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6549260da8b423585a12b789
|
10.26434/chemrxiv-2023-rcjt2
|
The role of Manganese in CoMnOx Catalysts for Selective Fischer-Tropsch Synthesis
|
The origin of the high selectivity of cobalt-manganese oxide (CoMnOx) catalysts in the Fischer−Tropsch synthesis (FTs) reaction towards long-chain hydrocarbon products was investigated using model systems of CoMnOx in the form of crystalline nanoparticles and amorphous thin films where Co and Mn are intimately mixed rather than separated in two phases. Using ambient pressure X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy, the chemical structure of the catalyst and adsorbed species were determined under reaction conditions. We found that the catalytically active phase contains an outer layer enriched in metallic Co relative to the bulk. Molecular CO adsorbs on Co0 sites, where it dissociates by reaction with H2 to form cobalt carbide and CHx species. The concentration of CHx increases rapidly with exposure to CO/H2 syngas on the CoMnOx catalyst, while no such increase was observed in the absence of Mn. Density Functional Theory (DFT) simulations indicate that MnO acts as a reservoir of H atoms bound to the basic O sites, which makes it less accessible to CHx moieties, thus hindering chain termination to form short chain hydrocarbons. In contrast, the increasing concentration of CHx moieties helps chain growth.
|
HAO CHEN; Zan Lian; Xiao Zhao; Jiawei Wan; Priscilla F. Pieters; Judit Oliver Meseguer ; Ji Yang ; Elzbieta Pach; Sophie Carenco; Laureline Treps; Nikos Liakakos; Yu Shan; Maria Virginia Altoe ; Ed Wong; Zengqing Zhuo; Feipeng Yang ; Ji Su; Jinghua Guo; Monika Blum; Lapidus Saul H; Hunt Adrian; Waluyo Iradwikanari; Ogasawara Hirohito; Haimei Zheng ; Peidong Yang; Alexis T. BELL; Nuria López ; Miquel Salmeron
|
Physical Chemistry; Catalysis; Nanoscience; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6549260da8b423585a12b789/original/the-role-of-manganese-in-co-mn-ox-catalysts-for-selective-fischer-tropsch-synthesis.pdf
|
620ccaa6e0f52961eab46103
|
10.26434/chemrxiv-2022-v76pk
|
Surface Segregation in AgAuCuPdPt High Entropy Alloy: Insights From Molecular Simulations
|
High entropy alloys (HEAs) are emerging as a novel class of superior catalysts for diverse chemical conversions. The activity of a catalyst is intimately related to the composition and atomic structure at its surface. In this work, we used embedded atom (EAM) potential based Monte Carlo – Molecular Dynamics simulations to study surface segregation in the equimolar AuAgCuPdPt HEA, that was recently shown to be an efficient catalyst for CO2 electrochemical reduction. Firstly, EAM potentials were extensively validated against experimental segregation data for several different binary and ternary compositions. Subsequently, simulations on the HEA were carried out for four different surface orientations, spherical and cubical nanoparticles, to obtain detailed structural and concentration profiles normal to the surface. In all cases, Ag atoms were found to preferentially segregate to the surface while the subsurface layer mainly consisted of Au atoms. No Pt atoms were found on the surface layer for all systems. A detailed analysis neighborhood of each surface site revealed that the atoms formed a finite number of chemically unique clusters. The percentage of chemically unique sites were larger for elements with lower concentration at the surface. Together with the physical diversity surrounding each site, the enrichment of one or more element(s) at the surface also increased its number of unique catalytically active sites. Results from our work suggest that HEAs are prone to surface segregation and such effects must be taken into consideration while modeling the surface chemistry of these materials.
|
Chinmay Dahale; Sriram Goverapet Srinivasan; Shashank Mishra; Soumyadipta Maiti; Beena Rai
|
Physical Chemistry; Materials Science; Catalysis; Catalysts; Structure; Surface
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620ccaa6e0f52961eab46103/original/surface-segregation-in-ag-au-cu-pd-pt-high-entropy-alloy-insights-from-molecular-simulations.pdf
|
664d151b21291e5d1de509f5
|
10.26434/chemrxiv-2024-g4gqm
|
Crystallography reveals metal-triggered restructuring of β-hairpins
|
Metal binding to β-sheets occurs in many metalloproteins and is also implicated in the pathology of Alzheimer's disease. De novo designed metallo-β-sheets have been pursued as models and mimics of these proteins. However, no crystal structures of canonical β-sheet metallopeptides have yet been obtained, in stark contrast to many examples for ɑ-helical metallopeptides, leading to a poor understanding for their chemistry. To address this, we have engineered tryptophan zippers, stable 12-residue β-sheet peptides, to bind Cu(II) ions and obtained crystal structures through single crystal X-ray diffraction (SC-XRD). We find that metal binding triggers several unexpected supramolecular assemblies that demonstrate the range of higher-order structures available to metallo-β-sheets. Overall, these findings underscore the importance of crystallography in elucidating the rich structural landscape of metallo-β-sheet peptides.
|
Viet Thuc Dang; Aryan Engineer; Dan McElheny; Alexander Drena; Joshua Telser; Kyle Tomczak; Andy Nguyen
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Ligands (Inorg.); Supramolecular Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664d151b21291e5d1de509f5/original/crystallography-reveals-metal-triggered-restructuring-of-hairpins.pdf
|
662b964691aefa6ce17f8d32
|
10.26434/chemrxiv-2024-klzjq
|
Selective C3- or C5-Borylation of Furfural Derivatives: Enabling the Synthesis of Tri- and Tetra-Substituted Furan Analogues
|
A strategy of C3/C4 and C5/C4 bis-C–H functionalization of furfural and 5-hydroxymethylfurfural is presented. This task has been accomplished by the initial iridium-catalyzed C–H borylation of furfural, equipped with an appropriate imine function. Depending on the nature of the ligand employed, the borylation takes place selectively at C3 or C5, the products serving in turn as partners in Suzuki-Miyaura cross-couplings. After aldehyde function regeneration, some of the resulting heterobiaryl compounds underwent a, C3- or C5-directed, C4-selective Pd-catalyzed Fujiwara-Moritani olefination. These hitherto unknown serial C3/C4 and C5/C4 bis C–H functionalization strategies allow the straightforward conversion of the bio-sourced platform molecules furfural and 5-hydroxymethylfurfural into tri- and tetra-substituted furaldehyde derivatives
|
Alessia Mori; Mariana Isabel Crespo Monteiro; Filipa Siopa; Giovanni Poli; Julie Oble
|
Catalysis; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662b964691aefa6ce17f8d32/original/selective-c3-or-c5-borylation-of-furfural-derivatives-enabling-the-synthesis-of-tri-and-tetra-substituted-furan-analogues.pdf
|
670d2ba451558a15ef0a875d
|
10.26434/chemrxiv-2024-9wms4
|
Novel Therapeutic Applications of Stem Cell-Derived Exosomes in Enhancing Neurological Regeneration and Repair
|
Exosome-based therapies have emerged as a promising frontier in the field of regenerative medicine, particularly for neural repair. Exosomes, which are microvesicles derived from mesenchymal stem cells (MSCs), neural stem cells (NSCs), and induced pluripotent stem cells (iPSCs), exhibit significant regenerative potential. This manuscript aims to explore the therapeutic prospects of exosome-based treatments in neural injury and neurodegenerative conditions. Recent advancements have deepened our understanding of exosome cargo, including microRNAs (miRNAs), proteins, and growth factors, which are critical to their regenerative capacity. Exosomes operate at various levels to support neuroprotection, enhance axonal growth, promote synaptic plasticity, and modulate immune responses. This paper further discusses the efficacy of exosome treatments, highlighting ongoing and recent clinical studies that investigate the therapeutic benefits of exosomes, particularly through intranasal and intravenous administration routes. Despite their potential, several challenges remain, notably in the large-scale production, distribution, and immune compatibility of exosome-based therapies. This review also addresses future directions for enhancing exosome targeting within neural tissues, with a focus on bioengineering strategies to improve treatment precision. While exosome therapies hold promise for addressing neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and stroke, further research is needed before they can be fully integrated into clinical practice.
|
Arshia Farmahini Farahani
|
Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d2ba451558a15ef0a875d/original/novel-therapeutic-applications-of-stem-cell-derived-exosomes-in-enhancing-neurological-regeneration-and-repair.pdf
|
67737c70fa469535b9519dad
|
10.26434/chemrxiv-2025-tzpxn
|
Cobaloxime-Based Metalloradical Catalysis: A Versatile Strategy for the Synthesis of Cyclopropenes and Oxazoles
|
Metalloradical catalysis (MRC), predominantly exemplified by metalloporphyrin complexes, has emerged as a promising strategy for regulating radical reactions and broadening their synthetic applications. Here, an efficient catalytic method has been devised for the radical [2 + 1] cyclopropenation of alkynes and radical [3 + 2] oxazolation of nitriles using α-aryldiazoacetates via MRC. Cobaloxime proves effective in facilitating the metalloradical [2 + 1] cyclopropenation of alkynes and radical [3 + 2] oxazolation cycloaddition reaction under mild conditions. The reactions demonstrate broad substrate tolerance, accommodating gram-scale transformations and the synthesis of pharmaceutical compounds. Our findings highlight the significant potential of cobaloxime-catalyzed cycloaddition as a valuable tool in organic synthesis and broaden the scope of metalloradical systems in catalysis.
|
Liming Tan; Keyang Wu; Gang Li
|
Organic Chemistry; Inorganic Chemistry; Catalysis; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67737c70fa469535b9519dad/original/cobaloxime-based-metalloradical-catalysis-a-versatile-strategy-for-the-synthesis-of-cyclopropenes-and-oxazoles.pdf
|
63e39a85cdb6a7f57b4b9a1b
|
10.26434/chemrxiv-2023-v2t2f
|
Chemical Synthesis of Glycopeptides containing L-Arabinosylated Hydroxyproline and Sulfated Tyrosine
|
Post-translationally modified peptides are important regulating molecules for living organisms. Here we report the stereoselective total synthesis of beta-1,2-linked L-arabinosylated Fmoc-protected hydroxyproline building blocks and their incorporation, together with sulfated tyrosine and hydroxyproline, into the plant peptide hormone PSY1. Clean glycopeptides were obtained by perform-ing acetyl removal from the L-arabinose groups prior to deprotection of the neopentyl-protected sulfated tyrosine.
|
Jasper van de Sande; Bauke Albada
|
Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2023-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e39a85cdb6a7f57b4b9a1b/original/chemical-synthesis-of-glycopeptides-containing-l-arabinosylated-hydroxyproline-and-sulfated-tyrosine.pdf
|
6436e4101d262d40ea53fbc9
|
10.26434/chemrxiv-2023-1q64v
|
Towards a Realistic Surface State of Ru in Aqueous and Gaseous Environments
|
Identifying the surface species is critical towards a realistic understanding of supported metal catalysts working in water. To this end, we have characterized the surface species present at a Ru/water interface by employing a hybrid computational approach involving an explicit description of the liquid water and a possible pressure of H2. On close-packed, most stable Ru(0001) facet, the solvation tends to favor the full dissociation of water into atomic O and H in contrast with the partially-dissociated water layer reported for ultra-high vacuum conditions. The solvation stabilization was found to be as high as -0.279 J.m2 which results in stable O and H species on Ru(0001) in presence of liquid water even at room temperature. Conversely, introducing even a small H2 pressure (10−2 bar) results in a monolayer of chemisorbed H at the interface, a general trend found on the three most exposed facets of Ru nanoparticles. While hydroxyls were often hypothesized as possible surface species at the Ru/water interface, this computational study clearly demonstrates that they are not stabilized by liquid water and are not found in realistic reductive catalytic conditions.
|
Muhammad Akif Ramzan; Raphaël Wischert; Stephan N. Steinmann; Carine Michel
|
Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Theory - Computational; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6436e4101d262d40ea53fbc9/original/towards-a-realistic-surface-state-of-ru-in-aqueous-and-gaseous-environments.pdf
|
60c7409cbdbb890828a3818b
|
10.26434/chemrxiv.7665734.v2
|
Di-Palladium Complexes are Active Catalysts for Mono-N-Protected Amino Acid Accelerated Enantioselective C-H Functionalization
|
The role of mono-protected amino acid (MPAA) ligands in accelerating enantioselective cyclopalladation and palladium catalyzed C-H func-tionalization was investigated using kinetic, spectroscopic, and computational methods. Single crystal X-ray diffraction and NMR spectroscopy demonstrate that MPAA ligands bind catalytically competent di-palladium complexes as bridging carboxylates. The catalytic relevance of the observed di-palladium species was evaluated by kinetic analysis. The kinetic method of continuous variation demonstrated that a complex contain-ing a single MPAA-bridged di-palladium core (Pd2(MPAA)1) is an active catalyst for the reactions studied. The experimental studies are con-sistent with density functional theory calculations that indicate enantioinduction can be achieved by a single MPAA ligand bridging a di-palladium catalyst through secondary sphere hydrogen-bonding interactions that lower the barrier to C-H activation of the major enantiomer.<br />
|
Joseph Gair; Brandon E. Haines; Alexander S. Filatov; Djamaladdin G. Musaev; Jared C. Lewis
|
Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7409cbdbb890828a3818b/original/di-palladium-complexes-are-active-catalysts-for-mono-n-protected-amino-acid-accelerated-enantioselective-c-h-functionalization.pdf
|
6231ef5c658bc04c0aacfda0
|
10.26434/chemrxiv-2022-qf75v
|
Four-dimensional spacetime atomistic artificial intelligence models
|
We demonstrate that artificial intelligence (AI) can learn four-dimensional (4D) atomistic systems in the spacetime continuum. Given the initial conditions – nuclear positions and velocities at time zero – the proposed 4D-atomistic AI (4D-A2I) models can predict nuclear positions at any time in the future or past for the simplest systems as we show for H2. For larger polyatomic molecules, AI is capable of learning distant but finite future as we demonstrate for an ethanol molecule. 4D-A2I models provide direct access to a multitude of properties at a given time such as geometries, velocities, forces, and energies which can be used in simulating physicochemical transformations and spectra. Our approach can be used as a cost-efficient alternative to traditional molecular dynamics. We show an example of a 4D-A2I model describing the dynamical behavior of ethanol at the coupled-cluster level with the speed of one nanosecond simulation time per one hour wall-clock time on a single GPU card – a previously unachievable feat with traditional Born–Oppenheimer molecular dynamics. 4D-A2I model is also demonstrated to provide direct access to atomistic time-resolved details of physicochemical transformations.
|
Fuchun Ge; Lina Zhang; Arif Ullah; Pavlo O. Dral
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6231ef5c658bc04c0aacfda0/original/four-dimensional-spacetime-atomistic-artificial-intelligence-models.pdf
|
673363ed7be152b1d0d78956
|
10.26434/chemrxiv-2024-pg6bx-v2
|
Innovative Optimization of LDI-MS Porous Silicon Substrates Using Thermometer ions
|
This study presents a methodical procedure for optimizing laser desorption/ionization mass spectrometry (LDI-MS) supports using porous silicon (PSi) substrates. The approach involves the use of substituted benzyl-pyridinium salts (thermometer ions) to obtain one metric that assesses analyte fragmentation (the effective temperature of vibration). Porous silicon substrates were synthesized via electrochemical etching of p-type silicon wafers (10-20 mΩ⋅cm), with etching pa-rameters adjusted to vary porosity while maintaining a layer thickness between 700 and 1200 nm. The results revealed that PSi substrates with 40-60% porosity achieved the lowest fragmentation levels. This finding was validated through the analysis of N-Acetyl glucosamine, a carbohydrate, which confirmed the effective temperature trend. Further analysis involving peptides, specifically P14R and a peptide mix (Peptide Calibration Standard II, Bruker), demonstrated that the optimized PSi substrates enabled the desorption and ionization of peptides with a maximum mass at m/z 2465, corresponding to ACTH clip 1-17. These results highlight the critical role of substrate porosity in minimizing analyte fragmentation and enhancing LDI-MS performance.
|
Clara Whyte Ferreira; Bastien Cabrera-Tejera; Bernard Leyh; Romain Tuyaerts; Gilles Scheen; Yannick Coffinier; Edwin De Pauw; Gauthier Eppe
|
Physical Chemistry; Materials Science; Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673363ed7be152b1d0d78956/original/innovative-optimization-of-ldi-ms-porous-silicon-substrates-using-thermometer-ions.pdf
|
61f9069d537af8d593ac76fb
|
10.26434/chemrxiv-2022-ntgxg-v2
|
Atomic force microscopy characterization of polyethylene terephthalate grafting with poly(styrene sulfonate)
|
Polyethylene terephthalate (PET) is widely used to elaborate biomaterials and medical devices in particular for long-term implant applications but tuning their surface properties remains challenging. We investigate surface functionalization by grafting poly(sodium 4-styrene sulfonate, PNaSS) with the aim of enhancing protein adhesion and cellular activity. Elucidating the topography and molecular level organization of the modified surfaces is important for understanding and predicting biological activity. In this work, we explore several grafting methods including thermal grafting, thermal grafting in the presence of Mohr's salt, and UV activation. We characterize the different surfaces obtained using atomic force microscopy (AFM), contact angle (CA), and X-ray photoelectron spectroscopy (XPS). We observe an increase in the percentage of sulfur atoms (XPS) that correlates with changes in (CA), and we identify by AFM characteristic features, which we interpret as patches of polymers on the PET surfaces. This work demonstrates tuning of biomaterials surface by functionalization and illustrates the capability of atomic force microscopy to provide insights into the spatial organization of the grafted polymer.
|
Tuan Nguyen; Vincent Humblot; Veronique Migonney; Raphael Levy
|
Materials Science; Polymer Science; Nanoscience; Biodegradable Materials; Nanostructured Materials - Materials; Polyelectrolytes - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f9069d537af8d593ac76fb/original/atomic-force-microscopy-characterization-of-polyethylene-terephthalate-grafting-with-poly-styrene-sulfonate.pdf
|
64e4dba0dd1a73847f4dc904
|
10.26434/chemrxiv-2023-h02j4
|
Fine-tuning GPT-3 for machine learning electronic and functional properties of organic molecules
|
We evaluate the effectiveness of fine-tuning GPT-3 for the prediction of electronic and functional properties of organic molecules. Our findings show that fine-tuned GPT-3 can successfully identify and distinguish between chemically meaningful patterns, and discern subtle differences among them, exhibiting robust predictive performance for the prediction of molecular properties. We focus on assessing the fine-tuned models' resilience to information loss, resulting from the absence of atoms or chemical groups, and to noise that we introduce via random alterations in atomic identities. We discuss the challenges and limitations inherent to the use of GPT-3 in molecular machine-learning tasks and suggest potential directions for future research and improvements to address these issues.
|
Zikai Xie; Xenophon Evangelopoulos; Ömer Omar; Alessandro Troisi; Andrew I. Cooper; Linjiang Chen
|
Theoretical and Computational Chemistry; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e4dba0dd1a73847f4dc904/original/fine-tuning-gpt-3-for-machine-learning-electronic-and-functional-properties-of-organic-molecules.pdf
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62378a51d7562723041f69ce
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10.26434/chemrxiv-2022-kqnpk
|
Predicting Surface Strain Effects on Adsorption Energy with
Graph Neural Networks
|
Modifying the adsorption energies of reaction intermediates on different material surfaces can significantly improve heterogeneous catalysis by reducing energy barriers for intermediate elementary reaction steps. Surface strain can increase or decrease the adsorption energy depending on the surface composition, adsorbate composition, surface facet, and adsorbate site, breaking traditional scaling relationships which inhibit energy barrier alteration in reactions such as ammonia synthesis. We aim to generate a model that maps the adsorption energy response to a given input strain for a range of adsorbates and catalyst structures. After generating a training dataset of strained copper binary alloy catalyst + adsorbate complexes from the Open Catalyst Project and calculating the adsorption energy with first-principles calculations (dataset made
available), we train a graph neural network to learn the relationship between catalyst + adsorbate structure, surface strain, and adsorption energy. The model successfully predicts the nature of the adsorption energy response for 85% of surface strains, outperforming simpler model baselines. Using the ammonia synthesis reaction as an example system, we identify Cu-S alloy catalysts as promising candidates for strain engineering since the majority of surface strain patterns raise the adsorption energy of the *NH intermediate. We find that the strain response of similar adsorbates on the same surface can greatly vary due to the competition between surface
relaxation under strain and relaxation of the coordination environment. Our presented machine learning approach can be applied to additional datasets to identify target strain patterns that can reduce energy barriers in heterogeneous catalysis.
|
Christopher Price; Akash Singh; Nathan Frey; Vivek Shenoy
|
Theoretical and Computational Chemistry; Materials Science; Catalysis; Theory - Computational; Machine Learning; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62378a51d7562723041f69ce/original/predicting-surface-strain-effects-on-adsorption-energy-with-graph-neural-networks.pdf
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610727820b093e36c8e4fa96
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10.26434/chemrxiv-2021-f7rhr
|
ICP-MS Analysis of Mercury in Fish: Exploration of Method Validation, Matrix Effect, and Kinetic Energy Discrimination
|
Inductively coupled plasma-mass spectrometry (ICP-MS) is a powerful analytical technique that can quantify elements of interest at parts-per-trillion concentrations. In this laboratory class, students performed ICP-MS analysis to quantify mercury concentration of standard reference material (SRM) 1947 (Lake Michigan fish tissue) and canned tuna from a local supermarket. These two samples were digested in two different matrices (HNO3/ H2O2 or HNO3/HCl/H2O2) and then analyzed using no-gas mode or helium mode with two different kinetic energy discrimination voltages (2V or 4V). The inclusion of HCl in the matrix produced more accurate results and stabilized mercury over the 8-day period after the digestion. Based on their analysis, the students were asked to draw their own conclusions about what they perceived to be the most accurate representation of the true mercury concentration of the tuna samples. This laboratory class provides students with a wide range of scientific concepts to explore such as method verification with SRM, kinetic energy discrimination, matrix effect, and trace metal stability over time.
