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65a03d069138d23161b5eb10
|
10.26434/chemrxiv-2024-3w0nc
|
A Spanish Chemoinformatics GitBook for Chemical Data retrieval and Analysis using Python Programming
|
Searching, retrieving, and analyzing chemical information is one of the main tasks faced by students and professionals in chemistry-related scientific disciplines. Currently, freely available modules developed in programming languages, such as Python, allow efficient data management and facilitate obtaining information and knowledge from the data. This manuscript describes an electronic handbook generated on the GitBook platform to introduce the Python programming language and the Analysis, computational representation, and visualization of chemical data. This manual explores the most common molecular representations of low molecular weight organic compounds and their applications in various contexts. It also illustrates the acquisition of chemical information from large public molecular databases such as ChEMBL and PubChem and the Analysis and visualization of chemical information using concepts such as chemical space. The GitBook is freely available and is expected to foster open science and facilitate learning for chemistry students at the undergraduate and graduate levels and professionals interested in chemical data analysis and visualization.
|
Fernanda I. Saldívar-González; Diana L. Prado-Romero; B. Raziel Cedillo-González; Ana L. Chávez-Hernández; Juan F. Avellaneda-Tamayo; Alejandro Gómez-García; Luis Juárez-Rivera; José L. Medina-Franco
|
Theoretical and Computational Chemistry; Chemical Education; Chemical Education - General; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a03d069138d23161b5eb10/original/a-spanish-chemoinformatics-git-book-for-chemical-data-retrieval-and-analysis-using-python-programming.pdf
|
67c5a47b6dde43c9084acebc
|
10.26434/chemrxiv-2025-8p9j3
|
Roles of Sixth Bound Copper in Reductive Inactivation of Copper Efflux Oxidase
|
Copper efflux oxidase (CueO) is involved in copper homeostasis in Escherichia coli by catalyzing the oxidation of cuprous ion (Cu+) to cupric ion (Cu2+). CueO has been studied as a direct electron transfer (DET)-type bioelectrocatalyst owing to its high dioxygen-reducing activity. Our previous study demonstrated reductive inactivation in the DET-type bioelectrocatalysis of CueO in the presence of Cu2+, which was known to facilitate substrate oxidation in solution. Considering the structural data, we hypothesized that sixth-bound copper (Cu6) induced reductive inactivation. CueO variants deleting putative Cu6 ligands (His145, His406, and Met417) were characterized bioelectrochemically. As expected, the reductive inactivation was significantly suppressed in H145A while slightly suppressed in H406A variants. In contrast, Cu2+ tolerance was slightly decreased in the M417A variant. These results indicate that His145 and His406 are the major and minor ligands of Cu6 that induce reductive inactivation, respectively, whereas Met417 might contribute to stabilizing the Cu6 coordination sphere. Furthermore, kinetic analysis of chronoamperograms representing the time-dependent Cu2+ response revealed that the deletion of Cu6 ligands affected both the binding and redox kinetics of the enzyme-substrate-copper complex. Additionally, Cu6-induced inactivation was observed using an enzymatic assay in solution for the oxidation of 1,1′-ferrocenedimethanol. Therefore, reductive inactivation likely occurs in concert with biological Cu+ oxidation, which may contribute to the regulation of the Cu2+/Cu+ ratio.
|
Taiki Adachi; Toshitada Takei; Takumi Nishiyama; Kenji Kano; Satoshi Yamashita; Kunishige Kataoka; Keisei Sowa
|
Catalysis; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c5a47b6dde43c9084acebc/original/roles-of-sixth-bound-copper-in-reductive-inactivation-of-copper-efflux-oxidase.pdf
|
664ab481418a5379b0c270e0
|
10.26434/chemrxiv-2024-z7mgb
|
Mapping lipid C=C isomer profiles of human gut bacteria by a novel structural lipidomics workflow assisted by chemical epoxidation
|
The unsaturated lipids produced by human gut bacteria exhibit extraordinary structural diversity, largely attributed to the isomerism of the carbon-carbon double bond (C=C) in terms of position and stereochemistry. Characterizing these distinct C=C configurations poses a significant challenge in the research field, primarily due to limitations in current bioanalytical methodologies. In this study, we developed a novel structural lipidomic workflow by integrating an epoxidation protocol using meta-chloroperoxybenzoic acid for C=C derivatization and liquid chromatography-tandem mass spectrometry for C=C characterization. We utilized this workflow to quantitatively assess over 50 C=C positional and cis/trans isomers of fatty acids and phospholipids from selected human gut bacteria. The strain-specific isomer profiles revealed unexpected and remarkable productivity of trans-10-octadecenoic acid by Enterococcus faecalis, Bifidobacterium longum, and Lacto-bacillus acidophilus, among numerous other trans fatty acid isomers produced by gut bacteria. Isotope-tracking experiments suggest that gut bacteria produce trans-10-octadecenoic acid through isomeric biotransformation of oleic acid in vitro and that such isomeric biotransformation of dietary oleic acid is dependent on the presence of gut bacteria in vivo.
|
Kai-Li Chen; Ting-Hao Kuo; Cheng-Chih Hsu
|
Analytical Chemistry; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664ab481418a5379b0c270e0/original/mapping-lipid-c-c-isomer-profiles-of-human-gut-bacteria-by-a-novel-structural-lipidomics-workflow-assisted-by-chemical-epoxidation.pdf
|
60c740eb702a9b200e18a196
|
10.26434/chemrxiv.7886165.v1
|
Hidden Bias in the DUD-E Dataset Leads to Misleading Performance of Deep Learning in Structure-Based Virtual Screening
|
<p>Recently much effort has been invested in using convolutional neural
network (CNN) models trained on 3D structural images of protein-ligand
complexes to distinguish binding from non-binding ligands for virtual screening.
However, the dearth of reliable protein-ligand x-ray structures and binding affinity
data has required the use of constructed datasets for the training and
evaluation of CNN molecular recognition models. Here, we outline various
sources of bias in one such widely-used dataset, the Directory of Useful
Decoys: Enhanced (DUD-E). We have constructed and performed tests to
investigate whether CNN models developed using DUD-E are properly learning the
underlying physics of molecular recognition, as intended, or are instead
learning biases inherent in the dataset itself. We find that superior
enrichment efficiency in CNN models can be attributed to the analogue and decoy
bias hidden in the DUD-E dataset rather than successful generalization of the
pattern of protein-ligand interactions. Comparing additional deep learning
models trained on PDBbind datasets, we found that their enrichment performances
using DUD-E are not superior to the performance of the docking program AutoDock
Vina. Together, these results suggest that biases that could be present in
constructed datasets should be thoroughly evaluated before applying them to
machine learning based methodology development. </p>
|
Lieyang Chen; Anthony Cruz; Steven Ramsey; Callum
J. Dickson; José S. Duca; Viktor Hornak; David R. Koes; Tom Kurtzman
|
Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-03-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740eb702a9b200e18a196/original/hidden-bias-in-the-dud-e-dataset-leads-to-misleading-performance-of-deep-learning-in-structure-based-virtual-screening.pdf
|
60c7483a337d6c77e6e274e6
|
10.26434/chemrxiv.11862669.v1
|
Reactions of PhIX2 I(III) Oxidants with Heavy Triphenyl Pnictines
|
The reactions of [PhI(pyridine)2]2+, PhI(OAc)2 and PhI(OTf)(OAc) with Ph3As, Ph3Sb and Ph3Bi are described. The reactions of [PhI(pyridine)2]2+ with Ph3Sb and Ph3Bi affords dicationic Pn(V) complexes ligated by pyridine in one step. These were previously reported by Burford in multi step syntheses. Reactions with PhI(OAc)2, which were already known for Sb and Bi giving Pn(V) diacetates, was confirmed to give the same type of compound for As. Reactions with <br />PhI(OAc)(OTf) were less clean, resulting in the isolation of iodonium cations [Ph-I-Ph]+ for As and Bi, while Ph3Sb gave an oxobridged di-antimony species characteristic of the decomposition of a high valent triflate bound species.
|
Sathsara Egalahewa; Antonino Aprile; Jason Dutton
|
Main Group Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7483a337d6c77e6e274e6/original/reactions-of-ph-ix2-i-iii-oxidants-with-heavy-triphenyl-pnictines.pdf
|
63875fe7c5675373bc9c4c7b
|
10.26434/chemrxiv-2022-2r6d5
|
Breaking bonds and breaking rules: [(iPr3P)Ni]5H4 as the key intermediate in cooperative C-H activation and carbon atom abstraction from alkenes and catalytic stereospecific dimerization of norbornene
|
The facile carbon atom abstraction reaction by [(iPr3P)Ni]5H6 (1) with various terminal alkenes to give [(iPr3P)Ni]5H4(μ5-C) (2) occurs via a common highly reactive intermediate [(iPr3P)Ni]5H4 (3), which was isolated by the reaction of 1 with norbornene. Temperature dependent 1H and 31P{1H} NMR chemical shifts of 3 are consistent with a thermally populated triplet excited state only 2 kcal·mol–1 higher energy than the diamagnetic ground state. Complex 3 catalyzes the dimerization of norbornene to stereoselectively provide exclusively (Z) anti-(bis-2,2'-norbornylidene).
|
Junyang Liu; Manar Shoshani; Kethya Sum; Samuel Johnson
|
Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bond Activation; Catalysis; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63875fe7c5675373bc9c4c7b/original/breaking-bonds-and-breaking-rules-i-pr3p-ni-5h4-as-the-key-intermediate-in-cooperative-c-h-activation-and-carbon-atom-abstraction-from-alkenes-and-catalytic-stereospecific-dimerization-of-norbornene.pdf
|
6761091481d2151a02fe55ef
|
10.26434/chemrxiv-2024-lhlmt
|
Machine-Learning-Driven Exploration of Surface Reconstructions of Reduced Rutile TiO2
|
Titanium dioxide (TiO2) is widely used as catalyst support due to its stability, tunable electronic properties, and surface oxygen vacancies, which are crucial for catalytic processes such as the reverse water-gas shift (RWGS) reaction. Reduced TiO2 surfaces undergo complex surface reconstructions that endow unique properties, but are computationally challenging to describe. In this study, we utilize machine-learning interatomic potentials (MLIPs) integrated with an active-learning workflow to efficiently explore reduced rutile TiO2 surfaces. This approach enabled the prediction of a phase diagram as a function of oxygen chemical potential, revealing a variety of reconstructed phases, including a previously unreported subsurface shear plane structure. We further investigate the electronic properties of these surfaces and validate our results experimentally. To illustrate their catalytic implications, we examined the behavior of Rh single atoms on the reconstructed surfaces, focusing on CO2 activation, the rate-limiting step in the RWGS reaction. Our findings provide new insights into how extreme surface reductions influence the structural and electronic properties of TiO2, with potential implications for catalyst design.
|
Yonghyuk Lee; Xiaobo Chen; Sabrina Gericke; Meng Li; Dmitri Zakharov; Ashley Head; Judith Yang; Anastassia Alexandrova
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6761091481d2151a02fe55ef/original/machine-learning-driven-exploration-of-surface-reconstructions-of-reduced-rutile-ti-o2.pdf
|
6709954dcec5d6c142e3db7b
|
10.26434/chemrxiv-2024-cfkj4
|
Determination of stable proton configurations by black-box optimization using an Ising machine
|
Stable proton configurations in solid-state materials are a prerequisite for the theoretical microscopic investigation of solid-state proton-conductive materials. However, a large number of initial atomistic configurations should be considered to find stable proton configurations, and relaxation calculations using the density functional theory approach are required for each initial configuration. Consequently, the determination of stable configurations is a difficult and time-consuming task. Furthermore, when the size of the simulation cells or the number of doped atoms increases, the number of initial configurations leads to a combinatorial explosion, rendering the computation infeasible. In this study, black-box optimization was combined with an Ising machine and density functional calculations to perform an efficient search for stable proton configurations. Scandium-doped barium zirconate, a typical high-proton conductive oxide, was selected as the model system. The Ising machine was able to rapidly select the initial atomistic configuration, ultimately leading to stable proton configurations after subsequent relaxation calculations. This optimization strategy should be able to solve various issues related to configuration optimization in solid-state materials, thereby promoting novel scientific discoveries.
|
Jianbo Lin; Tomofumi Tada; Ai Koizumi; Masato Sumita; Koji Tsuda; Ryo Tamura
|
Materials Science
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6709954dcec5d6c142e3db7b/original/determination-of-stable-proton-configurations-by-black-box-optimization-using-an-ising-machine.pdf
|
60c747ae4c8919c607ad2d8a
|
10.26434/chemrxiv.11763792.v1
|
Influence of Network Topology on the Viscoelastic Properties of Dynamically Crosslinked Hydrogels
|
Biological materials combine stress relaxation and self-healing with non-linear stress-strain responses. These characteristic features are a direct result of hierarchical self-assembly, which often results in fiber-like architectures. Even though structural knowledge is rapidly increasing, it has remained a challenge to establish relationships between microscopic and macroscopic structure and function. Here, we focus on understanding how network topology determines the viscoelastic properties, i.e. stress relaxation, of biomimetic hydrogels. We have dynamically crosslinked two different synthetic polymers with one and the same crosslink. The first polymer, a polyisocyanopeptide (PIC), self-assembles into semi-flexible, fiber-like bundles and thus displays stress-stiffening, similar to many biopolymer networks. The second polymer, 4-arm poly(ethylene glycol) (starPEG), serves as a reference network with well-characterized structural and viscoelastic properties. Using one and the same coiled coil crosslink allows us to decouple the effects of crosslink kinetics and network topology on the stress relaxation behavior of the resulting hydrogel networks. We show that the fiber-containing PIC network displays a relaxation time approximately two orders of magnitude slower than the starPEG network. This reveals that crosslink kinetics is not the only determinant for stress relaxation. Instead, we propose that the different network topologies determine the ability of elastically active network chains to relax stress. In the starPEG network, each elastically active chain contains exactly one crosslink. In the absence of entanglements, crosslink dissociation thus relaxes the entire chain. In contrast, each polymer is crosslinked to the fiber bundle in multiple positions in the PIC hydrogel. The dissociation of a single crosslink is thus not sufficient for chain relaxation. This suggests that tuning the number of crosslinks per elastically active chain in combination with crosslink kinetics is a powerful design principle for tuning stress relaxation in polymeric materials. The presence of a higher number of crosslinks per elastically active chain thus yields materials with a slow macroscopic relaxation time but fast dynamics at the microscopic level. Using this principle for the design of synthetic cell culture matrices will yield materials with excellent long-term stability combined with the ability to locally reorganize, thus facilitating cell motility, spreading and growth.
|
Emilia M. Grad; Isabell Tunn; Dion Voerman; Alberto S. de Léon; Roel Hammink; Kerstin Blank
|
Hydrogels
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747ae4c8919c607ad2d8a/original/influence-of-network-topology-on-the-viscoelastic-properties-of-dynamically-crosslinked-hydrogels.pdf
|
6593cb949138d2316101090e
|
10.26434/chemrxiv-2024-kdx3g
|
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition
|
Stakeholders of machine learning models desire explainable artificial intelligence (XAI) to produce human-understandable and consistent interpretations. In computational toxicity, augmentation of text-based molecular representations has been used successfully for transfer learning on downstream tasks. Augmentations of molecular representations can also be used at inference to compare differences between multiple representations of the same ground-truth. In this study, we investigate the robustness of eight XAI methods using test-time augmentation for a molecular-representation model in the field of computational toxicity prediction. We report significant differences between explanations for different representations of the same ground-truth, and show that randomized models have similar variance. We hypothesize that text-based molecular representations in this and past research reflect tokenization more than learned parameters. Furthermore, we see a greater variance between in-domain predictions than out-of-domain predictions, indicating XAI measures something other than learned parameters. Finally, we investigate the relative importance given to expert-derived structural alerts and find similar importance given irregardless of applicability domain, randomization and varying training procedures. We therefore caution future research to validate their methods using a similar comparison to human intuition without further investigation.
|
Peter B. R. Hartog; Fabian Krüger; Samuel Genheden; Igor V. Tetko
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6593cb949138d2316101090e/original/using-test-time-augmentation-to-investigate-explainable-ai-inconsistencies-between-method-model-and-human-intuition.pdf
|
60c73d8df96a003844285da3
|
10.26434/chemrxiv.5497099.v2
|
Junction potentials bias measurements of ion exchange membrane permselectivity
|
<div>Ion exchange membranes (IEMs) are versatile materials relevant to a variety of water and waste treatment, energy production, and industrial separation processes. The defining characteristic of IEMs is their ability to selectively allow positive or negative ions to permeate, which is referred to as the permselectivity. Measured values of permselectivity that equal unity (corresponding to a perfectly-selective membrane) or exceed unity (theoretically impossible) have been reported for cation exchange membranes (CEMs). Such non-physical results call into question our ability to correctly measure this crucial membrane property. Since weighing errors, temperature, and measurement uncertainty have been shown to not explain these anomalous permselectivity results, we hypothesized that a possible explanation are junction potentials that occur at the tips </div><div>of reference electrodes. In this work, we tested this hypothesis by comparing permselectivity values obtained from bare Ag/AgCl wire electrodes (which have no junction) to values obtained from single-junction reference electrodes containing two different electrolytes. We show that permselectivity values obtained using reference electrodes with junctions were greater than unity for CEMs. By contrast, electrodes without junctions always produced permselectivities lower than unity. Electrodes with junctions also resulted in artificially low permselectivity values for AEMs compared to electrodes without junctions. Thus, we conclude that junctions in reference electrodes introduce two biases into results in the IEM literature: (i) permselectivity values larger than unity for CEMs, and (ii) lower permselectivity values for AEMs compared to those for CEMs. These biases can be avoided by using electrodes without a junction. </div>
|
Ryan Kingsbury; Sophie Flotron; Shan Zhu; Douglas F. Call; Orlando Coronell
|
Transport Phenomena (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-10-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d8df96a003844285da3/original/junction-potentials-bias-measurements-of-ion-exchange-membrane-permselectivity.pdf
|
651a483f0065940912440d61
|
10.26434/chemrxiv-2023-zn0qw
|
Intersystem Crossing as Vibronically-Induced Phonon Emission and Absorption Processes: A Unified View of Nonradiative Transitions in a Molecule
|
An analytical expression for the nonradiative rate constant is derived based on Fermi's golden rule within the mixed-spin crude adiabatic (CA) approximation. The mixed-spin CA basis is defined by a set of eigenstates for the electronic Hamiltonian that comprises the nonrelativistic electronic Hamiltonian and spin-orbit coupling clumped at the reference nuclear configuration. The mixed-spin basis differs from the pure-spin basis defined by a set of eigenstates for the nonrelativistic electronic Hamiltonian. The mixed-spin CA representation provides a unified view of the nonradiative transition; both internal conversion and intersystem crossing (ISC) are regarded as vibronically-induced phonon emission and absorption processes. The analytical expression enables us to determine important vibrational modes responsible for phonon emission/absorption (promoting modes) and accepting excitation energy (accepting modes) according to the selection rule of vibronic coupling. An advantage of the CA representation is that the spatial distribution of vibronic coupling is elucidated based on its density form, i.e., vibronic coupling density, which can be applied to theoretical molecular design with controlled nonradiative processes. The calculated ISC rate constant of tetracene reproduces the experimental result well.
|
Wataru Ota; Motoyuki Uejima; Naoki Haruta; Tohru Sato
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651a483f0065940912440d61/original/intersystem-crossing-as-vibronically-induced-phonon-emission-and-absorption-processes-a-unified-view-of-nonradiative-transitions-in-a-molecule.pdf
|
6412d142aad2a62ca1d86505
|
10.26434/chemrxiv-2023-q2jkb
|
Automatic Screen-out of Ir(III) Complex Emitters by Combined Machine Learning and Computational Analysis
|
Organic light-emitting diodes (OLEDs) have gained widespread commercial use, yet there is a continuous need to identify innovative emitters that offer higher efficiency and broader color gamut. To effectively screen out promising OLED molecules that are yet to be synthesized, we perform a representation learning aided high throughput virtual screening (HTVS) over millions of Ir(III) complexes, a prototypical type of phosphorescent OLED material, constructed via a random combination of 278 reported ligands. We successfully screen out a decent amount of promising candidates for both display and lighting purposes, which are worth further experimental investigation. The high efficiency and accuracy of our model are largely attributed to the pioneering attempt of using representation learning to organic luminescent molecules, which is initiated by a pre-training procedure with over 1.6 million 3D molecular structures and frontier orbital energies predicted via semi-empirical methods, followed by a fine-tune scheme via the quantum mechanical computed properties over around 1500 candidates. Such workflow enables an effective model construction process that is otherwise hindered by the scarcity of labeled data, and can be straightforwardly extended to the discovery of other novel materials.
