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63d4e631ae221a107d403393
|
10.26434/chemrxiv-2023-78fk0
|
Cu(I)-BOX Catalyzed Asymmetric 3-Component Reaction for the Synthesis of Trifluoromethylated Propargylic Ethers and Anilines
|
An asymmetric 3-component reaction between EthynylBenziodoXoles (EBxs), 2,2,2-trifluorodiazoethane and nucleophiles catalyzed by a Cu(I)Box catalyst is described. This protocol gives access to chiral trifluoromethylated propargyl ethers and anilines, which are valuable building blocks in synthetic and medicinal chemistry. The reaction proceeds with high enantioselectivity and yield with different nucleophiles such as primary, secondary and tertiary alcohols, as well as both electron-rich and electron-poor anilines. Aryl-, Alkyl- and silyl-substituted alkynes can be successfully introduced as electrophiles. In case of chiral substrates, high catalyst control was observed, leading to good diastereoselectivity.
|
Nieves P. Ramirez; Jerome Waser
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d4e631ae221a107d403393/original/cu-i-box-catalyzed-asymmetric-3-component-reaction-for-the-synthesis-of-trifluoromethylated-propargylic-ethers-and-anilines.pdf
|
60c75308f96a0011e728838c
|
10.26434/chemrxiv.13373249.v1
|
Labeling Preferences of Diazirines with Protein Biomolecules
|
<p>Diazirines are widely used in photoaffinity labeling (PAL) to trap non-covalent interactions with biomolecules. However, design and interpretation of PAL experiments is challenging without a molecular understanding of the reactivity of diazirines with protein biomolecules. Here, we report a systematic evaluation of the labeling preferences of alkyl and aryl diazirines with individual amino acids, single proteins, and in the whole cell proteome. We find that aryl-fluorodiazirines react primarily through a carbene intermediate, while alkyl diazirines generate a reactive alkyl diazo intermediate on route to the carbene. The generation of a reactive diazo intermediate leads to preferential labeling of acidic amino acids in a pH-dependent manner. From a survey of 32 alkyl diazirine probes, we use this reactivity profile to rationalize why these probes preferentially enrich highly acidic proteins or those embedded in membranes and why probes with a net positive-charge tend to produce higher labeling yields. These results indicate that alkyl diazirines are an especially effective chemistry for surveying the membrane proteome, and will facilitate probe design and interpretation of biomolecular labeling experiments with diazirines.<b></b></p>
|
Alexander West; Giovanni Muncipinto; Hung-Yi Wu; Andrew Huang; Matthew T. Labenski; Christina Woo
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75308f96a0011e728838c/original/labeling-preferences-of-diazirines-with-protein-biomolecules.pdf
|
60c74849567dfefc91ec49a1
|
10.26434/chemrxiv.11879193.v1
|
Is Domain Knowledge Necessary for Machine Learning Materials Properties?
|
<div>New methods for describing materials as vectors in order to predict their properties using machine learning are common in the field of material informatics. However, little is known about the comparative efficacy of these methods. This work sets out to make clear which featurization methods should be used across various circumstances. Our findings include, surprisingly, that simple one-hot encoding of elements can be as effective as traditional and new descriptors when using large amounts of data. However, in the absence of large datasets or data that is not fully representative we show that domain knowledge offers advantages in predictive ability.</div><div><br /></div>
|
Ryan Murdock; Steven Kauwe; Anthony Wang; Taylor Sparks
|
Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74849567dfefc91ec49a1/original/is-domain-knowledge-necessary-for-machine-learning-materials-properties.pdf
|
60c74e7f702a9b397718ba03
|
10.26434/chemrxiv.12765953.v1
|
Prediction of Single Point Mutations in Ganglioside-Binding Domain of SARS-CoV-2 S and Their Effects on Binding of 9-O-Acetylated Sialic Acid and Hidroxychloroquine
|
The infectious disease CoViD-19 is caused by a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also referred to as hCoV-19. A possible infection mechanism includes dual host receptor recognitions by the SARS-CoV-2 transmembrane spike (S) glycoproteins. SARS-CoV-2 S contains two different domains, the receptor-binding domain (RBD) and the N-terminal domain (NTD), which interact with the angiotensin-converting enzyme 2 (ACE2) and the ganglioside-rich domain of the plasma membrane at the surface of respiratory cell, respectively. The NTD amino acid residues (111-162) form a functional ganglioside-binding domain (GBD) that is conserved in all clinical isolates. Herein, the single point mutations (SPMs) of the GBD residues to which the virus is prone during genetic adaptation are predicted using an in silico protein engineering approach. Consequently, their effects on the attachment of SARS-CoV-2 S to the ganglioside-linked 9-O-acetylated sialic acid (9-O-Ac-Sia) are explored using molecular docking simulations. Val120Tyr and Asn122Trp are found to be the most likely SPMs in the GBD of SARS-CoV-2 S being involved in very specific recognition with 9-O-Ac-Sia through electrostatic interactions. Val120Tyr and Asn122Trp are also found to be the most likely SPMs in the GBD of SARS-CoV-2 S that is involved in conspicuously hydrophobic recognition with hidroxychloroquine (Hcq), thereby indicating the ability of Hcq to competitively inhibit GBD interactions with lipid rafts. However, the considerably non-specific binding of Hcq and the micromolar range of the dissociation constants of the SARS-CoV-2 S/Hcq complexes do not support the proposal of treating Hcq as a drug candidate. Maintaining a clear resemblance of the structure of a potential drug candidate to a natural substrate, accompanied by essential functional group modifications, may be a usable guideline for the structure-based design of anti-CoViD-19 drugs.<br />
|
Petar M. Mitrasinovic
|
Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e7f702a9b397718ba03/original/prediction-of-single-point-mutations-in-ganglioside-binding-domain-of-sars-co-v-2-s-and-their-effects-on-binding-of-9-o-acetylated-sialic-acid-and-hidroxychloroquine.pdf
|
63175dbefaf4a46a540863c8
|
10.26434/chemrxiv-2022-3j82b
|
Ion mobility-mass spectrometry and collision induced unfolding of designed bispecific antibody therapeutics
|
Bispecific antibodies (bsAbs) represent a critically important class of emerging therapeutics capable of simultaneously two different antigens simultaneously. As such, bsAbs have been developed as effective treatment agents for diseases that remain challenging for conventional monoclonal antibody (mAb) therapeutics to access. Despite this, bsAbs are intricate molecules, requiring both the appropriate engineering and pairing of linked heavy and light chains derived from separate parent mAbs. Current analytical tools for tracking the bsAb construction process have demonstrated a limited ability to robustly probe the higher order structure (HOS) of bsAbs. Native ion mobility-mass spectrometry (IM-MS) and collision induced unfolding (CIU) have proven to be useful tools in probing the HOS of mAb therapeutics. In this report, we de-scribe a series of comprehensive IM-MS and CIU datasets that reveal HOS details associated with knob-into-hole (KiH) bsAb model system. We find that quantitative analysis of CIU data indicates that global bsAb stability occupies and in-termediate space between the stabilities recorded for its parent mAbs. Furthermore, our CIU data identifies the hole-containing half of the bsAb construct to be least stable, thus driving much of the overall stability of the bsAb. An analysis of both intact bsAb and enzymatic fragments allows us to link the first and second CIU transitions observed for intact bsAbs to the Fab and Fc domains, respectively. This result is likely general for CIU data collected from low charge state mAb ions and is supported by data acquired for deglycosylated bsAb and mAb constructs, each of which of which indi-cate greater destabilization of the second CIU transition observed in our data. When integrated, our CIU analysis allows us to link changes in the first CIU transition primarily to the Fab region of the hole-containing halfmer, while the second CIU transition is likely strongly connected to the Fc region of the knob-containing half of the bsAb construct. Taken together, our results provide an unprecedented roadmap for evaluating the domain-level stabilities and HOS of both bsAbs and mAb constructs using CIU.
|
Rosendo Villafuerte-Vega; Henry Li; Thomas Slaney; Naresh Chennamsetty; Guodong Chen; Li Tao; Brandon Ruotolo
|
Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63175dbefaf4a46a540863c8/original/ion-mobility-mass-spectrometry-and-collision-induced-unfolding-of-designed-bispecific-antibody-therapeutics.pdf
|
64e475a3dd1a73847f498f17
|
10.26434/chemrxiv-2023-35mmv
|
Regioselective glycosylation of polyphenols by family 1 glycosyltransferases: experiments and simulations
|
Family 1 glycosyltransferases (GT1s, UGTs) form natural product glycosides with exquisite control over regio- and stereoselectivity, representing attractive biotechnological targets. However, regioselectivity cannot be predicted and large-scale activity assessment efforts of UGTs are commonly performed via mass spectrometry or indirect assays that are blind to regioselectivity. Here, we present a large HPLC screening discriminating between regioisomeric products of 40 diverse UGTs (28.6% average pairwise sequence identity) against 32 polyphenols, identifying enzymes able to reach high glycosylation yields (≥90% in 24h) in 26/32 cases. In reactions with >50% yield, we observed perfect regioselectivity for 47% (75/158) on polyphenols presenting two hydroxyl groups, and for 30% (43/143) on polyphenols presenting ≥3 hydroxyl groups. Moreover, we developed an NMR-based procedure to identify the site of glycosylation directly on enzymatic mixtures. We further selected seven regiospecific reactions catalyzed by four enzymes on five dihydroxycoumarins. We characterized the four enzymes, showing that temperature optima are functions of the acceptor substrate, varying by up to 20°C for the same enzyme. Furthermore, we performed short molecular dynamics simulations of 311 ternary complexes (UGT, UDP-Glc, glycosyl acceptor) to investigate the molecular basis for regioselectivity. Interestingly, it appeared that most UGTs can accommodate acceptors in configurations favorable to the glycosylation of either hydroxyl. In contrast, evaluation of hydroxyl nucleophilicity appeared a strong predictor of the hydroxyl predominantly glycosylated by most enzymes.
|
Ruben Marcel de Boer; Dovydas Vaitkus; Kasper Enemark-Rasmussen; Sören Maschmann; David Teze; Ditte Hededam Welner
|
Catalysis; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e475a3dd1a73847f498f17/original/regioselective-glycosylation-of-polyphenols-by-family-1-glycosyltransferases-experiments-and-simulations.pdf
|
62269fd9daa4fbafcb835483
|
10.26434/chemrxiv-2022-8l577
|
Site-selective deuteration of amino acids through dual protein catalysis
|
Deuterated amino acids have been recognized for their utility in drug development, for facilitating NMR analysis, and as probes for enzyme mechanism. Small molecule-based methods for the site-selective synthesis of deuterated amino acids typically involve de novo synthesis of the compound from deuterated precursors. In comparison, enzymatic methods for introducing deuterium offer improved efficiency, operating directly on free amino acids to achieve hydrogendeuterium (H/D) exchange. However, site-selectivity remains a significant challenge for enzyme-mediated deuteration, limiting access to desirable deuteration motifs. Here we use enzyme-catalyzed deuteration, combined with steady-state kinetic
analysis and UV-vis spectroscopy to probe the mechanism of a two-protein system responsible for the biosynthesis of L-alloIle. We show an aminotransferase (DsaD) can pair with a small partner protein (DsaE) to catalyze Cα and Cβ H/D exchange
of amino acids, while reactions without DsaE lead exclusively to Cα-deuteration. With conditions for improved catalysis, we
evaluate the substrate scope for Cα/Cβ-deuteration and demonstrate the utility of this system for preparative-scale, selective labeling of amino acids.
|
Tyler Doyon; Andrew Buller
|
Biological and Medicinal Chemistry; Catalysis; Biochemistry; Bioengineering and Biotechnology; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62269fd9daa4fbafcb835483/original/site-selective-deuteration-of-amino-acids-through-dual-protein-catalysis.pdf
|
640814ea0e6a36fabae9cfd8
|
10.26434/chemrxiv-2023-4gskt
|
Maximization of Hydrogen Peroxide Utilization in PEM H2O2 Electrolyzer for Efficient Power-to-Hydrogen Conversion
|
The hydrogen peroxide electrolyzer (HPEL) is the workhorse for the energy storage system based on the electrochemical cycle of H2O2. The high H2O2 utilization towards power-to-hydrogen conversion (EH2O2-HER) in the HPEL is essential to ensure the efficiency and cyclability of the system. Unfortunately, the disproportionation of H2O2 at the anode and its crossover to the cathode in a proton exchange membrane (PEM) HPEL is detrimental to H2O2 utilization and must be mitigated. This work investigates the effects of catalyst type, catalyst loading, and membrane thickness on H2O2 utilization in PEM HPEL. The results show that cobalt- and nitrogen-doped carbon (Co-N-C) catalyst exhibits higher H2O2 utilization than the Fe-N-C and Pt/C catalysts due to its higher selectivity towards the hydrogen peroxide oxidation reaction (HPOR) and the lesser H2O2 disproportionation reaction (HPDR). Increasing the loading of the Co-N-C catalyst and membrane thickness can effectively inhibit the H2O2-crossover and improve the H2O2 utilization. On the other hand, the portion of HPDR and the ohmic loss increases with the catalyst loading and membrane thickness, respectively. A maximum H2O2 utilization of over 98% can be achieved by balancing these factors and the cell operating condition. These results provide valuable guides to the catalyst design and device optimization for highly efficient energy storage systems based on the electrochemical H2O2-H2 cycle.
|
Jie Yang; Ruimin Ding; Chang Liu; Lifang Chen; Qi Wang; Shanshan Liu; Qinchao Xu; Xi Yin
|
Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Electrocatalysis; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640814ea0e6a36fabae9cfd8/original/maximization-of-hydrogen-peroxide-utilization-in-pem-h2o2-electrolyzer-for-efficient-power-to-hydrogen-conversion.pdf
|
60c752864c89191ddcad412c
|
10.26434/chemrxiv.13311881.v1
|
Unraveling the Growth Mechanism of Magic-Sized Semiconductor Nanocrystals
|
Magic-sized clusters (MSCs) of semiconductor are typically defined as specific molecular-scale arrangements of atoms that exhibit enhanced stability. They often grow in discrete jumps, creating a series of crystallites, without the appearance of intermediate sizes. However, despite their long history, the mechanism behind their special stability and growth remains poorly understood. This is particularly true considering experiments that have shown discrete evolution of MSCs to sizes well beyond the “cluster” regime and into the size range of colloidal quantum dots. Here, we study the growth of these larger magic-sized CdSe nanocrystals to unravel the underlying growth mechanism. We first introduce a synthetic protocol that yields a series of nine magic-sized nanocrystals of increasing size. By investigating these crystallites, we obtain important clues about the mechanism. We then develop a microscopic model that uses classical nucleation theory to determine kinetic barriers and simulate the growth. We show that magic-sized nanocrystals are consistent with a series of zinc-blende crystallites that grow layer by layer under surface-reaction-limited conditions. They have a tetrahedral shape, which is preserved when a monolayer is added to any of its four identical facets, leading to a series of discrete nanocrystals with special stability. Our analysis also identifies strong similarities with the growth of semiconductor nanoplatelets, which we then exploit to increase further the size range of our magic-sized nanocrystals. Although we focus here on CdSe, these results reveal a fundamental growth mechanism that can provide a different approach to nearly monodisperse nanocrystals.
|
Aniket S. Mule; Sergio Mazzotti; Aurelio A. Rossinelli; Marianne Aellen; P. Tim Prins; Johanna C. van der Bok; Simon F. Solari; Yannik M. Glauser; Priyank V. Kumar; Andreas Riedinger; David J. Norris
|
Nanostructured Materials - Materials; Optical Materials; Nanostructured Materials - Nanoscience; Theory - Computational; Clusters; Optics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752864c89191ddcad412c/original/unraveling-the-growth-mechanism-of-magic-sized-semiconductor-nanocrystals.pdf
|
60c7578c702a9b118b18cafe
|
10.26434/chemrxiv.14416133.v1
|
Transformer Neural Network for Structure Constrained Molecular Optimization
|
Finding molecules with a desirable balance of multiple properties is a main challenge in drug discovery. Here, we focus on the task of molecular optimization, where a starting molecule with promising properties needs to be further optimized towards the desirable properties. Typically, chemists would apply chemical transformations to the starting molecule based on their intuition. A widely used strategy is the concept of matched molecular pairs where two molecules differ by a single transformation. In particular, a chemist would be interested in keeping one part of the starting molecule (core) constant, while substituting the other part (R-group), to optimize the starting molecule towards desirable properties. Motivated by this, we train a Transformer model, Transformer-R, to generate R-groups given the starting molecule (with its core and R-group specified) and the specified desirable properties. The generated R-groups will be attached to the core to form the final molecules, which are guaranteed to keep the core of interest and are expected to satisfy the desirable properties in the input. Our model could accelerate the process of optimizing antiviral drug candidates in terms of various properties of interest, e.g. pharmacokinetics.
|
Jiazhen He; Felix Mattsson; Marcus Forsberg; Esben Jannik Bjerrum; Ola Engkvist; eva nittinger; Christian Tyrchan; Werngard Czechtizky
|
Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7578c702a9b118b18cafe/original/transformer-neural-network-for-structure-constrained-molecular-optimization.pdf
|
677ce2216dde43c90896dcbe
|
10.26434/chemrxiv-2025-xjj46
|
Phenylboronic acids as pH-selective ligands for arylsulfatase B: a lead for pharmacological chaperones against Maroteaux–Lamy syndrome
|
Loss of function in lysosomal arylsulfatase B (ARSB) leads to Maroteaux–Lamy syndrome, a form of the mucopolysaccharidoses. Mutations in ARSB, at least those characterized in detail, often destabilize and interfere with the folding of the ARSB protein, resulting in the loss of functional ARSB in lysosomes. Pharmacological chaperones, which are ligands that assist in protein folding by binding to folding intermediates in the endoplasmic reticulum, are proposed to be potential drug candidates for such protein misfolding diseases. However, small-molecule ligands for ARSB have not been widely studied and most of the known ligands are sulfate compounds, which are highly polar and do not readily cross the membrane. Since pharmacological chaperones must be able to enter the cell and the endoplasmic reticulum, a surrogate pharmacophore with membrane permeable properties is needed. In this study, we identified phenylboronic acid as an effective sulfate surrogate with membrane permeability, via competitive enzymatic assay against ARSB. Additionally, phenylboronic acids were more potent at neutral pH and less so at acidic pH, exhibiting a pH selective activity profile ideal for pharmacological chaperones. Subsequent structure-activity relationship studies identified more potent derivatives, and ARSB was protected from thermal denaturation in the presence of the derivatives, supporting direct binding of the phenylboronic acids. Although further studies will be required to determine if these phenylboronic acids could act as pharmacological chaperones for ARSB mutants, our finding of phenylboronic acid as a pH-selective surrogate pharmacophore for the aryl sulfate should be valuable for designing pharmacological chaperones for sulfatases in the future.
|
Fumika Karaki; Kyoko Hidaka; Yuko Nishiyama; Ami Taniguchi; Yuichi Hashimoto; Kenji Ohgane; Hideaki Fujii
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677ce2216dde43c90896dcbe/original/phenylboronic-acids-as-p-h-selective-ligands-for-arylsulfatase-b-a-lead-for-pharmacological-chaperones-against-maroteaux-lamy-syndrome.pdf
|
657c3fe8e9ebbb4db9f2917b
|
10.26434/chemrxiv-2023-rc4t5
|
Flooded mineshaft compressed air energy storage in the Witwatersrand Goldmine Complex – case study of a proposed novel energy storage method
|
With renewable energy sources representing a rapidly-growing share of the global energy mix, their intermittent nature has led to growing interest in mechanisms of storing energy during periods of high availability, for use during times of high demand. Several different types of compressed-air energy storage have been considered, including constant-volume approaches such as salt dome or artificial vessel storage and newer constant-pressure approaches such as submerged cavern storage. This manuscript proposes a novel approach where abandoned, flooded mineshafts are pressurized with air, displacing water downward in the shaft but upward in other hydraulically-linked shafts in the same geological complex. This approach is something of a hybrid between compressed-air storage and pumped storage and is thermodynamically distinct in that neither pressure nor volume are constant. An application to the abandoned goldmine shafts of South Africa’s Witwatersrand geological complex is considered, and thermodynamic analysis indicates that this approach offers around 10% greater energy density than conventional compressed air energy storage, and that a single mineshaft could have isothermal storage capacity exceeding 1GWh, with some operational advantages specific to the Witwatersrand context, meriting further research to design processes.
|
Neil Thomas Stacey; Peter Stacey; Diane Hildebrandt; James Fox; David Glasser
|
Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657c3fe8e9ebbb4db9f2917b/original/flooded-mineshaft-compressed-air-energy-storage-in-the-witwatersrand-goldmine-complex-case-study-of-a-proposed-novel-energy-storage-method.pdf
|
6344000b114b7e0e21304d7b
|
10.26434/chemrxiv-2022-shhck-v2
|
Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links
protein dynamics to active-site electrostatic preorganisation
|
ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.
