26434/chemrxiv-2022-nzrr3 | A Generalized Machine Learning Model for Predicting Ionic Conductivity for Ionic Liquids | Ionic liquids are currently being considered as potential electrolyte candidates for next-generation batteries and energy storage devices due to their high thermal and chemical stability. However, high viscosity and low conductivity at lower temperatures have severely hampered their commercial applications. To overcome these challenges, it is necessary to develop structure-property models for ionic liquid transport properties to guide the ionic liquid design. This work expands our previous effort in developing a machine learning model on imidazolium-based ionic liquids to now include ten different cation families, representing structural and chemical diversity. The model dataset contains 2869 ionic conductivity values over a temperature range of 238-472 K collected from the NIST ILThermo database and literature values for 397 unique ionic liquids. The database covers 214 unique cations and 68 unique anions. Three machine learning models, multiple linear regression, random forest, and extreme gradient boosting, are applied to correlate the ionic liquid conductivity data with cation and anion features. Shapely additive analysis is performed to glean insights into cation and anion features with significant impact on ionic conductivity. Finally, the extreme gradient boosting model is used to predict ionic conductivity of ionic liquids from all the possible combinations of unique cations and anions to identify ionic liquids crossing the ionic conductivity threshold of 2.0 S/m | Pratik Dhakal; Jindal Shah | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Machine Learning; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62353091202c0621f9d8f02b/original/a-generalized-machine-learning-model-for-predicting-ionic-conductivity-for-ionic-liquids.pdf |
66fc1fc3cec5d6c142cc9656 | 10.26434/chemrxiv-2024-kpr4t | Exploring CRISPR-Cas9 HNH-Domain Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation | The target DNA (tDNA) cleavage catalyzed by the CRISPR Cas9 enzyme is a critical step in the Cas9-based genome editing technologies. Previously, the tDNA cleavage from an active SpyCas9 enzyme conformation was modeled by Palermo and coworkers [Nierzwicki et al., Nat. Catal. 5, 912 (2022)] using ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulations, where the free energy barrier was found to be more favorable than that from a pseudoactive enzyme conformation. In this work, we performed ai-QM/MM simulations based on another catalytically active conformation (PDB 7Z4J) of the Cas9 HNH domain from cryo-electron microscopy experiments.For the wildtype enzyme, we acquired a free energy profile for the tDNA cleavage that is largely consistent with the previous report. Furthermore, we explored the role of the active-site K866 residue on the catalytic efficiency by modeling the K866A mutant, and found that the K866A mutation increased the reaction free energy barrier, which is consistent with the experimentally observed reduction in the enzyme activity. | Richard Van ; Xiaoliang Pan; Saadi Rostami ; Jin Liu ; Pratul Agarwal; Bernard Brooks; Rakhi Rajan ; Yihan Shao | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc1fc3cec5d6c142cc9656/original/exploring-crispr-cas9-hnh-domain-catalyzed-dna-cleavage-using-accelerated-quantum-mechanical-molecular-mechanical-free-energy-simulation.pdf |
66ceb7fef3f4b05290578d70 | 10.26434/chemrxiv-2024-ts4vf | Birch Reductive Arylation by Mechanochemical Anionic Activation of Polycyclic Aromatic Compounds | Birch reduction is a well-known process for producing aromatic compounds. The reduction of aromatic rings using alkali metals produces anionic species that react with protons or electrophiles. However, this reaction is generally accompanied by signifi-cant restrictions on the available substrates because only alkyl halides are available in most cases. For example, most Birch reduction/transformation reactions are related to the alkylation of aromatic compounds, whereas reactions with other elec-trophiles are rare and have not yet been completely established. In particular, the arylation of unfunctionalized polycyclic ar-omatic hydrocarbons (PAHs), so-called Birch reductive arylation has not yet been investigated. Herein, we report a Birch re-ductive arylation for the first time by mechanochemical anionic activation using a lithium(0) wire followed by addition of vari-ous fluoroarenes. Specifically, we found that the not only Birch reductive arylation products but also formal C–H arylation products were obtained from unfunctionalized PAHs, achieving one-pot fissure-region annulative π-extension to give nanogra-phenes. This newly found process is a unique reaction that is rarely achieved in solution, and showed the interesting reactivity of metal lithium and organofluorine compounds in the solid state. | Yoshifumi Toyama; Akiko Yagi; Kenichiro Itami; Hideto Ito | Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Main Group Chemistry (Organomet.); Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ceb7fef3f4b05290578d70/original/birch-reductive-arylation-by-mechanochemical-anionic-activation-of-polycyclic-aromatic-compounds.pdf |
67b01e25fa469535b964ccdd | 10.26434/chemrxiv-2025-2mc0h | Repurposing Polymeric Waste from the Textile Industry for Sustainable Biodegradable Composites: Challenges and Opportunities | The textile industry generates significant amounts of polymeric waste, primarily from synthetic fibers like polyester and nylon, which are non-biodegradable and contribute to environmental pollution. This review explores the potential of repurposing textile polymeric waste into sustainable biodegradable composites, offering a promising solution to reduce waste and address environmental concerns. Biodegradable composites, made by recycling textile waste, can replace conventional non-biodegradable materials in industries such as construction, automotive, and packaging. This paper discusses the various methods for repurposing polymeric waste, including mechanical, chemical, and biological recycling techniques. It also examines the challenges involved in converting textile waste into high-quality biodegradable composites, such as issues with material properties, processing difficulties, and cost-effectiveness. The review highlights the opportunities for integrating this waste into a circular economy, with a focus on environmental benefits, economic potential, and future research directions. | Jerusha Evangeline Nallarajah | Polymer Science; Chemical Engineering and Industrial Chemistry; Biopolymers; Industrial Manufacturing; Quality Control; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b01e25fa469535b964ccdd/original/repurposing-polymeric-waste-from-the-textile-industry-for-sustainable-biodegradable-composites-challenges-and-opportunities.pdf |
60c745e5469df4bd93f4359b | 10.26434/chemrxiv.10283990.v1 | Inverse Thermogelation of Aqueous Triblock Copolymer Solutions into Macroporous Shear-Thinning 3D Printable Inks | Amphiphilic block copolymers that undergo (reversible) physical gelation in aqueous media are of great interest in different areas including drug delivery, tissue engineering, regenerative medicine and biofabrication. We investigated a small library of ABA-type triblock copolymers comprising poly(2-methyl-2-oxazoline) as the hydrophilic shell A and different aromatic poly(2-oxazoline)s and poly(2-oxazine)s cores B in aqueous solution at different concentrations and temperatures. Interestingly, aqueous solutions of poly(2-methyl-2-oxazoline)-block-poly(2-phenyl-2-oxazine)-block-poly(2-methyl-2-oxazoline) (PMeOx-b-PPheOzi-b-PMeOx) undergo inverse thermogelation below a critical temperature. The viscoelastic properties of the resulting gel can be conveniently tailored by the concentration and the polymer composition. Storage moduli of up to 110 kPa could be obtained while the material remains shear-thinning and retains rapid self-healing properties. We demonstrate 3D-printing of excellently defined and shape persistent 24-layered scaffolds at different aqueous concentrations to highlight its application potential e.g. in the research area of biofabrication. A mesoporous microstructure, which is stable throughout the printing process, could be confirmed via cryo-SEM analysis. The absence of cytotoxicity even at very high concentrations opens wide range of different applications for this first-in-class material in the field of biomaterials.<br /> | Lukas Hahn; Matthias Maier; Philipp Stahlhut; Matthias Beudert; Alexander Altmann; Fabian Töppke; Tessa Lühmann; Robert Luxenhofer | Aggregates and Assemblies; Biocompatible Materials; Carbon-based Materials; Nanostructured Materials - Materials; Surfactants; Hydrogels; Organic Polymers; Fluid Mechanics; Pharmaceutical Industry | CC BY 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745e5469df4bd93f4359b/original/inverse-thermogelation-of-aqueous-triblock-copolymer-solutions-into-macroporous-shear-thinning-3d-printable-inks.pdf |
621aea06011b58f911b6308c | 10.26434/chemrxiv-2022-vznv4 | Clusteroluminescence in Maleimide: from Well-Known Phenomenon to Unknown Mechanism | Maleimide compounds have a long history related to colour reactions. It has been reported that maleimide yields bright colour when it reacts with basic reagents. Inspired by its colour formation, we investigated the maleimide polymer produced by an organic base 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU). The resultant polyimide contains exceptional fluorescence, which is virtually non-emissive in dilute solutions but exhibits strong pink emission (430nm and 580nm) in the concentrated solution and solid state. The intense colour comes from such a simple chemical structure, the unconventional fluorophore can be undoubtedly categorized into clusteroluminogens. By controlling the organic base amount, the intensity ratio of purple and orange-red emission can be controlled. The interaction between maleimide and base is rapid, and it can be achieved in the solid-solid interface or solid-gas interface. The aim herein is to highlight the recent observation and hold strong implications for further potential applications in anti-counterfeiting, gas sensors. | Yuan Xie; Dan Liu; Haoke Zhang; Dong Wang; Zheng Zhao; Ben Zhong Tang | Physical Chemistry; Organic Chemistry; Polymer Science; Clusters; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621aea06011b58f911b6308c/original/clusteroluminescence-in-maleimide-from-well-known-phenomenon-to-unknown-mechanism.pdf |
644f5efd6ee8e6b5ed644fb1 | 10.26434/chemrxiv-2023-58sfj-v3 | Disruption of the FMN-A524 interaction cascade and Glu513 induced collapse of the hydrophobic barrier promotes light induced Jα-helix unfolding in AsLOV2 | The C terminal Jα-helix of the Avena Sativa’s Light Oxygen and Voltage (AsLOV2) protein, unfolds on exposure to blue light. This characteristic seeks relevance in applications related to engineering novel biological photoswitches. Using Molecular Dynamic (MD) simulations and the Markov State Modeling (MSM) approach we provide the mechanism that explains the stepwise unfolding of the Jα-helix. The unfolding was resolved into seven steps represented by the structurally distinguishable states distributed over the initiation and the post initiation phases. Wherein, the initiation phase occurs due to the collapse of the interaction cascade FMN-Q513-N492-L480-W491-Q479-V520-A524, the onset of the post initiation phase is marked by breaking of the hydrophobic interactions between the Jα-helix and the Iβ-sheet. This study indicates that the displacement of N492 out of the FMN binding pocket, not necessarily requiring Q513, is essential for the initiation of the Jα-helix unfolding. Rather, the structural reorientation of Q513 activates the protein to cross the hydrophobic barrier and enter the post initiation phase. Similarly, the structural deviations in N482, rather than its integral role in unfolding, could enhance the unfolding rates. Further, the MSM studies on the wild type and the Q513 mutant, provide the spatio-temporal roadmap that layout the possible pathways of structural transition between the dark and the light states of the protein. Overall, the study provides insights useful to enhance the performance of AsLOV2 based photoswitches. | Syeda Amna Arshi; Manisha Chauhan; Amit Sharma | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644f5efd6ee8e6b5ed644fb1/original/disruption-of-the-fmn-a524-interaction-cascade-and-glu513-induced-collapse-of-the-hydrophobic-barrier-promotes-light-induced-j-helix-unfolding-in-as-lov2.pdf |
66b359bdc9c6a5c07a4978f5 | 10.26434/chemrxiv-2024-3t818 | Multi-fidelity graph neural networks for predicting toluene/water partition coefficients | Accurate prediction of toluene/water partition coefficients of neutral species is crucial in drug discovery and separation processes; however, data-driven modeling of these coefficients remains challenging due to limited available experimental data. To address the limitation of available data, we apply multi-fidelity learning approaches leveraging a quantum chemical dataset (low fidelity) of approximately 9000 entries generated by COSMO-RS and an experimental dataset (high fidelity) of about 250 entries collected from the literature. We explore the transfer learning, feature-augmented learning, and multi-target learning approaches in combination with graph neural networks, validating them on two external datasets: one with molecules similar to training data (EXT-Zamora) and one with more challenging molecules (EXT-SAMPL9). Our results show that multi-target learning significantly improves predictive accuracy, achieving a Root-Mean-Square Error (RMSE) of 0.44 logP units for the EXT-Zamora, compared to an RMSE of 0.63 logP units for single-task models. For the EXT-SAMPL9 dataset, multi-target learning achieves an RMSE of 1.02 logP units, indicating reasonable performance even for more complex molecular structures. These findings highlight the potential of multi-fidelity learning approaches that leverage quantum chemical data to improve toluene/water partition coefficient predictions and address challenges posed by limited experimental data. We expect applicability of the methods used beyond just toluene/water partition coefficients. | Thomas Nevolianis; Jan Gerald Rittig; Alexander Mitsos; Kai Leonhard | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b359bdc9c6a5c07a4978f5/original/multi-fidelity-graph-neural-networks-for-predicting-toluene-water-partition-coefficients.pdf |
63768b0356c6f40f5871bbb0 | 10.26434/chemrxiv-2022-lvgbf | Q-RepEx: A Python Pipeline to Increase the Sampling of Empirical Valence Bond Simulations | The exploration of chemical systems occurs on complex energy landscapes. Comprehensively sampling rugged energy landscapes with many local minima is a common problem for molecular dynamics simulations. These multiple local minima trap the dynamic system, preventing efficient sampling. This is a particular challenge for large biochemical systems with many degrees of freedom. Replica exchange molecular dynamics (REMD) is an approach that accelerates the exploration of the conformational space of a system, and thus can be used to enhance the sampling of complex biomolecular processes. In parallel, the empirical valence bond (EVB) approach is a powerful approach for modeling chemical reactivity in biomolecular systems. Here, we present an open-source Python-based tool that interfaces with the Q simulation package, and increases the sampling efficiency of the EVB free energy perturbation / umbrella sampling approach by means of REMD. This approach, Q-RepEx, both decreases the computational cost of the associated REMD-EVB simulations, and opens the door to more efficient studies of biochemical reactivity in systems with significant conformational fluctuations along the chemical reaction coordinate. | Sebastian Brickel; Andrey O. Demkiv; Rory M. Crean; Gaspar P. Pinto; Shina Caroline Lynn Kamerlin | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63768b0356c6f40f5871bbb0/original/q-rep-ex-a-python-pipeline-to-increase-the-sampling-of-empirical-valence-bond-simulations.pdf |
675f32a3085116a133812367 | 10.26434/chemrxiv-2024-dcpqv-v2 | NO Oxidation States in Nonheme Iron Nitrosyls:
A DMRG-CASSCF Study of {FeNO}6 –10 Complexes
| Building upon an earlier study of heme-nitrosyl complexes (Inorg. Chem. 2023, 62, 20496–20505), we examined a wide range of nonheme {FeNO}6–10 complexes (the superscript represents the Enemark-Feltham count) and two dinitrosyl iron complexes using DMRG-CASSCF calculations. Analysis of the wave functions in terms of resonance forms with different [π*(NO)]i occupancies (where i = 0-4 for mononitrosyl complexes) identified the dominant electronic configurations of {FeNO}6 and {FeNO}7 complexes as FeIII-NO0 and FeII-NO0, respectively, mirroring our previous findings on heme-nitrosyl complexes. A trigonal-bipyramidal S = 1 {FeNO}8 complex with an equatorial triscarbene ligand set appears best described as a resonance hybrid of FeI-NO0 and FeII-NO−. Reduction to the corresponding S = 1/2 {FeNO}9 state was found to involve both the metal and the NO, leading to an essentially FeI-NO− complex. Further reduction to the {FeNO}10 state was found to be primarily metal-centered, leading to a predominantly Fe0-NO− configuration. Based on the weights wi of the [π*(NO)]i resonance forms, an overall DMRG-CASSCF-based π*(NO) occupation number could be derived, which was found to exhibit a linear correlation with both the NO bond distance and NO stretching frequency, allowing a readout of the NO oxidation state from the NO bond distance. | Quan Phung; Ho Nam; Vic Austen; Takeshi Yanai; Abhik Ghosh | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675f32a3085116a133812367/original/no-oxidation-states-in-nonheme-iron-nitrosyls-a-dmrg-casscf-study-of-fe-no-6-10-complexes.pdf |
63b0ef12e8047ae9c3fc035f | 10.26434/chemrxiv-2023-zljjp | Formation and structures of palladium-cyanomethyl complexes generated under unexpectedly mild conditions: quantifying the acidification of acetonitrile coordinated to a palladium center | Abstract The reaction of the palladium-triphosphine complex [Pd(triphos)(PPh3)]2+ with guanidine and phosphazene bases in acetonitrile forms the cyanomethyl complex [Pd(triphos)(CH2CN)]+, where triphos is the triphosphine ligand PhP(CH2CH2PPh2)2. A cyanomethyl complex with a tridentate PNHP ligand, HN(CH2CH2PPh2)2, was also formed in a similar reaction with solvent, demonstrating that this acidification is relatively general. The crystal structures of these cyanomethyl complexes possess distorted square planar geometries with the cyanomethyl group trans to the central P and N atoms, demonstrating a trans influence that is significantly greater than observed in analogous halide complexes but weaker than complexes with monodentate phosphines. The bases used to form the triphosphine complex are too weak to deprotonate free acetonitrile, and the observed reaction demonstrates a dramatic acidification of the solvent in the presence of the palladium ion. The pKa of the coordinated acetonitrile is estimated to be approximately 25 from these results, which represents a decrease of at least 8 pKa units relative to the free solvent; through a thermodynamic cycle, the heterolytic M–C bond energies can also be estimated as 11 kcal/mol using the H–C bond energies as a reference. | Nicholas Garcia; Bianca Catungal; Christopher Zall | Inorganic Chemistry; Organometallic Chemistry; Inorganic Acid/Base Chemistry; Bond Activation; Coordination Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2023-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b0ef12e8047ae9c3fc035f/original/formation-and-structures-of-palladium-cyanomethyl-complexes-generated-under-unexpectedly-mild-conditions-quantifying-the-acidification-of-acetonitrile-coordinated-to-a-palladium-center.pdf |
