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6721d9017be152b1d03f9cce
|
10.26434/chemrxiv-2024-bznm6
|
Performance Insights for Small Molecule Drug Discovery Models: Data Scaling, Multitasking, and Generalization
|
Predictive models hold considerable promise in enabling the faster discovery of safe, efficacious therapeutics. To better understand and improve the performance of small molecule predictive models, we conducted multiple experiments with deep learning and traditional machine learning approaches, leveraging our large internal datasets as well as publicly available datasets. These experiments included assessing performance on random, temporal, and reverse-temporal data ablation tasks as well as tasks testing model extrapolation to different property spaces. We were able to identify factors that contribute to higher performance of predictive models built using graph neural networks versus traditional methods such as XGboost and random forest. Expanding upon these learnings, we were able to derive a scaling relationship that accounts for 81% of the variance in model performance across different assays and data regimes. This relationship can be used to estimate the performance of models for ADMET (absorption, distribution, metabolism, excretion, and toxicity) endpoints as well as drug discovery assay data in general. The results provide insights into how to further improve model performance.
|
Jacky Chen; Yunsie Chung; Jonathan Tynan; Chen Cheng; Song Yang; Alan Cheng
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6721d9017be152b1d03f9cce/original/performance-insights-for-small-molecule-drug-discovery-models-data-scaling-multitasking-and-generalization.pdf
|
60c743bcbb8c1a40243da3c1
|
10.26434/chemrxiv.8325668.v1
|
Sodium Ion Conductivity in Superionic IL-Impregnated Metal-Organic Frameworks: Enhancing Stability Through Structural Disorder
|
<p>Metal—organic frameworks
(MOFs) are intriguing host materials in composite electrolytes due to their
ability for tailoring host-guest interactions by chemical tuning of the MOF
backbone. Here, we introduce particularly high sodium ion conductivity into the
zeolitic imidazolate framework ZIF-8 by impregnation with the
sodium-salt-containing ionic liquid (IL) (Na0.1¬EMIM0.9)TFSI. We demonstrate an
ionic conductivity exceeding 2×10-4 S ⋅cm-1 at room
temperature, with an activation energy as low as 0.26 eV, i.e., the highest
reported performance for room temperature Na+-related ion conduction in
MOF-based composite electrolytes to date. Partial amorphization of the ZIF-backbone
by ball-milling results in significant enhancement of the composite stability,
reflecting in persistent and stable ionic conductivity during exposure to
ambient air over up to 20 days. While the introduction of network disorder
decelerates IL exudation and interactions with ambient contaminants, the ion
conductivity is only marginally affected, decreasing linearly with decreasing
crystallinity but still maintaining superionic behavior. This highlights the
general importance of 3D networks of interconnected pores for efficient ion
conduction in MOF/IL blends, whereas pore symmetry is a presumably less
stringent condition.</p>
|
Vahid Nozari; Courtney Calahoo; Joshua M. Tuffnell; Philipp Adelhelm; Katrin Wondraczek; Siân E. Dutton; Thomas Bennett; Lothar Wondraczek
|
Hybrid Organic-Inorganic Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743bcbb8c1a40243da3c1/original/sodium-ion-conductivity-in-superionic-il-impregnated-metal-organic-frameworks-enhancing-stability-through-structural-disorder.pdf
|
60c74de0bb8c1a3c973db653
|
10.26434/chemrxiv.12666296.v1
|
The Structure of PAMAM DAB-dendr(NH2)4 – the First Crystal Structure of a PAMAM-Dendrimer
|
The first crystal structure of an amino terminated PAMAM-dendrimer (DABdendr(NH2)4) is reported. The structure features a compact dendrimer conformation without
voids, held together by intermolecular hydrogen bonds between dendrimers<br />
|
Jesper Bendix; Joern Christensen
|
Organic Polymers; Nanostructured Materials - Nanoscience; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de0bb8c1a3c973db653/original/the-structure-of-pamam-dab-dendr-nh2-4-the-first-crystal-structure-of-a-pamam-dendrimer.pdf
|
673ded2e7be152b1d0dd04aa
|
10.26434/chemrxiv-2024-jqgzs
|
Graphene Encapsulated Ni Catalyzed Reductive Amination of VOC Aldehydes to High Value Chemicals by industrial continuous flow synthesis
|