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Wonhyeuk Jung; Christopher Dunham; Katie Perrotta; Yu Chen; James Gimzewski; Joseph Loo
|
Analytical Chemistry; Chemical Education; Agriculture and Food Chemistry; Chemical Education - General; Mass Spectrometry
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-08-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610727820b093e36c8e4fa96/original/icp-ms-analysis-of-mercury-in-fish-exploration-of-method-validation-matrix-effect-and-kinetic-energy-discrimination.pdf
|
63e2bb533067856f18b6e6b1
|
10.26434/chemrxiv-2023-6v632
|
Synthesis and characterization of low-cost ceramic membranes using red mud from the eastern Amazon as waste from the Bayer process
|
This research presents the development and characterization of ceramic membranes from a mixture of Red Mud and Clay. Characterized as for the Apparent Porosity (AP), Water Absorption (WA), Linear Retraction (LR), Apparent Density (AD), Pore Distribution, Hydraulic Permeability and Rejection to a solute of interest. XRD, SEM / EDS, and Rietveld Technique were used to characterize the raw materials. The composition L35A65 shows the best results, with WA = 29.55 ± 0.2, AP = 44.72 ± 0.62, AD = 1.5 ± 0.01, LR =1.67 ± 0.0, mean diameter of pores equal to 0.418µm and hydraulic permeability, Lp = 721.4 Lh/m2.bar. The rejection for yeasts was 99.9% and for starch was 96.8%.
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Yasmim Lima; Renan Baia; Vitor Auzier; Patrick De Alencar; Kleber Oliveira
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e2bb533067856f18b6e6b1/original/synthesis-and-characterization-of-low-cost-ceramic-membranes-using-red-mud-from-the-eastern-amazon-as-waste-from-the-bayer-process.pdf
|
64f5ef1179853bbd78177206
|
10.26434/chemrxiv-2023-bczdm
|
Room Temperature Electroreductive Carboxylation of Unactivated Alkyl Chlorides with CO2 Using a Ni(II) NNN-Pincer Complex. Towards Polyvinyl chloride (PVC) Upgrading
|
In organic synthesis, direct carboxylation of organohalides with carbon dioxide is a highly desirable transformation because it uses feedstock chemicals and produces carboxylic acids, which are among the most widely used classes of organic compounds. Alkyl carboxylic acids are favored motifs in many medicines and physiologically active substances. Carbon dioxide (CO2) is an ideal C1 source for organic synthesis because of its high abundance, low cost, nontoxicity, and recyclability. This article describes a nickel-catalyzed electrochemical method for producing alkyl carboxylic acids via carboxylation of unactivated alkyl chlorides with CO2. The development of a Ni pincer complex (complex 1) with a redox-active ligand as an electrocatalyst to convert unactivated alkyl chlorides to the corresponding acids over less desirable homocoupling products is presented. Electronic structure calculations revealed that CO2 binding occurs in a resting state to yield an 2-CO2 adduct and that the C-Cl bond activation step is the TOF-determining transition state, which has an activation energy of 19.3 kcal/mol. A combination of electroanalytical methods, control experiments, and computational studies revealed the mechanism of the electrocarboxylation reaction. In addition, complex 1 has been demonstrated as an efficient catalyst to upgrade polyvinyl chloride to polyacrylate in 95% yield.
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Prasenjit Sarkar; Sandeep Dash; Jeanette Krause; Julien Panetier; Jianbing Jiang
|
Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f5ef1179853bbd78177206/original/room-temperature-electroreductive-carboxylation-of-unactivated-alkyl-chlorides-with-co2-using-a-ni-ii-nnn-pincer-complex-towards-polyvinyl-chloride-pvc-upgrading.pdf
|
632344fbe615029a9d19a490
|
10.26434/chemrxiv-2022-tqg48-v2
|
Gold(I)-Catalyzed Benzylic C(sp3)-H Functionalizations: Product Bifurcation towards Indole[a]- and [b]-Fused Polycycles
|
Phenylazides substituted by an (alkylphenyl)ethynyl group facilitate divergent benzylic sp3(C-H) functionalization in the presence of a JohnPhosAu catalyst, via N- or C-cyclization, resulting in indole-fused tetra- and pentacycles. The chemoselectivity is influenced depending on the counter-anion (SbF6 or BARF), the electron density of the alpha-imino gold(I) carbene, and the alkyl groups stabilizing the benzylic carbocation originating from a 1,5-hydride shift. An isotop-ic labeling experiment demonstrates the involvement of an indolylgold(I) species resulting in a tautomerization that is much faster than deauration is. The formation of a benzylic sp3(C-H) functionalization resulting in an indole-fused sev-en-membered ring is also demonstrated.
|
Luca Greiner; Norihito Arichi; Shinsuke Inuki; Hiroaki Ohno
|
Catalysis; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632344fbe615029a9d19a490/original/gold-i-catalyzed-benzylic-c-sp3-h-functionalizations-product-bifurcation-towards-indole-a-and-b-fused-polycycles.pdf
|
64cc49ec69bfb8925a50ee18
|
10.26434/chemrxiv-2023-h7v5z
|
Synthesis and Characterization of Quinone Compounds Derived from Doubly- and Triply-Linked Diporphyrins and Tuning of Their Absorption Properties
|
Porphyrins are attracting increasing attention in materials science and photochemistry owing to their unique properties and diverse applications. This study focuses on modifying and tuning the absorption properties of porphyrins, specifically those of quinoidal porphyrins, to extend their spectral range into the near-infrared (NIR) region. We report the synthesis and structural and physical properties of quinone compounds derived from doubly- and triply-linked diporphyrins and their metal complexes. Doubly-linked diporphyrinquinone exhibits broad panchromatic absorption properties in solution owing to its low symmetry. Metal complexation markedly extends its absorption range to the near-infrared region. In contrast, the metal complexes of the triply-linked diporphyrinquinones exhibit sharp and strong absorption bands in the visible to near-infrared region owing to their higher symmetry. The longest absorption wavelength of the triply-linked diporphyrinquinones was approximately 1500 nm, which was significantly more red-shifted than that of the doubly-linked ones.
|
Ken-ichi Yamashita; Daisuke Hirano; Ken-ichi Sugiura
|
Organic Chemistry; Physical Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cc49ec69bfb8925a50ee18/original/synthesis-and-characterization-of-quinone-compounds-derived-from-doubly-and-triply-linked-diporphyrins-and-tuning-of-their-absorption-properties.pdf
|
64188380aad2a62ca10f7080
|
10.26434/chemrxiv-2023-9rqvp
|
Templated Total Synthesis of Cu(I)-Methanobactin OB3b
|
Methanobactin OB3b (Mbn-OB3b) is a unique natural product featuring two ene-thiolate-azlactone rings incorporated in a rigidified peptide backbone. The stunning affinity of this chalkophore for copper (Ka ≈ Cu(I) 10E34) makes it a prominent lead compound for Cu-transport, metabolism, and detoxification. Its exceptional structure poses particular challenges for biosynthesis and chemical manipulation. Here, we report the first total synthesis of Cu(I)-bounded methanobactin OB3b featuring as key transformations a cyclodehydration-thioacylation sequence, to generate the conjugated heterocyclic systems, and a copper-templated cyclization, to complete the caged structure of the sensitive chalkophore.
|
Emilia Cupioli; Frédéric Gaigne; Anna Sachse; Philipp Buday; Wolfgang Weigand; Phil Liebing; Hans-Dieter Arndt
|
Biological and Medicinal Chemistry; Organic Chemistry; Inorganic Chemistry; Natural Products; Organic Synthesis and Reactions; Bioinorganic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64188380aad2a62ca10f7080/original/templated-total-synthesis-of-cu-i-methanobactin-ob3b.pdf
|
654a230248dad2312042ae94
|
10.26434/chemrxiv-2023-127s9
|
A deep learning approach for quantum dots sizing from wide-angle X-ray scattering data
|
Disclosing the full potential of functional nanomaterials requires the optimization of synthethic protocols and an effective size screening tool, aiming at efficiently triggering their size-dependent properties. Here we demonstrate the successful combination of a wide-angle X-ray total scattering approach with a deep learning classifier for directly sizing quantum dots in both colloidal and dry states. This work offers a compelling alternative to the lengthy process of deriving sizing curves from transmission electron microscopy coupled with spectroscopic measurements, especially in the ultra-small size regime, where traditional empirical functions exhibit larger discrepancies.
The core of our algorithm is an all-convolutional neural network trained on Debye scattering equation X-ray simulations, incorporating atomistic models to capture structural and morphological features, and augmented with physics-informed perturbations to account for different predictable experimental conditions. The model performances are evaluated using both wide-angle X-ray total scattering simulations and experimental datasets collected on lead sulfide quantum dots, resulting in size classification accuracies surpassing 97%. With the developed deep learning size classifier, we overcome the need for calibration curves for quantum dots sizing and thanks to the unified modeling approach at the basis of the total scattering method implemented, we include simultaneously structural and microstructural aspects in the classification process,
This algorithm can be complemented by incorporating input information from other experimental observations (e.g. small angle X-ray scattering data) and can be easily extended to other classes of nanocrystals, providing the nanoscience community with a powerful and broad tool to accelerate the development of novel functional (nano)materials.
|
Lucia Allara; Federica Bertolotti; Antonietta Guagliardi
|
Materials Science; Nanoscience; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654a230248dad2312042ae94/original/a-deep-learning-approach-for-quantum-dots-sizing-from-wide-angle-x-ray-scattering-data.pdf
|
65d732149138d23161b61907
|
10.26434/chemrxiv-2022-mnh4n-v2
|
Substituent-dependent spin-state switching in isomeric iron(II) complexes: from bi-stable spin-state switching with T1/2 centred at room temperature to trapped high-spin state
|
Spin-state switching in iron(II) complexes composed of ligands featuring moderate ligand-field strength—for example, 2,6-bi(1H-pyrazol-1-yl)pyridine (BPP)—is dependent on many factors—examples include lattice solvent, counter anion, and substituent. Herein, we show that spin-state switching in isomeric iron(II) complexes (1·CH3CN and 2) composed of tridentate all nitrogen coordinating ligands—ethyl 2,6-bis(1H-pyrazol-1-yl)isonicotinate (BPP-COOEt, L1) and (2,6-di(1H-pyrazol-1-yl)pyridin-4-yl)methylacetate (BPP-CH2OCOMe, L2)—is controlled by the nature of substituent at the fourth position of the pyridine ring of the BPP skeleton. Complex 1·CH3CN, crystallized with acetonitrile solvent, undergoes abrupt and hysteretic spin-state switching, hence bistable switching, with a thermal hysteresis width (ΔT1/2) of 44 K and switching temperature (T1/2) = 298 K in the first cycle. Conversely, the isomeric counterpart of 1·CH3CN—complex 2—crystallized with no lattice solvent; the complex was trapped in the high-spin (HS) state upon cooling from 300 K. Molecular structures of the LS and HS forms of complex 1·CH3CN revealed that spin-state switching induces a pronounced angular distortion, creating an energy barrier separating the LS and HS states. Traversing the barrier requires substantial molecular rearrangement in the presence of constraints imposed by the crystal lattice, rendering the spin-state switching of 1·CH3CN hysteretic in the solid-state. The observation of bistable spin-state switching with T1/2 centred at room temperature for 1·CH3CN as well as the attribution of pronounced angular distortion and conformational variation of the COOEt substituent as causes behind the observed hysteretic spin-state switching indicates that technologically relevant spin-state switching profiles based on mononuclear iron(II) complexes can be obtained.
|
Senthil Kumar Kuppusamy; Asato Mizuno; Lea Spieker; Soma Salamon; Benoît Heinrich; Corinne Bailly; Heiko Wende; Mario Ruben
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Transition Metal Complexes (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d732149138d23161b61907/original/substituent-dependent-spin-state-switching-in-isomeric-iron-ii-complexes-from-bi-stable-spin-state-switching-with-t1-2-centred-at-room-temperature-to-trapped-high-spin-state.pdf
|
62ff931dd858fb9013546243
|
10.26434/chemrxiv-2022-9c7kg-v3
|
Isolation and Catalytic Reactivity of Mononuclear Palladium(I) Complexes
|
<p>Palladium
complexes are among the most commonly used transition metal catalysts for
different organic transformations with wide applications in the chemical
synthesis. Currently, catalytic transformations involving Pd(0)/Pd(II)
catalytic cycles are very well-known, and processes involving Pd(II)/Pd(III)/Pd(IV)
intermediates are also gaining interest in recent years due to the increasing relevance
of high-valent Pd species. By contrast, isolated low-valent Pd(I) complexes,
especially mononuclear Pd(I) species, are very rare. Herein, we report the
isolation of two heteroleptic Pd(I) complexes stabilized by dithiapyridinophane
ligands that were fully characterized by single-crystal X-ray diffraction, EPR,
IR, and UV-Vis spectroscopies, and computational studies. Excitingly, these Pd(I)
complexes are shown to be superior catalysts for the C<i>sp<sup>2</sup></i>-C<i>sp<sup>3</sup>
</i>Kumada cross-coupling reaction vs. their Pd(0) or Pd(II) analogs.</p>
|
Giang N. Tran; Bailey S. Bouley; Liviu M. Mirica
|
Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Transition Metal Complexes (Inorg.); Coordination Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ff931dd858fb9013546243/original/isolation-and-catalytic-reactivity-of-mononuclear-palladium-i-complexes.pdf
|
60c755ab842e655d2bdb435b
|
10.26434/chemrxiv.14135783.v1
|
Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation
|
Cyclotide-induced membrane disruption is studied at the microsecond timescale by Dissipative Particle Dynamics (DPD) to quantitatively estimate a kinetic rate constant for membrane lipid extraction with a “sandwich” interaction model where two bilayer membranes enclose a cyclotide/water compartment. The obtained bioactivity trends for cyclotides Kalata B1, Cycloviolacin O2 and selected mutants with different membrane types are in agreement with experimental findings: For all membranes investigated, Cycloviolacin O2 shows a higher lipid extraction activity than Kalata B1. The presence of cholesterol leads to a decreased cyclotide activity compared to cholesterol-free membranes. Phosphoethanolamine-rich membranes exhibit an increased membrane disruption. A cyclotide’s “hydrophobic patch” surface area is important for its bioactivity. A replacement of or with charged amino acid residues may lead to super-mutants with above-native activity but without simple charge-activity patterns. Cyclotide mixtures show linearly additive bioactivities without significant sub- or over-additive effects.<br />
|
Karina van den Broek; Matthias Epple; Lisa Sophie Kersten; Hubert Kuhn; Achim Zielesny
|
Bioinformatics and Computational Biology; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755ab842e655d2bdb435b/original/quantitative-estimation-of-cyclotide-induced-bilayer-membrane-disruption-by-lipid-extraction-with-mesoscopic-simulation.pdf
|
664b077721291e5d1dc57de7
|
10.26434/chemrxiv-2024-ssxk5
|
Direct Ion-Exchange Method for Preparing a Solution Allowing Spontaneous Perovskite Passivation via Hole Transport Material Deposition
|
We propose a direct ion-exchange (DI) method for preparing a hole transport material (HTM) solution undergoing spontaneous perovskite passivation via HTM deposition and verify its applicability for the photovoltaic performance enhancement of perovskite solar cells (PSCs). The simple synthesis of a Spiro-OMeTAD HTM solution based on ion exchange via dissolving and mixing multiple solid materials in a chlorobenzene solution produces an HTM solution similar to that obtained with an n-octylammonium bis(trifluoromethanesulfonyl)imide ionic liquid functioning as a spontaneous perovskite passivator. Using the resulting HTM solution, the power conversion efficiency of PSCs was enhanced up to 23.0% without conventional post-passivation processes.
|
Naoyuki Nishimura; Hiroyuki Kanda; Takurou N. Murakami
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664b077721291e5d1dc57de7/original/direct-ion-exchange-method-for-preparing-a-solution-allowing-spontaneous-perovskite-passivation-via-hole-transport-material-deposition.pdf
|
60c750a44c8919272fad3dd7
|
10.26434/chemrxiv.13065278.v1
|
De Novo Synthetic Design for Ultrafast Formation of Disulfide Bonds in Peptides and Proteins .pdf
|
<p><b>Despite
six decades of efforts to synthesize peptides and proteins bearing multiple
disulfide bonds, this synthetic challenge remains an unsolved problem in most
targets (e.g. knotted mini proteins). Here we show a de novo general synthetic
strategy for the ultrafast, high-yielding formation of two and three disulfide
bonds in peptides and proteins. We developed an approach based on the combination
of a small molecule, UV-light, and palladium for chemo- and regio-selective
activation of Cys, which enables the one-pot formation of multiple disulfide
bonds in various peptides and proteins. We prepared bioactive targets of high
therapeutic potential, including conotoxin, RANTES, EETI-II, and plectasin
peptides and the linaclotide drug. We anticipate that this strategy will be a
game-changer in preparing millions of inaccessible targets for drug discovery.</b><br /></p>
|
Shay Laps; Fatima Atamleh; Guy Kamnesky; Hao Sun; ashraf brik
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750a44c8919272fad3dd7/original/de-novo-synthetic-design-for-ultrafast-formation-of-disulfide-bonds-in-peptides-and-proteins-pdf.pdf
|
61f2a4708d70c356400f7edd
|
10.26434/chemrxiv-2022-tfkk1
|
Structure-based relaxation analysis reveals C-terminal [1-13C]glycine-d2 in peptides has long spin-lattice relaxation time that is applicable to in vivo hyperpolarized magnetic resonance studies
|
Dissolution-dynamic nuclear polarization (d-DNP) is a state-of-the-art technology that can dramatically enhance the detection sensitivity of nuclear magnetic resonance (NMR). DNP NMR has been applied to small molecules with stable isotopes and has been used to obtain metabolic and physiological information in vivo. However, the hyperpolarized state exponentially decays back to the thermal equilibrium state, depending on the spin-lattice relaxation time (T1). This signal decay has remained a major problem associated with this technology. Therefore, DNP NMR molecular probes useful for in vivo analysis have been limited to naturally occurring small molecules that inherently show long T1. While peptides are promising targets for DNP NMR studies, because of the limitation in T1, DNP NMR molecular probes applicable in vivo have been limited to amino acids or dipeptides. Herein we propose a 13C-labeling strategy to utilize the C-terminal [1-13C]Gly-d2 residue for realizing long T1 in peptides. Structure-based T1 relaxation analysis of amino acids and peptides revealed that (1) T1 does not decrease monotonically with increasing molecular weight and (2) T1 is not significantly affected by a side chain on the neighboring amino acid residue. These findings suggest that the C-terminal [1-13C]Gly-d2 residue affords sufficiently long T1 for biological uses, even in oligopeptides, and allowed us to develop 13C-b- casomorphin-5 (Tyr-Pro-Phe-Pro-[1-13C]Gly-d2, T1 = 24 ± 4 s at 3 T in H2O) and 13C-glutathione (g-Glu-Cys-[1-13C]Gly-d2, T1 = 58 ± 3 s at 3 T in H2O) as DNP NMR probes with long T1. We succeeded in in vivo detection of enzymatic conversions of these two probes. These results demonstrate the utility of our strategy and would contribute to further expansion of the substrate scope for DNP applications.
