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64fb484b99918fe537984a6b | 10.26434/chemrxiv-2023-63qfl-v2 | E Pluribus Unum: Functional Aggregation of Cell-Free Proteins Enables Fungal Ice Nucleation | Biological ice nucleation plays a key role in the survival of cold-adapted organisms. Several species of bacteria, fungi, and insects produce ice nucleators (INs) that enable ice formation at temperatures above -10 oC. Bacteria and fungi produce particularly potent INs that can promote water crystallization above -5 oC. Bacterial INs consist of extended protein units that aggregate to achieve superior functionality. Despite decades of research, the nature and identity of fungal INs remain elusive. Here we combine ice nucleation measurements, physicochemical characterization, numerical modeling and nucleation theory to shed light on the size and nature of the INs from the fungus Fusarium acuminatum. We find ice-binding and ice-shaping activity of Fusarium IN, suggesting a potential connection between ice growth promotion and inhibition. We demonstrate that fungal INs are composed of small 5.3 kDa protein subunits which assemble into ice nucleating complexes that can contain more than 100 subunits. Fusarium INs retain high ice-nucleation activity even when only the ~12 kDa fraction of size-excluded proteins are initially present, suggesting robust pathways for their functional aggregation in cell-free aqueous environments. We conclude that the use of small proteins to build large assemblies is a common strategy among organisms to create potent biological INs. | Ralph Schwidetzky; Ingrid de Almeida Ribeiro; Nadine Bothen ; Anna Backes; Arthur L. DeVries; Mischa Bonn; Janine Frhlich-Nowoisky; Valeria Molinero; Konrad Meister | Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Biophysical Chemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fb484b99918fe537984a6b/original/e-pluribus-unum-functional-aggregation-of-cell-free-proteins-enables-fungal-ice-nucleation.pdf |
672ce7dff9980725cf764d24 | 10.26434/chemrxiv-2024-93qp3 | Organic Solubility Prediction at the Limit of Aleatoric Uncertainty | Small molecule solubility is a critically important property which affects the efficiency, environmental impact, and phase behavior of synthetic processes. Experimental determination of solubility is a time- and resource-intensive process and existing methods for in silico estimation of solubility are limited by their generality, speed, and accuracy. This work presents two models derived from the fastprop and chemprop architectures and trained on BigSolDB which are capable of predicting solubility at arbitrary temperatures for any small molecule in organic solvent. Both extrapolate to unseen solutes 2-3 times more accurately than the current state-of-the-art model and we demonstrate that they are approaching the aleatoric limit (0.5-1 logS), suggesting that further improvements in prediction accuracy require more accurate datasets. These models, collectively referred to as fastsolv, are open source, freely accessible via a Python package and web interface, highly reproducible, and up to 50 times faster than the next best alternative. | Lucas Attia; Jackson W. Burns; Patrick S. Doyle; William H. Green | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672ce7dff9980725cf764d24/original/organic-solubility-prediction-at-the-limit-of-aleatoric-uncertainty.pdf |
664da3ef418a5379b0f08ef0 | 10.26434/chemrxiv-2023-z668v-v2 | Expedient and Stereoselective Access to Diverse Alkaloid-like Scaffolds via an Oxidation/Double-Mannich Reaction Sequence | Sequential oxidative cleavage and double-Mannich reactions enable the stereoselective conversion of simple norbornenes into complex alkaloid-like structures. The products undergo a wide range of derivatization reactions, including a regioselec-tive enol triflate formation/cross-coupling sequences and highly efficient conversion to an unusual tricyclic-8,5,5 fused lac-tam. Overall, the process represents a formal 1-atom aza-ring expansion with concomitant bridging annulation, making it of interest for the broader derivatization of alkene feedstocks. | Charles Mikan; Joseph Watson; Ryan Walton; Paul Waddell; Jonathan Knowles | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry | CC BY 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664da3ef418a5379b0f08ef0/original/expedient-and-stereoselective-access-to-diverse-alkaloid-like-scaffolds-via-an-oxidation-double-mannich-reaction-sequence.pdf |
65248ca245aaa5fdbba1cc26 | 10.26434/chemrxiv-2023-70tx9 | Chemical bond overlap descriptors from multiconfiguration wavefunctions | Chemical bonds are fundamental in chemistry, serving as the foundation for understanding molecular properties. Over time, various theories and descriptors have evolved to characterize these bonds since the inception of quantum mechanics. This report focuses on extending overlap density and its topological descriptors (OP/TOP) using Multiconfigurational Self-Consistent Field (MCSCF) wavefunctions, highlighting their importance. We present a comparative analysis of OP/TOP descriptors using CASSCF and DCD-CAS(2) wavefunctions for a diverse range of molecular systems, including X$-$O bonds in X$-$OH (where X = H, Li, Na, H$_2$B, H$_3$C, H$_2$N, HO, F) and Li$-$X' (where X' = F, Cl, and Br) molecular test systems. CAS(10,16) and CAS(6,20) calculations challenge the MCSCF-based OP/TOP bond descriptors, with comparisons to QTAIM and LVM descriptors. Additionally, we examine the Li--F dissociation profile using OP/TOP descriptors. Our study reveals that chemical bonds formed between atoms with varying electronegativities exhibit overlap density shifted towards the more electronegative atom, as predicted by the OP/TOP descriptors. Quantitative assessments using critical point overlap density and its Laplacian descriptors show reduced spreading in bonds with increasing electronegativity differences. The sensitivity of OP/TOP descriptors to ionic/neutral inversion during Li--F dissociation showcased their potential in elucidating intricate bond phenomena. These insights into multiconfigurational wavefunctions, facilitated by OP/TOP descriptors, open new avenues for understanding chemical bond dynamics across multiconfigurational and multireference wavefunction classes, offering novel applications in the field of chemistry. | Carlos Santos-Jr; Renaldo Moura Jr. | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65248ca245aaa5fdbba1cc26/original/chemical-bond-overlap-descriptors-from-multiconfiguration-wavefunctions.pdf |
6310b901faf4a42b51031654 | 10.26434/chemrxiv-2022-2vz00-v2 | Direct photolysis of 4-tert-alkyl-1,4-dihydropyridines under blue-light irradiation for the generation of tertiary alkyl radicals | Herein, we disclose a direct photolysis approach for the generation of tertiary alkyl radicals from 4-tert-alkyl-1,4-dihydropyridines (DHPs) under blue LED irradiation, as exemplified in a photochemical Giese reaction. Radical generation occurs under mild conditions, does not require the use of exogenous photocatalysts or oxidants, and the Giese reaction is compatible with a range of 4-tert-alkyl-DHPs and Michael acceptors (23 examples, up to 86% yield). Mechanistic investigations reveal that the presence of base is crucial for radical generation. | Prasadi Gallage; Spencer Pitre | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6310b901faf4a42b51031654/original/direct-photolysis-of-4-tert-alkyl-1-4-dihydropyridines-under-blue-light-irradiation-for-the-generation-of-tertiary-alkyl-radicals.pdf |
66bc0a75f3f4b05290cbabd1 | 10.26434/chemrxiv-2024-hvfgp | Functionalization of Pt(IV)–Ammines Enables Site-Directed Covalent Modification of mRNA | Developing chemical toolkits for mRNA modification has remained an immense challenge driven by inherent difficulties in targeting mRNA molecules. Antisense oligonucleotides (ASOs) offer a promising framework for targeting specific mRNA sequences, yet they do not possess the capacity to alter the covalent structure of mRNA except through enzyme-mediated hydrolysis. The requirement of relying on an enzyme for modifying mRNA incurs several limitations on the application, design, and delivery of ASOs. To address these limitations, we developed a Pt(IV)-ASO strategy that combines the reactivity of platinum with the sequence specificity of ASOs to covalently modify nucleic acids, including short RNA and mRNA, in a selective, enzyme-free manner. Access to Pt(IV)-ASO constructs was made possible by an innovative equatorial Pt(IV) ammine functionalization strategy, allowing for conjugation of carboxylic acids directly to the Pt core. Reactivity with 21-mer RNA and full-length mRNA by Pt-ASO con-structs was demonstrated, and the covalently modified products were characterized using a suite of orthogonal techniques, such as electrophoretic mobility shift assay, MALDI-TOF MS, temperature-dependent dissociation assay, and RT-qPCR. Constructs were optimized for their reactivity and selectivity, allowing for Pt(IV)-PMO constructs with sub-nanomolar IC50 values in an RNA competition assay. This Pt(IV)-ASO plat-form facilitates new avenues for RNA modification by providing a strategy for covalent modification of nucleic acids with potential applications for molecular biology research. | Edward Miller; Charlotte E. Farquhar; Jacob Rodriguez; Andrei Loas; Bradley L. Pentelute | Biological and Medicinal Chemistry; Organic Chemistry; Organometallic Chemistry; Bioengineering and Biotechnology; Coordination Chemistry (Organomet.); Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bc0a75f3f4b05290cbabd1/original/functionalization-of-pt-iv-ammines-enables-site-directed-covalent-modification-of-m-rna.pdf |
60c75320337d6c7424e28806 | 10.26434/chemrxiv.13388753.v1 | Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome | The 20S Proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells as well as in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome, an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy and boronic acid containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics and Bayesian optimization of non-bonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach to the reevaluation of non-bonded potentials making use of QM/MM dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the inhibitor. | Jon Uranga; Lukas Hasecke; Jonny Proppe; Jan Fingerhut; Ricardo A. Mata | Biochemistry; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75320337d6c7424e28806/original/theoretical-studies-of-the-acid-base-equilibria-in-a-model-active-site-of-the-human-20s-proteasome.pdf |
60c749f09abda21c3ff8cd28 | 10.26434/chemrxiv.12129975.v1 | Interaction of Hydroxychloroquine with SARS-CoV2 Functional Proteins Using All-atoms Non-equilibrium Alchemical Simulations | <div>The paper presents an accurate in silico measurement of the dissociation constant of HCQ on three important SARS-Cov2 protein targets, namely the main protease (3CLpro) and the Papain-like protease (PLpro) and the RNA dependent RNA polimerase (RdRp), using the recently the released PDB stuructures of these protein. Calculations are done using state-of-the art force fields and advanced simulation methodologies combining enhanced sampling and nonequilibrium techniques amenable to massive parallelization on a dedicated HPC cluster.<br /></div><div><div><br /></div><div>We have shown that HCQ may act as a mild inhibitor for all the three viral proteins, with potency increasing in the series PLpro, 3CLpro, RdRp. By analyzing the bound state configurations, we were able to improve the potency for the 3CLpro target, designing a novel HCQ-inspired compound, named PMP329, with predicted nanomolar activity. If confirmed in vitro, our results provide a convincing molecular rationale for the use of HCQ or of strictly related derivatives in the treatment of Covid-19.</div></div><div><br /><br /></div> | Piero Procacci; Marina Macchiagodena; Marco Pagliai; Guido Guarnieri; Francesco Iannone | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749f09abda21c3ff8cd28/original/interaction-of-hydroxychloroquine-with-sars-co-v2-functional-proteins-using-all-atoms-non-equilibrium-alchemical-simulations.pdf |
655d692f6e0ec7777f70329e | 10.26434/chemrxiv-2023-wssrh-v2 | Pore Structure Compartmentalization for Advanced
Characterization of Metal-Organic Framework Materials | Metal-Organic Frameworks (MOFs) are nanoporous crystals which are widely used as selective adsorbents, separation membranes, catalysts, gas and energy storage media, and drug delivery vehicles. The unique adsorption and transport properties of MOFs are determined by their complex three-dimensional (3D) networks of pores, cages, and channels, that differ in size, shape, and chemical composition. While the morphological structure of MOF crystals is known, practical MOF materials are rarely ideal crystals. They contain secondary phases, binders, residual chemicals, and various types of defects. It is of paramount importance to evaluate the degree of crystallinity and accessibility of different pore compartments to adsorbing guest molecules. To this end, we recently suggested the method of fingerprint isotherms based on the comparison of the experimentally measured adsorption isotherms and theoretical isotherms on ideal MOF crystals produced by Monte Carlo (MC) simulations and decomposed with respect to different pore compartments. In this work, we develop an automated algorithm of pore network compartmentalization that is a prerequisite for calculations of the fingerprint isotherms. The proposed algorithm partitions the unit cell into realistically shaped compartments based on the geometric pore size distribution. The proposed method is demonstrated on several characteristic systems, including Cu-BTC, IRMOF-1, UiO-66, PCN-224, and ZIF-412 and 56 structures from the CoRE MOF database. | Shivam Parashar; Alexander V. Neimark | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655d692f6e0ec7777f70329e/original/pore-structure-compartmentalization-for-advanced-characterization-of-metal-organic-framework-materials.pdf |
62a732fdbb751998ce4ca45b | 10.26434/chemrxiv-2022-3lsjg-v2 | Efficient photoredox cycles to control perylenediimide self-assembly | Photoreduction of perylenediimide (PDI) derivatives has been widely studied for use in photocatalysis, hydrogen evolution, photo-responsive gels, and organic semiconductors. Upon light irradiation, the radical anion (PDI•–) can readily be obtained, whereas further reduction to the dianion (PDI2–) is rare. Here we show that full 2-electron photoreduction can be achieved using UVC light: 1) in anaerobic conditions by ‘direct photoreduction’ of PDI aggregates, or 2) by ‘indirect photoreduction’ in aerobic conditions due to acetone ketyl radicals. The latter strategy is also efficient for other dyes, such as naphthalenediimide (NDI) and methylviologen (MV2+). Efficient photoreduction on the minute time-scale using simple LED light in aerobic conditions is attractive for use in dissipative light-driven systems and materials. | Chunfeng Chen; Jorge Valera; Takuji Adachi; Thomas Hermans | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a732fdbb751998ce4ca45b/original/efficient-photoredox-cycles-to-control-perylenediimide-self-assembly.pdf |
646e20d04f8b1884b735b999 | 10.26434/chemrxiv-2023-2tq29 | Phototrophic microbial fuel cells for sustainable power generation and wastewater treatment | Microbial fuel cells (MFCs) rely on the capacity of electrode-adhered electroactive bacteria to oxidize organic matter and generate electrons. Typical MFCs are highly engineered systems that can be applied as green tools to alleviate the burden of waste streams. Phototrophic MFCs (PhMFCs) are a promising variant that can be implemented indoors or outdoors and use the power of the sun to boost efforts in on-site environmental remediation, biomass generation, and power generation. PhMFC variations include plant-based and algal-based MFCs. Algal-based MFCs can incorporate special photosynthetic action at either the anode or cathode, enhancing or replacing the role of other bacteria in regular bacterial MFCs. Plant-based MFCs can be more complex due to the role of the root system near an electrode and its interaction with electrode-adhered bacteria, and they are nearly universally operated outdoors in either natural or engineered conditions. This review considers PhMFCs such as algal-based MFCs, algal carbon capture cells (ACCCs) and anode algal microbial fuel cells (AAMFCs), and also plant-based MFCs which include natural plant MFCs (NPMFCs), constructed wetland MFCs (CWMFCs), and marine-rooted plant MFCs (MPMFCs). After summaries of the fabrication and function of different PhMFCs, we elaborate with a literature review and discussion on each variant, followed by suggestions for future directions that will enhance the impact and accelerate the uptake of these promising multi-functional biosystems. | Jayesh Sonawane; Ankisha Vijay; Tianyang Deng; Prakash C. Ghosh; Jesse Greener | Energy; Agriculture and Food Chemistry; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e20d04f8b1884b735b999/original/phototrophic-microbial-fuel-cells-for-sustainable-power-generation-and-wastewater-treatment.pdf |
60c74967f96a003ea9287237 | 10.26434/chemrxiv.12058437.v1 | Nanocrystals of Lead Chalcohalides: A Series of Kinetically Trapped Metastable Nanostructures | We report
the colloidal synthesis of a series of surfactant-stabilized lead chalcohalide
nanocrystals. Our work is mainly focused on Pb<sub>4</sub>S<sub>3</sub>Br<sub>2</sub>,
a chalco-halide phase unknown to date that does not belong to the ambient-pressure
PbS – PbBr<sub>2</sub> phase diagram. The Pb<sub>4</sub>S<sub>3</sub>Br<sub>2</sub>
nanocrystals herein feature a remarkably narrow size distribution (with a size
dispersion as low as 5%) a good size tunability (from 7 to ∼30 nm), an indirect bandgap, photoconductivity (responsivity
= 4 ± 1
mA/W) and stability for months
under air. A crystal structure is proposed for this new material by combining the
information from 3D electron diffraction and electron tomography of a single
nanocrystal, X-Ray powder diffraction and density functional theory
calculations. Such a structure is closely related to that of the recently
discovered high-pressure chalcohalide Pb<sub>4</sub>S<sub>3</sub>I<sub>2</sub>
phase, and indeed we were able to extend our synthesis scheme to Pb<sub>4</sub>S<sub>3</sub>I<sub>2</sub>
colloidal nanocrystals, whose structure matches the one that has been published
for the bulk. Finally, we could also prepare nanocrystals of Pb<sub>3</sub>S<sub>2</sub>Cl<sub>2</sub>,
which proved to be a structural analogue of the recently reported bulk Pb<sub>3</sub>Se<sub>2</sub>Br<sub>2</sub>
phase. It is remarkable that one high-pressure structure (for Pb<sub>4</sub>S<sub>3</sub>I<sub>2</sub>)
and two metastable structures that had not yet been reported (for Pb<sub>4</sub>S<sub>3</sub>Br<sub>2</sub>
and Pb<sub>3</sub>S<sub>2</sub>Cl<sub>2</sub>) can be prepared on the nanoscale
by wet-chemical approaches. This highlights the important role of colloidal
chemistry in the discovery of new materials and motivates further exploration into
metal chalcohalides nanocrystals. | Stefano Toso; Quinten A. Akkerman; Beatriz Martín-García; Mirko Prato; Juliette Zito; Ivan Infante; Zhiya Dang; Anna Moliterni; Cinzia Giannini; Eva Bladt; Ivan Lobato; Julien Ramade; Joka Buha; Sara Baals; Davide Spirito; Enrico Mugnaioli; mauro gemmi; Liberato Manna | Nanostructured Materials - Materials; Optical Materials; Crystallography; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74967f96a003ea9287237/original/nanocrystals-of-lead-chalcohalides-a-series-of-kinetically-trapped-metastable-nanostructures.pdf |
67924b156dde43c908ff22f5 | 10.26434/chemrxiv-2025-79ts7 | Boosting Ru Atomic Efficiency of LaFe0.97Ru0.03O3 via Knowledge-Driven Synthesis Design | We use the process of exsolution of ruthenium from a 3 at% ruthenium substituted LaFeO3 (LFR3) perovskite oxide to produce a high performing ruthenium supported catalyst. To increase the atomic efficiency of the catalyst, the exsolution process is designed to produce a high density of small Ru particles and thus a high atomic efficiency of ruthenium. A high-temperature redox pretreatment at 800 °C enriches the Ru concentration in the near-surface region of LFR3, while a subsequent mild reduction step with H2 at 500 °C leads to the Ru exsolution from the Ru-enriched near-surface region (LFR3_Redox_500R), resulting in a high density of small particles that are not passivated by LaOx. This catalyst is tested on two prototypical catalytic reactions, namely the oxidation in propane combustion and the reduction in CO2 hydrogenation. For both reactions, the activity of the redox-pretreated sample LFR3_Redox_500R is significantly higher than that of the untreated sample (LFR3_500R). For the catalytic hydrogenation of CO2, the high selectivity is switched from methane for LFR3_Redox_500R to CO for LFR3_500R. | Herbert Over; Yu Wang; Paul Paciok; Lukas Pielsticker; Alexander Spriewald-Luciano; Lorena Glatthaar; Aijie Xu; Zimo He; Min Ding; Walid Hetaba; Jaime Gallego; Yanglong Guo; Bernd Smarsly | Catalysis; Electrocatalysis; Heterogeneous Catalysis; Redox Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67924b156dde43c908ff22f5/original/boosting-ru-atomic-efficiency-of-la-fe0-97ru0-03o3-via-knowledge-driven-synthesis-design.pdf |
60c742af469df4034ff4302b | 10.26434/chemrxiv.8428217.v1 | Coverage and Stability of NHx Terminated Cobalt and Ruthenium Surfaces: a First Principles Investigation | <div>In the atomic layer deposition (ALD) of Cobalt (Co) and Ruthenium (Ru) metal using nitrogen plasma, the structure and composition of the post N-plasma NHx terminated (x = 1 or 2) metal surfaces are not well known but are important in the subsequent metal containing pulse. In this paper, we use the low-index (001) and (100) surfaces of Co and Ru as models of the metal polycrystalline thin films. The (001) surface with a hexagonal surface structure is the most stable surface and the (100) surface with a zigzag structure is the least stable surface but has high reactivity. We investigate the stability of NH and NH2 terminations on these surfaces to determine the saturation coverage of NHx on Co and Ru. NH is most stable in the hollow hcp site on (001) surface and the bridge site on the (100) surface, while NH2 prefers the bridge site on both (001) and (100) surfaces. The differential energy is calculated to find the saturation coverage of NH and NH2. We also present results on mixed NH/NH2-terminations. The results are analyzed by thermodynamics using Gibbs free energies (ΔG) to reveal temperature effects on the stability of NH and NH2 terminations. Ultra-high vacuum (UHV) and standard ALD</div><div>operating conditions are considered. Under typical ALD operating conditions we find that the most stable NHx terminated metal surfaces are 1 ML NH on Ru (001) surface (350K-550K), 5/9 ML NH on Co (001) surface (400K-650K) and a mixture of NH and NH2 on both Ru (100) and Co (100) surfaces.</div> | Ji Liu; Michael Nolan | Materials Processing; Thin Films; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742af469df4034ff4302b/original/coverage-and-stability-of-n-hx-terminated-cobalt-and-ruthenium-surfaces-a-first-principles-investigation.pdf |
63c51584d19cc569bb078f61 | 10.26434/chemrxiv-2023-5pvl2 | Absolute value of bond dissociation energy as a reaction direction marker. | The calculation problem of bond-dissociation energy D0(M+-S) for M = Sc, Ti, V, Y, Zr, Nb was solved using the fundamental law of nature determining the dependence of chemical bond dissociation energy on its length. The recommended experimental values from literature are as follows D0(Sc+-S)=4.97±0.05 eV, D0(Ti+-S)=4.74±0.07 eV, D0(V+-S)=3.78±0.10 eV, D0(Y+-S)=5.49±0.18 eV, D0(Zr+-S)=5.69±0.10 eV, D0(Nb+-S)=5.20±0.21 eV. The theoretical data calculated in this article are 4.967 eV, 4.72 eV, 3.772 eV, 5.505 eV, 5.694 eV, 5.209 eV correspondingly which is in good agreement with the literature. Besides the recommended D0(M+-S) values, there are more data referring to D0(M+-S) in reactions of transition metal sulfides (M = Sc, Ti, V, Y, Zr, Nb) with oxygen-bearing substrates such as COS, CO, and CO2. It should be noted that different directions of the reaction corresponded to different observed values of bond dissociation energies (M+-S). The experimental D0 values for metal sulfide species from literature were calculated with high accuracy. In our calculations, we used the bond lengths from the literature calculated for various electronic configurations. Therefore, we assume that the previously obtained data allow us to define correlation between reagent electronic state and corresponding reaction direction.