60c74542567dfe758aec4432 | 10.26434/chemrxiv.10002122.v1 | Emergence of Light-Driven Protometabolism upon Recruitment of a Photocatalytic Cofactor by a Self-Replicator | This work shows how a designed co-factor can be recruited and activated by a self-replicator to do photo-redox catalysis and generate the precursors from which the self-replicator can grow. It constitutes an important step in the direction of the de-novo synthesis of life by intergrating self-replication with a protometabolism. <br /> | Guillermo Monreal Santiago; Kai Liu; Wesley R Browne; Sijbren Otto | Combinatorial Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Homogeneous Catalysis; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74542567dfe758aec4432/original/emergence-of-light-driven-protometabolism-upon-recruitment-of-a-photocatalytic-cofactor-by-a-self-replicator.pdf |
60c7463dbb8c1ab6323da848 | 10.26434/chemrxiv.11188709.v1 | Recoverable Microparticle-Supported Metal Nanocatalysts | Metal nanoparticles have been widely
exploited in catalysis, but their full impact on the
environment and human health is still under debate. Here we describe the one-step
fabrication of polymer microbead-supported metal and metal oxide nanoparticles and
their application as recoverable nanocatalysts for reactions under batch and
flow conditions. Au, Ag and Fe<sub>3</sub>O<sub>4</sub> nanoparticles were
prepared directly at the surface of benzylamine-coated spherical polymer beads
in water by using low energy microwave radiation. The morphology and size of
the nanoparticles, and therefore their catalytic properties, were tuned by modifying
the bead surface using betalamic acid, an antioxidant from plant origin. The
catalytic performance and recovery of these environmentally friendly
nanocatalysts was demonstrated towards model redox chemical transformations. We anticipate the
results reported herein can provide important insights into the controlled and
facile synthesis of microparticle supported nanocatalysts under mild
conditions. | Arthur Bonfá Fernandes; Mariia V. Pavliuk; Cristina Paun; Alexandrina C. Carvalho; Cassiana S. Nomura; Erik Lewin; Rebecka Lindblad; Pedro H. C. Camargo; Jacinto Sa; Erick Leite Bastos | Natural Products; Biocompatible Materials; Magnetic Materials; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7463dbb8c1ab6323da848/original/recoverable-microparticle-supported-metal-nanocatalysts.pdf |
668858ad5101a2ffa880e714 | 10.26434/chemrxiv-2024-w86rz | Bench-scale Microfluidic Manufacturing of Cross-linked Polyester Microparticles | Polymeric microparticles used as long-acting drug delivery systems provide advantages relative to conventional oral dosage forms including improved efficacy and safety. However, development of these formulations, including generics, is constrained by current manufacturing techniques. Conventional approaches have limited control over process parameters and are difficult to scale. Droplet microfluidic techniques produce individual particles sequentially enabling unparalleled consistency on key material properties including particle size and dispersity. While microfluidics approaches have much promise, including affording continuous rather than batch production; designing, constructing, and operating these systems is challenging reducing adoption by formulation scientists. Herein, we describe the operation of a modular microfluidic system built with commercially available components to prepare photo-cross-linked microparticles by droplet generation, inline dilution, and inline irradiation with UV. We synthesized monodisperse cross-linked polyester microparticles with a median size of 37.6 ± 0.4 μm at 20, 60 and 120 mg batch sizes with average yields of 92 ± 5 %. Additionally, as a means to tailor material properties, particles were produced at varying degrees of cross-linking. The particle’s properties were further characterized, loaded with celecoxib at a low and a high level, then the in vitro drug release evaluated. Overall, the degree of cross-linking and drug loading modulated key formulation properties such as in vitro release rate. With this work, we showcase the potential of microfluidic systems and aim to foster further adoption of microfluidic techniques to manufacture comparable materials. | Jack Bufton; Darcy Burns; Jeffrey Watchorn; Seoyeon Lee; Christine Allen | Materials Science; Polymer Science; Biocompatible Materials; Controlled-Release Systems; Drug delivery systems; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668858ad5101a2ffa880e714/original/bench-scale-microfluidic-manufacturing-of-cross-linked-polyester-microparticles.pdf |
64870e30be16ad5c57d26bd7 | 10.26434/chemrxiv-2023-r97bm | CGCompiler: Automated coarse-grained molecule parameterization via noise-resistant mixed-variable optimization | Coarse-grained force-fields (CG FF) such as the Martini model entail a predefined, fixed set of Lennard-Jones parameters (building blocks) to model virtually all possible non-bonded interactions between chemically relevant molecules. Owing to its universality and transferability, the building block coarse-grained approach has gained a tremendous popularity over the last decade. The parameterization of molecules can be highly complex and often involves the selection and fine tuning of a large number of parameters (e.g., bead types and bond lengths) to optimally match multiple relevant targets simultaneously. The parameterization of a molecule within the building block CG approach is a mixed-variable optimization problem: The non-bonded interactions are discrete variables whereas the bonded interactions are continuous variables. Here, we pioneer the utility of mixed-variable particle swarm optimization in automatically parameterizing molecules within the Martini 3 coarse-grained force-field by matching both structural (e.g., RDFs) as well as thermodynamic data (phase-transition temperatures). For sake of demonstration, we parameterize the linker of the lipid sphingomyelin. The important advantage of our approach is that both bonded- and non-bonded interactions are simultaneously optimized while conserving the search efficiency of vector guided particle swarm optimization (PSO) methods over other metaheuristic search methods such as genetic algorithms. In addition, we explore noise-mitigation strategies in matching the phase transition temperatures of lipid membranes, where nucleation and concomitant hysteresis introduces a dominant noise term within the objective function. We propose that noise-resistant mixed-variable PSO methods can both improve as well as automate parameterization of molecules within building block CG FFs, such as Martini. | Kai S. Stroh; Paulo C. T. Souza; Luca Monticelli; H. Jelger Risselada | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64870e30be16ad5c57d26bd7/original/cg-compiler-automated-coarse-grained-molecule-parameterization-via-noise-resistant-mixed-variable-optimization.pdf |
6652a458418a5379b04acb7b | 10.26434/chemrxiv-2024-7t6h7-v2 | Nanobody Engineering: Computational Modelling and Design for Biomedical and Therapeutic Applications | Nanobodies, the smallest functional antibody fragment derived from camelid heavy-chain-only antibodies, have emerged as powerful tools for diverse biomedical applications. In this comprehensive review, we discuss the structural characteristics, functional properties, and computational approaches driving the design and optimisation of synthetic nanobodies. We explore their unique antigen-binding domains, highlighting the critical role of complementarity-determining regions in target recognition and specificity. This review further underscores the advantages of nanobodies over conventional antibodies from a biosynthesis perspective, including their small size, stability, and solubility, which make them ideal candidates for economical antigen capture in diagnostics, therapeutics, and biosensing. We discuss the recent advancements in computational methods for nanobody modelling, epitope prediction, and affinity maturation, shedding light on their intricate antigen-binding mechanisms and conformational dynamics. Finally, we examine a direct example of how computational design strategies were implemented for improving a nanobody-based immunosensor, known as a Quenchbody. Through combining experimental findings and computational insights, this review elucidates the transformative impact of nanobodies in biotechnology and biomedical research, offering a roadmap for future advancements and applications in healthcare and diagnostics. | Nehad El Salamouni; Jordan Cater; Lisanne Spenkelink; Haibo Yu | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Biophysics; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6652a458418a5379b04acb7b/original/nanobody-engineering-computational-modelling-and-design-for-biomedical-and-therapeutic-applications.pdf |
65c521f09138d23161b3eb1c | 10.26434/chemrxiv-2023-1s6n8-v2 | Engineering a molecular electrocatalytic system for energy-efficient ammonia production from wastewater nitrate | Haber-Bosch ammonia production and utilization has sustained exponential population growth but exacerbated wastewater nitrate pollution. Abundant nitrate pollutants could be refined to purified nitrogenous chemicals with the electrochemical nitrate reduction reaction (NO3RR). However, the dilute and impure composition of nitrate-rich wastewaters presents barriers to realizing practical electrocatalytic systems that to date operate most efficiently in concentrated, pure electrolytes. These barriers inform our investigation of the ammonia-selective homogeneous molecular NO3RR catalyst Co(DIM). In this work, we elucidate interfacial mechanisms of catalysis inhibition that describe Co(DIM)-mediated NO3RR performance in complex electrolyte compositions. These mechanisms inform design principles for a novel reactive separations platform, electrocatalyst-in-a-box (ECaB), that exhibits the lowest reported energy consumption for purified ammonia production from a real wastewater (90.0 ± 2.7 kWh kg-N–1). This work demonstrates a use-informed design approach that iterates between mutually informative mechanistic insights and performance of electrochemical wastewater refining systems in complex aqueous streams. | Dean Miller; Matthew Liu; Kristen Abels; Anna Kogler; Kindle Williams; William Tarpeh | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Water Purification; Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c521f09138d23161b3eb1c/original/engineering-a-molecular-electrocatalytic-system-for-energy-efficient-ammonia-production-from-wastewater-nitrate.pdf |
6144360539ef6a6c8b1ef7d8 | 10.26434/chemrxiv-2021-vfvkd-v2 | Reactant-Induced Photoactivation of a Gold-Catalyzed Csp2-Csp Cross-Coupling Leading to Indoles | A novel access to 2,3-disubstituted indoles from o-alkynyl aniline and iodoalkyne derivatives via a gold-catalyzed sequence under visible-light irradiation and in the absence of an exogenous photocatalyst was uncovered. A wide scope of the process was observed. Of note, 2-iodo-ynamides that have never been used in any organometallic cross-coupling reaction could be used as electrophiles. The resulting N-alkynyl indoles lend themselves to post-functionalization affording valuable scaffolds, notably benzo[a]carbazoles. Mechanistic studies converged on the fact that a potassium sulfonyl amide generates emissive aggregates in the reaction medium. Static quenching of these aggregates by a vinylgold(I) intermediate yields to an excited state of the latter, which can react with an electrophile via oxidative addition and reductive elimination to forge the key C-C bond. This reactant-induced photoactivation of an organogold intermediate opens rich perspectives in the field of cross-coupling reactions. | Fen Zhao; Mehdi Abdellaoui; Jérome Berthet; Vincent Corcé; Stéphanie Delbaere; Héloïse Dossmann; Agathe Espagne; Jérémy Forté; Ludovic Jullien; Thomas Le Saux; Virginie Mouriès-Mansuy; Cyril Ollivier; Louis Fensterbank | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6144360539ef6a6c8b1ef7d8/original/reactant-induced-photoactivation-of-a-gold-catalyzed-csp2-csp-cross-coupling-leading-to-indoles.pdf |
641c59cf91074bccd0277272 | 10.26434/chemrxiv-2023-kjwkq-v2 | Alginate/Xanthan gum hydrogels as forensic blood substitutes for bloodstain formation and analysis. | Understanding the behaviour of human blood outside of the body has important implications in forensic research, especially related to bloodstain pattern analysis (BPA). The design of forensic blood substitutes (FBSs) can provide many advantages, including the incorporation of multiple physiological components for use as safe and reliable materials for forensic applications. In this work, we present the design of synthetic alginate and xanthan gum-based hydrogels that contain electrosprayed microparticles (MPs) with and without crosslinked DNA. In addition to the MPs, the alginate/xanthan gum FBS materials include fillers to alter the physical appearance and fluid properties of the material. The optimized FBS consisted of alginate (1% w/v) and xanthan gum (5.0 x10-3 w/v %), 2 mM CaCl2, ferric citrate (0.5% w/v), magnesium silicate (0.25% w/v), Allura red (2% w/v), 0.025% v/v Tween 20 and 9.5% v/v MPs. The FBS was tested in passive dripping experiments relevant to BPA scenarios at various impact angles. The spreading ratio (Ds/D0) was determined for 90 degree stains made on a paper surface and compared to bovine blood where the FBS was shown to simulate accurate and predictable spreading behaviour. In addition, we simulated other common BPA scenarios (e.g., impact patterns) and evidence processing potential. The FBS could be swabbed, and the DNA could be extracted, amplified, and genotyped analogous to human blood evidence. A stability test was also conducted which revealed a shelf-life of up to 4 weeks where the material remains relevant to human blood at physiological temperature. | Amanda Orr; Paul Wilson; Theresa Stotesbury | Materials Science; Polymer Science; Biological Materials; Biopolymers; Hydrogels; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641c59cf91074bccd0277272/original/alginate-xanthan-gum-hydrogels-as-forensic-blood-substitutes-for-bloodstain-formation-and-analysis.pdf |
670f3ce012ff75c3a18f22a0 | 10.26434/chemrxiv-2024-st481 | Structure-signal relationships of the δ-opioid-receptor (DOR)-selective agonist KNT-127 - Part I: Impact of the morphinan skeleton on the G-protein-biased DOR agonism | The δ-opioid receptor (DOR) is a promising target for developing novel analgesics due to its lower risk of causing side effects compared to the μ-opioid receptor (MOR), which is commonly associated with dependence, respiratory depression, and other adverse effects. KNT-127, a DOR-selective agonist with a morphinan skeleton, offers analgesic and antidepressant benefits without inducing convulsions at therapeutic doses, unlike the conventional DOR agonist SNC80. While previous studies have suggested that KNT-127 exhibits reduced β-arrestin recruitment, a signaling pathway implicated in adverse opioid effects, the ligand structural basis for this biased signaling remains unclear. In this study, we explored the structure–signal relationships of KNT-127, focusing on its quinoline moiety. Modifying the quinoline moiety by removing the aromatic rings reduced DOR selectivity and potency in relation to G-protein activation while diminishing both the potency and efficacy of β-arrestin recruitment. These results suggest that the morphinan skeleton is critical for reduced β-arrestin recruitment, while the quinoline moiety differentially modulates G-protein activation and β-arrestin recruitment. Together, our study thus provides structural insights into the G-protein-biased agonism of DOR agonists, guiding the design of safer DOR-targeting therapeutics. | Keita Kajino; Tomoya Sugai; Ryoji Kise; Riko Suzuki; Akihisa Tokuda; Yuki Sekiya; Tomoya Kakumoto; Risako Katamoto; Noriki Kutsumura; Yasuyuki Nagumo; Asuka Inoue; Tsuyoshi Saitoh | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670f3ce012ff75c3a18f22a0/original/structure-signal-relationships-of-the-opioid-receptor-dor-selective-agonist-knt-127-part-i-impact-of-the-morphinan-skeleton-on-the-g-protein-biased-dor-agonism.pdf |
60c748bfbb8c1ab62d3dad19 | 10.26434/chemrxiv.11962503.v1 | The impact of defects and crystal size on negative gas adsorption in DUT-49 analyzed by in situ 129Xe NMR spectroscopy. | The origin of crystal size-dependent adsorption behavior of flexible metal-organic frameworks is increasingly studied. In this contribution, we probe the solid-fluid interactions of DUT-49 crystals of different size by in situ 129Xe NMR spectroscopy at 200 K. With decreasing size of the crystals, the average solid-fluid interactions are found to decrease reflected by a decrease in chemical shift of adsorbed xenon from 230 to 200 ppm explaining the lack of adsorption-induced transitions for smaller crystals. However, recent studies propose that these results can also originate from the presence of lattice defects. To investigate the influence of defects on the adsorption behavior of DUT-49 we synthesized a series of samples with tailored defect concentrations and characterized them by in situ 129Xe NMR. In comparison to the results obtained for crystals with different size we find pronounced changes of the adsorption behavior and influence of the chemical shift only for very high concentrations of defects, which further emphasizes the important role of particle size phenomena. | Simon Krause; Florian Reuter; Sebastian Ehrling; Volodymyr Bon; Irena Senkovska; Stefan Kaskel; Eike Brunner | Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748bfbb8c1ab62d3dad19/original/the-impact-of-defects-and-crystal-size-on-negative-gas-adsorption-in-dut-49-analyzed-by-in-situ-129xe-nmr-spectroscopy.pdf |
6651f62d418a5379b042a0bd | 10.26434/chemrxiv-2024-z139t | GOLD RECOVERY FROM WASTE PRINTED CIRCUIT BOARD IODIDE LEACHATES USING A NOVEL MEMBRANE-BASED ELECTROWINING PROCESS
| The hydrometallurgical recovery of gold from waste printed circuit boards is considered a promising recycling technique. This paper presents the findings from a study investigating the feasibility of a hydrometallurgical technique to recover gold from waste printed circuit board iodide leachates using a novel membrane-based electrowinning process. Findings showed that the investigated novel process has the potential to be technically feasible if employed in a real-life industrial-scale waste printed circuit board recycling operation. This is primarily because high purity (>99%) Au was effectively recovered using the investigated process with a 95.50 % yield under the following conditions: 6.0 hrs time, constant cell voltage of 12.9 V, temperature of 25 degrees celsius, 250 rpm agitation speed, average current of 5 A, 1429 A/m2 equivalent current density, and 8.4 × 10-6 mol/m2.s Au flux. Overall, the simultaneous recovery of iodide lixiviant with Au makes the recovery process simple as well as potentially cost-effective. Further studies on the process scale-up are required to accurately evaluate the overall costing of the gold recovery process via the proposed technology. | Ngeleka Marco Mukuna; Jochen Petersen ; Thandazile Moyo | Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6651f62d418a5379b042a0bd/original/gold-recovery-from-waste-printed-circuit-board-iodide-leachates-using-a-novel-membrane-based-electrowining-process.pdf |
60c743acbb8c1abbf03da362 | 10.26434/chemrxiv.9404945.v1 | Carbocations as Secondary Coordination Sphere Z-Type Ligands – Anion-Induced Au(I)/Au(III) Oxidation and Impact on Reactivity | We
describe our efforts towards the design of phosphine-based ligands featuring an
electrophilic carbocationic moiety positioned to enter the secondary
coordination sphere of the phosphine-bound metal atom. Using simple synthetic protocols, we have
been able to obtain and fully characterize the complexes [(<i>o</i>-Ph<sub>2</sub>P(C<sub>6</sub>H<sub>4</sub>)Acr)AuCl]<sup>+</sup>
([<b>3</b>]<sup>+</sup>, Acr = 9-<i>N</i>-methylacridinium) and [(<i>o</i>-Ph<sub>2</sub>P(C<sub>6</sub>H<sub>4</sub>)Xan)AuCl]<sup>+</sup>
([<b>4</b>]<sup>+</sup>, Xan =
9-xanthylium). While only weak
interactions occur between the gold atom and the methylium centers of these
complexes, the more Lewis acidic [<b>4</b>]<sup>+</sup>
readily reacts with chloride to afford a trivalent phosphine gold dichloride
derivative (<b>7</b>) in which the metal
atom is covalently bound to the former methylium center. This anion-induced Au(I)/Au(III) oxidation is
accompanied by a conversion of the Lewis acidic methylium center in [<b>4</b>]<sup>+</sup> into an X-type ligand in
<b>7</b>.