|
Yohei Kondo; Yutaro Saito; Tomohiro Seki; Yoichi Takakusagi; Jumpei Morimoto; Hiroshi Nonaka; Koichiro Miyanishi; Wataru Mizukami; Makoto Negoro; Abdelazim Elsayed Elhelaly; Fuminori Hyodo; Masayuki Matsuo; Natarajan Raju; Rolf Swenson; Murali C. Krishna; Kazutoshi Yamamoto; Shinsuke Sando
|
Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Biochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f2a4708d70c356400f7edd/original/structure-based-relaxation-analysis-reveals-c-terminal-1-13c-glycine-d2-in-peptides-has-long-spin-lattice-relaxation-time-that-is-applicable-to-in-vivo-hyperpolarized-magnetic-resonance-studies.pdf
|
646e11064f8b1884b7350b2c
|
10.26434/chemrxiv-2023-vb0hr
|
The protein matrix of plastocyanin supports long-distance charge transport with photosystem I and the copper ion regulates its spatial span and conductance
|
Charge exchange is the fundamental process that sustains cellular respiration and photosynthesis by shuttling electrons in a cascade of electron transfer (ET) steps between redox cofactors. While intraprotein charge exchange is well characterized in protein complexes bearing multiple redox sites, interprotein processes are less understood due to the lack of suitable experimental approaches and the dynamic nature of the interactions. Proteins constrained between electrodes are known to support electron transport (ETp) through the protein matrix even without redox cofactors, as the charges housed by redox sites in ET are furnished by the electrodes in ETp configuration. However, it is unknown whether protein ETp mechanisms apply to the interprotein medium that is present in physiological conditions. Here, we study interprotein charge exchange between plant photosystem I (PSI) and its soluble redox partner plastocyanin (Pc) and address the role of the Pc copper center. Using electrochemical scanning tunnelling spectroscopy (ECSTS) current-distance and blinking measurements we respectively quantify the spatial span of charge exchange between individual Pc/PSI pairs and ETp through transient Pc/PSI complexes. Pc devoid of the redox center (Pcapo) can exchange charge with PSI and it does so at longer distances than with the copper ion (Pcholo). Conductance bursts associated to Pcapo/PSI complex formation are higher than in Pcholo/PSI. Thus, copper ions are not required for long distance ETp between PSI and Pc but regulate its spatial span and conductance. Our results suggest that the redox center that carries the charge in Pc is not necessary to exchange it in interprotein ET through the aqueous solution, and question the canonical view of tight complex binding between redox protein partners.
|
Manuel López-Ortiz; Ricardo A. Zamora; Marina I. Giannotti; Pau Gorostiza Langa
|
Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Chemical Biology; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e11064f8b1884b7350b2c/original/the-protein-matrix-of-plastocyanin-supports-long-distance-charge-transport-with-photosystem-i-and-the-copper-ion-regulates-its-spatial-span-and-conductance.pdf
|
60c754174c8919ab54ad4430
|
10.26434/chemrxiv.13607438.v1
|
Enantioselective Conjugate Addition of Catalytically Generated Zinc Homoenolate
|
<div>
<div>
<div>
<p>We report herein an enantioselective
conjugate addition reaction of a zinc homoenolate,
catalytically generated via ring opening of a
cyclopropanol, to an α,β-unsaturated ketone. The reaction
is promoted by a zinc aminoalkoxide catalyst generated
from Et2Zn and a chiral β-amino alcohol to afford 1,6-
diketones, which undergo, upon heating, intramolecular
aldol condensation to furnish highly substituted
cyclopentene derivatives with good to high
enantioselectivities. The reaction has proved applicable to
various 1-substituted cyclopropanols as well as chalcones
and related enones. The chiral amino alcohol has proved
to enable ligand-accelerated catalysis of the homoenolate
generation and its conjugate addition. Positive nonlinear
effects and lower reactivity of a racemic catalyst have
been observed, which can be attributed to a stable and
inactive heterochiral zinc aminoalkoxide dimer.
</p>
</div>
</div>
</div>
|
Yoshiya Sekiguchi; Naohiko Yoshikai
|
Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754174c8919ab54ad4430/original/enantioselective-conjugate-addition-of-catalytically-generated-zinc-homoenolate.pdf
|
6605ade166c1381729184780
|
10.26434/chemrxiv-2024-s3mhn-v2
|
Exploring the Light-Emitting Agents in Renilla Luciferases by an Effective QM/MM Approach
|
Bioluminescence is a remarkable natural process in which living organisms produce light via specific biochemical reactions. Among these organisms, Renilla luciferase (RLuc), derived from the sea pansy Renilla reniformis, is notable for its blue light emission, making it one of the promising candidates for bioluminescent tagging. Our study focuses on RLuc8, a modified variant of RLuc characterized by eight amino acid substitutions. Recent findings have illuminated that its luminescent emitter, coelenteramide, is capable of existing in multiple protonation states. These states may significantly be influenced by adjacent proton acceptor residues at the enzyme's active site, highlighting the complex interplay between the protein structure and its bioluminescent activity. Herein employing the Quantum Mechanical Consistent Force Field (QCFF/PI) method and the semi-macroscopic Protein Dipole-Langevin Dipole method with Linear Response Approximation (PDLD/S-LRA), we show that the phenolate state of coelenteramide in RLuc8 is the predominant light-emitting species, corroborating experimental results. Our calculations also demonstrate that proton transfer from neutral coelenteramide to Asp162 is integral to the bioluminescence mechanism. Furthermore, our calculations reproduce the observed emission maximum for the amide anion in RLuc8-D120A mutant. In the case of RLuc8-D162A, we predicted that the pyrazine anion, existing in the presence of a Na+ counterion, has an emission maximum consistent with experimental data, suggesting its primary role as potential emitter. Additionally, our calculations on the engineered AncFT-D160A enzyme, structurally similar to RLuc8-D162A but with a significantly blue-shifted emission peak, show that the emission peak of its neutral form of the emitter agrees well with observed data. This agreement may explain the variations in observed emission peaks. This study not only showcases an effective way for investigating the bimolecular states of chromophores in light emission but also introduces an efficient approach that integrates the proton transfer process into the calculations of the emission spectra, proving vital for further research of proton transfer and light emission in photoproteins.
|
Ashim Nandi; Aoxuan Zhang; Zhen Tao Chu; Wen Jun Xie; Zhongxin Xu; Suwei Dong; Arieh Warshel
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Computational Chemistry and Modeling; Biocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6605ade166c1381729184780/original/exploring-the-light-emitting-agents-in-renilla-luciferases-by-an-effective-qm-mm-approach.pdf
|
639302dbb103af371611a2cd
|
10.26434/chemrxiv-2022-23311
|
Calculation of number-average functionality and gel-point for stepwise polymerization
|
The number-average functionality is proposed a simplified equation which can be used to predict the reaction progress of the stepwise polymerization expediently. According to the equation, once the average functionality of one reactant ((f_b ) ̅, for example) is fixed, there will be a critical functionality of (f_a ) ̅. The reaction system has no risk to gel with the increase of component A if (f_a ) ̅ is below the critical functionality, while gelation will occur with the increase of component A if (f_a ) ̅ is higher than the critical functionality, and the gel point is the degree of reaction when (f_nb ) ̅ diverges to indefinitely large. The deduced equation is suitable for polymerization between R-An and R’-Bn, in which one of the components could be consumed completely, such as polyurethane, polyester, or other stepwise polymerization reactions. The equation can calculate the number-average functionality of polymer mixtures, especially for grafting or branched polymerization.
|
Hui Deng; Yan Han
|
Theoretical and Computational Chemistry; Polymer Science; Polymerization (Polymers); Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2022-12-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639302dbb103af371611a2cd/original/calculation-of-number-average-functionality-and-gel-point-for-stepwise-polymerization.pdf
|
60c74516842e6537d0db25a0
|
10.26434/chemrxiv.9961937.v1
|
Intermolecular 3+3 Ring Expansion of Aziridines to Dehydropiperidines through the Intermediacy of Aziridinium Ylides
|
Bicyclic aziridines undergo formal [3+3] ring expansion reactions when exposed to rhodium-bound vinyl carbenes to form complex dehydropiperidines in a highly stereocontrolled rearrangement. Mechanistic studies and DFT computations indicate the reaction proceeds through the formation of a vinyl aziridinium ylide; this reactive intermediate undergoes a concerted, asynchronous, pseudo-[1,4]- sigmatropic rearrangement to directly furnish the heterocyclic products with net retention at the new C-C bond. In combination with an asymmetric silver-catalyzed aziridination developed in our group, this method quickly delivers enantioenriched scaffolds with up to three contiguous stereocenters. The mild reaction conditions, functional group tolerance, and high stereochemical retention of this method are especially well-suited for appending piperidine motifs to natural product and complex molecules. Ultimately, our work establishes the value of underutilized aziridinium ylides as key intermediates in strategies to convert small, strained rings to larger N-heterocycles.
|
Jennifer Schomaker; Josephine Eshon; Kate A. Nicastri; Steven C. Schmid; William T. Raskopf; Ilia A. Guzei,; Israel Fernández
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74516842e6537d0db25a0/original/intermolecular-3-3-ring-expansion-of-aziridines-to-dehydropiperidines-through-the-intermediacy-of-aziridinium-ylides.pdf
|
65198a6800659409123d282b
|
10.26434/chemrxiv-2023-4hgnm
|
Modelling the solubility of gases in aqueous solutions in the context of renewable energy production with focus on geothermal plants, energy storage, and carbon sequestration
|
The interactions between aqueous solutions, gases, and minerals dictate the extent of issues such as scaling, degassing, and corrosion, which have a major impact on the performance of a vast number of industrial applications (e.g., geothermal plants, oil and gas production facilities, natural gas storage in saline aquifers, flue gas scrubbing, carbon sequestration, etc.). Among the different software programs available for aqueous chemistry calculations, PHREEQC and Reaktoro were tested and validated against a wide dataset of gas solubility measurements. For the datasets considered, the two programs essentially led to the same outcome with only a few discrepancies observed. Yet, the agreement between the models and experimental data was greatly affected by the selected database. The models implemented in PHREEQC and Reaktoro were also compared with the experimental bubble point pressure of fluids sampled at several geothermal wells. The satisfactory performance of both PHREEQC and Reaktoro for describing different chemical systems at a wide range of pressures and temperatures showcases their versatility and practicality for assisting in the design and optimization of various processes relevant to the energy transition (e.g., geothermal exploitation, CO2 /H2 transport and storage).
|
Maria Bonto; Anders Andreasen
|
Physical Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Energy Storage; Solution Chemistry; Thermodynamics (Physical Chem.)
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CC BY 4.0
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CHEMRXIV
|
2023-10-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65198a6800659409123d282b/original/modelling-the-solubility-of-gases-in-aqueous-solutions-in-the-context-of-renewable-energy-production-with-focus-on-geothermal-plants-energy-storage-and-carbon-sequestration.pdf
|
613f7d59d5f0800e38c3ae11
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10.26434/chemrxiv-2021-6bs54
|
Comparative study between adsorbents based on magnetic nanoferrite.
Application to the removal of methyl orange from wastewater
|
Magnetic ferrite (Mg-doped bismuth ferrite) and its clay-based composite (Mg-doped bismuth ferrite-bentonite) were prepared by self-combustion method utilizing glycine as fuel and served for the removal of methyl orange (MO) from aqueous solutions.
The ferrite-based adsorbents were characterized by the measurement of specific surface area (BET), scanning electron microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), X-ray diffraction (XRD). The different experimental parameters that affect the performance of this reaction such as: temperature, contact time, initial dye concentration and mass of adsorbent were investigated. The point of zero charge pH (pHPZC) was determined for the two adsorbents. Langmuir and Freundlich adsorption models were employed to provide a description of the equilibrium isotherms. Adsorption tests showed that the equilibrium time is a function of the initial concentration of dye. The adsorption kinetic study indicated that the equilibrium adsorption is established after 300 minutes for Mg-doped bismuth ferrite, while it is established after 180 minutes for Mg-doped bismuth ferrite-bentonite composite. Furthermore, this suggests that the adsorption of MO on both adsorbents can be perfectly described by pseudo-second order kinetics. The maximum adsorption capacity determined by the mathematical model of Langmuir is equal to 181.8 mg.g-1 for Mg-doped bismuth ferrite and to 188.7 mg.g-1 for its composite, at 298 K. Adsorption isotherms shows that the Freundlich model perfectly represents adsorption of methyl orange to the prepared Mg-doped bismuth ferrite. The ferrite/bentonite composite has 2-50 nm-sized pores and is indeed a mesoporous material. The small pores observed on the surface of the adsorbents are in line with type IV isotherm, with possible capillary condensation of the adsorbate. Moreover, Langmuir model seems to be the most suitable model for the absorption of methyl orange on the Mg-doped bismuth ferrite-bentonite composite. The thermodynamic parameters related to the sorbent/adsorbate system indicate that adsorption is spontaneous and exothermic. The determination of isosteric heat of adsorption suggested that it is indeed a physisorption characterized by weak intermolecular forces between MO and the surface.
|
Sabrine Saad; Sarra Ben Amor; Amel Ben Slimane
|
Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Solid State Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-09-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613f7d59d5f0800e38c3ae11/original/comparative-study-between-adsorbents-based-on-magnetic-nanoferrite-application-to-the-removal-of-methyl-orange-from-wastewater.pdf
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6467c7e5fb40f6b3eedb5648
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10.26434/chemrxiv-2023-v73sk
|
Revised Nitrogen Reduction Scaling Relations from Potential-Dependent Modeling of Chemical and Electrochemical Steps
|
The electrochemical nitrogen reduction reaction (NRR) is a promising route to enable carbon-free ammonia production. However, it is limited by the poor activity and selectivity of current catalysts. The rational design of superior NRR electrocatalysts requires a detailed mechanistic understanding of current material limitations to inform how these can be overcome. The current understanding of how scaling limits NRR on metal catalysts is predicated on a simplified reaction pathway that only considers proton-coupled electron transfer (PCET) steps. Here, we apply grand canonical density functional theory to investigate a more comprehensive NRR mechanism that includes both electrochemical and chemical steps on 23 metal surfaces in solvent under an applied potential. We applied Φmax, a grand canonical adaptation of the Gmax descriptor, to evaluate trends in catalyst activity. This approach produces a Φmax “volcano” diagram for NRR activity scaling on metals that qualitatively differs from the scaling relations identified when only PCET steps are considered. NH3* desorption was found to limit NRR activity for materials at the top of the volcano and truncates the volcano’s peak at increasingly reducing potentials. These revised scaling relations may inform the rational design of superior NRR electrocatalysts. This approach is transferable to study additional materials and reaction chemistries where both electrochemical and chemical steps are modeled under an applied potential.
|
Cooper Tezak; Nicholas Singstock; Abdulaziz AlHerz; Derek Vigil-Fowler; Christopher Sutton; Ravishankar Sundararaman; Charles Musgrave
|
Theoretical and Computational Chemistry; Materials Science; Catalysis; Theory - Computational; Electrocatalysis; Heterogeneous Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6467c7e5fb40f6b3eedb5648/original/revised-nitrogen-reduction-scaling-relations-from-potential-dependent-modeling-of-chemical-and-electrochemical-steps.pdf
|
60c75269bdbb89c2e8a3a280
|
10.26434/chemrxiv.13296311.v1
|
Phospha-Wittig Reagents Rediscovered
|
Phospha-Wittig reagents, RPPMe<sub>3</sub> (R = Mes* 2,4,6-<i>t</i>Bu<sub>3</sub>-C<sub>6</sub>H<sub>2</sub>;
<sup>Mes</sup>Ter 2,6-(2,4,6-Me<sub>3</sub>C<sub>6</sub>H<sub>2</sub>)-C<sub>6</sub>H<sub>3</sub>;
<sup>Dip</sup>Ter 2,6-(2,6-<i>i</i>Pr<sub>2</sub>C<sub>6</sub>H<sub>3</sub>)-C<sub>6</sub>H<sub>3</sub>),
can be considered as phosphine-stabilized phosphinidenes. In this study we show
that PMe<sub>3</sub> can be displaced by NHCs or NHOs. Interestingly,
phosphinidene-like reactivity results in a subsequent C(sp<sup>2</sup>)-H
activation of the exocyclic CH<sub>2</sub> in NHOs. This concept was further
extended to allyl-apended NHOs, which results in phosphine-substituted allyl
species.
|
Priyanka Gupta; Jan-Erik Siewert; Tim Wellnitz; Malte Fischer; Wolfgang Baumann; Torsten Beweries; Christian Hering-Junghans
|
Main Group Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75269bdbb89c2e8a3a280/original/phospha-wittig-reagents-rediscovered.pdf
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6470b8a0be16ad5c57f4b8bc
|
10.26434/chemrxiv-2023-2nf51
|
Data-driven approaches for identifying hyperparameters in multi-step retrosynthesis
|
Multi-step retrosynthesis problem can be solved by a search algorithm, such as Monte Carlo tree search (MCTS). The performance of multistep retrosynthesis, as measured by a trade-off in search time and route solvability, therefore depends on the hyperparameters of the search algorithm. In this paper, we demonstrated the effect of three MCTS hyperparameters (number of iterations, tree depth, and tree width) on metrics such as Linear integrated speed-accuracy score (LISAS) and Inverse efficiency score which consider both route solvability and search time. This exploration was conducted by employing three data-driven approaches, namely a systematic grid search, Bayesian optimization over an ensemble of molecules to obtain static MCTS hyperparameters, and a machine learning approach to dynamically predict optimal MCTS hyperparameters given an input target molecule. With the obtained results on the internal dataset, we demonstrated that it is possible to identify a hyperparameter sets which outperform the current AiZynthFinder default setting and appeared optimal across a variety of target input molecules, both on proprietary and public datasets. The settings identified with the in-house dataset reached a solvability of 93% and median search time of 151s for the in-house dataset, and a 74% solvability and 114s for the ChEMBL dataset. These numbers can be compared to the current default settings which solved 85% and 73% during a median time of 110s and 84s, for in-house and ChEMBL, respectively.