| Adel iakubov | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Computing; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c51584d19cc569bb078f61/original/absolute-value-of-bond-dissociation-energy-as-a-reaction-direction-marker.pdf |
60c7473a0f50db6ca3396572 | 10.26434/chemrxiv.11559693.v1 | Expressed Protein Ligation Without Intein | Proteins with a
functionalized <i>C</i>-terminus such as a <i>C</i>-terminal thioester are key to the
synthesis of larger proteins via expressed protein ligation. They are usually
made by recombinant fusion to intein. Although powerful, the intein fusion
approach suffers from premature hydrolysis and low compatibility with denatured
conditions. To totally bypass the involvement of an enzyme for expressed
protein ligation, here we showed that a cysteine in a recombinant protein was
chemically activated by a small molecule cyanylating reagent at its <i>N</i>-side amide for undergoing nucleophilic
acyl substitution with amines including a number of L- and D-amino acids and
hydrazine. The afforded protein hydrazides could be used further for expressed
protein ligation. We demonstrated the versatility of this approach with the
successful synthesis of ubiquitin conjugates, ubiquitin-like protein
conjugates, histone H2A with a posttranslational modification, RNAse H that
actively hydrolyzed RNA, and exenatide that is a commercial therapeutic
peptide. The technique, which is exceedingly simple but highly useful, expands
to a great extent the synthetic capacity of protein chemistry and will
therefore make a large avenue of new research possible. | Yuchen Qiao; Ge Yu; Xiaoyan Wang; Kaci C. Kratch; Wesley
Wei Wang; Jared S. Morse; Sunshine Z. Leeuwon; Wenshe Liu | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7473a0f50db6ca3396572/original/expressed-protein-ligation-without-intein.pdf |
60c748cdbb8c1a5a2b3dad35 | 10.26434/chemrxiv.11977839.v1 | Quantum Accurate Prediction of Plutonium–Plutonium Dihydride Phase Equilibrium Using a Spin-Lattice Model | <div>
<div>
<div>
<p>Plutonium-based materials are vital for use as nuclear fuels and as portable power
sources for space vehicles. However, elucidating their sensitivity to hydriding corrosion
represents an extreme challenge due to the toxicity of Pu as well as its anomalous magnetic properties. In this work, we develop a spin-lattice model of plutonium–plutonium
dihydride (Pu–PuH2) phase equilibrium that retains the accuracy of density functional
theory (DFT) while yielding many orders of magnitude improvement in computational
efficiency. Using Monte Carlo and free energy sampling algorithms, we compute a
number of Pu–PuH2 equilibrium properties that are difficult to probe experimentally,
including equilibrium pressures and phase compositions at room temperature and the
PuH2 heat of formation. Our method will have particular impact on these types of
materials studies, where there is a strong need for computationally efficient approaches
to bridge time and length scale gaps between quantum calculations and experiments.
</p>
</div>
</div>
</div> | Ryan Gotchy Mullen; Nir Goldman | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748cdbb8c1a5a2b3dad35/original/quantum-accurate-prediction-of-plutonium-plutonium-dihydride-phase-equilibrium-using-a-spin-lattice-model.pdf |
60c75229bb8c1aea6c3dbe27 | 10.26434/chemrxiv.13135136.v3 | Sol–Gel Processing of Water-Soluble Carbon Nitride Enables High-Performance Photoanodes | In
spite of the enormous promise that polymeric carbon nitride (PCN) materials
hold for various applications, the fabrication of high-quality, binder-free PCN
films and electrodes has been a largely elusive goal to date. Here we tackle
this challenge by devising, for the first time, a sol–gel approach that enables
facile preparation of thin films based on poly(heptazine imide) (PHI), a
polymer belonging to the PCN family. The sol–gel process capitalizes on the use
of a water-soluble PHI precursor that allows formation of a non-covalent
hydrogel. The hydrogel can be deposited on conductive substrates resulting in
formation of mechanically stable polymeric thin layers. The resulting
photoanodes exhibit unprecedented PEC performance in alcohol reforming and
selective (~100%)
conversions with very high photocurrents down to ~0 V vs. RHE, which enables
even effective operation under bias-free conditions. The robust binder-free
films derived from sol–gel processing of water-soluble PCN thus represent a new
paradigm for high-performance ‘soft-matter’ photoelectrocatalytic systems, and
pave the way for further applications in which high-quality PCN films are
required. | Christiane Adler; Igor Krivtsov; Dariusz Mitoraj; Lucía dos Santos-Gómez; Santiago García-Granda; Christof Neumann; Julian Kund; Christine Kranz; Boris Mizaikoff; Andrey Turchanin; Radim Beranek | Thin Films; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75229bb8c1aea6c3dbe27/original/sol-gel-processing-of-water-soluble-carbon-nitride-enables-high-performance-photoanodes.pdf |
6288c03e87d01f75acece6d0 | 10.26434/chemrxiv-2022-z22q6 | CO2 Conversion at High Current Densities: Stabilization of Bi(III) Containing Electrocatalysts under CO2 Gas Flow Conditions | Herein, we demonstrate the superior performance of novel bismuth subcarbonate ((BiO)2CO3) film catalysts for formate production using a fluidic CO2-fed electrolyzer device. The subcarbonate catalyst readily forms in situ from a CO2-absorbing Bi2O3 precursor material during the CO2 reduction reaction (CO2RR). In 1 mol dm–3 KOH electrolyte solution, a maximum Faradaic efficiency of FEformate = 97.4% (corresponding partial current density of formate formation: PCDformate = –111.6 mA cm–2) was achieved at a comparably low applied electrolysis potential of –0.8 V versus the reversible hydrogen electrode (RHE). Even higher values of PCDformate = –441.2 mA cm–2 (FEformate = 62%) were observed at more cathodic potential, –2.5 V vs. RHE. As the alkalinity of the liquid electrolyte is further increased (e.g., by using 5 mol dm–3 KOH solution), the performance of formate production is boosted beyond PCDformate values of –1 A cm–2. Combined X-ray diffraction and Raman spectroscopic investigations demonstrate an extraordinarily high stability of Bi(III) cations in the catalytically active subcarbonate catalyst phase down to cathode potentials of –1.5 V vs. RHE. This stabilization effect can clearly be attributed to the high abundance of gaseous CO2 under the operating conditions of the gas-fed electrolyzer. In the absence of any CO2 supply, however, the reductive Bi(III)-to-Bi(0) transition already occurs at much milder conditions of –0.3 V vs. RHE, as evidenced by in situ Raman spectroscopy in CO2-free 1 mol dm–3 KOH electrolyte solution. Advanced X-ray diffraction computed tomography (XRD-CT) technique was applied to gain deeper insights into the spatial distribution of the metallic and subcarbonate phases comprising the active composite catalyst layer (CL) during the CO2RR. | Iván Zelocualtecatl Montiel; Abhijit Dutta; Kiran Kiran; Alain Rieder; Anna Iarchuk; Soma Vesztergom; Marta Mirolo; Isaac Martens; Jakub Drnec; Peter Broekmann | Catalysis; Energy; Electrocatalysis; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6288c03e87d01f75acece6d0/original/co2-conversion-at-high-current-densities-stabilization-of-bi-iii-containing-electrocatalysts-under-co2-gas-flow-conditions.pdf |
63f054d59da0bc6b331df5fd | 10.26434/chemrxiv-2023-mjzdv | Second-order moment of kinetic theory of granular flow for multi-type particles | In this study, a numerical method, second-order moment of kinetic theory of granular flow for multitype particles (SOM-KTGF-MP) is proposed. The SOM-KTGF is used for particle flow with higher concentration and high inertia where inter-particle collisions exist; however, the particle fluctuation is far from equilibrium to satisfy the Boussinesq approximation. The model, SOM-KTGF-MP, is derived here as an extension of SOM-KTGF for mono-sized particles to be applied to multi-type particles with different sizes,
densities, and other properties. In SOM-KTGF-MP, the conservation equations of the volume fraction, velocity,
and second-order moment of the fluctuating velocity of particles are solved for each particle species in the multitype mixture. A binary mixture of particles in a simple shear flow was predicted using the SOM-KTGF-MT
method. This result is in good agreement with the discrete molecular dynamics method. The SOM-KTGF-MT
method increased the fidelity of the prediction of the binary mixture flow of particles based on the kinetic theory. | Dan Sun | Chemical Engineering and Industrial Chemistry; Fluid Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f054d59da0bc6b331df5fd/original/second-order-moment-of-kinetic-theory-of-granular-flow-for-multi-type-particles.pdf |
60c746e3f96a002be5286e20 | 10.26434/chemrxiv.11424000.v1 | Nanoengineered Light-Harvested Proteins for Optogenetics and Photopharmacology | <p>Chemical modification with nanometer
precision can be used to probe and to improve the function of complex molecular
entities, from organic materials to proteins and their assemblies. Using the
pigment arrangement in photosynthetic light-harvesting as inspiration, we show
that molecular photosensitizers can be located at well-defined distances from
photoisomerizable units in proteins in order to enhance and spectrally shift their
photoresponses. The approach is demonstrated in Channelrhodopsin-2 (ChR2) and
in the light-gated ionotropic glutamate receptor (LiGluR), two archetypical
actuators in optogenetics and photopharmacology that have been used both for
fundamental and therapeutic purposes. These proof-of-concept experiments together
with theoretical simulations predict that the photosensitivity can be increased
several orders of magnitude using these means, thus providing a unique
methodology to boost the performance of current optogenetic and
photopharmacological toolboxes.</p> | Aida Garrido-Charles; Gisela Cabré; Marta Gascón-Moya; Félix Busqué; Ramon Alibés; Jordi Hernando; Pau Gorostiza | Nanodevices; Nanostructured Materials - Nanoscience; Biochemistry; Bioengineering and Biotechnology; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746e3f96a002be5286e20/original/nanoengineered-light-harvested-proteins-for-optogenetics-and-photopharmacology.pdf |
60c74414ee301ccbdec790ed | 10.26434/chemrxiv.9741335.v1 | Elucidating the Impact of Charge Selective Contact in Halide Perovskite Through Impedance Spectroscopy | <p>The electron and hole selective contact (SC) play a pivotal role in
the performance of perovskite solar cells. In order to separate the interfacial
phenomenon from bulk, the influence of charge SC was elucidated, by means of impedance
spectroscopy. The specific role played by TiO<sub>2</sub> and <i>Spiro-OMeTAD</i>
as electron and hole SC in perovskite solar cells was investigated at short circuit condition at
different temperatures. We have probed MAPbI<sub>3</sub> and (FAPbI<sub>3</sub>)<sub>0.85</sub>(MAPbBr<sub>3</sub>)<sub>0.15
</sub>and elucidated parameters such as charge carrier mobility, recombination
resistance, time constant and charge carrier kinetics in perovskite layer and
at the interface of perovskite/SC. Charge carrier mobility in mixed perovskite
was found to be nearly two order of magnitude higher as compared to MAPbI<sub>3</sub>.
Moreover, the carrier mobility in devices with only electron SC was found to be
higher as compared only hole SC. The charge accumulation at TiO<sub>2</sub>/perovskite/<i>Spiro</i>-OMeTAD
interfaces were studied via frequency dependent capacitance, revealing higher
charge accumulation at perovskite/S<i>piro</i>-OMeTAD than at TiO<sub>2</sub>/perovskite
interface. By performing varying temperature frequency dependent capacitance measurements
the distribution of density of state within the bandgap of the perovskites, the
emission rate of electrons from the trap states and traps activation energy was
determined. </p> | Mohd Taukeer Khan; Manuel Salado; Abdullah R. D. Almohammedi; Samrana Kazim; Shahzada Ahmad | Hybrid Organic-Inorganic Materials; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74414ee301ccbdec790ed/original/elucidating-the-impact-of-charge-selective-contact-in-halide-perovskite-through-impedance-spectroscopy.pdf |
60c74087702a9be34418a0d8 | 10.26434/chemrxiv.7757210.v1 | Self-Assembled Nanostructure Library from Monodisperse Sequence-Defined Oligo(phosphodiester)s | <p><a>Natural biopolymers achieve information
storage, molecular recognition and catalysis efficiently through
sequence-control. To be able to mimic such properties, self-assembly studies of
artificial sequence-defined oligomers is of great interest. In this paper, we show
the use of hydrophilic, lipophilic, aromatic and fluorophilic monomers to
synthesize a large library of truly monodisperse sequence-defined block co-oligo(phosphodiester)s.