Volatile organic compounds (VOCs) include many types of organic compounds, such as alkanes, olefins, aldehydes, etc. They have attracted widespread attention in various fields such as food and flavor analysis, environmental and atmospheric research, safety, or healthcare. Developing efficient, practical, and high-value industrial VOC utilization technologies is crucial for sustainable social and human development. Aldehydes are one of the main components of VOCs, with C=O functional groups. Therefore, various conversion pathways such as reduction and oxidation can be used to achieve the utilization of VOC aldehyde compounds. One of the technologies is the reductive amination of aldehydes into amines, which are widely used as raw materials, drugs, pharmaceuticals, pesticides, etc. The synthesis of benzylamine by reductive amination of benzaldehyde is difficult to produce benzylamine specifically with high selectivity due to the complex pathway, and the currently applied catalysts generally have disadvantages such as poor cyclability. Enantioselective hydrogenation reactions over heterogeneous catalysts are advantageous for implementation in flow reactor systems for industrial applications due to their inherent operational and economic advantages, such as easy separation, low cost and environmental friendliness of heterogeneous catalysts. This work reports a catalyst with Ni nanoparticles encapsulated in a thin graphene shell, which successfully achieved the efficient of benzaldehyde to benzylamine under mild conditions (60 °C, 1 MPa), with the conversion of 99.99% and the selectivity of 94.59%. The catalyst is simple and inexpensive to prepare, and the graphene shell reduces the loss of catalyst during the reaction while increasing the catalytic active sites, making the catalyst efficient and stable with excellent recyclability. The reaction system is carried out in a flow reactor, where H2 and NH3 are involved simultaneously, ensuring safety while improving the mass and heat transfer of the reaction, and the overall conversion is substantially improved compared to that of the batch reactor.
|
Weidong Liu; Shanshan Lin; Siyi Mi; Sang-Hyun Pyo; Jianguo Liu
|
Catalysis; Base Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ded2e7be152b1d0dd04aa/original/graphene-encapsulated-ni-catalyzed-reductive-amination-of-voc-aldehydes-to-high-value-chemicals-by-industrial-continuous-flow-synthesis.pdf
|
623b5418d6d3edef1d9c3016
|
10.26434/chemrxiv-2022-hb7v3
|
Reconstructing Reactivity in Dynamic
Host-Guest Systems at Atomistic Resolution:
Amide Hydrolysis Under Confinement in the
Cavity of a Coordination Cage
|
Spatial confinement is widely employed by Nature to attain unique efficiency in controlling chemical reactions. Notable examples are enzymes, which selectively bind reactants and exquisitely regulate their conversion into products. In the attempt to mimic natural catalytic systems, supramolecular metal-organic cages capable of encapsulating guests in their cavity and of controlling/accelerating chemical reactions under confinement are attracting increasing interest. However, the complex nature of these systems, where reactants/products continuously exchange in-and-out the host, makes it often difficult to elucidate the factors controlling the reactivity in dynamic regimes. As a case study, here we focus on a coordination cage that can encapsulate amide guests and enhance their hydrolysis by favoring their mechanical twisting towards reactive
molecular configurations under confinement. We designed an advanced multiscale simulation approach that allows us to reconstruct the reactivity in such host-guest systems in dynamic regimes. In this way, we can characterize the amide encapsulation/expulsion in/out the cage cavity (thermodynamics and kinetics), coupling such host-guest dynamic equilibrium with the characteristic hydrolysis reaction constants. All computed kinetic/thermodynamic data are then combined, obtaining a statistical estimation of reaction acceleration in the host-guest system that is found in optimal agreement with the available experimental trends. This shows how, to understand the key factors controlling accelerations/variations in the reaction under confinement, it is necessary to take into account all dynamic processes that occur as intimately entangled
in such host-guest systems. This also provides us with a flexible computational framework, useful to build structure-dynamics-property relationships for a variety of reactive
host-guest systems.