This transformation leads us to conclude that the methylium center acts
as a latent Z-type ligand poised to increase the Lewis acidity of the gold
center, a notion supported by the carbophilic reactivity of these complexes. | Lewis Wilkins; Francois Gabbai | Catalysis; Coordination Chemistry (Organomet.); Ligand Design; Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743acbb8c1abbf03da362/original/carbocations-as-secondary-coordination-sphere-z-type-ligands-anion-induced-au-i-au-iii-oxidation-and-impact-on-reactivity.pdf |
62ba9c830bba5dbd987829a0 | 10.26434/chemrxiv-2022-tgw6p | Strategies for Transferring Photobiocatalysis to Continuous Flow Exemplified by the Photodecarboxylation of Fatty Acids | The challenges of light-dependent biocatalytic transformations of lipophilic substrates in aqueous media are manifold. For instance, photolability of the catalyst as well as insufficient light penetration into the reaction vessel may be further exacerbated by a heterogeneously dispersed substrate. Light penetration may be addressed by performing the reaction in continuous flow, which allows two modes of applying the catalyst: (i) heterogenously, immobilized on a carrier, which requires light-permeable supports, or (ii) homogenously, dissolved in the reaction mixture. Taking the light-dependent photodecarboxylation of palmitic acid catalyzed by the fatty-acid photodecarboxylase from Chlorella variabilis (CvFAP) as a showcase, strategies for the transfer of a photoenzyme-catalyzed reaction into continuous flow were identified. A range of different supports was evaluated for the immobilization of CvFAP, whereby Eupergit C250 L was the carrier of choice. As the photostability of the catalyst was a limiting factor, a homogeneous system was preferred instead of employing the heterogenized enzyme. This implied that photolabile enzymes may preferably be applied in solution if repair mechanisms cannot be provided. Furthermore, when comparing different wavelengths and light intensities, extinction coefficients may be considered to ensure comparable absorption at each wavelength. Employing homogenous conditions in the CvFAP-catalyzed photodecarboxylation of palmitic acid afforded a space-time yield unsurpassed by any reported batch process (5.7 g/L·h, 26.9 mmol/L·h) for this reaction, demonstrating the advantage of continuous flow in attaining higher productivity of photobiocatalytic processes. | Stefan Simić; Miglė Jakštaitė; Wilhelm T. S. Huck; Christoph K. Winkler; Wolfgang Kroutil | Organic Chemistry; Catalysis; Biocatalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ba9c830bba5dbd987829a0/original/strategies-for-transferring-photobiocatalysis-to-continuous-flow-exemplified-by-the-photodecarboxylation-of-fatty-acids.pdf |
6736dabb7be152b1d021a16e | 10.26434/chemrxiv-2024-ztx08-v3 | Pristine and Cu-decorated ψ-graphene-based materials for CO2 activation: A DFT(D)+ U Study | Capturing and repurposing anthropogenic carbon dioxide (CO2) is the traditional way to deal with climate change and lack of fossil fuel. CO2 adsorption (reduction) is the first step in this process. We have employed density functional theory-based calculations to investigate CO2 activation over the pristine and Cu-decorated carbon-based two-dimensional ψ-graphene material and its hydrogenated forms, i.e., ψ-graphone (half hydrogenated) and ψ-graphane (fully hydrogenated). ψ-graphene is a metallic allotrope of graphene containing 5-6-7 membered carbon rings. Our study found exothermic binding of CO2 with all three materials (for both pristine and Cu-decorated materials), indicating spontaneous physisorption. The presence of single atoms of the transition metal plays a significant role in increasing the activity of materials towards CO2 activation. We observed that the adsorption energy increases about three times after decorating a ψ-graphene sheet with Cu atoms. In contrast, no significant variation is observed on ψ-graphone or ψ-graphane materials. Our Bader charge analysis confirms the charge transfer from 2d nano-sheets to the molecule, where the values of calculated adsorption energies and the density of states suggest that the interaction between CO2 and these three materials can be categorized as weak physisorption., while Cu decoration enhances the CO2 adsorption. | Kamal Kumar; Nora de Leeuw; Jost Adam; Abhishek Kumar Mishra | Theoretical and Computational Chemistry; Materials Science; Catalysis; Carbon-based Materials; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6736dabb7be152b1d021a16e/original/pristine-and-cu-decorated-graphene-based-materials-for-co2-activation-a-dft-d-u-study.pdf |
60c74a70ee301c755cc79c54 | 10.26434/chemrxiv.12185634.v1 | As-Indaceno[3,2,1,8,7,6-Ghijklm]terrylene: A Near-Infrared Absorbing C70-Fragment | <div><div><div><p>Carbon and hydrogen are fundamental components of organic molecules and a fascinating plethora of functions can be generated using these two elements. Yet, realizing attractive electronic structures only by using carbon and hydrogen remains challenging. Herein, we report the synthesis and properties of the C70 fragment as- indaceno[3,2,1,8,7,6-ghijklm]terrylene, which exhibits near-infrared (NIR) absorption (up to ca. 1300 nm), even though this molecule consists of only 34 carbon and 14 hydrogen atoms. A remarkably small HOMO–LUMO gap was confirmed by electrochemical measurement and theoretical calculations. Nevertheless, as-indacenoterrylene is surprisingly stable despite the absence of peripheral substituents, which contrasts with the cases of other NIR-absorbing hydrocarbons such as biradicaloids and antiaromatic molecules. The low-energy absorption was attributed to the intramolecular charge- transfer from the electron-rich terrylene segment to the electron-deficient as- indacenopyrene segment. The results of this study thus offer fundamental insights into the design of hydrocarbons with a small band gap.</p></div></div></div> | Yuki Tanaka; Norihito Fukui; Hiroshi Shinokubo | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a70ee301c755cc79c54/original/as-indaceno-3-2-1-8-7-6-ghijklm-terrylene-a-near-infrared-absorbing-c70-fragment.pdf |
60c74e40469df424daf4443a | 10.26434/chemrxiv.12730553.v1 | Improving Hydride Conductivity in Layered Perovskites via Crystal Engineering | Hydride ion conduction in layered perovskites is of great interest for sustainable-energy applications. In this report we study Ba2ScHO3, a recently synthesized oxyhydride with an unusual anion ordering, using a multifaceted density functional theory approach involving both transition state calculations and molecular dynamics simulations. Beyond simply identifying the key ion migration pathways, we perform detailed analysis of transition states and identify key interactions which drive trends in ionic mobility. Our key findings are that ionic mobility is, remarkably, independent of hydride-oxide disorder, the dominant migration pathway changes under pressure, and a reduction in A-site cation size accelerates hydride diffusion. Local structural flexibility along migration pathways is understood in terms of dimensionality and ionic size, and we thus identify crystal engineering principles for rational design of ion conductors. On the basis of our new insights into these materials, we predict that Sr2ScHO3 will show improved conductivity over existing analogues. | Harry W. T. Morgan; Harry J. Stroud; Neil Allan | Solid State Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e40469df424daf4443a/original/improving-hydride-conductivity-in-layered-perovskites-via-crystal-engineering.pdf |
64e37c7e01042bc1cc6f0818 | 10.26434/chemrxiv-2023-h1459-v3 | Evaluating sentinel pipe racks for monitoring lead release
and optimizing corrosion control | Orthophosphate can limit lead contamination of tap water, but its benefits are difficult to quantify since lead concentrations are so site-specific. Sentinel homes serviced by lead pipe are ideal for monitoring orthophosphate treatment, but best practices dictate the removal of lead once identified. The best sentinel homes, then, are often short-lived. Here we explore an alternative: recovered lead pipe racks supplied with distributed drinking water at locations throughout a water system. We also propose a strategy for analyzing the data based on the generalized additive model, which approximates time series as sums of smooth functions. Geometric mean lead release from pipe racks exhibited a pronounced dose-response, falling by 54% after an increase from 1 to 2 mg PO4 L-1, and then climbing by 55% after a decrease to 1.5 mg PO4 L-1. Data from nine sentinel homes were consistent with those from pipe racks: geometric mean lead at the high orthophosphate dose was 60% of that at the low dose. Our results demonstrate sentinel pipe racks as a viable alternative to at-the-tap sampling for non-regulatory corrosion control monitoring. They also provide a Bayesian framework for quantifying changes in lead release that can incorporate information from multiple sources. | Benjamin F Trueman; Javier A Locsin; Wendy H Krkošek; Graham A Gagnon | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC 4.0 | CHEMRXIV | 2023-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e37c7e01042bc1cc6f0818/original/evaluating-sentinel-pipe-racks-for-monitoring-lead-release-and-optimizing-corrosion-control.pdf |
60c759009abda2008cf8e9f9 | 10.26434/chemrxiv.14622462.v1 | Rh2(II)-Catalyzed Intermolecular N-Aryl Aziridination of Olefins using Nonactivated N-Atom Precursors | The development of the first intermolecular Rh<sub>2</sub>(II)-catalyzed aziridination of di-, tri-, or tetraubstituted olefins using aryl- or heteroaryl amines as nonactivated N-atom precursors and an iodine(III) reagent as the stoichiometric oxidant is reported. The Rh<sub>2</sub>(II)-catalyzed N-atom transfer to the olefin is stereospecific, chemo- and diastereoselective to produce the <i>N</i>-aryl aziridine as the only amination product. | Wrickban Mazumdar; Tianning Deng; Yuki Yoshinaga; Pooja B. Patel; Dana Malo; Tala Malo; Donald Wink; Tom Driver | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759009abda2008cf8e9f9/original/rh2-ii-catalyzed-intermolecular-n-aryl-aziridination-of-olefins-using-nonactivated-n-atom-precursors.pdf |
628e4d986cae1c6dce16cbb7 | 10.26434/chemrxiv-2022-bl6mf-v2 | CrystalNets.jl: Identification of Crystal Topologies | We present here an open-source Julia library for the topological identification of crystalline materials, with algorithmic and computational improvements over the previously available software in the field, resulting in a speed increase of one order of magnitude. This new algorithm and implementation can therefore be used at large scale in high-throughput screening methodologies. We have validated and benchmarked CrystalNets.jl against a diverse set of crystal databases, covering in particular metal–organic frameworks, aluminophosphates, zeolites, and other inorganic compounds. | Lionel Zoubritzky; François-Xavier Coudert | Theoretical and Computational Chemistry; Materials Science | CC BY 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e4d986cae1c6dce16cbb7/original/crystal-nets-jl-identification-of-crystal-topologies.pdf |
60c754cc9abda2e4b5f8e231 | 10.26434/chemrxiv.13724827.v1 | Synthesis of Multi-Substituted Bicycloalkyl Boronates: An Intramolecular Coupling Approach to Alkyl Bioisosteres | <p>Bicyclic hydrocarbons, bicyclo[1.1.1]pentanes (BCPs) in particular, play an emerging role as saturated bioisosteres in pharmaceutical, agrochemical, and material chemistry. Taking advantage of strain release strategies, prior synthetic studies have featured the synthesis of bridgehead-substituted (C1, C3) BCPs from [1.1.1]propellane. This work describes a novel approach to accessing multi-substituted BCPs via a new type of intramolecular cyclization. In addition to the C1, C3-disubstituted BCPs, this method also enables the construction of yet underexplored tri-substituted (C1, C2 and C3) BCPs from readily accessible cyclobutanones. The broad generality of this cyclization is examined through synthesis of a variety of caged bicyclic molecules, ranging from [1.1.1] to [3.2.1] scaffolds. The modularity afforded by the pendant bridgehead Bpin resulted from the cyclization is demonstrated via several downstream functionalizations, highlighting the ability of this approach for programmed and divergent synthesis of multi-substituted bicyclic hydrocarbons.<br /></p> | Yangyang Yang; Jet Tsien; Jonathan Hughes; Byron Peters; Rohan Merchant; Tian Qin | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754cc9abda2e4b5f8e231/original/synthesis-of-multi-substituted-bicycloalkyl-boronates-an-intramolecular-coupling-approach-to-alkyl-bioisosteres.pdf |
67c8aa9e6dde43c908a18433 | 10.26434/chemrxiv-2025-77q13 | Off-equilibrium reactivity of boron-enriched metal diboride surfaces in electro-reduction conditions | Boron-based material, featuring B-dependent reactivity and diverse phases, is emerging as a promising catalyst system. However, catalytic mechanism on many borides remains poorly understood due to complex surface reconstructions under reaction conditions. Here, we investigate the MoB2 surface in conditions of hydrogen evolution reaction in acidic media, using grand canonical global optimization, grand canonical density functional theory, ab initio molecular dynamics, free energy surface sampling, and an analytical model for electrochemical barrier evaluation. We propose a boron enrichment strategy to tune the surface reactivity of the hexagonal face of MoB2. We reveal the dynamic nature of the B-enriched surface under H coverage and kinetic trapping of the system in the metastable regime, with an extensive examination on the deactivation pathways. The metastable center B site on B-enriched surfaces, featuring buckled-up configuration and a usual relaxation effect, is found to be highly active towards HER via Volmer-Heyrovsky mechanism. This work demonstrates how off-equilibrium behaviors can arise from the interplay between adsorbate coverage and surface reconstruction on a seemingly simple surface, and we present a theoretical framework and computational workflows to address them, along with other realistic complexities, in kinetics simulations. | Zisheng Zhang; Frank Abild-Pedersen | Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Theory - Computational; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c8aa9e6dde43c908a18433/original/off-equilibrium-reactivity-of-boron-enriched-metal-diboride-surfaces-in-electro-reduction-conditions.pdf |
62f3fc261ea5f6e03e6fdbb7 | 10.26434/chemrxiv-2022-vzf0w | Diverse Reactivity of an Iron–Aluminium Complex with Substituted Pyridines | The reaction of an Fe–Al complex with an array of substituted pyridines is reported. Depending on the substitution pattern of the substrate site-selective sp2 or sp3 C–H bond activation is observed. A series of reaction products are observed based on (i) C–Al bond formation, (ii) C–C bond formation by nucleophilic addition or (iii) deprotonation of the β-diketiminate ligand. A divergent set of mechanisms involving a common intermediate is proposed. | Nikolaus Gorgas; Andrew White; Mark Crimmin | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Kinetics and Mechanism - Organometallic Reactions; Main Group Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2022-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f3fc261ea5f6e03e6fdbb7/original/diverse-reactivity-of-an-iron-aluminium-complex-with-substituted-pyridines.pdf |
60c74d79f96a0054d2287965 | 10.26434/chemrxiv.12388772.v2 | Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents? | We investigate the self-assembly process of a surfactant with inverted polarity in water and cyclohexane using both all-atom and coarse grained hybrid particle-field molecular<br />dynamics simulations. Unlike conventional surfactants, the molecule under study proposed in a recent experiment is<br /><div>formed by a rigid and compact hydrophobic adamantane moiety, and a long and floppy triethylene glycol tail. In water, we report the formation of stable inverted micelles with the adamantane heads grouping together into a hydrophobic core, and the tails forming hydrogen bonds with water. By contrast, multi-microsecond simulations do not provide evidence of stable micelle formation in cyclohexane. Validating the computational results by comparison with experimental diffusion constant and small-angle neutron scattering intensity, we show that at laboratory thermodynamic conditions the mixture resides in the supercritical region of the phase diagram, where aggregated and free surfactant states co-exist in solution. Our simulations also provide indications about how to escape this region, to produce thermodynamically stable micellar forms.</div> | Manuel Carrer; Tatjana Skrbic; Sigbjørn Løland Bore; Giuseppe Milano; Michele Cascella; Achille Giacometti | Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d79f96a0054d2287965/original/can-polarity-inverted-surfactants-self-assemble-in-nonpolar-solvents.pdf |