|
Annie Westerlund; Bente Barge; Lewis Mervin; Samuel Genheden
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6470b8a0be16ad5c57f4b8bc/original/data-driven-approaches-for-identifying-hyperparameters-in-multi-step-retrosynthesis.pdf
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66cc884620ac769e5fe4275b
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10.26434/chemrxiv-2024-jjdsq
|
Latin American Natural Product Database (LANaPDB): an update
|
Natural product (NP) databases are crucial tools in computer-aided drug design (CADD). Over the last decade, there has been a worldwide effort to assemble information regarding natural products (NPs) isolated and characterized in certain geographical regions. In 2023, it was published LANaPDB, to our knowledge, it is the first attempt to gather and standardize all the NP databases of Latin America. Herein, we present and analyze in detail the contents of an updated version of LANaPDB, which includes 619 newly added compounds from Colombia, Costa Rica, and Mexico. The present version of LANaPDB has a total of 13,578 compounds, coming from ten databases of seven Latin American countries. A chemoinformatic characterization of LANAPDB was carried out, which includes the structural classification of the compounds, calculation of six physicochemical properties of pharmaceutical interest, visualization of the chemical space, determination of the structural diversity, molecular complexity, synthetic feasibility, commercial availability, predicted and reported biological activity. In addition, the LANaPDB compounds were cross-referenced to two of the largest public chemical compound databases annotated with biological activity: ChEMBL and PubChem. The Latin American natural product collection LANaPDB is publicly available and can be downloaded at https://github.com/alexgoga21/LANaPDB-version-2/tree/main.
|
Alejandro Gómez-García; Daniel A. Acuña Jiménez; William J. Zamora; Haruna L. Barazorda-Ccahuana; Miguel Á. Chávez-Fumagalli; Marilia Valli; Adriano D. Andricopulo; Vanderlan da S. Bolzani; Dionisio A. Olmedo; Pablo N. Solís; Marvin J. Núñez; Johny R. Rodríguez Pérez; Hoover A. Valencia Sánchez; Héctor F. Cortés Hernández; Oscar M. Mosquera Martinez; Jose L. Medina-Franco
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cc884620ac769e5fe4275b/original/latin-american-natural-product-database-la-na-pdb-an-update.pdf
|
66f57c99cec5d6c1424be6a6
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10.26434/chemrxiv-2024-mdldd
|
Unveiling the Impact of Impurity Phases on the Electrochemical Performance of Cobalt-Free Analogs of (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O as anode for Lithium-ion Batteries
|
Micrometer-size particles of the pure single-phase rock salt multi-metals oxide, (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O, have demonstrated long-term cycling stability and excellent rate performance as an anode for lithium-ion batteries. Such a feat has only been achieved with the nanostructuring of binary transition metal oxides. This success has led to the preparation of several pure single-phase spinel multi-metal oxides with significantly higher capacities. A common belief regarding these complex oxides is that the pure single-phase is a prerequisite for their outstanding electrochemical performance. Deviation from a pure single-phase is thought to harm their electrochemical performance. Here, we prepare and characterize the cobalt-free analogs of (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O using a traditional solid-state synthesis method by replacing cobalt with iron and manganese to give (Mg0.2Fe0.2Ni0.2Cu0.2Zn0.2)O and (Mg0.2Mn0.2Ni0.2Cu0.2Zn0.2)O respectively. These analogs were prepared in an air and an argon atmosphere to yield several compositions with different mixtures of crystalline secondary phases. The electrochemical performance of the pure single-phase (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O is used as a benchmark to compare the performance of the cobalt-free multi-phase analogs. The results indicate that although these cobalt-free analogs are not pure single-phase materials, their electrochemical performance is similar to that observed with (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O, suggesting that a pure single-phase might not be a prerequisite for an excellent electrochemical performance for these complex multi-metal oxides.
|
Modeste Tegomoh; Anne Co
|
Materials Science; Energy; Ceramics; Materials Processing; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f57c99cec5d6c1424be6a6/original/unveiling-the-impact-of-impurity-phases-on-the-electrochemical-performance-of-cobalt-free-analogs-of-mg0-2co0-2ni0-2cu0-2zn0-2-o-as-anode-for-lithium-ion-batteries.pdf
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67bc864681d2151a02da1b13
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10.26434/chemrxiv-2025-mwspf-v2
|
A new perspective on aqueous electrolyte solutions
|
Aqueous electrolyte solutions are central to many natural phenomena and industrial applications leading to continuous development of increasingly complex analytical models. These are based on an atomistic description of ion-ion electrostatic interactions combined with mean-field approaches for the dielectric response of water. Despite many achievements, these concepts fail to quantitatively describe situations where ion-ion correlation and specific solvation become relevant, such as for concentrated electrolyte solutions. Here, we propose a change of perspective, by introducing a statistical, coarse-grained view to describe the average thermodynamic properties of aqueous electrolyte solutions. This approach bypasses the need to define ion-pairs or ion-complexes and does not require any prior knowledge on specific solvation. We base our concept on separating the solution into a spherical observation droplet whose size and average composition are uniquely determined by the solution parameters, and its environment consisting of the remaining solution. This allows us to express the droplet-environment interaction in terms of a generalized multipole expansion, i.e. in a convenient, additive way. We applied this approach to 135 electrolytes including some notoriously complex electrolytes, such as LiCl or ZnCl$_2$ over the full solubility range. This paves the road toward understanding super-saturated and water-in-salt solutions and electrolyte nucleation.
|
Gerhard Schwaab; Simone Pezzotti
|
Physical Chemistry; Chemical Engineering and Industrial Chemistry; Physical and Chemical Properties; Solution Chemistry; Thermodynamics (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc864681d2151a02da1b13/original/a-new-perspective-on-aqueous-electrolyte-solutions.pdf
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65fd8566e9ebbb4db944c542
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10.26434/chemrxiv-2023-0qrs7-v4
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Improving the sustainability of enzymatic synthesis of poly(butylene adipate)-based copolyesters. Polycondensation reaction in bulk vs in diphenyl ether
|
In response to mounting global concerns such as CO2 emissions, environmental pollution, and the depletion of fossil resources, the field of polymer science is shifting its focus toward sustainability. This research investigates the synthesis of poly(butylene adipate)-co-(dilinoleic adipate) (PBA-DLA) copolymers using two distinct methods: bulk polycondensation and polycondensation in diphenyl ether. The objective is to assess the environmental impact, chemical structure, composition, and key properties of the resulting copolymers, with a particular emphasis on determining the viability of bulk synthesis as a more sustainable approach. Various analytical methods, including nuclear magnetic resonance spectroscopy (NMR), Fourier transform infrared spectroscopy (FTIR), and size exclusion chromatography (SEC), were employed to confirm successful copolymerization and highlight differences in molecular weight and microstructure. Additionally, thermal and dynamic mechanical analyses were conducted to thoroughly characterize the copolymers' properties. This research provides significant findings into the sustainable production of PBA-DLA copolymers, offering a more environmentally friendly approach without compromising product quality or performance.
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Martyna Sokołowska; Kristof Molnar; Judit E. Puskas; Miroslawa El Fray
|
Catalysis; Polymer Science; Polymerization (Polymers); Biocatalysis; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
|
2024-03-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fd8566e9ebbb4db944c542/original/improving-the-sustainability-of-enzymatic-synthesis-of-poly-butylene-adipate-based-copolyesters-polycondensation-reaction-in-bulk-vs-in-diphenyl-ether.pdf
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6438b39d73c6563f14d15151
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10.26434/chemrxiv-2023-b3m9b
|
Same Day Access to Proteins Enabled by Folding Selections
|
From laundry detergent to biomedicines, proteins are core components of modern technology. However, despite significant progress, modern recombinant protein expression still requires days to months to deliver pure, functional material. Chemical protein synthesis can also afford proteins for study with similar timeframes at the chemistry stage, with additional time dedicated post-synthesis for handling as separation of the numerous closely related side-products requires weeks to months. To overcome these rate-limiting barriers, we propose folding selection as a new framework to understand synthetic side products and enable rapid purification. We demonstrate that the minor chemical modifications present on synthetic side products result in substantially altered physical-chemical properties and that simple bio-purification techniques can separate them from the native protein in hours. With this strategy, we demonstrate the production of nine functional synthetic proteins in under ten hours each, including disulfide-containing enzymes and transcription factor domains with non-natural amino acids. Furthermore, only possible with this technology, we access homogeneous, post-translationally modified (e.g., by phosphorylation or acetylation) proteins in milligram amounts in hours. Understanding protein function is a cornerstone of modern biology, and the same-day protein production described here is uniquely suited to accelerate these efforts.
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Alex J. Callahan; Aurélie Rondon; Lia Lozano Salazar; Satish Gandhesiri; Jacob Rodriguez; Andrei Loas; Bradley Pentelute
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Biological and Medicinal Chemistry; Organic Chemistry; Polymer Science; Biopolymers; Bioengineering and Biotechnology; Chemical Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-04-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6438b39d73c6563f14d15151/original/same-day-access-to-proteins-enabled-by-folding-selections.pdf
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62963bf197e76a533fc0a2bd
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10.26434/chemrxiv-2022-vw55l
|
The Crystal Structure of Carbonic Acid
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Ubiquitous carbonic acid, H2CO3, a key molecule in biochemistry, geochemistry, and also extraterrestrial chemistry, is known from a plethora of physicochemical studies. Its crystal structure has now been determined from neutron-diffraction data on a deuterated sample in a specially built hybrid clamped cell. At 1.85 GPa, D2CO3 crystallizes in the monoclinic space group P21/c with a = 5.392(2), b = 6.661(4), c = 5.690(1) Å, β = 92.66(3)°, Z = 4, with one symmetry-inequivalent anti-anti shaped D2CO3 molecule forming dimers, as previously predicted. Quantum chemistry evidences π bonding within the CO3 molecular core, very strong hydrogen bonding between the molecules, and a massive influence of the crystal field on all bonds; phonon calculations emphasize the locality of the vibrations, being rather insensitive to the extended structure.
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Sebastian Benz; Da Chen; Andreas Möller; Michael Hofmann; David Schnieders; Richard Dronskowski
|
Inorganic Chemistry; Crystallography – Inorganic
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-06-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62963bf197e76a533fc0a2bd/original/the-crystal-structure-of-carbonic-acid.pdf
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6346a7551037d6ad7840f0be
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10.26434/chemrxiv-2022-d37lg
|
A crystalline aluminum/carbon-based ambiphile capable of activation and catalytic transfer of ammonia
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We report on a rare combination of an aluminum Lewis acid and a carbon Lewis base in the field of frustrated Lewis pair chemistry. A new class of hidden frustrated Lewis pairs consisting of a phosphorus ylide featuring an aluminum fragment in the ortho position of a phenyl ring scaffold is introduced. Although the formation of the Lewis acid/base adduct was observed in the solid state, the title compound readily reacts with ammonia under thermoneutral and reversible N–H bond splitting at ambient temperature. Furthermore, previously unprecedented NH3 transfer reactions mediated by a main group catalyst are presented.
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Felix Krämer; Jan Paradies; Israel Fernández; Frank Breher
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Organometallic Chemistry; Main Group Chemistry (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-10-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6346a7551037d6ad7840f0be/original/a-crystalline-aluminum-carbon-based-ambiphile-capable-of-activation-and-catalytic-transfer-of-ammonia.pdf
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60c73e16bdbb895770a37da2
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10.26434/chemrxiv.6143732.v2
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Large–Scale Computational Screening of Molecular Organic Semiconductors Using Crystal Structure Prediction
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Predictive computational methods have the potential to significantly accelerate the discovery of new materials with targeted properties by guiding the choice of candidate materials for synthesis. Recently, a planar pyrrole azaphenacene molecule (pyrido[2,3-b]pyrido[3`,2`:4,5]-pyrrolo[3,2-g]indole, <b>1</b>) was synthesized and shown to have promising properties for charge transport, which relate to stacking of molecules in its crystal structure. Building on our methods for evaluating small molecule organic semiconductors using crystal structure prediction, we have screened a set of 27 structural isomers of <b>1</b> to assess charge mobility in their predicted crystal structures. Machine--learning techniques are used to identify structural classes across the landscapes of all molecules and we find that, despite differences in the arrangement of hydrogen bond functionality, the predicted crystal structures of the molecules studied here can be classified into a small number of packing types. We analyze the predicted property landscapes of the series of molecules and discuss several metrics that can be used to rank the molecules as promising semiconductors. The results suggest several isomers with superior predicted electron mobilities to <b>1</b> and suggest two molecules in particular that represent attractive synthetic targets.
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Jack Yang; Sandip De; Joshua E Campbell; Sean Li; Michele Ceriotti; Graeme Day
|
Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Self-Assembly; Structure
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CC BY 4.0
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CHEMRXIV
|
2018-04-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e16bdbb895770a37da2/original/large-scale-computational-screening-of-molecular-organic-semiconductors-using-crystal-structure-prediction.pdf
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66f4cce5cec5d6c14239516f
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10.26434/chemrxiv-2024-f80wf-v2
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Sulfenylnitrene-Mediated Nitrogen-Atom Insertion into Pyrroles, Indoles, and Imidazoles
|
Given the prevalence of nitrogen-containing heterocycles in FDA-approved drugs, selectively incorporating a single nitrogen atom emerges as a promising scaffold-hopping approach to enhance chemical diversity in drug discovery libraries. In this study, we harness the distinct reactivity of sulfenylnitrenes, which insert a single nitrogen atom to transform readily available pyrroles, indoles, and imidazoles into synthetically challenging pyrimidines, quinazolines, and triazines, respectively. Our additive-free method for skeletal editing employs easily accessible, benchtop-stable sulfenylnitrene precursors over a broad temperature range (–30 to 150 ºC). This chemical approach is compatible with diverse functional groups, including oxidation-sensitive functionalities like phenols and thioethers, and has been applied to various natural products, amino acids, and pharmaceuticals. Furthermore, we have conducted mechanistic studies and explored regioselectivity outcomes through DFT calculations.
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Bidhan Ghosh; Prakash Kafle; Rishav Mukherjee; Randall Welles; Deacon Herndon; Kenneth Nicholas; Yihan Shao; Indrajeet Sharma
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f4cce5cec5d6c14239516f/original/sulfenylnitrene-mediated-nitrogen-atom-insertion-into-pyrroles-indoles-and-imidazoles.pdf
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60c74333469df4957df4312a
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10.26434/chemrxiv.8984009.v1
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From Concept to Crystals via Prediction: Multi-Component Organic Cage Pots by Social Self-Sorting
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<p>We describe the <i>a priori </i>computational prediction and realization of multi-component cage pots, starting with molecular predictions based on candidate precursors through to crystal structure prediction and synthesis using robotic screening. The molecules were formed by the social self-sorting of a tri-topic aldehyde with both a tri-topic amine and di-topic amine, without using orthogonal reactivity or precursors of the same topicity. Crystal structure prediction suggested a rich polymorphic landscape, where there was an overall preference for chiral recognition to form heterochiral rather than homochiral packings, with heterochiral pairs being more likely to pack window-to-window to form two-component capsules. These crystal packing preferences were then observed in experimental crystal structures. <br /></p>
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Rebecca L. Greenaway; Valentina Santolini; Angeles Pulido; Marc A. Little; Ben M. Alston; Michael Briggs; Graeme Day; Andrew
I. Cooper; Kim Jelfs
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Supramolecular Chemistry (Org.)
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CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74333469df4957df4312a/original/from-concept-to-crystals-via-prediction-multi-component-organic-cage-pots-by-social-self-sorting.pdf
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672d137a5a82cea2fa6a5229
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10.26434/chemrxiv-2024-pjx2h
|
Nonenzymatic Carboxylate Phosphorylation in Water
|
The core pathways of autotrophic microbial metabolism have been proposed to be fossils of self-organized prebiotic chemistry. In recent years, numerous reactions within these pathways have been shown to occur nonenzymatically, supporting this hypothesis. However, the phosphorylation of carboxylic acids to the corresponding acyl phosphates, a recurring metabolic reaction, has yet to be demonstrated without enzymes. Here we show that carboxylate phosphorylation is promoted by diamidophosphate (DAP) and sodium nitrite in the presence of water, driven by the release of dinitrogen. The reaction occurs in minutes at 0-50 °C to convert carboxylic acids to acyl amidophosphate intermediates, which then undergo nitrite-promoted hydrolysis to give the corresponding acyl phosphates. Though we do not claim the conditions used here were directly relevant to the origin of life, the observation of aqueous nonenzymatic carboxylate phosphorylation to simple acyl phosphates in the absence of adenosine triphosphate (ATP) raises the enticing prospect that it might also be achieved using driving forces more congruent with the principles of cellular bioenergetics.
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Weiqiang Chen; Joris Zimmermann; Jonas Dechent; Joseph Moran
|
Organic Chemistry; Bioorganic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672d137a5a82cea2fa6a5229/original/nonenzymatic-carboxylate-phosphorylation-in-water.pdf
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649e24be9ea64cc167319508
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10.26434/chemrxiv-2023-rgm98
|
Thienoisoindigo-based recyclable conjugated polymers for organic electronics
|
In transient electronics, imine-based semiconducting polymers based on thiophene-flanked diketopyrrolopyrrole (TDPP) are widely used to realize naturally disposable electronic devices. However, TDPP units easily decomposed even under mildly acidic conditions in the biodegradation of electronic devices. Herein, we have designed and synthesized two chemically recyclable thienoisoindigo (TII)-based polymers bearing an imine bond at the depolymerized position, in which these polymers were prepared from polycondensation reactions of dialdehyde-functionalized monomer TII-(CHO)2 with p-phenylenediamine (PPD) to produce p(TII-PD) and 2,6-naphtalenediamine (2,6ND) to produce p(TII-2,6ND), respectively. Especially, we have examined the recyclability of both polymers. In the degradation process under mildly acidic conditions, our polymers showed excellent degradability within one day, and the TII-(CHO)2 monomer was retrieved with over 90% yield and exhibited remarkable chemical stability over 6 months under the degradation conditions. We prepared the same recycled polymers as p(TII-PD) and p(TII-2,6ND) by utilizing the recovered TII-(CHO)2 monomer. The recycled polymers displayed almost the same physicochemical properties and field-effect mobilities in the order of 10-2-10-3 cm2/Vs as the pristine polymers. These reproducible results suggest that the TII-based monomer unit is an excellent building block for developing fully recyclable semiconducting polymers.
|
Naoya Nozaki; Azalea Uva; Hidetoshi Matsumoto; Helen Tran; Minoru Ashizawa
|
Materials Science; Polymer Science; Biodegradable Materials; Conducting polymers; Organic Polymers; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649e24be9ea64cc167319508/original/thienoisoindigo-based-recyclable-conjugated-polymers-for-organic-electronics.pdf
|
6715ff65d433919392b38e16
|
10.26434/chemrxiv-2024-0mdvs
|
Identification of the novel synthetic opioid N-pyrrolidino isotonitazene at an Australian drug checking service.
|
2-Benzylbenzimidazole opioids and related derivatives, also known as ‘nitazenes’, present a growing threat to public health. Emerging in Europe in 2019, the nitazene group of drugs is a recent addition to the novel synthetic opioid class and has been associated internationally with adverse effects in drug users, overdose clusters and significant mortality. The high potency of many nitazene derivatives, which can in many cases exceed that of fentanyl, poses a significant challenge to the public health and early warning systems used to detect and respond to the emergence of new high-risk substances. This report describes close collaboration between an Australian drug checking service and a nearby university laboratory to identify and characterise the novel synthetic opioid N-pyrrolidino isotonitazene in an expected oxycodone sample presented by a member of the public. Though no prior publications are available describing the presence of this nitazene in the drug market, previously reported in vitro evaluation of this compound reveals it to be among the most potent nitazene opioid agonists known. The study highlights the rapid response possible though engaging drug users with drug checking services as a market monitor and early warning system to alert health services and the broader community to the presence of unexpected, high-risk substances. Integration of well-resourced and supported drug checking services provides a powerful approach to tackle the public health threats associated with new synthetic opioids and other drugs of concern.