|
Massimo Delle Piane; Luca Pesce; Matteo Cioni; G. M. Pavan
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623b5418d6d3edef1d9c3016/original/reconstructing-reactivity-in-dynamic-host-guest-systems-at-atomistic-resolution-amide-hydrolysis-under-confinement-in-the-cavity-of-a-coordination-cage.pdf
|
67603dd581d2151a02f2f7b8
|
10.26434/chemrxiv-2024-rp81v
|
The surprising ineffectiveness of molecular dynamics coordinates for predicting bioactivity with machine learning
|
Accurate prediction of protein-ligand binding affinity remains a major challenge in drug discovery, despite the rapid progress of machine learning. Interestingly, machine learning approaches based on two-dimensional molecular information (e.g., binary fingerprints) often outperform those using three-dimensional (3D) information, possibly due to the usage of minimum-energy conformations. This raises questions about how to incorporate more sophisticated three-dimensional information (e.g., ligand flexibility and binding-induced conformational changes) for bioactivity prediction. To this end, we systematically investigate whether coordinates derived from molecular dynamics (MD) can improve prediction performance over minimum-energy conformations. MD-derived coordinates capture dynamic molecular interactions, which are hypothesized to reflect a more realistic representation of ligand-protein binding events. Using over 2600 protein-ligand complexes across three macromolecular targets, we compared multiple machine learning approaches using well-established 3D descriptor sets. Surprisingly, our results show that MD-derived coordinates do not consistently outperform ‘static’ 3D structures, despite their ability to capture dynamic molecular interactions. These findings highlight the persistent challenge of effectively leveraging three-dimensional and dynamic information for bioactivity prediction and underscore the need for improved representations approaches to bridge this gap.
|
Emanuele Criscuolo; Rıza Özçelik; Derek van Tilborg; Francesca Grisoni
|
Theoretical and Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-12-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67603dd581d2151a02f2f7b8/original/the-surprising-ineffectiveness-of-molecular-dynamics-coordinates-for-predicting-bioactivity-with-machine-learning.pdf
|
62f975e01803732409a53aae
|
10.26434/chemrxiv-2022-3zxps
|
Boosting CO2-to-CO Evolution Using a Bimetallic Diketopyrrolopyrrole Tethered Rhenium Bipyridine Catalyst
|
The use of homogenous electro- and photo- catalysis involving molecular catalysts offers valuable insight into reaction mechanisms as it relates to the structure-function of these tunable systems. However, supported molecular catalysts (i.e., hybrid electrodes) are multiplexed and not fully understood with regards to specific support-catalyst interactions. Even so, it still remains that catalyst activity for CO2 electroreduction can be tuned by modifying specific functional groups to achieve performance enhancement. Herein, a series of derivatized [Re(bpy)(CO)3Cl] catalysts were prepared with molecular structures having variability in both the number of Re-centers and π-conjugated diketopyrrolopyrrole (DPP) units. While tethering [Re(bpy)(CO)3Cl] to the DPP unit had a negligible effect on molecular electro- and photo- catalyst properties in organic solvent, the DPP chromophore enabled facile coupling of two [Re(bpy)(CO)3Cl] moieties. As a homogenous species, the bimetallic system effectively doubles the rate of CO2-to-CO conversion in the reaction-diffusion layer achieving a TOFCO = 1000 s-1 and FEco% = 98 % for up to 6 hours of electrolysis as the two catalytic centers act independently. Immobilization onto carbon hybrid electrodes was found to evolve H2, where the ratio of CO:H2 produced during electrolysis depended on both the molecular structure of the catalyst and the additive(s) to the carbon surface used to suppress the hydrogen evolution reaction (HER). Introducing a commercial DPP-based polymer and/or colloid imprinted carbons (CICs) into carbon paper favours CO evolution from the catalyst by suppressing the HER at carbon and by dispersing the molecular catalyst across a larger more wettable surface to mitigate mass transport limitations. Once again, the bimetallic catalyst has the highest activity in comparison to the monometallic analogues, with a selectivity (FEco% = 53%), activity (TOF = 39 hr-1), and longevity (active for up to 5 hours) for CO2-to-CO evolution from aqueous electrolyte.