|
Zheng Cheng; Jiapeng Liu; Tong Jiang; Mohan Chen ; Fuzhi Dai; Zhifeng Gao; Guolin Ke; Zifeng Zhao ; Qi Ou
|
Theoretical and Computational Chemistry; Materials Science; Optical Materials; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6412d142aad2a62ca1d86505/original/automatic-screen-out-of-ir-iii-complex-emitters-by-combined-machine-learning-and-computational-analysis.pdf
|
60c7453e0f50db52e939622c
|
10.26434/chemrxiv.9999545.v1
|
Microsecond Timescale Simulations at the Transition State of PmHMGR Predict Remote Allosteric Residues
|
<p>Understanding the mechanisms of enzymatic
catalysis requires a detailed understanding of the complex interplay of structure
and dynamics of large systems that is a challenge for both experimental and
computational approaches. QM/MM methods have been
extensively used to study these reactions, but the difficulties arising from
the hybrid treatment of the system are well documented. More importantly, the
computational demands of QM/MM simulations mean that the dynamics of the
reaction can only be considered on a timescale of nanoseconds even though the
conformational changes needed to react the catalytically active state happen on
a much slower timescale. Here we demonstrate an alternative
approach that uses transition state force fields (TSFFs) derived by the
quantum-guided molecular mechanics (Q2MM) method that provides a consistent
treatment of the entire system at the classical molecular mechanics level and
allows simulations at the microsecond timescale. Application of this approach
the second hydride transfer transition state of HMG-CoA reductase from <i>Pseudomonas mevalonii </i>(<i>Pm</i>HMGR) identified three remote residues, R396 E399 and L407, (15-27 Å away from the
active site) that have a remote dynamic effect on enzyme activity. The
predictions were subsequently validated experimentally via site-directed
mutagenesis. These results show that microsecond
timescale MD simulations of transition states are possible and can predict rather
than just rationalize remote allosteric residues.</p>
|
Taylor Quinn; Calvin N. Steussy; Brandon E. Haines; Jinping Lei; Wei Wang; Fu Kit Sheong; Cynthia V. Stauffacher; Xuhui Huang; Per-Ola Norrby; Paul Helquist; Olaf Wiest
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453e0f50db52e939622c/original/microsecond-timescale-simulations-at-the-transition-state-of-pm-hmgr-predict-remote-allosteric-residues.pdf
|
60c752cc0f50db7508397a40
|
10.26434/chemrxiv.13208063.v3
|
Consecutive Photocatalysis vs Electro-Photocatalysis. Excitation of Radical Anions of Naphthalene Diimides.
|
<p>Photo- and electrochemical transformations represent excellent opportunities for the development of methodologies environmentally friendly and combination of both techniques would result in improved methodologies. Recently, photochemical transformations involving the excitation of open-shell species has become a reality. Photostimulated electron transfer (PET) from radical anions of organic dyes have been used in consecutive photoredox catalysis and electro-photocatalysis transformation, allowing the transformation of aryl halides in valuable compounds under mild conditions. The similarities of both techniques raises the question of the convenience of using one or other related and a close evaluation is necessary to drive further development and have been shyly done in previous works. However, an objective comparison of both approaches will require using the same chemical system. We present here a direct comparison of a “pure” photochemical and an electrophotochemical transformartion studying a model transformation, namely, a C-H substitution in (hetero)aromatic systems with a C-C bond formation through reaction of halogenated substrates. Through a detailed investigation of both mechanisms, we identify a system that could be applied in both approaches with minor (necessaries) changes in the reaction conditions and clearly identify the excitation of radical anion of naphthalene diimides as the key intermediates. Both approaches are comparable in yields and kinetics with slightly better yields for the consecutive PET reaction and better selectivity for the electro-PET process. Our work offers a system that could be used for a more profound comparison of the experimental setups which could include, for instance, the important factor of energy consumption.<br /></p>
|
Sofia Caby; Lydia
M. Bouchet; Juan E. Argüello; Roberto A. Rossi; Javier Bardagi
|
Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry; Electrocatalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752cc0f50db7508397a40/original/consecutive-photocatalysis-vs-electro-photocatalysis-excitation-of-radical-anions-of-naphthalene-diimides.pdf
|
66fabc5351558a15ef993cc1
|
10.26434/chemrxiv-2024-6349z
|
Evaluating the Sensitivity, Selectivity, and Cross-reactivity of Lateral Flow Immunoassay Xylazine Test Strips
|
Background The rise of xylazine-adulterated substances poses significant public health risks due to its severe side effects and this pressing concern calls for reliable xylazine detection methods. Lateral flow immunoassay-based xylazine test strips (XTS) have emerged as a potential harm reduction tool for quick, easy, and field-based drug checking but their effectiveness remains underexplored. Although commercial XTS from multiple vendors are available, the absence of regulatory standards raises concerns regarding their accuracy and effectiveness.
Method This study evaluated the performance of commonly used commercially available XTS from different vendors to investigate the inter-product comparison of sensitivity, precision (reproducibility and robustness), cross-reactivity, and stability over changes in pH and extended storage under ambient and extreme temperature conditions.
Results All test strips demonstrated effective sensitivity, and reproducibility and maintained their efficacy despite changes in urinary pH and storage temperatures over six weeks. Interfering compounds including lidocaine, levamisole, ketamine, methamphetamine, diphenhydramine, promethazine, and cetirizine displayed varying degrees of cross-reactivity with different XTS.
Conclusion This study highlights the variability in performance among commercially available XTS, with implications for their use in harm reduction and forensic settings. While XTS can detect xylazine in low concentrations, the potential for false positives due to cross-reactivity with other drugs necessitates caution in their interpretation. Hence, xylazine test strips may serve as a viable harm reduction tool, provided that their cross-reactivity limitations are thoroughly documented and they are incorporated as part of a broader harm reduction strategy.
|
Lena Scott; Katherine Davis; Ju Park; Saman Majeed
|
Biological and Medicinal Chemistry; Analytical Chemistry; Chemical Education; Analytical Chemistry - General; Biochemical Analysis; Biochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fabc5351558a15ef993cc1/original/evaluating-the-sensitivity-selectivity-and-cross-reactivity-of-lateral-flow-immunoassay-xylazine-test-strips.pdf
|
60c74958bb8c1ae03d3dae19
|
10.26434/chemrxiv.12053601.v1
|
Palladium-Catalysed C–F Alumination of Fluorobenzenes: Mechanistic Diversity and Origin of Selectivity
|
A palladium pre-catalyst, [Pd(PCy<sub>3</sub>)<sub>2</sub>] is reported for the efficient and selective C–F alumination of fluorobenzenes with the aluminium(I) reagent [{(ArNCMe)<sub>2</sub>CH}Al] (<b>1</b>, Ar = 2,6-di-iso-propylphenyl). The catalytic protocol results in the transformation of sp<sup>2</sup> C–F bonds to sp<sup>2</sup> C–Al bonds and provides a route into reactive organoaluminium complexes (<b>2a-h</b>) from fluorocarbons. The catalyst is highly active. Reactions proceed within 5 minutes at 25 ºC (and at appreciable rates at even –50 ºC) and the scope includes low-fluorine-content substrates such as fluorobenzene, difluorobenzenes and trifluorobenzenes. The reaction proceeds with complete chemoselectivity (C–F vs C–H) and high regioselectivities ( >90% for C–F bonds adjacent to the most acidic C–H sites). The heterometallic complex [Pd(PCy<sub>3</sub>)(<b>1</b>)<sub>2</sub>] was shown to be catalytically competent. Catalytic C–F alumination proceeds with a KIE of 1.1–1.3. DFT calculations have been used to model potential mechanisms for C–F bond activation. These calculations suggest that two competing mechanisms may be in operation. Pathway 1 involves a ligand-assisted oxidative addition to [Pd(<b>1</b>)<sub>2</sub>] and leads directly to the product. Pathway 2 involves a stepwise C–H to C–F functionalisation mechanism in which the C–H bond is broken and reformed along the reaction coordinate, allowing it to act as a directing group for the adjacent C–F site. This second mechanism explains the experimentally observed regioselectivity. Experimental support for this C–H activation playing a key role in C–F alumination was obtained by employing [{(MesNCMe)<sub>2</sub>CH}AlH<sub>2</sub>] (<b>3</b>, Mes = 2,4,6-trimethylphenyl) as a reagent in place of 1. In this instance, the kinetic C–H alumination intermediate could be isolated. Under catalytic conditions this intermediate converts to the thermodynamic C–F alumination product.
|
Feriel Rekhroukh; Wenyi Chen; Ryan Brown; Andrew J. P. White; Mark Crimmin
|
Coordination Chemistry (Inorg.); Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Organometallic Compounds; Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.); Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74958bb8c1ae03d3dae19/original/palladium-catalysed-c-f-alumination-of-fluorobenzenes-mechanistic-diversity-and-origin-of-selectivity.pdf
|
60c74f58567dfe524eec5673
|
10.26434/chemrxiv.12893825.v1
|
Comparison of Computational Chemistry Methods for the Discovery of Quinone-Based Electroactive Compounds for Energy Storage
|
High-throughput computational screening (HTCS) is an approach that can enable rational and time-efficient discovery of electroactive compounds. The effectiveness of HTCS is dependent on the accuracy and speed at which the performance descriptors can be estimated for possibly millions of candidate compounds. Here, a systematic evaluation of computational methods, including force field (FF), semi-empirical quantum mechanics (SEQM), density functional based tight binding (DFTB), and density functional theory (DFT), is performed on the basis of their accuracy in predicting the redox potentials of redox-active organic compounds. Geometry optimizations at lower level theories followed by single point energy (SPE) DFT calculations including an implicit solvation model are found to offer equipollent accuracy as the higher level DFT methods, albeit at significantly lower computational costs. Effects of implicit solvation on molecular geometries and SPEs, and their overall effects on the prediction accuracy of redox potentials are analyzed in view of computational cost versus prediction accuracy, which outlines the best choice of methods corresponding to a desired level of accuracy. The modular computational approach presented here is expected to be applicable for accelerating virtual studies on functional quinones and the respective discovery of candidate compounds for energy storage.
|
Qi Zhang; Abhishek Khetan; Süleyman Er
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f58567dfe524eec5673/original/comparison-of-computational-chemistry-methods-for-the-discovery-of-quinone-based-electroactive-compounds-for-energy-storage.pdf
|
642be240db1a20696e7f0436
|
10.26434/chemrxiv-2023-dp14j
|
Reactivity, Regioselectivity, and Synthetic Application of 2-Pyrenyl Units in Scholl Reactions
|
We herein report the reactivity and regioselectivity of 2-pyrenyl as a coupling unit in Scholl reactions. On the basis of the Scholl reactions of hexaarylbenzene substrates, we have found that pyrenyl units are preferably oxidized over naphthyl and phenyl units under appropriate Scholl reaction conditions, allowing divergent synthesis through a highly controllable intramolecular coupling sequence. The C1 and C3 positions of 2-pyrenyl unit are found as the favorable sites for intramolecular coupling while C4 is not reactive to allow further coupling. The reactivity and regioselectivity pattern can be explained by the spin density distribution, which shows that carbon-carbon bonds form preferably at sites with higher positive spin density. Guided by these findings, we successfully synthesized a double helicene and a sextuple helicene through the controlled Scholl reactions of 2-pyrenyl units.
|
Sai Ho Pun; Ethan Chi Ho Wen; Zeming Xia; Han Chen; Felix R. Fischer; Qian Miao
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642be240db1a20696e7f0436/original/reactivity-regioselectivity-and-synthetic-application-of-2-pyrenyl-units-in-scholl-reactions.pdf
|
65e9021ae9ebbb4db9190e80
|
10.26434/chemrxiv-2024-lx8dn
|
Using Dynamic Interaction Fingerprints to Derive Baseline Machine Learning Model for the Prediction of Protein-Ligand Dissociation Rate Constant
|
Model building for the prediction of protein-ligand unbinding kinetics gaining popularity with the increasing availability of experimental structural data for the protein-ligand complexes and their relevant kinetic parameters. Limited but major effort has been already put forward in choosing appropriate machine learning (ML) methods among the popular ones like least squares (LS), support vector machine (SVM), random forest (RF), and a few more. The RF and Bayesian neural network (BNN) algorithms have been reported to be promising when combined with advanced descriptors representing ligand properties and protein-ligand interactions. However, the selection of descriptors that would correlate well with the unbinding kinetic properties is still a challenge. In this work, we derived a baseline RF model using descriptors representing the protein-ligand interaction fingerprints (IFPs) along the ligand unbinding pathway otherwise can be called dynamic IFPs. We found that the dynamic IFPs in addition to the static or binding pocket IFPs significantly improved the quality of our model for the prediction of ligand dissociation rate constant (koff). To the best of our knowledge, this work is the first attempt towards using the dynamic IFPs in deriving a quantitative structure-kinetics relationship (QSKR) model for the prediction of koff.
|
Muhammad Jan Akhunzada; Hyun Jung Yoon; Abdennour Braka; Indrajit Deb; Sangwook Wu
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-03-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e9021ae9ebbb4db9190e80/original/using-dynamic-interaction-fingerprints-to-derive-baseline-machine-learning-model-for-the-prediction-of-protein-ligand-dissociation-rate-constant.pdf
|
672cadd47be152b1d051dc27
|
10.26434/chemrxiv-2023-wq2c1-v3
|
Correlation Between NMR Coupling Constants and σ-Donating Properties of N-Heterocyclic Carbenes and Their Derivatives
|
Is the 1JC-H coupling constant for protonated carbene a relevant measure of its σ-donation ability? This paper addresses this question by comparing calculated 1JC-H values with various experimental and theoretical approaches across a broad spectrum of carbene compounds. We have examined not only Arduengo-type NHCs based on the 2-imidazolylidene scaffold but also many other derivatives with modified frameworks, such as carbenes with extended, saturated, or conjugated rings, those with reduced heteroatom stabilization, those stabilized by alternative heteroatoms, permanently charged carbenes, acyclic carbenes, amidocarbenes, and cyclic amino(alkyl/aryl) carbenes, as well as carbodicarbenes and carbodiphosphoranes. Our findings reveal a nuanced relationship between different parameters associated with σ-interaction, such as 1JC-H, Huynh electronic parameter (HEP), σ-donation from ETS-NOCV, and lone pair energy. Notably, the best correlation was observed between 1JC-H and the ETS-NOCV method, particularly for mono- and diaminocarbenes, highlighting the utility of 1JC-H in comparing σ-donation among structurally similar carbene types. However, the use of 1JC-H as a universal measure across all carbene classes appears limited, especially when considering carbenes with significantly different structural frameworks. While HEP is less effective for carbenes with diverse structural backbones, our study suggests that 1JC-H has potential across a broader range of systems. Additionally, the analysis demonstrates that lone pair energy reflects basicity rather than σ-donor ability.
|
Radhika Gupta; Gilles Frison
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672cadd47be152b1d051dc27/original/correlation-between-nmr-coupling-constants-and-donating-properties-of-n-heterocyclic-carbenes-and-their-derivatives.pdf
|
6389afbe9e687b05db39b1e4
|
10.26434/chemrxiv-2022-x0c5g
|
Copper-Catalyzed C(3+1) Copolymerization of Propargyl Carbonates and Aryldiazomethanes
|
Controlling the composition and sequence during diazo copolymerization with vinyl or acetylenic monomers is challenging. Here we disclose a Cu-catalyzed C(3+1) copolymerization reaction using propargyl carbonates and aryldiazomethanes derived from N-tosylhydrazones as the C3 and C1 building blocks, respectively. This reaction rapidly produces alternating-like poly(1,4-diaryl-2-butyne-1,4-diyl)s (Mn up to 31.0 kg/mol) in a modular fashion, without detectable homopolymer segments. This work provides a new strategy for the synthesis of hydrocarbon polymers through diazo copolymerization.
|
Hao-Ze Su; Bin Wu; Jianbo Wang; Rong Zhu
|
Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Polymerization (Polymers)
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-12-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6389afbe9e687b05db39b1e4/original/copper-catalyzed-c-3-1-copolymerization-of-propargyl-carbonates-and-aryldiazomethanes.pdf
|
67d34feffa469535b922cf4d
|
10.26434/chemrxiv-2025-6wm8s
|
Improvement of Electrospray Ionization Response Linearity and Quantification in Dissolved Organic Matter using Synthetic Deuterated Internal Standards
|
Aquatic dissolved organic matter (DOM) is an ultra-complex mixture of compounds covering a wide range of masses and with an unknown extent of isomeric complexity, making its structural elucidation and quantification highly challenging. Electrospray ionization high-resolution mass spectrometry (ESI-HRMS) has advanced DOM analysis, but accurate concentration determination remains limited by the lack of response factor correction. Here, we address this limitation by introducing novel deuterated compounds as internal standards that mimic DOM structures. Using a d5-labeled compound free of isobaric interferences in DOM, we assessed ionization suppression in various aquatic sample extracts, and improved concentration-based linearity in a coastal DOM reference material. Our results show that deuterated carboxylic acid-rich standards enable ‘pseudo-quantification’ by correcting for ionization suppression and instrument drift. Applying this approach, we estimate that ionizable acids constitute 15-30% of DOM in river, coastal, and deep-ocean samples using an Orbitrap system and 11-24% using a 15T FT-ICR-MS, highlighting platform differences. Additionally, we establish a ~1 ng L⁻¹ feature detection limit for DOM compounds in seawater via a standard LC-MS gradient method. These findings demonstrate that deuterated standards provide a simple, practical way to improve DOM semi-quantification, enhancing our understanding of its chemical composition in environmental studies.
|
Alexander J. Craig; Mustapha Adekomi Ganiyu; Lindon W. K. Moodie; Sofja Tshepelevitsh; Koit Herodes; Heike Simon; Thorsten Dittmar; Jeffrey A. Hawkes
|
Analytical Chemistry; Environmental Analysis; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d34feffa469535b922cf4d/original/improvement-of-electrospray-ionization-response-linearity-and-quantification-in-dissolved-organic-matter-using-synthetic-deuterated-internal-standards.pdf
|
6655783f91aefa6ce12aa62e
|
10.26434/chemrxiv-2024-cfncv
|
Unraveling C4 selectivity in the light-driven C–H fluoroalkylation of pyridines and quinolines
|
Given the prevalence of pyridine motifs in FDA-approved drugs, selective fluoroalkylation of pyridines and quinolines is essential for preparing diverse bioisosteres. However, conventional Minisci reactions often face challenges in achieving precise regioselectivity due to competing reaction sites of pyridine and the limited availability of fluoroalkyl radical sources. Herein, we present a light-driven, C4-selective fluoroalkylation of azines utilizing N-aminopyridinium salts and readily available sulfinates. Our approach employs electron donor-acceptor complexes, achieving highly C4-selective fluoroalkylation under mild conditions without an external photocatalyst. This practical method not only enables the installation of CF2H groups but also allows for the incorporation of CF2-alkyl groups with diverse functional entities, surpassing the limitations of previous methods. The versatility of the radical pathway is further demonstrated through straightforward three-component reactions involving alkenes and [1.1.1]propellane. Detailed experimental and computational studies have elucidated the origins of regioselectivity, providing profound insights into the mechanistic aspects.