60c744b4842e65b257db24e3 | 10.26434/chemrxiv.9887846.v1 | Design Guidelines for Membrane-separated Organic Electrosynthesis: The Case of Adiponitrile Production | <div>
<p>The on-going
efforts to transition from thermal to electricity-driven processes can enable
the easy integration of renewable energy sources and sustainable practices in
chemical manufacturing. Organic electrosynthetic processes are key players in
this transition, but face important challenges regarding selectivity and energy
efficiency. Although membrane-separated flow reactors can help address these
issues, a deeper understanding of membrane behavior in organic electrosynthesis
electrolytes is required. In this study, we evaluate the effect of organic
reactants on the conductivity and permeability of one cation exchange membrane
(Nafion 117) and two anion exchange membranes (Sustainion and Fumasep FAB), and
later assess the advantages of their implementation in flow reactors for
organic electrosynthesis. This is done in the context of the
electrohydrodimerization of acrylonitrile to adiponitrile, the largest organic
electrosynthesis in industry. The presence of organic molecules led to
important losses in membrane conductivity, however no significant contribution
to reactor overpotential was observed from their implementation in
membrane-separated reactors. Furthermore, permeabilities between 0.4 – 1.2 x 10-6
cm2 s-1 towards organic molecules led to low crossover of organics and improved
reactor selectivity. Undivided reactors yielded selectivities as high as 48%
(40 mA cm-2 and 4 V), while selectivities of 77% (20 mA cm-2 and 2.7 V) and 81%
(40 mA cm-2 and 3 V) were obtained with Nafion and Sustainion-separated
reactors, respectively. The demonstrated improvement in energy efficiency for continuous
organic electrosynthesis processes makes the insights from this work a
significant step in the development of sustainable electrochemical
manufacturing processes. </p>
</div>
<br /> | Daniela Blanco; Purnima Prasad; Kaylee Dunnigan; Miguel Modestino | Industrial Manufacturing; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b4842e65b257db24e3/original/design-guidelines-for-membrane-separated-organic-electrosynthesis-the-case-of-adiponitrile-production.pdf |
66d6e5cb12ff75c3a141e666 | 10.26434/chemrxiv-2024-2w2cs | Visible Light-Controlled Intracellular Synthesis of Supramolecular Peptide Nanostructures | The complex dynamics and transience of supramolecular pathways in living cellular environments impede the correlation between diverse hierarchical species and their biological functions. The necessary breakthrough requires the precise control of supramolecular events at discrete time points via synthetic chemistry and their real-time visualization in native cells. Herein, we designed two peptide sequences that undergo a cascade of visible light-induced molecular and supramolecular transformations to form various assembly species in cells. In contrast to endogenous stimulus-responsive self-assembling systems, the irradiation with light enable full control over the reaction cascade where the monomer generation and concentration in turn regulates the assembly kinetics. Phasor-fluorescence lifetime imaging (phasor-FLIM) traced the formation of various assembly states in cells and revealed subsequent out-of-equilibrium dynamics associated with monomer activation and consumption. These temporally resolved assemblies show that the emergence of cytotoxicity is correlated to the accumulation of oligomers beyond the cellular efflux threshold. | Yong Ren; Zhixuan Zhou; Iain Harley; Özlem Aydin; Jiaqi Xing; Konrad Maxeiner; Ingo Lieberwirth; Katharina Landfester; David Y.W. Ng; Tanja Weil | Organic Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d6e5cb12ff75c3a141e666/original/visible-light-controlled-intracellular-synthesis-of-supramolecular-peptide-nanostructures.pdf |
66eb056f12ff75c3a1b7ba0a | 10.26434/chemrxiv-2024-6dnl2 | A Near-Infrared-Absorbing Osmium(II) Complex as a Photosensitizer for Photodynamic Therapy inducing Immunogenic Cell Death | Immunogenic cell death (ICD), which converts tumor cells into their own vaccine, plays a pivotal role in the development of novel anti-cancer therapies. Here, a small series of osmium(II) polypyridyl complexes were synthesized and their biological activity in the dark and upon light irradiation against various cancer cell lines was studied. The compound Os2 (bearing two 4,7-diphenyl-1,10-phenanthrolines and one substituted bipyridine ligand) was discovered to be the most effective photosensitizer (PS) for photodynamic therapy (PDT) of this series through the photogeneration of 1O2 and •OH. In addition, Os2 was found to exhibit promising toxicity upon near-infrared (NIR) irradiation under both normoxia and hypoxia. These observations indicate that this PS is working through a mixture of Type-I and Type-II mechanisms. More interestingly, upon 740 nm irradiation, Os2 can stimulate a strong ICD response both in vitro and in vivo. A comprehensive immune analysis showed that mice vaccinated with Os2-treated CT26-luc cells boosted the systemic specific adaptive immune responses, including the activation of CD8+ T cells and reprograming of macrophages, leading to effective inhibition of tumor growth. Os2 is, to the best of our knowledge, the first photoactive osmium-based complex inducing ICD.
| Yiyi Zhang; Pierre Mesdom; Eduardo Izquierdo-García; João António; Bruno Saubamea; Johanne Seguin; Morgane Moinard; Philippe Arnoux; Céline Frochot; Kevin Cariou; Bich-Thuy Doan; Gilles Gasser | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66eb056f12ff75c3a1b7ba0a/original/a-near-infrared-absorbing-osmium-ii-complex-as-a-photosensitizer-for-photodynamic-therapy-inducing-immunogenic-cell-death.pdf |
613fd60090051e7604f263e5 | 10.26434/chemrxiv-2021-9q343 | Epoxidation and late-stage C-H functionalization by P450 TamI is mediated by variant heme-iron oxidizing species | P450-catalyzed hydroxylation reactions are well understood mechanistically including the identity of the active oxidizing species. However, the catalytically active heme-iron species in P450 iterative oxidation cascades that involve mechanistically divergent pathways and distinct carbon atoms within a common substrate remains unexplored. Recently, we reported the enzymatic synthesis of tri-functionalized tirandamycin O (9) and O’ (10) using a bacterial P450 TamI variant and developed mechanistic hypotheses to explore their formation. Here, we report the ability of bacterial P450 TamI L295A to shift between different oxidizing species as it catalyzes the sequential epoxidation, hydroxylation and radical-catalyzed epoxide-opening cascade to create new tirandamycin antibiotics. We also provide evidence that the TamI peroxo-iron species could be a viable catalyst to enable nucleophilic epoxide opening in the absence of iron-oxo Compound I. Using site-directed mutagenesis, kinetic solvent isotope effects, artificial oxygen surrogates, end-point assays, and density functional theory (DFT) calculations, we provide new insights into the active oxidant species that P450 TamI employs to introduce its unique pattern of oxidative decorations. | Rosa V. Espinoza; Mark A. Maskeri; Aneta Turlik; Anjanay Nangia; Yogan Khatri; John Montgomery; Ken N. Houk; David H. Sherman | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Chemoinformatics - Computational Chemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613fd60090051e7604f263e5/original/epoxidation-and-late-stage-c-h-functionalization-by-p450-tam-i-is-mediated-by-variant-heme-iron-oxidizing-species.pdf |
64db89f4dfabaf06ff50b7dc | 10.26434/chemrxiv-2023-6f0d9 | Real-time monitoring of cell adhesion on to a soft substrate by a graphene impedance biosensor | Soft substrates are interesting for a range of applications from mimicking cellular micro-environment to implants. Conductive electrodes on soft substrates open a broad spectrum of possibilities such as electrical and electrochemical sensing coupled with the flexibility, elasticity and transparency of the underlying substrate. Single layer graphene on a soft substrate as a candidate for such flexible electrodes brings the additional advantage that the active area of the sensor is transparent and conformal to the underlying substrate. Here, we overcome several challenges facing the routine realization of graphene cell sensors on a canonical soft substrate namely poly(dimethylsiloxane) (PDMS). Specifically, we have systematically studied the effect of surface energy before, during and after the transfer of graphene. Based on this, we have identified a suitable support polymer, optimal substrate (pre-) treatment and an appropriate solvent for the removal of the support. Using this procedure, we can reproducibly obtain stable and intact graphene sensors in millimeter-scale on PDMS, which can withstand continuous measurements in cell culture media for several days. From local nanomechanical measurements with an AFM, we infer that the softness of the substrate is slightly affected after graphene transfer. However, we can modulate the stiffness using PDMS of differing composition. Finally, we show that graphene sensors on PDMS can be successfully used as electrodes for real-time monitoring of cell adhesion kinetics on a soft substrate. The routine availability of single layer graphene electrodes on a flexible soft substrate with tunable stiffness will open a new avenue for a range of studies, where the PDMS-liquid interface is made conducting with minimal alteration of the intrinsic material properties such as softness, flexibility, elasticity and transparency. | Victoria Guglielmotti; Emil Fuhry; Tilmann J Neubert; Michel Kuhl; Diego Pallarola; Kannan Balasubramanian | Materials Science; Analytical Chemistry; Nanoscience; Carbon-based Materials; Biochemical Analysis; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64db89f4dfabaf06ff50b7dc/original/real-time-monitoring-of-cell-adhesion-on-to-a-soft-substrate-by-a-graphene-impedance-biosensor.pdf |
614212c765636904502d7541 | 10.26434/chemrxiv-2021-zhxf2 | Conduction of Electric Current to Organic Molecules observed by Carrier Transport Mobility Measurements | Organic semiconductors have been studied for many years, but electric current conduction through organic materials has proven difficult in practice. To evaluate the carrier mobility of newly synthesized modified polyacenes, we prepared suitable techniques for determining the physical properties of the polyacenes from electrical measurements. In a transparent electrode cell based on a low-melting-point material, we observed the dark-current dependence on the cooling rate and evaluated the sample impurity. We then developed a vertical field-effect transistor (FET) device for high- melting-point materials that easily measures the transconductance of a single drop of a sample solution. The vertical FET device provides indirect evidence of Marcus’ theory of electric conduction phenomena in aggregated organic materials. | Toshiki Komatsu | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614212c765636904502d7541/original/conduction-of-electric-current-to-organic-molecules-observed-by-carrier-transport-mobility-measurements.pdf |
60c750a5bb8c1a35683dbb46 | 10.26434/chemrxiv.13065290.v1 | Consistent Inclusion of Continuum Solvation in Energy Decomposition Analysis: Theory and Application to Molecular CO2 Reduction Catalysts | <p>To facilitate computational investigation of intermolecular interactions in the solution phase, we report the development
of ALMO-EDA(solv), a scheme that allows the application of continuum solvent models within the framework of
energy decomposition analysis (EDA) based on absolutely localized molecular orbitals (ALMOs). In this scheme, all
the quantum mechanical states involved in the variational EDA procedure are computed with the presence of solvent
environment so that solvation effects are incorporated in the evaluation of all its energy components. After validation on
several model complexes, we employ ALMO-EDA(solv) to investigate substituent effects on two classes of complexes
that are related to electrochemical CO<sub>2</sub>
reduction catalysis. For [FeTPP(CO<sub>2</sub>−κC)]<sup>2−</sup>
(TPP = tetraphenylporphyrin), we
reveal that two ortho substituents which yield most favorable CO2
binding, −N(CH<sub>3</sub>)<sub>3</sub><sup>+</sup> (TMA) and −OH, stabilize the
complex via through-structure and through-space mechanisms, respectively. The Coulombic interaction between the
positively charged TMA group and activated CO<sub>2</sub>
is found to be largely attenuated by the polar solvent. Furthermore, we
also provide computational support for the design strategy of utilizing bulky, flexible ligands to stabilize activated CO<sub>2</sub>
via long-range Coulomb interactions, which creates biomimetic solvent-inaccessible “pockets” in that electrostatics is
unscreened. For the reactant and product complexes associated with the electron transfer from the <i>p</i>-terphenyl radical
anion to CO<sub>2</sub>
, we demonstrate that the double terminal substitution of <i>p</i>-terphenyl by electron-withdrawing groups
considerably strengthens the binding in the product state while moderately weakens that in the reactant state, which are
both dominated by the substituent tuning of the electrostatics component. These applications illustrate that this new
extension of ALMO-EDA provides a valuable means to unravel the nature of intermolecular interactions and quantify
their impacts on chemical reactivity in solution.<br /></p> | Yuezhi Mao; Matthias Loipersberger; Kareesa Kron; Jeffrey Derrick; Christopher Chang; Shaama Mallikarjun Sharada; Martin Head-Gordon | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750a5bb8c1a35683dbb46/original/consistent-inclusion-of-continuum-solvation-in-energy-decomposition-analysis-theory-and-application-to-molecular-co2-reduction-catalysts.pdf |
64ac44b5ba3e99daefdc324b | 10.26434/chemrxiv-2023-mrp3k | Stereoselective Alder-ene Reactions of Bicyclo[1.1.0]butanes: Facile Synthesis of Cyclopropyl- and Aryl-substituted Cyclobutenes | Bicyclo[1.1.0]butanes (BCBs), strained carbocycles comprising two fused cyclopropane rings, have become well-established building blocks in organic synthesis, medicinal chemistry and chemical biology due to their diverse reactivity profile with radicals, nucleophiles, cations and carbenes. The constraints of the bicyclic ring system confers high p-character on the interbridgehead C–C bond, leading to this broad reaction profile; however the use of BCBs in pericyclic processes has to date been largely overlooked in favor of such stepwise, non-concerted additions. Here we describe the use of BCBs as substrates for ene-like reactions with strained alkenes and alkynes, which give rise to cyclobutenes decorated with highly-substituted cyclopropanes and arenes. The former products are obtained from highly stereoselective reactions with cyclopropenes, generated in situ from vinyl diazoacetates under blue light irradiation (440 nm). Cyclo-butenes featuring a quaternary aryl-bearing carbon atom are prepared from equivalent reactions with arynes, which proceed in high yields under mild conditions. Mechanistic studies highlight the importance of electronic effects in this chemistry, while computational investiga-tions support a concerted pathway, and rationalize the excellent stereoselectivity of reactions with cyclopropenes. | Ayan Dasgupta; Subrata Bhattacharjee; Zixuan Tong; Avishek Guin; Ryan McNamee; Kirsten Christensen; Akkattu Biju; Edward Anderson | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ac44b5ba3e99daefdc324b/original/stereoselective-alder-ene-reactions-of-bicyclo-1-1-0-butanes-facile-synthesis-of-cyclopropyl-and-aryl-substituted-cyclobutenes.pdf |
6304df790c5277c820bfaf44 | 10.26434/chemrxiv-2022-xxfqd | Discovery, structure, and mechanism of a class II sesquiterpene cyclase
| Terpene cyclases (TCs), the extraordinary enzymes that create the structural diversity seen in terpene natural products, are traditionally divided into two classes. Although the structural and mechanistic features in class I TCs are well-known, the corresponding details in class II counterparts have not been fully characterized. Here, we report the genome mining discovery and structural characterization of two class II sesquiterpene cyclases (STCs) from Streptomyces. These drimenyl diphosphate synthases (DMSs) are the first STCs shown to possess β,γ-didomain architecture. High-resolution X-ray crystal structures of SsDMS in complex with both a farnesyl diphosphate and Mg2+ unveiled an induced-fit mechanism with an unprecedented Mg2+ binding mode, finally solving one of the lingering questions in class II TC enzymology. This study supports continued genome mining for novel bacterial TCs and provides new mechanistic insights into canonical class II TCs that will lead to advances in TC engineering and synthetic biology.