Automated and accurate control over the sequence allowed to rationally study the
degree of polymerisation, blocks ratio, chemical composition and orthogonal
supramolecular interactions influence on self-assembly. Interestingly, our
studies revealed remarkable morphological changes (spheres to nanosheets) caused
by very small differences between polymers, e.g., polymers differing by a
single monomer unit. Inverting block sequence in multi-block copolymers also caused
a dramatic increase in micelle size. Conventional polymerization does not allow
the exploration of these subtle variations in polymer sequence or composition. Therefore,
fast synthesis and purification of a variety of oligomers with slightly
different sequences allows studying the supramolecular chemistry of precision
oligomers in a systematic way. It paves the way to the rational design of
functional sequence-defined polymers.</a></p> | Donatien de Rochambeau; Maciej Barlog; Hassan S. Bazzi; Hanadi Sleiman | Biopolymers; Polymer morphology; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74087702a9be34418a0d8/original/self-assembled-nanostructure-library-from-monodisperse-sequence-defined-oligo-phosphodiester-s.pdf |
61df409df51b22070013e56d | 10.26434/chemrxiv-2022-2dr03 | Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances | The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states that make several super-resolved single-molecule localization microscopy (SMLM) methods possible. However, studies quantifying the timescales and nature of dark state behavior for commonly used FPs under conditions typical of widefield and total internal reflection fluorescence (TIRF) microscopy remain scarce and pre-date many new SMLM techniques. FusionRed is a relatively bright red FP exhibiting fluorescence intermittency and has thus been identified as a potential candidate for SMLM. We herein characterize the rates for dark-state conversion and the subsequent ground-state recovery of FusionRed and its 2.5-fold brighter descendent FusionRed L175M M42Q (FusionRed-MQ) at low irradiances (1-10 W/cm2), which were previously unexplored experimental conditions. We characterized the kinetics of dark state transitions in these two FPs by using single molecule blinking and ensemble photobleaching experiments bridged with a dark state kinetic model. We find that at low irradiances, the recovery process to the ground state is minimally light-driven and FusionRed-MQ has a 1.3-fold higher ground state recovery time indicating a conformationally restricted dark-state chromophore in comparison to FusionRed. Our studies indicate that the brighter FusionRed-MQ exhibits higher tendency in dark state conversion, thus it is potentially a better candidate for SMLM applications than its progenitor FusionRed. | Srijit Mukherjee; Connor Thomas; Ryan Wilson; Emma Simmerman; ShengTing Hung; Ralph Jimenez | Physical Chemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61df409df51b22070013e56d/original/characterizing-dark-state-kinetics-and-single-molecule-fluorescence-of-fusion-red-and-fusion-red-mq-at-low-irradiances.pdf |
60c7569af96a00bede288b06 | 10.26434/chemrxiv.13500960.v2 | Origins of Clustering of Metalate-Extractant Complexes in Liquid-Liquid Extraction | Effective and energy efficient separation of precious and rare metals is very important for a variety of advanced technologies. Liquid-liquid extraction (LLE) is a relatively less energy intensive separation technique, widely used in separation of lanthanides, actinides, and platinum group metals (PGMs). In LLE, the distribution of an ion between an aqueous phase and an organic phase is determined by enthalpic (coordination interactions) and entropic (fluid reorganization) contributions. The molecular scale details of these contributions are not well understood. Preferential extraction of an ion from the aqueous phase is usually correlated with the resulting fluid organization in the organic phase, as the longer-range organization increases with metal loading. However, it is difficult to determine the extent to which organic phase fluid organization causes, or is caused by, metal loading. In this study, we demonstrate that two systems with the same metal loading may impart very different organic phase organization; and investigate the underlying molecular scale mechanism. Small angle X-ray scattering shows that the structure of a quaternary ammonium extractant solution in toluene is affected differently by the extraction of two metalates (octahedral PtCl<sub>6</sub><sup>2-</sup> and square-planar PdCl<sub>4</sub><sup>2-</sup>), although both are completely transferred into the organic phase. The aggregates formed by the metalate-extractant complexes (approximated as reverse micelles) exhibit more long-range order (clustering) with PtCl<sub>6</sub><sup>2-</sup> compared to that with PdCl<sub>4</sub><sup>2-</sup>. Vibrational sum frequency generation spectroscopy, and complimentary atomistic molecular dynamics simulations on model Langmuir monolayers, indicate that the two metalates affect the interfacial hydration structures differently. Further,
the interfacial hydration is correlated with water extraction into the organic
phase. These results support a strong relationship between the organic phase organizational structure and different local hydration present within the aggregates of metalate-extractant complexes, which is independent of metalate concentration. | Srikanth Nayak; Raju R. Kumal; Zhu Liu; Baofu Qiao; Aurora Clark; Ahmet Uysal | Aggregates and Assemblies; Surfactants; Nanostructured Materials - Nanoscience; Interfaces; Self-Assembly; Surface; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7569af96a00bede288b06/original/origins-of-clustering-of-metalate-extractant-complexes-in-liquid-liquid-extraction.pdf |
669a212c01103d79c5830c0a | 10.26434/chemrxiv-2024-mcjpn | An Evolved Artificial Radical Cyclase Enables the Construction of Bicyclic Terpenoid Scaffolds via an H-Atom Transfer Pathway | While natural terpenoid cyclases generate complex terpenoid structures via cationic mechanisms, alternative radical cyclization pathways are underexplored. The metal-catalyzed hydrogen-atom-transfer (M-HAT) reaction offers an attractive means for hydrofunctionalizing olefins, providing access to terpenoid-like structures. Artificial metalloenzymes offer a promising strategy for introducing M-HAT reactivity into a protein scaffold. Herein, we report our efforts towards engineering an artificial radical cyclase (ARCase), resulting from anchoring a biotinylated [Co(Schiff-base)] cofactor within an engineered chimeric streptavidin. After two rounds of directed evolution, a double mutant catalyzed a radical cyclization to afford bicyclic products with a cis-5-6-fused ring structure and up to 97% enantiomeric excess. The involvement of a histidine ligation to the Co-cofactor was confirmed by crystallography. A time-course experiment revealed a cascade reaction catalyzed by the ARCase, combining a radical cyclization with a conjugate reduction. The ARCase exhibited tolerance towards variations in the dienone substrate, highlighting its potential to access terpenoid scaffolds. | Dongping Chen; Xiang zhang; Anastassia Vorobieva; Ryo Tachibana; Alina Stein; Roman Jakob; Zhi Zou; Damian Graf; Ang Li; Timm Maier; Bruno Correia; Thomas Ward | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a212c01103d79c5830c0a/original/an-evolved-artificial-radical-cyclase-enables-the-construction-of-bicyclic-terpenoid-scaffolds-via-an-h-atom-transfer-pathway.pdf |
60c744db9abda24b5ff8c460 | 10.26434/chemrxiv.6970301.v2 | Microfluidics of Binary Liquid Mixtures with Temperature-Dependent Miscibility | Liquid-liquid microfluidic systems rely on the intricate control over the fluid properties of either miscible or immiscible mixtures. Herein, we report on the use of partially miscible binary liquid mixtures that lend their microfluidic properties from a highly temperature-sensitive mixing and phase separation behaviour. For a blend composed of the thermotropic liquid crystal 4-Cyano-4'-pentylbiphenyl (5CB) and methanol, mixing at temperatures above the upper critical solution temperature (UCST; 24.4°C) leads to a uniform single phase while partial mixing can be achieved at temperatures below the UCST. Thermally-driven phase separation inside the microfluidic channels results in the spontaneous formation of very regular phase arrangements, namely in droplets, plug, slug and annular flow. We map different flow regimes and relate findings to the role of interfacial tension and viscosity and their temperature dependence. Importantly, different flow regimes can be achieved at constant channel architecture and flow rate by varying the temperature of the blend. A consistent behaviour is observed for a binary liquid mixture with lower critical solution temperature, namely 2,6-lutidine and water. This temperature-responsive approach to microfluidics is an interesting candidate for multi-stage processes, selective extraction and sensing applications. | Maximiliano J. Fornerod; Esther Amstad; Stefan Guldin | Nanofluidics; Fluid Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744db9abda24b5ff8c460/original/microfluidics-of-binary-liquid-mixtures-with-temperature-dependent-miscibility.pdf |
65114495ed7d0eccc32d00f8 | 10.26434/chemrxiv-2023-r843x | PFΔScreen – An open-source tool for automated PFAS feature prioritization in non-target HRMS data | Per- and polyfluoroalkyl substances (PFAS) are a huge group of anthropogenic chemicals with unique properties that are used in countless products and applications. Due to the high stability of their C–F bonds, PFAS or their transformation products (TPs) are persistent in the environment, leading to ubiquitous detection in various samples worldwide. Since PFAS are industrial chemicals, the availability of authentic PFAS reference standards is limited, making non-target screening (NTS) approaches based on high-resolution mass spectrometry (HRMS) necessary for a more comprehensive characterization. NTS usually is a time-consuming process, since only a small fraction of the detected chemicals can be identified. Therefore, efficient prioritization of relevant HRMS signals is one of the most crucial steps. We developed PFΔScreen, a Python-based open-source tool with a simple graphical user interface (GUI) to perform efficient feature prioritization by several PFAS specific techniques such as the highly promising MD/C-m/C approach, Kendrick mass defect analysis, diagnostic fragments (MS2), fragment mass differences (MS2) and suspect screening. Feature detection from vendor-independent MS raw data (mzML, data-dependent acquisition) is performed via pyOpenMS (or custom feature lists) with subsequent calculations for prioritization and identification of PFAS in both HPLC- and GC-HRMS data. The PFΔScreen workflow is presented on four PFAS-contaminated agricultural soil samples from south-western Germany. Over 15 classes of PFAS (more than 80 single compounds with several isomers) could be identified, including four novel classes, potentially TPs of the precursors fluorotelomer mercapto alkyl phosphates (FTMAPs). PFΔScreen can be used within the Python environment and is easily automatically installable and executable on Windows. Its source code is freely available on GitHub (https://github.com/JonZwe/PFAScreen). | Jonathan Zweigle; Boris Bugsel; Joel Fabregat-Palau; Christian Zwiener | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Analysis; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65114495ed7d0eccc32d00f8/original/pf-screen-an-open-source-tool-for-automated-pfas-feature-prioritization-in-non-target-hrms-data.pdf |
6449276f83fa35f8f64819f5 | 10.26434/chemrxiv-2023-2cl67-v2 | Smooth Things Come in Threes: A Diabatic Surrogate Model for Conical Intersection Optimization | The optimization of conical intersection structures is complicated by the non-differentiability of the adiabatic potential energy surfaces. In this work, we build a pseudo-diabatic surrogate model, based on Gaussian process regression, formed by three smooth and differentiable surfaces that can adequately reproduce the adiabatic surfaces. Using this model with the restricted variance optimization method results in a notable decrease of the overall computational effort required to obtain minimum energy crossing points. | Ignacio Fdez. Galván; Roland Lindh | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6449276f83fa35f8f64819f5/original/smooth-things-come-in-threes-a-diabatic-surrogate-model-for-conical-intersection-optimization.pdf |
60c74a9af96a000e7a287485 | 10.26434/chemrxiv.12227336.v1 | Collisional Dynamics Simulations Revealing Fragmentation Properties of Zn(II)-Bound Poly-Peptide | <div>
<div>
<div>
<p>Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with
the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analogue methanobactin peptide-5, amb5) and in particular to explore the role of zinc
binding on reactivity. Fragmentation pathways, their mechanisms, and collision energy transfer are discussed. The probability distributions of
the pathways are compared with the results of the experimental IM-MS, MS/MS spectrum and previous thermal simulations. Collisional
activation gives both statistical and non-statistical fragmentation pathways with non-statistical shattering mechanisms accounting for a relevant
percentage of reactive trajectories, becoming dominant at higher energies. The tetra-coordination of zinc changes qualitative and quantitative
fragmentation, in particular the shattering. The collision energy threshold for the shattering mechanism was found to be 118.9 kcal/mol which
is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal/mol identified previously during thermal simulations. This
difference can be attributed to the tetra-coordinated zinc complex that hinders the availability of the sidechains to undergo direct collision with
the Ar projectile.
</p>
</div>
</div>
</div> | Abdul Malik; Laurence A. Angel; Riccardo Spezia; William L. Hase | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a9af96a000e7a287485/original/collisional-dynamics-simulations-revealing-fragmentation-properties-of-zn-ii-bound-poly-peptide.pdf |
64d54bb5dfabaf06ff112c9f | 10.26434/chemrxiv-2023-hzzg4 | Cations Mediate Lithium Polysulfide Adsorption in Metal-Organic Framework Coatings for Lithium-Sulfur Batteries | Lithium-sulfur (Li-S) batteries are one promising alternative to Li-ion batteries due to their higher theoretical specific capacity and energy density. However, several technical challenges such as polysulfide shuttling remain. As liquid polysulfide diffusion into the electrolyte causes a loss of capacity, different material classes have been explored to anchor lithium polysulfides and reduce active material loss. The metal-organic framework (MOF) UiO-66 has been identified as one candidate material due to its porosity, high surface area, and zirconium oxide nodes that could anchor liquid polysulfides. MOFs also allow for post-synthetic modifications that can increase their adsorption specificity towards liquid polysulfides and reduce shuttling. In this work, we combined atomistic simulations and experimental characterization to probe the molecular interactions between lithium polysulfides and functionalized UiO-66 nodes. We explored how lithium polysulfides adsorb to open sites caused by missing linker defects, as well as sites functionalized with alkali cations. Our results demonstrate that lithium polysulfides adsorb favorably to UiO-66 through Li-O electrostatic interactions. In addition, we found that nodes functionalized with alkali metals demonstrated stronger adsorption of long chain lithium polysulfides (Li2S4-8) by facilitating charge transfer to the nodes. Experimental UV-Vis and 7Li-NMR measurements on Zr polyoxometallates and UiO-66 provided further evidence that lithiation favors adsorption of long chain polysulfides. Our findings show how UiO-66 functionalization may inhibit the shuttle effect through polysulfide adsorption, and consequently im-prove Li-S battery performance. The fundamental insights into polysulfide adsorption shown here provide quantitative principles to design functionalized moieties and further inhibit polysulfide shuttling. | Roberto A. Jarrín; Kevin Bennett; V. Sara Thoi; Brandon C. Bukowski | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d54bb5dfabaf06ff112c9f/original/cations-mediate-lithium-polysulfide-adsorption-in-metal-organic-framework-coatings-for-lithium-sulfur-batteries.pdf |
61ddeabdf51b222af6129124 | 10.26434/chemrxiv-2022-qbxjs | Highly Durable Graphene Monolayer Electrode on Insulating Substrate under Long-term Hydrogen Evolution Cycling | Electrochemical hydrogen evolution reaction (HER) at single graphene sheets has been investigated widely either in its pristine form or after chemical modification. One important challenge is the long-term stability of single graphene sheets on Si/SiO2 substrates under HER. Previous reports have found that due to stress developing under gas evolution, the sheets tend to break apart, with a very low lifetime limited to just a few cycles of HER. Here, we show through appropriate electrode preparation that it is possible to achieve highly durable single graphene electrodes on insulating substrates, which can survive several hundreds of HER cycles with virtually no damage to the sp2-carbon framework. Through systematic investigations including atomic force microscopy, Raman spectroscopy and electroanalysis, we show that even after so many cycles, the sheet is physically intact and the electron transfer capability of the electrodes remain unaffected. This extremely high stability of a single atomic sheet of carbon, when combined with appropriate chemical modification strategies, will pave way for the realization of novel 2D electrocatalysts. | Michel Wehrhold; Tilmann J Neubert; Tobias Grosser; Kannan Balasubramanian | Materials Science; Catalysis; Nanoscience; Carbon-based Materials; Nanostructured Materials - Nanoscience; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ddeabdf51b222af6129124/original/highly-durable-graphene-monolayer-electrode-on-insulating-substrate-under-long-term-hydrogen-evolution-cycling.pdf |
67cd559281d2151a02b7e327 | 10.26434/chemrxiv-2025-p1734 | Dynamic Clustering of Aqueous Ti(IV) Cations | Titanium (Ti), the ninth-abundant element of the Earth crust, distributes widely in rocks, soils, waters and bodies of almost all organisms. The solution chemistry of Ti(IV), the most stable oxidation state of Ti, is the key of distribution, transformation and utilization of Ti element. Despite its pervasiveness in nature and chemical industry, the speciation of Ti(IV) cations in aqueous solution remains controversial after decades of researches. Herein, aided by combined state-of-the-art characterizations, we discover that hydrated Ti(IV) cations predominantly exist as atomically precise [Ti8O12(H2O)24]8+ clusters at higher concentrations and as [Ti(H2O)n(OH)]3+ (n = 4 or 5) monomers at lower concentrations, instead of commonly believed titanyl ions. The two structures transform into each other spontaneously and reversibly when diluting or concentrating the solution. More importantly, the transformation also governs the hydrothermal growth behavior of rutile-phase TiO2 from solution. Our work addresses a long-standing controversy regarding the structure of Ti(IV) (aq), reveals a highly dynamic clustering and dissociation behavior of Ti(IV) (aq), and benefits fundamental understanding of Ti chemistry. | Lijing Fan; Fan Wu; Yang Lu; Yanxin Chen; Yi-Fan Huang; Pengxin Liu | Inorganic Chemistry; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cd559281d2151a02b7e327/original/dynamic-clustering-of-aqueous-ti-iv-cations.pdf |
6318ca5afaf4a4de5209bfc0 | 10.26434/chemrxiv-2022-hlbk6 | Tricolor Visible Wavelength-selective Photodegradable Hydrogel Biomaterials | Photodynamic hydrogel biomaterials have demonstrated great potential for user-triggered therapeutic release, patterned organoid development, and 4D control over advanced cell fates in vitro. Current photosensitive materials are constrained by their reliance on high-energy ultraviolet (UV) light (<400 nm) that offers poor tissue penetrance and limits access to the broader visible spectrum. Here, we report a family of three photolabile material crosslinkers that respond rapidly and with unique tricolor wavelength-selectivity to low-energy visible light (400 – 617 nm). When mixed with multifunctional poly(ethylene glycol) macromolecular precursors, novel ruthenium polypyridyl- and ortho-nitrobenzyl (oNB)-based crosslinkers yield cytocompatible biomaterials that can undergo spatiotemporally patterned, uniform bulk softening, and multiplexed degradation several centimeters deep through complex tissue. Encapulated living cells within these photoresponsive gels show high viability (>85%) and can be successfully recovered from the hydrogels following photodegradation. Moving forward, we anticipate that these advanced material platforms will enable new studies in 3D mechanobiology, controlled drug delivery, and next-generation tissue engineering applications. | Teresa Rapp; Cole DeForest | Materials Science; Polymer Science; Controlled-Release Systems; Optical Materials; Hydrogels; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6318ca5afaf4a4de5209bfc0/original/tricolor-visible-wavelength-selective-photodegradable-hydrogel-biomaterials.pdf |
62b222d3486c989a6dadcf9e | 10.26434/chemrxiv-2022-g77x5 | The HEALED SBU library of chemically realistic building blocks for construction of hypothetical metal-organic frameworks | Advancements in hypothetical metal-organic framework (hMOF) databases and construction tools have resulted in a rapidly expanding chemical design space for nanoporous materials. The bulk of these hypothetical structures are constructed using structural building units (SBUs) derived from experimental MOF structures, often collected from the CoRE-MOF database. Recent investigations into the state of these deposited experimental structures’ chemical accuracy identified an array of common structural errors—including omitted protons, missing counterions, and disordered structures. These structural errors propagate into the SBUs mined from experimental MOFs, culminating in inaccurate hMOF structures possessing net charges or missing atoms which were not accounted for previously. This work demonstrates how manual investigation was applied to diagnose structural errors in SBUs obtained from several popular hMOF construction tools and databases. An analysis of the prevailing errors discovered during the examination process is provided along with representative cases to aid with error detection in future studies involving SBU extraction and hMOF construction. A novel repair protocol was established and employed to generate a library of SBUs that are hand-examined and labeled with enhanced detail (HEALED). This repaired library of SBUs contains 952 inorganic SBUs and 568 organic SBUs ideally suited for the generation of hypothetical frameworks that are chemically accurate and properly charge labelled. Additionally, case studies following the effects of SBU errors on electrostatic potential-fitted charges and GCMC-simulated gas adsorption predictions are presented to highlight the significance of using chemically accurate hMOF structures exclusively in all screening efforts going forward. | Marco Gibaldi; Ohmin Kwon; Andrew White; Jake Burner; Tom K. Woo | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b222d3486c989a6dadcf9e/original/the-healed-sbu-library-of-chemically-realistic-building-blocks-for-construction-of-hypothetical-metal-organic-frameworks.pdf |
662fd96121291e5d1d085ae6 | 10.26434/chemrxiv-2024-m6kj8 | In-vivo Lifetime Imaging of the Internal O2 Dynamics in Corals with NIR-emitting Sensor Nanoparticles | Mapping of O2 with luminescent sensors within intact animals is challenging due to attenuation of excitation and emission light caused by tissue absorption and scattering, as well as interfering background fluorescence. Here we show the application of luminescent O2 sensor nanoparticles (~40-50 nm) composed of the O2 indicator platinum(II) tetra(4-fluoro)phenyltetrabenzoporphyrin (PtTPTBPF) immobilized in poly(methyl methacrylate-co-methacrylic acid) (PMMA-MA). We injected the sensor nanoparticles into the gastrovascular system of intact colony fractions of reef-building, tropical corals that harbor photosynthetic microalgae in their tissues. The sensor nanoparticles are ex-cited by red LED light (617 nm) and emit in the near-infrared (780 nm), which enhances transmission of excitation and emission light through biological materials. This enabled us to map the internal O2 concentration via time-domain luminescence lifetime imaging through the outer tissue layers across several coral polyps in flowing seawater. After injection, nanoparticles dispersed within the coral tissue over several hours. While luminescence intensity imag-ing showed some local aggregation of sensor particles, lifetime imaging showed a more homogenous O2 distribution across a larger area of the coral colony. Local stimulation of symbiont photosynthesis in corals induced oxygenation of illuminated tissue areas and formation of lateral O2 gradients toward surrounding respiring tissues, which were dissi-pated rapidly after onset of darkness. Such measurements are key to improve our understanding of how corals regulate their internal chemical microenvironment and metabolic activity and how they are affected by environmental stress such as ocean warming, acidification and deoxygenation. Our experimental approach can also be adapted for in vivo O2 imaging in other natural systems such as biofilms, plant and animal tissues, as well as in organoids and other cell con-structs, where imaging internal O2 conditions are relevant and challenging due to high optical density and back-ground fluorescence. | Michael Kühl; Daniel Aagren Nielsen; Sergey M. Borisov | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Analysis; Imaging | CC BY NC 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662fd96121291e5d1d085ae6/original/in-vivo-lifetime-imaging-of-the-internal-o2-dynamics-in-corals-with-nir-emitting-sensor-nanoparticles.pdf |
66489b3a91aefa6ce1583506 | 10.26434/chemrxiv-2024-ljd5f | Interfacial structures and mechanical response of highly viscous polymer melt on solid surfaces investigated by atomic force microscopy | The interfacial structures and mechanical response of the highly viscous poly(dimethylsiloxane) (PDMS, 9750 mPa･s, Mn ~ 59000) on solid surfaces were investigated by frequency-modulation atomic force microscopy (FM-AFM) using a quartz tuning fork sensor. A layered density distribution on a PDMS/mica interface was visualized on a 29 h-settling sample by two-dimensional frequency shift (∆ƒ) mapping, and the result exhibited that the layered structure was metastable. It was also found that the damping coefficient of tip vibration (∆γ) increased in the region of ~1 nm from the solid surface, which suggests the limited mobility of the liquid molecules closest to the solids. After settling for more extended time or heating the sample, the layered density distribution was suppressed, and the conservative repulsive force near the solid surface in 2-3 nm were observed over longer distances by settling for a more extended time or heating. The suppression of the layered density distribution showed the similar temperature dependence with the bulk viscoelastic relaxation. In contrast, the elongation of conservative repulsive force near the solid surface showed steeper temperature dependence than the bulk, which suggests that it was rate-limited by the attraction between the solid surface and the closest liquid molecules. | Yuto Nishiwaki; Yuya Yamada; Toru Utsunomiya; Hiroyuki Sugimura; Takashi Ichii | Physical Chemistry; Polymer Science; Interfaces | CC BY 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66489b3a91aefa6ce1583506/original/interfacial-structures-and-mechanical-response-of-highly-viscous-polymer-melt-on-solid-surfaces-investigated-by-atomic-force-microscopy.pdf |