|
Sungwoo hong; Leejae Kim; Wooseok Lee
|
Organic Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6655783f91aefa6ce12aa62e/original/unraveling-c4-selectivity-in-the-light-driven-c-h-fluoroalkylation-of-pyridines-and-quinolines.pdf
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60c74265337d6c0225e26a59
|
10.26434/chemrxiv.8224538.v1
|
The Dual Role of Histidine as General Base and Recruiter of a Third Metal Ion in HIV-1 RNase H
|
<div>RNase H is a prototypical example for two metal ion catalysis in enzymes. An RNase H activity is present in the HIV-1 reverse transcriptase but also in many other nucleases such as Homo sapiens (Hs) or Escherichia coli (Ec) RNase H. The mechanism of the reaction has already been extensively studied based on the Bacillus halodurans (Bh) RNase H crystal structures, most recently using time-resolved X-Ray crystallography. However, kinetic and mutation experiments with HIV-1, Hs and Ec RNase H implicate a catalytic histidine in the reaction that is not present in Bh RNase H, and the protonation of the leaving group also remains poorly understood. We use quantum mechanics/molecular mechanics (QM/MM) calculations combining Hamiltonian replica exchange with a finite-temperature string method to study the cleavage of the ribonucleic acid (RNA) backbone of a DNA/RNA hybrid catalyzed by the HIV-1 RNase H with a focus on the proton transfer pathway and the role of the histidine. The reported pathway is consistent with kinetic data obtained with mutant HIV-1, Hs and Ec RNase H, the calculated pK<sub>a</sub> values of the DEDD residues and crystallographic studies. The overall reaction barrier of ∼18 kcal mol<sup>-1</sup>, encountered in the first step, matches the slow experimental rate of ∼1-100 min<sup>-1</sup>. Using Molecular dynamics (MD) calculations we are able to sample the recently identified binding site for a third transient divalent metal ion in the vicinity of the scissile phosphate in the product complex. Our results account for the experimental observation of a third metal ion facilitating product release in an Aquifex aeolicus RNase III crystal structure and the Bh RNase H in crystallo reaction. Based on our data we are able to show that the third ion and the histidine are key to product release as had been hypothesized.</div>
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Simon L. Dürr; Olga Bohuszewicz; Reynier Suardiaz; Pablo G. Jambrina; Christine Peter; Yihan Shao; Edina Rosta
|
Biochemistry; Biophysics; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2019-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74265337d6c0225e26a59/original/the-dual-role-of-histidine-as-general-base-and-recruiter-of-a-third-metal-ion-in-hiv-1-r-nase-h.pdf
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657850bc7acf130c320f146e
|
10.26434/chemrxiv-2023-3zg5f
|
Pure Water Splitting Driven by Overlapping Electric Double Layers
|
In pursuit of a sustainable future powered by renewable energy, hydrogen production through water splitting should achieve high energy efficiency with economical materials. Here, we present a nanofluidic electrolyzer that leverages overlapping cathode and anode electric double layers (EDLs) to drive the splitting of pure water. The strong electric field within the overlapping EDLs enhances ion migration and facilitates the dissociation of water molecules. Acidic and basic environments, that are created in situ at cathode and anode, respectively, enable the use of non-precious metal catalysts. All these merits allow the reactor to exhibit a current density of 2.8 A·cm-2 at 1.7 V with a nickel anode. This paves the way towards a new type of water electrolyzers without membranes, supporting electrolytes, or precious metal catalysts.
|
Haosen Xu; Jianbo Zhang; Michael Eikerling; Jun Huang
|
Catalysis; Nanoscience; Energy; Nanofluidics; Electrocatalysis; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657850bc7acf130c320f146e/original/pure-water-splitting-driven-by-overlapping-electric-double-layers.pdf
|
65fdc33ee9ebbb4db948fe8f
|
10.26434/chemrxiv-2024-gtwdx
|
Cationic and anionic dual redox activity of MoS2 for electrochemical potassium storage
|
MoS2 is receiving intensive attention in the research area of potassium-ion batteries (PIBs) and regarded as one of the most promising PIB anodes. Great progress has been made to enhance the electrochemical performance of MoS2, but understanding of the electrochemical mechanism to store K-ion in MoS2 remains unclear. This work reports that the K storage process in MoS2 follows a complex reaction pathway involving the conversion reactions of both Mo and S and as a result, the storage process shows both cationic redox activity of Mo and anionic redox activity of S. The presence of dual redox activity, characterized in-depth through synchrotron X-ray absorption, X-ray photoelectron, Raman, and UV-vis spectroscopies, reveals the irreversible Mo oxidation during the depotassiation process redirects the reaction pathway towards S oxidation, which leads to the progression of K-S electrochemistry in the (de)potassiation process. Moreover, the dual reaction pathway can be regulated by controlling the discharge depth at different cycling stages of MoS2, realizing a long-term stable cycle life of MoS2 as a PIB anode.
|
Ajay Piriya Vijaya Kumar Saroja; Yupei Han; Charlie Nason; Gopinathan Sankar; Yi Lu; Henry Tinker; Andrew Stewart; Veronica Celorrio; Min Zhou; Jiayan Luo; Yang Xu
|
Materials Science; Energy; Energy Storage; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fdc33ee9ebbb4db948fe8f/original/cationic-and-anionic-dual-redox-activity-of-mo-s2-for-electrochemical-potassium-storage.pdf
|
60c74d77842e65027fdb3499
|
10.26434/chemrxiv.12623504.v1
|
Visible-Light-Induced Dearomatization via [2+2] Cycloaddition or 1,5-Hydrogen Atom Transfer: Regulating Reaction Pathways of Diradicals on Excited States
|
Visible-light-induced
dearomatization reaction <i>via</i> energy
transfer mechanism is an emerging strategy for the synthesis of highly strained
polycyclic molecules. Transient, high-energy
diradical species on excited states are typically involved in this type of
reactions as key intermediates. Herein, we report the
visible-light-induced divergent dearomatization of indole-tethered O-methyl
oximes, in which the reactivity of the open-shelled singlet diradical
intermediates towards competitive reaction pathways, namely [2+2] cycloaddition
and 1,5-hydrogen atom transfer, can be well regulated. The mechanism has been well
supported by a series of experimental and computational investigations. The
dearomatization reactions allow the facile synthesis of structurally appealing
indoline-fused azetidines and related polycyclic molecules with high efficiency
and exclusive selectivity.
|
Shu-Li You; Min Zhu; Xiao Zhang; Chao Zheng
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d77842e65027fdb3499/original/visible-light-induced-dearomatization-via-2-2-cycloaddition-or-1-5-hydrogen-atom-transfer-regulating-reaction-pathways-of-diradicals-on-excited-states.pdf
|
6750d5abf9980725cf14fee3
|
10.26434/chemrxiv-2024-sr8sl
|
Coherent Vibrational Dynamics in an Isolated Peptide Captured with 2D IR Spectroscopy
|
Quantum mechanical vibrational coherence transfer processes play important roles in energy relaxation, charge transfer, and reaction dynamics in chemical and biological systems, but are difficult to directly measure using traditional condensed-phase nonlinear spectroscopies. Recently, we developed a new experimental capability to obtain two-dimensional infrared (2D IR) spectra of molecular systems in the gas phase that enables the direct measurement of coherence pathways. Herein, we report ultrafast 2D IR spectroscopy of the peptide glutathione (GSH) isolated and cryogenically cooled in the gas phase. Six vibrational modes were simultaneously excited within the amide I and II region. The spectral dynamics of both diagonal and off-diagonal cross peak features exhibit long-lived oscillatory behavior consistent with the presence of coherent vibrational dynamics. The oscillatory signatures deviate significantly from the expected quantum beating pathways predicted from standard nonlinear response theories. These deviations indicate the presence of additional nonlinear pathways, including coherence transfer processes. Quantum chemistry calculations indicate large anharmonic couplings between the excited vibrational modes in GSH and, critically, strong coupling between the excited modes and numerous low-frequency modes that act as a bath to mediate coherence transfer. The data provide important new benchmarks for modeling coherence transfer dynamics and system bath interactions in open quantum systems free from solvent effects.
|
Zifan Ma; Laura McCaslin; Joseph Fournier
|
Physical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6750d5abf9980725cf14fee3/original/coherent-vibrational-dynamics-in-an-isolated-peptide-captured-with-2d-ir-spectroscopy.pdf
|
6446b78883fa35f8f630301a
|
10.26434/chemrxiv-2023-kqqtt
|
A Wearable Electrochemical Biosensor for Lactate Monitoring in Sweat
|
This study aimed to optimize the inkjet printing process for the fabrication of rGO- based lactate biosensors. The ink used for printing possessed proper fluidic properties, and the droplets were connected on the film by repeated printing process. The ink also contained ethyl cellulose, which reduced the coffee ring effect and resulted in a uniform film of rGO. The optimal density of Anti-L on the surface of the sensor was found to be 200 mM, and the incubation time for lactate samples was optimized to 60 minutes. The device showed linear responses from 100 to 500 μM with a high sensitivity of about 0.5 per 100 μM lactate and a low detection limit at 23 μM at S/N=3. This study demonstrates that optimized inkjet printing can be used to fabricate highly sensitive lactate biosensors for various applications.
|
Mohammed Hassan Ali; Ahmed Tariq Mahmoud; Karim Hisham Abdullah
|
Analytical Chemistry; Analytical Apparatus
|
CC BY 4.0
|
CHEMRXIV
|
2023-04-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6446b78883fa35f8f630301a/original/a-wearable-electrochemical-biosensor-for-lactate-monitoring-in-sweat.pdf
|
67c5692dfa469535b9b9a95b
|
10.26434/chemrxiv-2025-zm61f
|
Novel iPrRu-MACHO Salts: Synthesis and Catalytic Applications with Diverse H-trans Ligands
|
The Ru-MACHO complex acts as a pre-catalyst for a plethora of significant catalytic transformations. However, since its discovery approximately two decades ago, most enhancement attempts have been limited to varying the P-substituents for increasing catalyst performance or replacing Ru for greener alternatives. In this study we synthesize novel trans-L monohydrido iPrRu-MACHO complex derivatives that can act as pre-catalysts operating under mild conditions while maintaining high activity and selectivity in a variety of chemical transformations. Specifically, we investigated their catalytic efficiency for CO2 hydrogenation, formic acid dehydrogenation, and levulinic acid hydrogenation and we compared their activity with their commercially available precursor (iPrRu-MACHO).
|
Tu Anh Tran; Valeria Nori; Alexander Tobias Nikol; Andreas Schoeler; Mathias Thor Nielsen; Mike Steffen Bernhard Jørgensen; René Wugt Larsen; Martin Nielsen
|
Catalysis; Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligands (Organomet.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-03-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c5692dfa469535b9b9a95b/original/novel-i-pr-ru-macho-salts-synthesis-and-catalytic-applications-with-diverse-h-trans-ligands.pdf
|
665d8fa221291e5d1df68c08
|
10.26434/chemrxiv-2024-rs2v8-v2
|
A Positive Charge in an Antimalarial Compound Unlocks Broad-spectrum Antibacterial Activity
|
In this study, we synthesised a library of eNTRy-rule-complying compounds by introducing ionisable nitrogens to an antimalarial compound. These positively-charged derivatives gained activity against both Gram-negative and -positive bacteria, Mycobacterium tuberculosis and boosted Plasmodium falciparum inhibition to the double-digit nanomolar range. Overcoming and remaining inside the cell envelope of Gram-negative bacteria is one of the major difficulties in antibacterial drug development. The eNTRy rules (N = ionisable nitrogen, T = low three-dimensionality, R = rigidity) can be a useful structural guideline to improve accumulation of small molecules in Gram-negative bacteria. With the aim of unlocking Gram-negative activity, we added amines and (cyclic) N-alkyl guanidines to an already flat and rigid pyrazole-amide class. To test their performance, we compared these eNTRy-rule-complying compounds to closely related non-complying ones through phenotypic assay screenings of various pathogens (P. falciparum, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, and M. tuberculosis) obtaining a handful of broad-spectrum hits. The results support the working hypothesis and even extend its applicability, the studied pyrazole-amide class adheres to the eNTRy rules; non-compliant compounds do not kill any of the bacteria tested, while compliant compounds largely showed inhibition of Gram-negative, -positive, and M. tuberculosis bacteria in the single-digit micromolar range.
|
Maria Braun-Cornejo; Mitchell Platteschorre; Vincent de Vries; Patricia Bravo; Vidhisha Sonawane; Mostafa M. Hamed; Jörg Haupenthal; Norbert Reiling; Matthias Rottmann; Dennis Piet; Peter Maas; Eleonora Diamanti; Anna K. H. Hirsch
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665d8fa221291e5d1df68c08/original/a-positive-charge-in-an-antimalarial-compound-unlocks-broad-spectrum-antibacterial-activity.pdf
|
60c73e19337d6ccd4fe262ba
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10.26434/chemrxiv.6683010.v1
|
Cs Retention and Diffusion in C-S-H at Different Ca/Si Ratios
|
<div>Cement and concrete have been widely used as a barrier to isolate many types of contaminants, including radioactive waste, in repository sites. Nevertheless, the intrusion of groundwater in those nuclear repositories may release those contaminants by leaching mechanisms. Because of this, the retention and diffusion processes in cement matrix require to be analyzed in depth. The adsorption in cement and C‐S-H gel, its main hydration product, is influenced by factors as the pH, the composition or the alkali and alkaline earth content. In this work, molecular dynamics simulations were employed to study the role of Ca/Si ratio of the C‐S‐H in the capacity to retain Cs and diffusivity of these ions in gel pores. For that purpose, we built four different C‐S‐H models with Ca/Si ratios from 1.1 to 2.0. The results indicate better cationic retention at low Ca/Si ratios due to the interaction of the cations with the bridging silicate tetrahedrons. However, the average diffusion coefficients of the cations decrease at higher Ca/Si ratios because the high ionic constraint in the nanopore that induces a longrange ordering of the water molecules.</div>
|
Eduardo Duque-Redondo; Kazuo Yamada; Iñigo López-Arbeloa; Hegoi Manzano
|
Nanostructured Materials - Materials; Computational Chemistry and Modeling; Physical and Chemical Processes; Surface; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-06-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e19337d6ccd4fe262ba/original/cs-retention-and-diffusion-in-c-s-h-at-different-ca-si-ratios.pdf
|
60c7516b9abda2472cf8dbf1
|
10.26434/chemrxiv.13160453.v1
|
Catalyst-Free Polymerization with 100% Atom Economy: Facile Synthesis of Polysulfonates with Multifunctionalities
|
Catalyst-free spontaneous
polymerization for the synthesis of halogen-rich polysulfonates at room
temperature in air with 100% atom economy in high yields was developed. The
resulting polymers possess various properties, including
post-functionalization, extraordinarily high refractive index, visible
photodegradation, photoacid generation, multi-color and 3D fluorescent
photopatterning, and practical broad-spectrum antibacterial activity.
|
XIAOLIN LIU; Xin Liang; YUBING HU; Qing Qu; Dongming Liu; Haotian Bai; Anjun Qin; Jacky W. Y. Lam; Ryan Tsz Kin Kwok; Lei Han; Ben Zhong Tang
|
Organic Polymers
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7516b9abda2472cf8dbf1/original/catalyst-free-polymerization-with-100-atom-economy-facile-synthesis-of-polysulfonates-with-multifunctionalities.pdf
|
60c757d1bb8c1a808a3dc8fe
|
10.26434/chemrxiv.14198768.v2
|
Quasi-Steady-State and Partial-Equilibrium Approximations in Chemical Kinetics: One Stage Beyond the Elimination of a Fast Variable
|
<pre>Classical approximations in chemical kinetics, the quasi-steady-state approximation (QSSA) and the partial-equilibrium approximation (PEA), are used to reduce rate equations for the concentrations and the extents of the reaction steps, respectively. We make precise two conditions on the rate constants necessary and sufficient to eliminate a well-chosen variable in the vicinity of a steady state. The first condition expresses that dynamics admits a small characteristic time associated with a fast variable. The second condition ensures that the fast variable is a concentration for QSSA and an extent for PEA. Both approximations exploit the zeroth order of a singular perturbation method. Eliminating a fast variable does not mean that it has reached a steady state. The fast evolution is considered over and the slow evolution of the eliminated variable is governed by the slow variables. The evolution of the slow variables occurs on a slow manifold in the space of the concentrations or the extents. In some cases the dynamics of the slow variables can be associated with a reduced chemical scheme. QSSA and PEA are applied to three chemical schemes associated with linear and nonlinear dynamics. We find that QSSA cannot be identified with the elimination of a reactive intermediate. The nonlinearities of the rate equations induce a more complex behavior.</pre>
|
Agnès Pellissier-Tanon; Gabriel Morgado; Ludovic Jullien; Annie Lemarchand
|
Chemical Education - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757d1bb8c1a808a3dc8fe/original/quasi-steady-state-and-partial-equilibrium-approximations-in-chemical-kinetics-one-stage-beyond-the-elimination-of-a-fast-variable.pdf
|
6544b0b0a8b423585adb7d04
|
10.26434/chemrxiv-2023-580rb
|
Model-Independent Statistical Averages
of the Hydrodynamic Radius via Dynamic Light Scattering
|
I present new, robust, and measurable nonparametric statistical averages that summarize major features of the distribution of the hydrodynamic radius. I explain how these descriptive statistical averages—the mean, standard deviation, and skewness of the intensity-weighted distribution—are obtained. Next, I demonstrate that—unlike the well-known and widely used Z-average and polydispersity index—these statistical averages bear a direct and physically meaningful interpretability. At the same time, these statistical averages are straightforward to obtain from experimental correlograms, and therefore, they merit a place in characterizing particle systems via DLS.
|
Sandor Balog
|
Physical Chemistry; Materials Science; Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6544b0b0a8b423585adb7d04/original/model-independent-statistical-averages-of-the-hydrodynamic-radius-via-dynamic-light-scattering.pdf
|
6773efb381d2151a027b696f
|
10.26434/chemrxiv-2025-552f9
|
Preparation of Sequence-controlled Aliphatic Polysulfones by Group Transfer Radical Polymerization
|
The integration of sulfur atoms into polymer backbones to synthesize S-containing polymers, such as aliphatic polysulfones, renders many unique properties of the materials. Conventional methods are facing great challenges to achieve sequence-controlled aliphatic polysulfones with high molecular weight (MW), significantly restricting the use of these polymers. We devise a novel approach for the preparation of aliphatic polysulfones via sulfonyl radical-mediated group transfer radical polymerization (GTRP). The polymerization proceeds through a practical SO2-free pathway, producing a series of ABC sequence-defined high-MW polymers (up to 199 kg/mol). DFT calculations are conducted, which support the radical Smiles rearrangement pathway involved in the GTRP process.
|
Kexiong Gao; Xianjin Wang; Tongkun Wang; Silin Song; Chen Zhu
|
Polymer Science
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6773efb381d2151a027b696f/original/preparation-of-sequence-controlled-aliphatic-polysulfones-by-group-transfer-radical-polymerization.pdf
|
6750a1b05a82cea2fafec8d7
|
10.26434/chemrxiv-2024-46fll
|
Resolution of selectivity steps of CO reduction reaction on copper by quantum Monte Carlo
|
Electrochemical reduction of carbon monoxide to valuable fuels and chemicals on copper surfaces remains a challenging area in catalysis due to a limited understanding of adsorption mechanisms and reaction pathways. Although density functional theory (DFT) based studies have investigated these processes, their accuracy varies across different functionals. Here, we present the first application of fixed-node diffusion Monte Carlo (FNDMC) to benchmark the adsorption energies of CO*, H*, and key CO reduction reaction (CORR) intermediates, COH* and CHO* on the Cu(111) surface. Our results for CO* and H* adsorption energies closely align with experimentally measured chemisorption reactions, highlighting the limitations of DFT, and providing site-specific energy comparisons that are often not available experimentally. Additionally, we explore the effect of explicit solvation, demonstrating how water stabilizes the COH* over CHO*, thus suggesting a critical role of COH* in CORR. Finally, we release our high-accuracy FNDMC benchmarks for testing and developing new DFT functionals for electrocatalysis. Overall, this study underscores the potential of FNDMC for detailed surface chemistry studies and offers new insights into catalytic processes.
|
Roman Fanta; Michal Bajdich
|
Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6750a1b05a82cea2fafec8d7/original/resolution-of-selectivity-steps-of-co-reduction-reaction-on-copper-by-quantum-monte-carlo.pdf
|
6557d0086e0ec7777f288186
|
10.26434/chemrxiv-2023-9l4wm
|
Halobenzene adducts of a dysprosocenium single-molecule magnet
|
Dysprosium complexes with strong axial crystal fields are promising candidates for single-molecule magnets (SMMs), which could be used for high-density data storage. Isolated dysprosocenium cations, [Dy(CpR)2]+ (CpR = substituted cyclopentadienyl), have recently shown magnetic hysteresis (a memory effect) above the temperature of liquid nitrogen. Synthetic efforts have focused on reducing strong transverse ligand fields in these systems, as they are known to enhance magnetic relaxation by spin-phonon mechanisms. Here we show that equatorial coordination of the halobenzenes PhX (X = F, Cl, Br) and o-C6H4F2 to the cation of a recently reported dysprosocenium complex [Dy(Cpttt)(Cp*)][Al{OC(CF3)3}4] (Cpttt = C5H2tBu3-1,2,4; Cp* = C5Me5) reduces magnetic hysteresis temperatures compared to the parent cation. We find that this is due to increased effectiveness of both one- (Orbach) and two-phonon (Raman) relaxation mechanisms, which correlate with the electronegativity and number of interactions with the halide. We observe unusual divergent behavior of relaxation rates at low temperature in [Dy(Cpttt)(Cp*)(PhX)][Al{OC(CF3)3}4], which we attribute to a phonon bottleneck effect. We find that, despite the transverse fields introduced by the monohalobenzenes in these cations, the interactions are sufficiently weak that the effective barriers to magnetization reversal remain above 1000 cm–1, being only ca. 100 cm–1 lower than the parent complex, [Dy(Cpttt)(Cp*)][Al{OC(CF3)3}4].