| Xingming Pan; Wenyu Du; Xiaowei Zhang; Xiaoxu Lin; Fang-Ru Li; Qian Yang; Hang Wang; Jeffrey D. Rudolf; Bo Zhang; Liao-Bin Dong | Biological and Medicinal Chemistry; Catalysis; Biochemistry; Chemical Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304df790c5277c820bfaf44/original/discovery-structure-and-mechanism-of-a-class-ii-sesquiterpene-cyclase.pdf |
663cf4b291aefa6ce194ecf3 | 10.26434/chemrxiv-2024-6tg5n | Zirconium Hydride Catalysis Initiated by Tetrabutylammonium Fluoride | In our drug discovery campaigns to target the oncogenic drivers of cancers, the demand for a chemoselective, stereoselective and economical synthesis of chiral benzylamines drove the development of a catalytic zirconium hydride reduction. This methodology uses the inexpensive, bench stable zirconocene dichloride, and a novel tetrabutylammonium fluoride activa-tion tactic to catalytically generate a metal hydride under ambient conditions. The diastereo- and chemoselectivity of this reaction was tested with the preparation of key intermediates from our discovery programs and in the scope of sulfinyl ketimines and carbonyls relevant to medicinal chemistry and natural product synthesis. A preliminary mechanistic investi-gation conducted into the role of tetrabutylammonium fluoride indicates that formation of a zirconocene fluoride occurs to initiate catalysis. The implications of this convenient activation approach may provide expanded roles for zirconium hy-drides in catalytic transformations. | Stephen Harwood; Athenea Aloiau; Briana Bobek; Kelly Pearson; Kendall Cherry; Christopher Smith; John Ketcham; Matthew Marx | Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663cf4b291aefa6ce194ecf3/original/zirconium-hydride-catalysis-initiated-by-tetrabutylammonium-fluoride.pdf |
60c74c1dbdbb89490ea396eb | 10.26434/chemrxiv.9759581.v7 | Geometry-Wave Potential Quantified and Unified Properties in General Chemistry | Many long-known but never-quantified properties in chapters of general chemistry have for the first time been quantitatively compared and consistently unified, using the newly introduced geometro-wave (GW) potential of particles (i.e. atoms, molecules, clusters, ions, and nanoparticles). Th GW Potential has helped update the electrochemistry, Lewis acid-base chemistry, redox chemistry, self-assembly, surface chemistry, catalysis, and inter-nanoparticle bonding. | Zheng Tian | Nanostructured Materials - Nanoscience; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Physical and Chemical Properties; Self-Assembly; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c1dbdbb89490ea396eb/original/geometry-wave-potential-quantified-and-unified-properties-in-general-chemistry.pdf |
60c74f80f96a0039fa287c74 | 10.26434/chemrxiv.12804032.v2 | Carbenaporphyrins: A Missing Ligand in N-Heterocyclic Carbene Chemistry | The successful synthesis of a
carbenaporphyrin ligand based on carbazole and triazolylidene (CTP) is
reported. Instead of a macrocyclic aromatic or antiaromatic character, the
aromaticity of each heterocyclic moiety is preserved, which results in optical
properties different from porphyrins, e.g. fluorescence. In Li<sup>+</sup> and Sc<sup>3+</sup> complexes
the ligand reveals striking geometric similarity to porphyrins, but is stronger
electron donating. | Theo Maulbetsch; Doris Kunz | Coordination Chemistry (Organomet.); Ligand Design; Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f80f96a0039fa287c74/original/carbenaporphyrins-a-missing-ligand-in-n-heterocyclic-carbene-chemistry.pdf |
60c73f5bee301c2f50c788a1 | 10.26434/chemrxiv.7323995.v1 | CuH-Catalyzed Enantioselective Alkylation of Indole Derivatives with Ligand-Controlled Regiodivergence | <b>Enantioenriched molecules bearing indole-substituted stereocenters form a class of privileged compounds in biological, medicinal, and organic chemistry. Thus, the development of methods for asymmetric indole alkylation is highly valuable in organic synthesis. Traditionally, achieving N-selectivity in indole alkylation reactions is a significant challenge, since there is an intrinsic preference for alkylation at C3, the most nucleophilic position. Furthermore, selective and predictable access to either N- and C3-alkylated chiral indoles using catalyst control has been a long-standing goal in indole functionalization. Herein, we report a ligand-controlled regiodivergent synthesis of N- and C3-alkylated chiral indoles that relies on a polarity reversal strategy. In contrast to conventional alkylation reactions in which indoles are employed as nucleophiles, this transformation employs electrophilic indole derivatives, N-(benzoyloxy)indoles, as coupling partners. N- or C3-alkylated indoles are prepared with high levels of regio- and enantioselectivity using a copper hydride catalyst. The regioselectivity is governed by the use of either DTBM-SEGPHOS or Ph-BPE as the supporting ligand. Density functional theory (DFT) calculations are conducted to elucidate the origin of the ligand-controlled regiodivergence.</b> | Yuxuan Ye; Seoung-Tae Kim; Jinhoon Jeong; Mu-Hyun Baik; Stephen L. Buchwald | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5bee301c2f50c788a1/original/cu-h-catalyzed-enantioselective-alkylation-of-indole-derivatives-with-ligand-controlled-regiodivergence.pdf |
678bfa1c6dde43c90815ccc5 | 10.26434/chemrxiv-2023-kss3r-v3 | Emergence of molecular structures from repository-scale self-supervised learning on tandem mass spectra | Tandem mass spectrometry (MS/MS) is the primary method for characterizing biological and environmental samples at a molecular level. Despite this, the interpretation of tandem mass spectra from untargeted metabolomics experiments remains a challenge. Existing computational methods for predictions from mass spectra heavily rely on limited spectral libraries and on hard-coded human expertise. Here we introduce a transformer-based neural network pre-trained in a self-supervised way on millions of unannotated tandem mass spectra from our new GeMS (GNPS Experimental Mass Spectra) dataset mined from the MassIVE GNPS repository. We show that pre-training our model to predict masked spectral peaks and chromatographic retention orders leads to the emergence of rich representations of molecular structures, which we name DreaMS (Deep Representations Empowering the Annotation of Mass Spectra). Fine-tuning the pre-trained neural network to predict spectral similarity, molecular fingerprints, chemical properties, and the presence of fluorine from tandem mass spectra yields state-of-the-art performance across all the tasks. This underscores the practical utility of DreaMS across diverse mass spectrum interpretation tasks and establishes it as a stepping stone for future advances in the field. We make our new dataset and pre-trained models available to the community and release the DreaMS Atlas -- a molecular network of 201 million MS/MS spectra constructed using DreaMS annotations. | Roman Bushuiev; Anton Bushuiev; Raman Samusevich; Corinna Brungs; Josef Sivic; Tomáš Pluskal | Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678bfa1c6dde43c90815ccc5/original/emergence-of-molecular-structures-from-repository-scale-self-supervised-learning-on-tandem-mass-spectra.pdf |
60c744740f50db329d3960a6 | 10.26434/chemrxiv.9794588.v1 | Rapid Crystallization and Kinetic Freezing of Site-Disorder in the Lithium Superionic Argyrodite Li6PS5Br | <p>Lithium argyrodite superionic conductors are currently being investigated as solid electrolytes for all-solid-state batteries. Recently, in the lithium argyrodite Li<sub>6</sub>PS<sub>5</sub>X (X = Cl, Br, I), a site-disorder between the anionsS<sup>2–</sup>and X<sup>–</sup>has been observed, which strongly affects the ionic transport and appears to be a function of the halide present. In this work, we show how such disorder in Li<sub>6</sub>PS<sub>5</sub>Br can be engineered <i>via</i>the synthesis method. By comparing fast cooling (<i>i.e. </i>quenching) to more slowly cooled samples, we find that anion site-disorder is higher at elevated temperatures, and that fast cooling can be used to kinetically trap the desired disorder, leading to higher ionic conductivities as shown by impedance spectroscopy in combination with <i>ab-initio</i>molecular dynamics. Furthermore, we observe that after milling, a crystalline lithium argyrodite can be obtained within one minute of heat treatment. This rapid crystallization highlights the reactive nature of mechanical milling and shows that long reaction times with high energy consumption are not needed in this class of materials. The fact that site-disorder induced <i>via</i>quenching is beneficial for ionic transport provides an additional approach for the optimization and design of lithium superionic conductors.</p> | Ajay Gautam; Marcel Sadowski; Nils Prinz; Henrik Eickhoff; Nicolo Minafra; Michael Ghidiu; Sean Culver; Karsten Albe; Thomas Fässler; Mirijam Zobel; Wolfgang Zeier | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744740f50db329d3960a6/original/rapid-crystallization-and-kinetic-freezing-of-site-disorder-in-the-lithium-superionic-argyrodite-li6ps5br.pdf |
67a2dd26fa469535b916b697 | 10.26434/chemrxiv-2024-vhmz3-v2 | Single atom alloys 2.0: Exploiting undercoordination for stronger dissociative CH4 chemisorption | Efficient C-H bond activation is key to low temperature methane oxidation in catalytic converters of natural gas-powered vehicles. Through ab initio calculations, we investigate the potential enhancement of dissociative CH₄ chemisorption on single atom doped (211) facets of Pt and Pd, the preferred platinum group metals (PGMs) for methane oxidation. Single atom doping at undercoordinated edge sites induces surface relaxation, leading to stronger methane dissociation energies due to dopant-induced expansive lattice strain. Conversely, geometrically restricted subsurface doping imposes compressive strain, resulting in weaker chemisorption energies. Our findings indicate that the d-band model fails to capture these strain-dominated activity trends at single-atom sites. Although subsurface sites are thermodynamically stable for single atom doping under inert conditions, we demonstrate that dopant segregation to exposed edge sites becomes more favorable when dissociated methane is chemisorbed on the surface. This study adds a new dimension to the design of single-atom alloy catalysts and encourages experimental efforts to synthesize edge-doped dilute single-atom PGM alloys for enhanced CH₄ activation. | Debtanu Maiti; Michael Harold; Lars Grabow | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a2dd26fa469535b916b697/original/single-atom-alloys-2-0-exploiting-undercoordination-for-stronger-dissociative-ch4-chemisorption.pdf |
60c74d59bdbb891e12a39968 | 10.26434/chemrxiv.12612278.v1 | First-Principles Study of CaB12H12 as a Potential Solid-State Conductor for Ca | Calcium dodecahydro-closo-dodecaborate, CaB12H12, was
calculated to have a percolating Ca migration path with low
activation barrier (650 meV). The formation of Ca vacancies
required for diffusion was calculated to be thermodynamically
feasible by substitution of Ca with Al, Bi, or a number of trivalent
rare-earth cations | Julius Koettgen; Christopher Bartel; Jimmy-Xuan Shen; Kristin Persson; Gerbrand Ceder | Solid State Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d59bdbb891e12a39968/original/first-principles-study-of-ca-b12h12-as-a-potential-solid-state-conductor-for-ca.pdf |
60c7498d9abda22658f8cc68 | 10.26434/chemrxiv.12073869.v1 | General Cluster Sorption Isotherm | <p>Adsorption
isotherms are an essential tool in chemical physics of surfaces. However,
several approaches based on a different theoretical basis exist and for
isotherms including capillary condensation existing approaches can fail. Here,
a general isotherm equation is derived and applied to literature data both concerning
type IV isotherms of argon and nitrogen in ordered mesoporous silica, and type
II isotherms of disordered macroporous silica. The new isotherm covers the full
range of partial pressure (10<sup>-6</sup> - 0.7). It relies firstly on the
classical thermodynamics of cluster formation, secondly on a relationship
defining the free energy during the increase of the cluster size. That equation
replaces the Lennard-Jones potentials used in the classical density functional
theory. The determination of surface areas is not possible by this isotherm
because the cross-sectional area of a cluster is unknown. Based on the full
description of type IV isotherms, most known isotherms are accessible by
respective simplifications. </p> | Christoph Buttersack | Clusters; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7498d9abda22658f8cc68/original/general-cluster-sorption-isotherm.pdf |
62f10de16948b956e3b07f4d | 10.26434/chemrxiv-2022-p8hg6-v2 | Comparison of co-refining of fast pyrolysis oil from Salix via catalytic cracking and hydroprocessing | Lignocellulosic biomass from energy crops, i.e., short rotation coppice willows such as Salix spp., can be used as feedstock to produce transportation biofuels. An attractive thermochemical route for the introduction of large-scale production of biofuels in the transport sector in the near future is to convert the biomass to a liquid (pyrolysis oil) via fast pyrolysis followed by co-processing with fossil oil in existing refinery infrastructures. In this study, Salix was first liquefied using ablative fast pyrolysis in a pilot scale unit. The resulting pyrolysis oil, rich in oxygenates, was co-refined in 20 wt.% ratio with fossil feedstocks using two different technologies, a fluidized catalytic cracking (FCC) laboratory unit, and a continuous slurry hydroprocessing pilot plant.
In the FCC route, the pyrolysis oil was cracked at 525 °C using a commercial FCC catalyst at atmospheric pressures and resulted in significant deoxygenation (97 wt.%). To determine the biogenic carbon in the co-refined liquid product, C14 analysis was conducted. The whole conversion route resulted in 11 wt.% of the biogenic carbon from Salix ended up in liquid products, the rest being gaseous products, bio-char from the pyrolysis, and coke (16 wt.%) from the FCC upgrading. The hydroprocessing was conducted at 420 °C, at a hydrogen pressure of 150 bars at a liquid hourly space velocity of 0.67 h-1, in the presence of an unsupported molybdenum sulfide catalyst. The hydroprocessing resulted also in significant deoxygenation of the liquid product (93 wt.%). The whole conversion route resulted in 26 wt.% of the biogenic carbon from Salix ending up as liquid hydrocarbons, the rest was mainly gaseous hydrocarbons, carbon oxides, and bio-char.