|
Blake Curtis; Douglas Lawes; David Caldicott; Malcolm D. McLeod
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Spectroscopy (Anal. Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6715ff65d433919392b38e16/original/identification-of-the-novel-synthetic-opioid-n-pyrrolidino-isotonitazene-at-an-australian-drug-checking-service.pdf
|
66792dc9c9c6a5c07a415a4e
|
10.26434/chemrxiv-2024-428c6
|
Glycosylation-Enhanced Luminescence of Nonaromatic Amino Acids
|
Nonaromatic amino acids with intrinsic photoluminescence (PL) have drawn growing attention due to their crucial role in the luminescence of natural proteins. Nevertheless, the faint luminescence significantly constrains the mechanism exploration of biomolecules as well as their practical applications. We here report a serendipitous finding of synergetic PL enhancement by coupling both weakly emissive nonaromatic amino acids and sugars via glycosidic bonds. Namely, glycosylation drastically boosted the quantum yields of nonaromatic amino acids from 0.3% to as high as 9.2%, accompanied by the emergence of pro-nounced persistent room temperature phosphorescence (p-RTP). This synergistic PL enhancement arises from the ingenious integration of the electron-rich oxygen clusters present in sugar with the charge separation characteristics of amino acids. Driven by amino acids, ample electrons supplied by the sugar rings are directionally induced to promote electron delocaliza-tion, as well as subsequently enhanced absorption, resulting in a more efficient excitation process. Furthermore, the ultrafast femtosecond to nanosecond transient absorption (fs-TA, ns-TA) spectroscopy and theoretical calculations further reveal the importance of hybridization of the locally excited (LE) and the charge transfer (CT) states for PL enhancement and p-RTP features. These results not only provide a universal strategy for constructing efficient nonconventional luminophores but also shed new light on the underlying mechanism of biological autofluorescence.
|
Qiang Zhang; Zihao Zhao; Guangxin Yang; Anze Li; Yijing Cui; Yusong Cai; Zhuojie Yin; Yuntian Tan; Chenyang Zhou; Qian Peng; Wang Zhang Yuan
|
Physical Chemistry; Organic Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66792dc9c9c6a5c07a415a4e/original/glycosylation-enhanced-luminescence-of-nonaromatic-amino-acids.pdf
|
64871b1be64f843f41add544
|
10.26434/chemrxiv-2023-k7jl7
|
Prospects of Single-Cell NMR Spectroscopy with Quantum Sensors
|
Single-cell analysis can unravel functional heterogeneity within cell populations otherwise obscured by ensemble measurements. However, non-invasive techniques that probe chemical entities and their dynamics are still lacking. This challenge could be overcome by novel sensors based on nitrogen-vacancy (NV) centers in diamond, which enable nuclear magnetic resonance (NMR) spectroscopy on unprecedented sample volumes. In this perspective, we briefly introduce NV-based quantum sensing and review the progress made in microscale NV-NMR spectroscopy. Lastly, we discuss approaches to enhance the sensitivity of NV ensemble magnetometers to detect biologically relevant concentrations and provide a roadmap towards their application in single-cell analysis.
|
Nick Ruben Neuling; Robin Derek Allert; Dominik Benjamin Bucher
|
Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Spectroscopy (Anal. Chem.); Cell and Molecular Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64871b1be64f843f41add544/original/prospects-of-single-cell-nmr-spectroscopy-with-quantum-sensors.pdf
|
67b5c6db81d2151a022438fb
|
10.26434/chemrxiv-2025-0mhwm
|
Towards carbon-free cathodes for fluoride ion batteries: deconvoluting effects of active material and conductive additive on charging and cyclic stability
|
In this study, conductive, fluorine and antimony co-doped tin oxide nanoparticles (FATO-NPs) are highlighted as a possible alternative for conductive carbon additives in fluoride ion batteries, successfully circumventing oxidative side reactions. Since good cyclability with high and stable discharge capacities was achieved with both types of conductive additive, it was concluded that conductive carbon is well suitable for high-voltage fluoride ion batteries, contrary to prior assumptions. The utilization of almost completely side-reaction free FATO-NPs as the conductive additive enables the deconvolution of other side reactions in initial cycles.
|
Tommi Hendrik Aalto; Roham Talei; Guido Schmitz; Oliver Clemens
|
Materials Science; Nanoscience; Energy; Nanostructured Materials - Materials; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b5c6db81d2151a022438fb/original/towards-carbon-free-cathodes-for-fluoride-ion-batteries-deconvoluting-effects-of-active-material-and-conductive-additive-on-charging-and-cyclic-stability.pdf
|
60c758c6567dfe9e58ec68f2
|
10.26434/chemrxiv.14582913.v1
|
Gold Nanoclusters as Nano-Antibiotic Auranofin Analogues
|
Auranofin, a gold(I)-complex with tetraacetylated thioglucose and
triethylphosphine ligands, is an FDA-approved drug used as an
anti-inflammatory aid in the treatment of rheumatoid arthritis. In
repurposing auranofin for other diseases, it was found that the drug
showed significant activity against Gram-positive bacteria but was
inactive against Gram-negative bacteria. Herein, we report the design
and synthesis of gold nanoclusters (AuNCs) based on the structural motif
of auranofin. Phosphine-capped AuNCs were synthesized and glycosylated,
yielding auranofin AuNC analogues with mixed phosphine/thioglucose
ligand shells. These AuNCs were active against both Gram-negative and
Gram-positive bacteria, including a panel of resistant ESKAPE pathogens.
Notably, an auranofin analogue, a mixed-ligand 1.6 nm AuNC (<strong>4b</strong>) was ~4 times more active than auranofin against <em>Pseudomonas aeruginosa</em>,
while exhibiting 24 times lower toxicity against human A549 cells. The
enhanced antibacterial activity of these AuNCs was characterized by a
greater uptake of Au by the bacteria compared to Au<sup>I</sup>-complexes (20% for AuNC <strong>4b</strong>).
Additional factors include increased oxidative stress, moderate
inhibition of thioredoxin reductase (TrxR), and DNA damage. Most
intriguingly, the AuNCs were not affected by the bacterial outer
membrane (OM) barrier or by extracellular proteins. This contrasts with
Au<sup>I</sup>-complexes like auranofin that are susceptible to protein binding and hindered by the OM barrier.
|
William Ndugire; N. G. Hasitha Raviranga; Jingzhe Lao; Olof Ramstrom; Mingdi Yan
|
Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758c6567dfe9e58ec68f2/original/gold-nanoclusters-as-nano-antibiotic-auranofin-analogues.pdf
|
669f71c4c9c6a5c07a9bd826
|
10.26434/chemrxiv-2024-7f8sn
|
A BODIPY-Containing Covalent Organic Framework as a Highly Porous Photosensitizer for Environmental Remediation and Pollutants Adsorption
|
The direct incorporation of borondipyrromethene (BODIPY) subunits into the structural backbone of covalent organic frameworks (COFs) gives facile access to porous photosensitizers but is still a challenging task. Here, we introduce β ketoenamine-linked BDP TFP COF, which crystallizes in AA stacking mode with hcb topology. A comprehensive characterization reveals high crystallinity and enhanced stability in a variety of solvents, excellent porosity (SABET = 1042 m2/g), broad light absorption in the visible region, and red emission upon the exfoliation of few-layer COF nanosheets. The versatility of multifunctional BODIPY-COFs is highlighted in various applications. Pollutants Bisphenol A (BPA, qmax = 426 mg/g) and Methylene Blue (MB, qmax = 96 mg/g) have been efficiently removed from H2O. Fluorescence quenching or enhancement of exfoliated BDP TFP COF nanosheets have been utilized for dual-mode sensing of MB or NEt3, respectively. Ultimately, the photosensitizing effect of the BODIPY units is retained in the COF. Thus, BPD TFP COF was established as a metal-free triplet photosensitizer, which efficiently oxidized a mustard gas simulant under visible light irradiation.
|
Roberto Sánchez-Naya; Florian Beuerle
|
Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669f71c4c9c6a5c07a9bd826/original/a-bodipy-containing-covalent-organic-framework-as-a-highly-porous-photosensitizer-for-environmental-remediation-and-pollutants-adsorption.pdf
|
61b37b69476fcd56f70ef9ea
|
10.26434/chemrxiv-2021-41mn8
|
Machine learning to explain printability induced by rheology additives
|
With the continuous growth of extrusion bioprinting techniques, ink formulations based on rheology modifiers are becoming increasingly popular, as they enable 3D printing of non-printable biologically-favored materials. However, benchmarking and characterization of such systems are inherently complicated due to the variety of rheology modifiers and differences in mechanisms of inducing printability. This study tries to explain induced printability in formulations by incorporating machine learning algorithms that describe the underlying basis for decision-making in classifying a printable formulation. For this purpose, a library of rheological data and printability scores for 180 different formulations of hyaluronic acid solutions with varying molecular weights and concentrations and three rheology modifiers were produced. A feature screening methodology was applied to collect and separate the impactful features, which consisted of physically interpretable and easily measurable properties of formulations. In the final step, all relevant features influencing the model’s output were analyzed by advanced yet explainable statistical methods. The outcome provides a guideline for designing new formulations based on data-driven correlations from multiple systems.
|
Ali Nadernezhad; Jürgen Groll
|
Materials Science; Polymer Science; Materials Processing; Biopolymers; Polymer scaffolds
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b37b69476fcd56f70ef9ea/original/machine-learning-to-explain-printability-induced-by-rheology-additives.pdf
|
61631eb18b620d34bd4ad785
|
10.26434/chemrxiv-2021-2frpz
|
Computational data analysis shows that key developments towards the periodic system occurred in the 1840s
|
The periodic system arose from knowledge about substances, which constitute the chemical space. Despite the importance of this interplay, little is known about how the expanding space affected the system. Here we show, by analysing the space between 1800 and 1869, how the periodic system evolved until its formulation. We found that after an unstable period culminating around 1826, the system began to converge to a backbone structure, unveiled in the 1860s, which was clearly evident in the 1840s. Hence, contrary to the belief that the ``ripe moment'' to formulate the system was in the 1860s, it was in the 1840s. The evolution of the system is marked by the rise of organic chemistry in the first quarter of the nineteenth-century, which prompted the recognition of relationships among main group elements and obscured some of transition metals, which explains why the formulators of the periodic system struggled accommodating them. We also introduced an algorithm to adjust the chemical space according to different sets of atomic weights, which allowed for estimating the resulting periodic systems of chemists using one or the other nineteenth-century atomic weights. These weights produce orderings of the elements very similar to that of 1869, while providing different similarity relationships among the elements, therefore producing different periodic systems. By analysing these systems, from Dalton up to Mendeleev, we found that Gmelin's atomic weights of 1843 produce systems remarkably similar to that of 1869, a similarity that was reinforced by the atomic weights on the years to come.
|
Wilmer Leal; Eugenio J. Llanos; Andres Bernal; Peter F. Stadler; Jürgen Jost; Guillermo Restrepo
|
Theoretical and Computational Chemistry; Chemical Education; Chemical Education - General; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61631eb18b620d34bd4ad785/original/computational-data-analysis-shows-that-key-developments-towards-the-periodic-system-occurred-in-the-1840s.pdf
|
6533273dc3693ca993c427eb
|
10.26434/chemrxiv-2023-b71mn-v2
|
Counting electrons in electrides
|
The wave nature of electrons makes the quantification of charge fundamentally challenging. In complex materials like electrides, this challenge is amplified by the small charge and complex shape of electride wavefunctions. For these reasons, popular integration methods like the Bader method usually fail to assign any charge to the bare electrons in an electride. To address this challenge, we develop an algorithm that instead partitions the charge based on the electron localization function (ELF), a popular scheme for visualizing chemically important features in molecules and solids. The algorithm uses Bader segmentation of the ELF to find the electride electrons and Voronoi segmentation of the ELF to identify atoms. We apply this method, “BadELF”, to the quantification of atomic radii and oxidation states in both ionic compounds and electrides. For ionic compounds, we find that the BadELF method yields radii that agree closely with Shannon crystal radii, while the oxidation states agree closely with the Bader method. When applied to electrides, however, only the BadELF algorithm yields chemically meaningful charges. We argue that the BadELF method provides a useful strategy to identify electrides and obtain new insight about their most essential property: the quantity of electrons within them.
|
Samuel Weaver; Jack Sundberg; Connor Slamowitz; Rebecca Radomsky; Matthew Lanetti; Lauren McRae; Scott Warren
|
Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Bonding; Solid State Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6533273dc3693ca993c427eb/original/counting-electrons-in-electrides.pdf
|
6673b179c9c6a5c07ae62579
|
10.26434/chemrxiv-2024-m9qp7
|
Continuous and reversible transformation of the polymorphs of an MGAT2 inhibitor (S-309309) from the anhydrate to the hydrate in response to relative humidity
|
Quality control is a strict requirement of pharmaceutical manufacture. The stability of a drug can be enhanced by crystallization owing to the relatively low energy of a crystal lattice. Herein, we investigated the hydrate and anhydrate polymorphs of a monoacylglycerol acyltransferase 2 inhibitor (S-309309) to elucidate their relationship with each other. Polymorphic screening by solvent evaporation and slurry conversion revealed two polymorphs: Form I (the hydrate) and Form II (the solvate). Form II transformed to Form I during thermogravimetry–differential thermal analysis. X-ray powder diffraction demonstrated that Form I transformed to the anhydrate via an intermediate state when heated. These crystal forms were confirmed under controlled humidity conditions; the presence of the anhydrate, the intermediate hydrate, or the hydrate depended on the relative humidity at 25°C. The stoichiometry of S-309309 to water in the hydrate form was 4:1. The hydrate and anhydrate had similar crystal structures. The water of hydration in the intermediate hydrate was 0.1–0.15 mol according to the dynamic vapor sorption profile. We discovered a mechanism of reversible crystal transformation between the anhydrate and pseudo-polymorphs of the hydrate at ambient humidity. We conclude that S-309309 should be treated carefully because the experimental conditions affect its crystal form.
|
Hiroshi Ueda; Katsuji Sugita; Tetsuya Miyano
|
Organic Chemistry; Analytical Chemistry; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6673b179c9c6a5c07ae62579/original/continuous-and-reversible-transformation-of-the-polymorphs-of-an-mgat2-inhibitor-s-309309-from-the-anhydrate-to-the-hydrate-in-response-to-relative-humidity.pdf
|
60c744dbf96a0054b2286ad5
|
10.26434/chemrxiv.9917189.v1
|
Asymptotic Behavior of the Exchange-Correlation Energy Density and the Kohn-Sham Potential in Density Functional Theory: Exact Results and Strategy for Approximations
|
The present work is a review of two analytical properties of the exact exchange-correlation (xc) functional in density-functional theory. These properties are the asymptotic behavior of the xc energy density per particle and the asymptotic behavior of the Kohn-Sham potential, in finite many-electron systems. The derivation of the asymptotic forms for both quantities is reviewed, employing the concepts of the adiabatic connection and of the xc hole with relation to the first quantity and the electron exact factorization approach for the second one. Furthermore, it is shown that the correct asymptotic behavior of one of the aforementioned quantities does not guarantee a correct behavior of the other. In this process, a new quantity, the xc hole response function, is defined and its exact exchange part is analytically derived. The extent to which existing xc approximations satisfy the named exact properties is reviewed and the relationship between correct asymptotics and freedom from one-electron self-interaction in DFT is discussed. Finally, a strategy for development of advanced approximations for exchange and correlation with a correct asymptotic behavior is suggested.<br />
|
Eli Kraisler
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744dbf96a0054b2286ad5/original/asymptotic-behavior-of-the-exchange-correlation-energy-density-and-the-kohn-sham-potential-in-density-functional-theory-exact-results-and-strategy-for-approximations.pdf
|
60c74ec2702a9b06da18ba5e
|
10.26434/chemrxiv.12798134.v1
|
Rheological Investigation of Collagen, Fibrinogen, and Thrombin Solutions for Drop-on-Demand 3D Bioprinting
|
<p>Collagen, fibrinogen, and thrombin proteins in aqueous buffer solutions are widely used as precursors of natural biopolymers for three-dimensional (3D) bioprinting applications. The proteins are sourced from animals and their quality may vary from batch to batch, inducing differences in the rheological properties of such solutions. In this work, we investigate the rheological response of collagen, fibrinogen, and thrombin protein solutions in bulk and at the solution/air interface. Interfacial rheological measurements show that fibrous collagen, fibrinogen and globular thrombin proteins adsorb and aggregate at the solution/air interface, forming a viscoelastic solid film at the interface. The viscoelastic film corrupts the bulk rheological measurements in rotational rheometers by contributing to an apparent yield stress, which increases the apparent bulk viscosity up to shear rates as high as 1000 s<sup>-1</sup>. The addition of a non-ionic surfactant, such as polysorbate 80 (PS80) in small amounts between 0.001 and 0.1 v/v%, prevents the formation of the interfacial layer, allowing the estimation of true bulk viscosity and viscoelastic properties of the solutions. The estimation of viscosity not only helps in identifying those protein solutions that are potentially printable with drop-on-demand (DOD) inkjet printing but also detects inconsistencies in flow behavior among the batches.</p>
|
Hemanth Gudapati; Daniele Parisi; Ralph H. Colby; Ibrahim Ozbolat
|
Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ec2702a9b06da18ba5e/original/rheological-investigation-of-collagen-fibrinogen-and-thrombin-solutions-for-drop-on-demand-3d-bioprinting.pdf
|
65b9cbdb9138d23161163118
|
10.26434/chemrxiv-2024-gm4g2
|
Beyond Explored Functionals: A Computational Journey of Two-Photon Absorption
|
We present a thorough investigation into the efficacy of 19 DFT functionals, relative to RI-CC2 results, for computing two-photon absorption (2PA) cross-sections (σ2PA) and key dipole moments (µ00, µ11, Δµ, µ01) for a series of coumarin dyes in the gas-phase. The functionals include different categories, including local density approximation (LDA), generalized gradient approximation (GGA), hybrid-GGA (H-GGA), range separated hybrid-GGA (RSH-GGA), meta-GGA (M-GGA), and hybrid M-GGA (HM-GGA), with 14 of them being subjected to analysis for the first time with respect to predicting σ2PA values. Analysis reveals that functionals integrating both short-range (SR) and long-range (LR) corrections, particularly those within the RSH GGA and HM-GGA classes, outperform others. Furthermore, the range-separation approach was found more impactful compared to the varying percentages of Hartree-Fock exchange (HF Ex) within different functionals. The functionals traditionally recommended for 2PA do not appear among the top 9 in our study, which is particularly interesting as these top-performing functionals have not been previously investigated in this context. This list is dominated by M11, QTP variants, ωB97X, ωB97X-V, and M06-2X, surpassing the performance of other functionals, including the commonly used CAM-B3LYP.
|
Ismael A. Elayan; Laura Rib; Rodrigo A. Mendes; Alex Brown
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b9cbdb9138d23161163118/original/beyond-explored-functionals-a-computational-journey-of-two-photon-absorption.pdf
|
6343b4772984c924b57f7a35
|
10.26434/chemrxiv-2022-znpz2
|
Direct Suzuki–Miyaura Coupling of Naphthalene-1,8-diaminato (dan)-Substituted Cyclopropylboron Compounds
|
We herein describe the direct Suzuki–Miyaura coupling of dan-substituted, saturated organoboron compounds. Despite its Lewis acidity-diminished and robust character of the boron center, cyclopropyl–B(dan) can be activated by t-BuOK to under-go transmetalation with a palladium complex. The increased s-character of the C–B(dan) bond as compared with other alkyl–B(dan) should be the key to the smooth reaction.
|
Mikinao Koishi; Kazuki Tomota; Masaaki Nakamoto; Hiroto Yoshida
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6343b4772984c924b57f7a35/original/direct-suzuki-miyaura-coupling-of-naphthalene-1-8-diaminato-dan-substituted-cyclopropylboron-compounds.pdf
|
62bbb2f37b3b3029ab061842
|
10.26434/chemrxiv-2022-413k7
|
General and Practical Metal-Free Aziridination and Cyclopropanation of XH2 (X = N, C) with Alkenes by Thianthrenation
|
Three-membered cyclic structures are widely existing in natural products and serve as enabling intermediates in organic synthesis. However, the efficient and straightforward access to such structures with diversity remains a formidable challenge. Herein, a general and practical protocol to aziridines and cyclopropanes synthesis using free XH2 (X = C or N) with alkenes by thianthrenation is presented. This metal-free protocol features the direct aziridination and cyclopropanation of unprotected NH2 under mild conditions. Free sulfonamides, amides, carbamates, amines, and methylene with acidic protons, are good precursors for three-membered ring formation, providing an attractive alternative for straightforward synthesis of aziridines and cyclopropanes from easily available starting materials.