64e0db8000bbebf0e67352ae | 10.26434/chemrxiv-2023-dzrp1 | Ligand-Enabled Palladium(II)-Catalyzed γ-C(sp3)−H Arylation of Primary Aliphatic Amines | Amines are common scaffolds in bioactive molecules as well as building blocks for chemical synthesis. Despite significant advances in palladium-catalyzed C(sp3)−H functionalization of amines over the past decades, it remains challenging to perform directed C−H metalation with native amine groups rather than amine-derived or transient directing groups (DGs). Recently, our group developed the Pd(II)/sulfoxide-2-hydroxypyridine (SOHP) catalytic system, in which SOHP ligands play a pivotal role as a crucial functional module, enabling regioselective C(sp2)−H and enantioselective C(sp3)−H functionalization reactions. In this work, we demonstrate that this chemistry provides an ideal solution for native primary amine-directed γ-C(sp3)-H arylation. Primary amines of varying degrees of complexity, encompassing amino acid esters and aminol silyl ethers, were found to be compatible with the established methodology. Additionally, we achieved a preliminary implementation of the asymmetric variant of this γ-C−H arylation reaction by employing a chiral SOHP ligand. Moreover, the range of applicable substrates could be extended to pyridine, oxime ether, and pyridine-N-oxide. | Chen-Hui Yuan; Lei Jiao | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e0db8000bbebf0e67352ae/original/ligand-enabled-palladium-ii-catalyzed-c-sp3-h-arylation-of-primary-aliphatic-amines.pdf |
60c759e59abda253eff8eb91 | 10.26434/chemrxiv.14540358.v2 | Approximate Models for the Lattice Thermal Conductivity of Alloy Thermoelectrics | Thermoelectric generators (TEGs) convert waste heat to electricity and are a leading contender for improving energy efficiency at a range of scales. Ideal TE materials show a large Seebeck effect, high electrical conductivity, and low thermal conductivity. Alloying is a widely-used approach to engineering the heat transport in TEs, but despite many successes the underlying mechanisms are poorly understood. In previous work, first-principles modelling has successfully been used to study the thermodynamics of alloy formation and to investigate its effect on the electronic structure and phonon spectrum. However, it has so far only been possible to examine qualitatively the impact of alloying on the lattice thermal conductivity. In this work, we develop and test two new approaches to addressing this. The constant relaxation-time approximation (CRTA) assumes the primary effect of alloying is on the phonon group velocities, and allows the thermal conductivity to be calculated assuming a suitable constant lifetime. Alternatively, setting the three-phonon interaction strengths to a constant further enables an assessment of how changes to the phonon frequency spectrum influence the lifetimes. We test both approaches for the <i>Pnma</i> Sn(S<sub>1-<i>x</i></sub>Se<sub><i>x</i></sub>) alloy system and are able to account for the substantially-reduced thermal conductivity measured in experiments. | Jonathan Skelton | Alloys; Computational Chemistry and Modeling; Theory - Computational; Piezoelectricity and Thermoelectricity; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759e59abda253eff8eb91/original/approximate-models-for-the-lattice-thermal-conductivity-of-alloy-thermoelectrics.pdf |
63adc7ce518c16486a3c9a4b | 10.26434/chemrxiv-2022-s2q7g | Toward in silico Catalyst Optimization | In this minireview, we overview a computational pipeline that can be used to successfully reproduce the enantiomeric ratios of homogeneous catalytic reactions. At the core of this pipeline is the SCINE Molassembler module, a graph-based software that provides algorithms for molecular construction of all periodic table elements. With this pipeline, we are able to simulataneously functionalize and generate ensembles of transistion state conformers, which permits facile exploration of the influence of various substituents on the overall enantiomeric ratio. This allows preconceived back-of-the-envelope design models to be tested and subsequently refined by providing quick and reliable access to energetically low-lying transition states, which represents a key step in undertaking in silico catalyst optimization. | Matthew Wodrich; Ruben Laplaza; Nicolai Cramer; Markus Reiher; Clemence Corminboeuf | Theoretical and Computational Chemistry; Organic Chemistry; Organometallic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63adc7ce518c16486a3c9a4b/original/toward-in-silico-catalyst-optimization.pdf |
673ba816f9980725cfa3c405 | 10.26434/chemrxiv-2024-n3fc1 | Sorbent Mediated Electrocatalytic Reduction of Dilute CO2 to Methane | Efficient CO2 utilization is a critical component of closing the anthropogenic carbon cycle. Most studies have focused on using pure streams of CO2. However, CO2 is generally only available in dilute streams, which requires capture by sorbents followed by energy intensive regeneration to release concentrated CO2. Direct utilization of sorbed-CO2 avoids the costly regeneration step. Furthermore, the sorbent-CO2 interaction can kinetically activate CO2 and tune its reactivity to access products that could otherwise be inaccessible with direct CO2 reduction. We demonstrate that an N-heterocyclic carbene, 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (DPIy), can capture CO2 from dilute streams (0.04% and 10%) to form 1,3-bis(2,6-diisopropylphenyl)imidazolium-2-carboxylate (DPICx) quantitatively. Electrocatalyst iron tetraphenylporphyrin chloride (Fe(TPP)Cl) typically reduces CO2 to CO; however, with DPICx as the substrate, the 8-electron reduced product methane (CH4) is produced with high (>85%) Faradaic efficiency and regeneration of the sorbent DPIy. In addition to the overall energy and capital advantages of integrated CO2 capture and conversion, these studies illustrate how sorbents can serve a dual purpose for both CO2 capture and chemical auxiliary to access unique products. CO2 has a spectrum of reactivity with different types of sorbents; these results reveal how sorbent-CO2 interactions can be leveraged for integrated capture and utilization platforms to access a wider range of CO2-derived products. | Jared Stanley; Hunter Pauker; Erin Kuker; Vy Dong; Robert Nielsen; Jenny Yang | Inorganic Chemistry; Catalysis; Energy; Electrocatalysis; Redox Catalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ba816f9980725cfa3c405/original/sorbent-mediated-electrocatalytic-reduction-of-dilute-co2-to-methane.pdf |
60c74fafbb8c1a2f543db98d | 10.26434/chemrxiv.12894050.v2 | Anomalous Nanoparticle Surface Diffusion in Liquid Cell TEM is Revealed by Deep Learning-Assisted Analysis | The motion of nanoparticles near surfaces is of fundamental importance in physics, biology, and chemistry. Liquid cell transmission electron microscopy (LCTEM) is a promising technique for studying motion of nanoparticles with high spatial resolution. Yet, the lack of understanding of how the electron beam of the microscope affects the particle motion has held back advancement in using LCTEM for in situ single nanoparticle and macromolecule tracking at interfaces. Here, we experimentally studied the motion of a model system of gold nanoparticles dispersed in water and moving adjacent to the silicon nitride membrane of a commercial liquid cell in a broad range of electron beam dose rates. We find that the nanoparticles exhibit anomalous diffusive behavior modulated by the electron beam dose rate. We characterized the anomalous diffusion of nanoparticles in LCTEM using a convolutional deep neural network model and canonical statistical tests. The results demonstrate that the nanoparticle motion is governed by fractional Brownian motion at low dose rates, resembling diffusion in a viscoelastic medium, and continuous time random walk at high dose rates, resembling diffusion on an energy landscape with pinning sites. Both behaviors can be explained by the presence of silanol molecular species on the surface of the silicon nitride membrane and the ionic species in solution formed by radiolysis of water in presence of the electron beam. | Vida Jamali; Cory Hargus; Assaf Ben Moshe; Amirali Aghazadeh; Hyun Dong Ha; Kranthi K. Mandadapu; Paul Alivisatos | Imaging; Microscopy; Nanofluidics; Machine Learning; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fafbb8c1a2f543db98d/original/anomalous-nanoparticle-surface-diffusion-in-liquid-cell-tem-is-revealed-by-deep-learning-assisted-analysis.pdf |
60c74fd8ee301c737ec7a77b | 10.26434/chemrxiv.12950804.v1 | Efficient Emission in Halide Layered Double Perovskites: The Role of Sb3+ Substitution in Cs4Cd1–xMnxBi2Cl12 Phosphors | Layered halide perovskites and double perovskites optoelectronic properties have recently been the subject of intense research. Layered double perovskites represent the merging of both worlds, and as such, have the potential to further expand the already vast space of optoelectronic properties and applications of halide perovskites. Despite having more than 40 known members, to date, only the <111>-oriented layered double perovskites: Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub><b>Bi</b><sub>2</sub>Cl<sub>12</sub>, have shown efficient photoluminescence (PL). In this work, we replaced Bi with Sb to further investigate the electronic structure and PL properties of these materials, resulting in two new families of layered inorganic perovskites alloys with full solubility. The first family, Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<b>Sb</b><sub>2</sub>Cl<sub>12</sub>, exhibits a PL emission at 605 nm ascribed to Mn<sup>2+</sup> centers in octahedral coordination, and a maximum photoluminescence quantum yield PLQY of 28.5%. The second family of alloys, also with full solubility, Cs<sub>4</sub>Cd<sub>0.8</sub>Mn<sub>0.2</sub>(Sb<sub>1</sub>–<sub>y</sub>Bi<sub>y</sub>)<sub>2</sub>Cl<sub>12</sub>, contains a fixed amount of Mn<sup>2+</sup> and Cd<sup>2+</sup> cations but different concentrations of the trivalent metals. This variability allows the tuning of the PL emission from 603 nm to 614 nm. We show that the decreased efficiency of the Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub>Sb<sub>2</sub>Cl<sub>12</sub>family compared to Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub><b>Bi</b><sub>2</sub>Cl<sub>12</sub>, is mostly due to a decreased spin-orbit coupling in Sb and the subsequent increased electronic delocalization compared to the Bi alloys, reducing the energy transfer to Mn<sup>2+</sup> centers. This work lays out a roadmap to understand and achieve high photoluminescence efficiencies in layered double perovskites.<p></p> | Brenda Vargas; Eduardo Coutiño-Gonzalez; Oscar Ovalle-Encinia; Citlali Sánchez-Aké; Diego Solis-Ibarra | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fd8ee301c737ec7a77b/original/efficient-emission-in-halide-layered-double-perovskites-the-role-of-sb3-substitution-in-cs4cd1-x-mnx-bi2cl12-phosphors.pdf |
60c75019842e658f7cdb397f | 10.26434/chemrxiv.12990830.v1 | Multireference Description of Nickel–Aryl Homolytic Bond Dissociation Processes in Photoredox Catalysis | <p>Multireference electronic structure calculations consistent with known experimental data have elucidated a novel mechanism for photo-triggered Ni(II)–C homolytic bond dissociation in Ni 2,2’-bipyridine (bpy) photoredox catalysts. Previously, a thermally assisted dissociation from the lowest energy triplet ligand field excited state was proposed and supported by density functional theory (DFT) calculations that reveal a barrier of ~30 kcal mol<sup>-1</sup>. In contrast, multireference ab initio calculations suggest this process is disfavored, with barrier heights of ~70 kcal mol<sup>-1</sup>, and highlight important ligand noninnocent contributions to excited state relaxation and bond dissociation processes that are not captured with DFT. In the multireference description, photo-triggered Ni(II)–C homolytic bond dissociation occurs via initial population of a singlet Ni(II)-to-bpy metal-to-ligand charge transfer (<sup>1</sup>MLCT) excited state followed by intersystem crossing and aryl-to-Ni(III) charge transfer, overall a formal two-electron transfer process driven by a single photon. This results in repulsive triplet excited states from which spontaneous homolytic bond dissociation can occur, effectively competing with relaxation to the lowest energy, nondissociative triplet Ni(II) ligand field excited state. These findings guide important electronic structure considerations for the experimental and computational elucidation of the mechanisms of ground and excited state cross-coupling catalysis mediated by Ni heteroaromatic complexes.</p> | David Cagan; Gautam Stroscio; Alexander Cusumano; Ryan Hadt | Organic Synthesis and Reactions; Bonding; Coordination Chemistry (Inorg.); Kinetics and Mechanism - Inorganic Reactions; Ligands (Inorg.); Spectroscopy (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Homogeneous Catalysis; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75019842e658f7cdb397f/original/multireference-description-of-nickel-aryl-homolytic-bond-dissociation-processes-in-photoredox-catalysis.pdf |
657ea30ae9ebbb4db915becd | 10.26434/chemrxiv-2023-fdjbl-v2 | Biofabrics from Sodium Alginate | This was a study meant to understand the properties and nature of
biofabrics made with the help of sodium alginate, which is an extract of
brown seaweed, sodium alginate as a substance is often used for baking
purposes. The research aimed at the making of biofabrics from many
different organic and inorganic materials like tea, beetroot, coffee, sugar,
water, colored water and even salt water. The study aims at
understanding and taking a step further at progressing the development
of sustainable fabrics. Our biofabrics showcase the potential to
significantly reduce the environmental impact associated with
conventional textile manufacturing. Its properties can be customized to
cater to a wide array of applications. | Mohammad Farhan | Biological and Medicinal Chemistry; Biochemistry; Environmental biology | CC BY 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657ea30ae9ebbb4db915becd/original/biofabrics-from-sodium-alginate.pdf |
60c74de1469df46a86f44378 | 10.26434/chemrxiv.12668651.v1 | BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization | <div><div><div><p>With a large amount of research dedicated to decoding how metallic species bind to protein, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal binding templates. These approaches are fundamentally focused on the first coordination sphere of the metal. Here, we present the BioMetAll predictor that is based on a different postulate: the formation of a potential metal-binding site is related to the geometric organization of the protein backbone. We first report the set of convenient geometric descriptors of the backbone needed for the algorithm and their parametrization from a statistical analysis. Then, the successful benchmark of BioMetAll on a set of more than 50 metal-binding X-Ray structures is presented. Because BioMetAll allows structural predictions regardless of the exact geometry of the side chains, it appears extremely valuable for systems which structures (either experimental or theoretical) are not optimal for metal binding sites. We report here its application on three different challenging cases i) the modulation of metal-binding sites during conformational transition in human serum albumin, ii) the identification of possible routes of metal migration in hemocyanins, and iii) the prediction of mutations to generate convenient metal-binding sites for de novo biocatalysts. This study shows that BioMetAll offers a versatile platform for numerous fields of research at the interface between inorganic chemistry and biology, and allows to highlight the role of the preorganization of the protein backbone as a marker for metal binding.</p></div></div></div> | José-Emilio Sánchez-Aparicio; Laura Tiessler-Sala; Lorea Velasco-Carneros; Lorena Roldán-Martín; Giuseppe Sciortino; Jean-Didier Maréchal | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de1469df46a86f44378/original/bio-met-all-identifying-metal-binding-sites-in-proteins-from-backbone-preorganization.pdf |
639b20fce8047a6844e9c93d | 10.26434/chemrxiv-2022-dpsx9 | Mechanochemical Desymmetrization of Unbiased Bis- and Tris-alkynes to Access 3,5-Isoxazoles-Alkyne Adducts and Unsymmetrical Bis-3,5-isoxazoles | A mechanochemical desymmetrization of symmetrical bis- and tris-alkynes via a controlled 1,3-dipolar cycloaddition reaction with nitrile oxide dipoles has been developed. This convenient, efficient, and simple protocol allows access to 3,5-isoxazole-alkyne adducts from easily prepared or commercially available symmetrical bis- and tris-alkynes in moderate to excellent yield. The synthetic utility of 3,5-isoxazole-alkyne was demonstrated by developing a route to access β-ketoenamine-alkyne derivatives and the synthesis of unsymmetrical bis-3,5-isoxazoles products in good to excellent yields. | Rafael A. Hernandez R.; Irini Trakakis; Jean-Louis Do; Louis A. Cuccia; Tomislav Friščić; Pat Forgione | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b20fce8047a6844e9c93d/original/mechanochemical-desymmetrization-of-unbiased-bis-and-tris-alkynes-to-access-3-5-isoxazoles-alkyne-adducts-and-unsymmetrical-bis-3-5-isoxazoles.pdf |
667e545bc9c6a5c07aa7f7d8 | 10.26434/chemrxiv-2024-7h93h | Functional Aptamers in vitro Evolution for Protein-protein Interaction Blockage | As aptamer development progresses, their applications have expanded significantly beyond high affinity to include functional capabilities. Currently, identifying functional aptamers relies on traditional SELEX techniques, followed by functional validation and computer-assisted redesign of high-affinity aptamers. However, high affinity does not guarantee optimal functionality, making the search for functional aptamers from binding pools time consuming and labor-intensive. Addressing this challenge, we introduce Functional Aptamers in vitro Evolution (FAIVE), a novel screening method that links sequence functionality to fluorescence intensity. We demonstrated the effectiveness of FAIVE by obtaining modified DNA aptamers capable of disrupting the interaction between SARS-CoV-2 spike receptor-binding domain (RBD) and hACE2, targeting protein-protein interaction inhibition. Furthermore, we investigated the criteria for validating the quality of the bead library generated for selection by modeling the process of emulsion PCR, thus providing theoretical insights for future applications. The concept of incorporating fluorescent signal reporting of aptamer functionality into the aptamer selection process has the potential of facilitate the identification of aptamers with diverse functionalities, and is readily adaptable to various research contexts. | Tongxuan Wei; Qinguo Liu; Jun Li; Liqin Zhang | Biological and Medicinal Chemistry; Analytical Chemistry; High-throughput Screening; Bioengineering and Biotechnology | CC BY NC 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667e545bc9c6a5c07aa7f7d8/original/functional-aptamers-in-vitro-evolution-for-protein-protein-interaction-blockage.pdf |
64526d5527fccdb3ea6e13c8 | 10.26434/chemrxiv-2023-545nv-v2 | Morphology and porosity of pure and magnetite nanoparticles decorated porous cellulose nanocrystal cryogel monoliths | The investigation of porosity and porous materials have been of great interest to the medical field. Cellulose nanocrystals (CNC) are an attractive biocompatible natural material currently under development for use in tissue engineering. Herein, we probe the fabrication of carboxylated CNC-based cryogel scaffolds using the freeze-casting technique. We also employed a combination of characterization techniques to probe scaffold porosity, including scanning electron microscopy (SEM), small-angle X-ray scattering (SAXS), and dynamic vapor sorption (DVS). Our findings showed that macropore morphologies of the CNC-based cryogel scaffolds depend on the conditions under which water freezing takes place. The SAXS data fitted using the mass fractal model and power law suggest that the CNCs aggregated to form well-defined walls in the range of 96.7 nm – 27.3 nm for all samples, while the incorporation of nanoparticles disrupted this compactness in the range of 27.3 – 4.8 nm. The nanoparticles also showed a direct influence on water uptake of the cryogel scaffolds by reducing water sorption mesopores with a radius of 5 – 6 nm, as shown by the DVS technique. | Xining Chen; Mark Andrews | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64526d5527fccdb3ea6e13c8/original/morphology-and-porosity-of-pure-and-magnetite-nanoparticles-decorated-porous-cellulose-nanocrystal-cryogel-monoliths.pdf |
6196adc562372e6fe7be162a | 10.26434/chemrxiv-2021-0npvq | Aerobic Oxidation Reactivity of Well-Defined CoII and CoIII Aminophenol Complexes | This article describes the synthesis and reactivity studies of three cobalt complexes bearing aminophenol-derived ligands without nitrogen substitution: CoII(tBu2APH)2(tBu2AP)2 (1), Co2III(tBu2APH)2(tBu2AP)2(μ-tBu2BAP)2 (2), and CoIII(tBu2AP)3 (3) (tBu2APH = 2-amino-4,6-di-tert-butylphenol, tBu2AP = 2-amino-4,6-di-tert-butylphenolate, μ-tBu2BAP = bridging 2-amido-4,6-di-tert-butylphenolate). Stoichiometric reactivity studies of these well-defined complexes demonstrate the catalytic com-petency of both CoII and CoIII complexes in the aerobic oxidative cyclization of tBu2APH with tert-butyl isonitrile. Reactions with O2 reveal the aerobic oxidation of CoII complex 1 to generate the CoIII species 2 and 3. UV-visible time-course studies and EPR spectroscopy indicate that this oxidation proceeds through a ligand-based radical intermediate. These studies repre-sent the first example of well-defined cobalt-aminophenol complexes that participate in catalytic aerobic oxidation reactions and highlight a key role for a ligand radical in the oxidation sequence. | Jiaqi Liu; Brian Dolinar; Jessica Hoover | Organic Chemistry; Inorganic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6196adc562372e6fe7be162a/original/aerobic-oxidation-reactivity-of-well-defined-co-ii-and-co-iii-aminophenol-complexes.pdf |
60c744b8f96a003806286a85 | 10.26434/chemrxiv.9784607.v2 | Felkin-Anh Model from an Orbital Phase Perspective: Diastereoselectivity in Nucleophilic Addition to 2,3-Bis(trifluoromethyl)bicyclo[2.2.1]heptan-7-one | <p>To address the electronic effect in
nucleophilic addition, we often use the Felkin-Anh model, in which the most sigma-electron-withdrawing
group (.sigma.EWG) at the a-position of the carbonyl should be located anti to the nucleophile
approach. The diastereoselectivity is often explained by the antiperiplanar
effect of the .sigma.EWG. Reetz and Frenking reported that the FMO, the LUMO in the a-substituted
ketone, has greater expansion anti the .sigma.EWG. Thus, the FMO theory
can also apply to this diastereoselectivity. However, there is still no
explanation for why the LUMO has greater expansion anti to the .sigma.EWG and toward
the nucleophile approach with this conformation, as is suggested by the FMO
theory. We show here that the phase-continuous cyclic orbital interaction among
n<sub>Nu:-</sub>-.pi.*<sub>C=O</sub>-.sigma.*<sub>C-<i>A</i>/vic</sub>-.sigma.*<sub>CC/gem</sub>-
controls the diastereoselectivity, which is confirmed with theoretical
calculations and the bond model analysis using a conformationally-fixed
bicyclic molecule, 2,3-bis(trifluoromethyl)bicyclo[2.2.1]heptan-7-one
<b>1</b>, as a model.</p> | Yuji Naruse; Hayata Hibino; Atsushi Takamori | Organic Synthesis and Reactions; Stereochemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b8f96a003806286a85/original/felkin-anh-model-from-an-orbital-phase-perspective-diastereoselectivity-in-nucleophilic-addition-to-2-3-bis-trifluoromethyl-bicyclo-2-2-1-heptan-7-one.pdf |
64a2f0abba3e99daef73a144 | 10.26434/chemrxiv-2023-crmpg | Vendi Sampling For Molecular Simulations: Diversity As A Force For Faster Convergence And Better Exploration | Molecular dynamics (MD) is the method of choice for understanding the structure, function, and interactions of molecules. However, MD simulations are limited by the strong metastability of many molecules, which traps them in a single conformation basin for an extended amount of time. Enhanced sampling techniques, such as metadynamics and replica exchange, have been developed to overcome this limitation and accelerate the exploration of complex free energy landscapes. In this paper, we propose Vendi Sampling, a replica-based algorithm for increasing the efficiency and efficacy of the exploration of molecular conformation spaces. In Vendi sampling, replicas are simulated in parallel and coupled via a global statistical measure, the Vendi Score, to enhance diversity. Vendi sampling allows for the recovery of unbiased sampling statistics and dramatically improves sampling efficiency. We demonstrate the effectiveness of Vendi sampling in improving molecular dynamics simulations by showing significant improvements in coverage and mixing between metastable states and convergence of free energy estimates for four common benchmarks, including Alanine Dipeptide and Chignolin. | Amey Pasarkar; Gianluca Bencomo; Simon Olsson; Adji Bousso Dieng | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a2f0abba3e99daef73a144/original/vendi-sampling-for-molecular-simulations-diversity-as-a-force-for-faster-convergence-and-better-exploration.pdf |
67793cf981d2151a02dd8ea9 | 10.26434/chemrxiv-2025-78s3j | In situ NMR to monitor bulk photopolymerization kinetics | The ability to precisely measure photopolymerization kinetics is paramount to controlling curing characteristics and material properties in photocurable systems. However, traditional methods to measure kinetics, such as Fourier- transform infrared spectroscopy (FTIR), are often limited by broadening mechanisms intrinsic to the system and poor spectral resolution. In this work, we present an in situ NMR spectroscopy technique to monitor bulk photopolymerization reactions wherein the polymer system is separated from the locking solvent via a capillary insert and photoexcited using an LED-coupled fiber optic. This technique allows for the purity of the reaction to be preserved while also benefiting from the high spectral resolution and rich chemical information offered by NMR. Rate constants (kp’) and ultimate monomer conversion are determined for four systems: (a) neat hexyl acrylate, (b) isobornyl methacrylate, (c) N,N-dimethylacrylamide, and (d) hexyl acrylate in the presence of a crosslinking species. By observing kinetic data of simple photopolymer systems, this work demonstrates the utility of in situ NMR photopolymerization as a complementary technique to conventional FTIR for the kinetic monitoring of photopolymer materials. | Luis L. Jessen; Kameron Hansen; George B. Crull; Tanner L. Grover; C. Allan Guymon | Materials Science; Polymer Science; Thin Films; Polymerization kinetics | CC BY 4.0 | CHEMRXIV | 2025-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67793cf981d2151a02dd8ea9/original/in-situ-nmr-to-monitor-bulk-photopolymerization-kinetics.pdf |
619e3191c481c302bbf71ce4 | 10.26434/chemrxiv-2021-j18mg-v4 | Novel Pyrazolo[3,4-c]pyridine Antagonists with Nanomolar affinity for A1 / A3 Adenosine Receptors: Binding Kinetics and Exploration of their Binding Profile Using Mutagenesis Experiments, MD simulations and TI/MD calculations | Drugs targeting the four adenosine receptor (AR) subtypes can provide “soft" treatment of various significant diseases. Even for the two experimentally resolved AR subtypes the description of the orthosteric binding area and structure-activity relationships of ligands remains a demanding task due to the high similar amino acids sequence but also the broadness and flexibility of the ARs binding area. The identification of new pharmacophoric moieties and nanomolar leads and the exploration of their binding area with mutagenesis and state-of-the-art computational methods useful also for drug design purposes remains a challenging aim for all ARs.