The study showed that it is feasible to co-refine pyrolysis oil using both methods, the main difference being that hydroprocessing results in a significantly higher yield of hydrocarbon products but also would require an input of H2 while in the cracking route a significant part ends up as gas and as coke on the catalyst. The choice of routes is foremost dependent on the available amount of bio-oil and refining infrastructures. Besides liquid biofuel, it is also vital to utilize the biogenic carbon material in the bio-char and in the gaseous products.
| Ann-Christine Johansson; Niklas Bergvall; Roger Molinder; Elena Wikberg; Mirva Niinipuu; Linda Sandström | Energy; Chemical Engineering and Industrial Chemistry; Petrochemicals; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f10de16948b956e3b07f4d/original/comparison-of-co-refining-of-fast-pyrolysis-oil-from-salix-via-catalytic-cracking-and-hydroprocessing.pdf |
60c74228702a9bf3f418a3c5 | 10.26434/chemrxiv.8219057.v1 | BODIPY Fluorophores for Membrane Potential Imaging | Fluorophores based on the BODIPY scaffold are prized for their tunable excitation and emission profiles, mild syntheses, and biological compatibility. Improving the water-solubility of BODIPY dyes remains an outstanding challenge. The development of water-soluble BODIPY dyes usually involves direct modification of the BODIPY fluorophore core with ionizable groups or substitution at the boron center. While these strategies are effective for the generation of water-soluble fluorophores, they are challenging to implement when developing BODIPY-based indicators: direct modification of BODIPY core can disrupt the electronics of the dye, complicating the design of functional indicators; and substitution at the boron center often renders the resultant BODIPY incompatible with the chemical transformations required to generate fluorescent sensors. In this study, we show that BODIPYs bearing a sulfonated aromatic group at the meso position provide a general solution for water-soluble BODIPYs. We outline the route to a suite of 5 new sulfonated BODIPYs with 2,6-disubstitution patterns spanning a range of electron-donating and -withdrawing propensities. To highlight the utility of these new, sulfonated BODIPYs, we further functionalize them to access 13 new, BODIPY-based voltage-sensitive fluorophores. The most sensitive of these BODIPY VF dyes displays a 48% ΔF/F per 100 mV in mammalian cells. Two additional BODIPY VFs show good voltage sensitivity (≥24% ΔF/F) and excellent brightness in cells. These compounds can report on action potential dynamics in both mammalian neurons and human stem cell-derived cardiomyocytes. Accessing a range of substituents in the context of a water soluble BODIPY fluorophore provides opportunities to tune the electronic properties of water-soluble BODIPY dyes for functional indicators. | Jenna Franke; Benjamin Raliski; Steven Boggess; Divya Natesan; Evan Koretsky; Patrick Zhang; Rishikesh Kulkarni; Parker Deal; Evan Miller | Imaging; Spectroscopy (Anal. Chem.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74228702a9bf3f418a3c5/original/bodipy-fluorophores-for-membrane-potential-imaging.pdf |
60c74374842e6531e3db2298 | 10.26434/chemrxiv.7607078.v2 | Accurate Kd via Transient Incomplete Separation | <div>Current methods for finding the equilibrium dissociation constant, <i>K</i><sub>d</sub>, of protein-small molecule complexes have inherent sources of inaccuracy.</div><div><br /></div><div>We introduce “Accurate <i>K</i><sub>d</sub> via Transient Incomplete Separation” (AKTIS), an approach that is free of known sources of inaccuracy. Conceptually, in AKTIS, a short plug of the pre-equilibrated protein-small molecule mixture is pressure-propagated in a capillary, causing transient incomplete separation of the complex from the unbound small molecule. A superposition of signals from these two components is measured near the capillary exit as a function of time, for different concentrations of the protein and a constant concentration of the small molecule. Finally, a classical binding isotherm is built and used to find accurate <i>K</i><sub>d</sub> value. <br /></div><div><br /></div><div>Here we prove AKTIS validity theoretically and by computer simulation, present a fluidic system satisfying AKTIS requirements, and demonstrate practical application of AKTIS to finding <i>K</i><sub>d</sub> of protein-small molecule complexes.</div> | Nicolas Sisavath; Jean Luc Rukundo; J.C. Yves Le Blanc; Victor
A. Galievsky; Jiayin Bao; Sven Kochmann; Alexander
S. Stasheuski; Sergey N. Krylov | Analytical Chemistry - General; Analytical Apparatus; Biochemical Analysis; Chemoinformatics; Mass Spectrometry; Separation Science; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74374842e6531e3db2298/original/accurate-kd-via-transient-incomplete-separation.pdf |
652bb91b8bab5d205565a0f1 | 10.26434/chemrxiv-2023-m5z1r | Design, synthesis, chemical and biological evaluation of 2,5,5-trisubstituted-1,2-thiazepan-6-one 1,1-dioxides | In this article, we designed and synthesized a series of novel 2,5,5-trisubstituted (including spirocyclic) 1,2-thiazepan-6-one 1,1-dioxides (put simply, γ,γ-disubstituted β-keto ε-sultams), prepared a number of derivatives and evaluated their cytotoxic activity against MDA-MB-231 breast cancer cell line. In particular, alkylation of N-monosubstituted methanesulfonamides with α,α-disubstituted β-halogenated esters (including cyclic representatives) afforded the corresponding N-mesylated β-amino acid esters. The latters were involved in CSIC (Carbanion-mediated Sulfonamide Intramolecular Cyclization) reaction to give the target γ,γ-disubstituted β-keto ε-sultams (including spirocyclic representatives) in synthetically useful yields. This class of compounds can be considered as valuable building blocks since they possess carbonyl functionality and an EWG-activated methylene group capable of further functionalization. For instance, the condensation with DMFDMA afforded the corresponding α-dimethylaminomethylidene derivatives ‒ the direct precursors for the heterocyclization reactions. Their treatment with hydrazine hydrate or guanidine hydrochloride provided the corresponding pyrazolo- and pyrimidofused ε-sultams. Despite the prepared β-keto ε-sultams showing weak cytotoxicity against the MDA-MB-231 breast cancer cell line, their pyrazolofused derivatives appeared perspective pharmacological templates with stable cytotoxic effects. Moreover, β-keto ε-sultams and their heterofused derivatives form the water-soluble conjugates with branched polymers based on dextran-polyacrylamide (D-PAA) that can be used as the transport module for the targeted drug delivery in biological media. | Demyd Milokhov; Mykhailo Pomalin; Mykola Balabushko; Vladyslav Holubnychyi; Vasyl Hys; Pavlo Virych; Petro Virych; Nataliia Lukianova; Vasyl Chumachenko; Svitlana Shishkina; Yulian Volovenko; Alexey Dobrydnev | Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652bb91b8bab5d205565a0f1/original/design-synthesis-chemical-and-biological-evaluation-of-2-5-5-trisubstituted-1-2-thiazepan-6-one-1-1-dioxides.pdf |
64d293aa4a3f7d0c0dd52640 | 10.26434/chemrxiv-2022-j2mc1-v3 | Spin labelling via metabolic glycoengineering for studying post-translational protein modification by electron paramagnetic resonance spectroscopy | Post-translational modifications are involved in many cellular processes. The addition of O-linked β-N-acetylglucosamine (O-GlcNAc) is a ubiquitous post-translational modification essential for regulatory processes in mammalian cells. Here, we demonstrate specific spin labelling of post-translational modifications, namely glycosylation modifications, via metabolic glycoengineering and subsequent copper-catalyzed azide-alkyne cycloaddition. Electron paramagnetic resonance spectroscopy and subsequent quantitative spectral simulations allow for detection of the labelled post-translational modifications and for monitoring the levels of O-GlcNAcylation in presence of different inhibitors relevant for metabolic glycoengineering. | Anna Rubailo; Valentin Wittmann; Malte Drescher | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Biochemistry; Biophysics | CC BY NC 4.0 | CHEMRXIV | 2023-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d293aa4a3f7d0c0dd52640/original/spin-labelling-via-metabolic-glycoengineering-for-studying-post-translational-protein-modification-by-electron-paramagnetic-resonance-spectroscopy.pdf |
6727ed9cf9980725cffd5e3f | 10.26434/chemrxiv-2024-4mst2 | Close Electrohydrodynamic Fiber Deposition using a Partially Coated Glass Collector | This article outlines an electrohydrodynamic printing discovery that produces well-formed fibers from a normally difficult-to-process polymer that are positioned extremely close to each other. A solution of poly(vinylidene-co-trifluoroethylene-co-chlorotrifluoroethylene) P(VDF-co-TrFE-co-CTFE) in dimethyl sulfoxide (DMSO) is heated to 60°C to both enable solution flow and increased solvent evaporation from the jet. A glass microscope slide with a partially-coated platinum (Pt) region permitted the touching of direct written single parallel fibers to the level that they are touching. Such close-fiber positioning was unattainable on a non-coated microscope slide or metallic collectors. This discovery of a partially metal-coated glass collector expands the design possibilities for electrohydrodynamic continuous jetting. | Antonín Minařík; Aleš Mráček; Paul Dalton | Materials Science; Materials Processing | CC BY 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6727ed9cf9980725cffd5e3f/original/close-electrohydrodynamic-fiber-deposition-using-a-partially-coated-glass-collector.pdf |
6352327daca1987ef2ded616 | 10.26434/chemrxiv-2022-m399q | Protein Encapsulated Covellite CuS Nanospheres for the Efficient Oxidative Degradation of Organic Dyes in Wastewater | The existence of toxic, non-biodegradable organic pollutants in wastewater has become an indisputable and global remark for environmental problem. Interesting works have been performed on engineering/designing novel nano-catalyst to replace well-known Fe-fenton system in the degradation of such pollutants where the residual iron limits their wide application. Alternatively, Cu based materials have been explored in waste-water management mainly due to their ease of availability, cost-effectiveness, and efficient oxidative catalytic activity. However, synthesis of such pure phase water-soluble monodispersed Cu-based nanoparticles is challenging. In this study, we reported the synthesis of monodispersed covellite bovine serum albumin functionalized - copper sulfide (BSA-CuS) nanoparticles by simple thermal decomposition process. As-synthesized nanoparticles were characterized through advanced techniques such as UV-Visible spectra, XRD, FT-IR, HR-TEM and XPS. Finally, their potential for enhanced oxidative catalytic performance was investigated through experimental and theoretical studies for the degradation of wide range of dyes such as anionic dye, cationic dye, and industry effluent, which are commonly present in wastewater as contaminant. | Shamili Bandaru; Anik Sen; Goutam Pramanik; Goutam Kumar Dalapati; Sajal Biring; Sabyasachi Chakrabortty | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6352327daca1987ef2ded616/original/protein-encapsulated-covellite-cu-s-nanospheres-for-the-efficient-oxidative-degradation-of-organic-dyes-in-wastewater.pdf |
65a2807c66c13817295a6bfe | 10.26434/chemrxiv-2024-z93sj | First Cu-Nanostar as Sustainable Catalyst Realized through Synergistic Effects of Bowl-shaped Features and Surface Activation of Sporopollenin Exine | Recently, nanostar-shaped structures, including gold nanostars (NS), have drawn much attention for their potential use in surface-enhanced Raman spectroscopy (SERS) and catalysis. Yet, very few studies have been conducted on Cu-Au hybrid NS, and there are none for Cu-based NS. Herein, we describe an effective method for controlling copper oxide nanostar (ESP-PEI-CuI/IIO-NS) growth using sporopollenin as a sustainable template material. However, ESP-PEI-CuI/IIO-NS growth depends on sporopollenin surface functionalization. Sporopollenin surface activation was done by amine functionalization with polyethyleneimine (PEI), without which ESP-PEI-CuI/IIO-NS growth was not observed. The sporopollenin’s exine (outer wall) has bowl-like structures, which mediates the growth of Cu nanorods, resulting in an NS morphology. Furthermore, due to their increased surface area, ESP-PEI-CuI/IIO-NS showed excellent catalytic activity for Huisgen 1,3-dipolar cycloadditions even when used in H2O and without additives under greener conditions. This approach utilising biomass as a sustainable template would pave the way for developing controlled growth of nanostructures for SERS-related and catalytic applications. | Vijayendran Gowri; Sarita Kumari; Raina Sharma; Abdul Selim; Govindasamy Jayamurugan | Catalysis; Polymer Science; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a2807c66c13817295a6bfe/original/first-cu-nanostar-as-sustainable-catalyst-realized-through-synergistic-effects-of-bowl-shaped-features-and-surface-activation-of-sporopollenin-exine.pdf |
60c745c3bb8c1a0d063da73e | 10.26434/chemrxiv.10260353.v1 | Experimental and Topological Determination of the Pressure-Temperature Phase Diagram of Racemic Etifoxine, a Pharmaceutical Ingredient with Anxiolytic Properties | <div>
<div>
<div>
<p>Information about the solid-state properties of etifoxine has been lacking, even if the active pharmaceutical
ingredient has been used for its anxiolytic properties for decennia. The crystal structure of the racemic
compound possesses a monoclinic space group P21/n with cell parameters a = 8.489(2) Å, b = 17.674(2) Å,
c = 20.883(3) Å, b = 98.860(10)° and a unit-cell volume of 3095.8(9) Å3 at 293 K. The unit cell contains 8
molecules, while 2 independent molecules with different conformations are present in the asymmetric unit.
The density of the crystal is 1.291 g/cm3 and its melting point was found at 362.6 ±0.3 K with a melting
enthalpy of 85.6 ±3.0 J g-1. Its thermal expansion in the liquid and the solid state and the change in volume
on melting and between the vitreous state and the crystalline solid have been studied. The results confirm
the tendency of small organic molecules to increase about 11% in volume on melting, while the volume
difference between the glass and the crystal at the glass transition temperature is about half this value at
6%. These values can be used in the construction of phase diagrams in the case that the experimental data
for a given system is incomplete.