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Gemma Fisher; Marina Corbella; Magnus S. Alphey; John Nicholson; Benjamin J. Read; Shina C. L. Kamerlin; Rafael G. da Silva
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Computational Chemistry and Modeling; Biocatalysis
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CC BY 4.0
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CHEMRXIV
|
2022-10-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6344000b114b7e0e21304d7b/original/allosteric-rescue-of-catalytically-impaired-atp-phosphoribosyltransferase-variants-links-protein-dynamics-to-active-site-electrostatic-preorganisation.pdf
|
62e1040c5be0414c4d9d7e8f
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10.26434/chemrxiv-2022-866vj
|
Efficient machine learning configuration interaction for bond breaking problems
|
Machine learning-assisted configuration interaction (MLCI) has been shown earlier as a promising method in determining the electronic structure of the model and molecular Hamiltonians. In the MLCI approach to molecular Hamiltonians, it has been noticed that prediction is strongly dependent on the connectedness of the training and validation spaces. In this work, we have tested three different models with different output parameters (abs-MLCI, transformed-MLCI, and log-MLCI) to verify the robustness of training these models. We define robustness as the extent of error in prediction even when the spaces (training and validation) are nected. We notice that the log-MLCI model is best suited to this approach and is, therefore, a powerful model for accurate one-shot variational energies. This is tested not confor chemical bond breaking in water, carbon monoxide, nitrogen, and dicarbon molecules.
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Madhumita Rano; Debashree Ghosh
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Theoretical and Computational Chemistry; Theory - Computational; Machine Learning
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CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e1040c5be0414c4d9d7e8f/original/efficient-machine-learning-configuration-interaction-for-bond-breaking-problems.pdf
|
67922419fa469535b9703034
|
10.26434/chemrxiv-2025-61l4x-v2
|
Regioselective [3+2] Cycloaddition Reactions of the Phosphorus and Arsenic Analogues of the Thiocyanate Anion
|
Salt metathesis reactions of the tris-amide zirconium iodide complex ([NRR’]3ZrI (1-I) (with NRR’ = 3,5-Xylyl-tert-butylamide, N(Xyl)(tBu)) and sodium 2-phosphaethynthiolate (Na(diox)3SCP) or 2-arsaethynthiolate (Na(diox)3SCAs) in THF result in the formal [3+2] cycloaddition of the two SCE (E = P, As) units forming novel five membered 2-thio-1,3,4-thiadiphosphole and 2-thio-1,3,4-thiadiarsole heterocyclic ligands with an exocyclic sulfur atom, bridging two zirconium fragments with the general formula (N(RR’)3Zr(-C,S-(SCE)2-Zr(NRR’)3 with E = P (2-PP) or As (3-AsAs). The reactions are regioselective and only the P,P / As,As isomers are formed in THF. Switching the solvent to toluene, salt metathesis with NaSCP results in the selective formation of the other regioisomer 2-SP, with a 3-thio-1,2,4-thiadiphosphole bridge, while for NaSCAs both regioisomers with an As-As bond (3-AsAs) and an S-As bond (3-SAs; 3-thio-1,2,4-thiadiarsole bridge) are observed. Quantum chemical investigations to elucidate the mechanism and solvent dependency suggest a concerted ring formation (in line with a [3+2] cycloaddition reaction) with 2-SP and 3-AsAs being the thermodynamic products of the reaction.
|
Marc Baltrun; Florian Hett; Michael Seidl; Florian Weigend; Stephan Hohloch
|
Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67922419fa469535b9703034/original/regioselective-3-2-cycloaddition-reactions-of-the-phosphorus-and-arsenic-analogues-of-the-thiocyanate-anion.pdf
|
60c749deee301c4145c79b4f
|
10.26434/chemrxiv.12116943.v1
|
Prediction of T and B Cell Epitopes in the Proteome of SARS-CoV-2 for Potential Use in Diagnostics and Vaccine Design
|
<p>The world
is currently battling the Covid-19 pandemic for which there is no therapy
available. Prophylactic measures like vaccines can effectively thwart the
disease burden. The current methods of detection are PCR based and require
skilled manpower to operate. The availability of cheap and ready to use
diagnostics like serological methods can ease the detection of SARS-CoV-2
virus. In the current study, immunoinformatics tools have been used to predict
T and B cell epitopes present in all the proteins of this virus. NetMHCPan,
NetCTL and NetMHCII servers were used for T cell epitope prediction while
BepiPred and ABCPred were used for B cell epitope prediction. Population
coverage analysis for T cell epitopes revealed that these could provide
protection to the people throughout world. The T cell epitopes can exclusively
used for vaccine design whereas B cell epitopes can be used for both vaccine
design and developing diagnostic kits. </p>
<p> </p>
|
Parvez Slathia; Preeti Sharma,
|
Bioinformatics and Computational Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2020-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749deee301c4145c79b4f/original/prediction-of-t-and-b-cell-epitopes-in-the-proteome-of-sars-co-v-2-for-potential-use-in-diagnostics-and-vaccine-design.pdf
|
659d339c66c13817290c2088
|
10.26434/chemrxiv-2024-g7l32
|
Making 1H-1H couplings more accessible and accurate with selective 2DJ NMR experiments aided by 13C satellites
|
1H-1H coupling constants are one of the primary sources of information for NMR structural analysis. Several selective 2DJ experiments have been proposed that allow their individual measurement at pure shift resolution. However, all these experiments fail in the not uncommon case when coupled protons have very close chemical shifts. Firstly, the coupling between protons with overlapping multiplets is inaccessible due to the inability of a frequency-selective pulse to invert just one of them. Secondly, the strong coupling condition affects the accuracy of coupling measurements involving third spins. These shortcomings impose a limit on the effectiveness of state-of-the-art experiments, such as G-SERF or PSYCHEDELIC. Here, we introduce two new and complementary selective 2DJ experiments that we coin SERFBIRD and SATASERF. These experiments overcome the aforementioned issues by utilizing the 13C satellite signals at natural isotope abundance, which resolve the chemical shift degeneracy. We demonstrate the utility of these experiments on the tetrasaccharide stachyose and the challenging case of norcamphor, for the latter achieving measurement of all JHH couplings while only few were accessible with PSYCHEDELIC. The new experiments are applicable to any organic compound and will prove valuable for configurational and conformational analyses.
|
François-Xavier Cantrelle; Emmanuelle Boll; Davy Sinnaeve
|
Analytical Chemistry; Spectroscopy (Anal. Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659d339c66c13817290c2088/original/making-1h-1h-couplings-more-accessible-and-accurate-with-selective-2dj-nmr-experiments-aided-by-13c-satellites.pdf
|
65411ee048dad23120c7b181
|
10.26434/chemrxiv-2023-svjfl
|
Group 14 Metallocene Catalysts for Carbonyl Hydroboration and Cyanosilylation
|
A series of six Group 14 metallocene compounds (M = Ge, Sn, Pb) were studied as catalysts for carbonyl hydroboration and cyanosilylation reactions at room temperature. Both bis(pentamethylcyclopentadienyl) and tetramethyldisiloxa[3]metallocenophane compounds were compared. The tin and lead metallocenophanes exhibited the highest reactivity in hydroboration and cyanosilylation reactions. Hammett analysis of aldehyde hydroboration provided a rho value of 0.73, suggesting a buildup of negative charge during the turnover-limiting step, consistent with the transition state for hydride transfer to the carbonyl center. NMR studies of Lewis acidity indicate that the Ge, Sn, and Pb tetramethyldisiloxa[3]metallocenophane compounds are weak Lewis acids.
|
Haley Robertson; Mallory Fujiwara; Allegra Liberman-Martin
|
Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Main Group Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65411ee048dad23120c7b181/original/group-14-metallocene-catalysts-for-carbonyl-hydroboration-and-cyanosilylation.pdf
|
619b49b92bf8a962d4e7a1b4
|
10.26434/chemrxiv-2021-j5vb5-v2
|
On the electro-oxidation of small organic molecules: towards a fuel cell catalyst testing platform
|
The electrocatalytic oxidation of small organic compounds such as methanol or formic acid has been the subject of numerous investigations in the last decades. The motivation for these studies is often their use as fuel in so-called direct methanol or direct formic acid fuel cells, promising alternatives to hydrogen-fueled proton exchange membrane fuel cells. The fundamental research spans from screening studies to identify the best performing catalyst materials to detailed mechanistic investigations of the reaction pathway. These investigations are commonly performed in standard three electrode electrochemical cells with a liquid supporting electrolyte to which the methanol or formic acid is added. In fuel cell devices, however, no liquid electrolyte will be present, instead membrane electrolytes are used. The question therefore arises, to which extend results from conventional electrochemical cells can be extrapolated to conditions found in fuel cells. We previously developed a gas diffusion electrode setup to mimic “real-life” reaction conditions and study electrocatalysts for oxygen gas reduction or water splitting. It is here demonstrated that the setup is also suitable to investigate the properties of catalysts for the electro-oxidation of small organic molecules. Using the gas diffusion electrode setup, it is seen that employing a catalyst - membrane electrolyte interface as compared to conventional electrochemical cells can lead to significantly different catalyst performances. Therefore, it is recommended to implement gas diffusion electrode setups for the investigation of the electro-oxidation of small organic molecules.
|
Damin Zhang; Jia Du; Jonathan Quinson; Matthias Arenz
|
Catalysis; Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619b49b92bf8a962d4e7a1b4/original/on-the-electro-oxidation-of-small-organic-molecules-towards-a-fuel-cell-catalyst-testing-platform.pdf
|
60c75112567dfe1b45ec59ba
|
10.26434/chemrxiv.11833470.v3
|
Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes
|
<p>Molecular dynamics (MD) simulations are increasingly used to elucidate relationships between protein structure, dynamics and their biological function. Currently it is extremely challenging to perform MD simulations of large-scale structural rearrangements in proteins that occur on millisecond timescales or beyond, as this requires very significant computational resources, or the use of cumbersome ‘collective variable’ enhanced sampling protocols. Here we describe a framework that combines ensemble MD simulations and virtual-reality visualization (eMD-VR) to enable users to interactively generate realistic descriptions of large amplitude, millisecond timescale protein conformational changes in proteins. Detailed tests demonstrate that eMD-VR substantially decreases the computational cost of folding simulations of a WW domain, without the need to define collective variables <i>a priori</i>. We further show that eMD-VR generated pathways can be combined with Markov State Models to describe the thermodynamics and kinetics of large-scale loop motions in the enzyme cyclophilin A. Our results suggest eMD-VR is a powerful tool for exploring protein energy landscapes in bioengineering efforts. </p>
|
Jordi Juárez-Jiménez; Philip Tew; Michael o'connor; Salome Llabres; Rebecca Sage; David Glowacki; Julien Michel
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75112567dfe1b45ec59ba/original/combining-virtual-reality-visualization-with-ensemble-molecular-dynamics-to-study-complex-protein-conformational-changes.pdf
|
613f7d5490051e3277f20d9a
|
10.26434/chemrxiv-2021-9h59t
|
On the Role of the Electron-Dipole Interaction in Photodetachment Angular Distributions
|
The importance of including long-range electron-molecule interactions in treatments of photodetachment/photoionization is demonstrated. A combined experimental and computational study of CN− detachment is presented in which near threshold anisotropy parameters (β) are measured via photoelectron imaging. Calculated β values, based on an EOM-IP-CCSD/aug-cc-pVTZ Dyson orbital, are obtained using free particle and point dipole models. The results demonstrate the influence of the molecular dipole moment in the detachment process, and provide an explanation of the near threshold behavior of the overall photodetachment cross section in CN− detachment [J. Chem. Phys. 2020, 153, 184309]
|
C. Annie Hart; Justin Lyle; Joseph Spellberg; Anna I. Krylov; Richard Mabbs
|
Physical Chemistry; Quantum Mechanics; Spectroscopy (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-09-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613f7d5490051e3277f20d9a/original/on-the-role-of-the-electron-dipole-interaction-in-photodetachment-angular-distributions.pdf
|
6388c8747b7c916681de9f50
|
10.26434/chemrxiv-2022-cgcdk
|
Nitrogen atom insertion into indenes to access isoquinolines
|
We report a convenient protocol for a nitrogen atom insertion into indenes to afford isoquinolines. The reaction uses a combination of commercially available (diacetoxy¬iodo)benzene (PIDA) and ammonium carbamate to furnish a wide range of isoquinolines. Various substitution patterns and commonly used functional groups are well tolerated and the operational simplicity renders this protocol broadly applicable. Furthermore, this strategy enables the facile synthesis of 15N labeled isoquinolines, using 15NH4Cl as a commercial 15N source.
|
Patrick Finkelstein; Julia Reisenbauer; Ori Green; Bence Botlik; Andri Florin; Bill Morandi
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6388c8747b7c916681de9f50/original/nitrogen-atom-insertion-into-indenes-to-access-isoquinolines.pdf
|
60c74ba4f96a0056ca28765e
|
10.26434/chemrxiv.12366938.v1
|
Identification of Drugs Targeting Multiple Viral and Human Proteins Using Computational Analysis for Repurposing Against COVID-19
|
<p>The SARS-CoV2 is a highly contagious pathogen that causes a
respiratory disease named COVID-19. The COVID-19 was declared a pandemic by the
WHO on 11th March 2020. It has affected about 5.38 million people globally
(identified cases as on 24th May 2020), with an average lethality of ~3%.
Unfortunately, there is no standard cure for the disease, although some drugs
are under clinical trial. Thus, there is an urgent need of drugs for the treatment
of COVID-19. The molecularly targeted therapies have proven their utility in
various diseases such as HIV, SARS, and HCV. Therefore, a lot of efforts are
being directed towards the identification of molecules that can be helpful in
the management of COVID-19. </p>
<p>In the current studies, we have
used state of the art bioinformatics techniques to screen the FDA approved
drugs against thirteen SARS-CoV2 proteins in order to identify drugs for quick
repurposing. The strategy was to identify potential drugs that can target
multiple viral proteins simultaneously. Our strategy originates from the fact that individual viral proteins play
specific role in multiple aspects of viral lifecycle such as attachment, entry,
replication, morphogenesis and egress and targeting them simultaneously will
have better inhibitory effect.</p>
<p>Additionally, we analyzed if
the identified molecules can also affect the host proteins whose expression is
differentially modulated during SARS-CoV2 infection. The differentially
expressed genes (DEGs) were identified using analysis of NCBI-GEO data (GEO-ID:
GSE-147507). A pathway and protein-protein interaction network analysis of the
identified DEGs led to the identification of network hubs that may play
important roles in SARS-CoV2 infection. Therefore, targeting such genes may
also be a beneficial strategy to curb disease manifestation. We have identified
29 molecules that can bind to various SARS-CoV2 and human host proteins. We
hope that this study will help researchers in the identification and
repurposing of multipotent drugs, simultaneously targeting the several viral
and host proteins, for the treatment of COVID-19.</p>
|
Sugandh Kumar; Pratima Kumari; Geetanjali Agnihotri; Preethy VijayKumar; Shaheerah Khan; Gulam Hussain Syed; Anshuman Dixit
|
Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ba4f96a0056ca28765e/original/identification-of-drugs-targeting-multiple-viral-and-human-proteins-using-computational-analysis-for-repurposing-against-covid-19.pdf
|
60c74881bdbb89e4d1a38fbb
|
10.26434/chemrxiv.11861124.v2
|
An Intelligent AIEgen with Nonmonotonic Multi-Responses to Multi-Stimuli
|
<p>Intelligent stimulus-response (S/R) systems are the basis of natural process and machine control, and have been intensively explored in biomimetic design, analytical chemistry and biological applications. However, nonmonotonic multi-S/R systems are still rarely studied so far. Now, we propose a rational design strategy to achieve such a unique S/R system by integrating opposite luminescence behaviors in one molecule. When solvent polarity increases, many heterocycles often become more emissive due to the suppression of the proximity effect. However, molecules with donor-acceptor (D-A) structures tend to be less emissive because of the twisted intramolecular charge transfer. Meanwhile, protonation on D/A moieties will weaken/strengthen the D-A interaction to result in blue/red-shifted emissions. By combining a protonatable heterocyclic acceptor and a protonatable donor together in one molecule, we can easily achieve nonmonotonic brightness responses to polarity stimuli and nonmonotonic color responses to pH stimuli. In this work, a simple molecule, namely ASQ is chosen as the model compound to verify the design strategy feasibility. It successfully shows two opposite trends of responses to polarity and pH stimuli, and aggregation-induced emission (AIE) with a nonmonotonic AIE curve. Moreover, the acidified ASQ solution is also a pure organic up-conversion and white-light-emitting system. A new mechanistic viewpoint is established to explain its unique anti-Stokes emission. Besides, ASQ shows multivalent functionalities including albumin protein sensing, ratiometric pH sensing, and amine gas sensing, etc. Therefore, ASQ is proved to be a fundamentally important and versatile functional “intelligent” AIE luminogen with nonmonotonic multi-responses to multi-stimuli. <br /></p>
|
Yujie Tu; Yeqing Yu; Diwen Xiao; Junkai Liu; zheng zhao; zhiyang liu; Jacky W. Y. Lam; Ben Zhong Tang
|
Dyes and Chromophores; Optical Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74881bdbb89e4d1a38fbb/original/an-intelligent-ai-egen-with-nonmonotonic-multi-responses-to-multi-stimuli.pdf
|
67b722916dde43c908b286d4
|
10.26434/chemrxiv-2025-swjjx
|
Quantification of azides on the surface of nanoparticles: towards precise bioconjugation
|
The precise design of bioconjugated nanoparticles is crucial for effective cell targeting and cellular uptake. Therefore, an accurate approach to creating and quantifying
the organic ligand shell with a specific number of conjugated targeting ligands is essential. Click-chemistry has emerged as a robust method for bioconjugation, with
azide-alkyne cycloaddition as the most prevalent method. Although nanoparticles are typically functionalized with azides, their quantification has rarely been reported. Here,
we present two spectroscopic methods for the surface azide quantification of catechol-stabilized hafnium oxide nanoparticles as a model system. The first method exploits
the intrinsic ability of catechol ligands to quench the fluorescence of conjugated fluorophores, whereas the second method represents a general strategy based on monitoring the alkyne absorbance during the click reaction. The latter method is independent of both inorganic core and the ligand shell, allowing it to be generally used. We also
demonstrate the broader applicability on hafnium oxide nanoparticles capped with polyphosphonate ligands.