Here, we identified several low nanomolar ligands and potent competitive antagonists against A1R / A3R, containing the novel pyrazolo[3,4-c]pyridine pharmacophore for ARs, from a screen of an in-house library of only 52 compounds, originally designed for anti-proliferative activity. We identified L2-L10, A15, A17 with 3-aryl, 7-anilino and a electronegative group at 5-position as low micromolar to low nanomolar A1R / A3R antagonists. A17 has for A1R Kd = 5.62 nM and a residence time (RT) 41.33 min and for A3R Kd = 13.5 nM, RT = 47.23 min. The kinetic data showed that compared to the not potent or mediocre congeners the active compounds have similar association, for example at A1R Kon = 13.97 x106 M-1 (A17) vs Kon = 3.36 x106 M-1 (A26) but much lower dissociation rate Koff = 0.024 min-1 (A17) vs 0.134 min-1 (A26). Using molecular dynamics (MD) simulations and mutagenesis experiments we investigated the binding site of A17 showing that it can interact with an array of residues in transmembrane helix 5 (TM5), TM6, TM7 of A1R or A3R including residues E5.30, E5.28, T7.35 in A1R instead of Q5.28, V5.30 , L7.35 in A3R. A striking observation for drug design purposes is that for L2506.51A the binding affinity of A17 significantly increased at A1R.
A17 provides a lead representative of a promising series and by means of the Thermodynamics Integration coupled with MD simulations (TI/MD) method, first applied here on whole GPCR- membrane system and showing a very good agreement between calculated and experimental relative binding free energies for A1R and A3R (spearman rank correlation p = 0.82 and 0.84, respectively), and kinetic experiments can lead to ligands with improved profile against ARs.
| Margarita Stampelou; Anna Suchankova; Efpraxia Tzortzini; Lakshiv Dhingra; Kerry Barkan; Nikolaos Lougiakis; Panagiotis Marakos; Nikole Pouli; Graham Ladds; Antonios Kolocouris | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619e3191c481c302bbf71ce4/original/novel-pyrazolo-3-4-c-pyridine-antagonists-with-nanomolar-affinity-for-a1-a3-adenosine-receptors-binding-kinetics-and-exploration-of-their-binding-profile-using-mutagenesis-experiments-md-simulations-and-ti-md-calculations.pdf |
66f27ec612ff75c3a14e0111 | 10.26434/chemrxiv-2023-brst4-v3 | Polymer of Intrinsic Microporosity as Light Absorber for Luminescent Solar Concentrators | Luminescent solar concentrators (LSCs) hold the promise to make solar electricity more affordable by reducing the need for expensive photovoltaic cells and enabling less conventional forms of photovoltaics such as solar windows or roofs, and other architectural elements. Here we demonstrate the use of a polymer of intrinsic microporosity (PIM-1) as an efficient light absorber in an LSC, combined with a red-emitting dye. The prepared prototype LSC displays a good internal efficiency (25.3%) and external efficiency (11.4%), and performance metrics that show promise for the use of polymers of intrinsic microporosity as light harvesters. This work significantly broadens the potential applications of PIMs beyond their more traditional functions in molecular separations and other adsorption-based processes. | Yuxing Wang; Meihuizi Jiang; Saif A. Haque; Sebastien Rochat | Physical Chemistry; Energy; Interfaces; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f27ec612ff75c3a14e0111/original/polymer-of-intrinsic-microporosity-as-light-absorber-for-luminescent-solar-concentrators.pdf |
60c75856bdbb897726a3ad4e | 10.26434/chemrxiv.14540178.v1 | Nutritional Analysis of Biovalorisaton of Homogeneous Food Processing By-products | <div>
<div>
<div>
<p>Okara and Brewer's Spent Grain (BSG), the food by-products generated during soybean and
beer production, respectively, are two of the many food processing side streams that are
suitable for human consumption but often discarded. Okara and BSG offer good amounts of
both macro and micronutrients. More importantly, they are an exceptional source of proteins.
Solid-state fermentation was used to enhance the bioavailability of their intrinsic nutrients. In
this study, eight unique strains of Aspergillus Oryzae were used to ferment both Okara and
BSG. Subsequently, various quantitative and qualitative analyses were conducted to determine
the Total Polyphenolic Content (TPC) and Total Flavonoids Content (TFC) of the fermented
biomasses. TPC and TFC were determined via spectroscopic analysis. The microbial
fermentation of Okara by Black Koji resulted in the highest increase of TPC and TFC (5- and
13-fold respectively), compared to the control Okara. Meanwhile for BSG, the microbial
fermentation by M-1 resulted in the highest increase of TPC in BSG (7-fold).
</p>
</div>
</div>
</div> | Winnie Faustinelie; Ken Chi Lik Lee | Analytical Chemistry - General; Feed; Food | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75856bdbb897726a3ad4e/original/nutritional-analysis-of-biovalorisaton-of-homogeneous-food-processing-by-products.pdf |
62b662e85983a9cd5e6e42cf | 10.26434/chemrxiv-2022-m5fgw-v2 | Dipole Switching by Intramolecular Electron Transfer in Single-Molecule Magnetic Complex [Mn12O12(O2CR)16(H2O)4] | We study intramolecular electron transfer in the single-molecule magnetic complex [Mn12O12(O2CR)16 (H2O)4] for R = -H, -CH3, -CHCl2, -C6H5, -C6H4F ligands as a mechanism for switching of the molecular dipole moment. Energetics are obtained using the density functional theory (DFT) with onsite Coulomb energy correction (DFT+U). Lattice distortions are found to be critical for localizing an extra electron on one of the easy sites on the outer ring in which localized states can be stabilized. We find that the lowest energy path for charge transfer is for the electron to go through the center via superexchange mediated tunneling. The energy barrier for such a path ranges from 0.4 meV to 54 meV depending on the ligands and the isomeric form of the complex. The electric field needed to move the charge from one end to the other, thus reversing the dipole moment, is 0.01 - 0.04 V/Å. | Dmitry Skachkov; Shuang-Long Liu; Jia Chen; George Christou; Arthur Hebard; Xiao-Guang Zhang; Samuel Trickey; Hai-Ping Cheng | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b662e85983a9cd5e6e42cf/original/dipole-switching-by-intramolecular-electron-transfer-in-single-molecule-magnetic-complex-mn12o12-o2cr-16-h2o-4.pdf |
61537057cea2e9c72d011600 | 10.26434/chemrxiv-2021-6cxlq | First-Principles Plane-Wave-Based Exploration of Cathode and Anode Materials for Li and Na-ion Batteries involving Complex Nitrogen-based Anions | We present a first-principles study based on plane-wave derived Löwdin population analysis and other local bonding descriptors to investigate cathode and anode materials for lithium and sodium ion batteries, with a special emphasis on complex nitrogen chemistry. By comparing the Löwdin charges of commonly used electrode materials to other phases such as salts of dicyanamide and nanoporous carbon-based compounds, new conclusions of an improved intercalation behavior of the latter are derived. In addition, we explore the stability of the dicyanamide salts upon Li and Na removal, some of them resulting in dimerized structures. In particular, having a look at the different kinds of bonds and the corresponding covalency indicators reveals insights into the bonding changes during dimerization. Considering the astonishing thermal stability of metal dicyanamide salts, which are solid at room temperature, their electrochemical activity as well as non toxicity of alkali metal-based compounds, these materials are potential alternatives to commercially available electrodes, particularly as they show some flexibility in exhibiting anodic and cathodic behavior and allow for transition metal-free cathode materials. | Christina Ertural; Ralf P. Stoffel; Peter Christian Müller; Christian Alexander Vogt; Richard Dronskowski | Theoretical and Computational Chemistry; Inorganic Chemistry; Solid State Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61537057cea2e9c72d011600/original/first-principles-plane-wave-based-exploration-of-cathode-and-anode-materials-for-li-and-na-ion-batteries-involving-complex-nitrogen-based-anions.pdf |
636f1eccb58850373b492c01 | 10.26434/chemrxiv-2022-5v338 | Quasi-reversible photoinduced displacement of aromatic ligands from semiconductor nanocrystals | Organic-inorganic nanohybrids using semiconductor nanocrystals (NCs) coordinated with aromatic organic molecules have been widely studied in the fields of optoelectronic materials, such as solar cells, photocatalysis, and photon upconversion. In these materials, coordination bonds of ligand molecules are usually assumed to be stable during optical processes. However, this assumption is not always valid. In this study, we demonstrate that the coordination bonds between ligand molecules and NCs by carboxyl groups are displaced quasi-reversibly by light irradiation using zinc sulfide (ZnS) NCs coordinated with perylenebisimide (PBI) as a model system. Ultrafast spectroscopy and density functional theory calculations show that the photoinduced ligand displacement is driven by ultrafast hole transfer from PBI to ZnS NCs, and that the dissociated radical anion of PBI survives over the second timescale. This study opens up a new avenue for advanced photofunctional materials utilizing colloidal NCs, such as photocatalysts that can expose their active facets of NCs on demand, and sub-micropatterning of photoconductive circuits on solid-state NC films. | Daisuke Yoshioka; Yusuke Yoneda; I-Ya Chang; Hikaru Kuramochi; Kim Hyeon-Deuk; Yoichi Kobayashi | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Photochemistry (Physical Chem.); Physical and Chemical Processes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636f1eccb58850373b492c01/original/quasi-reversible-photoinduced-displacement-of-aromatic-ligands-from-semiconductor-nanocrystals.pdf |
62849bd53f1e7c502bc1eab0 | 10.26434/chemrxiv-2022-c0md8 | Growth of silicon carbide multilayers with varying preferred growth orientation | SiC multilayer coatings were deposited via thermal chemical vapor deposition (CVD) using
silicon tetrachloride (SiCl4) and various hydrocarbons under identical growth conditions, i.e.