</p>
</div>
</div>
</div> | Maria Barrio; Hassan Allouchi; Josep-Lluis Tamarit; René Céolin; L Berthon-Cédille; Ivo Rietveld | Physical and Chemical Properties; Structure; Thermodynamics (Physical Chem.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c3bb8c1a0d063da73e/original/experimental-and-topological-determination-of-the-pressure-temperature-phase-diagram-of-racemic-etifoxine-a-pharmaceutical-ingredient-with-anxiolytic-properties.pdf |
60d353a5afe54f5ff6a4c474 | 10.26434/chemrxiv-2021-35cn8 | Programmable zwitterionic droplets as biomolecular sorters and model of membraneless organelles | It is emerging that cells can regulate biochemical functions by generating open compartments with well-defined composition. One important mechanism underlying this control is simple coacervation driven by disordered proteins that encode multivalent interactions. Inspired by these observations, here we develop programmable droplets based on simple coacervation of synthetic responsive polymers that mimic the architecture of these biological disordered proteins. We have adopted a bottom-up approach starting from zwitterionic polymers, demonstrating that they can form liquid droplets that exclude most molecules. Starting from this reference material we have progressively introduced in the polymer architecture an increasing number of different intermolecular interactions. With this strategy, we can independently control multiple properties of the droplets, such as stimulus responsiveness, polarity, selective uptake of client molecules and miscibility. We demonstrate that these droplets can separate and enable the detection of target molecules even within complex mixtures, opening attractive applications in bioseparation and in diagnostics. | Umberto Capasso Palmiero; Carolina Paganini; Marie Kopp; Miriam Linsenmeier; Andreas Kuffner; Paolo Arosio | Physical Chemistry; Materials Science; Polymer Science; Biophysical Chemistry; Interfaces; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d353a5afe54f5ff6a4c474/original/programmable-zwitterionic-droplets-as-biomolecular-sorters-and-model-of-membraneless-organelles.pdf |
66dca3da12ff75c3a1b864bc | 10.26434/chemrxiv-2024-rhf99 | On the Origin of Superior Hydrogen Evolution Activity on Composite Ni/Ni3S2 Catalysts: A First Principles Investigation | Nickel-based compound catalysts have been shown to have significantly higher alkaline HER activity than pure Ni. Here we attempt to explain this behavior with composite Ni/Ni-3S2. First, simulated annealing of a previously generated Ni/Ni3S2 heterostructure uncovered S-diffusion to the Ni surface. GCDFT calculations show that pristine Ni is likely to be lightly modified by adsorbed OH at alkaline conditions, in contrast to other metals, and reveal that the OH- and S-modified surfaces are mutually exclusive. These light modifications did not significantly change the activity of the Ni surface. Seeing no effect on the static Volmer step (the RDS of alkaline HER), we performed dynamic calculations of the alkaline Volmer barrier. Using metadynamics to sample the reaction along our defined collective variable (CV), we first estimate the barrier on Ni and Pt, obtaining a similar gap between static and dynamic barriers. Low temperature (100K) sampling on Ni found a significantly lower barrier relating to the more consistent hydrogen-bondng at low temperatures. Our characterization of the Ni and Pt interfaces from unbiased AIMD showed similar solvent structures, further supporting this line of thinking. Finally, calculations on OH- and S-modified Ni surfaces found that the former surface had a greater Volmer barrier by 0.16 eV. This OH-modified surface had a significantly less consistent solvation environment, with an average hydrogen bond lifetime 14 fs less than that of the S-modified surface. From these results, we contend that the enhanced activity of composite Ni/Ni3S2 catalysts originates from adsorbed S on Ni preventing OH-binding and the associated decline in interfacial solvation. Our calculations emphasize the importance of interface dynamics on electrochemical reaction barriers. | Dipam Manish Patel; Gyeong Hwang | Theoretical and Computational Chemistry; Materials Science; Catalysis; Computational Chemistry and Modeling; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dca3da12ff75c3a1b864bc/original/on-the-origin-of-superior-hydrogen-evolution-activity-on-composite-ni-ni3s2-catalysts-a-first-principles-investigation.pdf |
649efc619ea64cc1673a2e00 | 10.26434/chemrxiv-2023-bm5qc-v2 | Inelastic Scattering of Formaldehyde on Au(111) surface | Inelastic scattering between gas molecules and surfaces is a fundamental process that has been investigated extensively. During this process, the energy exchange between the gas and the surface changes the internal and translational degrees of freedom of the scattered gas molecules. However, the energy transfer mechanism between the molecule and surface is quite complicated and not well understood. In recent gas-surface scattering experiments [Phys. Chem. Chem. Phys. 19, 19896 (2017)] on formaldehyde scattering off the gold surface, the scattered formaldehyde molecules had a high propensity to excite twirling motion about the C-O bond axis. In the work presented here, we used classical dynamics simulation to understand energy transfer in formaldehyde-surface collisions and to probe the mechanism of interconversion of translational energy to rotational energy. Our simulations capture the trend of the experiments for the formaldehyde-Au scattering, both in terms of rotational energy distribution and trapping probabilities, and provide an atomic-level mechanism for the energy transfer process during the scattering process. | Rupayan Biswas; Upakarasamy Lourderaj | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649efc619ea64cc1673a2e00/original/inelastic-scattering-of-formaldehyde-on-au-111-surface.pdf |
66bba0d920ac769e5f7d9a2b | 10.26434/chemrxiv-2024-f14jv-v2 | Thionation of poly(2-ethyl-2-oxazoline) and its effect on solubility and cloud point | Many water-soluble polymers undergo phase separation above their lower critical solution temperature (LCST) in aqueous solutions. Generally, the LCST is controlled via the polymer-solvent interactions, which in turn are highly structure dependent and typically tuned via the polymer side chain. For example, the LCST for the poly(2-oxazoline) family can be tuned via the length of the polymer side chain. In particular, the LCST of poly(2-ethyl-2-oxazoline) varies between 60-100 °C, depending on its molar mass, polymer architecture and concentration. Here, we introduce LCST adjustment via modification of the carbonyl of the amide moiety of poly(2-oxazoline)s. We introduce poly(2-ethyl-2-oxazoline-co-N-propiothioacetyl ethylene imine), synthesized from poly(2-ethyl-2-oxazoline) using Lawesson’s reagent. The degree of thionation of the polymers was varied and characterized using spectroscopic methods and elemental analysis. While the glass transition temperatures of the copolymers increase with increasing thionation degree, decomposition temperatures decrease. Interestingly, polymers with less than 20% thionation degree were soluble in water with LCST behavior. The cloud point temperatures decrease with increasing thionation degree, due to weaker hydrogen bonding ability of thioamides and decreased polarity. | Askican Hacioglu; Vikram Baddam; Andrew Kerr; Josef Kehrein; Alex Bunker; Robert Luxenhofer | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Organic Polymers; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bba0d920ac769e5f7d9a2b/original/thionation-of-poly-2-ethyl-2-oxazoline-and-its-effect-on-solubility-and-cloud-point.pdf |
60e846feaf9cdb9b44da2eb9 | 10.26434/chemrxiv-2021-cqbws | Tuning the excited state properties of [2.2]paracyclophane-based antennas to ensure efficient sensitization of lanthanide ions or singlet oxygen generation. | The multi-step synthesis of original antennas incorporating substituted [2.2]paracyclophane (pCp) moieties in the -conjugated skeleton is described. These antennas, functionalized with electron an donor alkoxy fragment (A1) or with a fused coumarin derivative (A2) are incorporated in a triazacyclonane macrocyclic ligand L1 or L2, respectively for the design of Eu(III), Yb(III) and Gd(III) complexes. A combined photophysical/theoretical study reveals that A1 presents a charge transfer character via the through-space paracyclophane conjugation, whereas A2 presents only local excited states centered on the coumarin-paracyclophane moiety, strongly favoring triplet state population via intersystem crossing. The resulting complexes EuL1 and YbL2 are fully emissive in the red and near infrared, respectively whereas the GdL2 complex acts as photosensitizer for the generation of singlet oxygen.
| Shiqi Wu; Laura Abad Galan; Margaux Roux; François Riobé; Boris Le Guennic; Yannick Guyot; Tangui Le Bahers; Laurent Micouin; Olivier Maury; Erica Benedetti | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2021-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e846feaf9cdb9b44da2eb9/original/tuning-the-excited-state-properties-of-2-2-paracyclophane-based-antennas-to-ensure-efficient-sensitization-of-lanthanide-ions-or-singlet-oxygen-generation.pdf |
630d3e2dd147b27510bd60ad | 10.26434/chemrxiv-2022-f61pb | Expedited Total Synthesis of Brevianamide A via the Strategic Use of Gold(I)-Catalysis | Two concise and complementary routes to the polycyclic alkaloid brevianamide A from readily available amino acid building blocks is presented. Key to the synthesis is the strategic use of a gold(I)-catalyzed cascade process that quickly assembles the characteristic pseudoindoxyl motif of the natural product along with the two adjacent quaternary centers in a single step. This sequence, which exemplifies the structural complexity that can be achieved with gold catalysis, allowed for the shortest and highest yielding synthesis of brevianamide A to date (4 steps LLS, 14% overall yield) | Ali Mansour; Fabien Gagosz | Organic Chemistry; Catalysis; Natural Products; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630d3e2dd147b27510bd60ad/original/expedited-total-synthesis-of-brevianamide-a-via-the-strategic-use-of-gold-i-catalysis.pdf |
67ac7427fa469535b9021143 | 10.26434/chemrxiv-2025-2hs17 | Nitroreductase-triggered indazole formation | Biocatalysis contributes significantly to the development of more sustainable synthetic pathways by using mild reaction conditions and water as a solvent. However, many relevant classes of compounds, including privileged groups in drug design, are not yet accessible via enzymatic pathways. In this context, the development of an enzymatic route to indazoles remains an unmet challenge. Here, we present the first example of nitroreductase-triggered indazole formation, in which 2-nitrobenzylamine derivatives are converted to reactive nitrosobenzylamine intermediates that spontaneously cyclize and aromatize to indazoles. Two nitroreductases, NfsA and BaNTR1, were found to accept a
series of 2-nitrobenzylamine derivatives with excellent conversions (up to >99 %). In the case of N-substituted nitrosobenzylamines, 2H-indazoles were formed, whereas other derivatives led to 1H-indazoles. The synthetic value of the nitroreductase-triggered indazole formation was further demonstrated by successful coupling with an imine reductase (IRED15) in a sequential cascade reaction. With this cascade, N-methyl-2Hindazole was accessible from cheap 2-nitrobenzaldehyde and methylamine, resulting in 62 % isolated yield. | Henrik Terholsen; Lisa Medema; Elizaveta Chernyshova; Alejandro Prats Luján; Gerrit J. Poelarends; Sandy Schmidt | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ac7427fa469535b9021143/original/nitroreductase-triggered-indazole-formation.pdf |
67ddda8181d2151a025ec170 | 10.26434/chemrxiv-2025-2gxjp | Polymorphism in Cysteine Adsorption on Au Surfaces: Zwitterions versus Uncharged Molecules | The adsorption of amino acids on coinage metal surfaces has been of interest for a range of biological applications. Core to the advancements of these applications is understanding the structure of the adsorbed molecules and the state they are present in. Cysteine, the focus of this study, has been studied extensively, both experimentally and theoretically. Here, density functional theory (DFT) and molecular dynamics are used to examine the different adsorption modes of the cysteine monomer on an Au(111) surface in vacuum. Dimeric structures and their influence on the adsorption mode of the individual molecules are also considered. We find that the most stable monomeric binding mode is an unconventional zwitterion the ammonium group is formed by do- nation of the mercapto hydrogen. Moreover, we observe the transformation of neu- tral adsorbed molecules to unconventional zwitterion through direct or indirect proton transfer. On the other hand, conventional zwitterions are unstable in monomeric form, either in gas phase or adsorbed structure calculations. | Clayton B. Smith; Aishat Idris; Elvis C. M. Ting; Irina Paci | Materials Science; Aggregates and Assemblies; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ddda8181d2151a025ec170/original/polymorphism-in-cysteine-adsorption-on-au-surfaces-zwitterions-versus-uncharged-molecules.pdf |
62120d2cbd05a083a50d76a9 | 10.26434/chemrxiv-2022-qsjzm | Based-Catalyzed Stereoselective Thiosulfonylation of Ynones | The first catalytic vicinal thiosulfonylation of ynones has been developed. Under the catalysis of 1-10 mol% Cs2CO3, various thiosulfonates underwent Michael addition/nucleophilic substitution tandem reaction with different ynones to form C-SO2 and C-S bonds simultaneously and produce multifunctional vinyl sulfones in high yields and excellent E-selectivity. | Lin He; Jinyun Luo; Muze Lin; Guangfen Du; Zhihua Cai | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62120d2cbd05a083a50d76a9/original/based-catalyzed-stereoselective-thiosulfonylation-of-ynones.pdf |
60c744bc567dfe6804ec4344 | 10.26434/chemrxiv.9904781.v1 | A Coherent Picture of the Hydrogen Oxidation and Evolution Reactions in Aqueous Solutions | <p>Recent studies show the limitations of catalytic activity descriptor-based approaches to rationalize the kinetics of the hydrogen oxidation and evolution reactions (HOR/HER). Herein, we deposited several transition metals (TMs) onto Pt surfaces to disturb and probe the interface in alkaline solutions. The redox transition of these TMs in association with adsorption and desorption of reaction intermediates during the HOR/HER was monitored via <i>in situ</i> X-ray absorption spectroscopy. We propose that the TM facilitates the HOR by anchoring H<sub>2</sub>O with the H-up configuration (↑H<sub>2</sub>O<sub>ad</sub>) that removes H<sub>ad</sub> on Pt via the bifunctional mechanism, based on the first in situ experimental evidence for the presence of ↑H<sub>2</sub>O<sub>ad</sub> on surface Ru. Meanwhile, the TM promotes the HER of Pt by anchoring OH<sub>ad</sub> to trigger the hard–soft acid–base (HSAB) mechanism for OH<sub>ad</sub> removal. The revised 2B theory depicts a coherent picture of the HOR/HER kinetics in aqueous solutions.<br /></p> | Ershuai Liu; Li Jiao; Jingkun Li; Thomas Stracensky; Lynne K. LaRochelle Richard; Qiang Sun; Sanjeev Mukerjee; Qingying Jia | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744bc567dfe6804ec4344/original/a-coherent-picture-of-the-hydrogen-oxidation-and-evolution-reactions-in-aqueous-solutions.pdf |
60c74c23702a9b6dff18b5e0 | 10.26434/chemrxiv.11980827.v2 | Multiconfigurational Dynamics Explain Photochemical Reactivity and Torquoselectivity Towards Fluorinated Polyacetylenes | The discovery of the conductivity of polyacetylene ignited the field of organic electronic materials. Functionalizing polyacetylenes with electron withdrawing groups (e.g., fluorine), has theoretically been shown to increase the air-stability of PAs and open new avenues in organic electronics. Burns and coworkers recently reported a novel synthetic route to fluorinated polyacetylenes which utilizes as a key step the completely stereoselective photochemical electrocyclic ring-closing of hexafluorinated dienes. This photochemical torquoselective (photo-torquoselective) reaction is, to our knowledge, the first of its kind. While the torquoselectivity model (Houk and co-workers) describes the stereospecificity of thermal electrocyclic reactions, no such reactivity model exists for their photochemical counterpart. We have used multiconfigurational quantum chemical calculations and ab initio molecular dynamics simulations to describe this reaction and to determine the origin of its stereoselectivity. We show that the reaction proceeds through the S1 excited state with a lifetime of 988 fs. This reaction lies along an energetically unfavorable pathway which results in a reaction quantum yield of approximately 0.9%. We predict that the reaction pathway to the unobserved product lies 0.2 eV (4.6 kcal mol−1) higher in energy than the pathway to the observed isomer. The unobserved isomer brings adjacent fluorine substituents to within 2.67 and 2.60 Å of each other at the S1/S0 crossing point, resulting in a closed-shell repulsion. This repulsion is responsible for increasing the energy of the unobserved pathway which directs the reaction exclusively to the observed product. | Jordan Cox; Steven Lopez | Photochemistry (Org.); Physical Organic Chemistry; Stereochemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c23702a9b6dff18b5e0/original/multiconfigurational-dynamics-explain-photochemical-reactivity-and-torquoselectivity-towards-fluorinated-polyacetylenes.pdf |
671e6c3b98c8527d9e8aeefb | 10.26434/chemrxiv-2024-qt1z4 | Photooxygenation reactions under flow conditions: An experimental and in-silico study | The photooxygenation reaction of a different set of olefins was investigated in LED flow reactor module from both experimental and in silico point of view. Initially, operating parameters potentially affecting the photoreaction efficiency, including the loading of the photosensitizer (methylene blue) (mol%), residence time and temperature were screened. The optimal conditions were then applied for the synthesis of 1,2-dioxetanes proving a straightforward and scalable approach to important chemiluminescent molecular probes for bioanalytical and diagnostic applications. Moreover, the scope of the reaction was tested for the oxidation of diverse alkenes under Schenck ene conditions providing synthetically useful allyl hydroperoxides. From this, a chemometric analysis was performed to propose a preliminary in silico model useful to both rationalize and predict the photooxygenation reaction outcome. | Giada Moroni; Yi-Hsuan Tsai; Marco Ballarotto; Andrea Carotti; Jean-Christophe M. Monbaliu; Antimo Gioiello | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671e6c3b98c8527d9e8aeefb/original/photooxygenation-reactions-under-flow-conditions-an-experimental-and-in-silico-study.pdf |
6583b1bee9ebbb4db964da21 | 10.26434/chemrxiv-2023-txxmf | Soliton based Dynamic Nuclear Polarization: an unexpected Overhauser effect in cyclic polyacetylene at high field and room temperature | Polyacetylene, a versatile material with an electrical conductivity that can span seven orders of magnitude, is the prototypical conductive polymer. In this letter, we report an unexpected and unprecedented Overhauser Effect that increases with temperature, observed under high magnetic field of 14.1 T, in both linear and cyclic polyacetylene. Significant NMR signal enhancements ranging from 24 to 45 are obtained. The heightened sensitivity enabled the characterization of chain defects at natural abundance. The absence of end methyl group carbon-13 signals provides proof of the closed-loop molecular structure of the cyclic polyacetylene. This efficiency of the soliton based Overhauser Effect DNP mechanism at high temperature and high field holds promise for applications and extension to other conductive polymer systems. | Zhihui Miao; Faith J. Scott; Johan van Tol; Russel Bowers; Adam S. Veige; Frederic Mentink-Vigier | Physical Chemistry; Catalysis; Homogeneous Catalysis; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6583b1bee9ebbb4db964da21/original/soliton-based-dynamic-nuclear-polarization-an-unexpected-overhauser-effect-in-cyclic-polyacetylene-at-high-field-and-room-temperature.pdf |
61eea96b0716a8ed4f3a6a60 | 10.26434/chemrxiv-2022-hngjc | Appraisal of dispersion damping functions for the effective fragment potential method | The effective fragment potential (EFP) is a polarizable force field whose physically-motivated functional form is parameterized in an automated way from ab initio
calculations, and whose dispersion potential has been suggested as a correction for Hartree-Fock or density functional theory calculations. However, the parameter-free dispersion damping potentials that are currently used in EFP do not follow from a rigorous derivation and do not satisfy simple limits for the dispersion energy.