|
Elizaveta Maksimova; David E. Salazar Marcano; Jonathan De Roo
|
Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b722916dde43c908b286d4/original/quantification-of-azides-on-the-surface-of-nanoparticles-towards-precise-bioconjugation.pdf
|
60c748e3842e65f2e7db2c78
|
10.26434/chemrxiv.11993487.v1
|
DNAzyme Sensor for the Detection of Metal Ions Using Resistive Pulse Sensing
|
<b>DNAzymes are DNA based catalysts that can undergo cleavage upon binding of the target analyte. The cleavage reaction is highly specific, and DNAzymes exists for a wide range of metal ions. The change of structure upon binding of a specific metal ion has given rise to many sensing strategies, but few exist with nanopore sensors. Resistive Pulse Sensing, RPS, is a platform that has emerged in recent years capable of identifying changes in DNA structure and sequence. Here we develop the use of DNAzymes with RPS technologies for the detection of Ca2+ ions in solution. Ca2+ plays an important role in biological processes, critical for cell signally, protein folding and catalysis. Extreme concentrations of Ca2+ within drinking water have also been linked to problems with corrosion, scaling and the taste of water. Using DNAzyme functionalised nanocarriers and RPS, it was possible follow the Ca2+ ions binding to the DNAzyme. The binding of Ca2+ caused a conformation change in the DNAzyme which was monitored as a change in translocation speed. By following the changes to the translocation speed, it is hypothesised that RPS can verify the changes in structure. In addition, the assay allowed the quantification of Ca2+ between 1 – 9 μM, and due its catalytic nature, increasing incubation time from 30 to 90 minutes allowed lower detection limits, down to 0.3 μM. We demonstrate that the speed changes are specific to Ca2+ in the presence of other metal ions, and we can quantify Ca2+ in tap and pond water samples.</b><br />
|
Imogen Heaton; Mark Platt
|
Hydrology and Water Chemistry; Electrochemical Analysis; Nanodevices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748e3842e65f2e7db2c78/original/dn-azyme-sensor-for-the-detection-of-metal-ions-using-resistive-pulse-sensing.pdf
|
658551a9e9ebbb4db97c3290
|
10.26434/chemrxiv-2023-16rwj
|
Bioorthogonal Aza-Michael Addition to Dehydrated Amino Acids in Antimicrobial Peptides
|
We report the efficient and site selective modification of non-canonical dehydroamino acids in ribosomally synthesized and post-transationally modified peptides (RiPPs) by β-amination. The singly modified thiopeptide Thiostrepton showed an up to 35-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity was maintained.
|
Michela Vargiu; Yanli Xu; Oscar Kuipers; Gerard Roelfes
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658551a9e9ebbb4db97c3290/original/bioorthogonal-aza-michael-addition-to-dehydrated-amino-acids-in-antimicrobial-peptides.pdf
|
678698726dde43c9087fc99f
|
10.26434/chemrxiv-2025-ll55t
|
Magnetic Field-Induced Drug Delivery from ZIF-8 Metal-Organic Frameworks-Based Nanocomposites through Magnetic Nanoparticles Heating or Motion
|
Metal-organic frameworks (MOFs) hold great promise for drug delivery applications due to their large tuna-ble porosity and structural flexibility, which facilitate designs with high drug-loading capacities and biocom-patibility. Despite these advantages, controlling off-target, uncontrolled drug release remains challenging. This study develops a magnetic field-responsive magnetic nanocomposite based on MOFs to enable spatio-temporal controlled drug delivery. The design features a superparamagnetic iron oxide nanoparticle core and a nanometric zeolitic imidazolate framework (ZIF-8) shell, loaded with cresyl violet as a fluorescent probe and stabilized with a fluorescein-labelled amphiphilic polymer. The nanocomposites demonstrate biocom-patibility up to 1 pM with MiaPaCa-2 cancer cells and cancer-associated fibroblasts (CAF) and preferentially accumulate in endolysosomes. Exposure to high-frequency alternating or low-frequency rotating magnetic fields significantly increases the release of cresyl violet into the cytosol of MiaPaca-2 and CAF cells. This release —whether thermal or mechanical— reduces the viability of cells in 2D culture and the size of 3D spheroids composed of MiaPaCa2 and CAF cells, illustrating precise spatiotemporal control over the drug delivery process. The proposed MOF-based magnetic nanocomposites represent promising platforms for developing magnetic field-responsive drug delivery systems.
|
Ahmed Abdelhamid; Aitor Alvarez; Loubna Laib; Pascal Clerc; Manuel Ceballos; Justine Journaux; Anil Misra; Mohammad S Alavijeh; Géraldine Ballon; Corinne Bousquet; Beatriz Pelaz; Pablo del Pino; Julian Carrey; Véronique Gigoux
|
Biological and Medicinal Chemistry; Nanoscience; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678698726dde43c9087fc99f/original/magnetic-field-induced-drug-delivery-from-zif-8-metal-organic-frameworks-based-nanocomposites-through-magnetic-nanoparticles-heating-or-motion.pdf
|
634985f14a1876cb95e3dde7
|
10.26434/chemrxiv-2022-1b24c
|
BICePs v2.0: Software for Ensemble Reweighting using Bayesian Inference of Conformational Populations
|
Bayesian Inference of Conformational Populations (BICePs) version 2.0 (v2.0) is a free, open-source Python package that reweights theoretical predictions of conformational state populations using sparse and/or noisy experimental measurements. In this article, we describe the implementation and usage of the latest version of BICePs (v2.0), a powerful, user-friendly and extensible package which makes several improvements upon the previous version. The algorithm now supports many experimental NMR observables (NOE distances, chemical shifts, J-coupling constants, and hydrogen-deuterium exchange protection factors), and enables convenient data preparation and processing. BICePs v2.0 can perform automatic analysis of the sampled posterior, including visualization, and evaluation of statistical significance and sampling convergence. We provide specific coding examples for these topics, and present a detailed example illustrating how to use BICePs v2.0 to reweight a theoretical ensemble using experimental measurements.
|
Robert Raddi; Yunhui Ge; Vincent Voelz
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634985f14a1876cb95e3dde7/original/bi-ce-ps-v2-0-software-for-ensemble-reweighting-using-bayesian-inference-of-conformational-populations.pdf
|
60c73f87f96a000d272860de
|
10.26434/chemrxiv.7396757.v1
|
La Chimie en Couleurs: Socially-Relevant and Original Research in Chemistry at High-Schools Using Modest Resources
|
<div><div><div><p>Teaching chemistry at high school level has the potential of playing a major role for the development of our society, in particular, to form future leaders in chemistry who will address social challenges such as the need for better healthcare, improved agricultural techniques and more efficient use of energy resources. In general, the high school’s chemistry teaching programs tend to illustrate the great historic discoveries and glorious past of chemical research. It is hoped that this historical perspective will help to provide students with the basic understanding necessary for the development of the chemistry of tomorrow. Unfortunately, in general, the emphasis on established chemical research and on the reassuringly solid-foundations of the field is ubiquitous not only in the theoretical classes, but also in more practical aspects of teach- ing, such as in student maturity work: these small, often laboratory-oriented research projects are often limited to reproducing the scientific literature often printed in black white- and/or adding minor modifications to estab- lished scientific protocols, instead of exploring the colourful world of current scientific discovery and the excitement of pushing back the boundaries of knowledge. Practicing innovative and original research with chemistry stu- dents is therefore a challenge for the mentor of any maturity work. Here, I describe the implementation of a practical program nicknamed La Chimie en Couleurs- for carrying out original research work in chemistry, making science live, colourful and vivid to students, i.e. not something that has already been done by others before, but something that one can pursue oneself and that is totally new and original. The program is taught during high-school courses and carried by students, using inexpensive equipment, easily-accessible, non- toxic chemicals and simple chemical concepts. Part of the research work was presented by students at the Swiss Chemical Society Annual Meeting and merited a Poster-Prize in the Inorganic Chemistry Runner-Up category. The La Chimie en Couleurs program presented here illustrates that up-to-date and socially-relevant chemistry (not just historically-relevant chemistry!) can be taught to teenagers in a creative way through the implementation of serious, albeit inexpensive, scientific research at highschool level.</p></div></div></div>
|
Thibaud Rossel; Marc Creus
|
Chemical Education - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f87f96a000d272860de/original/la-chimie-en-couleurs-socially-relevant-and-original-research-in-chemistry-at-high-schools-using-modest-resources.pdf
|
60c745e2bdbb894826a38afb
|
10.26434/chemrxiv.10282112.v1
|
Autonomous Discovery of Battery Electrolytes with Robotic Experimentation and Machine-Learning
|
<div>
<div>
<div>
<p>Innovations in batteries take years to formulate, requiring extensive experimentation during the design and optimization phases. We approach the design of a battery electrolyte as
a black-box optimization problem. We report here the discovery of a novel battery electrolyte by a robotic electrolyte experiment guided by machine-learning software. Motivated
by the recent trend toward super-concentrated aqueous electrolytes for high-performance
batteries, we utilize Dragonfly - a Bayesian machine-learning software package - to search
mixtures of commonly used lithium and sodium salts for super-concentrated aqueous electrolytes with wide electrochemical stability windows. Dragonfly autonomously managed the
robotic test-stand, recommending electrolyte designs to test and receiving experimental feed-
back in real time. Within 40 hours of continuous experimentation, Dragonfly discovered a
novel, high-performing aqueous sodium electrolyte that a human-guided design process may
have missed. This result demonstrates the possibility of integrating robotics with machine-learning to rapidly and autonomously discover novel battery materials.</p></div></div></div>
|
Adarsh Dave; Jared Mitchell; Kirthevasan Kandasamy; Sven Burke; Biswajit Paria; Barnabas Poczos; Jay Whitacre; Venkatasubramanian Viswanathan
|
Electrocatalysis; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745e2bdbb894826a38afb/original/autonomous-discovery-of-battery-electrolytes-with-robotic-experimentation-and-machine-learning.pdf
|
64d955d769bfb8925ae1d27c
|
10.26434/chemrxiv-2023-6cwhw
|
Ultra small Pd clusters in FER zeolite alleviate CO poisoning for effective low temperature carbon monoxide oxidation
|
Ultra small Pd4 clusters form inside FER zeolite during low temperature treatment (100 °C) in the presence of humid CO gas. They effectively catalyze CO oxidation below 100°C, whereas Pd nanoparticles are not active as they are poisoned by CO. Using catalytic measurements, infrared (IR) spectroscopy, X-ray absorption spectroscopy (EXAFS), microscopy, and density functional theory calculations we provide the molecular level insight into this previously unreported phenomenon. Pd nanoparticles get covered with CO at low temperatures which effectively blocks O2 activation until CO desorption occurs. Small Pd clusters in zeolites, in contrast, demonstrate fluxional behavior in the presence of CO, which significantly increases their affinity for binding O2. Our study shows a pathway for achieving low temperature CO oxidation activity on the basis of well-defined Pd/zeolite system.
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Inhak Song; Iskra Z. Koleva; Hristiyan A. Aleksandrov; Linxiao Chen; Jaeyoung Heo; Dongsheng Li; Yong Wang; Janos Szanyi; Konstantin Khivantsev
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Physical Chemistry; Catalysis; Heterogeneous Catalysis; Statistical Mechanics; Surface
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CC BY NC ND 4.0
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CHEMRXIV
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2023-08-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d955d769bfb8925ae1d27c/original/ultra-small-pd-clusters-in-fer-zeolite-alleviate-co-poisoning-for-effective-low-temperature-carbon-monoxide-oxidation.pdf
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63e81a7afcfb27a31f9b6e66
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10.26434/chemrxiv-2022-hspwv-v2
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Development and Validation of a Chemoinformatic Workflow for Predicting Reaction Yield for Pd-Catalyzed C-N Couplings with Substrate Generalizability
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A machine learning-based tool that provides conditions and predicted yields for Buchwald-Hartwig couplings from a ChemDraw™ structure input is described. The tool is built on an in-house generated experimental dataset that explores a diverse network of reactant pairings. To minimize the number of experiments necessary to produce models and maximize data value, a workflow based on unsupervised machine leaning tools was created. The workflow enables the construction of models which can successfully generalize—making predictions for reactants which are not represented in the dataset.
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N. Ian Rinehart; Rakesh K. Saunthwal; Joël Wellauer; Andrew F. Zahrt; Lukas Schlemper; Alexander S. Shved; Raphael Bigler; Serena Fantasia; Scott E. Denmark
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Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2023-02-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e81a7afcfb27a31f9b6e66/original/development-and-validation-of-a-chemoinformatic-workflow-for-predicting-reaction-yield-for-pd-catalyzed-c-n-couplings-with-substrate-generalizability.pdf
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61d58007828c2f6cafd76709
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10.26434/chemrxiv-2021-14mng-v2
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The role of language in students’ justifications of scientific phenomena
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Making decisions and constructing arguments with scientific evidence and reasoning are essential skills for all members of society, especially in a world facing complex socioscientific issues (climate change, global pandemics, etc.). Argumentation is a complex linguistic practice, but little is known about how students from diverse language backgrounds engage in argumentation. The goal of this study was to identify how students’ English language proficiency/history was associated with the reasoning demonstrated in their written arguments. We found that students with lower English proficiency and less English history produced fewer causal responses compared to students with higher English language proficiency and history. Follow-up interviews with fifteen participants revealed that students’ comfort communicating in English on assessments depended on a combination of general and academic language experiences. Findings suggest a need to identify what barriers students from diverse language backgrounds encounter during argumentation to ensure students from all language backgrounds have equitable opportunities to demonstrate their abilities.
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Jacky Deng; Malek Rahmani; Alison Flynn
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Chemical Education; Chemical Education - General
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CC BY NC ND 4.0
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CHEMRXIV
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2022-01-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d58007828c2f6cafd76709/original/the-role-of-language-in-students-justifications-of-scientific-phenomena.pdf
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662553d421291e5d1d52dc1a
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10.26434/chemrxiv-2024-5ckg0
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From Digital Blueprint to Chemical Reality: Methanol to Formaldehyde at Ambient Conditions
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Partial oxidation of methanol to value added product presents an intriguing yet challenging process. Among these products, formaldehyde is the simplest and one of the most vital aliphatic aldehydes, which has extensive application across various domains. Industrially, silver and iron-molybdenum oxides are used as catalysts for the conversion of methanol to formaldehyde at elevated temperatures (600 ◦ C and 250-400 ◦ C, respectively). However, in this computational and experimental study, we have demonstrated the efficacy of ZnO as a catalyst. Notably, in the presence of ZnO, methanol readily converts to formaldehyde even under ambient conditions. We employed periodic density functional theory (DFT) to explore (1011) facet of ZnO to elucidate its inter- action with methanol. Our comprehensive analysis identified the most active facet (1011) involved in the spontaneous conversion of methanol to formaldehyde. Subsequently, experimental validation supported our theoretical findings, demonstrating the conversion of methanol to formaldehyde with 100% selectivity at room temperature and atmospheric pressure in the presence of ZnO. This study exemplifies the pivotal role of theory in catalyst design.
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Shweta Mehta; Mirabai Kasabe; Shubhangi Umbarkar; Kavita Joshi
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Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2024-04-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662553d421291e5d1d52dc1a/original/from-digital-blueprint-to-chemical-reality-methanol-to-formaldehyde-at-ambient-conditions.pdf
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60c73feb9abda27d3ef8bba4
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10.26434/chemrxiv.7570664.v1
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Integrated CO2 Capture and Conversion into Valuable Hydrocarbons
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The alarming atmospheric concentration and continuous emissions of carbon dioxide (CO2) require immediate action. As a result of advances in CO2 capture and sequestration technologies (generally involving point sources such as energy generation plants), large amounts of pure CO2 will soon be available. In addition to geological storage and other applications of the captured CO2, the development of technologies able to convert this carbon feedstock into commodity chemicals may pave the way towards a more sustainable economy. Here, we present a novel multifunctional catalyst consisting of Fe2O3 encapsulated in K2CO3 that can capture and simultaneously transform CO2 into olefins. In contrast to traditional systems in Fischer-Tropsch reactions, we demonstrate that when dealing with CO2 activation (in contrast to CO), very high K loadings are key to capturing the CO2 via the well-known ‘potassium carbonate mechanism’. The proposed catalytic process is demonstrated to be as productive as existing commercial processes based on synthesis gas while relying on economically and environmentally advantageous CO2 feedstock.
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Adrian Ramirez; Samy Ould-Chikh; Lieven Gevers; Abhishek Dutta Chowdhury; Edy Abou-hamad; Antonio Aguilar-Tapia; Jean-Louis Hazemann; Nimer Wehbe; Abdullah J. Al Abdulghani; Sergey M. Kozlov; Luigi Cavallo; Jorge Gascon
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Heterogeneous Catalysis; Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-01-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73feb9abda27d3ef8bba4/original/integrated-co2-capture-and-conversion-into-valuable-hydrocarbons.pdf
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679ce55afa469535b99170d9
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10.26434/chemrxiv-2025-75jk6-v2
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Total Synthesis of (+)-Hazuntiphylline, (–)-Anhydrohazuntiphyllidine, and (–)-Hazuntiphyllidine
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The first total synthesis of the bisindole alkaloids (+)-hazuntiphylline, (–)-anhydrohazuntiphyllidine, and (–)-hazuntiphyllidine is described. We envisioned an efficient synthetic strategy based on a plausible biosynthetic hypothesis for the rapid assembly of these complex alkaloids via successive methylenation of an oxidized variant of the natural product (–)-mehranine. Our concise synthesis of these alkaloids required the development of completely stereoselective double alkylation sequences of transiently formed C3-enamines and precise timing for hydration of intricate intermediates. Whereas homodimerization of a C3-methylene mehranine-derivative exclusively gave (–)-3-epi-anhydrohazuntiphyllidine, an alternative alkylation cascade was developed to afford the natural products (–)-anhydrohazuntiphyllidine and (+)-hazuntiphylline. Insights gained in these studies concerning the intermediacy of hydrated intermediates enabled a completely stereoselective synthesis of (–)-hazuntiphyllidine, the most complex member of the Hazunta alkaloids. We discuss our hypothesis for the rapid assembly of these intriguing alkaloids, including our completely controlled access to both the natural and epimeric C3-quaternary stereochemistry of anhydrohazuntiphyllidine, and analysis of plausible biosynthetic intermediates including a highly sensitive methylenebisdesmethylmehranine, highlighting divergent pathways to each natural alkaloid based on the order of C–C and C–N bond formation and the hydration of putative intermediates.