|
Sophie Corner; Gemma Gransbury; Inigo Vitorica-Yrezabal; George Whitehead; Nicholas Chilton; David Mills
|
Inorganic Chemistry; Organometallic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6557d0086e0ec7777f288186/original/halobenzene-adducts-of-a-dysprosocenium-single-molecule-magnet.pdf
|
675c5d3df9980725cff830d6
|
10.26434/chemrxiv-2024-6fb7g-v2
|
PathInHydro, a set of machine learning models to identify unbinding pathways of gas molecules in [NiFe] hydrogenases
|
Machine learning (ML) is a powerful tool for the automated data analysis of molecular dynamics (MD) simulations. Recent studies showed that ML models can be used to identify protein-ligand unbinding pathways and understand the underlying mechanism. To expedite the examination of MD simulations, we constructed PathInHydro, a set of supervised ML models capable of automatically assigning unbinding pathways for the dissociation of gas molecules from [NiFe] hydrogenases, using the unbinding trajectories of CO and H2 from Desulfovibrio fructosovorans [NiFe] hydrogenase as a training set. [NiFe] hydrogenases are receiving increasing attention in biotechnology due to their high efficiency in the generation of H2, which is considered by many to be the fuel of the future. However, some of these enzymes are sensitive to O2 and CO. Many efforts have been made to rectify this problem and generate air-stable enzymes by introducing mutations that selectively regulate the access of specific gas molecules to the catalytic site. Herein, we showcase the performance of PathInHydro for the identification of unbinding paths in different test sets, including another gas molecule and a different [NiFe] hydrogenase, which demonstrates its feasibility for the trajectory analysis of a diversity of gas molecules along enzymes with mutations and sequence differences. PathInHydro allows the user to skip time-consuming manual analysis and visual inspection, facilitating data analysis for MD simulations of ligand unbinding from [NiFe] hydrogenases. The codes and data sets are available online: https://github.com/FarzinSohraby/PathInHydro.
|
Farzin Sohraby; Jing-Yao Guo; Ariane Nunes-Alves
|
Theoretical and Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-12-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c5d3df9980725cff830d6/original/path-in-hydro-a-set-of-machine-learning-models-to-identify-unbinding-pathways-of-gas-molecules-in-ni-fe-hydrogenases.pdf
|
66e2f68451558a15efc94baf
|
10.26434/chemrxiv-2024-hzlgd-v2
|
Decoding the Promotional Effect of Iron in Bimetallic Pt-Fe-Nanoparticles for the Low Temperature Reverse Water-Gas Shift Reaction
|
The reverse water-gas shift reaction (RWGS) is a key technology of the chemical industry, central to the emerging circular carbon economy. Pt-based catalysts have previously been shown to effectively promote the RWGS, especially when modified by promoter elements. However, their active state is still poorly understood. Here, we show that the intimate incorporation of an iron promoter into metal-oxide supported Pt-based nanoparticles can increase their activity and selectivity for the low temperature reverse water-gas shift (LT-RWGS) substantially and drastically outperform unpromoted Pt-based materials. Specifically, the study explores the promotional effect of iron in Pt-Fe bimetallic systems supported on silica (PtxFey@SiO2) prepared by surface organometallic chemistry (SOMC). The most active catalyst (Pt1Fe1@SiO2) shows high selectivity (>99% CO) towards CO at a formation rate of 0.192 molCO h-1 gcat-1, which is significantly higher than that of monometallic Pt@SiO2 (96% sel. and 0.022 molCO h-1 gcat-1). In-situ diffuse reflectance FT-IR spectroscopy (DRIFTS) and X-ray absorption spectroscopy (XAS) indicate a dynamic process at the catalyst surface under reaction conditions, revealing distinct reaction pathways for the monometallic Pt@SiO2 and bimetallic PtxFey@SiO2 systems.
|
Colin Hansen; Wei Zhou; Enzo Brack; Yuhao Wang; Chunliang Wang; James Paterson; Jamie Southouse; Christophe Copéret
|
Inorganic Chemistry; Catalysis; Organometallic Chemistry; Small Molecule Activation (Inorg.); Heterogeneous Catalysis; Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e2f68451558a15efc94baf/original/decoding-the-promotional-effect-of-iron-in-bimetallic-pt-fe-nanoparticles-for-the-low-temperature-reverse-water-gas-shift-reaction.pdf
|
60c742f7842e6521d2db21ab
|
10.26434/chemrxiv.8868701.v1
|
[3+2] Fragmentation of a Pentaphosphido Ligand by Cyanide
|
The activation of white phosphorus (P4) by transition metal complexes has been studied for decades, but the functionalization and release of the resulting (organo)phosphorus ligands has rarely been achieved. Herein we describe the formation of unusal diphosphanides from a P5 ligand by treatment with cyanide. New cobalt diorganopentaphosphido complexes have been synthesized by a stepwise reaction sequence involving a low-valent dimine cobalt complex, white phosphorus and diorganochlorophosphanes. Reactions of such complexes with tetraalkylammonium or potassium cyanide afford the first cyclotriphosphido cobaltate anion 5 and rare 1-cyano-diphosphan-1-ide anions [R2PPCN]− (6-R). The molecular structure of a related product 7 suggests a novel reaction mechanism, where cyanide anion coordination to cobalt induces a ligand rearrangement. This is followed by nucleophilic attack of a second cyanide anion at a P atom, releasing the P2 fragment. <br />
|
Christian M. Hoidn,; Thomas M. Maier; Karolina Trabitsch; Jan J. Weigand; Robert Wolf
|
Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Organometallic Compounds; Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f7842e6521d2db21ab/original/3-2-fragmentation-of-a-pentaphosphido-ligand-by-cyanide.pdf
|
61f9fbe063acba2fe5226c44
|
10.26434/chemrxiv-2022-cx8pz
|
Laser-Induced Graphene-Based Electrochemical Sensor for 4-Nitrophenol from Polyimide and Polyethersulfone Precursors
|
Electrochemical sensors provide an excellent alternative for the in-situ detection of pollutants in water. 4-Nitrophenol is a critical pollutant owing to its acute toxicity and adverse health effects on humans and other living organisms. It is known to have carcinogenic, mutagenic, and teratogenic effects on aquatic life plants and human beings at very low concentrations. In this work, a facile electrochemical sensor for 4-Nitrophenol detection is proposed by laser-induced graphene (LIG) printed on polyethersulfone (PES) and polyimide (PI) films respectively. The laser irradiation of polymeric films results in 3D porous graphene structure formation that increases electron transfer rate as well as the electrochemically active surface area (EASA). This fabrication approach by laser-scribing provides a simple, fast, chemical-free, mask-free, and scalable solution to produce graphene-based electrochemical sensors for 4-Nitrophenol. Cyclic voltammetry is used as the electrochemical technique for the highly sensitive detection of 4-Nitrophenol. PES-based LIG sensors exhibit a higher sensitivity of 3793 µAmM-1cm-2 as compared to that of PI-based LIG sensors with a sensitivity of 3025 µAmM-1cm-2.
|
Vikram P. Wanjari; Ashish Kumar; Siddhartha P. Duttagupta; Swatantra P. Singh
|
Materials Science; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Carbon-based Materials; Environmental Science; Electrochemical Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f9fbe063acba2fe5226c44/original/laser-induced-graphene-based-electrochemical-sensor-for-4-nitrophenol-from-polyimide-and-polyethersulfone-precursors.pdf
|
66a0eda2c9c6a5c07ac1da46
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10.26434/chemrxiv-2024-0b4vd
|
Fluorogenic detection of cyanide ions in pure aqueous media through intramolecular crossed-benzoin reaction: limitations unveiled and possible solutions
|
Reaction-based fluorogenic sensing of lethal cyanide anion in aqueous matrices remains a big challenge. We have revisited the approach proposed by the Kim group (Chem. Commun. 2015, 51, 7709-7712) and highlighted its limitations related to poor aqueous stability of probes and impossibility to achieve molecular amplification despite the assumed catalytic activation mechanism. Self-immolative linker strategies were considered to obtain usable cyanide-responsive chemodosimeters and statistical analyses of fluorescence data have been deepened to accurately delineate their sensing performances, especially limit of detection (LOD).
|
Vincent GAUMERD; Yoan CAPELLO; Quentin BONNIN; Pierre-Yves RENARD; Anthony ROMIEU
|
Organic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a0eda2c9c6a5c07ac1da46/original/fluorogenic-detection-of-cyanide-ions-in-pure-aqueous-media-through-intramolecular-crossed-benzoin-reaction-limitations-unveiled-and-possible-solutions.pdf
|
60c75a419abda27db8f8ebdc
|
10.26434/chemrxiv.7234721.v5
|
Vacuum-Field Catalysis: Accelerated Reactions by Vibrational Ultra Strong Coupling
|
<p>In conventional catalysis, the reactants interact with specific sites of the catalyst in such a way that the reaction barrier is lowered by changing the reaction path, causing the reaction rate to be accelerated. Here we take a radically different<br />approach to catalysis by ultra-strongly coupling the vibrations of the reactants to the infrared vacuum electromagnetic field. To demonstrate the possibility of such<br />vacuum-field catalysis (or cavity catalysis), we have studied hydrolysis reactions under the vibrational ultra strong coupling (V-USC) of the OH stretching mode of water to a Fabry-Pérot microfluidic cavity mode. This results in a giant Rabi splitting energy (92 meV), indicating the system is in the V-USC regime. We have found that V-USC water enhances the hydrolysis reaction rate of cyanate ions by<br />10<sup>2</sup>-fold and that of ammonia borane by 10<sup>4</sup>-fold. This catalytic ability is found to depend upon the coupling ratio of the vibrational light-matter interaction. Given the vital importance of water for life and human activities, we expect that our finding not only offers an unconventional way of controlling chemical reactions by vacuum-field catalysis but also brings a fresh perspective to science and technology.</p>
|
Hidefumi Hiura; Atef Shalabney
|
Catalysis; Chemical Kinetics; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75a419abda27db8f8ebdc/original/vacuum-field-catalysis-accelerated-reactions-by-vibrational-ultra-strong-coupling.pdf
|
60c745f6bdbb891a2aa38b37
|
10.26434/chemrxiv.10292759.v1
|
Solid-State Phase Transformation and Self-Assembly of Amorphous Nanoparticles into Higher-Order Mineral Structures
|
Digging into nonclassical pathways to crystallization to unearth design principles for
fabricating advanced functionalized materials shapes the future of materials science. Nature
has long since been exploiting such nonclassical pathways to crystallization to build
inorganic-organic hybrid materials that fulfill support, mastication, defense, attack, or optical
functions. Especially, various biomineralizing taxa such as stony corals deposit metastable,
magnesium-rich, amorphous calcium carbonate nanoparticles that further transform into
higher-order mineral structures. Here we examine whether a similar process can be duplicate
in abiogenic conditions using synthetic, amorphous calcium magnesium carbonate
nanoparticles. Applying a combination of ultrahigh-resolution imaging, and, in situ, solidstate nuclear magnetic resonance (NMR) spectroscopy, we reveal the underlying mechanism
of the phase transformation of these synthetic amorphous nanoparticles into crystals. When
soaked in water, these synthetic amorphous nanoparticles are coated by a rigid hydration layer
of bound water molecules. In addition, fast chemical exchanges occur between hydrogens
from the nanoparticles and those from the free water molecules of the surrounding aqueous
medium. At some stage, crystallization spontaneously occurs, and we provide spectroscopic
evidence for a solid-state phase transformation of the starting amorphous nanoparticles into
crystals. Depending on their initial chemical composition, and especially on the amount of
magnesium, the starting amorphous nanoparticles can aggregate and form ordered mineral
structures through crystal growth by particle attachment, or rather dissolve and reprecipitate
into another crystalline phase. The former scenario offers promising prospects for exerting
some control over such non-classical pathway to crystallization to design mineral structures
that could not be achieved through a classical layer-by-layer growth.<br />
|
Stanislas Von Euw; Viacheslav Manichev; Margarita Rivers; Nagarajan Murali; Daniel J. Kelly; Paul G Falkowski
|
Aggregates and Assemblies; Ceramics; Nanostructured Materials - Materials; Microscopy; Nanostructured Materials - Nanoscience; Minerals; Solid State Chemistry; Self-Assembly; Spectroscopy (Physical Chem.); Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745f6bdbb891a2aa38b37/original/solid-state-phase-transformation-and-self-assembly-of-amorphous-nanoparticles-into-higher-order-mineral-structures.pdf
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67cef4f96dde43c908479cb5
|
10.26434/chemrxiv-2025-x0sv0
|
Environmental Control of Regio-/Stereoselectivity Across Mechanistically Similar Transformations
|
The control of regio- and stereoselectivity in organic transformations remains a foundational challenge in synthetic chemistry. While chemoselectivity can often be influenced by careful selection of reagents or protective groups, controlling regio- and stereoselectivity is far more nuanced, often requiring highly specific reaction conditions. In this work, we explore a unified approach to controlling both regio- and stereoselectivity across mechanistically related transformations, specifically focusing on epoxide openings and carbonyl additions. We demonstrate that the same environmental factors, here the nature of the Lewis Acid (LA), can be leveraged to influence divergent outcomes in these two reaction types by amplifying inherent differences between reaction sites/faces, leading to highly selective transformations. Our systematic evaluation of over 30 Lewis acids revealed a dichotomy between "labile" and "strong" activation modes, where strong LAs, such as AlCl3 and SnCl4, drive the highest levels of regio- and diastereoselectivity for both transformations. Further, there exists nuanced differences between the degree of influence of some LA within these mechanistically related transformations. These findings suggest that environmental factors can be broadly applied across different mechanistic classes to achieve selectivity, offering a versatile strategy for reaction optimization.
|
Anushka Asurumunige; Doris Itubo; Kerry Gilmore
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Acid Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cef4f96dde43c908479cb5/original/environmental-control-of-regio-stereoselectivity-across-mechanistically-similar-transformations.pdf
|
60c74355f96a003c9b286789
|
10.26434/chemrxiv.9104693.v1
|
Low Concentration Measurements of Nuclear Spin-Induced Optical Rotation Using SABRE Hyperpolarization
|
Nuclear spin-induced optical rotation (NSOR) is a promising phenomenon for molecular structure elucidation due to its sensitivity to electronic structure near atomic nuclei. It is the only experimentally verified nuclear magneto-optic effect, so far observed usually in neat liquids or in concentrated binary mixtures, with the proportion of the minor component at least 10\%. We report a method to extend the lower concentration range of NSOR measurements by two orders of magnitude by employing continuous-flow SABRE (signal amplification by reversible exchange) hyperpolarization. This approach significantly increases sensitivity of NSOR and enables its detection in dilute samples, as demonstrated with measurements of NSOR of 90 mmol/l solutions of pyridine and pyrazine. The results are compared with first principles calculations and a good agreement is found. The possibility to measure low concentration solutions significantly extends the pool of samples available for further studies of nuclear magneto-optic effects.
|
Petr Štěpánek; Anu M. Kantola
|
Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
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CHEMRXIV
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2019-07-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74355f96a003c9b286789/original/low-concentration-measurements-of-nuclear-spin-induced-optical-rotation-using-sabre-hyperpolarization.pdf
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651abe10ade1178b2486e455
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10.26434/chemrxiv-2023-z49qp
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Broadband APT (BAPT): a Versatile APT Experiment with Improved J-Compensation and Optimal Suppression of Artifacts in Cq-only Spectra
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A modified version of the CAPT (Compensated APT) experiments, the Broadband-APT (BAPT) sequence is proposed, that allows the user to record APT- and Cq-only spectra in a simple manner and that improves both the tolerance for wide ranges of 1JCH values in the APT spectra and the suppression of residual CHn signals in the Cq-only spectra. Compared to the original version with delays d1, of equal lengths, these improvements can be achieved with three different delays d1, d2, and d3, which can be set for three different one-bond coupling constants. The recording of APT and Cq-only spectra is governed most simply by a single constant, which adjusts the delay d2 and the phase programs for the two proton 90° pulses accordingly. These attributes make this experiment attractive for 13C analysis of small molecules, including spectral editing, particularly in high-throughput analysis laboratories.
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Peter Bigler; Ilche Gjuroski; julien Furrer
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Analytical Chemistry; Spectroscopy (Anal. Chem.)
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CC BY NC 4.0
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CHEMRXIV
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2023-10-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651abe10ade1178b2486e455/original/broadband-apt-bapt-a-versatile-apt-experiment-with-improved-j-compensation-and-optimal-suppression-of-artifacts-in-cq-only-spectra.pdf
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67a73cc981d2151a029f9b52
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10.26434/chemrxiv-2025-8q8jd
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Tuning the electric dipole transitions (5D0 → 7F2, and 5D0 → 7F4) in thin Eu-doped BiOCl nanosheets
|
The polarization and depolarization of layered ferroelectric materials can be tuned by altering the thickness of nanosheets apart from controlling inter/intra layer distances, doping of ions, surrounding dielectric environments, etc. In two-dimensional (2D) single-crystalline ferroelectric nanosheets, the reduction in the thickness facilitates the internal electric field, which leads to enhanced depolarization. BiOCl is a characteristic layered ferroelectric material that contains [Bi2O2]2+ layers arranged anisotropically along the c-direction. However, the depolarization and polarisation of BiOCl are significantly influenced by the thickness of its nanosheets. In this study, europium (Eu3+)-doped BiOCl nanosheets resembling a 2D-dimensional structure have been synthesized using the solid-state grinding method at ambient temperature. As a result of the depolarization effect, the intensity of the electric dipole (ED) transitions 5D0 → 7F2 and 5D0 → 7F4 increases in Eu3+-doped BiOCl nanosheets. Further, electric force microscopy (EFM) confirms that the electric field is present in close proximity to the surface of Eu3+-doped BiOCl. However, thiol capping helps in synthesizing uniform 2D nanosheets with reduced vertical dimensions (c-direction). It is observed that all the prepared samples with varying Eu ion concentrations show uniform nanosheet-like morphology. As the concentration of Eu ions increases in the BiOCl host lattice, the intensity of electric dipole transitions also increases. Fourier transform infrared spectroscopy (FT-IR) discloses the coating of 1-dodecanthiol on Eu-doped BiOCl molecules. Furthermore, the Eu-doped BiOCl samples demonstrated a prominent far-red emission at 700 nm, corresponding to the 5D0 → 7F4 transition. Moreover, this work emphasizes the synthesis of Eu-doped phosphor at an ambient temperature of 24 + 2 ˚C and generates a deeper understanding of the abnormal electric dipole (5D0 → 7F4) transition.
|
Dinesh Singh; Pankaj Poddar
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Physical Chemistry; Materials Science; Physical and Chemical Properties
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CC BY 4.0
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CHEMRXIV
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2025-02-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a73cc981d2151a029f9b52/original/tuning-the-electric-dipole-transitions-5d0-7f2-and-5d0-7f4-in-thin-eu-doped-bi-o-cl-nanosheets.pdf
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655b4d386e0ec7777f524821
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10.26434/chemrxiv-2023-mm3jk
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Cross-Linked Gold Nanoparticle Assemblies: What can we Learn from Single Flat Interfaces?
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Cross-linked gold nanoparticle (GNP) assemblies are valuable for a variety of applications, such as transducers for strain or gas sensors. To pave the way for understanding their sensing behavior on an atomistic scale, we ask whether their properties can be modeled by a single, flat, particle–particle interface. Employing reactive force field (ReaxFF) molecular dynamics simulations and a tight-binding density functional the- ory approach to coherent tunneling, we find that for alkane dithiolates, where most molecules will typically bridge between the gold surfaces, the interparticle distances, as well as the conductivity of the assembly, can be modeled to even quantitative accuracy with a single-interface model — if comparing to sufficiently large GPNs for which the flat surface is a good approximation. For alkane monothiols, where each molecule is only attached on one side, the difficulty of estimating surface density and the resulting degree of interlacing results, in our case, in underestimating the interparticle distances by around 5 Å. The increase of these distances (and the decrease of conductivity) as going to longer alkane chains, however, is still well reproduced. We discuss shortcomings of ReaxFF, such as not being able to describe thiol physisorption and producing spurious reactions between dithiolates, as well as factors influencing the validity of a single, flat, particle–particle interface model. Our model reduces the system complexity significantly compared to simulating entire GNP assemblies, enabling further mechanistic investigations of sensing properties of these systems with atomistic approaches, and, potentially, screening of ligands for specific sensing applications.