|
Wei Shu; Ming-Shang Liu; Hai-Wu Du
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bbb2f37b3b3029ab061842/original/general-and-practical-metal-free-aziridination-and-cyclopropanation-of-xh2-x-n-c-with-alkenes-by-thianthrenation.pdf
|
6328a71b2984c91c8764dbea
|
10.26434/chemrxiv-2022-9qhw3
|
Engineering a Conformationally Switchable Artificial Metalloprotein
|
Most naturally occurring metalloenzymes are gated by rate-limiting conformational changes and there exists a critical inter-play between macroscopic structural rearrangements of the protein, and subatomic changes affecting the electronic struc-ture of embedded metallocofactors. Despite this connection, most artificial metalloproteins (ArMs) are prepared in structur-ally rigid protein hosts. To better model the natural mechanisms of metalloprotein reactivity, we have developed conforma-tionally switchable ArMs (swArMs) that undergo a large-scale structural rearrangement upon allosteric effector binding. The swArMs reported here contain a Co(dmgH)2(X) cofactor (dmgH = dimethylglyoxime, X = N3–, H3C–, iPr–). We used UV-vis absorbance and energy-dispersive X-ray fluorescence spectroscopies, along with protein assays, and mass spectrometry to show that these metallocofactors are installed site-specifically and stoichiometrically via direct Co‒S cysteine ligation within the E. coli glutamine binding protein (GlnBP). Structural characterization by single-crystal X-ray diffraction (2.99 Å resolu-tion) unveils the precise positioning and microenvironment of the metallocofactor within the protein fold. Fluorescence and circular dichroism spectroscopies, along with isothermal titration calorimetry reveal that allosteric Gln binding drives a large-scale protein conformational change. In swArMs containing a Co(dmgH)2(CH3) cofactor, we show that the protein stabilizes the otherwise labile Co‒S bond relative to the free complex. Kinetics studies performed as a function of temperature and pH reveal that the protein conformational change accelerates this bond dissociation in a pH-dependent fashion. We present swArMs as a robust platform for investigating the interplay between allostery and metallocofactor regulation.
|
Saman Fatima; David G. Boggs; Peter J. Thompson; Noor Ali; Megan C. Thielges; Jennifer Bridwell-Rabb; Lisa Olshansky
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Biophysics; Chemical Biology
|
CC BY NC ND 4.0
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CHEMRXIV
|
2022-09-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6328a71b2984c91c8764dbea/original/engineering-a-conformationally-switchable-artificial-metalloprotein.pdf
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61c1ae9b1e13eb5d2c00a191
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10.26434/chemrxiv-2021-jv6rk
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Combinatorial library screening of quinadoline B derivatives against SARS-CoV-2 RNA-dependent RNA polymerase
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The unprecedented global health threat of SARS-CoV-2 has sparked a continued interest to discover novel anti-COVID-19 agents. To this end, we present here a computer-based protocol for identifying potential compounds targeting RNA-dependent RNA polymerase (RdRp). Starting from our previous study in which, by a virtual screening campaign, we identified a fumiquinazolinone alkaloid quinadoline B (Q3), an antiviral fungal metabolite with significant activity against SARS-CoV-2 RdRp, we applied an in silico combinatorial methodologies for generating and screening a library of anti-SARS-CoV-2 candidates with strong in silico affinity for RdRp. For this study, the quinadoline pharmacophore was subjected to structural iteration obtaining a Q3-focused library of over 900,000 unique structures. This chemical library was explored to identify binders of RdRp with greater affinity with respect to the starting compound Q3. Coupling this approach with the evaluation of physchem profile, we found 26 compounds with significant affinities for the RdRp binding site. Moreover, top-ranked compounds were submitted to molecular dynamics to evaluate the stability of the systems during a selected time, and for deeply investigating the binding mode of the most promising derivatives. Among the generated structures, five compounds, obtained by inserting nucleotide-like scaffolds (1, 2, and 5), heterocyclic thiazolyl benzamide moiety (compound 3), and a peptide residue (compound 4), exhibited enhanced binding affinity for SARS-CoV-2 RdRp, deserving further investigation as possible antiviral agents. Remarkably, the presented in silico procedure provides a useful computational procedure for hit-to-lead optimization, having implications in anti-SARS-CoV-2 drug discovery and in general in the drug optimization process.
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simone brogi; Mark Tristan Quimque; Kin Israel Notarte; Jeremiah Gabriel Africa ; Jenina Beatriz Hernandez; Sophia Morgan Tan; Vincenzo Calderone; Allan Patrick Macabeo
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY NC 4.0
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CHEMRXIV
|
2021-12-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c1ae9b1e13eb5d2c00a191/original/combinatorial-library-screening-of-quinadoline-b-derivatives-against-sars-co-v-2-rna-dependent-rna-polymerase.pdf
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673db9795a82cea2fae25715
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10.26434/chemrxiv-2024-88rh7
|
Helical Polymer-Based Polycarboxylic Acids as a Chiroptical Chemosensor for Detection and Quantification of Small Enantiomeric Imbalances of Chiral Amines in Water
|
Achiral dynamic helical polymers, poly(quinoxaline-2,3-diyl)s (P1 and P2) bearing achiral carboxylic acid side chains, i.e., carboxymethoxymethyl (in P1) and carboxyethoxymethyl (in P2), with different polymerization degrees were synthesized. They exhibited induced circular dichroism (ICD) in the presence of chiral amines such as 1-phenylalkylamines and nicotine, 1,2-amino alcohols such as valinol, leucenol, and prolinol, and the basic amino acid, arginine, in response to the induction of right- or left-handed helical conformation. The efficiency of helix induction depends on the compatibility of the structures of amines and polymers, with no clear structural correlation. The highly sensitive and formulated nature of ICD with the helical polymer-based polycarboxylic acids allowed their use as CD-based sensors to detect and quantify minute imbalances of enantiomeric excess of chiral molecules. We determined 0.2%–0.6% ee in the commercially available 1-phenylethylamine from three different suppliers, which have the label of “dl” or no indication of enantiopurity using P1 as a chemosensor.
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Tomonori Yamawaki; Takuma Kuroda; Takeshi Yamamoto; Yuuya Nagata; Michinori Suginome
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Polymer Science; Organic Polymers
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CC BY NC 4.0
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CHEMRXIV
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2024-11-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673db9795a82cea2fae25715/original/helical-polymer-based-polycarboxylic-acids-as-a-chiroptical-chemosensor-for-detection-and-quantification-of-small-enantiomeric-imbalances-of-chiral-amines-in-water.pdf
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611133603b558f0ce5f9ff97
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10.26434/chemrxiv-2021-l42ch
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Hybrid Computational-Experimental Data-Driven Design of Self-Assembling Pi-Conjugated Peptides
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Biocompatible molecules with electronic functionality provide a promising substrate for biocompatible electronic devices and electronic interfacing with biological systems. Synthetic oligopeptides composed of an aromatic pi-core flanked by oligopeptide wings are a class of molecules that can self-assemble in aqueous environments into supramolecular nanoaggregates with emergent optical and electronic activity. We present an integrated computational-experimental pipeline employing all-atom molecular dynamics simulations and experimental UV-visible spectroscopy within an active learning workflow using deep representational learning and Bayesian optimization to design pi-conjugated peptides programmed to self-assemble into elongated pseudo-1D nanoaggregtes with a high degree of H-type co-facial stacking of the pi-cores. We consider as our design space the 694,982 unique pi-conjugated peptides comprising a quaterthtiophene pi-core flanked by symmetric oligopeptide wings up to five amino acids in length. After sampling only 1181 molecules (~0.17% of the design space) by computation and 28 (~0.004%) by experiment, we identify and experimentally validate a diversity of previously unknown high-performing molecules and extract interpretable design rules linking peptide sequence to emergent supramolecular structure and properties.
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Kirill Shmilovich; Sayak Panda; Anna Stouffer; John Tovar; Andrew Ferguson
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Self-Assembly; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2021-08-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611133603b558f0ce5f9ff97/original/hybrid-computational-experimental-data-driven-design-of-self-assembling-pi-conjugated-peptides.pdf
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66e8679e12ff75c3a18544ed
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10.26434/chemrxiv-2024-trlwf
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A Universal Oxygen Scavenger for Oxidase-based Biosensors
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Enzyme-based electrochemical biosensors are extensively deployed for point-of-use applications due to their low cost, simplicity, and high selectivity. However, oxygen from ambient air often causes interferences, leading to inaccurate results. Here, we developed a universal enzymatic O2 scavenger composed of alcohol oxidase, catalase, and paraformaldehyde, designed to convert O2 into water within the sensor strip. The O2 scavenging was evaluated for implementation in oxidase-based biosensors. Alcohol oxidase is advantageous as a catalyst for O2 scavenging because it exclusively donates electrons to O₂, thereby preventing interferences with other sensor components. Additionally, paraformaldehyde acts as a solid precursor to formaldehyde, which can be oxidized by alcohol oxidase. This bypasses the need for any volatile compound in the sensor, thus allowing for long-term storage. The O2 scavenger was validated for glucose sensing across a glucose concentration range relevant to diabetes management. In the presence of the O2 scavenger, the sensing accuracy in ambient air was 99% of that achieved under inert gas conditions. In contrast, sensors without the scavenger exhibited readings that were less than 50% of those under inert gas conditions. Implementation in biosensors for lactate and creatinine show that the alcohol oxidase-based O2 scavenger is generally compatible with oxidase-based electrochemical biosensors for point-of-care applications.
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Huijie Zhang; Mohamed Saadeldin; Darren Buesen; Hamzah Elfaitory; Jakob Burger; Vincent Friebe; Jonas Honacker; Tobias Voepel; Alaa Oughli; Nicolas Plumeré
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Analytical Chemistry
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CC BY 4.0
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CHEMRXIV
|
2024-09-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e8679e12ff75c3a18544ed/original/a-universal-oxygen-scavenger-for-oxidase-based-biosensors.pdf
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659fb97466c1381729323825
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10.26434/chemrxiv-2023-szkt8-v2
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Design, synthesis, and biological characterization of proteolysis targeting chimera (PROTACs) for the Ataxia telangiectasia and RAD3-related (ATR) kinase
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The Ataxia telangiectasia and RAD3-related (ATR) kinase is a key regulator of DNA replication stress responses and DNA-damage checkpoints. Several potent and selective ATR inhibitors are reported and four of them are currently in clinical trials in combination with radio- or chemotherapy. Based on the idea of degrading target proteins rather than inhibiting them, we designed, synthesized and biologically characterized a library of ATR-targeted proteolysis targeting chimera (PROTACs). Among the synthesized compounds, the lenalidomide-based PROTAC 42i was the most promising. In pancreatic and cervix cancer cells cancer cells (MIA PaCa-2), it reduced ATR to 40% of the levels in untreated cells. 42i selectively degraded ATR through the proteasome, dependent on the E3 ubiquitin ligase component cereblon, and without affecting the associated kinases ATM and DNA-PKcs. 42i may be a promising candidate for further optimization and biological characterization in various cancer cells.
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Abdallah M. Alfayomy; Ramy Ashry; Anita Kansy; Anne-Christin Sarnow; Frank Erdmann; Matthias Schmidt; Oliver H. Krämer; Wolfgang Sippl
|
Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-01-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659fb97466c1381729323825/original/design-synthesis-and-biological-characterization-of-proteolysis-targeting-chimera-prota-cs-for-the-ataxia-telangiectasia-and-rad3-related-atr-kinase.pdf
|
61dba158db142e7ee6ba7971
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10.26434/chemrxiv-2022-71rkz
|
Stereoselective Nanocarbon Imides Featuring 12-fold [5]helicenes
|
Despite the great progress in research on chiral molecular nanocarbons containing multiple helicenes, controlling the stereoselectivity is still a major challenge, especially when attempting to increase the number of helicene moieties. Herein, a novel molecular nanocarbon imides composed of C204 skeleton and eighteen imide groups was successfully synthesized via an inside–out ring closing strategy involving repeated Suzuki–Miyaura coupling for C–C bond formation and photocyclic aromatization. Because of the presence of quad–core twelvefold [5]helicenes, there are, in theory, more than one hundred stereoisomers. However, only one pair of stereoisomers with D3 symmetry was observed. Despite the large and rigid skeleton, the (3M,3M,3M,3M)+(3P,3P,3P,3P) enantiomers were successfully separated by chiral HPLC, and the chiroptical properties were investigated by CD spectroscopy.
|
Guogang Liu; Marvin Nyenhuis; Dong Meng; Nikos L. Doltsinis; Yan Li; Zhaohui Wang; He Tian
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Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-01-11
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dba158db142e7ee6ba7971/original/stereoselective-nanocarbon-imides-featuring-12-fold-5-helicenes.pdf
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64ca6585dfabaf06ff958a4f
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10.26434/chemrxiv-2023-nrxtl
|
Artificial Design of Organic Emitters via a Genetic Algorithm Enhanced by a Deep Neural Network
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The design of molecules requires multi-objective optimizations in high-dimensional chemical space with often conflicting target properties. To navigate this space, classical workflows rely on the domain knowledge and creativity of human experts, which can be the bottleneck in high-throughput approaches. Herein, we present an artificial molecular design workflow relying on a genetic algorithm and a deep neural network to find a new family of organic emitters with inverted singlet-triplet gaps and appreciable fluorescence rates. We combine high-throughput virtual screening and inverse design infused with domain knowledge and artificial intelligence to accelerate molecular generation significantly. This enabled us to explore more than 800,000 potential emitter molecules and find more than 10,000 candidates estimated to have inverted singlet-triplet gaps (INVEST) and appreciable fluorescence rates, many of which likely emit blue light. This class of molecules has the potential to realize a new generation of organic light-emitting diodes.
|
AkshatKumar Nigam; Robert Pollice; Pascal Friederich; Alán Aspuru-Guzik
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Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-08-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca6585dfabaf06ff958a4f/original/artificial-design-of-organic-emitters-via-a-genetic-algorithm-enhanced-by-a-deep-neural-network.pdf
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65675cc729a13c4d4744f4c7
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10.26434/chemrxiv-2023-n0lnl
|
Visible light-triggered desorption of CO2 in green coordination polymers
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Efficient, facile, and energy-efficient desorption processes are highly sought after in industrial processes. Visible light exists all around us and can be considered a ubiquitous energy source that can be used to drive photothermal processes such as the release of guest molecules from porous sorbents. Herein, we present four sustainably synthesized porous coordination polymers, M(dhbq)(H2O)2 (where dhbq = 2,5-dihydroxy-1,4-benzoquinone, and M = Fe, Mg, Mn, or Zn) with visible light photoresponsive properties. Efficient desorption of CO2 corresponding to up to 47.6 % of the total uptake capacity was achieved upon visible light irradiation for 10 min. A negligible decrease (< 97 %) in CO2 uptake was observed for up to 10 light-swing adsorption cycles and working capacities of up to 37.5 g kg- were obtained in Fe(dhbq). M(dhbq) possess highly desirable properties that make them interesting for applications related to cost-effective and energy-efficient desorption processes.
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Ocean Cheung; Michelle Åhlén; Ribooga Chang; Maria Strømme
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Materials Chemistry
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CC BY NC 4.0
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CHEMRXIV
|
2023-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65675cc729a13c4d4744f4c7/original/visible-light-triggered-desorption-of-co2-in-green-coordination-polymers.pdf
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60c74c7dee301c251bc7a0ad
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10.26434/chemrxiv.12479837.v1
|
Barium Selective Chemosensing by Diazacrown Ether Naphthalimide Turn-on Fluorophores for Single Ion Barium Tagging
|
Single molecule fluorescence detection of barium is investigated for enhancing the sensitivity and robustness of a neutrinoless double beta decay ($0\nu\beta\beta$) search in $^{136}$Xe, the discovery of which would alter our understanding of the nature of neutrinos and the early history of the Universe. A key developmental step is the synthesis of barium-selective chemosensors capable of incorporation into ongoing experiments in high-pressure $^{136}$Xe gas. Here we report turn-on fluorescent naphthalimide chemosensors containing monoaza- and diaza-crown ethers as agents for single Ba$^{2+}$ detection. Monoaza-18-crown-6 ether naphthalimide sensors showed sensitivity primarily to Ba$^{2+}$ and Hg$^{2+}$, whereas two diaza-18-crown-6 ether naphthalimides revealed a desirable selectivity toward Ba$^{2+}$. Solution-phase fluorescence and NMR experiments support a photoinduced electron transfer mechanism enabling turn-on fluorescence sensing in the presence of barium ions. Changes in ion-receptor interactions enable effective selectivity between competitive barium, mercury, and potassium ions, with detailed calculations correctly predicting fluorescence responses. With these molecules, dry-phase single Ba$^{2+}$ ion imaging with turn-on fluorescence is realized using oil-free microscopy techniques. This represents a significant advance toward a practical method of single Ba$^{2+}$ detection within large volumes of $^{136}$Xe, plausibly enabling a background-free technique to search for the hypothetical process of $0\nu\beta\beta$.
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pawan thapa; Nick Byrnes; Alena Denisenko; Frank Foss; Ben Jones; James X. Mao; Austin McDonald; Kwangho Nam; Charleston Newhouse; David Nygren; Thanh Thuy Vuong; Katherine Woodruff
|
Photochemistry (Org.); Imaging Agents; Imaging; Sensors
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-06-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c7dee301c251bc7a0ad/original/barium-selective-chemosensing-by-diazacrown-ether-naphthalimide-turn-on-fluorophores-for-single-ion-barium-tagging.pdf
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60c74d21469df4a76ef4422e
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10.26434/chemrxiv.12587450.v1
|
Solvated Proton and the Origin of the High Onset Overpotential in the Oxygen Reduction Reaction on Pt(111)
|
<p>For the oxygen reduction reaction
(ORR) in acidic media, proton is a key component in the hydrogenation of O<sub>2</sub>,
O, and OH. Modeling a proton requires the explicit account of its solvation and
dynamic nature in the interfacial solution region. We employed ab initio
molecular dynamics method to study such reactions on Pt(111), a model problem
in electro-catalysis. Our results show that the branching ratio for the two hydrogenation
channels of O atoms adsorbed on Pt(111) shifts dramatically with the electrode
potential. This kinetic factor underlies the electrochemical observations
peculiar to ORR on Pt(111), and provides an explanation for the long standing
puzzle of its high onset overpotential. </p>
|
Yuke Li; Zhi-Feng Liu
|
Electrochemistry - Mechanisms, Theory & Study
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CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d21469df4a76ef4422e/original/solvated-proton-and-the-origin-of-the-high-onset-overpotential-in-the-oxygen-reduction-reaction-on-pt-111.pdf
|
66739f59c9c6a5c07ae5223e
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10.26434/chemrxiv-2024-5rzt9-v2
|
Discovery of a Novel Mutant-Selective Epidermal Growth Factor Receptor Inhibitor Using in silico Enabled Drug Discovery Platform
|
Despite the success of first, second and third generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in treatment of non-small cell lung cancer (NSCLC) with classical EGFR mutations (L858R or Exon 19 deletions), disease progression often occurs due to the acquisition of additional mutations in the EGFR kinase domain that confer TKI resistance. Specifically, acquisition of both T790M and C797S resistance mutations results in an EGFR variant that is resistant to all approved EGFR TKIs. Herein, we report a physics-based computationally-driven lead identification approach which successfully identified structurally-unique imidazo[3.2-b]pyrazole derivatives as reversible inhibitors of EGFR classical mutations bearing both T790M and C797S. Importantly, they spare EGFR WT to avoid known EGFR WT-driven cutaneous toxicities. During profiling of imidazo[3.2-b]pyrazole derivatives, we elucidated the bioactivation mechanism causing CYP3A4/5 time-dependent inhibition (TDI) and found key modifications to suppress bioactivation and mitigate the TDI risk. Representative lead compound 31 inhibited EGFR L858R/T790M/C797S in biochemical assays with a Ki = 2.1 nM, and EGFR del19/T790M/C797S in a Ba/F3 cellular assay with a IC50 = 56.9 nM. Deuterated analog of 31 (38) demonstrated dose-dependent tumor growth inhibition in a Ba/F3 EGFR del19/T790M/C797S CDX model by 47% at 50 mg/kg BID and 92% at 100 mg/kg BID.