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Robert-Cristian Raclea; Marius Mewald; Kolby L. White; Mohammad Movassaghi
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Organic Chemistry; Natural Products; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
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2025-02-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679ce55afa469535b99170d9/original/total-synthesis-of-hazuntiphylline-anhydrohazuntiphyllidine-and-hazuntiphyllidine.pdf
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60c73d0e469df404c4f42677
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10.26434/chemrxiv.5410807.v1
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Tandem Mass Spectrometric Evaluation of Core Structures of Aromatic Compounds after Catalytic Deoxygenation
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Catalytic deoxygenation of coal enhances the stability and combustion performance of coal-derived liquids. However, determination of the selectivity of removal of oxygen atoms incorporated in or residing outside of aromatic rings is challenging. This limits the ability to evaluate the success of catalytic deoxygenation processes. A mass spectrometric method, in-source collision-activated dissociation (ISCAD), combined with high resolution product ion detection, is demonstrated to allow the determination of whether the oxygen atoms in aromatic compounds reside outside of aromatic rings or are part of the aromatic system, because alkyl chains can be removed from aromatic cores via ISCAD. Application of this method for the analysis of a subbituminous coal treated using a supported catalyst revealed that the catalytic treatment reduced the number of oxygen-containing heteroaromatic rings but not the number of oxygen atoms residing outside the aromatic rings.<br />
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Xueming Dong
|
Mass Spectrometry
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CC BY NC ND 4.0
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CHEMRXIV
|
2017-09-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e469df404c4f42677/original/tandem-mass-spectrometric-evaluation-of-core-structures-of-aromatic-compounds-after-catalytic-deoxygenation.pdf
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60c74d38337d6c8f7ee27d69
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10.26434/chemrxiv.12600488.v1
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Novel Water-Soluble Far-Red Nitroreductase-Responsive Bodipy-Based Fluorescent Probe for the Detection of Hypoxic Status in A549 Non-Small Cell Lung Cancer Cells
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Over expression of nitroreductase (NTR) enzymes is closely related to the hypoxic status in living organisms for which molecular oxygen is vital. The development of effective methods for real-time monitoring of NTR activity is of great significance for medical diagnosis and cancer research. Here, we present a novel water-soluble Bodipy-based chemodosimeter (NBB) effective in imaging the hypoxic status of human non-small-cell lung cancer A549 cells. We assumed that NTR-mediated activation of the probe NBB is based on the reductive release of meso-phenol Bodipy dye to finally produce unusual fluorescence "ON-OFF" response.
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Sergey A. GORBATOV; Denis Y. UVAROV; Alexander M. SCHERBAKOV; Igor V. ZAVARZIN; Yulia A. VOLKOVA; Anthony ROMIEU
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Bioorganic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-07-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d38337d6c8f7ee27d69/original/novel-water-soluble-far-red-nitroreductase-responsive-bodipy-based-fluorescent-probe-for-the-detection-of-hypoxic-status-in-a549-non-small-cell-lung-cancer-cells.pdf
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65ce1e8266c1381729b4a90a
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10.26434/chemrxiv-2024-w4vgb
|
Effect of extended defects on phonon confinement in polycrystalline Si and Ge films
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We present Raman spectroscopy of the polycrystalline Si and Ge films deposited by molecular beam deposition on a dielectric substrate. The Raman study has been made using lasers with different wavelengths. Structural properties of the poly-films have been studied by XRD and TEM. The Raman spectra are characterized by appearance of the additional wide peaks around 500 cm–1 and 290 cm–1 in the main vibrational bands of TO(c-Si) and TO(c-Ge) phonons, respectively. It is shown that these peaks correspond to scattering in grain boundary area. For the poly–Si films, both a downward shift and an asymmetrical broadening of the vibrational band of TO(c-Si) near 520 cm–1 are observed, whereas there is only a symmetric broadening in the spectra of poly-Ge. The Raman line shape has been modeled within the framework of the phonon confinement theory taking into account the sizes of coherent scattering domains obtained using XRD. The model includes a symmetrical band broadening observed in polycrystalline films. It is shown that confinement of phonon propagation might be in the poly–Si films. The phonon dispersion and the density of phonon states have been simulated using density functional theory. It has been found that phonon confinement relates to grain boundaries rather than other extended defects such as twins (multiple twins, twin boundaries), the appearance of which does not lead to significant changes in phonon dispersion and density of phonon states.
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Larisa V. Arapkina; Kirill V. Chizh; Oleg V. Uvarov; Valery V. Voronov; Vladimir P. Dubkov; Mikhail S. Storozhevykh; Maksim V. Poliakov; Lidiya S. Volkova; Polina A. Edelbekova; Alexey A. Klimenko; Alexander A. Dudin; Vladimir A. Yuryev
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Materials Science; Nanoscience; Optical Materials; Nanostructured Materials - Nanoscience
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ce1e8266c1381729b4a90a/original/effect-of-extended-defects-on-phonon-confinement-in-polycrystalline-si-and-ge-films.pdf
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63d9649229feaa4475003452
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10.26434/chemrxiv-2023-cb6pc-v2
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Electrostatic Interactions in Asymmetric Organocatalysis
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Electrostatic interactions are ubiquitous in catalytic systems and are often decisive in determining reactivity and stereoselectivity. However, a lack of understanding of the fundamental underlying principles has long stymied our ability to fully harness the power of these interactions. Fortunately, advances in affordable computing power together with new quantum chemistry methods have increasingly enabled a detailed atomic-level view. Empowered by this more nuanced perspective, synthetic practitioners are now adopting these techniques with growing enthusiasm.
In this review, we narrate our recent results rooted in state-of-the-art quantum chemical computations, describing pivotal roles for electrostatic interactions in the organization of transition state (TS) structures to direct reactivity and selectivity in the realm of asymmetric organocatalysis. To provide readers with a fundamental foundation in electrostatics, we first introduce a few guiding principles, beginning with a brief discussion of electrostatic interactions and electrostatics-dominated non-covalent interactions as well as and their modulating factors. We then describe computational approaches to capture these effects, primarily through representative case studies. Subsequently, we cover some general strategies that have been utilized to impart stereocontrol in asymmetric organocatalysis, presenting our own results along with selected highlights from other groups.
We then briefly cover our most significant recent computational investigations in three specific branches of asymmetric organocatalysis, beginning with chiral phosphoric acid (CPA) catalysis. We disclose how CPA-catalyzed asymmetric ring openings of meso-epoxides are driven by stabilization of a transient partial positive charge in the SN2-like TS by the chiral electrostatic environment of the catalyst. We also report on substrate-dependent electrostatic effects from our study of CPA-catalyzed intramolecular oxetane desymmetrizations. For non-chelating oxetane substrates, electrostatic interactions with the catalyst confers stereoselectivity, whereas oxetanes with chelating groups adopt a different binding mode that overrides this electrostatic stereodetermination and erodes selectivity. In another example, computational approaches revealed a pivotal role of CH···O and NH···O hydrogen bonding in CPA-catalyzed asymmetric synthesis of 2,3-dihydroquinazolinones. These interactions control selectivity during the enantiodetermining intramolecular amine addition step, and their strength is modulated by substrate positioning within the electrostatic environment created by the catalyst, allowing us to rationalize the effect of introducing o-substituents. Next, we describe our efforts to understand selectivity in a series of NHC-catalyzed kinetic resolutions. We discovered that electrostatic interactions are the common driver of selectivity. Finally, we discuss our breakthrough in understanding asymmetric silylium ion-catalyzed Diels–Alder cycloaddition of cinnamate esters to cyclopentadienes. The diastereoselectivity of these transformations is guided by CH···O electrostatic interactions that selectively stabilize the endo-transition state. Additionally, we deduced the geometry of the preferred binding mode to explain the requirement for a 9-fluorenylmethyl ester to achieve high selectivity.
We conclude with a brief overview of the outstanding challenges and the potential roles of computational chemistry in enabling the exploitation of electrostatic interactions in asymmetric organocatalysis.
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Rajat Maji; Sharath Chandra Mallojjala; Steven Wheeler
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Catalysis; Organocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-02-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d9649229feaa4475003452/original/electrostatic-interactions-in-asymmetric-organocatalysis.pdf
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60c750239abda2b689f8d99b
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10.26434/chemrxiv.12999035.v1
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A Fused Thiophene-S,S-Dioxide-Based Super-Photostable Fluorescent Marker for Lipid Droplets
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Lipid droplets (LDs) are essential organelle in most eukaryotes, and tracking intracellular LDs dynamics using synthetic small molecules is crucial for biological studies. However, only a limited number of fluorescent markers that satisfy all requirements, such as the selective staining of LDs, high photostability, and sufficient biocompatibility, have been developed. Herein, we report a series of donor-p-acceptor dyes based on the thiophene-containing fused polycyclic scaffold [1]benzothieno[3,2-<i>b</i>][1]benzothiophene (BTBT), in which either or both thiophene rings are oxidized into thiophene-<i>S</i>,<i>S</i>-dioxide to form an electron-accepting building block. Among these dyes, LAQ1 satisfied all the aforementioned requirements, and allowed us capturing ultra-small LDs on the endoplasmic reticulum (ER) membrane by stimulation emission depletion (STED) microscopy with a super-resolution below the diffraction limit of light. Moreover, the extremely high photostability of LAQ1 enabled recording the lipolysis of LDs and the concomitant lipogenesis as well as long-term trajectory analysis of micro LDs at the single particle level in living cells.
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Masayasu Taki; Keiji Kajiwara; Eriko Yamaguchi; Yoshikatsu Sato; Shigehiro Yamaguchi
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Imaging; Chemical Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-09-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750239abda2b689f8d99b/original/a-fused-thiophene-s-s-dioxide-based-super-photostable-fluorescent-marker-for-lipid-droplets.pdf
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6580490ae9ebbb4db931472d
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10.26434/chemrxiv-2023-gzfhv
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Cyclic ion mobility for hydrogen/deuterium exchange-mass spectrometry applications
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Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localisation of dynamic changes. Consequently, HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase data quality by providing an orthogonal mode of peptide ion separation in the gas-phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage and/or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multi-pass IM separations. Using 1-pass and multi-pass cIM routines, we use the recently commercialised SELECT SERIES™ Cyclic™ IM spectrometer for HDX-MS analyses of 4 detergent solubilised IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multi-pass cIM data. Interestingly, use of 1-pass and multi-pass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM which has the potential to enable the analysis of more complex systems with greater accuracy and speed.
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Damon Griffiths; Malcolm Anderson; Keith Richardson; Satomi Inaba-Inoue; William J. Allen; Ian Collinson; Konstantinos Beis; Michael Morris; Kevin Giles; Argyris Politis
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Analytical Chemistry; Mass Spectrometry
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CC BY 4.0
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CHEMRXIV
|
2023-12-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6580490ae9ebbb4db931472d/original/cyclic-ion-mobility-for-hydrogen-deuterium-exchange-mass-spectrometry-applications.pdf
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66db6d07cec5d6c1425ad518
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10.26434/chemrxiv-2024-rpst3-v2
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Design and Crystallographic Screening of a Highly Sociable and Diverse Fragment Library Towards Novel Antituberculotic Drugs
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Missing synthetic tractability is a common pitfall that is often impeding fragment-to-lead campaigns. Ideally, the follow-up fragment extension would be performed quickly and exhaustively, leading to novel hit or lead compounds in rapid succession without the need for tediously developing synthetic methodologies. However, no fragment library currently has this so-called “sociability” as its primary design principle. Herein, we describe the development of a 96-membered, highly diverse, and entirely sociable fragment library suitable for crystallographic screening. Hundreds to thousands of follow-up compounds modified at all growth vectors are available for each fragment from Enamine’s REAL Space. Additionally, tens to hundreds of thousands of larger and more complex leadlike molecules are accessible per library member, further expanded by scaffold-modified, alternative fragments. This allows for rapid exploration of the chemical space around a fragment of interest without much effort. Here, this library was used for a crystallographic fragment screening on a mycobacterial thioredoxin reductase to identify new starting points for developing new anti-tuberculotic agents. Several hits have been identified in a preliminary analysis of the screening.
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Philipp Janssen; Fabrice Becker; Friederike T. Füsser; Nataliya Tolmachova; Tetiana Matviiuk; Ivan Kondratov; Manfred Weiss; Daniel Kümmel; Oliver Koch
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry
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CC BY 4.0
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CHEMRXIV
|
2024-09-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66db6d07cec5d6c1425ad518/original/design-and-crystallographic-screening-of-a-highly-sociable-and-diverse-fragment-library-towards-novel-antituberculotic-drugs.pdf
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60c7451dbdbb89d650a3894d
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10.26434/chemrxiv.9963989.v1
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Monolithic Solder-on Nanoporous Si-Cu Contacts for Stretchable Silicone Composite Sensors
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We report a method of creating solderable, mechanically robust, electrical contacts to interface (soft) silicone-based strain sensors with conventional (hard) solid-state electronics using a nanoporous Si-Cu composite. The Si-based solder-on electrical contact consists of a copper-plated nanoporous Si top surface formed through metal-assisted chemical etching and electroplating, and a smooth Si bottom surface which can be covalently bonded onto silicone-based strain sensors through plasma bonding. We investigated the mechanical and electrical properties of the contacts proposed under relevant ranges of mechanical stress for applications in physiological monitoring and rehabilitation. We also produced a series of proof-of-concept devices, including a wearable respiration monitor, leg band for exercise monitoring and Squeeze-ball for monitoring rehabilitation of patients with hand injuries or neurological disorders, to demonstrate the mechanical robustness and versatility of the technology developed, in real-world applications.
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Guder Research; Estefania Nunez-Bajo; Max Grell; Yasin Cotur; Giandrin Barandun; Ji-Seon Kim; Firat Güder
|
Biocompatible Materials; Carbon-based Materials; Composites; Elastic Materials; Nanostructured Materials - Materials
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-10-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7451dbdbb89d650a3894d/original/monolithic-solder-on-nanoporous-si-cu-contacts-for-stretchable-silicone-composite-sensors.pdf
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64d8ff8969bfb8925ade3a64
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10.26434/chemrxiv-2023-v3zgd
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Site Isolated Rh(II) Metalloradicals Catalyze Olefin Hydrosilylation
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Rh(II) porphyrin complexes display pronounced metal-centered radical character and the ability to activate small molecules under mild conditions, but catalysis with Rh(II) porphyrins is extremely rare. In addition to facile dimerization, Rh(II) porphyrins readily engage in kinetically and thermodynamically facile reactions involving two Rh(II) centers to generate stable Rh(III)-X intermediates that obstruct turnover in thermal catalysis. Here we report site isolation of Rh(II) metalloradicals in a MOF host, which not only protects Rh(II) metalloradicals against dimerization, but also allows them to participate in thermal catalysis. Access to PCN-224 or PCN-222 in which the porphyrin linkers are fully metalated by Rh(II) in the absence of any accom-panying Rh(0) nanoparticles was achieved via the first direct MOF synthesis with a linker containing a transition-metal alkyl moiety, followed by Rh(III)–C bond photolysis.
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Zihang Qiu; Hao Deng; Constanze N. Neumann
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Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Coordination Chemistry (Organomet.); Transition Metal Complexes (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-08-14
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d8ff8969bfb8925ade3a64/original/site-isolated-rh-ii-metalloradicals-catalyze-olefin-hydrosilylation.pdf
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671bb07298c8527d9e5d7f57
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10.26434/chemrxiv-2024-cbkp5
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Nickel-catalysed stereoselective α-vinylation and arylation of peptide electrophiles
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Stereoselective modification peptide α-carbons remains a challenge. In this context, transition metal-catalyzed C-C cross-coupling chemistry of peptidyl α-carbon-electrophiles has not been achieved. Herein, we report that racemic glycinyl α-C-Ts (α-TG) unit implanted in peptide backbones serves as an excellent electrophile element for vinylation/arylation with vinyl/aryl triflates/halides to afford the α-C(sp2)-modified peptides in excellent levels of diastereoselectivity, enabled by asymmetric Ni-catalyzed reductive coupling platform. The stereocontrol is essentially governed by the catalyst, on which the α-substituents of the neighboring amino acid elements showed minor effect. The scope of peptides was broad, comprising decapeptides and cyclic pentapeptides. A unique feature of the present work is the viability of modification of the internal sites of the peptides, which stands a sharp contrast to the contemporary studies that focus on the N- or C-terminal peptide α-carbons. This work may provoke a broader interest in peptide backbone modification based on cross-coupling chemistry.