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Karen Schaefer; Chih-Yin Liu; Andreas Meyer; Hendrik Schlicke; Tobias Vossmeyer; Carmen Herrmann
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Theoretical and Computational Chemistry; Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Theory - Computational; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2023-11-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655b4d386e0ec7777f524821/original/cross-linked-gold-nanoparticle-assemblies-what-can-we-learn-from-single-flat-interfaces.pdf
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62cf17f8a7d17e75e758ecca
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10.26434/chemrxiv-2022-wcjjj
|
Multi-element compound specific isotope analysis reveals aerobic biodegradation of 2,3-dichloroaniline at a complex site
|
Compound specific isotope analysis (CSIA) is an established tool for evaluating in situ transformation of organic contaminants. To date, CSIA has never been applied to understand the in situ fate of 2,3-dichloroaniline (2,3-DCA). Although persistent in the environment, several microorganisms were identified as able to degrade 2,3-DCA, thus making this contaminant a potential candidate for bioremediation. Using a controlled-laboratory experiment, we determined, for the first time, negligible carbon and hydrogen isotope fractionation, and a significant inverse nitrogen isotope effect during aerobic 2,3-DCA biodegradation via dioxygenation using a mixed enrichment culture. The corresponding AKIEN values ranged from 0.9938±0.0003 to 0.9922±0.0004. The ε_(N,bulk) values, ranging from +6.2±0.3 to +7.9±0.4‰ was applied to investigate the potential in situ 2,3-DCA biotransformation at a contaminated site, where the field-obtained carbon and nitrogen isotope signatures suggested aerobic biotransformation by native microorganisms. Under the assumption of the applicability of the Rayleigh model at the field site, the extent of 2,3-DCA transformation was estimated at up to 80 to 90%. This study proposes multi-element CSIA of 2,3-DCA as a novel application to study 2,3-DCA fate in groundwater and surface water.
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Shamsunnahar Suchana; Sofia Pimentel Araujo; Line Lomheim; Elizabeth Edwards; Elizabeth Erin Mack; Elodie Passeport
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Organic Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Bioorganic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2022-07-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cf17f8a7d17e75e758ecca/original/multi-element-compound-specific-isotope-analysis-reveals-aerobic-biodegradation-of-2-3-dichloroaniline-at-a-complex-site.pdf
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60c74c92ee301c05e9c7a0e1
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10.26434/chemrxiv.12456215.v1
|
How Good Are Polarizable and Flexible Models for Water: Insights from a Many-Body Perspective
|
<div>
<div>
<div>
<p>We present a systematic analysis of state-of-the-art polarizable and flexible water models from a many-body perspective, with a specific focus on their ability to represent the
Born-Oppenheimer potential energy surface of water, from the gas to the liquid phase. Using coupled cluster data in the completed basis set limit as a reference, we examine the
accuracy of the polarizable models in reproducing individual many-body contributions to
interaction energies and harmonic frequencies of water clusters, and compare their performance with that of MB-pol, an explicit many-body model that has been shown to correctly
predict the properties of water across the entire phase diagram. Based on these comparisons, we use MB-pol as a reference to analyze the ability of the polarizable models to
reproduce the energy landscape of liquid water at ambient conditions. We find that, while
correctly reproducing the energetics of minimum-energy structures, the polarizable models examined in this study suffer from inadequate representations of many-body effects for
distorted configurations. To investigate the role played by geometry-dependent representations of 1-body charge distributions in reproducing coupled cluster data for both interaction and many-body energies, we introduce a simplified version of MB-pol that adopts
fixed atomic charges and demonstrate that the new model retains the same accuracy as the
original MB-pol model. Based on the analyses presented in this study, we believe that
future developments of both polarizable and explicit many-body models should continue
in parallel and would benefit from synergistic efforts aimed at integrating the best aspects
of the two theoretical/computational frameworks.
</p>
</div>
</div>
</div>
|
Eleftherios Lambros; Paesani Lab
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Computational Chemistry and Modeling; Theory - Computational; Clusters; Physical and Chemical Properties; Quantum Mechanics; Spectroscopy (Physical Chem.); Statistical Mechanics; Structure; Thermodynamics (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-06-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c92ee301c05e9c7a0e1/original/how-good-are-polarizable-and-flexible-models-for-water-insights-from-a-many-body-perspective.pdf
|
63d8c3c5d1632f652bea45d4
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10.26434/chemrxiv-2023-l8440
|
Unusual selective monitoring of N,N-dimethylformamide in a two-dimensional layered field-effect transistor
|
N,N-Dimethylformamide (DMF) is an essential solvent in industries and pharmaceutics. Its market size range was estimated to be 2 billion US dollars in 2022. Monitoring DMF in solution environments in real time is significant because of its toxicity. However, DMF is not a redox-active molecule; therefore, selective monitoring DMF in solutions in real time requires an unprecedented design at the scale of atomic resolution. In this paper, we propose a selective DMF sensor using a molybdenum disulfide (MoS2) field-effect transistor (FET). The sensor responds to DMF molecules, but not to similar molecules of formamide, N,N-diethylformamide, and N,N-dimethylacetamide. The plausible atomic mechanism is the oxygen substitution sites on MoS2, on which the DMF molecule shows exceptional orientation. The thin structure of MoS2-FET can be incorporated into a microfluidic chamber, which leads to DMF monitoring in real time by exchanging solutions subsequently. The designed device shows DMF monitoring in NaCl ionic solutions from 1 to 200 L/mL. This work proposes the concept of selectively monitoring redox-inactive molecules based on the non-ideal atomic affinity site on the surface of two-dimensional semiconductors.
|
Akito Fukui; Keigo Matsuyama; Hiroaki Onoe; Shun Itai; Hidekazu Ikeno; Shunsuke Hiraoka; Kousei Hiura; Yuh Hijikata; Jenny Pirillo; Takahiro Nagata; Kuniharu Takei; Takeshi Yoshimura; Norifumi Fujimura; Daisuke Kiriya
|
Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Nanodevices; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-01-31
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d8c3c5d1632f652bea45d4/original/unusual-selective-monitoring-of-n-n-dimethylformamide-in-a-two-dimensional-layered-field-effect-transistor.pdf
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636969defbfd382f46d30947
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10.26434/chemrxiv-2022-g0bg9
|
Disturbance of Intermolecular Forces: Eutectics as a New Tool for the Preparation of Vapor-Phase Deposition Precursors
|
The volatile bis(tert-butylimido)-dichloromolybdenum(VI) compounds, (tBuN)2MoCl2·dad (dad = 1,4-di-tert-butyl-1,3-diazabutadiene) (1) and [(tBuN)2MoCl(μ-Cl)·(tBuNH2)]2 (2), form a eutectic, with a two to one composition (χ2 = 0.33). A decrease of 40 °C in the melting temperature has been observed between the eutectic mixture and the pure compounds. We have isolated a co-crystal of (tBuN)2MoCl2·dme (dme = 1,2-dimethoxyethane) (3) and 2, also in a two to one ratio, which serves as a structural model for such mixtures. The lower melting point of carefully chosen eutectic mixtures can offer more consistent precursor delivery in deposition processes.
|
Michael Land; Katherine Robertson; Jason Clyburne; Seán Barry
|
Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Physical and Chemical Properties; Materials Chemistry; Crystallography – Inorganic
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CC BY NC ND 4.0
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CHEMRXIV
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2022-11-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636969defbfd382f46d30947/original/disturbance-of-intermolecular-forces-eutectics-as-a-new-tool-for-the-preparation-of-vapor-phase-deposition-precursors.pdf
|
61afb738dcbea2719b99c4c9
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10.26434/chemrxiv-2021-wtjm2-v2
|
Proteoform-selective imaging of tissues using mass spectrometry
|
Unraveling the complexity of biological systems relies on the development of new approaches for spatially resolved proteoform-specific analysis of the proteome. Herein, we employ nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI) for the proteoform-selective imaging of biological tissues. Nano-DESI generates multiply charged protein ions, which is advantageous for their structural characterization using tandem mass spectrometry (MS/MS) directly on the tissue. Proof-of-concept experiments demonstrate that nano-DESI MSI combined with on-tissue top-down proteomics is ideally suited for the proteoform-selective imaging of tissue sections. Using rat brain tissue as a model system, we provide the first evidence of differential proteoform expression in different regions of the brain.
|
Manxi Yang; Hang Hu; Pei Su; Paul M. Thomas; Jeannie M. Camarillo; Joseph B. Greer; Bryan P. Early; Ryan T. Fellers; Neil L. Kelleher; Julia Laskin
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Analytical Chemistry; Imaging; Mass Spectrometry
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CC BY NC 4.0
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CHEMRXIV
|
2022-01-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61afb738dcbea2719b99c4c9/original/proteoform-selective-imaging-of-tissues-using-mass-spectrometry.pdf
|
60c74390f96a000def286835
|
10.26434/chemrxiv.9252680.v1
|
A Commercially Available Ruthenium Compound for Catalytic Hydrophosphination
|
Hydrophosphination with a commercially available ruthenium compound, bis(cyclopentadienylruthenium dicarbonyl) dimer ([CpRu(CO)2]2), was explored. Styrene derivatives or Michael acceptors react readily with either primary or secondary phosphines in the presence of 0.1 mol% of [CpRu(CO)2]2 under photolysis with an inexpensive and commercially available UV-A 9W lamp. In comparison to related photoactivated hydrophosphination reactions with [CpFe(CO)2]2 as a catalyst, these ruthenium-catalyzed reactions proceed at greater relative rates with lower catalyst loadings. <br />
|
Michael
P. Cibuzar; Steven G. Dannenberg; Rory Waterman
|
Catalysis; Main Group Chemistry (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-08-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74390f96a000def286835/original/a-commercially-available-ruthenium-compound-for-catalytic-hydrophosphination.pdf
|
60c74c19842e654d80db3268
|
10.26434/chemrxiv.12421196.v1
|
Metal-Chelating Benzothiazole Multifunctional Compounds for the Modulation and 64Cu PET Imaging of Aβ Aggregation
|
While Alzheimer’s Disease (AD) is the most common
neurodegenerative disease, there is still a dearth of efficient therapeutic and
diagnostic agents for this disorder. Reported herein are a series of new
multifunctional compounds (MFCs) with appreciable affinity for amyloid
aggregates that can be potentially used for both the modulation <a>of A</a>b aggregation
and its toxicity, as well as positron emission tomography (PET) imaging of Ab
aggregates. Firstly, among the six compounds tested <b>HYR-16</b> is shown to be capable to reroute the toxic Cu-mediated Ab
oligomerization into the formation of less toxic amyloid fibrils. In addition, <b>HYR-16</b> can also alleviate the formation
of reactive oxygen species (ROS) caused by Cu<sup>2+</sup> ions through
Fenton-like reactions. Secondly, these MFCs can be easily converted to PET imaging
agents by pre-chelation with the <sup>64</sup>Cu radioisotope, and the Cu
complexes of <b>HYR-4</b> and <b>HYR-17</b> exhibit good fluorescent staining
and radiolabeling of amyloid plaques both <i>in
vitro</i> and <i>ex vivo</i>. Importantly,
the <sup>64</sup>Cu-labeled <b>HYR-17</b> is
shown to have a significant brain uptake of up to 0.99 ± 0.04 %ID/g. Overall, by
evaluating the various properties of these MFCs valuable structure-activity
relationships were obtained that should aid the design of improved therapeutic
and diagnostic agents for AD.
|
Yiran Huang; Hong-Jun Cho; Nilantha Bandara; Liang Sun; Diana Tran; Buck E. Rogers; Liviu M. Mirica
|
Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
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CHEMRXIV
|
2020-06-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c19842e654d80db3268/original/metal-chelating-benzothiazole-multifunctional-compounds-for-the-modulation-and-64cu-pet-imaging-of-a-aggregation.pdf
|
6422b064647e3dca99a4752b
|
10.26434/chemrxiv-2023-j4fg9
|
The antimicrobial properties of Pd(II)- and Ru(II)-pyta complexes
|
Infections associated with antimicrobial resistance (AMR) are poised to become the leading cause of death in the next few decades, a scenario that can be ascribed to two phenomena: antibiotic over-prescription and a lack of antibiotic drug development. The crowd-sourced initiative CO-ADD has been testing research compounds contributed by researchers around the world to find new antimicrobials to combat AMR, and during this campaign has found that metallodrugs might be a promising, yet untapped source. To this end, we submitted 18 Pd(II) and Ru(II) – pyridyl-1,2,3-triazolyl complexes which were developed as catalysts for their antimicrobial properties. It was found that the Pd-complexes possessed potent antifungal activity, especially Pd1, with MICs between 0.06 – 0.125 µg/mL against C. glabrata. The in vitro studies were extended to in vivo studies in G. mellonella larvae where it was established that the compounds were non-toxic. Here we effectively demonstrate the potential of Pd(II)-pyta complexes as antifungal agents.
|
Angelo Frei; Annick Van Niekerk; Cassiem M. Joseph; Angela Kavanagh; Hue Dinh; Andrew J. Swarts; Selwyn F. Mapolie; Johannes Zuegg; Amy K. Cain; Alysha G. Elliott; Mark A. T. Blaskovich
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Organometallic Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422b064647e3dca99a4752b/original/the-antimicrobial-properties-of-pd-ii-and-ru-ii-pyta-complexes.pdf
|
60c75312bb8c1aa22a3dbf98
|
10.26434/chemrxiv.13377212.v1
|
Non-Hydrolytic Sol-Gel Route to a Family of Hybrid Mesoporous Aluminosilicate Ethanol Dehydration Catalysts
|
Organic-inorganic hybrid materials are nowadays intensely studied for potential applications in heterogeneous catalysis because their properties and catalytic behavior differ from pristine inorganic counterparts. The organic groups at the catalyst surface can modify not only its hydrophilicity, but also acidity, hydrothermal stability, porosity, etc. In some cases, such properties alteration leads to improved catalytic performance in terms of activity, selectivity, or stability. However, the choice of organic groups stays relatively narrow, as most reports focus on pendant methyl groups. Here, a series of mesoporous hybrid aluminosilicate materials containing various organic groups was prepared in one pot by non-hydrolytic sol-gel (NHSG). Both aromatic and aliphatic, pendant and bridging organic groups were incorporated. The presence of the organic groups in the bulk and at the outermost surface of the materials was verified by solid-state NMR and ToF-SIMS, respectively. Aluminum is mostly incorporated in tetrahedral coordination in the hybrid silica matrix. The organically modified mesoporous aluminosilicate samples were tested as catalysts in the gas phase ethanol dehydration (which relies on solid acids) and most of them outperformed the purely inorganic catalyst benchmark. While a direct influence of surface hydrophilicity or hydrophobicity (as probed by water sorption and water contact angle measurements) appeared unlikely, characterization of acidity (IR-pyridine) revealed that the improved performance for hybrid catalysts can be correlated with a modification of the acidic properties. In turn, acidity is determined by the quality of the dispersion of Al centers in the form of isolated sites in the hybrid silica matrix. All in all, this study establishes a "ranking" for a variety of organic groups in terms of their effect on gas-phase ethanol dehydration to ethylene; ethylene yield decreases in this order: bridging xylylene ≈ pendant methyl > pendant benzyl > bridging methylene ≈ inorganic benchmark (no organic groups) > bridging ethylene.<br />
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Ales Styskalik; Imène Kordoghli; Claude Poleunis; Arnaud Delcorte; Denis Dochain; Zdeněk Moravec; Julius Vida; Tomas Homola; Carmela Aprile; Luca Fusaro; François Devred; Damien Debecker
|
Hybrid Organic-Inorganic Materials; Nanocatalysis - Catalysts & Materials; Acid Catalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75312bb8c1aa22a3dbf98/original/non-hydrolytic-sol-gel-route-to-a-family-of-hybrid-mesoporous-aluminosilicate-ethanol-dehydration-catalysts.pdf
|
67c5963a81d2151a02ddaf51
|
10.26434/chemrxiv-2024-hs24g-v2
|
Citrus IntegroPectin: a computational insight
|
Imparted with uniquely high and broad-scope bioactivity including antioxidant, anti-inflammatory, cardioprotective, neuroprotective, antimicrobial and anticancer properties, the IntegroPectin bioconjugate obtained from citrus processing waste via hydrodynamic cavitation (HC) was investigated via Density Functional Theory computational approach. The main flavonoids of grapefruit (naringenin), orange (hesperidin), and lemon (eriocitrin) were taken into account along with a model structure for pectin including the RG-I rhamnogalacturonan chains. Results indicate that the pectin-flavonoid conjugate formation is slightly endergonic for all three conjugates, confirming the key role of HC in opening an energy window that allows overcoming the slightly positive ΔGform thanks to the energy released by the imploding cavitation bubbles. Remarkably, recent experimental results confirm these theoretical findings.
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Valeria Butera; Rosaria Ciriminna; Chiara Valenza; Giovanna Li Petri; Giuseppe Angellotti; Giampaolo Barone; Francesco Meneguzzo; Valentina Di Liberto; Angela Bonura; Mario Pagliaro
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling
|
CC BY NC 4.0
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CHEMRXIV
|
2025-03-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c5963a81d2151a02ddaf51/original/citrus-integro-pectin-a-computational-insight.pdf
|
64bf98f8b053dad33ad8c002
|
10.26434/chemrxiv-2023-fm49h
|
Accessing Metal-Specific Orbital Interactions in C-H Activation using Resonant Inelastic X-ray Scattering
|
Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C-H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the bidirectional charge-transfer between an incoming alkane C-H group and the transition metal is the decisive interaction in the C-H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, we propose metal specific and time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) at the transition metal L-edge as a method to provide a full account of the evolution of metal-alkane interactions during transition-metal mediated C-H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO)2), we demonstrate with a combination of experiment and quantum chemical simulation how the Rh-centered valence-excited final states probed with VtC-RIXS directly reflect changes in donation and back-donation between the alkane C-H group and the transition metal as the reaction proceeds via its intermediates. Following the initial photo-triggered CO dissociation, we find substantial reduction in charge donation onto the metal and the resulting stabilization of metal-centered states as the alkane coordinates to the Rh center in a σ-complex intermediate. C-H bond cleavage in the final oxidative addition step is instead characterized by a substantial increase in back-donation as the new Rh-hydrogen and Rh-carbon bonds are formed. We benchmark and validate our simulations against experimental steady-state measurements. With our study, we predict the key spectral fingerprints for future time-resolved experiments of C-H activation reactions with CpRh(CO)2 and related compounds.
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Ambar Banerjee; Raphael M. Jay; Torsten Leitner; Ru-Pan Wang; Jessica Harich; Robert Stefanuik; Michael R. Coates; Emma V. Beale; Victoria Kabanova; Abdullah Kahraman; Anna Wach; Dmitry Ozerov; Christopher Arrell; Christopher Milne; Philip J. M. Johnson; Claudio Cirelli; Camila Bacellar; Nils Huse; Michael Odelius; Philippe Wernet
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Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Spectroscopy (Inorg.); Theory - Inorganic; Photochemistry (Physical Chem.)
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CC BY NC 4.0
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CHEMRXIV
|
2023-07-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bf98f8b053dad33ad8c002/original/accessing-metal-specific-orbital-interactions-in-c-h-activation-using-resonant-inelastic-x-ray-scattering.pdf
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65a8bd0366c1381729b6413a
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10.26434/chemrxiv-2024-gt124
|
In situ monitoring of the Shikimate pathway: A combinatorial approach of Raman reverse stable isotope probing and hyperspectral imaging.
|
Our research is focused on evaluating the potentials of Raman reverse stable isotope probing for sensing and visualizing the Shikimate pathway activity in prokaryotic and eukaryotic model systems in a cost-effective and non-destructive manner at community and single cell level in situ. In this work, we have successfully demonstrated that by using unlabeled 12C-glucose as the sole carbon source in the 13C labelled microbial culture medium the Shikimate pathway can be monitored qualitatively and quasi-quantitatively. The Shikimate Pathway links central carbon metabolism to biosynthesis of aromatic ring containing metabolites such as aromatic amino acids, folates, salicylic acid, and others. The incorporation 12C in the 13C labelled metabolome pool causes a blue shift in the Raman spectra. Phenylalanine was selected as representative band shikimate pathway activity marker. Temporal changes in the intensity of representative bands over a period of 0 to 24 hours have been analyzed to demonstrate the feasibility of this approach. We have also visualized the Shikimate pathway activity and phenylalanine turnover using Raman hyperspectral imaging aided by multivariate curve resolution. The novelty of our study lies in the fact that for the first time Shikimate pathway activity has been monitored in situ in a cost-effective, extraction free, and non-destructive manner. The overall findings are very encouraging and support the prospective utility of this approach for monitoring pathways related to aromatic rings containing metabolites. This can have a wide range of applications in sensing commercially and medically relevant microbial metabolites in situ.