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Hideyuki Igawa; Zef A. Konst ; Eric Therrien; Mee Shelley; Heidi Koldsø; Pieter H. Bos ; Ana Negri ; Andreas Verras; Jiaye Guo; Markus Dahlgren; Adam Levinson; Brendan T. Parr; Suresh E. Kurhade; Prashant Latthe; Rajesha Shetty ; Sridhar Santhanakrishnan ; Katherine Amberg-Johnson ; Alan Futran; Christian Atsriku; Robert Pelletier; Zhijian Liu; Jeffery A. Bell; Sathesh Bhat; Mats Svensson ; Aleksey I. Gerasyuto
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66739f59c9c6a5c07ae5223e/original/discovery-of-a-novel-mutant-selective-epidermal-growth-factor-receptor-inhibitor-using-in-silico-enabled-drug-discovery-platform.pdf
|
64c13648658ec5f7e535bee4
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10.26434/chemrxiv-2023-qb8g3
|
Total Synthesis of Sclerotioloid A
|
A four-step total synthesis of a structurally unique N-propargyllated 2,5-diketopiperazine alkaloid sclerotioloid A has been achieved. Structural studies point towards sclerotioloid A being a helically chiral racemate in the solid state.
|
Juha Siitonen
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c13648658ec5f7e535bee4/original/total-synthesis-of-sclerotioloid-a.pdf
|
672349925a82cea2fa9b0e08
|
10.26434/chemrxiv-2024-5ppc5
|
Expanding the chemical coverage of polar compounds in water analysis by coupling supercritical fluid with hydrophilic interaction chromatography high-resolution mass spectrometry
|
Background: Persistent and mobile organic compounds (PMOC) are of great concern for water
quality and human health. The recent improvement and availability of high-resolution mass
spectrometry in combination with liquid chromatography have widely expanded the potential of
analytical workflows for their detection and quantitation in water. Given their high polarity, the
detection of some PMOC requires alternative techniques to reversed-phase chromatography,
such as hydrophilic interaction liquid chromatography (HILIC) and supercritical fluid
chromatography (SFC). Unified chromatography (UC), an SFC gradient in which the state of the
mobile phase changes continuously from supercritical to liquid at 100% polar co-solvent, has
shown potential for the analysis of very polar compounds.
Results: In the present study, for the first time, a UC-HILIC method coupled with high-
resolution mass spectrometry was set up for PMOC analysis in water. SFC and HILIC gradients
were run sequentially on the same bare-silica column, with the first separation running to 100%
modifier (UC) followed by a HILIC gradient transitioning to water. The UC and UC-HILIC
gradients were previously optimized on a mix of 18 representative PMOC to assess solvent and
mobile phase composition and for the instrumental system setup. The final method was
employed for the analysis of water samples in comparison with a traditional reversed-phase
separation, resulting in a significant increase in the number of annotated polar PMOC, including
compounds listed in the Candidate List of substances of very high concern for Authorisation by
the European Chemicals Agency.
Significance: The proposed approach represents a robust alternative to traditional methods for
broadening the chemical space of separation and mass spectrometric detection. The introduction
of the HILIC section of the gradient was necessary for the elution of strongly retained
compounds on the silica phase, thus also reducing the amount of compounds that would be stuck
onto the phase of the column, resulting in possible irreproducibility, pressure increase, and loss
of efficiency in the compound separation.
|
Andrea Cerrato; Thomas Holmark; Erik Emke; Elvio D. Amato; Andrea F. G. Gargano
|
Analytical Chemistry; Mass Spectrometry; Separation Science; High-throughput Screening
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672349925a82cea2fa9b0e08/original/expanding-the-chemical-coverage-of-polar-compounds-in-water-analysis-by-coupling-supercritical-fluid-with-hydrophilic-interaction-chromatography-high-resolution-mass-spectrometry.pdf
|
60c746c04c8919a0d5ad2bc1
|
10.26434/chemrxiv.11347994.v1
|
Is ADC(3) as Accurate as CC3 for Valence and Rydberg Transition Energies?
|
<div><div><div><p>The search for new ab initio models rapidly delivering accurate excited state energies and properties is one of the most active research lines of theoretical chemistry. Along with these methodological developments, the performances of known methods are constantly reassessed thanks to the emergence of new benchmark values. In this Letter, we show that, in contrast to previous claims, the third-order algebraic diagrammatic construction, ADC(3), does not yield transition energies of the same quality as the third-order coupled cluster method, CC3. There is indeed a significant difference in terms of accuracy between the two approaches, as we clearly and unambiguously demonstrate here thanks to extensive comparisons with several hundreds high-quality vertical transition energies obtained with FCI, CCSDTQ, and CCSDT. Direct comparisons with experimental 0-0 energies of small- and medium-size organic molecules support the same conclusion, which holds for both valence and Rydberg transitions, as well as singlet and triplet states. In regards of these results, we introduce a composite method that we named ADC(2.5) which consists in averaging the ADC(2) and ADC(3) excitation energies. Although ADC(2.5) does not match the CC3 accuracy, it significantly improves the ADC(3) results, especially for vertical energies. We hope that the present contribution will stimulate further developments and, in particular, improvements of the ADC-type methods which have the indisputable advantage of being computationally lighter than their equivalent-order CC variants.</p></div></div></div>
|
Pierre-Francois Loos; Denis Jacquemin
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c04c8919a0d5ad2bc1/original/is-adc-3-as-accurate-as-cc3-for-valence-and-rydberg-transition-energies.pdf
|
60c7485a0f50dbe13439676d
|
10.26434/chemrxiv.11899755.v1
|
Direct Reversible Decarboxylation from Stable Organic Acids in Solution
|
Many classical and emerging methodologies in organic chemistry rely on carbon dioxide extrusion to generate reactive intermediates for subsequent bond-forming events. Synthetic reactions that involve the microscopic reverse, the carboxylation of reactive intermediates such as organometallic nucleophiles, occur under vastly different reaction conditions. We found that under appropriate conditions chemically stable C(sp3) carboxylates undergo rapid, uncatalyzed reversible decarboxylation in solution. The decarboxylation/carboxylation process occurs through the generation and trapping of otherwise undetectable carbanion intermediates that are largely resistant to protodecarboxylation in the presence of Brønsted acids or to trapping by external electrophiles. Isotopically labelled carboxylic acids, including drug molecules and valuable synthetic intermediates, can be prepared in high chemical and isotopic yield by simply supplying an atmosphere of 13CO2 to carboxylate salts in polar aprotic solvents. Our results indicate that the reversibility of decarboxylation from organic acids should be taken into consideration when designing and executing decarboxylative functionalization processes.
|
Duanyang Kong; Patrick Moon; Erica K. J. Lui; Odey Bsharat; Rylan Lundgren
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7485a0f50dbe13439676d/original/direct-reversible-decarboxylation-from-stable-organic-acids-in-solution.pdf
|
66348d6f418a5379b0525822
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10.26434/chemrxiv-2024-xrtr3
|
Streamlining the Synthesis of Pyridones through Oxidative Amination
|
Herein we report the development of an oxidative amination process for the streamlined synthesis of pyridones from cyclopentenones. Cyclopentenone building blocks can undergo in situ silyl enol ether formation, followed by the introduction of a nitrogen atom into the carbon skeleton with successive aromatisation to yield pyridones. The reaction sequence is operationally simple, rapid, and carried out in one pot. The reaction proceeds under mild conditions, exhibits broad functional group tolerance, complete regioselectivity, and is well scalable. The developed method provides facile access to the synthesis of 15N-labelled targets, industrially relevant pyridone products and their derivatives in a fast and efficient way.
|
Bence Botlik; Micha Weber; Florian Ruepp; Kazuki Kawanaka; Patrick Finkelstein; Bill Morandi
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66348d6f418a5379b0525822/original/streamlining-the-synthesis-of-pyridones-through-oxidative-amination.pdf
|
671284a7cec5d6c14286294b
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10.26434/chemrxiv-2024-39b71
|
Development of a Second-Generation, In Vivo Chemical Probe for PIKfyve
|
We optimized our highly potent and cell-active chemical probe for phosphatidylinositol-3-phosphate 5-kinase (PIKfyve), SGC-PIKFYVE-1, resulting in compounds with improved potency and demonstrated in vivo stability. Use of an in-cell, kinome-wide selectivity panel allowed for confirmation of excellent in-cell selectivity of our lead compound, 40, and another promising analogue, 46. Evaluation of the pharmacokinetic (PK) profiles of these two compounds revealed that both are well tolerated systemically and orally bioavailable. Coupled with its sub-nanomolar cellular potency and impressive selectivity in cells, the long half-life of 40 makes it an ideal candidate for the evaluation of the consequences of PIKfyve inhibition in vivo. PIKfyve inhibition has been investigated clinically for indications including rheumatoid arthritis, Crohn’s disease, COVID-19, and ALS using a single compound (apilimod), supporting the development of orthogonal PIKfyve inhibitors with in vivo stability.
|
Sophia M. Min; Frances M. Bashore; Jeffery L. Smith; Tammy M. Havener; Stefanie Howell; Haoxi Li; Rafael M. Couñago; Konstantin I. Popov; Alison D. Axtman
|
Biological and Medicinal Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671284a7cec5d6c14286294b/original/development-of-a-second-generation-in-vivo-chemical-probe-for-pi-kfyve.pdf
|
63516794ca86b88e11bc1887
|
10.26434/chemrxiv-2022-xfrt5
|
Crystal plane dependent dispersion of cobalt metal on metastable aluminas
|
Metallic Co nanoparticles, widely used and studied as supported heterogeneous catalysts for Fischer-Tropsch synthesis (FTS), display catalytic properties that can vary significantly depending on their size and crystal structure. In this work, we used 59Co Internal Field NMR (59Co IF NMR) complemented by high-resolution transmission electron microscopy (HRTEM) to demonstrate the influence of strong metal-support interaction on two noticeably different metastable alumina phases - γ-Al2O3 and χ-Al2O3. According to 59Co IF NMR and HRTEM, the metallic particles supported on χ-Al2O3 were larger and displayed a significantly higher content of hcp Co phase, which are known to be more active and selective to C5+ in FTS. The 1H NMR chemical shifts of hydroxyl groups anchored to the (110) and (111) spinel crystal planes were calculated by DFT. It revealed that the hydroxyl coverage of γ-Al2O3 facilitates the dispersion of Co precursor over the surface of the support, ultimately leading to the formation of smaller metal Co nanoparticles on γ-Al2O3, than on χ-Al2O3 .
|
Ilya V. Yakovlev; Vladimir I. Zaikovskii; Mariya A. Kazakova; Evgeniy S. Papulovskiy; Olga B. Lapina; Jean-Baptiste d'Espinose de Lacaillerie
|
Inorganic Chemistry; Catalysis; Magnetism; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63516794ca86b88e11bc1887/original/crystal-plane-dependent-dispersion-of-cobalt-metal-on-metastable-aluminas.pdf
|
628760d5809e325281964813
|
10.26434/chemrxiv-2022-h3530
|
Efficient removal of aqueous pharmaceutical pollutants by a robust anionic zirconium ellagate framework
|
Emerging organic contaminants (EOCs) in water, such as pharmaceutical compounds, are of growing environmental concern and there is a need to develop new materials and technologies for their efficient removal. A highly porous and exceptionally stable anionic zirconium ellagate metal-organic framework (MOF), denoted SU-102, was developed and utilized to remove EOCs from water, including real municipal wastewater treatment plant (WWTP) effluent. SU-102 adsorbs cationic EOCs with particularly high efficiencies and of the 17 pharmaceutical EOCs detected in WWTP effluent all 9 cationic species were removed with efficiencies of at least 79.0-99.6%, emphasizing the significance of framework charge on selectivity. As a second mechanism of EOC removal, SU-102 photodegraded the antibiotic sulfamethazine under visible light. SU-102 is synthesized from ellagic acid, an edible polyphenol building unit, highlighting the possibility of creating stable high-performance multifunctional materials from sustainably sourced plant-based components.
|
Erik Svensson Grape; Antonio J. Chacón; Sara Rojas; Yolanda Pérez; Aleksander Jaworski; Mathias Nero; Michelle Åhlén; Eva Martínez-Ahumada; Mayumi Narongin-Fujikawa; Ilich Ibarra; Ocean Cheung; Christian Baresel; Tom Willhammar; Patricia Horcajada; A. Ken Inge
|
Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes; Crystallography – Inorganic
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-05-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628760d5809e325281964813/original/efficient-removal-of-aqueous-pharmaceutical-pollutants-by-a-robust-anionic-zirconium-ellagate-framework.pdf
|
60c749cf9abda21079f8cce5
|
10.26434/chemrxiv.12103515.v1
|
DNA Translocation Through Vertically Stacked 2D Layers of Graphene & Hexagonal Boron Nitride Heterostructure Nanopore
|
Cost effective, fast and reliable DNA sequencing can be enabled by
advances in nanopore based methods, such as the use of atomically thin graphene
membranes. However, strong interaction of DNA bases with graphene leads to
undesirable effects such as sticking of DNA strands to the membrane surface.
While surface functionalization is one way to counter this problem, here we present
another solution based on a heterostructure nanopore system, consisting of a
monolayer of graphene and hexagonal Boron Nitride (hBN) each. Molecular
dynamics studies of DNA translocation through this heterostructure nanopore
revealed a surprising and crucial influence of heterostructure layer order in
controlling the base specific signal variability. Specifically, the
heterostructure with graphene on top of hBN had nearly 3-10x lower signal
variability than the one with hBN on top of graphene. Simulations point to the
role of differential underside sticking of DNA bases as a possible reason for
the observed influence of layer order. Our studies can guide the development of
experimental systems to study and exploit DNA translocation through two-dimensional
heterostructure nanopores for single molecule sequencing and sensing
applications.
|
Ramkumar Balasubramanian; Sohini Pal; Anjana Rao; Akshay Naik; Banani Chakraborty; Prabal
K. Maiti; Manoj Varma
|
Bioengineering and Biotechnology; Bioinformatics and Computational Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749cf9abda21079f8cce5/original/dna-translocation-through-vertically-stacked-2d-layers-of-graphene-hexagonal-boron-nitride-heterostructure-nanopore.pdf
|
64e5d5f6dd1a73847f57bca3
|
10.26434/chemrxiv-2023-jfq48
|
Site-selective ring opening of bicyclo[n.1.0]alkanols: An Fe(II)-catalyzed 1,6-conjugate addition to p-quinone methides
|
Herein, we report an efficient synthetic strategy for an Fe(II)-catalyzed site-selective ring opening of bicyclo[n.1.0]alkanols and their concomitant 1,6-conjugate addition to p-quinone methides. The selectivity induced is tuned exclusively by the substrate, thereby forming carbocycles of distinct sizes. Diverse synthetic transformations further enhance the utility of the protocol.
|
Neha Jha; Subhadip Mondal; Manmohan Kapur
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e5d5f6dd1a73847f57bca3/original/site-selective-ring-opening-of-bicyclo-n-1-0-alkanols-an-fe-ii-catalyzed-1-6-conjugate-addition-to-p-quinone-methides.pdf
|
60c755dd842e65390bdb43d2
|
10.26434/chemrxiv.14174222.v1
|
Thermodynamic Exploration of Xenon/krypton Separation Based on a High-Throughput Screening
|
<div>
<div>
<div>
<p>Nanoporous framework materials are a promising class of materials for energy-efficient technology of
xenon/krypton separation by physisorption. Many studies on Xe/Kr separation by adsorption have fo-
cused on the determination of structure/property relationships, the description of theoretical limits of performance, and the identification of top-performing materials. Here, we provided a study based on high-throughput screening of the adsorption of Xe, Kr, and Xe/Kr mixtures in 12,020 experimental MOFs materials, in order to provide a better comprehension of the thermodynamics behind Xe/Kr separation in
nanoporous materials and the microscopic origins of Xe/Kr selectivity at both low and ambient pressure.
</p>
</div>
</div>
</div>
|
Emmanuel Ren; François-Xavier Coudert
|
Hybrid Organic-Inorganic Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755dd842e65390bdb43d2/original/thermodynamic-exploration-of-xenon-krypton-separation-based-on-a-high-throughput-screening.pdf
|
60c74f30567dfe5dd8ec5646
|
10.26434/chemrxiv.12861170.v1
|
Graphene Oxide based Rechargeable Respiratory Masks
|
<div><div><div><p>Respiratory masks having similar standards of ‘N95’, defined by U.S. National Institute for Occupational Safety and Health, will be highly sought after, post this COVID-19 related pandemic condition. Here such a low cost (~$1/mask) mask design having electrostatic rechargeability and also having the filtration efficiency of >95% and quality factor of ~20 kPa-1 is demonstrated for its filtration efficacy towards particles of size < 0.5 μm. A tri-layer mask named ‘PPDFGO tri’ is designed here - containing nylon, modified polypropylene (PPY), and cotton non- woven fabrics as three layers. The melt-spun PPY, available in a conventional N95 mask, modified with graphene oxide (GO) and polyvinylidene fluoride (PVDF) mixture containing paste using a simple solution casting method acts as active filtration layer, and this tri-layer filtration system is shown for its efficacy towards triboelectric rechargeability using small mechanical agitations. These triboelectric nanogenerator (TENG) assisted masks have high electrostatic charge retention capacity (~1 nC/cm2 after 5 days in ambient condition) and high rechargeability even in the very humid condition (>80% RH). A simple but robust permeability measurement set up is also constructed to test these TENG based membranes, where a flow rate of 30-35 L/min is maintained during the testing. Such a simple modification in the existing mask designs enabling their rechargeability via external mechanical disturbances, with enhanced usability for single use as well as for reuse with decontantamination, will be highly beneficial in the modern era of indispensable personal protective equipment.</p></div></div></div>
|
Stelbin Peter Figerez; Sudeshna Patra; G. Rajalakshmi; Tharangattu Narayanan
|
Carbon-based Materials; Materials Processing; Thin Films
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f30567dfe5dd8ec5646/original/graphene-oxide-based-rechargeable-respiratory-masks.pdf
|
66b722c001103d79c577393d
|
10.26434/chemrxiv-2024-6zhx4-v2
|
Origin of the High-Frequency Shoulder in the Raman Spectra of CdSe Quantum Dots
|
The origin of the high-frequency shoulder (HFS) observed above the longitudinal optical (LO) peak around 230 1/cm in the Raman spectra of CdSe quantum dots (QDs) has been a subject of intense debate. We use state-of-the-art ab initio density functional theory applied to small CdSe QDs with various realistic surface passivations and find an intense Raman signal around 230 1/cm, which corresponds to a stretching vibration of a defective twofold coordinated Se atom. We interpret this signal as being the origin of the HFS. Since the signal disappears in fully passivated and defect-free (magic size cluster) structures, it can be used as a fingerprint to distinguish defective from non-defective structures.
|
Surender Kumar; Torben Steenbock; Gabriel Bester
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Clusters; Physical and Chemical Properties; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-08-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b722c001103d79c577393d/original/origin-of-the-high-frequency-shoulder-in-the-raman-spectra-of-cd-se-quantum-dots.pdf
|
61ddf0dadb4d9fc72d9581ef
|
10.26434/chemrxiv-2022-xmh55
|
Gradually Fe-doped Co3O4 nanoparticles in 2-propanol and water oxidation catalysis with single laser pulse resolution.