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Jie Hu; Shengjie Su; Haodong Zhang; Yan Gao; Xiaoping Yang; Yunrong Chen; Hegui Gong
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Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-10-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671bb07298c8527d9e5d7f57/original/nickel-catalysed-stereoselective-vinylation-and-arylation-of-peptide-electrophiles.pdf
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674dd8787be152b1d0b11927
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10.26434/chemrxiv-2024-p504f
|
Spectroscopic Properties of SrH from Relativistic Coupled-Cluster Calculations
|
We have presented the calculations of hyperfine structure constants and P, T-odd sensitivity parameters of SrH, in its ground electronic state, 2Σ1/2, within the four-component (4-c) relativistic coupled-cluster singles and doubles (CCSD) framework. The calculated properties would be important
for studying high-precision spectroscopy with the SrH molecule, which shows promise for laser cooling. Results obtained through two analytic approaches− Z-vector (energy-derivative) technique and expectation-value method within the 4-c CCSD framework are in very good agreement with each other. We further examine the role of electron correlation, relativistic Hamiltonian, and basis set in the precise calculations of the studied molecular properties. Finally, this study reveals that the P, T-odd parameters of SrH are reasonably large, making it a promising candidate molecule for high-precision experiments.
|
Kaushik Talukdar; Malaya K. Nayak; Sourav Pal
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.)
|
CC BY NC 4.0
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CHEMRXIV
|
2024-12-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674dd8787be152b1d0b11927/original/spectroscopic-properties-of-sr-h-from-relativistic-coupled-cluster-calculations.pdf
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664219ca21291e5d1d23b8f5
|
10.26434/chemrxiv-2023-8k3sq-v4
|
Quantum Control of Nonlinear Dynamics in Confined Fluids
|
Investigating nonlinear fluid dynamics remains a challenge across physics from nanofluidics and biophysics to astrophysics. Here we introduce a quantum/classical theoretical approach that takes into account both quantum correlations and classical behaviour within a 2D fluid that is confined in a 3 μm side square. We employ a modified Gross-Pitaevskii equation, encompassing many-body interactions and confinement. This system reveals complex fluid dynamics characterised by dissipative solitons; a significant outcome is an asymptotic function that describes the soliton behaviour. The solitons exhibit intriguing geometrical and temporal transformations, guided by subtle phase gradients. We trace the soliton evolution from 1 ns to 83 ns, revealing the emergence of geometric oscillations in amplitude and phase angles. Under these phase gradients, solitons transition to states with reduced amplitude and expanded spatial profiles. These results show that geometric solitons can emerge from a quantum noisy environment, and lead us to propose an interesting possibility: it is feasible to control and manipulate nonlinear dynamics in systems with finite-range interactions and confinement using quantum control. By bridging quantum and classical dynamics, this study links various scientific disciplines, including non-equilibrium phases of condensed matter, unconventional/quantum computing and advanced control of nanofluidics. From a more fundamental perspective, this possibility of quantum control of classical behaviour advances our understanding of physics within multidimensional Hilbert spaces.
|
Vinitha Johny; Sonia Contera; Siddharth Ghosh
|
Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanofluidics; Quantum Computing; Statistical Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664219ca21291e5d1d23b8f5/original/quantum-control-of-nonlinear-dynamics-in-confined-fluids.pdf
|
65c47a69e9ebbb4db9e76b60
|
10.26434/chemrxiv-2024-2dk13
|
Near-Field Response of Resonant Molecule Coupled With Plasmonic Nanocavity in Atomic Resolution
|
The local field enhancement effect in plasmonic nanocavities has facilitated the development of plasmon-enhanced spectroscopy (PES) techniques. Despite recent progress in sensitivity of PES, there exists a necessity for a comprehensive understanding of mutual interactions between exciton modes and plasmonic responses of nanocavities in terms of relative positions, orientations, and excitation wavelengths. In this study, we observed that the hot-spot transfer effect, occurring upon the coupling of a single molecule with a plasmonic nanocavity, is induced by the exciton modes of the molecule. Bright spots within the exciton mode contribute positively to the near fields, while dark spots contribute negative impact on the fields in the plasmonic nanocavity. At the sub-nanometer scale, the coupling between the molecule and plasmonic nanocavity results in substantial deviations from a simple power law. We approach the understanding the local field enhancement from both aspects of plasmon excitation and molecule induction. Additionally, we comprehend the molecule induction arising from local charges and charge flows in molecules. Moreover, the influence of an asymmetric plasmonic nanocavity on near-field distributions was systematically quantified. Notably, the observation of the hot-spot transfer effect persists even when the molecular dipole moment is oriented perpendicular to the near-field direction. These findings provide crucial insights into the near-field modulation in molecules coupled with plasmonic nanocavities.
|
Huijie He; Xueyang Zhen; Shuang Li; Sibing Chen; Xing Chen
|
Theoretical and Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c47a69e9ebbb4db9e76b60/original/near-field-response-of-resonant-molecule-coupled-with-plasmonic-nanocavity-in-atomic-resolution.pdf
|
60c751ebf96a0074ea2880f0
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10.26434/chemrxiv.12933683.v2
|
High-Throughput Discovery of Hf Promotion on the Formation of Hcp Co and Fischer-Tropsch Activity
|
A proxy-based high-throughput experimental approach was used to explore
the stability and activity of Co-based Fischer Tropsch Synthesis catalysts with
different promoters on various supports. The protocol is based on the
estimation by XRD of active phase, Co, particle size and relative amounts of
crystalline phases, Co to support. Sequential libraries samples enabled
exploration of four Co loadings with five different promoters on six support
materials. Catalysts stable to aging in syngas, displaying minimal change of
particle size or relative area, were evaluated for their activity under
industrial conditions. This procedure identified SiC as support for stable
catalysts and a combination of Ru and Hf to promote the formation hcp Co.
Unsupported bulk samples of Co with appropriate amounts of Ru and Hf revealed
that the formation of hcp Co is independent of the support. The hcp Co
containing catalyst presented the highest catalytic activity and C<sub>5+</sub>
selectivity amongst the samples tested in this study confirming the effectiveness
of the proxy-based high-throughput method.
|
Luis Alvarado Rupflin; Hendrik. Van Rensberg; Marco Zanella; Elliot J Carrington; Alexios Grigoropoulos; Troy Manning; John Bleddyn Claridge; Alexandros P Katsoulidis; Robert
P. Tooze; Matthew J Rosseinsky
|
Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751ebf96a0074ea2880f0/original/high-throughput-discovery-of-hf-promotion-on-the-formation-of-hcp-co-and-fischer-tropsch-activity.pdf
|
625d8997ebac3a1b9ed9d769
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10.26434/chemrxiv-2022-28pt7-v2
|
Reaction SPL - extension of a public document markup standard to chemical reactions
|
There are numerous formats and data models for describing reaction-related data. However, each offers only a limited coverage of the multitude of information that can be of interest to a broad user base in the context of chemical reactions. Structured Product Labeling (SPL) is a robust yet fairly light public XML document standard. It uses a highly generic but usefully refinable data schema, which is, like a language, highly expressive. We are therefore presenting an extension of SPL to chemical reactions (“Reaction SPL”). This extension is designed to support chemical manufacturing processes, which include as a minimum the chemical reaction and the procedures and conditions to run it. We provide an overview of the SPL reaction specification structures followed by some examples of documents with reaction data: predicted single-step reactions, a two-step synthesis, an enzymatic reaction, an example how to represent a reaction center, a patent, and a fully annotated reaction with by-products. Special attention is given to a mechanism for atom-atom mapping of reactions as well as to the possibility to integrate Reaction SPL with laboratory automation equipment, in particular automated synthesis devices.
|
Gunther Schadow; Yulia Borodina; Victorien Delannée; Wolf-Dietrich Ihlenfeldt; Alexander Godfrey; Marc Nicklaus
|
Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-04-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625d8997ebac3a1b9ed9d769/original/reaction-spl-extension-of-a-public-document-markup-standard-to-chemical-reactions.pdf
|
6283d9776cae1ce7590d5628
|
10.26434/chemrxiv-2022-3n2t2
|
Response of sediment phosphorus partitioning to lanthanum-modified clay amendment and porewater chemistry in a small eutrophic lake.
|
Sustained eutrophication of the aquatic environment by the remobilization of legacy phosphorus (P) stored in soils and sediments is a prevailing issue worldwide. Fluxes of P from the sediments to the water column, referred to as internal P loading, often delays the recovery of water quality following a reduction in external P loads. Here, we report on the vertical distribution and geochemistry of P, lanthanum (La), iron (Fe) and carbon (C) in the culturally eutrophied Lake Bromont. This lake underwent remediation treatment using La- modified bentonite (LMB) commercially available as PhoslockTM. We investigated the effectiveness of LMB in decreasing soluble reactive phosphorus (SRP) availability in sediments and in reducing dissolved fluxes of P across the sediment-water interface. Sediment cores were retrieved before and after LMB treatment at three sites representing bottom sediment, sediment influenced by lakeside housing and finally littoral sediment influenced by the lake inflow. Sequential extractions were used to assess changes in P speciation. Depth profiles of dissolved porewater concentrations were obtained after LMB treatment at each site. Results indicate that SRP extracted from the sediments decreased at all sites, while total extracted P (PTOT) bound to redox-sensitive metal oxides increased. 31P NMR data on P extract reveals that 20-43% of total solid-phase P is in the form of organic P (Porg) susceptible to be released via microbial degradation. Geochemical modelling of porewater data provides evidence that LaPO4(s) mineral phases, such as rhabdophane and/or monazite, are likely forming. However, results also suggest that La3+ binding by dissolved organic carbon (DOC) hinders La-phosphate precipitation. We rely on thermodynamic modelling to suggest that high Fe2+ would bind to DOC instead of La3+, therefore promoting P sequestrations by LMB under anoxic conditions.
|
Wessam Neweshy; Dolors Planas; Elisabeth Tellier; Rémi Marsac; Marie Demers; Raoul-Marie Couture
|
Earth, Space, and Environmental Chemistry; Geochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6283d9776cae1ce7590d5628/original/response-of-sediment-phosphorus-partitioning-to-lanthanum-modified-clay-amendment-and-porewater-chemistry-in-a-small-eutrophic-lake.pdf
|
67dd44e56dde43c908b8f4df
|
10.26434/chemrxiv-2025-0czlj
|
A Radical Strategy to the Synthesis of Bicyclo[1.1.1]pentyl C−Glycosides
|
Aryl C-glycosides are widely represented in natural products and pharmaceuticals, yet their saturated analogs remain elusive. Here, we address this challenge with a diastereoselective radical strategy for the efficient synthesis of bicyclopentyl C-glycosides via addition of glycosyl radicals to [1.1.1]propellane. Experimental and DFT studies support a radical chain mechanism under kinetic control. The protocol is practical, mild, and general, and amenable to scalable synthesis in continuous flow. Products manipulations allow easy access to a variety of three-dimensional aryl C-glycosides analogs.
|
Giulio Goti; Alessia Marrese; Simone Baldon; Patricia Gómez Roibás; Giorgio Pelosi; Andrea Sartorel; Luca Dell'Amico
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd44e56dde43c908b8f4df/original/a-radical-strategy-to-the-synthesis-of-bicyclo-1-1-1-pentyl-c-glycosides.pdf
|
60c73f40337d6c5116e264eb
|
10.26434/chemrxiv.7289732.v1
|
Tunable Metal-Organic Frameworks Enable High Efficiency Cascaded Adsorption Heat Pumps
|
Rising global standards of living coupled with the recent agreement to eliminate<br />hydrofluorocarbon refrigerants are creating intense pressure to develop more sustainable climate<br />control systems. In this vein, the use of water as the refrigerant in adsorption heat pumps is highly<br />attractive, but such adsorption systems are constrained to large size and poor efficiency by the<br />characteristics of currently employed water sorbents. Here we demonstrate control of the relative<br />humidity of water uptake by modulating the pore size in a family of isoreticular triazolate metalorganic<br />frameworks. Using this method, we identify a pair of materials with stepped, nonoverlapping<br />water isotherms that can function in tandem to provide continuous cooling with a<br />record ideal coefficient of performance of 1.63. Additionally, when used in a single-stage heat<br />pump, the microporous Ni2Cl2BBTA has the largest working capacity of any material capable of<br />generating a 25 °C difference between ambient and chiller output.
|
Adam Rieth; Ashley M. Wright; Sameer Rao; Hyunho Kim; Alina LaPotin; Evelyn N. Wang; Mircea Dinca
|
Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-11-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f40337d6c5116e264eb/original/tunable-metal-organic-frameworks-enable-high-efficiency-cascaded-adsorption-heat-pumps.pdf
|
60c74786469df49a76f4383a
|
10.26434/chemrxiv.11626098.v1
|
DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet
|
<p>Computational protein design remains a challenging task despite its remarkable success in the past few decades. With the rapid progress of deep-learning techniques and the accumulation of three-dimensional protein structures, using deep neural networks to learn the relationship between protein sequences and structures and then automatically design a protein sequence for a given protein backbone structure is becoming increasingly feasible. In this study, we developed a deep neural network named DenseCPD that considers the three-dimensional density distribution of protein backbone atoms and predicts the probability of 20 natural amino acids for each residue in a protein. The accuracy of DenseCPD was 51.56±0.20% in a 5-fold cross validation on the training set and 54.45% and 50.06% on two independent test sets, which is more than 10% higher than those of previous state-of-the-art methods. Two approaches for using DenseCPD predictions in computational protein design were analyzed. The approach using the cutoff of accumulative probability had a smaller sequence search space compared to that of the approach that simply uses the top-k predictions and therefore enables higher sequence identity in redesigning three proteins with Rosetta. The network and the data sets are available on a web server at <a href="http://protein.org.cn/densecpd.html">http://protein.org.cn/densecpd.html</a>. The results of this study may benefit the further development of computational protein design methods.</p>
|
Yifei Qi; John Z.H. Zhang
|
Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74786469df49a76f4383a/original/dense-cpd-improving-the-accuracy-of-neural-network-based-computational-protein-sequence-design-with-dense-net.pdf
|
65bd797a66c1381729d75b36
|
10.26434/chemrxiv-2024-1ph89
|
Enantioselective Arbuzov Reaction Enabled by Catalytic Ion-Pair Reorganization
|
The stereocontrolled synthesis of stereogenic-at-phosphorus compounds is a long-standing challenge in organic chemistry that has received heightened research attention in recent years. None of the catalytic approaches taken to date have leveraged the rich manifold of transformations proceeding through nucleophilic dealkylation of phosphonium ion intermediates (e.g. Michaelis–Arbuzov, Pudovik, and Appel reactions). Here, we report enantioselective hydrogen-bond-donor-catalyzed Michaelis–Arbuzov reactions of dialkylphosphonites with hydrogen chloride to afford H-phosphinates, which are versatile P-chiral building blocks. Mechanistic and computational investigations reveal that the catalyst diminishes the reactivity of the chloride nucleophile, yet accelerates the rate-determining dealkylation step by preorganizing the phosphonium chloride resting state into a geometry that is primed to enter the SN2 transition state.
|
Gabriel Lovinger; Marcus Sak; Eric Jacobsen
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Organocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bd797a66c1381729d75b36/original/enantioselective-arbuzov-reaction-enabled-by-catalytic-ion-pair-reorganization.pdf
|
60c745b84c8919142dad2a3f
|
10.26434/chemrxiv.10119302.v1
|
A Sweet Galactose Transfer – Metabolic Oligosaccharide Engineering as a Tool to Study Glycans in Plasmodium Infection
|
The use of artificial galactose derivatives and labelling through iEDDA reaction in the liver stage of <i>Plasmodium </i>infection showed increased uptake in infected hepatic cells, through participation of GLUT1 transporters. Furthermore, unprotected derivatives are transferred from the mosquito host to the <i>Plasmodium</i> <i>berghei</i> parasite. This strategy has the potential to provide new insights into <i>Plasmodium</i> glycobiology.
|
Annabel Kitowski; Gonçalo Bernardes
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745b84c8919142dad2a3f/original/a-sweet-galactose-transfer-metabolic-oligosaccharide-engineering-as-a-tool-to-study-glycans-in-plasmodium-infection.pdf
|
64e3371800bbebf0e68ad25f
|
10.26434/chemrxiv-2023-93llx
|
A Telescoped Continuous Flow Enantioselective Process to Access Chiral Intermediates of Atomoxetine, Dapoxetine, Duloxetine and Ezetimibe
|
A telescoped continuous flow process is reported for the enantioselective synthesis of chiral precursors of 1-aryl-1,3-diols, intermediates in the synthesis of Ezetimibe, Dapoxetine, Duloxetine and Atomoxetine. The two-step sequence consists of an asymmetric allylboration of readily available aldehydes using a polymer-supported chiral phosphoric acid catalyst to introduce asymmetry, followed by selective epoxidation of the resulting alkene. The process is highly stable for at least 7 h and represents a transition-metal free enantioselective approach to valuable 1-aryl-1,3-diols.
|
Aitor Maestro; Bence Nagy; Sandor Ötvös; Oliver Kappe
|
Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Process Chemistry; Heterogeneous Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e3371800bbebf0e68ad25f/original/a-telescoped-continuous-flow-enantioselective-process-to-access-chiral-intermediates-of-atomoxetine-dapoxetine-duloxetine-and-ezetimibe.pdf
|
66aa8490c9c6a5c07a9f6106
|
10.26434/chemrxiv-2024-qpwsg-v2
|
First-principles data for solid solution niobium-tantalum-vanadium alloys with body-centered-cubic structures
|
We present four open-source datasets that provide results of density functional theory (DFT) calculations of ground-state properties of refractory solid solution binary alloys niobium-tantalum (NbTa), niobium-vanadium (NbV), tantalum-vanadium (TaV), and ternary alloys NbTaV ordered in body-centered-cubic (BCC) structures with 128 Bravais lattice sites. The first-principles code used to run the calculations is the Vienna Ab-Initio Simulation Package. The calculations have been collected by uniformly sampling chemical compositions across the entire compositional range. For each chemical composition, the calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. This sampling methodology resulted in running DFT simulations for a total of 3,100 randomized atomic configurations over 31 chemical compositions for each of the three binary alloys Nb-Ta, Nb-V, Ta-V, and a total of 10,500 randomized atomic structures over 105 chemical compositions for the ternary alloys Nb-Ta-V. For each atomic configuration, geometry optimization has been performed, and the data released contains information about each step of geometry optimization for each atomic configuration.
|
Massimiliano Lupo Pasini; German Samolyuk; Markus Eisenbach; Jong Youl Choi; Junqi Yin; Ying Yang
|
Materials Science; Alloys
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aa8490c9c6a5c07a9f6106/original/first-principles-data-for-solid-solution-niobium-tantalum-vanadium-alloys-with-body-centered-cubic-structures.pdf
|
657d2fce66c13817294bbc16
|
10.26434/chemrxiv-2023-jh199
|
Predicting Molecular Trajectories using Machine Learning Methods
|
Predicting molecular trajectories is a cornerstone of computational chemistry, with implications for drug discovery and molecular dynamics simulations. This study presents a comprehensive analysis of various machine learning models for the prediction of aspirin molecular trajectories, as captured in a dataset of 1500 frames calculated via the CCSD [Psi4, cc-pVDZ] method. We explore statistical sampling methods, including random walk and Monte Carlo Markov Chain (MCMC), alongside a suite of neural networks comprising feed-forward, recurrent neural network (RNN), Long Short-Term Memory (LSTM), and Gated Recurrent Unit (GRU) architectures. Additionally, we investigate the potential of Equivariant Neural Networks (E3NN) to enforce permutation and rototranslational invariance, as well as Graph Convolutional Networks (GCN) for leveraging the inherent graph structure of molecules. Our results highlight the comparative effectiveness of these methods, with GCNs unexpectedly outperforming others in trajectory prediction accuracy. The study also delves into the novel application of diffusion models, treating molecular pose prediction as a generative problem, despite challenges in maintaining physical plausibility. Though preliminary, our findings underscore the promise of graph-based methods in capturing molecular interactions and dynamics, paving the way for future advancements in efficient and accurate trajectory prediction in computational chemistry.
|
Sonny Young
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY 4.0
|
CHEMRXIV
|
2023-12-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657d2fce66c13817294bbc16/original/predicting-molecular-trajectories-using-machine-learning-methods.pdf
|
6565bf5acf8b3c3cd74f4ffb
|
10.26434/chemrxiv-2023-tnsnw-v2
|
Synthetic Protein-to-DNA Input Exchange for Protease Activity Detection Using CRISPR-Cas12a
|
We present a novel activity-based detection strategy for matrix metalloproteinase 2 (MMP2), a critical cancer protease biomarker, leveraging a mechanism responsive to the proteolytic activity of MMP2 and its integration with CRISPR-Cas12a-assisted signal amplification. We designed a chemical translator comprising two functional units — a peptide and a peptide nucleic acid (PNA) — fused together. The peptide presents the substrate of MMP2, while the PNA serves as a nucleic acid output for subsequent processing. This chemical translator was immobilized on micrometric magnetic beads as a physical support for an activity-based assay. We incorporated into our design a single-stranded DNA partially hybridized with the PNA sequence and bearing a region complementary to the RNA guide of CRISPR-Cas12a. The target-induced nuclease activity of Cas12a results in the degradation of FRET-labeled DNA reporters and amplified fluorescence signal, enabling detection of MMP2 in the low picomolar range, showing a limit of detection of 72 pg/mL. This study provides new design principles for a broader applicability of CRISPR-Cas-based biosensing.