|
Cody Carr; Joshua Koenig; Michael Grant; Warren Piers; Gregory Welch
|
Inorganic Chemistry; Catalysis; Electrochemistry; Small Molecule Activation (Inorg.); Electrocatalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f975e01803732409a53aae/original/boosting-co2-to-co-evolution-using-a-bimetallic-diketopyrrolopyrrole-tethered-rhenium-bipyridine-catalyst.pdf
|
63b83ebd53a45a4aeb50805d
|
10.26434/chemrxiv-2023-tkrq3
|
MESSI: a new method for stereochemical assignment of flexible and polyhydroxylated molecules inspired by wisdom of the crowd theory
|
The use of quantum-based NMR methods to complement and guide the connectivity and stereochemical assignment of natural and unnatural products has grown enormously. One of the unsolved problems is related to the improper calculation of the conformational landscape of flexible molecules that have functional groups capable of generating a complex network of intramolecular H-bonding (IHB) interactions. Here we present MESSI (Multi-Ensemble Strategy for Structural Identification), a method inspired by the wisdom of the crowd theory that breaks with the traditional mono-ensemble approach. By including independent mappings of selected artificially manipulated ensembles, MESSI greatly improves the sense of the assignment by neutralizing potential energy biases.
|
Maribel O. Marcarino; Lucas Passaglia; María Marta Zanardi; Ariel Marcelo Sarotti
|
Organic Chemistry; Natural Products; Stereochemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b83ebd53a45a4aeb50805d/original/messi-a-new-method-for-stereochemical-assignment-of-flexible-and-polyhydroxylated-molecules-inspired-by-wisdom-of-the-crowd-theory.pdf
|
60c75511842e659747db429a
|
10.26434/chemrxiv.14039141.v1
|
Production of High Value Amine Intermediates via Biocatalytic Cascades in Continuous Flow
|
<p>A key aim of biocatalysis is to mimic the
ability of eukaryotic cells to carry out compartmentalized multistep cascades
in a controlled and selective way. As biocatalytic cascades get longer and more
complex, reactions become unattainable under typical batch conditions. Here a
continuous flow multipoint injection reactor was combined with switching valves
to overcome batch incompatibility, thus allowing for successful biocatalytic
reaction cascades. As proof-of-principle, several reactive carbonyl intermediates
were generated <i>in situ </i>using galactose oxidase and engineered choline
oxidases, then passed directly to a series of packed-bed modules containing
different aminating biocatalysts which accordingly produced a range of
structurally distinct amines. The method was expanded to employ a batch
incompatible sequential amination cascade <i>via
</i>an oxidase-transaminase-imine reductase sequence, introducing different
amine reagents at each step without cross reactivity. The
combined approaches allowed for the biocatalytic synthesis of the natural
product alkaloid precursor 4O-methylnorbelladine. The
flow biocatalysis platform shown here significantly increases the scope of novel
biocatalytic cascades, removing previous limitations due to reaction and
reagent batch incompatibility.</p>
|
Ashley P. Mattey; grayson ford; Joan Citoler; Christopher Baldwin; James Marshall; Ryan Pamer; Matthew P. thompson; Nicholas Turner; Sebastian Cosgrove; Sabine Flitsch
|
Bioorganic Chemistry; Organic Synthesis and Reactions; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75511842e659747db429a/original/production-of-high-value-amine-intermediates-via-biocatalytic-cascades-in-continuous-flow.pdf
|
66f592aa51558a15ef3875a1
|
10.26434/chemrxiv-2024-vbh8g
|
PySIDT: Subgraph Isomorphic Decision Trees for Molecular Property Prediction
|
Accurate molecular property prediction is incredibly important across all fields of chemistry. Deep neural networks (DNNs) have become increasingly popular due to their ability to train automatically, avoiding the incredibly tedious process of constructing and extending traditional property estimation schemes. However, DNNs require large amounts of training data, are challenging to interpret, require large amounts of memory to load even during inference, and have severe difficulties incorporating qualitative chemical knowledge, which are often desired for molecular property prediction tasks. Here we present PySIDT (https://github.com/zadorlab/PySIDT) a software for training and running inference on Subgraph Isomorphic Decision Trees (SIDTs). SIDTs are graph-based decision trees made of nodes associated with molecular substructures. Inference is done by descending target molecular structures down the decision tree to nodes with matching subgraph isomorphic substructures and making predictions based on the final (most specific) node matched. SIDTs scale down well to dataset sizes much smaller than is feasible for DNNs. As trees of molecular substructures, SIDTs are inherently readable and easy to visualize making them easy to analyze. They are also straightforward to extend and retrain, facilitate uncertainty estimation, and enable easy integration of expert knowledge. We demonstrate the SIDT approach applying PySIDT to a diverse range of molecular prediction tasks: rate coefficient estimation, diffusion coefficient estimation, thermochemistry estimation, transition state bond stretch prediction, pKa prediction, stability of molecular structures, stability of surface structures, and prediction of surface lateral interactions.