|
Controlling the surface composition of colloidal nanoparticles is still a challenging yet mandatory prerequisite in catalytic studies to investigate composition-activity trends, active sites, and reaction mechanisms without superposition of particle size- or morphology-effects. Laser post-processing of colloidal nanoparticles has been employed previously to create defects in oxide nanoparticles, while the possibility of laser-based cation doping of colloidal nanoparticles without affecting their size, remains mostly unaccounted for. Consequently, at the example of doping iron into colloidal Co3O4 spinel nanoparticles, we developed a pulse-by-pulse laser cation doping method to provide catalyst series with gradual surface composition but maintained extrinsic properties such as phase, size, and surface area for catalytic studies. Laser pulse number-resolved doping series were prepared at laser intensity chosen to selectively heat the Co3O4-NPs to roughly 1000 K and enable cation diffusion of surface-adsorbed Fe3+ into the Co3O4 lattice while maintaining the spinel phase, particle size, and surface area. The combination of bulk-sensitive X-ray fluorescence (XRF) and surface-sensitive X-ray photoelectron spectroscopy (XPS) was used to confirm a surface enrichment of the Fe-dopant. XRD, Magnetometry, and Mössbauer spectroscopy revealed an increasing interaction between Fe and the antiferromagnetic Co3O4 with an increasing number of pulses, in line with a proposed laser-induced surface doping of colloidal Co3O4 with Fe. Using Fick’s second law the thermal diffusion-related doping depth was estimated to be roughly 2 nm after 4 laser pulses. At the example of gas-phase 2-propanol oxidation and liquid-phase oxygen evolution reaction, the activity of the laser-doped catalysts is in good agreement with previous observations on binary iron-cobalt oxides. The catalytic activity was found to linearly increases with the calculated doping depth in both reactions, while only catalysts processed with at least one laser pulse were catalytically stable, highlighting the presented method in providing comparable, active, and stable gradual catalyst doping series for future catalytic studies.
|
Swen Zerebecki; Kai Schott; Soma Salamon; Joachim Landers; Eko Budiyanto; Heiko Wende; Harun Tüysüz; Stephan Barcikowski; Sven Reichenberger
|
Catalysis; Nanoscience; Nanofabrication; Nanostructured Materials - Nanoscience; Heterogeneous Catalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ddf0dadb4d9fc72d9581ef/original/gradually-fe-doped-co3o4-nanoparticles-in-2-propanol-and-water-oxidation-catalysis-with-single-laser-pulse-resolution.pdf
|
60e696a60387b1181aca374d
|
10.26434/chemrxiv-2021-45h42-v3
|
Characterization of Cisplatin/Membrane Interactions by QM/MM Energy Decomposition Analysis
|
The intermolecular interactions established between anticancer drugs and lipid membranes play a key role in the permeation mechanism of the drugs inside the cells. Herein we extend a quantum mechanical energy decomposition analysis scheme based on deformation electron densities to a hybrid multiscale electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) framework, and apply it to characterize the interactions between the cisplatin drug and a dioleyl-phosphatidylcholine lipid membrane. The interaction energy decomposition into electrostatic, induction, dispersion and Pauli repulsion contributions is performed for ensembles of geometries taken from molecular dynamics simulations to account for conformational sampling and, thus, obtain a distribution of each of the energy components. Contrary to a previous energy decomposition using force fields, it is evidenced that the electrostatic component is predominant in both polar and non-polar regions of the bilayer, and the repulsive component is strong when considered quantum mechanically, while being largely underestimated by the force field.
|
Gustavo Cárdenas; Álvaro Pérez-Barcia; Marcos Mandado; Juan J. Nogueira
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-07-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e696a60387b1181aca374d/original/characterization-of-cisplatin-membrane-interactions-by-qm-mm-energy-decomposition-analysis.pdf
|
6787de5a81d2151a0248a785
|
10.26434/chemrxiv-2025-ffb6q
|
A tale of two mechanisms: The p53 modulator COTI-2 is a Zn metallochaperone
|
Mutations in, or misregulation of, Tp53 are found in approximately 50% of all cancers. p53 functions by ensuring that cells with irretrievably damaged DNA undergo apoptosis. When p53 is non-functional in cells that may also be undergoing uncontrolled cell growth (due to other mutations), cancer readily emerges. Consequently, restoring the function of misregulated and mutated Tp53 is an incredibly important goal in therapeutic oncology. Tp53 mutations often induce conformational changes that inhibit the protein’s ability to engage its DNA response element. Small molecule chaperones could theoretically restore the proper shape and activity, but this is a far more challenging design problem than the typical paradigm of designing inhibitors of protein function. Consequently, it is unsurprising that there are no approved p53-targeting drugs. COTI-2, a thiosemicarbazone with orphan-drug status for ovarian cancer, has proven an effective cytotoxic agent against various cancer cell lines in vitro, exhibited efficacy in vivo, and has demonstrated a good safety profile in Phase 1b human clinical trials. The proposed mechanism, direct engagement and refolding of mutant p53, has been supported by a combination of cell-based assays and transcriptomics data. We propose that this is an unlikely mechanism of action, and that instead COTI-2 is acting as a selective, well-tolerated, zinc chaperone to replace zinc ions lost to p53 mutants’ deficient zinc-binding. We discuss that COTI-2 likely also works through other mechanisms but demonstrate that zinc-binding is necessary for the exceptional bioactivity. The promising therapeutic potential of this molecule and additional evidence for its zinc chaperone activity is discussed. This would make it the first well-tolerated zinc chaperone with pharmacological implications not only for cancer but for other zinc deficiency-related diseases.
|
İrem Şimşek; Farsheed Shahbazi-Raz; Michael J. Krause; Azam Mohammadzadeh; Maryam Kosar; Peihan Xu; Samra Khan; Olena Tykhoniuk; Ashley DaDalt; Deya'a Almasri; Lara K. Watanabe; Kaitlyn Breault; John J. Hayward; Fraser S. Pick; Richard L. Ho; Jeremy M. Rawson; John F. Trant
|
Biological and Medicinal Chemistry; Biophysics; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6787de5a81d2151a0248a785/original/a-tale-of-two-mechanisms-the-p53-modulator-coti-2-is-a-zn-metallochaperone.pdf
|
60c753e2337d6c1d3de2891f
|
10.26434/chemrxiv.13567853.v1
|
Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution
|
<div>The rational design of foldable and functionalizable peptidomimetic scaffolds requires the concerted application of both computational and experimental methods. Recently, a new class of designed peptoid macrocycle incorporating spiroligomer proline mimics (Q-prolines) has been found to pre-organize when bound by monovalent metal cations. To determine the solution-state structure of these cation-bound macrocycles, we employ a Bayesian inference method (BICePs) to reconcile enhanced-sampling molecular simulations with sparse ROESY correlations from experimental NMR studies. The BICePs approach circumvents the need for bespoke force field parameterization, instead relying on experimental restraints to help narrow the possible set of <i>cis</i>/<i>trans</i> amide isomers in solution. Conformations predicted to be most populated in solution were then simulated in the presence of explicit cations to yield trajectories with observed binding events, revealing a highly-preorganized all-<i>trans</i> amide conformation, whose formation is likely limited by the slow rate of <i>cis</i>/<i>trans</i> isomerization. Interestingly, this conformation differs from a racemic crystal structure solved in the absence of cation. Free energies of cation binding computed from distance-dependent potentials of mean force suggest Na<sup>+</sup> has higher affinity to the macrocycle than K<sup>+</sup>, with both cations binding much more strongly in acetonitrile than water. The simulated affinities are able to correctly rank the extent to which different macrocycle sequences exhibit preorganization in the presence of different metal cations and solvents, suggesting our approach is suitable for solution-state computational design.</div>
|
Matthew Hurley; Justin Northrup; Yunhui Ge; Christian Schafmeister; Vincent Voelz
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753e2337d6c1d3de2891f/original/metal-cation-binding-mechanisms-of-q-proline-peptoid-macrocycles-in-solution.pdf
|
669b1a0401103d79c5a0a108
|
10.26434/chemrxiv-2024-k0sss
|
Unconventional charge compensation mechanism for proton insertion in aqueous Zn-ion batteries
|
Aqueous Zn-ion batteries have been proposed as safe and economical options for large-scale energy storage. In theory, they operate by reversibly shuttling zinc ions between a metallic zinc anode and a cathode material for Zn2+ ion intercalation through an aqueous electrolyte of a zinc salt solution. In practice, protons (H+) in the aqueous electrolyte can compete with and even predominate Zn2+ in the intercalation reaction. A diagnostic consequence of H+, as opposed to Zn2+, insertion is the precipitation of layered double hydroxide (LDH) crystals, which can be readily identified by electron microscopy and X-ray diffraction measurements. Absence of LDH formation has been perceived as evidence for Zn2+ insertion. Using a combination of X-ray diffraction, electron microscopy, X-ray photoelectron spectroscopy, we reveal a different charge compensation mechanism in a vanadyl phosphate electrode, where H+ insertion predominates in an aqueous Zn(CF3SO3)2 electrolyte. The H+ insertion induces a conformal deposition of an amorphous ZnO layer on the electrode particle, which cannot be captured by scanning electron microscopy or X-ray diffraction. Our work underlines the complexity of the charge compensation mechanism in aqueous Zn-ion batteries, which is relevant to other multivalent systems.
|
Jiwei Wang; Heran Huang; Linna Qiao; Haonan Wang; Krystal Lee; Guangwen Zhou; Hao Liu
|
Materials Science; Energy; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669b1a0401103d79c5a0a108/original/unconventional-charge-compensation-mechanism-for-proton-insertion-in-aqueous-zn-ion-batteries.pdf
|
60c74853702a9b11ed18af78
|
10.26434/chemrxiv.11124251.v2
|
Divergence of Many-Body Perturbation Theory for Noncovalent Interactions of Large Molecules
|
Prompted by recent reports of large errors in noncovalent interaction (NI) energies obtained from many-body perturbation theory (MBPT), we compare the performance of second-order Møller–Plesset MBPT (MP2), spin-scaled MP2, dispersion-corrected semilocal density functional approximations (DFA), and the post-Kohn–Sham random phase approximation (RPA) for predicting binding energies of supramolecular complexes contained in the S66, L7, and S30L benchmarks. All binding energies are extrapolated to the basis set limit, corrected for basis set superposition errors, and compared to reference results of the domain-based local pair-natural orbital coupled-cluster (DLPNO-CCSD(T)) or better quality. Our results confirm that MP2 severely overestimates binding energies of large complexes, producing relative errors of over 100% for several benchmark compounds. RPA relative errors consistently range between 5-10%, significantly less than reported previously using smaller basis sets, whereas spin-scaled MP2 methods show limitations similar to MP2, albeit less pronounced, and empirically dispersion-corrected DFAs perform almost as well as RPA. Regression analysis reveals a systematic increase of relative MP2 binding energy errors with the system size at a rate of approximately 0.1% per valence electron, whereas the RPA and dispersion-corrected DFA relative errors are virtually independent of the system size. These observations are corroborated by a comparison of computed rotational constants of organic molecules to gas-phase spectroscopy data contained in the ROT34 benchmark. To analyze these results, an asymptotic adiabatic connection symmetry-adapted perturbation theory (AC-SAPT) is developed which uses monomers at full coupling whose ground-state density is constrained to the ground-state density of the complex. Using the fluctuation–dissipation theorem, we obtain a nonperturbative “screened second-order” expression for the dispersion energy in terms of monomer quantities which is exact for non-overlapping subsystems and free of induction terms; a first-order RPA-like approximation to the Hartree, exchange, and correlation kernel recovers the macroscopic Lifshitz limit. The AC-SAPT expansion of the interaction energy is obtained from Taylor expansion of the coupling strength integrand. Explicit expressions for the convergence radius of the AC-SAPT series are derived within RPA and MBPT and numerically evaluated. Whereas the AC-SAPT expansion is always convergent for nondegenerate monomers when RPA is used, it is found to spuriously diverge for second-order MBPT, except for the smallest and least polarizable monomers. The divergence of the AC-SAPT series within MBPT is numerically confirmed within RPA; prior numerical results on the convergence of the SAPT expansion for MBPT methods are revisited and support this conclusion once sufficiently high orders are included. The cause of the failure of MBPT methods for NIs of large systems is missing or incomplete “electrodynamic” screening of the Coulomb interaction due to induced particle–hole pairs between electrons in different monomers, leaving the effective interaction too strong for AC-SAPT to converge. Hence, MBPT cannot be considered reliable for quantitative predictions of NIs, even in moderately polarizable molecules with a few tens of atoms. The failure to accurately account for electrodynamic polarization makes MBPT qualitatively unsuitable for applications such as NIs of nanostructures, macromolecules, and soft materials; more robust non-perturbative approaches such as RPA or coupled cluster methods should be used instead whenever possible.<br />
|
Brian Nguyen; Guo P Chen; Matthew M. Agee; Asbjörn M. Burow; Matthew Tang; Filipp Furche
|
Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74853702a9b11ed18af78/original/divergence-of-many-body-perturbation-theory-for-noncovalent-interactions-of-large-molecules.pdf
|
60c74ffd9abda2f619f8d952
|
10.26434/chemrxiv.12974714.v1
|
Identification and Analysis of Activity Cliffs Using 3D Similarity Techniques
|
<p>The analysis of activity landscapes and
activity cliffs is a widely used method to locate critical regions of SAR.
Knowledge of what changes in a series of molecules caused unexpectedly large
changes in affinity allows the chemist to focus on the molecular features which
are crucial for activity. We examine the usefulness of activity cliff analysis
with a metric based on 3D shape and electrostatic similarity, utilizing a
ligand-based alignment method. We demonstrate that 3D activity cliff analysis
is complementary to the more usual 2D fingerprint-based methods, in that each
finds cliffs that the other misses. Moreover, we show that analysis of the
activity landscape in the context of a consensus 3D alignment allows the source
of the activity cliff to be investigated in terms of the effect that a
structural change has on the steric and electrostatic properties of a molecule.
The technique is illustrated with two set of compounds with activity against
acetylcholinesterase and dipeptidyl peptidase.</p>
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Mark Mackey; Timothy J. Cheeseright; Paolo Tosco
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Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2020-09-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ffd9abda2f619f8d952/original/identification-and-analysis-of-activity-cliffs-using-3d-similarity-techniques.pdf
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661f7d96418a5379b0051b49
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10.26434/chemrxiv-2024-tvsb6
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Moiré Superlattices of Zn2+ Mediated 2D Assembly of Mn2+-Cysteine Complex Nanoparticles Alter Electron Spin Transitions in the X-band
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Ambient reaction-mediated assembly of cysteine-based nanoparticles of Mn complex, and Zn2+ ion led to the generation of moiré patterns in 2D films. Individually formed crystalline 2D films made of manganese cysteine complex nanoparticles and Zn2+ ions were stacked angularly against each other giving rise to the moiré films. Selected area electron diffraction patterns revealed a wide range of twist angles. Circular dichroism peaks appearing at 480 nm, 513 nm, and 643 nm; representing moiré chirality were observed irrespective of the chiral identity of the constituent ligand. The moiré films were constituted of two chemically different types of Mn2+ ions as revealed by electron spin resonance (ESR) spectroscopy. The ESR signal of Mn2+ ion was found to have been altered upon formation of the moiré films as a result of the prevalent interfacial magnetic field of the individual 2D films. The current work focuses on the generation of self-assembled moiré materials of manganese cysteine nanoparticles by Zn2+ ion and the influence of so formed moiré pattern on the chemical environment of the Mn2+ ions. The discovery of inorganic complex nanoparticle-based moiré material can offer structural, physical, and chemical diversity to materials science.
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Archismita Hajra; Arun Chattopadhyay
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Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Interfaces; Physical and Chemical Properties; Materials Chemistry
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CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f7d96418a5379b0051b49/original/moire-superlattices-of-zn2-mediated-2d-assembly-of-mn2-cysteine-complex-nanoparticles-alter-electron-spin-transitions-in-the-x-band.pdf
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60c7518c337d6c9eade28557
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10.26434/chemrxiv.13176413.v1
|
Multiple Objects Interacting with a Solidification Front
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The interaction of foreign objects suspended in a liquid melt with an advancing solidification front is of special interest in nature (e.g. frost heave) and engineering sciences (e.g. crystal growth). The front can engulf the object, trapping it into the growing crystal, or the front can repel the object, pushing it ahead of itself. Therefore, the object-front confrontation can have a strong influence on the properties of the solidified material. In particular, the spatial distribution of the objects in the resulting microstructure determines the material's structural and functional properties. The past theoretical models and experimental studies have mostly investigated the interaction of isolated, spherical, and hard objects in pure melts. However, the outcome of object-front interactions in complex (more realistic) systems, where multiple objects and solutes are present, is still poorly understood. Here we show the interaction of multiple oil droplets with an ice-water front in the absence and presence of solute effects using in situ cryo-confocal microscopy. We observe the formation of a compact agglomerated layer resulting in a force equilibrium different from the isolated object approach. We elucidate the role of solute during the evolution of a material microstructure in the presence of foreign objects. We report on how the object size, number of objects, and bulk solute concentration influence the front morphology and the subsequent object spatial distribution. Our results depict how the presence of multiple objects with varying solute concentration can modify the object-front interactions and hence, can lead to the formation of complex microstructures, difficult to predict theoretically. We suggest that the volume fraction of objects suspended in a liquid melt in conjunction with the amount of bulk solute concentration are two important criteria to be incorporated in the development of object-front interaction models. Furthermore, our simplified approach of using oil-in-water emulsions can serve as a good analogue for studying the development of material microstructure in presence of foreign objects. <br />
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Sidhanth Tyagi; Cécile Monteux; Sylvain Deville
|
Composites; Imaging Agents; Materials Processing; Surfactants; Interfaces
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7518c337d6c9eade28557/original/multiple-objects-interacting-with-a-solidification-front.pdf
|
60c7467f842e65e6addb2801
|
10.26434/chemrxiv.11338457.v1
|
Molten Salt Electrometallurgy
|
The experimental results are for electro-deoxidation in molten salt and the numerical results are for molten salt processes in electrometallurgy.<div>The internal cathode microstructure is analysed using SEM, Energy dispersive X-ray spectroscopy, and computerised X-ray tomography.<br /></div><div>Numerical simulations using COMSOL multiphysics report results for molten salt processes using theory from rotating disk electrodes and multiphase flow. Scale-up of electro-deoxidation is discussed using primary current distribution simulations in various electro-deoxidation cell designs.<br /></div><div>Experimental details of electro-deoxidation cell construction is referenced to and outlined in my earlier work: <i>Electrochim.
Acta</i> <b>164</b>,
48 (2015)<br /></div>
|
Charles Osarinmwian
|
Fluid Mechanics; Industrial Manufacturing; Reaction Engineering; Transport Phenomena (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7467f842e65e6addb2801/original/molten-salt-electrometallurgy.pdf
|
64fad159b338ec988a192157
|
10.26434/chemrxiv-2023-75k23
|
Simplified Preservation of Equal Paths Spectroscopy
|
Inspired by the recently proposed Transverse mixing Optimal control Pulses (TROP) approach for improving signal in multi-dimensional magic-angle spinning (MAS) NMR experiments, we present simplified preservation of equal paths spectroscopy (SPEPS). It transfers both transverse components of magnetization that occur during indirect evolutions, theoretically enabling a √2 improvement in sensitivity for each such dimension. We compare SPEPS transfer with TROP and cross polarization (CP) using membrane protein and fibril samples at MAS of 55 kHz and 100 kHz. In 3D (H)CANH spectra, SPEPS outperformed TROP and CP by factors of, on average, 1.16 and 1.69, respectively for the membrane protein, but only marginal improvement of 1.09 was observed for the fibril. These differences are discussed making note of the longer transfer time used for CP, 14 ms, as compared with 2.9 and 3.6 ms for SPEPS and TROP, respectively. Using SPEPS for two transfers in the 3D (H)CANCO experiment resulted in even larger benefit in signal intensity, with an average improvement of 1.82 as compared with CP. This results in a multifold time savings, in particular considering the weaker peaks that are observed to benefit the most from SPEPS.
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Evgeny Nimerovsky; Abel Cherian Varkey; Myeongkyu Kim; Stefan Becker; Loren B. Andreas
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Physical Chemistry; Biological and Medicinal Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fad159b338ec988a192157/original/simplified-preservation-of-equal-paths-spectroscopy.pdf
|
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