|
Luca Capelli; Federica Pedrini; Andrea C. Di Pede; Neda Bagheri; Simone Fortunati; Marco Giannetto; Monica Mattarozzi; Roberto Corradini; Alessandro Porchetta; Alessandro Bertucci
|
Analytical Chemistry; Nanoscience; Analytical Chemistry - General; Nanodevices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6565bf5acf8b3c3cd74f4ffb/original/synthetic-protein-to-dna-input-exchange-for-protease-activity-detection-using-crispr-cas12a.pdf
|
6629fbda21291e5d1da7bedf
|
10.26434/chemrxiv-2024-mf9mw
|
4-anilinoquinazoline derivatives as the first potent NOD1-RIPK2 signaling pathway inhibitors at the nanomolar range with potential anti-inflammatory activity
|
Inflammation is a defense mechanism that restores tissue damages and eliminates pathogens. Among the Pattern Recognition Receptors that recognize danger or pathogenic signals, Nucleotide Oligomerization Domain 1 and 2 (NOD1/2) have been identified to play an important role in innate immunity responses and inhibition of NOD1 could be interesting to treat severe infections and inflammatory diseases. In this work, we identified the first selective NOD1 vs NOD2 pathway inhibitors at the nanomolar range based on a 4-anilinoquinazoline scaffold. We demonstrated that NOD1 inhibition occurs through the inhibition of Receptor Interacting Protein Kinase 2 (RIPK2), involved in its downstream signaling pathways. Compound 37 demonstrates no cytotoxicity, a selectivity for RIPK2 over Epithelial and Vascular Endothelial Growth Factor Receptors (EGFR/VEGFR) and a capacity to reduce pro-inflammatory cytokine IL-8 secretion. The structure of the RIPK2-compound 37 complex was resolved by crystallography. The 4-anilinoquinazoline scaffold offers novel perspectives to design NOD1-RIPK2 inhibitors, potentially useful to treat inflammatory diseases.
|
Amélie BARCZYK; Perrine SIX; Morgane RIVOAL; Claire DEVOS; Xavier DEZITTER; Min-Jeong CORNU-CHOI; Karine HUARD; Erika PELLEGRINI; Stephen CUSACK; Laurent DUBUQUOY; Régis MILLET; Natascha LELEU-CHAVAIN
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6629fbda21291e5d1da7bedf/original/4-anilinoquinazoline-derivatives-as-the-first-potent-nod1-ripk2-signaling-pathway-inhibitors-at-the-nanomolar-range-with-potential-anti-inflammatory-activity.pdf
|
673473a17be152b1d0ed4665
|
10.26434/chemrxiv-2024-016md
|
Spatio-chemical deconvolution of the LiNi0.6Co0.2Mn0.2O2/Li6PS5Cl interphase layer in all-solid-state batteries using combined X-ray spectroscopic methods
|
The (electro-)chemical degradation at the interface between Li6PS5Cl (LPSC) and LiNi0.6Co0.2Mn0.2O2 (NCM622) is systematically investigated using non-destructive synchrotron X-ray absorption spectroscopy (XAS) and X-ray photoemission electron microscopy (XPEEM). These techniques provide surface chemical depth profiling (from 2 nm to several hundred nm) and high-resolution elemental imaging of both LPSC and NCM622 particles. This analysis was complemented by galvanostatic cycling, impedance spectroscopy, and operando cell pressure measurements. Several correlations between interphase evolution and cell electrochemical performance are clarified, while some inconsistencies are rationalized and discussed. Firstly, the intrinsic LPSC electrochemical oxidation mechanisms were studied using an LPSC:C65 working electrode. The results showed that increased cell resistance during the first charge stemmed from polysulfide by-products and particle contact loss due to LPSC volume shrinkage at the interface. Secondly, when using an NCM622:LPSC working electrode, species such as sulfites, sulfates and phosphates, were detected on both LPSC and NCM622 particles, while electrochemically inactive reduced transition metals (TMs) were observed only at NCM622 surfaces. These species, initially present at open circuit potential, increased after the first charge, due to the chemical reactions between LPSC and NCM622 surface lattice oxygen. The estimated interphase thickness on the LPSC and NCM622 surface over the cycling remains below ⁓3 nm. Our findings highlight that the formation of an electrochemically inactive NCM622 surface is a primary cause of impedance rise during the first charge, along with the formation of LPSC by-products and contact loss. However, the continuous increase in cell resistance could not be attributed to further interphase growth after the first charge. We hypothesize that this may result from slow and progressive LPSC polymerization reactions (e.g., form Li2PS6 and P2S5) and structural changes at the NCM622 surface.
|
Barthélémy Lelotte; Carlos A. F. Vaz; Linfeng Xu; Camelia Borca; Thomas Huthwelker; Pelé Vincent; Christian Jordy; Lorenz Gubler; Mario El Kazzi
|
Analytical Chemistry; Energy; Electrochemical Analysis; Imaging; Spectroscopy (Anal. Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673473a17be152b1d0ed4665/original/spatio-chemical-deconvolution-of-the-li-ni0-6co0-2mn0-2o2-li6ps5cl-interphase-layer-in-all-solid-state-batteries-using-combined-x-ray-spectroscopic-methods.pdf
|
60c745a5bdbb8926aaa38a7e
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10.26434/chemrxiv.10087298.v1
|
Directed Evolution of an Feᴵᴵ-Dependent Halogenase for Asymmetric C(sp³)-H Chlorination
|
By using structure-guided directed evolution, the substrate scope of the FeII and a‑ketoglutarate dependent halogenase Wi‑WelO15 from Westiella intricata HT-29-1 was engineered to enable chemo-, regio- and diastereoselective chlorination of unactivated C(sp3)-H bonds using NaCl as chlorine source. While FeII dependent enzymes are often oxygen sensitive, variants of this halogenase could be screened in lysates under aerobic conditions. The new biocatalysts offer a sustainable approach for mild, late-stage chlorination on mg-scale of non-natural hapalindoles containing a ketone instead of an isonitrile functionality, thereby unlocking them for preparative biocatalysis.<br />
|
Sabine Duewel; Luca Schmermund; Tabea Faber; Klaus Harms; Vasundara Srinivasan; Eric Meggers; Sabrina Hoebenreich
|
Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745a5bdbb8926aaa38a7e/original/directed-evolution-of-an-fe-ii-dependent-halogenase-for-asymmetric-c-sp3-h-chlorination.pdf
|
60c75758bb8c1aa0e33dc7fb
|
10.26434/chemrxiv.14396105.v1
|
Chemical Proportionality within Molecular Networks
|
Molecular networking of non-targeted tandem mass spectrometry data connects structurally related molecules based on similar fragmentation spectra. Here we report the Chemical Proportionality contextualization of molecular networks. ChemProp scores the changes of abundance between two connected nodes over sequential data series which can be displayed as a direction within the network to prioritize potential biological and chemical transformations or proportional changes of related compounds. We tested the ChemProp workflow on a ground truth data set of defined mixture and highlighted the utility of the tool to prioritize specific molecules within biological samples, including bacterial transformations of bile acids, human drug metabolism and bacterial natural products biosynthesis. The ChemProp workflow is freely available through the Global Natural Products Social Molecular Networking environment.<br /><b> </b>
|
Daniel Petras; Andrés Mauricio Caraballo-Rodríguez; Alan K. Jarmusch; Carlos Molina-Santiago; Julia
M. Gauglitz; Emily Gentry; Pedro Belda-Ferre; Diego Romero; Shirley M. Tsunoda; Pieter C. Dorrestein; Mingxun Wang
|
Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75758bb8c1aa0e33dc7fb/original/chemical-proportionality-within-molecular-networks.pdf
|
66d4bca8a4e53c487655dc67
|
10.26434/chemrxiv-2024-2v39h
|
C-H alkylation of heterocycles via light-mediated palladium catalysis
|
Methods enabling direct C-H alkylation of heterocycles are of fundamental importance in the late-stage modification of natural products, bioactive molecules, and medicinally relevant compounds. However, there is a scarcity of a general strategy for the direct C-H alkylation of a variety of heterocycles using commercially available alkyl surrogates. We report an operationally simple palladium-catalyzed direct C-H alkylation of heterocycles using alkyl halides under the visible light irradiation with good scalability and functional group tolerance. Our studies suggest that the photoinduced alkylation proceeds through cascade of events comprising, site-selective alkyl radical addition, base-assisted deprotonation, and oxidation. A combination of experiments and computations was employed for the generalization of this strategy, which was successfully translated towards the modification of natural products and pharmaceuticals.
|
Sudip Senapati; Sudhir K. Hota; Lennard Kloene; Claire Empel; Sandip Murarka; Rene M. Koenigs
|
Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d4bca8a4e53c487655dc67/original/c-h-alkylation-of-heterocycles-via-light-mediated-palladium-catalysis.pdf
|
627c4bc859f0d665418d9ae9
|
10.26434/chemrxiv-2022-5gk0z
|
Addressing Environmental- and Public Health through Urban Water Profiling of Emerging Contaminants in a South African Urban Setting
|
The study evaluated the mass balance of various contaminants of emerging concern (CEC) from a South African wastewater treatment works (WWTW) and surface waters located upstream and downstream from the point of discharge. A total of 45 CECs, that are grouped into 16 drug classes, were quantified during multiple sampling events that spanned over a period of two years in the study area. Daily loads (DL; in g/day) of the target analytes in the WWTW showed persistence of various CECs, along with population-normalised daily loads (PNDL; in mg/day/1000inh) of pharmaceuticals and drugs of abuse (DOA) that were estimated for the first time in the study area, using the wastewater-based epidemiology (WBE) approach. Multiple chemical markers were recorded in river water located upstream of the WWTW discharge, suggesting other urban pollution sources that contribute towards the CEC loading in the surface water environment. Environmental risk characterisation for the WWTW effluent and surface waters was done to calculate multiple risk quotients (RQs) for each CEC spanning over various sentinel trophic levels. High risk profiles (RQ>1.0) with a frequency of exceedance (FoE) larger than 75% were recorded for several CECs in both WWTW effluent and surface water locations that warrants the need for more refined surveillance of pollution hotspots in the urban catchment. These findings highlight the need for developing an urban water profiling (UWP) approach similar to conventional WBE approaches, at least for low- and middle-income countries (LMICs) where some (peri)urban communities are not connected to municipal sewage infrastructure and thus lead to direct discharge of human waste products into the natural environment.
|
Edward Archer; Elizabeth Holton; James Fidal; Barbara Kasprzyk-Hordern; Alno Carstens; Ludwig Brocker; Thomas Kjeldsen; Gideon Wolfaardt
|
Earth, Space, and Environmental Chemistry; Environmental Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627c4bc859f0d665418d9ae9/original/addressing-environmental-and-public-health-through-urban-water-profiling-of-emerging-contaminants-in-a-south-african-urban-setting.pdf
|
60c757759abda2195ef8e71c
|
10.26434/chemrxiv.14403188.v1
|
Ab Initio Electronic Dielectric “Constant” of Proteins: A Baseline for Electrostatic Interaction in Biomolecular Systems
|
<p>The protein dielectric constant reflects the molecular heterogeneity
of the proteins and can be decomposed into different components depending on
the size, structure, composition, locality, and environment of the protein in
general. The long history of its
computation and measurement attest to the vital importance of electrostatic
interactions in protein physics that engendered diverse theoretical approaches
based often on scattered methodologies with various adjustable parameters. We present a new robust computational method
anchored in rigorous <i>ab initio</i> quantum
mechanical calculation of explicit atomistic models, without any indeterminate
parameters to compute and gain insight into the <i>electronic component</i> of the static dielectric constants of small
proteins under different conditions. We implement the new methodology to the 20
canonical amino acids individually, a polypeptide RGD-4C (1FUV) in different
environments, and the SD1 domain in the Spike protein of SARS-COV-2. The
calculated electronic dielectric constants for 1FUV and SD1 in vacuum are 28.06 and 50.02 respectively.
They decrease in the presence of aqueous bathing solution.</p>
|
Puja Adhikari; Rudolf Podgornik; Bahaa Jawad; Wai-Yim Ching
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757759abda2195ef8e71c/original/ab-initio-electronic-dielectric-constant-of-proteins-a-baseline-for-electrostatic-interaction-in-biomolecular-systems.pdf
|
60c75313842e65b8b2db3ea4
|
10.26434/chemrxiv.13385228.v1
|
New Good Ionic Conductor: Ba-Deficient Ba3Y4O9 with Zr Substitution
|
<p>To lower operating
temperatures of solid oxide fuel cells (SOFCs), the development of ion-conducting
oxides with high conductivity and durability is desired. In this work, we investigated
Zr-substituted “Ba<sub>3</sub>Y<sub>4</sub>O<sub>9</sub>” as an ionic conductor
at intermediate temperatures and found that the Zr substitution for Y
dramatically improves the phase stability in humidified atmospheres at 300-800 °C. The total electrical conductivity of 20 mol% Zr-substituted Ba<sub>3</sub>Y<sub>4</sub>O<sub>9</sub>
is about 1 mS/cm at 700 °C in dry H<sub>2</sub> and O<sub>2</sub>
atmospheres and the contribution of electronic conduction (both hole and
electron) is relatively small compared with Y-doped BaZrO<sub>3</sub> (BZY) and
Gd-doped CeO<sub>2</sub> (GDC) which are typical intermediate-temperature
ionic conductors. Besides, in the Zr-substituted “Ba<sub>3</sub>Y<sub>4</sub>O<sub>9</sub>”
samples, we observed that BaO-rich amorphous phase coexists with the main phase
whose composition is estimated to be Ba:(Y+Zr) ~ 2:3. Therefore, the main
conducting phase might be Ba-deficient Ba<sub>3</sub>Y<sub>4</sub>O<sub>9</sub>.
The mechanism of the ionic conduction and the improvement of chemical stability
has not been revealed yet due to the lack of crystallographic information about
the Ba-deficient phase. While we are now working on further investigation, we
promptly report the characteristic of the new compound.</p>
|
Katsuhiro Ueno; Naoyuki Hatada; Tetsuya Uda
|
Ceramics; Solid State Chemistry; Fuel Cells
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75313842e65b8b2db3ea4/original/new-good-ionic-conductor-ba-deficient-ba3y4o9-with-zr-substitution.pdf
|
63d9c04eab681c2c9d255a7e
|
10.26434/chemrxiv-2023-vgs38
|
Topological Isomerism in Three-Dimensional Covalent Organic Frameworks
|
Although isomerism is a typical and significant phenomenon in organic chemistry, it is rarely found in covalent organic framework (COF) materials. Herein, for the first time, we report a controllable synthesis of topological isomers in three-dimensional COFs via a distinctive tetrahedral building unit under different solvents. Based on this strategy, both isomers with dia or qtz net (termed JUC-620 and JUC-621) have been obtained, and their structures are deter-mined by combining powder X-ray diffraction and transmission electron microscopy. Remarkably, these architectures show a dis-tinct difference in their porous features, e.g., JUC-621 with qtz net exhibits permanent mesopores (up to ~ 2.3 nm) and high surface area (~ 2060 m2 g-1), which far surpasses those of JUC-620 with dia net (pore size of ~1.2 nm and surface area of 980 m2 g-1). Further-more, mesoporous JUC-621 can remove dye molecules efficiently and achieves excellent iodine adsorption (up to 6.7 g g-1), which is 2.3 times that of microporous JUC-620 (~2.9 g g-1). This work thus provides a new way for constructing COF isomers and promotes structural diversity and promising applications of COF mate-rials.
|
Yaozu Liu; Jingwei Li; Jia Lv; Zitao Wang; Jinquan Suo; Junxia Reng; Jianchuan Liu; Dong Liu; Yujie Wang; Valentin Valtchev; Shilun Qiu; Daliang Zhang; Qianrong Fang
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d9c04eab681c2c9d255a7e/original/topological-isomerism-in-three-dimensional-covalent-organic-frameworks.pdf
|
63e46664068fd75979319983
|
10.26434/chemrxiv-2023-p478k-v2
|
Degenerate and Non-Degenerate Two-Photon
Absorption of Coumarin Dyes
|
Two-photon absorption (2PA) spectroscopy is a robust bioimaging tool that depends on the determined cross sections (σ2PA). The absorption of both photons occurs
simultaneously with equivalent (degenerate) or different (non-degenerate) photon energies, D-2PA and ND-2PA, respectively. The former has been investigated experimentally and computationally for many systems, while the latter remains relatively unexplored computationally and limited experimentally. In this study, response theory using time-dependent density functional theory (TD-DFT) and the 2-state model (2SM) have been utilized to investigate σD-2PA and σND-2PA for the excitation to the lowest energy singlet state (S1) of coumarin, coumarin 6, coumarin 120, coumarin 307, and coumarin 343. Solvents involved were methanol (MeOH), chloroform (ClForm), and dimethylsulfoxide (DMSO), where the latter leads to the largest σ2PA. Values of σ2PA are largest for coumarin 6 and lowest for coumarin, which illustrates the effect of substituents. The 2SM clarifies how the largest cross-sections correspond to molecules with the largest transition dipole moments, μ01. In general, σD-2SM computations agree with σD-2PA. Moreover, σND-2SM are in qualitative agreement with σND-2PA with comparable enhancement relative to σD-2PA. Overall, σND-2PA are larger than σD-2PA where the increase is in the range of 22% to 49%, depending on the coumarin as well as the relative energies of the two photons. This work aids in future investigations into various fluorophores to understand their photophysical properties for ND-2PA.
|
Ismael A. Elayan; Alex Brown
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Processes; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e46664068fd75979319983/original/degenerate-and-non-degenerate-two-photon-absorption-of-coumarin-dyes.pdf
|
62edaafb3b834e3d4be6cb84
|
10.26434/chemrxiv-2022-7999d
|
NO reduction with CO on low-loaded platinum-group metals (Rh, Ru, Pd, Pt, and Ir) atomically dispersed on Ceria
|
Low-loaded platinum-group single-atom catalysts on CeO2 (M1/CeO2) were synthesized via high-temperature atom trapping (AT) and tested for the NO + CO reaction under dry and wet condition. The activity of these catalysts for NO+CO reaction follows the order Rh > Pd ≈ Ru > Pt > Ir. For Rh, Ru, and Pd single-atom catalysts, the N2O byproduct is formed but not clearly observed on Ir and Pt cases, which may result from the higher reaction temperature (> 200oC) required for Pt and Ir catalysts. The presence of water can promote the activity of these M1/CeO2 catalysts for NO + CO reaction. Under wet conditions, significant NH3 formation occurred during the reaction, which is due to the co-existence of water-gas-shift reaction on these catalysts. Compared with Pt, Pd and Ir, the Rh and Ru single-atom catalysts show higher selectivity to NH3 species, resulting from the more hydride species on the surface. Among all tested catalysts, Ru1/CeO2 shows the highest production of ammonia and highest CO conversion due to excellent water-gas-shift activity, whereas Pd1/CeO2 shows lowest ammonia production.