We introduce several new damping expressions that correct these deficiencies, then evaluate their performance alongside existing damping functions using a new database of ionic liquid constituents. This data set, which we call IL195x8, consists of complete-basis coupled-cluster interaction energies for 195 ion pairs at each of 8 different intermolecular separations. Ultimately, we recommend a new parameter-free dispersion damping function as a replacement for the one that is currently used in EFP. | Kevin Carter-Fenk; John Herbert | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61eea96b0716a8ed4f3a6a60/original/appraisal-of-dispersion-damping-functions-for-the-effective-fragment-potential-method.pdf |
654923c548dad23120338ff4 | 10.26434/chemrxiv-2023-rp6q8 | Situating the Phosphonated Calixarene–Cytochrome C Association by Molecular Dynamics Simulations. | Protein-calixarenes binding plays an increasing, central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational ap- proaches such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit- solvent molecular dynamics simulations to capture the electrostatically-driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the X-ray struc- ture, the association has a larger structural impact in the protein dynamics. Our simulations, then, allow a direct comparison with analogous calixarenes, namely sulfonato, similarly re- ported as “molecular glue”. Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding. | Alessio Bartocci; Elise Dumont | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654923c548dad23120338ff4/original/situating-the-phosphonated-calixarene-cytochrome-c-association-by-molecular-dynamics-simulations.pdf |
639a46c8a2da4b91ee040fba | 10.26434/chemrxiv-2022-2mdnv | Interface Dielectric Constant of Water at the Surface of a Spherical Solute | Interface dielectric constant is used to quantify polar response of water interfacing a spherical solute. This interfacial parameter, affected by the interfacial structure within about two solvation layers, is fundamentally distinct from the bulk dielectric constant (a material property). Molecular dynamics simulations are used to extract the interface dielectric constant from fluctuation relations correlating the dipole moment of the interfacial layer with the medium electrostatics. For a probe ion, one has to calculate cross-correlations between the shell dipole and the electrostatic potential, while cross-correlations between the shell dipole and the electrostatic field are required for a probe dipole. All protocols produce dielectric constants of water interfacing a nonpolar solute significantly below the bulk value. We analyze corrections imposed on the fluctuation relations by protocols using periodic boundary conditions with Ewald sums to compute electrostatic interactions. These corrections are insignificant for typical simulation protocols. | Mohammadhasan Dinpajooh; Dmitry Matyushov | Physical Chemistry; Interfaces | CC BY NC 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639a46c8a2da4b91ee040fba/original/interface-dielectric-constant-of-water-at-the-surface-of-a-spherical-solute.pdf |
60c75842ee301c7b23c7b6df | 10.26434/chemrxiv.14529090.v1 | Magnetic Archimedean Tessellations in Metal-Organic Frameworks | The self-assembly of trivalent lanthanide ions with ditopic organic spacers results in the formation of complex tiling patterns that mimic the structural motifs of quasi-periodic 2D materials. The assembly of <i>trans</i>-{LnI<sub>2</sub>}<sup>+</sup> nodes (Ln = Gd, Dy) with both closed-shell and anion radicals of 4,4'-bipyridine affords rare examples of Archimedean tessellations in a metal-organic framework. We furthermore demonstrate occurrence of sizable magnetic exchange interactions and slow relaxation of magnetization behaviour in a complex tessellation pattern. The implementation of Archimedean tessellations in lanthanide(III) coordination solids couriers a strategy to design elusive quasi<i>-periodic metal-organic frameworks with inimitable magnetic properties</i> | Hua Chen; Laura Voigt; Mariusz Kubus; Dmytro Mihrin; Susanne Mossin; René Wugt Larsen; Søren Kegnæs; Stergios Piligkos; Kasper Pedersen | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Ligands (Inorg.); Magnetism; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75842ee301c7b23c7b6df/original/magnetic-archimedean-tessellations-in-metal-organic-frameworks.pdf |
650f4a9eb927619fe7b0923f | 10.26434/chemrxiv-2023-g82z3 | Deconvolution and Analysis of 1H NMR Spectra of Crude Reaction Mixtures | NMR spectroscopy is an important analytical technique in synthetic organic chemistry, but its integration into high-throughput experimentation workflows has been limited by the necessity to manually analyze NMR spectra of new chemical entities. Current efforts to automate the analysis of NMR spectra rely on comparisons to databases of reported spectra for known compounds, and, therefore, are incompatible with the exploration of new chemical space. By reframing the NMR spectrum of a reaction mixture as a joint probability distribution, we have used Hamiltonian Monte Carlo Markov Chain (HMCMC) and density functional theory (DFT) to fit predicted NMR spectra to those of crude reaction mixtures. This approach enables the deconvolution and analysis of spectra of containing mixtures of compounds, without relying on reported spectra. The utility of our approach to analyze crude reaction mixtures is demonstrated with experimental spectra of reactions that generate a mixture of isomers, such as Wittig olefination and C--H functionalization reactions. The correct identification of compounds in a reaction mixture and their relative concentrations is achieved with mean absolute error as low as 1%. | Maxwell Venetos; Masha Elkin; Connor Delaney; John Hartwig; Kristin Persson | Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650f4a9eb927619fe7b0923f/original/deconvolution-and-analysis-of-1h-nmr-spectra-of-crude-reaction-mixtures.pdf |
60c74b67bb8c1adcc53db1fd | 10.26434/chemrxiv.12326432.v1 | Ex-vivo Electrochemical pH Mapping of the Gastrointestinal Tract in the Absence and Presence of Pharmacological Agents | <i>Ex-vivo</i> pH profiling of the upper
gastrointestinal (GI) tract (of a mouse) in both the absence and presence of
pharmacological agents aimed at altering acid/bicarbonate production, is
reported using an electrochemical pH probe, for the first time. Three pH
electrodes were assessed for suitability using a GI tract biological mimic
buffer solution containing 0.5 % mucin. These include a traditional glass pH
probe, an iridium oxide (IrOx) coated electrode (both potentiometric) and a
quinone (Q) surface-integrated boron doped diamond (BDD-Q) electrode
(voltammetric). In mucin the timescale for both IrOx and glass to obtain stable
pH readings was in the ~100’s of s, most likely due to mucin adsorption, in
contrast to 6 s with the BDD-Q electrode. Both the glass and IrOx pH electrodes
were also compromised on robustness due to fragility and delamination (IrOx);
contact with the GI tissue was an experimental requirement. BDD-Q was deemed
the most appropriate. Ten measurements were made along the GI tract, esophagus
(1), stomach (5) and duodenum (4). Under untreated conditions (buffer only),
the BDD-Q probe tracked the pH from neutral in the esophagus, to acidic in the
stomach and rising to more alkaline in the duodenum. In the presence of
omeprazole, a proton pump inhibitor, the body regions of the stomach exhibited
elevated pH levels. Under melatonin treatment (a bicarbonate agonist and acid
inhibitor), both the body of the stomach and the duodenum showed elevated pH
levels. This study demonstrates the versatility of the BDD-Q pH electrode for
real-time <i>ex-vivo</i> biological tissue measurements. | Teena Rajan; Tania Read; Aya Abdalla; Bhavik Patel; Julie Macpherson | Biochemical Analysis; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b67bb8c1adcc53db1fd/original/ex-vivo-electrochemical-p-h-mapping-of-the-gastrointestinal-tract-in-the-absence-and-presence-of-pharmacological-agents.pdf |
60c743ae469df403b3f4322c | 10.26434/chemrxiv.9423011.v1 | Biaxial Strain Tuning of Interlayer Excitons in Bilayer MoS2 | <p>We show how
the excitonic features of biaxial MoS<sub>2</sub> flakes are very sensitive to
biaxial strain. We find a lower bound for the gauge
factors of the A exciton and B exciton of (-41 ± 2) meV/% and (-45 ± 2) meV/% respectively, which are larger
than those found for single-layer MoS<sub>2</sub>. Interestingly, the interlayer
exciton feature also shifts upon biaxial strain but with a gauge factor that is
systematically larger than that found for the A exciton, (-48 ± 4) meV/%. We attribute this larger gauge
factor for the interlayer exciton to the strain tunable van der Waals
interaction due to the Poisson effect (the interlayer distance changes upon
biaxial strain).</p> | Felix Carrascoso; Der-Yuh Lin; Riccardo Frisenda; Andres Castellanos-Gomez | Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ae469df403b3f4322c/original/biaxial-strain-tuning-of-interlayer-excitons-in-bilayer-mo-s2.pdf |
66024ff366c1381729d24d15 | 10.26434/chemrxiv-2024-xcdr8 | Characterization of deformational isomerization potential and interconversion dynamics with ultrafast x-ray solution scattering | Dimeric complexes composed of d8 square planar metal centers and rigid bridg- ing ligands provide model systems to understand the interplay between attractive dispersion forces and steric strain, in order to assist the development reliable meth- ods to model metal dimer complexes more broadly. [Ir2(dimen)4]2+ (dimen = para- diisocyanomenthane) presents a unique case study for such phenomena, as distortions of the optimal structure of a ligand with limited conformational flexibility counteracts the attractive dispersive forces from the metal and ligand to yield a complex with two ground state deformational isomers. Here, we use ultrafast X-ray solution scattering (XSS) and optical transient absorption spectroscopy (OTAS) to reveal the nature of the equilibrium distribution and the exchange rate between the deformational isomers. The two ground state isomers have spectrally distinct electronic excitations that enable the selective excitation of one isomer or the other using a femtosecond duration pulse of visible light. We then track the dynamics of the non-equilibrium depletion of the electronic ground state population – often termed the ground state hole – with ultra- fast XSS and OTAS, revealing a restoration of the ground state equilibrium in 2.3 ps. This combined experimental and theoretical study provides a critical test of various density functional approximations in the description of bridged d8-d8 metal complexes. The results show that density functional theory calculations can reproduce the primary experimental observations if dispersion interactions are added and a hybrid functional, which includes exact exchange, is used. | Natalia E. Powers-Riggs; Benedikt O. Birgisson; Sumana Raj; Elisa Biasin; Philipp Lenzen; Diana Bregenholt Zederkof; Morten Haubro; Dagrún K. V. Tveiten; Robert Hartsock; Tim B. van Driel; Kristjan Kunnus; Matthieu Chollet; Joseph Robinson; Silke Nelson; Ruaridh Forbes; Kristoffer Haldrup; Kasper Steen Pedersen; Gianluca Levi; Asmus Ougaard Dohn; Hannes Jónsson; Klaus Braagaard Møller; Adi Natan; Martin Meedom Nielsen; Kelly Gaffney | Physical Chemistry; Organometallic Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66024ff366c1381729d24d15/original/characterization-of-deformational-isomerization-potential-and-interconversion-dynamics-with-ultrafast-x-ray-solution-scattering.pdf |
664dfba521291e5d1df8a817 | 10.26434/chemrxiv-2024-v70lj | Polypharmacological Modulation of Atrial Fibrillation: Rational Design, Synthesis, and Evaluation of Novel Compounds Targeting NaV1.5, KV1.5, and K2P Channels | During atrial fibrillation (AF), electrical remodeling occurs, involving ion channels like NaV1.5, KV1.5, and TASK-1. A promising AF treatment encompasses inhibiting these channels. In this study, acetamide compounds were designed based on the local anesthetic pharmacophore as potential NaV1.5, KV1.5, and TASK-1 inhibitors. Compound 6f emerged as the most potent in the series, with IC50 values determined in Xenopus oocytes of approximately 0.3 µM in TASK-1, 81.5 µM in KV1.5, and 21.2 µM in NaV1.5. Unexpectedly, 6f activated at 100 µM another cardiac K2P channel (TASK-4) by about 40%. Next, we performed patch clamp experiments of human atrial cardiomyocytes from sinus rhythm (SR) or AF patients. In SR 6f reduced action potential amplitude (indicating NaV1.5 block) while in AF it increased action potential duration (APD), reflecting high affinity for TASK-1. Additionally, a hyperpolarization in resting membrane potential occurred in AF cardiomyocytes by 6f, consistent with the TASK-4 activation we observed. In a mathematical whole-atria model, 6f prolonged APD and tissue refractoriness, proving efficacious both for AF prevention and cardioversion. Favorable pharmacokinetic properties of 6f in silico, including good absorption and low toxicity, as well as its lack of cytotoxicity in a hemolytic assay, suggest its potential as an AF treatment. | Lorena Camargo-Ayala; Mauricio Bedoya; Albert Dasí; Merten Prüser; Luis Prent-Peñaloza; Francisco Adasme-Carreño; Aytug Kiper; Susanne Rinné; Paola Andrea Camargo-Ayala; Paula Andrea Peña-Martínez; Alfonso Bueno-Orovio; Diego Varela; Felix Wiedmann; José Carlos Estanislao Márquez-Montesinos; Constanze Schmidt; Blanca Rodriguez; Ursula Ravens; Niels Decher; Margarita Gutiérrez; Wendy González | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664dfba521291e5d1df8a817/original/polypharmacological-modulation-of-atrial-fibrillation-rational-design-synthesis-and-evaluation-of-novel-compounds-targeting-na-v1-5-kv1-5-and-k2p-channels.pdf |
65a6a80266c1381729940f80 | 10.26434/chemrxiv-2023-8s081-v2 | Charge regulation triggers condensation of short oligopeptides to polyelectrolytes | Electrostatic interactions between charged macromolecules are ubiquitous in bio- logical systems and they are important also in materials design. Attraction between oppositely charged molecules is often interpreted as if the molecules had a fixed charge, which is not affected by their interaction. Less commonly, charge regulation is invoked to interpret such interactions, i.e., a change of the charge state in response to a change of the local environment. Although some theoretical and simulation studies suggest that charge regulation plays an important role in intermolecular interations, experi- mental evidence supporting such view is very scarce. In the current study, we used a model system, composed of a long polyanion interacting with cationic oligolysines, containing up to 8 lysine residues. We showed using both simulations and experiments that while these lysines are only weakly charged in the absence of the polyanion, they charge up and condense on the polycations if the pH is close to the pKa of the lysine side chains. We show that the lysines coexist in two distinct populations within the same solution: 1. practically non-ionized and free in solution; 2. highly ionized and condensed on the polyanion. Using this model system, we demonstrate under what conditions charge regulation plays a significant role in the interactions of oppositely charged macromolecules and generalize our findings beyond the specific system used here. | Sebastian Pineda; Roman Staňo; Anastasiia Murmiliuk; Pablo Blanco; Patricia Montes; Zdeněk Tošner; Ondřej Groborz; Jiří Pánek; Martin Hrubý; Miroslav Štepánek; Peter Kosovan | Physical Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a6a80266c1381729940f80/original/charge-regulation-triggers-condensation-of-short-oligopeptides-to-polyelectrolytes.pdf |
60c744bb702a9b6ad318a8c6 | 10.26434/chemrxiv.8968508.v2 | Time-Resolved Dynamics in Iodide-Uracil-Water Clusters upon Excitation of the Nucleobase | The dynamics of iodide-uracil-water (I<sup>−</sup>·U·H<sub>2</sub>O) clusters following π-π*
excitation of the nucleobase are probed using time-resolved photoelectron
spectroscopy (TRPES). Photoexcitation of this cluster at 4.77 eV results in
electron transfer from the iodide moiety to the uracil, creating a
valence-bound (VB) anion within the cross-correlation of the pump and
probe laser pulses. This species can decay by a number of channels, including
autodetachment and dissociation to I<sup>−</sup> or larger anion fragments. Comparison
of the energetics of the photoexcited cluster and its decay dynamics with those
of the bare iodide-uracil (I<sup>−</sup>·U) complex provide a sensitive probe
of the effects of microhydration on these species. | Alice Kunin; Valerie S. McGraw; Katharine G. Lunny; Daniel Neumark | Clusters; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744bb702a9b6ad318a8c6/original/time-resolved-dynamics-in-iodide-uracil-water-clusters-upon-excitation-of-the-nucleobase.pdf |
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