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Jiro Karlo; Aryan Gupta; SURYA PRATAP SINGH
|
Biological and Medicinal Chemistry; Chemical Biology
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CC BY NC 4.0
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CHEMRXIV
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2024-01-19
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a8bd0366c1381729b6413a/original/in-situ-monitoring-of-the-shikimate-pathway-a-combinatorial-approach-of-raman-reverse-stable-isotope-probing-and-hyperspectral-imaging.pdf
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60f048b87e679770f54edfae
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10.26434/chemrxiv-2021-k4v9r
|
Pre-Nucleation Clusters Predict Crystal Structures in Models of Chiral Molecules
|
Kinetics can play an important role in the crystallization of molecules and give rise to polymorphism, the prevalent ability of molecules to form more than one crystal structure. Current computational methods of crystal structure prediction, however, focus almost exclusively on identifying the thermodynamically stable polymorph. Kinetic factors of nucleation and growth are often neglected because the underlying microscopic processes are thought to be complex and accurate rate calculations are numerically cumbersome. In this work, we use molecular dynamics computer simulations to study a simple molecular model that reproduces the crystallization behavior of real chiral molecules, including the formation of enantiopure and racemic crystals, as well as polymorphism. We show that in many cases, the crystal that robustly forms in simulations is not the one with the lowest free energy. We demonstrate that at high supersaturation the prevailing polymorph can be accurately predicted by considering the similarities between prevalent oligomeric species in solution and molecular motifs in the crystal structure. For the case of racemic mixtures, we even find that knowledge of crystal free energies is not necessary and kinetic considerations are sufficient to determine if the system will undergo spontaneous chiral separation. Our results suggest conceptually simple ways of improving current crystal structure prediction methods.
|
John E. Carpenter; Michael Gruenwald
|
Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Self-Assembly; Statistical Mechanics; Crystallography
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CC BY NC ND 4.0
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CHEMRXIV
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2021-07-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f048b87e679770f54edfae/original/pre-nucleation-clusters-predict-crystal-structures-in-models-of-chiral-molecules.pdf
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614494117c08d570df459beb
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10.26434/chemrxiv-2021-d6k2z
|
Red-Emissive Nanocrystals of Cs4MnxCd1-xSb2Cl12 Layered Perovskite
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Layered double perovskite are currently investigated as emerging halide-based materials for optoelectronic applications. Herein, we present the synthesis of Cs4MnxCd1-xSb2Cl12 (0 ≤ x ≤ 1) nanocrystals (NCs). X-ray powder diffraction evidences the retaining of the same crystal structure for all the inspected composition; transmission electron microscopy revealed monodisperse particles with a mean size of 10.6 nm. The absorption spectra seem to be mostly determined by transitions related to Sb3+, whereas Mn2+ induced a red emission in the 625 – 650 nm range. The emission intensity and position varies with the Mn2+ content and reaches the maximum for the composition with x = 0.12. Finally, we demonstrated that the photoluminescence quantum yield (PLQY) of the latter NCs was boosted from 0.3% to 3.9% through a post-synthesis treatment. The present work enlarges the knowledge of colloidal layered double perovskite nanocrystals, stimulating future investigations of this emerging class of material.
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Emanuela Sartori; Marta Campolucci; Dmitry Baranov; Min Zeng; Stefano Toso; Maurizio Ferretti; Zeger Hens; Liberato Manna; Federico Locardi
|
Nanoscience
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-09-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614494117c08d570df459beb/original/red-emissive-nanocrystals-of-cs4mnx-cd1-x-sb2cl12-layered-perovskite.pdf
|
60c740ab567dfe75f8ec3c2b
|
10.26434/chemrxiv.7808435.v1
|
Long-lived Triplet Excitons Formed by Exergonic Intramolecular Singlet Fission of an Adamantane-linked Tetracene Dyad
|
<div>An adamantane-linked tetracene dyad (Tc–Ad–Tc) undergoes exergonic intramolecular singlet fission (SF), producing longlived (τ = 175 μs) and high-energy (2 x 1.03 eV) multiexcitons. Timeresolved absorption, fluorescence decay, and electron paramagnetic resonance (EPR) spectroscopic analysis revealed that the long-lived triplet species is generated in this system via correlated triplet pair having singlet and quintet characteristics. Time-resolved EPR analysis revealed that conversion of <sup>1</sup>(<sup>3</sup>Tc–Ad–<sup>3</sup>Tc)* -> <sup>5</sup>(<sup>3</sup>Tc–Ad–<sup>3</sup>Tc)* requires small conformational dynamics accompanied by molecular motion. Analysis of the geometries of the quintet states shows that formation of the long-lived multiexciton is enabled by precise and close alignment of the tetracene moieties, which leads to their moderate interaction in the singlet excited state, while triplet–triplet annihilation is prevented by quintet generation. The presence of aliphatic linkages, like the rigid adamantane group, might enable effective conservation of intrinsic S<sub>1</sub> and T<sub>1</sub> levels of the original monomers, and moderate bridge-mediated σ–π interaction leading to exergonic intramolecular SF involving <sup>1</sup>Tc*–Ad–Tc -> <sup>1</sup>(<sup>3</sup>Tc–Ad–<sup>3</sup>Tc)*.</div><div><br /></div>
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Yasunori Matsui; Shuhei Kawaoka; Hiroki Nagashima; Tatsuo Nakagawa; Naoki Okamura; Takuya Ogaki; Eisuke Ohta; Seiji Akimoto; Shigeyuki Yagi; Yasuhiro Kobori; Hiroshi Ikeda
|
Physical Organic Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-03-11
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740ab567dfe75f8ec3c2b/original/long-lived-triplet-excitons-formed-by-exergonic-intramolecular-singlet-fission-of-an-adamantane-linked-tetracene-dyad.pdf
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6350b9d186473a47d31a8492
|
10.26434/chemrxiv-2022-zz776
|
A Unified System for Molecular Property Predictions: Oloren ChemEngine and its Applications
|
Molecular property predictors form the core of any AI-enabled drug discovery strategy. In recent years, there has been significant research in this area, resulting in the development of powerful predictors and representations. However, these diverse predictors have different software interfaces, dependencies, and levels of documentation. Due to lack of a unified API for molecular property prediction, an AI-enabled drug discovery endeavor often necessitates a tangled web of scripts, notebooks, and configuration. This makes it is needlessly difficult to share, distribute, and manage predictors, to ensemble predictors together, and to provide universal AI explainability tools. To this end, we present Oloren ChemEngine (OCE), an open-source Python library with a unified API for molecular property predictors with simplified model management and reproducibility. Using OCE, we create models which achieve superior performance on ADME/Tox prediction tasks by ensembling and integrating many different molecular property prediction methods. We include model-agnostic uncertainty quantification using calibrated confidence intervals and probabilities as well as interpretability using counterfactual methods.
|
David Huang; Sauhaarda (Raunak) Chowdhuri; Andrew Li; Alex Li; Ayush Agrawal; Kameron Gano; Andy Zhu
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry
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CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6350b9d186473a47d31a8492/original/a-unified-system-for-molecular-property-predictions-oloren-chem-engine-and-its-applications.pdf
|
65c3b62366c1381729295301
|
10.26434/chemrxiv-2024-8pqmg-v2
|
Imaging poly(ADP-ribose) polymerase-1 (PARP1) in vivo with 18F-labeled brain penetrant positron emission tomography (PET) ligand
|
Poly(ADP-ribose) polymerase 1 (PARP1) is a multifunctional protein involved in diverse cellular functions, notably DNA damage repair. Pharmacological inhibition of PARP1 holds potential therapeutic benefits for various pathologies. Despite the current FDA approval of PARP inhibitors, challenges persist in achieving PARP1 selectivity and effective blood-brain barrier (BBB) penetration. The development of a PARP1-specific positron emission tomography (PET) ligand is crucial for disease biology and target occupancy studies, aiding the development of PARP1-specific inhibitors. In this study, we leverage the recently identified PARP1 inhibitor, AZD9574, to introduce the design and development of its 18F-isotopologue ([18F]5). Our comprehensive approach, encompassing pharmacological, cellular, autoradiographical, and in vivo PET imaging in non-human primates, demonstrates the capacity of [18F]5 for specific binding to PARP1 and successful penetration of the BBB. These findings position [18F]5 as a viable molecular imaging tool, poised to facilitate the exploration of physiopathological changes of PARP1 across various diseases.
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Xin Zhou; Jiahui Chen; Jimmy S. Patel; Wenqing Ran; Yinlong Li; Richard S. Van; Mostafa M. H. Ibrahim; Chunyu Zhao; Yabiao Gao; Jian Rong; Ahmad F. Chaudhary; Guocong Li; Junqi Hu; April T. Davenport; James D. Daunais; Yihan Shao; Chongzhao Ran; Thomas L. Collier; Ahmed Haider; David M. Schuster; Allan Levey; Lu Wang; Gabriel Corfas; Steven H. Liang
|
Biological and Medicinal Chemistry; Organic Chemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-02-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c3b62366c1381729295301/original/imaging-poly-adp-ribose-polymerase-1-parp1-in-vivo-with-18f-labeled-brain-penetrant-positron-emission-tomography-pet-ligand.pdf
|
63452c67ba8a6d8ac9714c6f
|
10.26434/chemrxiv-2022-3f996
|
Active Machine Learning for Chemical Engineers: a Bright Future Lies Ahead!
|
By combining machine learning with design of experiments, so-called active machine learning, more efficient and cheaper research can be conducted. Machine learning algorithms are more flexible, and are better at investigating the processes spanning all length scales of chemical engineering. While the active machine learning algorithms are maturing, its applications are lacking behind. Three types of challenges faced by active machine learning are identified and ways to overcome them are discussed: the convincing of the experimental researcher, the flexibility of data creation, and the robustness of the active machine learning algorithms. A bright future lies ahead for active machine learning in chemical engineering thanks to increasing automation and more efficient algorithms to drive novel discoveries.
|
Yannick Ureel; Maarten R. Dobbelaere; Yi Ouyang; Kevin De Ras; Maarten K. Sabbe; Guy B. Marin; Kevin M. Van Geem
|
Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Heterogeneous Catalysis
|
CC BY 4.0
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CHEMRXIV
|
2022-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63452c67ba8a6d8ac9714c6f/original/active-machine-learning-for-chemical-engineers-a-bright-future-lies-ahead.pdf
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636a61c28e0d35483a11ce94
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10.26434/chemrxiv-2022-z7tc5-v2
|
Scrutinizing Formally NiIV Centers through the Lenses of Core Spectroscopy, Molecular Orbital Theory, and Valence Bond Theory
|
Nickel K- and L2,3-edge X-ray absorption spectra (XAS) are discussed for 13 molecules with nickel centers spanning a range of formal oxidation states from II to IV. K-edge XAS is shown to be an unreliable metric of physical oxidation state for these Ni complexes. Meanwhile, L2,3-edge XAS reveals that the physical d-counts of the formally NiIV compounds measured lie well above the d6 count implied by the oxidation state formalism. The generality of this phenomenon is explored computationally by scrutinizing 8 additional complexes. The extreme case of NiF62– is considered using high-level molecular orbital approaches as well as advanced valence bond methods. The emergent electronic structure picture reveals that even highly electronegative F– is incapable of supporting a physical d6 NiIV center. The reactivity of NiIV complexes in C–C bond forming reactions is then discussed, highlighting the dominant role of the ligands in this chemistry over that of the metal centers.
|
Ida DiMucci; Charles Titus; Dennis Nordlund; James Bour; Eugene Chong; Mikhail Kosobokov; Caleb Martin; Noel Nebra; David Vicic; Sam Yruegas; Samantha MacMillan; Jason Shearer; Kyle Lancaster
|
Inorganic Chemistry; Bonding; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-11-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636a61c28e0d35483a11ce94/original/scrutinizing-formally-ni-iv-centers-through-the-lenses-of-core-spectroscopy-molecular-orbital-theory-and-valence-bond-theory.pdf
|
669126075101a2ffa8300744
|
10.26434/chemrxiv-2024-98wtp
|
Combining Real-Space and Local Range Separation – The MH24 Locally Range-Separated Local Hybrid Functional
|
In this work, the development of a new general-purpose exchange-correlation hybrid functional based on the recent locally range-separated local hybrid (LRSLH) approach is presented. In particular, the new functional, denoted as MH24, combines a non-empirical treatment of the admixture of locally range-separated long-range exact exchange with a new real-space separation approach for the real-space exact-exchange admixture governed by the local mixing function (LMF) and a new empirical LYP-based approach for the correlation functional to enable a flexible description of same- and opposite-spin correlation effects. The nine empirical parameters of the MH24 model have been optimized using a state-of-the-art super-self-consistent-field approach, which exploits the sensitivity of specific properties such as core ionization potentials, electron affinities and atomization energies to the exact-exchange admixture in specific regions in real space and the separation of the LMF into a core, valence and asymptotic part. The optimized MH24 functionals are shown to be able to simultaneously provide good accuracy for valence and core properties as well as for electron affinities and noble gase dimer dissociation curves, while satisfying multiple known exact constraints related to the exact-exchange admixture in hybrid functionals. MH24 is thus a major step toward the development of more sophisticated hybrid functional models.
|
Toni M. Maier
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC 4.0
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CHEMRXIV
|
2024-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669126075101a2ffa8300744/original/combining-real-space-and-local-range-separation-the-mh24-locally-range-separated-local-hybrid-functional.pdf
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60c746c7842e65f251db289b
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10.26434/chemrxiv.7976474.v4
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Assessing the Calculation of Exchange Coupling Constants and Spin Crossover Gaps Using the Approximate Projection Model to Improve Density Functional Calculations
|
This work evaluates the quality of exchange coupling constant and spin crossover gap calculations using density functional theory corrected by the Approximate Projection model. Results show that improvements using the Approximate Projection model range from modest to significant. This study demonstrates that, at least for the class of systems examined here, spin-projection generally improves the quality of density functional theory calculations of $J$-coupling constants and spin crossover gaps. Furthermore, it is shown that spin-projection can be important for both geometry optimization and energy evaluations. The Approximate Projection model provides an affordable and practical approach for effectively correcting spin-contamination errors in such calculations.
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Xianghai Sheng; Lee Thompson; Hrant Hratchian
|
Theory - Computational; Transition Metal Complexes (Organomet.)
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CC BY 4.0
|
CHEMRXIV
|
2019-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c7842e65f251db289b/original/assessing-the-calculation-of-exchange-coupling-constants-and-spin-crossover-gaps-using-the-approximate-projection-model-to-improve-density-functional-calculations.pdf
|
60c751b8469df426f0f44a74
|
10.26434/chemrxiv.13194932.v1
|
Mechanistic Studies of Pd(II)-Catalyzed E/Z Isomerization of Unactivated Alkenes: Evidence for a Monometallic Nucleopalladation Pathway
|
Pd(II)-catalyzed <i>E</i>/<i>Z</i> isomerization of alkenes is a common process—yet is largely uncharacterized, particularly with non-conjugated alkenes. In this work, the mechanism of Pd(II)-catalyzed <i>E</i>/<i>Z</i> isomerization of unactivated olefins containing an aminoquinoline-based amide directing group is probed using <i>in situ</i> kinetic analysis, spectroscopic studies, kinetic modeling, and DFT calculations. The directing group allows for stabilization and monitoring of previously undetectable intermediates. Collectively, the data are consistent with isomerization occurring through a monometallic nucleopalladation mechanism.
|
Rei Matsuura; Malkanthi Karunananda; Mingyu Liu; Nhi Nguyen; Donna Blackmond; Keary Engle
|
Organic Compounds and Functional Groups; Physical Organic Chemistry; Stereochemistry; Computational Chemistry and Modeling; Homogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-11-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751b8469df426f0f44a74/original/mechanistic-studies-of-pd-ii-catalyzed-e-z-isomerization-of-unactivated-alkenes-evidence-for-a-monometallic-nucleopalladation-pathway.pdf
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661ab465418a5379b0c77930
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10.26434/chemrxiv-2024-f8rq5
|
Optimum Model-Based Design of Diagnostics Experiments (DOE) with Hybrid Pulse Power Characterization (HPPC) for Lithium-Ion Batteries
|
Diagnostics of lithium-ion batteries are frequently performed in battery management systems for optimized operation of lithium-ion batteries or for second-life usage. However, attempting to extract dominant degradation information requires long rest times between diagnostic pulses, which compete with the need for efficient diagnostics. Here, we design a set of efficient optimal hybrid pulse power characterization (HPPC) diagnostics using model-based design of experiment (DOE) methods, applying knowledge of degradation effects on pulse kinetics and cell properties. We validate that these protocols are effective through minimization of uncertainty, and robust with Markov Chain Monte Carlo (MCMC) simulations. Contrary to traditional HPPC diagnostics which use fixed pulse magnitudes at uniformly distributed state of charges (SOC), we find that well-designed HPPC protocols using our framework outperform traditional protocols in terms of minimizing both parametric uncertainties and diagnostic time. Trade-offs between minimizing parametric uncertainty and total diagnostic time can be made based on different diagnostics needs.
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Jinwook Rhyu; Debbie Zhuang; Martin Bazant; Richard Braatz
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Energy; Energy Storage
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-04-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661ab465418a5379b0c77930/original/optimum-model-based-design-of-diagnostics-experiments-doe-with-hybrid-pulse-power-characterization-hppc-for-lithium-ion-batteries.pdf
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6687207a5101a2ffa86cf532
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10.26434/chemrxiv-2024-0t7mw
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Analyzing the efficacy of different machine learning models for property prediction of solid polymer electrolytes
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In this work, we use machine learning to discover new polymer electrolytes for lithium-ion batteries. Polymer electrolytes are solid materials that can conduct ions and are safer than liquid electrolytes. However, they have lower ionic conductivity, which means they cannot transport ions as fast or as far. This limits their performance in batteries. Developing high ionic conductivity polymer electrolytes will result in high energy density and high-power density energy storage devices with rapid charging ability. Furthermore, polymer electrolytes need to have high mechanical stability to make safer solid-state batteries. However, developing new polymer electrolytes using multiple experiments is a tedious process. As such, machine learning can help in identifying the important parameters responsible for the discovery of high ionic conductivity polymer electrolytes. As part of this project, we study different copolymer electrolytes in context to their ionic conductivities and build a framework to identify the parameters governing the ionic conductivity of these electrolytes. We use different machine learning models including random forest, XGboost, KNN, linear regression, and chemprop model to predict the ionic conductivity of polymer electrolytes based on their chemical composition. The chemprop model uses a message-passing neural network, which is a type of deep learning that can learn from graph data, such as molecular structures. The model was trained on data from experimental publications, particularly, from Bradford et al. [1] that measured the ionic conductivity of different polymer electrolytes. The results showed that XG boost outperformed other models in predicting the ionic conductivity of polymer electrolytes. The significance of discovering new polymer electrolytes lies in addressing the current limitations of ionic conductivity. By identifying materials that exhibit improved conductivity, this work contributes to the development of high-performance lithium-ion batteries. Enhanced ionic conductivity translates to batteries with faster and more efficient ion transport, leading to improved battery performance and durability. This advancement is crucial for meeting the growing energy demands and ensuring the continued evolution of safe and reliable energy storage solutions.
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Urvashi Arora; Maninderjeet Singh; Siddharaj Dabade; Alamgir Karim
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Polymer Science; Energy
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-07-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687207a5101a2ffa86cf532/original/analyzing-the-efficacy-of-different-machine-learning-models-for-property-prediction-of-solid-polymer-electrolytes.pdf
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60c74744337d6cac60e27312
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10.26434/chemrxiv.8267837.v3
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A Relay Strategy Actuates Pre-Existing Trisubstituted Olefins in Monoterpenoids to Form New Trisubstituted Olefins by Cross Metathesis
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<b><u>Abstract:</u></b> A retrosynthetic disconnection-reconnection analysis of epoxypolyenes – substrates that can undergo cyclization to podocarpane-type tricycles – reveals relay-actuated Δ<sup>6,7</sup>-functionalized monoterpenoid alcohols for ruthenium benzylidene catalyzed olefin cross metathesis with homoprenyl benzenes. Successful implementation of this approach provided several epoxypolyenes as expected (<i>E</i>:<i>Z</i>, ca. 2-3:1). The method is further generalized for the cross metathesis of pre-existing trisubstituted olefins in other relay-actuated Δ<sup>6,7</sup>-functionalized monoterpenoid alcohols with various other trisubstituted alkenes to form new trisubstituted olefins. Epoxypolyene cyclization of an enantiomerically pure, but geometrically impure, epoxypolyene substrate provides an enantiomerically pure, trans-fused, podocarpane-type tricycle (from the <i>E</i>-geometrical isomer).<br />
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Karim Bahou; D. Christopher Braddock; Adam G. Meyer; G. Paul Savage; Zhensheng Shi; Tianyou He
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Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-12-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74744337d6cac60e27312/original/a-relay-strategy-actuates-pre-existing-trisubstituted-olefins-in-monoterpenoids-to-form-new-trisubstituted-olefins-by-cross-metathesis.pdf
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60c74a57bb8c1a5b763dafc7
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10.26434/chemrxiv.12178266.v1
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Distinct Helical Molecular Orbitals Through Conformational Lock
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Several theoretical studies have proposed strategies to reach helical molecular orbitals (Hel-MOs) in [n]cumulenes. While chiral even-[n] cumulenes feature Hel-MOs, odd-[n] cumulenes may also present them if the terminal groups lie on different planes. However, the hitherto proposed systems have been either experimentally unfeasible or resulted in opposite pseudo-degenerated Hel-MOs, impeding their use in real applicatons. To overcome this challenge, we hereby demonstrate the introduction of a remarkable energy difference between helical orbitals of opposite twist by fixing the torsion angle between the terminal groups in butadiyne fragments. In order to experimentally lock the conformation of the terminal groups, we designed cyclic architectures by combining acetylenes with chiral spirobifluorenes. A straightforward synthetic strategy along with the high stability allowed the isolation and full characterization of systems presenting distinct helical orbitals. Finally, a thorough computational analysis revealed that the most significant optical responses of these systems originate mainly from the exciton coupling between the featured diphenylbutadiyne fragments. This novel strategy opens now access to the development of systems with distinct helical molecular orbitals suitable for their implementation into chiroptical and optoelectronic applications.