|
Jinshu Tian; Konstantin Khivantsev; Yubing Lu; Sichuang Xue; Zihao Zhang; Janos Szanyi; Yong Wang
|
Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62edaafb3b834e3d4be6cb84/original/no-reduction-with-co-on-low-loaded-platinum-group-metals-rh-ru-pd-pt-and-ir-atomically-dispersed-on-ceria.pdf
|
613081aafc08e37e8488d521
|
10.26434/chemrxiv-2021-gvz7q
|
OLED from solution-processed crystalline poly(triazine imide)
|
Crystalline semiconducting carbon nitrides are chemically and physically resilient, consist of earth abundant elements, and can be exfoliated into 2D atomically thin layers. In particular, poly(triazine imide) (PTI) is a highly crystalline semiconductor, and though no techniques exist to date that enable synthesis of macroscopic monolayers of PTI, it is possible to study it in thin layer device applications that are compatible with its polycrystalline, nanoscale morphology. In our study, we find that the by-product of conventional PTI synthesis is a C-C carbon rich phase that is detrimental for charge transport and photoluminescence. An optimised synthetic protocol yields a PTI material with an increased quantum yield, enabled photocurrent and electroluminescence. In addition, we report that protonation of the PTI structure happens preferentially at the pyridinic nitrogen atoms of the triazine (C3N3) rings, is accompanied by exfoliation of PTI layers, and contributes to increases in quantum yield and exciton lifetimes. This study describes structure-property relationships in PTI that link (i) the nature of defects, their formation, and how to avoid them with (ii) the optical and electronic performance of PTI. On the basis of our findings, we create an OLED prototype with PTI as the active, metal-free material, and we lay the foundations for device integration of solution-processable graphitic carbon nitride dispersions in semiconductor devices.
|
David Burmeister; Ha Anh Tran; Johannes Müller; Michele Guerrini; Caterina Cocchi; Julian Plaickner; Michael Bojdys
|
Theoretical and Computational Chemistry; Polymer Science; Organic Polymers; Theory - Computational; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-09-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613081aafc08e37e8488d521/original/oled-from-solution-processed-crystalline-poly-triazine-imide.pdf
|
6455f59327fccdb3ea92da82
|
10.26434/chemrxiv-2023-vjn0d
|
Hydrogen-induced formation of surface acid sites on Pt/Al(PO3)3 enables remarkably efficient hydrogenolysis of C−O bonds in alcohols and ethers
|
The hydrogenolysis of oxygenates such as alcohols and ethers is central to the biomass valorization and also a valuable transformation in organic synthesis. However, there is lack of a mild and efficient catalyst system that is applicable to a wide range of alcohols and ethers. Here, we report an aluminum metaphosphate-supported Pt nanoparticles for the hydrogenolysis of a wide variety of primary, secondary, and tertiary alkyl and benzylic alcohols, and dialkyl, aryl alkyl, and diaryl ethers, including biomass-derived furanic compounds, under mild conditions (0.1–1 atm of H2, as low as 70 °C). Mechanistic studies suggested that H2 induces formation of the surface Brønsted acid sites via its cleavage by supported Pt nanoparticles. Accordingly, the high efficiency and the wide applicability of the catalyst system can be attributed to the cooperative activation and cleavage of C–O bonds of alcohols and ethers by the hydrogen-induced Brønsted acid sites and Lewis acidic Al sites on Al(PO3)3 surface. The high efficiency of the catalyst imply its potential application in energy efficient biomass valorization or fine chemical synthesis.
|
Kento Oshida; Kang Yuan; Yukari Yamazaki; Rio Tsukimura; Xiongjie Jin; Kyoko Nozaki
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6455f59327fccdb3ea92da82/original/hydrogen-induced-formation-of-surface-acid-sites-on-pt-al-po3-3-enables-remarkably-efficient-hydrogenolysis-of-c-o-bonds-in-alcohols-and-ethers.pdf
|
631cbf423e2e36d21131c130
|
10.26434/chemrxiv-2022-z6c5h
|
Breaking the tert-Butyllithium Contact Ion Pair:
A Gateway to Alternate Selectivity in Lithiation Reactions
|
The selective functionalization of saturated oxygen heterocycles at positions remote to the
embedded heteroatoms remains an outstanding challenge in organic synthesis. Although many
methods exist for the undirected replacement of C–H bonds with heteroatomic subunits the number
of site selective C–H functionalization reactions for the introduction of carbon-carbon bonds pales
in comparison. This paper describes the initial stages of a long-term program aimed at elucidating
how organolithium reagents can be re-engineered to selectively deprotonate and functionalize
saturated heterocycles at new locations. Through rigorous NMR spectroscopic investigations, it
was determined for the first time that the addition of Lewis basic phosphoramides can shift the
equilibrium of strong organolithium bases, such as t-BuLi, to include the triple ion pair (t-Bu–Li–t-Bu) / L4Li which serves as a reservoir for the highly reactive separated ion pair t-Bu / L4Li . Because the Li-atom’s valences are saturated the Lewis acidity is significantly decreased and the basicity is maximized which allowed for the typical directing effects within oxygen heterocycles to be overridden and for remote sp3-CH bonds to be deprotonated. In certain cases, this enabled the removal of stronger C–H bonds in the presence of weaker C–H bonds. Furthermore, these newly accessed lithium aggregation states were leveraged to develop a simple γ-lithiation and capture protocol (lithium nucleophilic coupling – “LiNC”) of chromane heterocycles with a variety of alkyl halide electrophiles in good yields.
|
Michael Crockett; Jeanette Piña; Andrew Nguyen; Andy Thomas
|
Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Kinetics and Mechanism - Organometallic Reactions; Small Molecule Activation (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631cbf423e2e36d21131c130/original/breaking-the-tert-butyllithium-contact-ion-pair-a-gateway-to-alternate-selectivity-in-lithiation-reactions.pdf
|
60c753e4702a9b756318c43d
|
10.26434/chemrxiv.13568669.v1
|
Phenylindolylmethyldiaminopyrimidines (PIDAPs) as Potent Antimicrobials Against Staphylococcus Aureus
|
We have ascertained that phenylindolylmethyldiaminopyrimidines (PIDAPs), stop the growth of USA300 MRSA at low micromolar concentrations. The controls, penicillin G and vancomycin, are able to stop the growth of MRSA at ~765 μM (256 μg/mL) and ~1.38 μM (2 μg/mL) respectively. We have also found out that PIDAPs are bactericidal at or close to the MIC. No activity was observed against Gram-negative pathogens. Other Gram-positive pathogens have not yet been tested. Based on a search through the ChEMBL database, PIDAPs are a novel class of chemicals with antimicrobial properties. A limited structure-function study suggests that the diaminopyrimidine is part of the pharmacophore. Unfortunately, we also detected potential dose-limiting toxicity on human cell lines. Further, detailed studies are needed.
|
Margaret Deming; Alatheia King; Robert A Coover; Cale D Fahrenholtz; Aurijit Sarkar
|
Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753e4702a9b756318c43d/original/phenylindolylmethyldiaminopyrimidines-pida-ps-as-potent-antimicrobials-against-staphylococcus-aureus.pdf
|
60c758ea9abda28daef8e9ba
|
10.26434/chemrxiv.14560581.v2
|
Atomic Structure-free Representation of Active Motifs for Expedited Catalyst Discovery
|
For CO* and H* binding energy prediction, we develop new representation of catalyst surface which split surface into three types of site, first nearest neighbor of adsorbates and second nearest neighbor in same layer and sublayer. From this representation and machine learning regression model, we achieve reasonable accuracy (0.120 eV for CO* and 0.105 eV for H*) with quick training (~200 sec using CPU). Because our representation does not require density functional calculation and atomic structure modelling, it can predict binding energies of possible active motifs without time-consuming steps.
|
Dong Hyeon Mok; Seoin Back
|
Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758ea9abda28daef8e9ba/original/atomic-structure-free-representation-of-active-motifs-for-expedited-catalyst-discovery.pdf
|
64be471cb605c6803b425da6
|
10.26434/chemrxiv-2023-604k3
|
Systematic handling of environmental fate data for model development – illustrated for the case of biodegradation half-life data
|
Environmental hazard endpoints describing persistence, mobility, toxicity, or bioaccumulation of chemicals are often associated with high variability in experimental outcomes. The assessment of persistence in the environment is particularly affected due to a multitude of influencing environmental factors, including the taxonomic composition and physiological state of the microbial community present. Biotransformation experiments may therefore result in half-lives spanning several orders of magnitude for the same substance tested with different environmental samples. Due to experimental limitations, values may further be beyond the limits of reliable half-life quantification (i.e., censored data points), and the number of data points per substance may vary considerably. However, reliable data describing average half-lives and their natural variability are an important foundation for building predictive models for environmental hazard endpoints, which are urgently needed by regulatory authorities to manage existing chemicals and by industry for the design of benign, non-persistent chemicals. Here, we propose the application of Bayesian inference to characterize the uncertainty of reported half-lives and to include censored data points to maximize the information extracted from experimental data. Our model estimates the true mean and standard deviation from a set of reported half-lives experimentally obtained for a single substance. Including censored data increases the available data volume, and reporting uncertainties helps estimating the reliability of the half-life data. We apply the inference model to 893 substances with experimental soil half-lives of varying data quantity and quality, and we estimate the true half-life distribution for each compound. Our approach can be easily adapted and applied to other environmental hazard endpoints to estimate uncertainty and to improve data quality for model development.
|
Jasmin Hafner; Kathrin Fenner; Andreas Scheidegger
|
Earth, Space, and Environmental Chemistry; Environmental Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64be471cb605c6803b425da6/original/systematic-handling-of-environmental-fate-data-for-model-development-illustrated-for-the-case-of-biodegradation-half-life-data.pdf
|
60c74a8f9abda2807cf8ce74
|
10.26434/chemrxiv.12170136.v2
|
Three-Phase Electrochemistry of a Highly Lipophilic Neutral Ru-Complex Having a Tridentate Bis(benzimidazolate)pyridine Ligand
|
Here we describe the
synthesis and electrochemical testing of a heteroleptic bis(tridentate) ruthenium(II) complex [Ru<sup>II</sup>(LR)(L)]<sup>0</sup>
(LR =2,6-bis(1-(2-octyldodecan)benzimidazol-2-yl)pyridine, L = 2,6-bis(benzimidazolate)pyridine). It
is a neutral complex which undergoes a quasireversible oxidation and reduction
at relatively low potential. The newly synthetized compound was used for
studies of ion-transfer at the three-phase junction because of the sensitivity
of this method to cation expulsion. The [Ru<sup>II</sup>(LR)(L)]<sup>0</sup>
shows exceptional stability during cycling and is sufficiently lipophilic even
after oxidation to persist in the organic phase also using very hydrophilic
anions such as Cl<sup>−</sup>. Given its low redox potential and strong
lipophilicity this compound will be of interest as an electron donor in
liquid-liquid electrochemistry.
|
Vishwanath R.S; Masa-aki Haga; Takumi Watanabe; Emilia Witkowska Nery; Martin Jönsson-Niedziolka
|
Electrochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a8f9abda2807cf8ce74/original/three-phase-electrochemistry-of-a-highly-lipophilic-neutral-ru-complex-having-a-tridentate-bis-benzimidazolate-pyridine-ligand.pdf
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61d9a87edb142e4068b86a1b
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10.26434/chemrxiv-2022-t1zsn
|
Predicting Ruthenium Catalysed Hydrogenation of Esters using Machine Learning
|
Catalytic hydrogenation of esters is a sustainable approach for the production of fine chemicals, and pharmaceutical drugs. However, the efficiency and cost of catalysts are often the bottlenecks in the commercialization of such technologies. The conventional approach of catalyst discovery is based on empiricism that makes the discovery process time-consuming and expensive. There is an urgent need to develop effective approaches to discover efficient catalysts for hydrogenation reactions. We demonstrate here the approach of machine learning for the prediction of out-comes for the catalytic hydrogenation of esters. Our models can predict the reaction yields with high mean accuracies of up to 91% (test set) and suggest that the use of certain chemical descriptors selectively can result in a more accurate model. Furthermore, cata-lysts and some of their corresponding descriptors can also be pre-dicted with mean accuracies of 85%, and >90%, respectively.
|
Challenger Mishra; Niklas von Wolff; Abhinav Tripathi; Eric Brémond; Annika Preiss; Amit Kumar
|
Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Machine Learning; Homogeneous Catalysis
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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/61d9a87edb142e4068b86a1b/original/predicting-ruthenium-catalysed-hydrogenation-of-esters-using-machine-learning.pdf
|
66f12b3ecec5d6c142ecdd8f
|
10.26434/chemrxiv-2024-6pk1d
|
Citric, Tartaric, and Succinic Acid Effects on C3S Dissolution and the Nucleation Kinetics of C-S-H and Portlandite
|
Functional additives like carboxylic acids modify the hydration mechanism of Portland cement and
are commonly used as set retarders. These retarders can affect the clinker phase dissolution and the
crystallization of hydrate phases. However, their specific effects are not fully understood. This study
focuses on understanding the role of citric, tartaric, and succinic acid in the dissolution of tricalcium
silicate (C3S) and the crystallization of C-S-H and portlandite. The results reveal that these acids
accelerate C3S dissolution, while their sodium salts exhibit minimal effects at high undersaturation.
At low undersaturation, citrate reduces the dissolution rate by 50%, and tartrate can fully suppress
dissolution in the model experiment. Potentiometric titration studies reveal that the additives inhibit
the nucleation and crystal growth of C-S-H and portlandite by stabilizing prenucleation clusters. In
summary, the additives’ relative impact on dissolution and crystallization suggests that the retarding
effect of citric and tartaric acid is predominantly caused by the inhibition of nucleation and crystal
growth.
|
Andreas Vohburger; Marie Collin; Arnaud Bouissonnié; Torben Gädt
|
Materials Chemistry
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CC BY 4.0
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CHEMRXIV
|
2024-09-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f12b3ecec5d6c142ecdd8f/original/citric-tartaric-and-succinic-acid-effects-on-c3s-dissolution-and-the-nucleation-kinetics-of-c-s-h-and-portlandite.pdf
|
60c74049bb8c1a09823d9d74
|
10.26434/chemrxiv.7688183.v1
|
Evaluation of Industrial Routes to Vinyl Chloride According to Material and Energy Efficiency Green Metrics Analysis
|
This work presents a detailed analysis of various industrial syntheses of vinyl chloride according to material and energy efficiency green metrics. The routes examined are hydrochlorination of acetylene, oxyhydrochlorination of ethane, and tandem hydrochlorination of ethylene and dehydrochlorination of 1,2-dichloroethane. The green metrics selected are process mass intensity (PMI) and input enthalpy per unit mass of product measured in MJ per ton.
|
john andraos
|
Organic Synthesis and Reactions; Catalysts
|
CC BY NC ND 4.0
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CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74049bb8c1a09823d9d74/original/evaluation-of-industrial-routes-to-vinyl-chloride-according-to-material-and-energy-efficiency-green-metrics-analysis.pdf
|
67d9d0effa469535b9b684b8
|
10.26434/chemrxiv-2025-tq3bh-v2
|
The Quasi-bound State as a Predictor of Relative Binding Free Energy
|
Relative binding free energy (ΔΔGbind) predictions have become the main approach to evaluate the potency of a congeneric series of compounds. They are enabled by alchemical transformations coupled to free energy methods, tools that have become essential in drug design. Yet, they are computationally expensive and are limited to small and relatively simple transformations. The ever-increasing size of virtual screening databases demands faster methods to assess virtual hits. Here, we show that the structural robustness of protein-ligand complexes, measured as the quasi-bound free energy (ΔGQB) by Dynamic Undocking (DUck), is well suited to detect outliers in the structure-activity continuum (i.e., activity cliffs), which are particularly challenging for knowledge-based approaches. On congeneric series of HSP90α, CDK2 and BACE-1 inhibitors, we demonstrate that ΔGQB can deliver excellent predictions, despite the local nature of the measurement, in some cases, comparable to the much more computationally demanding alchemical transformation methods. We find that for systems following a one-step dissociation model, ΔGQB actually informs about the free energy of the transition state, which allows us to predict relative binding kinetics and, when the series present relatively constant on-rates, also ΔΔGbind.This work has important implicatinos for drug discovery, as it shows that within a well-defined applicability domain, high-throughput computational dissociation studies can deliver ΔΔGbind predictions that compare well with rigorous alchemical transformation methods.
|
Álvaro Serrano-Morrás; Yvonne Westermaier; Maciej Majewski; Xavier Barril
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d9d0effa469535b9b684b8/original/the-quasi-bound-state-as-a-predictor-of-relative-binding-free-energy.pdf
|
63b06d6a963bf37f96ac52bf
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10.26434/chemrxiv-2023-7cl1d
|
Guanine quantum defects in carbon nanotubes for biosensing
|
Fluorescent single wall carbon nanotubes (SWCNTs) are used as nanoscale biosensors in diverse applications. Selectivity is built in by non-covalent functionalization with polymers such as DNA. In general, fluorescence sensing with SWCNTs would benefit from covalent DNA-conjugation but it is not known how changes in conformational flexibility and photophysics affect the sensing mechanism. Recently, covalent functionalization was demonstrated by conjugating guanine bases of adsorbed DNA to the SWCNT surface as guanine quantum defects (g-defects). Here, we create guanine defects in (GT)10 coated SWCNTs (Gd-SWCNTs) and explore how this affects molecular sensing. We vary the defect densities, which shifts the E11 fluorescence emission by 55 nm to max = 1049 nm for the highest defect density. Furthermore, the difference between absorption maximum and emission maximum (Stokes shift) increases with increasing defect density by 0.87 nm per nm of absorption shift and up to 27 nm in total. Gd-SWCNTs represent sensitive sensors and increase their fluorescence >70 % in response to the important neurotransmitter dopamine and decrease 93 % in response to riboflavin. Additionally, cellular uptake of Gd-SWCNTs decreases. These results show how physiochemical properties alter with guanine defects and that Gd-SWCNTs constitute a versatile optical biosensor platform.
|
Phillip Galonska; Jennifer M. Mohr; C. Alexander Schrage; Lena Schnitzler; Sebastian Kruss
|
Physical Chemistry; Nanoscience; Biophysical Chemistry; Interfaces; Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2023-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b06d6a963bf37f96ac52bf/original/guanine-quantum-defects-in-carbon-nanotubes-for-biosensing.pdf
|
60c746c3469df4839ef436ed
|
10.26434/chemrxiv.8148623.v2
|
Mechanisms of Two-Electron and Four-Electron Electrochemical Oxygen Reduction Reactions at Nitrogen-Doped Reduced Graphene Oxide
|
Doped carbon-based systems have been extensively studied over the past decade as active electrocatalysts for both the two-electron (2e-) and four-electron (4e-) oxygen reduction reaction (ORR). However, the mechanisms for ORR are generally poorly understood. Here we report an extensive experimental and first-principles theoretical study of the ORR at nitrogen-doped reduced graphene oxides (NrGO). We synthesize three distinct NrGO catalysts and investigate their chemical and structural properties in detail via X-ray photoelectron spectroscopy, infrared and Raman spectroscopy, high-resolution transmission electron microscopy and thin-film electrical conductivity. ORR experiments include the pH dependences of 2e- versus 4e- ORR selectivity, ORR onset potentials, Tafel slopes and H/D kinetic isotope effects. These experiments show very different ORR behavior for the three catalysts, both in terms of selectivity and the underlying mechanism which proceeds either via coupled proton-electron transfers (CPETs) or non-CPETs. Reasonable structural models developed from DFT rationalize this behavior. The key determinant between CPET vs. non-CPET mechanisms is the electron density at the Fermi level under operating ORR conditions. Regardless of the reaction mechanism or electrolyte pH, however, we identify the ORR active sites as sp2 carbons that are located next to oxide regions. This assignment highlights the importance of oxygen functional groups, while details of (modest) N-doping may still affect the overall catalytic activity, and likely also the selectivity, by modifying the general chemical environment around the active site.