at 1100 ℃ and 10 kPa. The coatings consisted of layers whose preferred growth orientation
alternated between random and highly <111>-oriented. The randomly oriented layers were
prepared with either methane (CH4) or ethylene (C2H4) as carbon precursor, whereas the highly
<111>-oriented layers were grown utilizing toluene (C7H8) as carbon precursor. In this work,
we demonstrated how to fabricate multilayer coatings with different growth orientations by
merely switching between hydrocarbons. Moreover, the success in depositing multilayer
coatings on both flat and structured graphite substrates has strengthened the assumption
proposed in our previous study that the growth of highly <111>-oriented SiC coatings using
C7H8 was primarily driven by chemical surface reaction. | Jing-Jia Huang; Christian Militzer; Charles Wijayawardhana; Urban Forsberg; Henrik Pedersen | Physical Chemistry; Materials Science; Multilayers; Thin Films; Surface; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62849bd53f1e7c502bc1eab0/original/growth-of-silicon-carbide-multilayers-with-varying-preferred-growth-orientation.pdf |
6169ed0135b406aeea15553a | 10.26434/chemrxiv-2021-4p7pq-v2 | Can prebiotic reaction systems survive in the wild? An interference chemistry approach | The origin of life occurred by a series of prebiotic reaction pathways (collectively a system) hosted in one or more geochemical environments (together forming an origin of life scenario). State-of-the-art prebiotic chemistry links together reactions to create systems, intended to be more representative of the diverse chemical pathways that may have proceeded on early Earth. By practical necessity, prebiotic systems chemistry must be investigated under simplified conditions in comparison to likely natural environments. The mismatch in complexity between lab and environment poses a challenge: how to build systems chemistry that is robust not only in the idealised conditions of a lab, but also under natural levels of environmental stress? Here, we propose and formalise a conceptual framework for such work: interference chemistry. We define interference chemistry as the interaction between prebiotic systems chemistry and the environmental scenarios proposed to host it. Natural environments in which prebiotic chemistry could have occurred are messy, containing many spectator ions, mineral phases, and spatially and temporally variable physical processes, e.g., wet/dry cycles. Each of these environmental variables may interfere either constructively or destructively with prebiotic pathways, respectively aiding or inhibiting their efficacy. Exploring interference chemistry for a reaction system will point towards favoured or disfavoured regions of environmental parameter space. To do so, innovation is needed in both the investigation of early planetary environmental conditions, and the continued incorporation of these constraints into experimental systems chemistry. We argue that interference chemistry provides a compelling way to assess combinations of system and environment, leading the way to increasingly prebiotically plausible scenarios for the origin of life on Earth. | Craig Walton; Paul B. Rimmer; Oliver Shorttle | Physical Chemistry; Organic Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6169ed0135b406aeea15553a/original/can-prebiotic-reaction-systems-survive-in-the-wild-an-interference-chemistry-approach.pdf |
61267dd2656369364419c7aa | 10.26434/chemrxiv-2021-90tc6 | Development and validation of AMBER-FB15-compatible force field parameters for phosphorylated amino acids | Phosphorylation of select amino acid residues is one of the most common tools for regulating protein structure and function. While computational modeling can be used to explore the detailed structural changes associated with phosphorylation, most molecular mechanics force fields developed for the simulation of phosphoproteins have been noted to be inconsistent with experimental data. In this work, we parameterize force fields for blocked dipeptide forms of the phosphorylated amino acids serine, threonine, and tyrosine using the ForceBalance software package with the goal of improving agreement with experiment for these residues. Our optimized force field, denoted as FB18, is parameterized using high-quality \textit{ab initio} potential energy scans and is designed to be fully compatible with the AMBER-FB15 protein force field. When utilized in MD simulations together with the TIP3P-FB water model, we find that FB18 consistently enhances the prediction of experimental quantities such as $^3J$ NMR couplings and intramolecular hydrogen-bonding propensities in comparison to previously published models. As was reported with AMBER-FB15, we also see improved agreement with the reference QM calculations in regions at and away from local minima. We thus believe that the FB18 parameter set provides a promising route for the further investigation of the varied effects of protein phosphorylation. | John P. Stoppelman; Tracey T. Ng; Paul S. Nerenberg; Lee-Ping Wang | Theoretical and Computational Chemistry; Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61267dd2656369364419c7aa/original/development-and-validation-of-amber-fb15-compatible-force-field-parameters-for-phosphorylated-amino-acids.pdf |
60c745c2842e65952fdb26af | 10.26434/chemrxiv.10255838.v1 | Orbital Shaped Standing Waves Using Chladni Plates | Chemistry
students are often introduced to the concept of atomic orbitals with a
representation of a one-dimensional standing wave. The classic example is the harmonic
frequencies which produce standing waves on a guitar string; a concept which is
easily replicated in class with a length of rope. From here, students are typically exposed to
a more realistic three-dimensional model, which can often be difficult to
visualize. Extrapolation from a
two-dimensional model, such as the vibrational modes of a drumhead, can be used
to convey the standing wave concept to students more easily. We have opted to use Chladni plates which may
be tuned to give a two-dimensional standing wave which serves as a cross-sectional
representation of atomic orbitals. The
demonstration, intended for first year chemistry students, facilitates the
examination of nodal and anti-nodal regions of a Chladni figure which students
can then connect to the concept of quantum mechanical parameters and their
relationship to atomic orbital shape. | Eric Janusson; Johanne Penafiel; Andrew Macdonald; Shaun MacLean; Irina Paci; J Scott McIndoe | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c2842e65952fdb26af/original/orbital-shaped-standing-waves-using-chladni-plates.pdf |
671747fcd433919392d13b5a | 10.26434/chemrxiv-2024-l31n8 | Electronic Absorption and Circular Dichroism Spectra of One-Dimensional Bay-Substituted Chiral PDIs: Effects of Intermolecular Interactions, Vibronic Coupling and Aggregate Size | Electronic circular dichroism (ECD) spectroscopy is the preferred tool for studying organic chiral supramolecules. However, it is a great challenge to experimentally clarify the contributions to ECD spectra from molecular vibrational motions and the intermolecular interactions, key factors for an efficient system architecture design of chemical sensors, catalysts or optoelectronics. Focusing on this issue, here, we per- form theoretical studies on the vibrationally resolved absorption and ECD spectra of two one dimensional bay-substituted chiral perylene diimides (PDIs) by employing the non-Markovian stochastic Schr¨odinger equation with respect to the model Hamiltonian in the diabatic representation, which includes the intramolecular local- ized excited states (LEs), inter molecular change-transfer excited states (CTEs) and the vibronic couplings (VC) as well. Our calculated results exhibit that the theoretical spectra with inclusion of VC effect agree better with the experimental ones than those without this effect, and that the difference between the traditional absorption spectra of two bay-substituted PDIs is much less obvious than that in their ECD spectra, veri- fied that ECD spectroscopy is sensitive to the absolute configuration and conformation of chiral supramolecules. We further make a comparison among the pure electronic spectra of aggregates with different aggregate size calculated by the time-dependent density functional theory, and the mixed exciton model with and without decoupling the LE and CTE states. It is shown that the hybridization between LE and CTE states results in the emergence of new peaks or trough in the high-energy band, and a significant deviation between the calculated ECD spectrum and that predicted by the exciton chirality rule. It is further shown that the ECD spectra of oligomers exhibit an odd-even alternation pattern with changes in aggregate size. | Yuchuan Xu; Yi Zhao; Wanzhen Liang | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671747fcd433919392d13b5a/original/electronic-absorption-and-circular-dichroism-spectra-of-one-dimensional-bay-substituted-chiral-pd-is-effects-of-intermolecular-interactions-vibronic-coupling-and-aggregate-size.pdf |
661fcd6d91aefa6ce1bf70b2 | 10.26434/chemrxiv-2024-04cx2 | Spectator exciton effects in nanocrystals III: Unveiling the stimulated emission cross section in quantum confined CsPbBr3 nanocrystals | Quantifying stimulated emission in semiconductor nanocrystals (NCs) remains challenging due to masking of its effects on pump-probe spectra by excited state absorption and ground state bleaching signals. Absence of this defining photo-physical parameter in turn impedes assignment of band edge electronic structure in many of these important fluorophores. Here we employ a generally applicable 3-pulse ultrafast spectroscopic method coined the “Spectator Exciton” (SX) approach to measure stimulated-emission efficiency in quantum confined inorganic perovskite CsPbBr3 NCs, band edge electronic structure of which is the subject of lively ongoing debate. Our results show that in 5-6 nm CsPbBr3 NCs, a single exciton bleaches more than half of the intense band edge absorption band, while the cross section for stimulated emission from the same state is nearly 6 times weaker. Discussion of these findings in light of several recent electronic structure models for this material proves them unable of simultaneously explaining both measures. proving the importance of this new input to resolving this debate. Along with femtosecond time resolved photoluminescence measurements on the same sample, SX results also verifies that biexciton interaction energy is intensely attractive with a magnitude of ~80 meV. In light of this observation, our previous suggestion that bi-exciton interaction is repulsive is reassigned to hot phonon induced slowdown of carrier relaxation leading to direct Auger recombination from an excited state. The mechanism behind the extreme slowing of carrier cooling after several stages of exciton recombination remains to be determined. | Apurba De; Soumyadip Bhunia; Yichao Cai; Tal Binyamin; Lioz Etgar ; Sanford Ruhman | Physical Chemistry; Materials Science; Nanoscience; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661fcd6d91aefa6ce1bf70b2/original/spectator-exciton-effects-in-nanocrystals-iii-unveiling-the-stimulated-emission-cross-section-in-quantum-confined-cs-pb-br3-nanocrystals.pdf |
60c75922ee301c56f6c7b848 | 10.26434/chemrxiv.14632611.v1 | Phosphorylation of the NBDY Microprotein Promotes Dissociation of Biomolecular Condensates | This study reports detection of specific phosphorylation sites installed on a small open reading frame-encoded polypeptide or microprotein called NBDY. NBDY phosphorylation sites were mapped using phosphoproteomics and antibody-based validation. NBDY is phosphorylated during growth factor signaling and cell division, and quantitative fluorescence microscopy was used to show that NBDY phosphorylation is required for disappearance of cytoplasmic RNA-protein granules called P-bodies during these cellular processes. Because P-bodies have properties of liquid-liquid phase separated membraneless orgaenelles, reductionist system to investigate NBDY phase separation. Purified NBDY was shown to form complex coacervates in the presence of RNA via fluorescence microscopy and turbidity measurements, and phosphorylation by a kinase in vitro promotes liquid phase remixing. | Zhenkun Na; Yang Luo; Danica
S. Cui; Alexandra Khitun; Stephanie Smelyansky; J. Patrick Loria; Sarah Slavoff | Mass Spectrometry; Microscopy; Biochemistry; Biophysics; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75922ee301c56f6c7b848/original/phosphorylation-of-the-nbdy-microprotein-promotes-dissociation-of-biomolecular-condensates.pdf |
62fd2adf60751b8cc4081dce | 10.26434/chemrxiv-2022-zp30w | Ultrafast photophysical studies of sulfonated polyaniline
in aqueous medium by femtosecond transient absorption
spectroscopy | In our previous work (Khatun et al., J. Phys. Chem. A 122 (2018) 7089-7098), synthesis and characterization of sulfonated polyaniline (SPANI) were discussed. Photophysical properties of SPANI in aqueous medium were also investigated using steady state spectroscopic techniques, which suggested the co-existence of two conformations (‘A’ and ‘B’) of SPANI in the normal working low acidic medium. Also, combined red-edge effect was observed from the two conformations of SPANI in aqueous medium. In the present work, a detailed investigation is carried out on the ultrafast photophysical properties of SPANI in aqueous medium by employing femtosecond transient absorption spectroscopy based on pump-probe technique. It is found that excited state absorption from the S1 state of SPANI in aqueous medium to higher electronic states originates mostly due to the conformation ‘A’ in the whole spectral range and very weakly due to the conformation ‘B’ on the blue side of the spectra. These new findings are extremely important keeping in mind various potential applications of SPANI in the field of polymer optoelectronics. | Rijia Khatun; Koushik Majhi; Subrata Sinha | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fd2adf60751b8cc4081dce/original/ultrafast-photophysical-studies-of-sulfonated-polyaniline-in-aqueous-medium-by-femtosecond-transient-absorption-spectroscopy.pdf |
611bd9165322c141b203b92a | 10.26434/chemrxiv-2021-12p4x-v2 | Boosting Palladium Catalyzed Aryl–Nitro Bond Activation Reaction by Understanding the Electronic, Electrostatic and Polarization Effect: A Computational Study from Basic Understanding to Ligand Design | Although cross coupling reaction with nitroarene as the electrophilic partner has gained high interest recently, the palladium catalyzed aryl–nitro bond activation reaction still requires rather high temperature and hash condition. In this work, based on Nakao’s nitrogen heterocyclic carbene (NHC) ligand, we systematically explored the substituent effect on the oxidative addition step, the known rate determining step of the whole reaction, by density functional theory (DFT) calculation. The key aryl ring on the ligand skeleton, namely Ring A, acts as a π-donor and stabilizes the palladium center of the transition state, as shown by Extended Transition State Natural Orbital of Chemical Valance (ETS-NOCV) analysis, and thus an electron-rich Ring A is expected to lower the barrier. On the other hand, however, the polarization and electrostatic effects were shown to be as or even more important, although they were often ignored before. These effects originate from through-space interaction with the nitro group in the resting state, and the overall effect is that any polarizable or partly negative group nearby the ortho- or meta¬- site of Ring A is harmful for the reaction. Based on these discoveries, we proposed a list of guidelines for successful ligand development, and designed several new ligands. These ligands exhibit significantly lower barrier than the reported Nakao’s ligand by as large as ~5 kcal/mol in both gas phase and solvation, and might be good candidates for further experimental study. | Yumiao Ma; Zhaohong Wang | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Bond Activation; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611bd9165322c141b203b92a/original/boosting-palladium-catalyzed-aryl-nitro-bond-activation-reaction-by-understanding-the-electronic-electrostatic-and-polarization-effect-a-computational-study-from-basic-understanding-to-ligand-design.pdf |
60c7453bbb8c1a0cd53da646 | 10.26434/chemrxiv.8170367.v2 | The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains | <div>
<div>
<div>
<p>Lipid-linked oligosaccharides (LLOs) plays an important role in the N-glycosylation
pathway as the donor substrate of oligosaccharyltransferases (OSTs), which are respon-
sible for the en bloc transfer of glycan chains onto a nascent polypeptide. The lipid
component of LLO in both eukarya and archaea consists of a dolichol, and an unde-
caprenol in prokarya, whereas the number of isoprene units may change between species.
Given the potential relevance of LLOs and their related enzymes to diverse biotechno-
logical applications, obtaining reliable LLO models from distinct domains of life could
support further studies on complex formation and their processing by OSTs, as well
as protein engineering on such systems. In this work, molecular modeling, such as
quantum mechanics calculations, molecular dynamics simulations, and metadynamics
were employed to study eukaryotic (Glc3-Man9-GlcNAc2-PP-Dolichol), bacterial (Glc1-
GalNAc5-Bac1-PP-Undecaprenol) and archaeal (Glc1-Man1-Gal1-Man1-Glc1-Gal1-Glc1-
P-Dolichol) LLO in membrane bilayers. Microsecond molecular dynamics simulations
and metadynamics calculations of LLOs revealed that glycan chains are more prone to
interact with the membrane lipid head groups, while the PP linkages are positioned at
the lipid phosphate head groups level. Dynamics of isoprenoid chains embedded within
the bilayer are described and membrane dynamics and its related properties are also
investigated. Overall, there are similarities regarding the structural and dynamics of
the eukaryotic, the bacterial and the archaeal LLOs in bilayers, which can support the
comprehension of their association with OSTs. This data may support future studies
on the transferring mechanism of the oligosaccharide chain to an acceptor protein. </p>
</div>
</div>
</div> | Pablo Ricardo Arantes; Conrado Pedebos; Marcelo D. Poleto; Laércio Pol-Fachin; Hugo Verli | Biochemistry; Bioinformatics and Computational Biology; Biophysics; Chemical Biology; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453bbb8c1a0cd53da646/original/the-lazy-life-of-lipid-linked-oligosaccharides-in-all-life-domains.pdf |
643d0c5208c86922ff2713ea | 10.26434/chemrxiv-2023-r1djt | Spatiotemporally tuned colloidal phoretic leap in an altering multivalent interaction field | Multivalency-mediated interactions play an important role in governing dynamicity and self-assembly in biological systems. Despite its significance in supramolecular material chemistry to biomedicine, the role of multivalency in modulating colloidal transport or phoresis remains largely unexplored. Here, combining theory and experiment, we report diffusiophoretic motion of a positively-charged catalytic microbead during its multivalent interactions with a gradient of adenosine mono-, di- and trinucleotides (AM/D/TP) both in micro- and macroscale regimes. We find that the extent of drift diminishes with increasing number of phosphates. Subsequently, we exhibit nucleotide-specificity of the colloid in catalyzing a proton-transfer reaction, which in turn alters its phoretic behaviour. Finally, we demonstrate spatiotemporal control over colloidal phoretic leap (a sudden increase in phoretic velocity) and population dynamics driven by enzymatic downregulation of multivalent interactivity, which has been achieved by controlling ATP hydrolysis in situ. These findings open up avenues for utilizing multivalent surface-mediated catalytic activity to achieve precise control of particle transport relevant to reaction-diffusion driven spatiotemporal processes. | Ekta Shandilya; Bhargav Rallabandi; Subhabrata Maiti | Catalysis; Nanoscience; Chemical Engineering and Industrial Chemistry; Nanocatalysis - Catalysts & Materials; Nanofluidics; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d0c5208c86922ff2713ea/original/spatiotemporally-tuned-colloidal-phoretic-leap-in-an-altering-multivalent-interaction-field.pdf |
672a3e93f9980725cf2f6517 | 10.26434/chemrxiv-2024-kb13g | Calcium Aluminate Cement Hydration Under the Influence of Mineral Acids | In technical mortars and refractory concrete, the reactivity of calcium aluminate cement (CAC) is typically controlled by retarders and accelerators. This study examines the retarding impact of five strong acids (HCl, HNO3, HClO4, H2SO4, and H3PO4) on CAC hydration (1) in dilute suspensions at a water-to-solid (w/s) ratio of 100, and (2) in pastes at a w/s of 0.3. Doing so, we identified several factors that affect the dissolution and hydration of CAC. In dilute suspensions, in-situ monitoring of the pH and conductivity reveals that the acids delay the initial dissolution of monocalcium aluminate (CA). The inhibition time depends exponentially on the proton concentration, and linearly on the available CA surface area, which is partially explained by the preferential formation of Al(OH)3 suggested by thermodynamic modeling. Notably, the acids’ efficiency varies at equimolar proton dosages. For H3PO4, we explain the outstanding inhibition efficiency by the joint formation of hydroxylapatite and Al(OH)3. For the other acids, the dissolution inhibition power follows an anion-specific sequence sulfate > chloride > nitrate > perchlorate, which aligns with the Hofmeister series and suggests a stabilization of calcium ion solvation by the anion. Isothermal calorimetry experiments performed on pastes show that the retardation order of these acids (H3PO4 > HClO4 > HNO3 > H2SO4 > HCl) differs from that observed at w/s of 100. Phosphoric acid still displays exceptional retardation properties suggesting a unique mechanism of action most likely related to early hydroxylapatite and Al(OH)3 formation. For the other acids, Al(OH)3 and anion-containing AFm phases formation may explain the differences in retardation maximum. | Lukas Deffner; Marie Collin; Torben Gädt | Inorganic Chemistry; Inorganic Acid/Base Chemistry; Kinetics and Mechanism - Inorganic Reactions; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a3e93f9980725cf2f6517/original/calcium-aluminate-cement-hydration-under-the-influence-of-mineral-acids.pdf |
6686fee6c9c6a5c07a4d962e | 10.26434/chemrxiv-2024-n6mzr | Dual Emissive and Long-lived Copper(I) Mesoionic Carbene Luminophores | We describe the synthesis of a family of photoemissive linear Cu(I) complexes bearing mesoionic carbenes (MIC) and amido ligands of the general formula Cu(MIC)NR2 (NR2 = carbazolide, diphenylamide). Careful tuning of the electronic and structural properties of both ligands enables modulation of the emission wavelengths from 400 to 520 nm. We observe that the emission mechanism is highly dependent on the nature of the ligands and exhibits a dichotomy in behavior. Complexes bearing diphenylamide ligands CuMesMICNaphNPh2 and CuMesMIC3,5-CF3PhNPh2 and complexes containing a combination of carbazolide and electron-rich MIC ligands such as CuMesMICNaphCz and Cu3,5-MePhMICNaph Cz emit from locally excited (LE) states, while complexes bearing electron-rich carbazolide and electron-poor MIC ligands emit from charge transfer (CT) states. A rational design of the ligands enabled us to exert exquisite control over the nature of the absorption and emission mechanisms of these emissive linear CuI complexes. | Felix León; Changfeng Si; Chenfei Li; Adisak Thanetchaiyakup; Thomas Papineau; Denis Jacquemin; Han Sen Soo; Eli Zysman-Colman | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligand Design; Spectroscopy (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6686fee6c9c6a5c07a4d962e/original/dual-emissive-and-long-lived-copper-i-mesoionic-carbene-luminophores.pdf |