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Ani Ozcelik; Daniel Aranda Ruiz; Sara Gil-Guerrero; Xaquín A. Pola-Otero; Maria Talavera; Liangxuan Wang; Santosh Kumar Behera; Johannes Gierschner; Ángeles Peña-Gallego; Fabrizio Santoro; Raquel Pereira-Cameselle; José Lorenzo Alonso Gómez
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Combinatorial Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Stereochemistry; Crystallography – Organic
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-04-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a57bb8c1a5b763dafc7/original/distinct-helical-molecular-orbitals-through-conformational-lock.pdf
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62c3c092e60d98588ef7d91b
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10.26434/chemrxiv-2022-56xw9-v2
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Predicting and rationalizing the Soret coefficient
of binary Lennard-Jones mixtures in the liquid state
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The thermodiffusion behavior of binary Lennard-Jones mixtures in the liquid state was investigated by combining the individual strengths of non-equilibrium molecular dynamics (NEMD) and equilibrium molecular dynamics (EMD) simulations. On the one hand, boundary-driven NEMD simulations are useful to quickly predict Soret coefficients because they are easy to set up and straightforward to analyze. However, careful interpolation is required because the mean temperature in the measurement region does not exactly reach the target temperature. On the other hand, EMD simulations attain the target temperature precisely and yield a multitude of properties that clarify the microscopic origins of Soret coefficient trends. An analysis of the Soret coefficient suggests a straightforward dependence on thermodynamic properties, whereas its dependence on dynamic properties is far more complex. Furthermore, a limit of applicability of a popular theoretical model, which mainly relies on thermodynamic data, was identified by virtue of an uncertainty analysis in conjunction with efficient empirical Soret coefficient predictions, which rely on model parameters instead of simulation output. Finally, the present study underscores that a combination of predictive models and EMD and NEMD simulations is a powerful approach to shed light onto the thermodiffusion behavior of liquid mixtures.
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Nils Edvin Richard Zimmermann; Gabriela Guevara-Carrion; Jadran Vrabec; Niels Hansen
|
Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Statistical Mechanics; Transport phenomena (Physical Chem.)
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CC BY 4.0
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CHEMRXIV
|
2022-07-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c3c092e60d98588ef7d91b/original/predicting-and-rationalizing-the-soret-coefficient-of-binary-lennard-jones-mixtures-in-the-liquid-state.pdf
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64485ecf83fa35f8f63f5439
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10.26434/chemrxiv-2023-s27dw
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Substrate effect on the structure and properties of Cu clusters supported on ZnO
|
To understand the interaction between the Cu clusters and the ZnO substrate, we performed density functional theory (DFT) calculations on the adsorptions of small copper clusters on the ZnO(100) surface. The PBE functional was used in the DFT calculations with a plane wave basis set. The structural changes of the Cu clusters upon adsorption on the ZnO surface were provided. Although a few different adsorption sites are available, a single Cu atom was found to be adsorbed on three positions on a ZnO(100) surface. The adsorption strength of a Cu dimer is increased with respect to the adsorption of a single Cu atom. In the adsorptions of tetramers, and pentamers, three-dimensional configurations of Cu clusters are more favorable than the planer.
|
Chasity Love-Nkansah; Peshala Jayamaha; Lichang Wang
|
Theoretical and Computational Chemistry; Materials Science; Catalysis; Nanostructured Materials - Materials; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64485ecf83fa35f8f63f5439/original/substrate-effect-on-the-structure-and-properties-of-cu-clusters-supported-on-zn-o.pdf
|
60c741884c8919375ead22e0
|
10.26434/chemrxiv.8060000.v1
|
Evaluating Polymer Representations via Quantifying Structure-Property Relationships
|
Machine learning techniques are being applied in quantifying structure-property relationships for a wide variety of materials, where the properly representing materials plays key roles. Although algorithms for representation learning are extensively studied, their applications to domain-specific areas, such as polymer, are limited largely due to the lack of benchmark databases. In this work, we investigate different types of polymer representations, including Morgan Fingerprint (MF), molecular embedding (ME) and molecular graph (MG), based on a benchmark database from a subset of PolyInfo. We evaluate the quality of different polymer representations via quantifying the relationships between the representations and polymer properties, including density, melting temperature and glass transition temperature. Different representation learning schemes, such as supervised learning, semi-supervised learning and transfer learning, are investigated. It is found that ME outperforms the other representations for structure-property relationship quantification in all cases studied, and MG is shown to be much inferior than ME and MF, likely due to the relatively small volumes of training data available. For MEs, it is found that the similarities of substructure MEs under different learning schemes (e.g., SL, SSL and TL) are differently estimated, thus leading to different performance scores in structure-property relation quantification. Several ME mixtures have shown to outperform the single MEs in the corresponding regression tasks, and this is attributed to the information gain when mixing different ME.
|
RUIMIN MA; Zeyu Liu; Quanwei Zhang; zhiyu liu; Tengfei Luo
|
Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741884c8919375ead22e0/original/evaluating-polymer-representations-via-quantifying-structure-property-relationships.pdf
|
65b111fb66c13817292b6b07
|
10.26434/chemrxiv-2024-gjvnc
|
The Cyanoketene Anion [NC3O]-
|
Cumulenes and heterocumulenes with three or more cumulative multiple bonds are usually reactive species, that serve as valuable building blocks to more complex molecules but tend to isomerize or cyclize and therefore are difficult to isolate. Until to date, numerous (hetero)cumulenes have been detected in the interstellar medium and are assumed to be important intermediates in prebiotic chemistry, in particular when containing nitrogen and oxygen functionalities. Using a mild ligand exchange reaction at carbon in metalated ylides, we have now succeeded in the synthesis and gram-scale isolation of the so far elusive cyanoketene anion, [NC3O]-. Despite its assumed cumulene-like structure and the delocalization of the negative charge across the whole 5-atomic molecule, it features a bent geometry in solid state with a nucleophilic central carbon atom. Computational studies reveal an ambiguous bonding situation in the anion, which can only be illustrated by a combination of different resonance structures. Nonetheless, the anion features a remarkable stability, thus allowing the storage of its potassium salt and its application as highly functional synthetic building block. The cyanoketene anion readily reacts with a series of small molecules to more complex organic compounds including industrially valuable compounds such as cyanoacetate. This work demonstrates that reactive species found in the interstellar medium can be made accessible by novel synthesis methods and open up new pathways to more complex compounds through reaction with small molecules, an atom economic strategy sought in sustainable chemistry.
|
Felix Krischer; Varre S. V. S. N. Swamy; Kai-Stephan Feichtner; Robert J. Ward; Viktoria H. Gessner
|
Organic Chemistry; Organometallic Chemistry; Earth, Space, and Environmental Chemistry; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.); Crystallography – Organic
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b111fb66c13817292b6b07/original/the-cyanoketene-anion-nc3o.pdf
|
636ea2dcfbfd385fefda8e13
|
10.26434/chemrxiv-2022-sn2kr
|
Reagent Prediction with a Molecular Transformer Improves Reaction Data Quality
|
Automated synthesis planning is key for efficient generative chemistry. Since reactions of given reactants may yield different products depending on conditions such as the chemical context imposed by specific reagents, computer-aided synthesis planning should benefit from recommendations of reaction conditions. Traditional synthesis planning software, however, typically proposes reactions without specifying such conditions, relying on human organic chemists who know the conditions to carry out suggested reactions. In particular, reagent prediction for arbitrary reactions, a crucial aspect of condition recommendation, has been largely overlooked in cheminformatics until lately. Here we employ the Molecular Transformer, a state-of-the-art model for reaction prediction and single-step retrosynthesis, to tackle this problem.
We train the model on the US patents dataset (USPTO) and test it on Reaxys to demonstrate its out-of-distribution generalization capabilities.
Our reagent prediction model also improves the quality of product prediction: the Molecular Transformer is able to substitute the reagents in the noisy USPTO data with reagents that enable product prediction models to outperform those trained on plain USPTO. This allows to improve upon the state-of-the-art in reaction product prediction on the USPTO MIT benchmark.
|
Mikhail Andronov; Varvara Voinarovska; Natalia Andronova; Michael Wand; Djork-Arné Clevert; Jürgen Schmidhuber
|
Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636ea2dcfbfd385fefda8e13/original/reagent-prediction-with-a-molecular-transformer-improves-reaction-data-quality.pdf
|
6334a9fbea6a22e834017b28
|
10.26434/chemrxiv-2022-9gj75-v2
|
Selectivity of Electrochemical Ion Insertion into Manganese Dioxide Polymorphs
|
The ion insertion redox chemistry of manganese dioxide has diverse applications in energy storage, catalysis, and chemical separations. Unique properties derive from the assembly of Mn-O octahedra into polymorphic structures that can host protons and non-protonic cations in interstitial sites. Despite many reports on individual ion-polymorph couples, much less is known about the selectivity of electrochemical ion insertion in MnO2. In this work, we use density functional theory to holistically compare the electrochemistry of AxMnO2 (where A = H+, Li+, Na+, K+, Mg2+, Ca2+, Zn2+ & Al3+) in aqueous and non-aqueous electrolytes. We develop an efficient computational scheme demonstrating that Hubbard-U correction has a greater impact on calculating accurate redox energetics than choice of exchange-correlation functional. Using PBE+U, we find that for non-protonic cations, ion selectivity depends on the oxygen coordination environments inside a polymorph. When H+ is present, however, the driving force to form hydroxyl bonds is usually stronger. In aqueous electrolytes, only three ion-polymorph pairs are thermodynamically stable within water’s voltage stability window (Na+ and K+ in 𝛼-MnO2, and Li+ in λ-MnO2), with all other ion insertion being metastable. We find Al3+ may insert into the 𝛿, R, and λ polymorphs across the full 2-electron redox of MnO2 at high voltage, however, electrolytes for multi-valent ions must be designed to impede formation of insoluble precipitates and facilitate cation desolvation. We also show that small ions co-insert with water in 𝛼-MnO2 to achieve greater coordination by oxygen, while solvation energies and kinetic effects dictate water co-insertion in 𝛿-MnO2. Taken together, these findings explain reports of mixed ion insertion mechanisms in aqueous electrolytes and highlight promising design strategies for safe, high energy density electrochemical energy storage, desalination batteries, and electrocatalysts.
|
Evan Zoltan Carlson; William Chueh; J. Tyler Mefford; Michal Bajdich
|
Theoretical and Computational Chemistry; Energy; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-09-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6334a9fbea6a22e834017b28/original/selectivity-of-electrochemical-ion-insertion-into-manganese-dioxide-polymorphs.pdf
|
66ed923fcec5d6c142ab3af7
|
10.26434/chemrxiv-2024-3x4rv
|
A Machine Learning Model for the Prediction of Water Contact Angles on Solid Polymers
|
The interaction between water and solid surfaces is an active area of research, and the interaction can be generally defined as hydrophobic or hydrophilic depending on the level of wetting of the surface. This wetting level can be modified, among other methods, by applying coatings, which often modify the chemistry of the surface. With the increase in available computing power and computational algorithms, methods to develop new materials and coatings have shifted from being heavily experimental to include more theoretical approaches. In this work we use a range of experimental and computational features to develop a supervised machine learning (ML) model using the XGBoost algorithm that can predict the water contact angle (WCA) on the surface of a range of solid polymers. The mean absolute error (MAE) of the predictions is below 5.0°. Models comprised of only computational features where also explored with good results (MAE < 5.0°), suggesting this approach could be used for the “bottom up” computational design of new polymers and coatings with specific water contact angle.
|
Jose Sena; Linus Johannissen; Jonny Blaker; Sam Hay
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ed923fcec5d6c142ab3af7/original/a-machine-learning-model-for-the-prediction-of-water-contact-angles-on-solid-polymers.pdf
|
62039693cbb4f46f4bbad5dd
|
10.26434/chemrxiv-2022-fgwj2
|
Spectroscopic characterization, docking studies and reactive properties by DFT calculations of halogen substituted 6-Chloro-N-(3-iodo-4-methylphenyl)-pyrazine-2-carboxamide with MD simulations.
|
The spectral characterization of 6-Chloro-N-(3-iodo-4-methylphenyl)-pyrazine-2-carboxamide (CIMPPC) was executed by FT-IR and FT-Raman spectroscopic methods and density functional theory (DFT) computations have been carried using B3LYP/gen method. On the basis of potential energy distribution (PED) the vibrational assignments of the wavenumbers were proposed. NBO analysis was performed to study donor acceptor interactions. Halogen substitution results in increase in the µ (chemical potential) value in comparison with the parent molecule, which is a minimum. Halogen substitution also results a decrease in electrophilicity index. Fundamental reactive properties of the title molecule is investigated by MEP analysis. Visualization of ALIE and Fukui functions evaluated the most probable sites for electrophilic attacks. Exposure of the title compound towards autoxidation and hydrolysis is evaluated using BDE and RDF. The compatible nature of the compound is investigated through the Hildebrand solubility parameter. CIMPPC exhibit inhibitory activity against the anti-inflammatory receptor transient receptor potential cation channel.
|
P. K. Ranjith; Angel Ignatious; C. Yohannan Panicker; B. Sureshkumar; Stevan Armakovic; Sanja. J. Armakovic; C. Van Alsenoy; P. L. ANTO
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-02-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62039693cbb4f46f4bbad5dd/original/spectroscopic-characterization-docking-studies-and-reactive-properties-by-dft-calculations-of-halogen-substituted-6-chloro-n-3-iodo-4-methylphenyl-pyrazine-2-carboxamide-with-md-simulations.pdf
|
6107db9e40c8bd04aa9a31d5
|
10.26434/chemrxiv-2021-cvvgp
|
Novel transformation products from the glucosinolate breakdown products isothiocyanates and thioglucose formed during cooking
|
Glucosinolates are secondary plant metabolites occurring in Brassicaceae plants. Upon tissue disruption these compounds can be enzymatically hydrolyzed into isothiocyanates. The latter are very reactive and can react with nucleophiles during food processing such as cooking. Here, a novel type of glucosinolate degradation product was identified resulting from the reaction of the isothiocyanates sulforaphane and allyl isothiocyanate with thioglucose during aqueous heat treatment. The cyclic compounds were isolated and their structure elucidated by NMR spectroscopy and high resolution mass spectrometry as 4-hydroxy-3-(4-(methylsulfinyl)butyl)thiazolidine-2-thione and 3-allyl-4-hydroxythiazolidine-2-thione. Based on experiments with isotope-labeled reagents, the determination of the diastereomeric ratio and further reactions, a reaction mechanism was proposed. Finally, the formation of the two 3-alk(en)yl-4-hydroxythiazolidine-2-thiones was quantified in boiled cabbage samples with contents of 92 pmol/g respectively 19 pmol/g fresh weight using standard addition method.
|
Holger Hoffmann; Lars Andernach; Clemens Kanzler; Franziska S. Hanschen
|
Agriculture and Food Chemistry; Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6107db9e40c8bd04aa9a31d5/original/novel-transformation-products-from-the-glucosinolate-breakdown-products-isothiocyanates-and-thioglucose-formed-during-cooking.pdf
|
62b0e8bae84dd12c2cfbdf1e
|
10.26434/chemrxiv-2022-w90r0
|
Isolation of a Californium(II) Crown-Ether Complex
|
Californium (Z = 98) is the first member of the actinide series displaying metastability of the 2+ oxidation state. Understanding the origin of this chemical behavior requires characterizing Cf(II) materials, but isolating a complex with this state has remained elusive. The source of its inaccessibility arises from the intrinsic challenges of manipulating this unstable element as well as a lack of suitable reductants that do not reduce Cf(III) to Cf(0). Herein we show that a Cf(II) crown-ether complex, Cf(18-crown-6)I2, can be prepared using an Al/Hg amalgam as a reductant. While spectroscopic evidence shows that Cf(III) can be quantitatively reduced to Cf(II), rapid radiolytic re-oxidation back to the Cf(III) parent occurs and co-crystallized mixtures of Cf(II) and Cf(III) complexes are isolated if the crystallization is not conducted over the Al/Hg amalgam. Quantum chemical calculations show that the Cf‒ligand interactions are highly ionic and that 5f/6d mixing is absent, resulting in remarkably weak 5f→5f transitions and an absorption spectrum dominated by 5f→6d transitions.
|
Todd Poe; Harry Ramanantoanina; Joseph Sperling; Hannah Wineinger; Brian Rotermund; Jacob Brannon; Zhuanling Bai; Benjamin Scheibe; Nicholas Beck; Brian Long; Samantha Justiniano; Thomas Albrecht-Schoenzart; Cristian Celis-Barros
|
Inorganic Chemistry; Lanthanides and Actinides; Nuclear Chemistry; Solid State Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-06-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b0e8bae84dd12c2cfbdf1e/original/isolation-of-a-californium-ii-crown-ether-complex.pdf
|
60c7567b9abda2afd4f8e53d
|
10.26434/chemrxiv.14254298.v1
|
Evidence of Bulk Proton Insertion in Nanostructured Anatase and Amorphous TiO2 Electrodes
|
Crystalline structures and lattice water
molecules are believed to strongly influence the ability of metal oxides to
reversibly and rapidly insert protons in aqueous batteries. In the present
work, we performed a systematic analysis of the electrochemical charge storage
properties of nanostructured TiO<sub>2</sub> electrodes composed of either
anatase or amorphous TiO<sub>2</sub> in a mild buffered aqueous electrolyte. We
demonstrate that both materials allow reversible bulk proton insertion up to a maximal
reversible gravimetric capacity of ~150
mA·h·g<sup>-1</sup>. We also
show that the TiO<sub>2 </sub>crystallinity governs the energetics of the
charge storage process, with a phase transition for anatase, while having little
effect on either the interfacial charge-transfer kinetics or the apparent rate
of proton diffusivity within the metal oxide. Finally, with both TiO<sub>2</sub>
electrodes, reversible proton insertion leads to gravimetric capacities as high
as 95 mA·h·g<sup>-1</sup> at 75
C. We also reveal two competitive reactions decreasing the Coulombic efficiency
at low rates, <i>i.e.</i> hydrogen evolution
and a non-faradaic self-discharge reaction. Overall, this work provides a
comprehensive overview of the proton-coupled electrochemical reactivity of TiO<sub>2</sub>
and highlights the key issues to be solved in order to truly benefit from the
unique properties of protons as fast charge carriers in metal oxides.
|
Nikolina Makivic; Jae-Young Cho; Kenneth D. Harris; Jean-Marie Tarascon; Benoit Limoges; Véronique Balland
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7567b9abda2afd4f8e53d/original/evidence-of-bulk-proton-insertion-in-nanostructured-anatase-and-amorphous-ti-o2-electrodes.pdf
|
60c74535bdbb89def4a3897f
|
10.26434/chemrxiv.7789454.v2
|
Stabilization of Super Electrophilic Pd+2 Cations in Small-Pore SSZ-13 Zeolite
|
<p>We
provide the first observation and characterization of super-electrophilic metal
cations on a solid support. For Pd/SSZ-13 the results of our combined
experimental (FTIR, XPS, HAADF-STEM) and density functional theory study reveal
that Pd ions in zeolites, previously identified as Pd<sup>+3</sup> and Pd<sup>+4</sup>,
are in fact present as super electrophilic Pd<sup>+2</sup> species (charge-transfer
complex/ion pair with the negatively charged framework oxygens). In this
contribution we re-assign the spectroscopic signatures of these species,
discuss the unusual coordination environment of “naked” (ligand-free) super-electrophilic
Pd<sup>+2</sup> in SSZ-13, and their complexes with CO and NO. With CO,
non-classical, highly positive [Pd(CO)<sub>2</sub>]<sup>2+</sup> ions are
formed with the zeolite framework acting as a weakly coordinating anion (ion
pairs). Non-classical carbonyl complexes also form with Pt<sup>+2</sup> and Ag<sup>+</sup>
in SSZ-13. The Pd<sup>+2</sup>(CO)<sub>2</sub>
complex is remarkably stable in zeolite cages even in the presence of water.