|
Hyo Won Kim; Vanessa Jane Bukas; Hun Park; Sojung Park; Kyle M. Diederichsen; Jinkyu Lim; Young Hoon Cho; Juyoung Kim; Wooyul Kim; Tae Hee Han; Johannes Voss; Alan C. Luntz; Bryan D. McCloskey
|
Physical Organic Chemistry; Carbon-based Materials; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c3469df4839ef436ed/original/mechanisms-of-two-electron-and-four-electron-electrochemical-oxygen-reduction-reactions-at-nitrogen-doped-reduced-graphene-oxide.pdf
|
60c748ce702a9bd93c18b057
|
10.26434/chemrxiv.11977887.v1
|
Melting Temperature Measurement and Mesoscopic Evaluation of Single, Double and Triple DNA Mismatches
|
Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bondings and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combination of canonical base pairs in the same location under the same conditions. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches.
|
Luciana M. Oliveira; Adam S. Long; Tom Brown; Keith R. Fox; Gerald Weber
|
Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748ce702a9bd93c18b057/original/melting-temperature-measurement-and-mesoscopic-evaluation-of-single-double-and-triple-dna-mismatches.pdf
|
64b6ce6dae3d1a7b0dee2707
|
10.26434/chemrxiv-2023-w152b
|
Serine-404 Phosphorylation and the R406W Modification in Tau Stabilize the cis-Proline Amide Bond, via Phosphoserine-Proline C–H/O and Proline-Aromatic C–H/π Interactions
|
Tau misfolding, oligomerization, and aggregation are central to the pathology of Alzheimer's disease (AD), chronic traumatic encephalopathy (CTE), frontotemporal dementia, and other tauopathies. Increased phosphorylation of tau is associated with conformational changes that are not fully understood. Moreover, tau oligomerization and aggregation are associated with proline cis-trans isomerism, with the phosphorylation-dependent prolyl isomerase Pin1 reducing tau hyperphosphorylation and aggregation. The FTDP-17 tau mutation R406W is frequently used in animal models of Alzheimer's disease, due to earlier onset of the AD phenotype. Despite its extensive application, the mechanisms by which tau-R406W leads to enhanced aggregation and neurotoxicity are poorly understood. Peptides derived from the tau C-terminal domain were examined by NMR spectroscopy as a function of residue 406 identity (Arg versus Trp) and Ser404 phosphorylation state. The R406W modification led to an increased population of Pro405 cis amide bond, which is stabilized by cis-proline-aromatic C–H/π interactions. Ser404 phosphorylation also resulted in an increase in cis amide bond, via a proposed C–H/O interaction between the Pro Hα and the phosphate that stabilizes the cis conformation. An analogous C–H/O interaction was observed in Glu-cis-Pro sequences in the PDB, and is proposed to be the basis of the increased propensity for cis amide bonds in Glu-Pro sequences. The higher activation barriers for proline cis-trans isomerization observed at pSer-Pro and pThr-Pro sequences are proposed to be due to both (a) an intraresidue phosphate-amide bond that stabilizes the trans-proline conformation and (b) the cis-stabilizing proline-phosphate C–H/O interaction identified herein. The combination of both pSer404 and R406W resulted in a further increase in the population of cis amide bond. In contrast to expectations, the R406W modification led to increased dephosphorylation of either pSer404 or pSer409 by PP2A, and had no effect on phosphorylation of Ser404 by cdk5, suggesting that R406W does not inherently increase Ser404 phosphorylation via changes in the actions of these enzymes. Modestly increased phosphorylation of Ser404 was observed by GSK-3β in tau R406W. Collectively, these data suggest a potential role for conformational change to a cis amide bond at Pro405, via Ser404 phosphorylation and/or R406W modification, as a possible mechanism involved in protein misfolding in AD, CTE, and FTDP-17. Alternatively, both Ser404 phosphorylation and the R406W modification lead to increased order, including induced turn formation, in both the trans-proline and cis-proline conformations.
|
Himal K. Ganguly; Michael B. Elbaum; Neal J. Zondlo
|
Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Bioinformatics and Computational Biology; Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b6ce6dae3d1a7b0dee2707/original/serine-404-phosphorylation-and-the-r406w-modification-in-tau-stabilize-the-cis-proline-amide-bond-via-phosphoserine-proline-c-h-o-and-proline-aromatic-c-h-interactions.pdf
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60c749de842e65275ddb2e24
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10.26434/chemrxiv.12117024.v1
|
Coexistence of Förster and Dexter Energy Transfer Pathways from an Antenna Ligand to Lanthanide Ion in Trivalent Europium Complexes through Phosphine-Oxide Bridges
|
<br />Trivalent europium (Eu3+) complexes are attractive materials for luminescence applications if energy transfer from antenna ligands to the lanthanide ion is efficient. However, the microscopic mechanisms of the transfer remain elusive and fundamental physical chemistry questions still require answers. We track the energy transfer processes in a luminescent complex Eu(hfa)3(DPPTO)2 (hfa: hexafluoroacetylacetonate, DPPTO: 2-diphenylphosphoryltriphenylene) using time-resolved photoluminescence spectroscopy. In addition to the conventional Dexter-type energy transfer pathway through the T1 state of the ligands, we discovered the Forster energy transfer pathway from the S1 of the DPPTO ligands to the 5D1 state of Eu3+ through the weak electronic interaction of a phosphine-oxide bridge. The short timescale of the energy transfer (16 ns, 127 ns) results in its high quantum yield. The coexistence of the distinct energy transfer pathways from a single chromophore is important for establishing design strategies of luminescent complexes. <br />
|
Shiori Miyazaki; Kiyoshi Miyata; Haruna Sakamoto; Fumiya Suzue; Yuichi Kitagawa; Yasuchika Hasegawa; Ken Onda
|
Lanthanides and Actinides; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749de842e65275ddb2e24/original/coexistence-of-forster-and-dexter-energy-transfer-pathways-from-an-antenna-ligand-to-lanthanide-ion-in-trivalent-europium-complexes-through-phosphine-oxide-bridges.pdf
|
64697af5fb40f6b3eeea55bb
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10.26434/chemrxiv-2023-prmwp
|
Defect Control Strategies for Al(1-x)Gd(x)N Alloys
|
Tetrahedrally-bonded III-N and related alloys are useful for a wide range of applications, from optoelectronics to dielectric electromechanics. Heterostructural AlN-based alloys offer unique properties for piezoelectrics, ferroelectrics, and other emerging applications. Atomic-scale point defects and impurities can strongly affect the functional properties of materials, and therefore, it is crucial to understand the nature of these defects and mechanisms through which their concentrations may be controlled in AlN-based alloys. In this study, we employ density functional theory with alloy modeling and point defect calculations to investigate native point defects and unintentional impurities in Al(1-x)Gd(x)N alloys. Among the native defects that introduce deep mid-gap states, nitrogen vacancies (V_N) are predicted to be in the highest concentration, especially under N-poor growth conditions. We predict and experimentally demonstrate that V_N formation can be suppressed in thin films through growth in N-rich environments. We also find that Al(1-x)Gd(x)N alloys are prone to high levels of unintentional O incorporation, which indirectly leads to even higher concentrations of deep defects. Growth under N-rich/reducing conditions is predicted to minimize and partially alleviate the effects of O incorporation. The results of this study provide valuable insights into the defect behavior in wurtzite nitride-based alloys, which can guide their design and optimization for various applications.
|
Naseem Ud Din; Cheng-Wei Lee; Keisuke Yazawa; William Nemeth; Rebecca W. Smaha; Nancy M. Haegel; Prashun Gorai
|
Materials Science; Inorganic Chemistry; Alloys; Ceramics; Theory - Inorganic; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64697af5fb40f6b3eeea55bb/original/defect-control-strategies-for-al-1-x-gd-x-n-alloys.pdf
|
60c7426b842e651e64db207c
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10.26434/chemrxiv.8279609.v1
|
Enumeration of de novo Inorganic Complexes for Chemical Discovery and Machine Learning
|
<p>Despite being attractive targets for functional materials, the discovery of transition metal complexes with high-throughput computational screening is challenged by the amount of feasible coordination numbers, spin states, or oxidation states and the potentially large sizes of ligands. To overcome these limitations, we take inspiration from organic chemistry where full enumeration of neutral, closed shell molecules under the constraint of size has enriched discovery efforts. We design monodentate and bidentate ligands from scratch for the construction of mononuclear, octahedral transition metal complexes with up to 13 heavy atoms (i.e., metal, C, N, O, P, or S). From > 11,000 theoretical ligands, we develop a heuristic score for ranking a chemically feasible 2,500 ligand subset, only 71 of which were previously included in common organic molecule databases. We characterize the top 20% of scored ligands with density functional theory (DFT) in an octahedral homoleptic ligand database (OHLDB). The OHLDB contains i) the geometry optimized structures of 1,250 homoleptic octahedral complexes obtained from the enumerated pool of ligands and an open-shell transition metal (M(II)/M(III), M = Cr, Mn, Fe, or Co), and ii) the resulting high-spin/low-spin adiabatic electronic energies (<b>Δ</b><i>E</i><sub>H-L</sub>) obtained with hybrid DFT. Over the OHLDB, we observe structure–property (i.e., <b>Δ</b><i>E</i><sub>H-L</sub>) relationships different from those expected on the basis of ligand field arguments or from our prior data sets. Finally, we demonstrate how incorporating OHLDB data into artificial neural network (ANN) training improves ANN out-of-sample performance on much larger transition metal complexes.</p>
|
Stefan Gugler; Jon Paul Janet; Heather Kulik
|
Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426b842e651e64db207c/original/enumeration-of-de-novo-inorganic-complexes-for-chemical-discovery-and-machine-learning.pdf
|
60c7538af96a003baf288491
|
10.26434/chemrxiv.13168139.v2
|
Polymer Cyclization as a General Strategy for the Emergence of Hierarchical Nanostructures
|
The creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here wedemonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike structures and higher-ordered networks. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.
|
Chaojian Chen; Manjesh Kumar Singh; Katrin Wunderlich; Sean Harvey; Manfred Wagner; George Fytas; Kurt Kremer; Debashish Mukherji; David Yuen Wah Ng; Tanja Weil
|
Nanostructured Materials - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7538af96a003baf288491/original/polymer-cyclization-as-a-general-strategy-for-the-emergence-of-hierarchical-nanostructures.pdf
|
64544b051ca6101a45cbb398
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10.26434/chemrxiv-2023-v9vsf
|
Hydrogen sulfide-releasing nanocascade templated by glucose oxidase for diabetic infection treatment
|
Diabetic ulcer receives much attention in recent years due to its high incidence and mortality, promoting the scientific community to develop various strategies for such chronic disease treatments. However, the therapeutic outcome of these approaches is highly compromised by the invasive bacteria and severe inflammatory ulcer microenvironment. To overcome these dilemmas, microenvironment-responsive self-delivery GOx@MnS nanoparticles (NPs) are developed by a one-step biomineralization. When encountered with high glucose level in the ulcer site, GOx catalyze glucose to decrease the local pH and trigger the steady release of both manganese ions (Mn2+) and hydrogen sulfide (H2S). Mn2+ react with hydrogen peroxide to generate hydroxyl radical for the elimination of bacterial infection, meanwhile H2S is able to suppress the inflammatory response and accelerate diabetic wound healing through macrophage polarization. The excellent biocompatibility, strong bactericidal activity, and considerable immunomodulatory effect promise GOx@MnS NPs great therapeutic potential for diabetic wound treatment.
|
Yuxuan Ge; Fan Rong; Yujia Lu; Zixin Wang; Jinyu Liu; Junsheng Chen; Wei Li; Yin Wang
|
Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64544b051ca6101a45cbb398/original/hydrogen-sulfide-releasing-nanocascade-templated-by-glucose-oxidase-for-diabetic-infection-treatment.pdf
|
60c74224bb8c1aec713da068
|
10.26434/chemrxiv.8216060.v1
|
Multi-Target Dopamine D3 Receptor Modulators: Actionable Knowledge for Drug Design from Molecular Dynamics and Machine Learning
|
Building on our previously reported studies on the combination of molecular dynamics and machine learning (Decherchi et al., Nature Comm 2015; Decherchi et al., JCIM 2018), we applied a combination of these techniques to identify the structural determinants causing efficacy cliffs at the D3 receptor in a small series of previously reported multi-target compounds.<br />
|
Mariarosaria Ferraro; Sergio Decherchi; Alessio De Simone; Maurizio Recanatini; Andrea Cavalli; Giovanni Bottegoni
|
Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74224bb8c1aec713da068/original/multi-target-dopamine-d3-receptor-modulators-actionable-knowledge-for-drug-design-from-molecular-dynamics-and-machine-learning.pdf
|
60c74ae8bdbb892b29a39477
|
10.26434/chemrxiv.12271847.v1
|
Molecular Embroidering of Graphene
|
In the present work, we developed
for the first time a practical approach to achieve multiply pattterning of graphene in a way of “molecular
graphene embroidery” (as analogy to the well-known fabric embroidery existing
in macroscopic world) by manipulating the graphene chemistry to generate
regular multiply functionalized patterns consisting of concentric regions of
covalent addend binding. Molecular graphene embroidery towards these spatially
resolved 2D-hetero-architectures was accomplished by repetitive electron-beam
lithography (EBL)/reduction/covalent-binding sequences starting with polymethyl
methacrylate (PMMA) covered graphene deposited on a reactive SiO<sub>2</sub>/Si
substrate, a key factor for strain-free antaratopic additions.<br />
|
Tao Wei; Malte Kohring; Heiko B. Weber; Frank Hauke; Andreas Hirsch
|
Carbon-based Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae8bdbb892b29a39477/original/molecular-embroidering-of-graphene.pdf
|
65ccb5d8e9ebbb4db9580550
|
10.26434/chemrxiv-2024-11wql
|
N-Heterocyclic carbene-catalyzed SuFEx reactions of functionalized secondary alcohols
|
An organocatalytic Sulfur (VI)-fluoride exchange (SuFEx) reaction of secondary alcohols is reported. Under the catalysis of 10 mol% NHC/MS 4Å, both trifluoromethyl and difluoromethyl benzyl alcohols reacted with aryl sulfonyl fluorides to produce the corresponding sulfonates in moderate to high yields.
|
Zhihang Wei; Muze Lin; Yu Xie; Zhihua Cai; Lin He; Guangfen Du
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ccb5d8e9ebbb4db9580550/original/n-heterocyclic-carbene-catalyzed-su-f-ex-reactions-of-functionalized-secondary-alcohols.pdf
|
67205bd61fb27ce124e57918
|
10.26434/chemrxiv-2024-1zl02
|
Noise Analysis and Data Refinement for Chemical Reactions from US Patents via Large Language Models
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The extraction of chemical reactions from U.S. Patent and Trademark Office (USPTO) documents has enabled significant advancements in machine learning models for organic synthesis. While the USPTO dataset offers a large and diverse collection of reaction data, recent studies have identified issues such as inconsistent or missing chemical entries, impacting data quality. To address these challenges, we employed fine-tuned large language models (LLMs) to revisit experimental sections in the US patents, performing a comprehensive analysis of noisy reaction data. Our findings demonstrate that LLMs produce fewer false reactions compared to existing datasets and reveal that many reactions in US patents involve multiple experimental steps, previously overlooked by standard extraction methods. Our analysis suggests that untraceable references and erroneous chemical names are primary sources of data noise. We also identify reaction types with high susceptibility to these issues, recommending scientists avoid using those high-risk reaction data.
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Chaewon Lee; Shuan Chen; Kai Tzu-iunn Ong; Jinyoung Yeo; Yousung Jung
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Theoretical and Computational Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2024-10-30
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67205bd61fb27ce124e57918/original/noise-analysis-and-data-refinement-for-chemical-reactions-from-us-patents-via-large-language-models.pdf
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60c74d36bdbb895058a39940
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10.26434/chemrxiv.12600443.v1
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Fast and Automatic Estimation of Transition State Structures Using Tight Binding Quantum Chemical Calculations
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We present a method for the automatic determination of transition states (TSs) that is based on Grimme’s RMSD-PP semiempirical tight binding reaction path method (<i>J. Chem. Theory Comput.</i> 2019, 15, 2847-2862), where the maximum energy structure along the path serves as an initial guess for DFT TS searches. The method is tested on 100 elementary reactions and located a total of 89 TSs correctly. Of the 11 remaining reactions, nine are shown not to be elementary reaction after all and for one of the two true failures the problem is shown to be the semiempirical tight binding model itself. Furthermore, we show that the RMSD-PP barrier is a good approximation for the corresponding DFT barrier for reactions with DFT barrier heights up to about 30 kcal/mol. Thus, RMSD-PP barrier heights, which can be estimated at the cost of a single energy minimisation, can be used to quickly identify reactions with low barriers, although it will also produce some false positives.
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Maria Harris Rasmussen; Jan H. Jensen
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Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
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2020-07-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d36bdbb895058a39940/original/fast-and-automatic-estimation-of-transition-state-structures-using-tight-binding-quantum-chemical-calculations.pdf
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660edfac91aefa6ce1cc3940
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10.26434/chemrxiv-2024-9fdqn
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Exploiting Photoredox Catalysis for Rapid Access to Unnatural α-Amino Acids through α-Amino C–H Bond Activation
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Unnatural amino acids (UAAs) have shown great potential to enhance the pharmacological properties of peptides and represent a key motif in a wide range of biologically relevant natural products. Herein, we disclose a protocol that facilitates the asymmetric synthesis of UAAs from widely abundant amines through photoredox-mediated α-amino C–H bond activation. The platform utilizes either the strongly oxidizing organic acridinium or decatungstate as a photocatalyst to generate α-amino radicals from a variety of amines, which are then effectively coupled with a chiral glyoxylate-derived N-sulfinyl imine. The disclosed platform provides a general entry to various decorated unnatural α-amino acid derivatives, accommodating a diverse array of functional groups.
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Gregory R. Alvey; Andrey Shatskiy; Elena V. Stepanova; Lucas Kusch; Moritz Schepp; Till Kalkuhl; Marco Bormetti; Chang Ho Lee; Ludwig Wåhlin; Markus D. Kärkäs
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Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.); Redox Catalysis
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CC BY 4.0
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CHEMRXIV
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2024-04-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660edfac91aefa6ce1cc3940/original/exploiting-photoredox-catalysis-for-rapid-access-to-unnatural-amino-acids-through-amino-c-h-bond-activation.pdf
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64b4dcb3b053dad33a63b7d9
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10.26434/chemrxiv-2023-3z3gc
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New insight into the electrochemical CO2 reduction reaction: radical reactions may govern the whole process
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In present paper, we wish to suggest a reaction mechanism for the electrochemical reduction of carbon dioxide. This mechanism can provide a reasonable interpretation to the formation of widely range of products on copper catalyst.
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Youyi Sun
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Catalysis; Electrocatalysis; Heterogeneous Catalysis
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CC BY 4.0
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CHEMRXIV
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2023-09-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b4dcb3b053dad33a63b7d9/original/new-insight-into-the-electrochemical-co2-reduction-reaction-radical-reactions-may-govern-the-whole-process.pdf
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