60c7424e842e651509db2043 | 10.26434/chemrxiv.8251076.v1 | Current Vortices in Aromatic Carbon Molecules | <div><div><div><p>The local current flow through three small aromatic carbon molecules, namely benzene, naphthalene and anthracene, is studied. Applying density functional theory and the non-equilibrium Green’s function method for transport, we demonstrate that pronounced current vortices exist at certain electron energies for these molecules. The intensity of these circular currents, which appear not only at the anti-resonances of the transmission but also in vicinity of its maxima, can exceed the total current flowing through the molecular junction and generate considerable magnetic fields. The π electron system of the molecular junctions is emulated experimentally by a network of macroscopic microwave resonators. The local current flows in these experiments confirm the existence of current vortices as a robust property of ring structures. The circular currents can be understood in terms of a simple nearest-neighbor tight-binding Hückel model. Current vortices are caused by the interplay of the complex eigenstates of the open system which have energies close-by the considered electron energy. Degeneracies, as observed in benzene and anthracene, can thus generate strong circular currents, but also non-degenerate systems like naphthalene exhibit current vortices. Small imperfections and perturbations can couple otherwise uncoupled states and induce circular currents.</p></div></div></div> | Thomas Stegmann; John A. Franco-Villafañe; Yenni P. Ortiz; Michael Deffner; Carmen Herrmann; Ulrich Kuhl; Fabrice Mortessagne; Francois Leyvraz; Thomas H. Seligman | Nanodevices; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Quantum Mechanics; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7424e842e651509db2043/original/current-vortices-in-aromatic-carbon-molecules.pdf |
62a14aeea784d1c9f0783de3 | 10.26434/chemrxiv-2022-1c530 | Catalytic Photochemical Enantioselective α-Alkylation with Pyridinium Salts | We have developed a chiral amine catalyzed enantioselective α-alkylation of aldehydes with amino acid derived pyridinium salts as alkylating reagents. The reaction proceeds in the presence of visible light (390 nm) and in the absence of a photocatalyst via a light activated charge-transfer complex. We apply this photochemical stereoconvergent process to the total synthesis of the lignan natural products (–)-enterolactone and (–)-enterodiol. Mechanistic studies support the ground-state complex-ation of the reactive components followed by divergent charge-transfer processes involving catalyst-controlled radical chain and in-cage radical recombination steps. | Santhivardhana Reddy Yetra; Nathan Schmitt; Uttam Tambar | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a14aeea784d1c9f0783de3/original/catalytic-photochemical-enantioselective-alkylation-with-pyridinium-salts.pdf |
6526a29745aaa5fdbbc5d8d6 | 10.26434/chemrxiv-2023-qzhr8 | A fluorescence approach for an online measurement technique of atmospheric microplastics | Microplastic particles in the atmosphere are regularly detected in urban areas as well as in very remote locations. Yet the sources, chemical transformation, transport, and abundance of airborne microplastics still remains largely unexplained. Therefore, their impact on health, weather and climate related processes lacks comprehensive understanding. Single particle detection presents a substantial challenge due to its time-consuming process and is conducted solely offline. To get more information about the distribution, fluxes and sources of microplastics in the atmosphere, a reliable and fast online measurement technique is of utmost importance. Here we demonstrate the use of autofluorescence of microplastic particles for their online detection with a high sensitivity towards different widely used polymers. We deploy online single particle fluorescence spectroscopy with a Wideband Integrated Bioaerosol Sensor WIBS 5/NEO (Droplet Measurement Technologies), which enables single particle fluorescence measurements at two excitation wavelengths (280 nm and 370 nm) and in two emission windows (310 – 400 nm and 420 – 650 nm). We investigated shredded (< 100 μm) everyday plastic products (drinking bottles, yogurt cups) and purchased pure powders of polyethylene terephthalate (PET), polyethylene (PE) and polypropylene (PP). For that broad range of typical plastic products analyzed, we detected fluorescence on a single particle level using the WIBS. The online detection is possible even for particles smaller than 2 μm, with a remarkable detection efficiency of microplastic particles from a PET bottle as small as 1.2 μm with 95% effectivity. Comparison with biological aerosol reveals that microplastics can be distinguished from two abundant pollen species and investigation of the complete fluorescence excitation emission maps of all samples show that online identification of microplastics might be possible with fluorescence techniques if multiple channels are available. | Jürgen Gratzl; Teresa M. Seifried; Dominik Stolzenburg; Hinrich Grothe | Physical Chemistry; Polymer Science; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6526a29745aaa5fdbbc5d8d6/original/a-fluorescence-approach-for-an-online-measurement-technique-of-atmospheric-microplastics.pdf |
6514b5ddade1178b243eaeae | 10.26434/chemrxiv-2023-rbr9x | Compound specific isotope analysis to evaluate in situ transformation of a complex mixture of substituted chlorobenzenes in a pilot constructed wetland system | Constructed wetlands can be a suitable remediation technique for the treatment of industrial contaminants via transfer (i.e., non-destructive) and transformation (i.e., destructive) processes. Providing direct evidence of in situ transformation using concentrations and biogeochemical parameters alone is challenging. Compound specific isotope analysis (CSIA) is a widely used tool to assess in situ transformation of contaminants based on changes in their stable isotope signatures. In this work, we evaluated the potential of CSIA to identify and possibly quantify the in situ transformation of six NO2- and NH2-chlorobenzenes in complex aqueous samples from a pilot constructed wetland system. No significant changes in δ13C, i.e., ≤2‰ were observed for any of the target compounds despite the contaminant concentration decreased by more than 99% between the inlet and outlet of the system. Using multi-element CSIA of carbon, hydrogen, and nitrogen and laboratory-derived isotope enrichment factors, we successfully identified and quantified the extent of in situ transformation of 2,3-dichloroaniline (2,3-DCA) in the pilot constructed wetlands. The isotopic trends provide evidence for aerobic biotransformation as a dominant pathway in the surface flow planted wetlands; whereas sorption was identified as the likely process in planted and unplanted upflow gravel bed wetlands during the initial wetland operation periods. Another major contaminant from the NO2-chlorobenzene group, i.e., 2-chloronitrobenzene (2-CNB), showed negligible δ13C, and small δ2H (±20‰) and δ15N (±2‰) isotope fractionation. No laboratory-controlled CSIA studies are yet available for 2-CNB biotransformation to characterize transfer and transformation processes. This study highlights the applicability of CSIA as a quantitative tool for 2,3-DCA in dynamic environmental conditions of wetlands and the need for pathway-specific isotope enrichment factors for the successful CSIA application of other target compounds. | Shamsunnahar Suchana; Line Lomheim; Elizabeth Edwards; Paola Barreto Quintero; Elizabeth Erin Mack; Silvia Mancini; Elodie Passeport | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6514b5ddade1178b243eaeae/original/compound-specific-isotope-analysis-to-evaluate-in-situ-transformation-of-a-complex-mixture-of-substituted-chlorobenzenes-in-a-pilot-constructed-wetland-system.pdf |
60c74d36bb8c1a802e3db574 | 10.26434/chemrxiv.12599618.v1 | Diagnosis of Fatty Liver Disease by a Bright, Multiphoton-Active and Lipid-Droplet-Specific AIEgen with Nonaromatic Rotors | Fatty liver disease (FLD) has become an increasing global health risk. However, an accurate diagnosis of FLD at an early stage remains a great challenge due to lack of suitable imaging tools. To this end, we developed the first fluorescent two-photon aggregationinduced emission (AIE) luminogen ABCXF for high-contrast imaging of FLD tissue. ABCXF has a large Stokes shift, good two-photon absorption cross-section, bright red emission, high fluorescence quantum yield in solid state, and excellent photostability. It shows abnormal intramolecular charge transfer effect instead of twisted intramolecular charge transfer effect in polar solvents. Photophysical and crystal data demonstrated that it exhibits nonaromatic rotors - trifluoromethyto contribute to its AIE effect. Biocompatible lipid droplet-targeting ABCXF can selectively light up lesions in the FLD tissue with a high signal-to-noise ratio. It shows superior imaging performances compared to Oil Red O. Thus, ABCXF can be a powerful tool for the diagnosis and evaluation of FLD from a liver biopsy. | Hojeong Park; Shijie Li; Guangle Niu; Haoke Zhang; Zhuoyue Song; Qing Lu; Jun Zhang; Chao Ma,; Ryan Tsz Kin Kwok; Jacky W. Y. Lam; Kam Sing Wong; Xiaoqiang Yu; Qingping Xiong; Ben Zhong Tang | Aggregates and Assemblies; Biological Materials; Dyes and Chromophores | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d36bb8c1a802e3db574/original/diagnosis-of-fatty-liver-disease-by-a-bright-multiphoton-active-and-lipid-droplet-specific-ai-egen-with-nonaromatic-rotors.pdf |
6523e580bda59ceb9a2c052a | 10.26434/chemrxiv-2023-2ccrw | Impedance of nanocapacitors from molecular simulations to understand the dynamics of confined electrolytes | Nanoelectrochemical devices have become a promising candidate technology across various applications, including sensing and energy storage, and provide new platforms for studying fundamental properties of electrode/electrolyte interfaces. In this work, we employ constant-potential molecular dynamics simulations to investigate the impedance of gold-aqueous electrolyte nanocapacitors, exploiting a recently-introduced fluctuation-dissipation relation. In particular, we relate the frequency-dependent impedance of these nanocapacitors to the complex conductivity of the bulk electrolyte in different regimes, and use this connection to design simple but accurate equivalent circuit models. We show that the electrode/electrolyte interfacial contribution is essentially capacitive and that the electrolyte response is bulk-like even when the interelectrode distance is only of a few nanometers, provided that the latter is sufficiently large compared to the Debye screening length. We extensively compare our simulation results with spectroscopy experiments and predictions from analytical theories. This work opens new avenues for the molecular interpretation of impedance measurements, and offers valuable contributions for future developments of accurate coarse-grained representations of confined electrolytes. | Giovanni Pireddu; Connie Fairchild; Samuel Niblett; Stephen J. Cox; Benjamin Rotenberg | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanodevices; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6523e580bda59ceb9a2c052a/original/impedance-of-nanocapacitors-from-molecular-simulations-to-understand-the-dynamics-of-confined-electrolytes.pdf |
62f173a442ddf55627b3ebce | 10.26434/chemrxiv-2022-r18wr | Particle or Cluster: On the Atomic Structure of the Seeds Used in Gold Nanoparticle Synthesis | Seed-mediated synthesis strategies, in which small nanoparticle precursors are added to a growth solution to initiate heterogeneous nucleation, are among the most prevalent, simple, and productive methodologies for generating well-defined colloidal anisotropic nanostructures. Here, we identify the majority component in the seed solution as an atomically-precise gold nanocluster, consisting of a 32 atom Au core with 8 halide ligands and 12 neutral ligands constituting a bound ion pair between a halide and the cationic surfactant: Au32X8[AQA+•X-]12 (X = Cl, Br; AQA = alkyl quaternary ammonium). Ligand exchange is dynamic and versatile, occurring on the order of minutes and allowing for the formation of 48 distinct Au32 clusters with AQAX (alkyl quaternary ammonium halide) ligands. Anisotropic nanoparticle syntheses seeded with solutions enriched in Au32X8[AQA+•X-]12 show narrower size distributions and fewer impurity particle shapes, indicating the importance of this cluster as a precursor to the growth of well-defined nanostructures. | Liang Qiao; Nia Pollard; Ravithree Senanayake; Zhi Yang; Minjung Kim; Arzeena Ali; Minh Tam Hoang; Nan Yao; Yimo Han; Rigoberto Hernandez; Andre Clayborne; Matthew Jones | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Ligands (Inorg.); Theory - Inorganic; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f173a442ddf55627b3ebce/original/particle-or-cluster-on-the-atomic-structure-of-the-seeds-used-in-gold-nanoparticle-synthesis.pdf |
644f5f5f80f4b75b5369fbff | 10.26434/chemrxiv-2023-lglgb | Electron configurations and the group 3 question | Twelve arguments based on or associated with electron configurations of the d or f block elements, absent of any other considerations, support (a) cerium-thorium and lutetium-lawrencium as the first and last dyads of the f-block; and hence (b) Group 3 as Sc-Y-La-Ac, on regularity grounds. The least common form of periodic table with Group 3 as Sc-Y-Lu-Lr does not accommodate the impact of the delayed appearance of the first f electron. | Rene Vernon | Inorganic Chemistry; Chemical Education; Chemical Education - General; Inorganic Acid/Base Chemistry; Lanthanides and Actinides | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644f5f5f80f4b75b5369fbff/original/electron-configurations-and-the-group-3-question.pdf |
61ed0983c18d6735d481b290 | 10.26434/chemrxiv-2022-ld189 | Thermal Functionalization of Alkanes with Carbon Electrophiles | Alkane functionalization with carbon-electrophiles remains virtually unexplored under thermo-driven hydrogen atom transfer (HAT) conditions due to a challenge of integrating oxidation and reduction in a single operation. We report here a Ni-catalyzed arylation and alkylation of alkane C‒H bonds with organohalides to forge C(sp3)‒C bonds by merging easily accessible Zn and tBuOOtBu (DTBP) as the external reductant and oxidant. The mild and easy-to-operate protocol enables facile carbofunctionalization of N-/O-α- and cyclohexane CH bonds, and preparation of a number of bioactive compounds and drug derivatives. Preliminary mechanistic studies implied a Ni(I)-mediated DTBP reduction followed by alkane HAT to tBuO radical. The marked compatibility of Zn and DTBP with nickel-catalysis may invoke the development of external oxidant and reductant co-trigged thermoredox bond forming approaches based upon challenging substrates. | Yuxin Gong; Lei Su; Zhaodong Zhu; Yang Ye; Hegui Gong | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ed0983c18d6735d481b290/original/thermal-functionalization-of-alkanes-with-carbon-electrophiles.pdf |
66e6e7dd12ff75c3a16735c7 | 10.26434/chemrxiv-2024-cr182 | Accelerated Zymonic Acid Formation from Pyruvic Acid at the Interface of Aqueous Nanodroplets | To explore the role of the liquid interface in mediating reactivity in small compartments, the formation kinetics of zymonic acid (ZA) is measured in submicron aerosols (average radius = 240 nm) using mass spectrometry. Formation of ZA, from a condensation reaction of two pyruvic acid (PA) molecules, proceeds over days in bulk solutions, while in submicron aerosols occurs in minutes. The experimental results are replicated in a kinetic model using an apparent interfacial reaction rate coefficient of krxn = 0.9 ± 0.2 × 10-3 M-1 · s-1. The simulation reveals that surface activity of PA coupled with enhanced interfacial reaction rate drive accelerated ZA formation in aerosols. Experimental and simulated results provide compelling evidence that the condensation reaction of PA occurs exclusively at the aerosol interface with a reaction rate coefficient that is enhanced by 4 orders of magnitudes (~104) relative to what is estimated for macroscale solutions. | Pyeongeun Kim; Ryan Reynolds; Alexandra Deal; Veronica Vaida; Musahid Ahmed; Kevin Wilson | Physical Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Chemical Kinetics; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e6e7dd12ff75c3a16735c7/original/accelerated-zymonic-acid-formation-from-pyruvic-acid-at-the-interface-of-aqueous-nanodroplets.pdf |
6762d904fa469535b9fc7a90 | 10.26434/chemrxiv-2024-f49zl | Semi-artificial leaf interfacing organic semiconductors and enzymes for solar fuel synthesis | Photoelectrochemical biohybrids combine the advantages of light harvesting semiconductors and biocatalysts into a single compact device. However, limited device stability, the use of toxic elements and non-innocent external components (buffers, mediators or sacrificial reagents) makes a sustainable artificial photosynthetic reaction, where fuel production is coupled to water oxidation, difficult to achieve. Here, we introduce organic photoelectrodes connected to an inverse opal TiO2 matrix that hosts efficient hydrogenase or formate dehydrogenase, driving direct solar fuel synthesis. By co-immobilising carbonic anhydrase, supported by simulations and spectroscopic investigations, the PCE10:EH-IDTBR photobiocathodes generate unprecedented photocurrent densities of up to −8 mA cm−2 in a pH neutral bicarbonate solution, attaining stable H2 production or selective CO2-to-formate conversion over 10 h. Semi-artificial photosynthesis is achieved by assembling the photobiocathode with a BiVO4 photoanode in an artificial leaf device for unassisted CO2 reduction coupled to O2 evolution, attaining a faradaic yield of 87% over 24 h of operation. | Celine Wing See Yeung; Yongpeng Liu; Samuel Cobb; Virgil Andrei; Ana Coito; Rita Manuel; Inês Pereira; Erwin Reisner | Catalysis; Energy; Biocatalysis; Electrocatalysis; Photovoltaics; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762d904fa469535b9fc7a90/original/semi-artificial-leaf-interfacing-organic-semiconductors-and-enzymes-for-solar-fuel-synthesis.pdf |
650f2f80b927619fe7afa9a5 | 10.26434/chemrxiv-2023-k6wbl | Optical and EPR Detection of a Triplet Ground State Phenyl Nitrenium Ion | Nitrenium ions are important reactive intermediates participating in synthetic chemistry and biological processes. Phenyl nitrenium ions (Ph-NH+) typically have closed-shell singlet ground states with large singlet–triplet energy gaps, while little is known of triplet nitrenium ions regarding their reactivity, lifetimes, spectroscopic signatures, and electronic configurations. In this work, m-pyrrolidinyl-phenyl hydrazine hydrochloride (1) is synthesized as the photoprecursor to photochemically generate the corresponding m-pyrrolidinyl-phenyl nitrenium ion (2), which is computed to adopt a π,π* triplet ground state. A combination of femtosecond (fs-) and nanosecond (ns-) transient absorption (TA) spectroscopy, cryogenic continuous-wave electronic paramagnetic resonance (CW-EPR) spectroscopy, computational analysis, and photoproduct studies, elucidated the complete photolysis pathway of this photoprecursor and offers the first direct experimental detection of a ground state triplet nitrenium ion. Upon photoexcitation, 1 is optically pumped to singlet excited states, followed by internal conversion (IC) to S1 on the sub-picosecond timescale, where bond heterolysis occurs and the NH3 leaving group is extruded in 1.8 ps, generating a vibrationally-hot, spin-conserving closed-shell singlet phenyl nitrenium ion (12) that undergoes vibrational cooling in 19 ps. Subsequent intersystem crossing (ISC) takes place in 534 ps, yielding the ground state triplet phenyl nitrenium ion (32), with a lifetime of 0.8 μs. Unlike electrophilic singlet phenyl nitrenium ions, this triplet phenyl nitrenium reacts through sequential H atom abstractions, resulting in the eventual formation of the reduced m-pyrrolidinyl-aniline as the predominant stable photoproduct. Supporting the triplet ground state, continuous irradiation of 1 in a glassy matrix at 80 K forms a paramagnetic species consistent with the triplet nitrenium ion by cryogenic CW-EPR spectroscopy. | Yunfan Qiu; Lili Du; Sarah Cady; David Phillips; Arthur Winter | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650f2f80b927619fe7afa9a5/original/optical-and-epr-detection-of-a-triplet-ground-state-phenyl-nitrenium-ion.pdf |
60c745399abda2276ef8c4d4 | 10.26434/chemrxiv.9974699.v1 | High Resolution Photoelectron Spectroscopy of Cryogenically-Cooled NO3ˉ | <p></p><p>High-resolution
anion photoelectron spectra of cryogenically cooled NO<sub>3</sub>ˉ anions obtained
using slow photoelectron velocity-map imaging are presented and provide new
insight into the vibronic structure of the corresponding neutral radical. A
combination of improved spectral resolution, measurement of energy-dependent
intensity effects, temperature control, and comparison to theory allows for
full assignment of the vibronic features observed in this spectrum. We obtain a
refined electron affinity of 3.9289(14) eV for NO<sub>3</sub>. Further, the
appearance of Franck-Condon forbidden transitions from vibrationally cold
anions to neutral states with excitation along the NO<sub>3</sub> <i>v</i><sub>4</sub>
mode confirms that these features arise from vibronic coupling with the excited state of NO<sub>3</sub> and are not hot bands as has
been suggested. Together, the suite of experimental and simulated results
provides clear evidence that the <i>v</i><sub>3</sub> fundamental of NO<sub>3</sub>
resides near 1050 cm<sup>−1</sup>, addressing a long-standing controversy
surrounding this vibrational assignment.</p>
<p> </p><br /><p></p> | Mark Babin; Jessalyn DeVine; John F. Stanton; Daniel Neumark; Martin DeWitt | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745399abda2276ef8c4d4/original/high-resolution-photoelectron-spectroscopy-of-cryogenically-cooled-no3.pdf |
63f8e25732cd591f126b821d | 10.26434/chemrxiv-2023-rlbk8 | Heteroleptic Tetravalent 𝛽-Diketonate Molybdenum Complexes as Highly Active Catalysts for Allylic Substitution Reactions | The synthesis and characterization of a series of Mo(IV) bis-𝛽-diketonate (^(R)diket, R = Me, tBu, Ph) dichloride (RMo^(IV)Cl_2) and bistriflate (^(R)Mo^(IV)(OTf)_2) complexes are reported. All complexes are characterized in solid and solution state by XRD and 1H NMR spectroscopy. We demonstrate that the bistriflate complexes constitute highly active catalysts for allylic substitution reactions. | Fabio Masero; Victor Mougel | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f8e25732cd591f126b821d/original/heteroleptic-tetravalent-diketonate-molybdenum-complexes-as-highly-active-catalysts-for-allylic-substitution-reactions.pdf |
61b1e15f9e56b8f9a7b3eeaa | 10.26434/chemrxiv-2021-xzkl8 | Gently Does It!: In Situ Preparation of Alkali Metal - Solid Electrolyte Interfaces for Photoelectron Spectroscopy | The key charge transfer processes in energy storage devices occur at the electrode-electrolyte interface, which is typically buried making it challenging to access the interfacial chemistry. In the case of Li-ion batteries, metallic Li electrodes hold promise for increasing energy and power densities, and when used in conjunction with solid electrolytes (SEs) adverse safety implications associated with dendrite formation in organic liquid electrolytes can potentially be overcome. To better understand the stability of SEs when in contact with alkali metals and the reactions that occur, here we consider the deposition of thin (~10 nm) alkali metal films onto SE surfaces, that are thin enough that X-ray photoelectron spectroscopy can probe the buried electrode-electrolyte interface. We highlight the importance of in situ alkali metal deposition, by assessing the contaminant species that are present after glovebox handling and the use of ‘inert’ transfer devices. Consequently, we compare and contrast three available methods for in situ alkali-metal deposition; Li sputter deposition, Li evaporation, and Li plating induced by e− flood-gun irradiation. Studies on both a sulphide SE (Li6PS5Cl), and a single-layer graphene probe surface reveal that the more energetic Li deposition methods, such as sputtering, can induce surface damage and interfacial mixing that is not seen with thermal evaporation. This indicates that appropriate selection of the Li deposition method for in situ studies is required to observe representative behaviour, and the results of previous studies involving energetic deposition may warrant further evaluation. | Joshua Gibson; Sudarshan Narayanan; Jack Swallow; Pardeep Kumar-Thakur; Mauro Pasta; Tien-Lin Lee; Robert Weatherup | Physical Chemistry; Nanoscience; Energy; Energy Storage; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b1e15f9e56b8f9a7b3eeaa/original/gently-does-it-in-situ-preparation-of-alkali-metal-solid-electrolyte-interfaces-for-photoelectron-spectroscopy.pdf |