Dicarbonyl and nitrosyl Pd<sup>+2</sup> complexes, in turn, serve as precursors
to the synthesis of previously inaccessible Pd<sup>+2</sup>-carbonyl-olefin
[Pd(CO)(C<sub>2</sub>H<sub>4</sub>)] and -nitrosyl-olefin [Pd(NO)(C<sub>2</sub>H<sub>4</sub>)]
complexes. Overall, we show that zeolite framework can stabilize super
electrophilic metal (Pd) cations, and show the new chemistry of Pd/SSZ-13
system with implications for adsorption and catalysis.<br /></p>
|
Konstantin Khivantsev; Nicholas
R. Jaegers; Iskra Z. Koleva; Hristiyan
A. Aleksandrov; Libor Kovarik; Mark Engelhard; Feng Gao; Yong Wang; Georgi N. Vayssilov; János Szanyi
|
Catalysts; Nanocatalysis - Catalysts & Materials; Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74535bdbb89def4a3897f/original/stabilization-of-super-electrophilic-pd-2-cations-in-small-pore-ssz-13-zeolite.pdf
|
62d701ebfe12e3bc06aa4d76
|
10.26434/chemrxiv-2022-b41qd
|
A systematic core-shell approach for coarsening nanoparticle-membrane interactions: application to silver nanoparticles
|
The continuous release of engineered nanomaterial (ENM) into the environment may bring along health concerns following human exposure. One important source of ENMs are silver nanoparticles (NPs) that are extensively used as anti-bacterial additives. The introduction of ENMs into the human body can occur via ingestion, skin uptake, or the respiratory system. Therefore, evaluating how NPs translocate over bio-membranes is essential in assessing their primary toxicity. Unfortunately, data regarding membrane-NP interaction is still scarce, as is a theoretical and in-silico insight that governs adhesion and translocation for the most relevant NPs and membranes. Coarse-grained (CG) molecular descriptions alleviate this situation but are hampered by the absence of a direct link to specific NP materials and membrane adhesion mechanisms. Here, we interrogate the relationship between the standard CG NP representation and the adhesion characteristics of a model lung membrane. We find that the standard model is inapt of describing silver (Ag) NPs of different sizes, meaning that a matching CG representation for one size is not transferable to other sizes. In addition, we identify two basic types of primary adhesion - (partial) NPs
wrapping by the membrane and NP insertion into the membrane - that depend on the NP’s overall hydrophobicity and significantly differ in terms of lipid coatings. The
non-transferability of the standard CG model forms an inspiration for introducing a core-shell model even for bare NPs that are uniform in composition. We show that this
extension allows us to reproduce the size-dependent adhesion properties of bare Ag NPs at the atomistic scales. Next, we evaluate adhesion signatures for bare Ag NPs up
to 10 nm diameter, illustrating that the previously atomically resolved lipid response to binding is correctly reproduced at the CG level. The simulation for the largest NP provides insight into the role of water in trapping NPs into defected mixed monolayer- bilayer states. This metastable situation is well beyond the previously considered elastic models and implicit-solvent molecular descriptions. We expect this development to be instrumental for simulating NP membrane adhesion towards experimental length and time scales for particular NP materials.
|
Ankush Singhal; Agur Sevink
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d701ebfe12e3bc06aa4d76/original/a-systematic-core-shell-approach-for-coarsening-nanoparticle-membrane-interactions-application-to-silver-nanoparticles.pdf
|
60c755020f50db1fbd397e15
|
10.26434/chemrxiv.13947575.v1
|
Translation of Collagen Ultrastructure to Biomaterial Fabrication for Material Independent but Highly Efficient Topographic Immunomodulation
|
<div>Supplement-free induction of cellular differentiation and polarization
solely through the topography of materials is an auspicious strategy but has so
far significantly lacked behind the efficiency and intensity of media-supplementation
based protocols. For immune cells, low intensity effects were achieved on
rhodent cells using standard technologically driven surface patterns and
scaffold geometries, but no effects could be achieved for human immune cells. <br /></div><p> </p>
<p>Consistent with the idea that 3D structural motives in the extracellular
matrix possess immunomodulatory capacity as part of the natural healing
process, we found that human monocyte-derived macrophages show a strong M2a
like pro-healing polarization when cultured on type I rat-tail collagen fibers
(hereafter termed "collagen I") but not on collagen I films. <br /></p><p>Therefore, we hypothesized that highly aligned nanofibrils also of synthetic
polymers, if packed into larger bundles in 3D topographical similarity to
native collagen I, would induce a localized macrophage polarization. <br /></p>
<p> </p>
<p>For the automated fabrication of such bundles in a 3D printing manner, we
pioneered the strategy of "Melt Electrofibrillation" by the
integration of flow directed polymer phase separation into Melt Electrowriting
and subsequent selective dissolution of the matrix polymer. This process yields
nano-fiber bundles with a remarkable structural similarity to native collagen I
fibers, particularly for medical grade polycaprolactone (PCL). </p>
<p> </p>
<p>These biomimetic fibrillar structures indeed induced a pronounced
elongation of human monocyte-derived macrophages and unprecedentedly triggered
their M2-like polarization as efficiently as IL-4 cytokine treatment.</p>
<p> </p>
<p>Our data evidence the
biological importance of human macrophage-elongation on collagen fibers and
pioneers a strategy to fabricate scaffolds that exploit this effect to drive
macrophage polarization through precise and biomimetic material design. </p>
|
matthias ryma; tina tylek; julia liebscher; robin fernandez; christoph böhm; carina blum; wolfgang kastenmüller; georg gasteiger; Jürgen Groll
|
Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755020f50db1fbd397e15/original/translation-of-collagen-ultrastructure-to-biomaterial-fabrication-for-material-independent-but-highly-efficient-topographic-immunomodulation.pdf
|
646e69bd4f8b1884b73829a2
|
10.26434/chemrxiv-2023-f1vh9
|
Comparison of Polarization Energies from B3LYP and MP2 Parameterizations: Spherical Benzene and Anthracene Clusters
|
To characterize polarization energies of organic small molecule based materials induced by aggregation, electronic structure calculations including density function theory (DFT) method become intractable when the size of the aggregates increases. A practical solution is to develop force field based on electronic structure calculations and molecular dynamics simulations. In this work, we performed B3LYP and MP2 calculations of neutral, cationic, and anionic benzene and anthracene and used these results to derive the state specific atomic polarizabilities (SSAPs) then to calculate the atomic dipole moments using QTAIM for better parameterization of the isotropic atomic polarizability for ionic systems. Ren’s atomic multipole parameterization method was also compared to a less computationally intensive B3LYP result and a grid quadrature method for multipole analysis in GDMA. Our results show that the trend in cluster size is the same for both parameterization methods, however, the magnitude of the apparent polarization energy is different for the bulk with a negatively charged carrier. B3LYP produces results closer to the experimental values for the positively charged carrier. The intramolecular electrostatic interactions of the negative charge carrier are a major depolarizing force. This relationship is reversed in the positive charge carrier.
|
Thomas Testoff; Lichang Wang
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Aggregates and Assemblies; Photosensitizers; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e69bd4f8b1884b73829a2/original/comparison-of-polarization-energies-from-b3lyp-and-mp2-parameterizations-spherical-benzene-and-anthracene-clusters.pdf
|
61e6fb42eab6ef9aeae57783
|
10.26434/chemrxiv-2021-ldqw5-v3
|
O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems
|
We propose a new strategy to solve the Many-Body Dispersion (MBD) model by Tkatchenko, DiStasio Jr. and Ambrosetti. Our approach overcomes the original O(N**3) computational complexity that limits its applicability to large molecular systems within the context of O(N) Density Functional Theory (DFT). First, in order to generate the required frequency-dependent screened polarizabilities, we introduce an efficient solution to the Dyson-like self-consistent screening equations. The scheme reduces the number of variables and, coupled to a DIIS extrapolation, exhibits linear-scaling performances. Second, we apply a stochastic Lanczos trace estimator resolution to the equations evaluating the many-body interaction energy of coupled quantum harmonic oscillators. While scaling linearly, it also enables communication-free pleasingly-parallel implementations. As the resulting O(N) stochastic massively parallel MBD approach is found to exhibit minimal memory requirements, it opens up the possibility of computing accurate many-body van der Waals interactions of millions-atoms’ complex materials and solvated biosystems with computational times in the range of minutes.
|
Pier Paolo Poier; Louis Lagardère; Jean-Philip Piquemal
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
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2022-01-19
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e6fb42eab6ef9aeae57783/original/o-n-stochastic-evaluation-of-many-body-van-der-waals-energies-in-large-complex-systems.pdf
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613802dd42198ef6576f36e8
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10.26434/chemrxiv-2021-zb25v
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Conductivity mechanism in ionic 2D carbon nitrides: from hydrated ion motion to enhanced photocatalysis
|
Carbon nitrides are among the most studied materials for photocatalysis, however, limitations arise from inefficient charge separation and transport within the material. Here, this aspect is addressed in the 2D carbon nitride poly(heptazine imide) (PHI) by investigating the influence of various counterions, such as M = Li+, Na+, K+, Cs+, Ba2+, NH4+ and tetramethyl ammonium, on the material’s conductivity and photocatalytic activity. These ions in the PHI pores affect the stacking of the 2D layers, which further influences the predominantly ionic conductivity in M-PHI. Na-containing PHI outperforms the other M-PHI in various relative humidity (RH) environments (0-42 %RH) in terms of conductivity, likely due to pore channel geometry and size of the (hydrated) ion. With increasing RH, the ionic conductivity increases by 4-5 orders of magnitude (for Na-PHI up to 10-5 S cm-1 at 42 %RH). At the same time, the highest photocatalytic hydrogen evolution rate is observed for Na-PHI, which is mirrored by increased photo-generated charge carrier lifetimes, pointing to efficient charge carrier stabilization by mobile ions. These results indicate that ionic conductivity is an important parameter that can influence the photocatalytic activity. Besides, RH-dependent ionic conductivity is of high interest for separators, membranes, or sensors.
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Julia Kröger; Filip Podjaski; Gökçen Savaşçı; Igor Moudrakovski; Alberto Jimenez-Solano; Maxwell W. Terban; Sebastian Bette; Viola Duppel; Markus Joos; Alessandro Senocrate; Robert Dinnebier; Christian Ochsenfeld; Bettina Valeska Lotsch
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Materials Science; Catalysis; Fuels - Materials; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-09-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613802dd42198ef6576f36e8/original/conductivity-mechanism-in-ionic-2d-carbon-nitrides-from-hydrated-ion-motion-to-enhanced-photocatalysis.pdf
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60c7416dbb8c1a13913d9f48
|
10.26434/chemrxiv.7864337.v2
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Capturing Nature's Oxonium Ions
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<p><a></a>Acetylcholine
and <i>S</i>-adenosylmethionine exemplify
the tetraalkylammonium (R<sub>4</sub>N<sup>+</sup>) and trialkylsulfonium (R<sub>3</sub>S<sup>+</sup>)
ions used by Nature. The corresponding trialkyloxonium ions (R<sub>3</sub>O<sup>+</sup>),
however, do not play a central role in biology most likely due to their
hydrolytic instability compared with their ammonium and sulfonium counterparts.
Indeed, Meerwein’s salts [(CH<sub>3</sub>)<sub>3</sub>O<sup>+</sup>BF<sub>4</sub><sup>–</sup>
and (CH<sub>3</sub>CH<sub>2</sub>)<sub>3</sub>O<sup>+</sup>BF<sub>4</sub><sup>–</sup>],
the simplest of the trialkyloxonium ions, are among the most powerful
alkylating agents known, and they too are unstable to water. Only recently have
water stable trialkyloxonium ions been reported which contain an oxatriquinane
skeleton. Interestingly, despite the inherent hydrolytic instability of the
vast majority of trialkyloxonium ions, they have been postulated as key
intermediates in the biosynthesis of a number of complex natural products from <i>Laurencia</i> species. The existence of
these complex trialkyloxonium ions has been implied from the structural and
stereochemical diversity of these natural products and is supported by elegant
biomimetic total syntheses, yet no direct evidence for their existence has been
forthcoming. Herein, we report the synthesis and full characterisation of one
family of these biosynthetically relevant trialkyloxonium ions - the most
structurally and stereochemically complex oxonium ions characterised to date.
Additionally, the elucidation of their <i>in
vitro </i>reactivity profile has resulted in the synthesis of more than ten
complex halogenated natural products. This work substantiates the existence of
complex trialkyloxonium ions as key reactive intermediates in the biosynthesis
of numerous halogenated natural products from <i>L. </i>spp. – expanding Nature’s rich inventory of onium ions.</p>
|
Hau Sun (Sam) Chan; Q. Nhu. N. Nguyen; Jonathan Burton; Robert Paton
|
Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7416dbb8c1a13913d9f48/original/capturing-nature-s-oxonium-ions.pdf
|
65b154a166c13817292fad82
|
10.26434/chemrxiv-2024-w0wvl
|
Deep learning for low-data drug discovery: hurdles
and opportunities
|
Deep learning is becoming increasingly relevant in drug discovery, from de novo design to protein structure prediction and synthesis planning. However, it is often challenged by the small data regimes typical of certain drug discovery tasks. In such scenarios, deep learning approaches – which are notoriously ‘data-hungry’ – might fail to live up to their promise. Developing novel approaches to leverage the power of deep learning in low-data scenarios is sparking great attention, and future developments are expected to propel the field further. This minireview provides an overview of recent low-data-learning approaches in drug discovery, analyzing their hurdles and advantages. Finally, we venture to provide a forecast of future research directions in low-data learning for drug discovery.
|
Derek van Tilborg; Helena Brinkmann; Emanuele Criscuolo; Luke Rossen; Rıza Özçelik; Francesca Grisoni
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b154a166c13817292fad82/original/deep-learning-for-low-data-drug-discovery-hurdles-and-opportunities.pdf
|
67852c1181d2151a02f24fdc
|
10.26434/chemrxiv-2025-kc3dz
|
Bimetallic Platinum(II) Complexes with Bridging Di-NHC and N^C^C Ligands: Synthesis and Photophysical Properties
|
Three new bimetallic Pt(II) compounds of the type [{Pt(N^C^C)}2{μ-(ImMe)2(CH2)n}] [n = 1 (1), 3 (2), 6 (3)], where N^C^C is the dimetalated terdentate ligand 2-(4,4''-dimethyl-[1,1':3',1''-terphenyl]-5'-yl)pyridine and ImMe is N-methylimidazol-N-yl-2-ylidene, have been synthesized in order to explore their ability to form molecular assemblies that affect their luminescence. Restricted rotation through the Pt-carbene bond gives rise to mixtures of stereoisomers, that hinder the obtention of single crystals. The complexes show efficient emissions with high phosphorescence quantum yields in 2 wt % doped PMMA films (PLQY: 73-77%). Significant modifications of their photophysical properties in fluid solution are observed upon variation of the solvent, with the highest efficiencies found in 2-methyltetrahydrofurane (up to 63% for complex 3). In the case of complex 1, which contains the shortest linkage, the formation of excimers in MeCN and MeOH causes a significant quenching of the emission, with a substantial decrease in the quantum yield.
|
Mariano Paredes; Dionisio Poveda; Pablo González-Herrero; Ángela Vivancos
|
Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67852c1181d2151a02f24fdc/original/bimetallic-platinum-ii-complexes-with-bridging-di-nhc-and-n-c-c-ligands-synthesis-and-photophysical-properties.pdf
|
633ca8cc114b7e27182885c8
|
10.26434/chemrxiv-2022-d75bh
|
Multiscale Engineering of Wood for a Sustainable Future
|
Wood has served humanity by providing tools, fuels, and engineering materials since the Paleolithic period. The composite and hierarchical structure of wood, which is a direct embodiment of stored solar energy and sequestered CO2, exhibits versatile utility. Top-down approaches have enabled recent advances in the engineering, functionalization, and conversion of wood and its derivatives. Its inherent hierarchical structure can be modified by physical and 25chemical methods. Moreover, ‘bottom-up’, targeted genetic engineering approaches have facilitated the modification of wood from molecular scale to nano-, micro-, and bulk scales. Herein, the strategies for manipulating the emergent properties of wood at several scales are reviewed to present sustainable solutions for meeting the current and future demands for materials and energy.
|
Qiang Li; Richard Dixon; Peter Ciesielski; Michael Himmel; Breeanna Urbanowicz; Daxian Cao; Hongli Zhu
|
Materials Science; Biological Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633ca8cc114b7e27182885c8/original/multiscale-engineering-of-wood-for-a-sustainable-future.pdf
|
673f4e447be152b1d035e616
|
10.26434/chemrxiv-2023-r7r6k-v2
|
Solid-state hydrogen storage in atomic layer deposited α−MoO3 thin films
|
Hydrogen is an energy vector capable of storing and supplying large amounts of energy, maximising the benefits of renewable and sustainable energy sources. Hydrogen is usually stored as compressed hydrogen gas, or liquid hydrogen. However, the former requires high pressure, the latter cryogenic temperatures, being a huge limit to the widespread adoption of these storage methods. Thus, new materials for solid-state hydrogen storage shall be developed. Here we show that a α−MoO3 thin film, grown via atomic layer deposition, is a material with potential for reversibly storing hydrogen. We found that hydrogen plasma is a convenient way to hydrogenate − at room temperature and relatively low pressures (200 mTorr) – layered α−MoO3 thin films. Hydrogen has been shown to locate itself in the van der Waals gap along the [010] oriented α−MoO3 film. The hydrogen absorption process has been found to be totally reversible, with desorption of hydrogen effective at 350 °C / 4 hours under nitrogen atmosphere, and recoverable after repeated cycles. Furthermore, a nominal 13 nm AlxOy capping layer, grown via atomic layer deposition, has been shown to be efficient in preventing hydrogen release. The volumetric hydrogen storage capacity of 28 kg.m−3 achieved in our films is comparable to that of pressurised steel cylinders, highlighting their potential for practical applications. Our essay could be a starting point to a transition from conventional (gas and liquid) to more advantageous solid-state hydrogen storage materials.
|
David Maria Tobaldi; Salvatore Mirabella; Gianluca Balestra; Daniela Lorenzo; Vittorianna Tasco; Maria Grazia Manera; Adriana Passaseo; Marco Esposito; Andreea Neacsu; Viorel Chihaia; Massimo Cuscunà
|
Materials Science; Energy; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673f4e447be152b1d035e616/original/solid-state-hydrogen-storage-in-atomic-layer-deposited-mo-o3-thin-films.pdf
|
62cd82f227b1e463bb36b984
|
10.26434/chemrxiv-2022-4gzm0-v2
|
Discovery of XL01126: A Potent, Fast, Cooperative, Selective, Orally Bioavailable and Blood Brain Barrier Penetrant Prote-olysis Targeting Chimera Degrader of Leucine Rich Repeat Kinase 2
|
Leucine Rich Repeat Kinase 2 (LRRK2) is one of the most promising targets for Parkinson’s Disease. LRRK2 targeting strategies have primarily focused on Type 1 kinase inhibitors, which however have limitations as the inhibited protein can interfere with natural mechanisms which could lead to undesirable side effects. Herein, we report the development of LRRK2 Proteolysis Targeting Chimeras (PROTACs), culminating in the discovery of degrader XL01126, as an alternative LRRK2 targeting strategy. Initial designs and screens of PROTACs based on ligands for E3 ligases von Hippel-Lindau (VHL), Cereblon (CRBN), and cellular inhibitor of Apoptosis (cIAP) identified the best degraders containing thioether-conjugated VHL ligand VH101. A second round of medicinal chemistry exploration led to qualifying XL01126 as a fast and potent degrader of LRRK2 in multiple cell lines, with DC50 values within 15-72 nM, Dmax values range from 82-90%, and degradation half-lives span from 0.6h to 2.4h. XL01126 exhibits high cell permeability and forms a positively cooperative ternary complex with VHL and LRRK2 (α=5.7), which compensates for a substantial loss of binary binding affinities to VHL and LRRK2, underscoring its strong degradation performance in cells. Remarkably, XL01126 is orally bioavailable (F=15%) and can penetrate the blood brain barrier after either oral or parenteral dosing in mice. Taken together, these experiments qualify XL01126 as a suitable degrader probe to study non-catalytic and scaffolding functions of LRRK2 in vitro and in vivo and offer an attractive starting point for future drug development.
|
Xingui Liu; Alexia Kalogeropulou; Sofia Domingos; Nikolai Makukhin; Raja Nirujogi; Francois Singh; Natalia Shpiro; Anton Saalfrank; Esther Sammler; Ian Ganley; Rui Moreira; Dario Alessi; Alessio Ciulli
|
Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2022-07-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cd82f227b1e463bb36b984/original/discovery-of-xl01126-a-potent-fast-cooperative-selective-orally-bioavailable-and-blood-brain-barrier-penetrant-prote-olysis-targeting-chimera-degrader-of-leucine-rich-repeat-kinase-2.pdf
|
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