60c74ebbbdbb895d63a39c0e | 10.26434/chemrxiv.12793685.v1 | Repurposing Known Drugs as Covalent and Non-Covalent Inhibitors of the SARS-CoV-2 Papain-like Protease | <p>In the absence of an approved vaccine,
developing effective SARS-CoV-2 antivirals is essential to tackle the current
pandemic health crisis due to the COVID-19 spread. As any traditional drug
discovery program is a time-consuming and costly process requiring more than
one decade to be completed, <i>in silico</i>
repurposing of existing drugs is the preferred way for rapidly selecting
promising clinical candidates. Herein we present a virtual screening campaign
to identify covalent and non-covalent inhibitors of the SARS-CoV-2 papain-like
protease (PLpro) showing potential multi-target activities for the COVID-19
treatment. A dataset including 688 phase III and 1702 phase IV clinical trial
drugs was downloaded from ChEMBL (version 27.1) and docked to the recently released
crystal structure of PLpro in complex with a covalently bound peptide
inhibitor. The obtained results were analyzed by combining protein-ligand
interaction fingerprint similarities, conventional docking scores and MMGBSA
binding free energies and allowed the identification of some interesting
candidates for further <i>in-vitro</i>
testing. To the best of our knowledge, this study represents the first attempt
to repurpose drugs for a covalent inhibition of PLpro and could pave the way
for new therapeutic strategies against COVID-19.<b></b></p> | Pietro Delre; Fabiana Caporuscio; Michele Saviano; Giuseppe Felice Mangiatordi | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ebbbdbb895d63a39c0e/original/repurposing-known-drugs-as-covalent-and-non-covalent-inhibitors-of-the-sars-co-v-2-papain-like-protease.pdf |
623d75905c8dae4906f64207 | 10.26434/chemrxiv-2021-bvf1l-v2 | A unified synthetic strategy to introduce heteroatoms via electrochemical functionalization of alkyl organoboron reagents | Based on systematic electrochemical analysis, an integrated synthetic platform of C(sp3)-based organoboron com- pounds was established for the introduction of heteroatoms. The electrochemically mediated bond-forming strategy was shown to be highly effective for the functionalization of sp3-hybridized carbon atoms with significant steric hindrance. Moreover, virtually all the nonmetallic heteroatoms could be utilized as reaction partners using one unified protocol. The observed reactivity stems from the two consecutive single-electron oxidations of the substrate, which eventually generates an extremely reactive carbocation as the key intermediate. The detailed reaction profile could be elucidated through multifaceted electrochemical studies. Ultimately, a new di- mension in the activation strategies for organoboron compounds was accomplished through the electrochemically driven reaction development. | Hong Geun Lee; Taek Dong Chung; Su Yong Go; Hyunho Chung; Samuel Jaeho Shin; Sohee An; Ju Hyun Youn; Tae Yeong Im; Ji Yong Kim | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623d75905c8dae4906f64207/original/a-unified-synthetic-strategy-to-introduce-heteroatoms-via-electrochemical-functionalization-of-alkyl-organoboron-reagents.pdf |
633c4301975e943fe99387e1 | 10.26434/chemrxiv-2022-cmzdf | Mechanism of Pd/Senphos-Catalyzed trans-Hydroboration of 1,3-Enynes: Experimental and Computational Evidence in Support of the Unusual Outer-Sphere Oxidative Addition Pathway | The reaction mechanism of the Pd/Senphos-catalyzed trans-hydroboration reaction of 1,3- enynes was investigated using various experimental techniques, including deuterium and double cross-over labeling experiments, X-ray crystallographic characterization of model reaction intermediates, and reaction progress kinetic analysis. Our experimental data are in support of an unusual outer-sphere oxidative addition mechanism where the catecholborane serves as a suitable electrophile to activate the Pd(0)-bound 1,3-enyne substrate to form a Pd-eta3-pi-allyl species, which has been determined to be the likely resting state of the catalytic cycle. Double cross-over labeling of the catecholborane points toward a second role played by the borane as a hydride delivery shuttle. DFT calculations reveal that the rate-limiting transition state of the reaction is the hydride abstraction by the catecholborane shuttle, which is consistent with the experimentally determined rate law: rate = k [enyne]0 [borane]1 [catalyst]1. The computed activation free energy DG‡ = 17.7 kcal/mol and KIE (kH/kD = 1.3) are also in line with experimental observations. Overall, this work experimentally establishes Lewis acids such as catecholborane as viable electrophilic activators to engage in an outer-sphere oxidative addition reaction and points towards this underutilized mechanism as a general approach to activate unsaturated substrates. | Yuanzhe Zhang; Ziyong Wang; Walid Lamine; Senmiao Xu; Bo Li; Anna Chrostowska; Karinne Miqueu; Shih-Yuan Liu | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c4301975e943fe99387e1/original/mechanism-of-pd-senphos-catalyzed-trans-hydroboration-of-1-3-enynes-experimental-and-computational-evidence-in-support-of-the-unusual-outer-sphere-oxidative-addition-pathway.pdf |
60c758cdee301c0a4cc7b7c7 | 10.26434/chemrxiv.14607771.v1 | Glass Surface as Strong Base, ‘Green’ Heterogeneous Catalyst and Degradation Reagent | Systematic screening of accelerated chemical reactions at solid/solution interfaces has been carried out in high-throughput fashion using desorption electrospray ionization mass spectrometry and it provides evidence that glass surfaces accelerate various base-catalyzed chemical reactions. The reaction types include elimination, solvolysis, condensation and oxidation, whether or not the substrates are pre-charged. In a detailed mechanistic study, we provide evidence using nanoESI showing that glass surfaces can act as strong bases and convert protic solvents into their conjugate bases which then act as bases/nucleophiles when participating in chemical reactions. In aprotic solvents such as acetonitrile, glass surfaces act as ‘green’ heterogeneous catalysts that can be recovered and reused after simple rinsing. Besides their use in organic reaction catalysis, glass surfaces are also found to act as degradation reagents for phospholipids with increasing extents of degradation occuring at low concentrations. This finding suggests that the storage of base/nucleophile-labile compounds or lipids in glass containers should be avoided. <br /> | Yangjie Li; Kai-Hung Huang; Nicolás Morato; R. Graham Cooks | Mass Spectrometry; High-throughput Screening; Base Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758cdee301c0a4cc7b7c7/original/glass-surface-as-strong-base-green-heterogeneous-catalyst-and-degradation-reagent.pdf |
63da9819d8f55fd0aa9b94ca | 10.26434/chemrxiv-2023-8t69b | Virtual Screening and binding mode analysis of selected FDA approved drugs against PLpro target: An effort to identify therapeutics to combat COVID-19 | Papain-like protease (PLpro) is one of the most promising targets for anti-SARS-CoV drugs. In this study, a bioactive library of FDA-approved drugs has virtually been screened using a new successful computational pipeline in the framework of the ensemble docking to identify potential binding molecules of PLpro. Based on our protocol, 20 FDA-approved drugs were found to bind the target enzyme with significant affinities and good geometries, suggesting their potential to be utilized against the virus. Our computational studies identified IMATINIB, a well-characterized drug used in the treatment of lymphoblastic and chronic myeloid leukemia, as a potential inhibitor against PLpro. Subsequently, SIMEPREVIR, NALDEMEDINE, TUCATINIB, and some other FDA-approved drugs exhibit great affinities to the PLpro. These drugs are used in the treatment of several diseases such as cancer, schizophrenia, hypertension, hepatitis C, HIV infection, and AIDS showed high affinities in the screening. The high affinity of ligands was rationalized by the newly identified allosteric site named BL2 groove. Occupying this groove may disrupt access to the catalytic site and affect the protein function. The best binding mode and the efficacy of hydrogen bonds and hydrophobic interactions on inhibitory activities of ligands were also disclosed. Furthermore, our studies provide significant molecular insight into PLpro inhibition that could aid in the development of new drugs for COVID-19 treatment. | Mitra Ashouri; Rohoullah Firouzi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da9819d8f55fd0aa9b94ca/original/virtual-screening-and-binding-mode-analysis-of-selected-fda-approved-drugs-against-p-lpro-target-an-effort-to-identify-therapeutics-to-combat-covid-19.pdf |
60c75281ee301c7e83c7ac0b | 10.26434/chemrxiv.13301372.v1 | COVID-19: Captures Iron and Generates Reactive Oxygen Species to Damage the Human Immune System | At present, the novel coronavirus pneumonia has been widespread worldwide, and there is no specific medicine. In response to the emergency, we adopted bioinformatics methods to study the virus's pathogenic mechanism and found possible control methods. We speculated in previous studies that E protein was related to viral infectivity. This study adopted the domain search techniques to analyze the E protein. The results showed that the E protein could bind iron or heme. The iron and heme bound by the E protein came from the attacked hemoglobin and phagocytes. When E protein attached to heme, it synthesized oxygen and water into superoxide anions, hydrogen peroxide, and hydroxyl radicals. When the iron-bound E protein and the heme-bound E protein worked together, they converted superoxide anions and hydrogen peroxide into oxygen and water. These were the “ROS attack” and “ROS escape” of the virus. “ROS attack” damaged the tissues or cells exposed on the surface of the virus, and “ROS escape” decomposed the superoxide anion and hydrogen peroxide that attacked the virus. When NK cells exposed to infected cells, viruses that had not shed from the infected cells’ surface damaged them through “ROS attack”. Lymphocytes such as T cells and B cells, which could be close to the antigen of the virus surface, were also easily damaged or killed by the "ROS attack", resulting in a decrease in lymphocytes. When memory B cells exposed to the virus’s surface antigen, “ROS attack” also damaged them, resulting in the patient's re-infection. The virus used the “ROS escape” to decompose hydrogen peroxide released by phagocytes into oxygen and water. The surrounding cells were replenished with oxygen, and the patient had a “happy hypoxia” state. When the phagocytes swallowed the virus, the E protein converted superoxide anions into oxygen and water. In this way, the virus parasitized in the vesicles of the phagocyte. While virus in the lysosome, the E protein generated ROS to damage nearby hydrolases. The virus parasitized the lysosome in this way. Excessive hydroxyl free radicals destroyed the membrane structure of the lysosome, causing the lysosome to release hydrolase, phagocytic cells autophagy and died. Therefore, the colonizing phagocytes of the virus was related to asymptomatic infection or retest-positive. In short, the virus inhibited the immune system through “ROS escape”, and damaged the immune system by “ROS attack”. The destruction instigated a strong cytokine storm and led to organ failure and complications. This theory is only used for academic discussion.We hoped this discovery would help prevent severe epidemics and save more lives. | liu wenzhong; Li hualan | Bioinformatics and Computational Biology; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75281ee301c7e83c7ac0b/original/covid-19-captures-iron-and-generates-reactive-oxygen-species-to-damage-the-human-immune-system.pdf |
623c9a07658bc08ff4b68175 | 10.26434/chemrxiv-2022-wg6cg-v3 | Fluorescent ligands targeting the intracellular allosteric binding site of the chemokine receptor CCR2 | Fluorescently labeled ligands are versatile molecular tools to study G protein-coupled receptors (GPCRs) and can be used for a range of different applications, including bioluminescence resonance energy transfer (BRET) assays. Here, we report the structure-based development of fluorescent ligands targeting the intracellular allosteric binding site (IABS) of the CC chemo-kine receptor 2 (CCR2), a class A GPCR that has been pursued as a drug target in oncology and inflammation. Starting from previously reported intracellular CCR2 antagonists, several tetramethylrhodamine (TAMRA) labeled CCR2 ligands were designed, synthesized and tested for their suitability as fluorescent reporters to probe binding to the IABS of CCR2. By means of these studies, we developed 14 as a fluorescent CCR2 ligand enabling cell-free as well as cellular NanoBRET-based binding studies in a non-isotopic and high-throughput manner. Further, we show that 14 can be used as a tool for fragment-based screening approaches as well. Thus, our small molecule-based fluorescent CCR2 ligand 14 represents a promising tool for future studies of CCR2 pharmacology. | Lara Toy; Max E. Huber; Maximilian F. Schmidt; Dorothee Weikert; Matthias Schiedel | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623c9a07658bc08ff4b68175/original/fluorescent-ligands-targeting-the-intracellular-allosteric-binding-site-of-the-chemokine-receptor-ccr2.pdf |
63ed1f9a9da0bc6b33fc6fcf | 10.26434/chemrxiv-2023-375jp | Direct Observation of Nanoplastics in Ocean Water | Plastic production surpasses all other synthetic materials globally, with 5-13 million tons of them entering the oceans every year, posing serious environmental challenges. Plastics in the environment can be fragmented by UV irradiation and mechanical means into micro- or even nano-particles. Although nanoplastics have been detected in ocean water using techniques like mass spectrometry, they have never been visually seen, and thus their morphological features are unknown, which are critical to their toxicity. Here we report the direct observation of nanoplastics in ocean water around the world leveraging a unique shrinking surface bubble deposition (SSBD) technique. SSBD concentrates suspended nanoplastic particles onto a surface, allowing direct visualization using electron microscopy. With the plasmonic nanoparticles co-deposited in the SSBD process, the surface-enhanced Raman spectroscopy effect is enabled for chemical identification of trace amounts of nanoplastics deposited on the surface. From the water samples collected from locations on the coastlines of China, South Korea, and the United States, and deep (>300 m) in the Gulf of Mexico, we observed nanoplastics with a variety of compositions, including polycaprolactam (Nylon), polystyrene (PS), and polyethylene terephthalate (PET) all commonly used in daily consumables (e.g., textiles, coffee cup lids and water bottles). The plastic particles we found possessed diverse morphologies, such as nanofibers, nanoflakes, and ball-stick nanostructures. These diverse nanoplastics may profoundly impact marine organisms, and our results can provide critical information for appropriately designing their toxicity studies. | Tengfei Luo; Seunghyun Moon; Leisha Martin; Seongmin Kim; Qiushi Zhang; Wei Xu | Polymer Science; Nanoscience; Earth, Space, and Environmental Chemistry; Organic Polymers; Wastes; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ed1f9a9da0bc6b33fc6fcf/original/direct-observation-of-nanoplastics-in-ocean-water.pdf |
679bf19781d2151a02991c58 | 10.26434/chemrxiv-2024-bdfr0-v2 | Molecular Simulations with a Pretrained Neural Network and Universal Pairwise Force Fields | Machine Learning Force Fields (MLFFs) promise to enable general molecular simulations that can simultaneously achieve efficiency, accuracy, transferability, and scalability for diverse molecules, materials, and hybrid interfaces. A key step toward this goal has been made with the GEMS approach to biomolecular dynamics [Sci. Adv. 10, eadn4397 (2024)]. This work introduces the SO3LR method that integrates the fast and stable SO3krates neural network for semi-local interactions with universal pairwise force fields designed for short-range repulsion, long-range electrostatics, and dispersion interactions. SO3LR is trained on a diverse set of 4 million neutral and charged molecular complexes computed at the PBE0+MBD level of quantum mechanics, ensuring a comprehensive coverage of covalent and non-covalent interactions. Our approach is characterized by computational and data efficiency, scalability to 200 thousand atoms on a single GPU, and reasonable to high accuracy across the chemical space of organic (bio)molecules. SO3LR is applied to study units of four major biomolecule types, polypeptide folding, and nanosecond dynamics of larger systems such as a protein, a glycoprotein, and a lipid bilayer, all in explicit solvent. Finally, we discuss the future challenges toward truly general molecular simulations by combining MLFFs with traditional atomistic models. | Adil Kabylda; J. Thorben Frank; Sergio Suarez Dou; Almaz Khabibrakhmanov; Leonardo Medrano Sandonas; Oliver T. Unke; Stefan Chmiela; Klaus-Robert Müller; Alexandre Tkatchenko | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679bf19781d2151a02991c58/original/molecular-simulations-with-a-pretrained-neural-network-and-universal-pairwise-force-fields.pdf |
60c7521af96a002d5c288158 | 10.26434/chemrxiv.13252373.v1 | Tapping the Unexplored Potential of Marine Fungi and Edible Mushrooms for in Silico Screening of Anti-Viral Bioactive Compounds Against SARS-CoV-2 for Rapid Development of Nutraceuticals | <p>Severe Acute Respiratory Syndrome Coronavirus 2 (SARS- CoV-2)
affects human respiratory function that causes COVID-19 disease. COVID-19 has
spread rapidly all over the world and became a pandemic within no time. Therefore,
it is the need of hour to screen potential lead candidates from natural
resources like edible mushrooms and marine fungi. These natural resources are
very less explored till now and known to be the source for many medicinal compounds
with several health benefits. These medicinal compounds can be easily exploited
for the faster development of nutraceuticals for controlling SARS-CoV-2
infections. Our in-silico research suggests that bioactive compounds originating
from mushroom and marine fungi shows strong potential to interact with ACE2
receptor or main protease of SARS-CoV-2, showing the inhibition activity
towards the enzymatic protease. We performed a series of in silico studies for
the validation of our results, which includes Molecular docking, drug likeness property
investigation by Swiss ADME tools, MD simulation, and thermodynamically stable
free binding energy calculation. Overall, these results suggest that Ganodermadiol
and Heliantriol
F bioactive compounds originating from edible mushroom has strong
potential to be developed as low-cost nutraceutical against SARS-CoV-2 viral
infection. The drug candidate isolated from marine fungi and edible mushroom
are highly unexplored for the development of potential alternative drug against
SARS-CoV-2 virus with minimum side effects. That is why we decided to screen
some active metabolites from the marine fungi and mushrooms, which offer some
encouraging results. Though our in-silico studies of these compounds are showing
a promising result against SARS-CoV-2 main protease and ACE2 receptor binding
domain, the effectiveness of these bioactive compounds should be further
validated by proper clinical trials.</p> | Amit Kumar Srivastav; Jyoti Jaiswal; Umesh Kumar | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7521af96a002d5c288158/original/tapping-the-unexplored-potential-of-marine-fungi-and-edible-mushrooms-for-in-silico-screening-of-anti-viral-bioactive-compounds-against-sars-co-v-2-for-rapid-development-of-nutraceuticals.pdf |
60c74f97ee301c7143c7a718 | 10.26434/chemrxiv.12924059.v1 | Does Liquid-Liquid Phase Separation Drive Peptide Folding? | <p>Proline-arginine (PR) dipeptide repeats have been shown to
undergo liquid-liquid phase separation and are an example of a growing number
of intrinsically disordered proteins that can assemble into membraneless
organelles. These structures have been posited as a nucleation site for
pathogenic protein aggregation. As such, a better understanding of the effects
that the increased local concentration and volumetric crowding within droplets
has on peptide secondary structure is necessary. Herein we use Fourier
transform infrared (FTIR) and two-dimensional infrared (2DIR) spectroscopy to
show that formation of droplets by PR20 accompany changes in the Amide-I
spectra consistent with folding into poly-proline helical structures. </p> | Dean N. Edun; Meredith R. Flanagan; Arnaldo Serrano | Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f97ee301c7143c7a718/original/does-liquid-liquid-phase-separation-drive-peptide-folding.pdf |
638e3dbf9e687be7aa3e8b3b | 10.26434/chemrxiv-2021-9pz8c-v5 | Soot and charcoal as reservoirs of extracellular DNA | The vast potential of using sediment adsorbed DNA as a window to past and present biodiversity rely on the ability of solid surfaces to adsorb environmental DNA. However, a comprehensive insight into DNA adsorption at surfaces in general is lacking. Soot and charcoal are carbonaceous materials widespread in the environment where they readily can come in contact with extracellular DNA shed from organisms. Using batch adsorption, we measured DNA adsorption capacity at soot and charcoal as a function of solution composition, time and DNA length. We observed that the adsorption capacity for DNA is highest at low pH, that it increases with solution concentration and cation valency and that the activation energy for DNA adsorption at both soot and charcoal is ~50 kJmol-1, suggesting strong binding. We demonstrate how the interaction between DNA and soot and charcoal partly occurs via terminal base pairs, suggesting that, besides electrostatic forces, hydrophobic interactions play an important role in binding. The large adsorption capacities and strong binding of DNA to soot and charcoal are features important for eDNA research and provide a motivation for use of carbonaceous materials from, e.g., anthropogenic pollution or wildfire as sources of biodiversity information. | Stanislav Jelavic; Lisbeth Garbrecht Thygesen; Valerie Magnin; Nathaniel Findling; Sascha Müller; Viktoriia Meklesh; Karina Krarup Sand | Earth, Space, and Environmental Chemistry; Geochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638e3dbf9e687be7aa3e8b3b/original/soot-and-charcoal-as-reservoirs-of-extracellular-dna.pdf |
6797f0876dde43c9089dcda4 | 10.26434/chemrxiv-2025-9kfw7 | Machine Learning-Driven Optimization of Output Force in Photo-Actuated Organic Crystals | Photo-actuated organic crystals, which can be remotely controlled by light, are gaining attention as next-generation actuator materials. In the practical application of actuator materials, not only the mode of deformation but also the output force is an important property. Since the output force depends on both the crystal properties and experimental conditions, it is necessary to explore the optimal conditions from a vast parameter space. In this study, we employed two types of machine learning for molecular design and experimental optimization, successfully maximizing the blocking force. Machine learning in molecular design led to the creation of a material pool of salicylideneamine derivatives. Bayesian optimization was used for efficient sampling from the material pool for force measurements, achieving a maximum blocking force of 37.0 mN. It was estimated that this method was at least 73 times more efficient than the grid search approach. | Kazuki Ishizaki; Toru Asahi; Takuya Taniguchi | Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6797f0876dde43c9089dcda4/original/machine-learning-driven-optimization-of-output-force-in-photo-actuated-organic-crystals.pdf |
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