|
Matthew S. Johnson; Hao-Wei Pang; Anna C. Doner; William H. Green; Judit Zador
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Chemical Kinetics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f592aa51558a15ef3875a1/original/py-sidt-subgraph-isomorphic-decision-trees-for-molecular-property-prediction.pdf
|
6159f6969f1b446bcddebb31
|
10.26434/chemrxiv-2021-x62pb-v2
|
Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels
|
The combination of free energy simulations in the alchemical and configurational spaces provides a feasible route to access the thermodynamic profiles under a computationally demanding target Hamiltonian. Normally, due to the significant differences between the computational cost of ab initio quantum mechanics (QM) calculations and those of semi-empirical quantum mechanics (SQM) and molecular mechanics (MM), this indirect method could be used to obtain the QM thermodynamics by combining the SQM or MM results and the SQM-to-QM or MM-to-QM corrections. In our previous works, a multi-dimensional nonequilibrium pulling framework for Hamiltonian variations has been introduced based on bidirectional pulling and bidirectional reweighting. The method performs nonequilibrium free energy simulations in the configurational space to obtain the thermodynamic profile along the conformational change pathway under a selected computationally efficient Hamiltonian, and uses the nonequilibrium alchemical method to correct or perturb the thermodynamic profile to that under the target Hamiltonian. The BAR-based method is designed to achieve the best generality and transferability and thus leads to modest (~20 folds) speedup. In this work, we explore the possibility of further accelerating the nonequilibrium free energy simulation by employing unidirectional pulling and using the selection criterion to obtain the initial configurations used to initiate nonequilibrium trajectories following the idea of adaptive steered molecular dynamics (ASMD). A single initial condition is used to seed the whole multi-dimensional nonequilibrium free energy simulation and the sampling is performed fully in the nonequilibrium ensemble. Introducing very short ps-length equilibrium sampling to grab more initial seeds could also be helpful. The ASMD scheme estimates the free energy difference with the unidirectional exponential average (EXP), but it does not follow exactly the requirements of the EXP estimator. Another deficiency of the seeding simulation is the inherently sequential or serial pulling due to the inter-segment dependency, which triggers some problems in the parallelizability of the simulation. Numerical tests are performed to grasp some insights and guidelines for using this selection-criterion-based ASMD scheme. The presented selection-criterion-based multi-dimensional ASMD scheme follows the same perturbation network of the BAR-based method, and thus could be used in various Hamiltonian-variation cases.
|
Zhaoxi Sun; Qiaole He
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6159f6969f1b446bcddebb31/original/seeding-the-multi-dimensional-nonequilibrium-pulling-for-hamiltonian-variation-indirect-nonequilibrium-free-energy-simulations-at-qm-levels.pdf
|
619d184d7848057fce9802df
|
10.26434/chemrxiv-2021-xnr5j
|
Enhanced N-directed Electrophilic C-H Borylation Generates BN-[5]- and [6]-helicenes with Improved Photophysical Properties
|
Helicenes are chiral polycyclic aromatic hydrocarbons (PAHs) of significant interest e.g. in supramolecular chemistry, materials science and asymmetric catalysis. Herein an enhanced N-directed electrophilic C-H borylation methodology has been developed that provides access to azaborine containing helicenes (BN-helicenes). This borylation process proceeds via protonation of an aminoborane with bistriflimidic acid. DFT calculations reveal the borenium cation formed by protonation to be more electrophilic than the product derived from aminoborane activation with BBr3. The synthesised helicenes include BN-analogues of archetypal all carbon [5]- and [6]helicenes. The replacement of a CC with a BN unit (that has a longer bond) on the outer helix increases the strain in the BN congeners and the racemization half-life for a BN-[5]helicene relative to the all carbon [5]helicene. BN incorporation also increases the fluorescence efficency of the helicenes, a direct effect of BN incorporation altering the distribution of the key frontier orbitals across the helical backbone relative to carbo-helicenes.
|
Kang Yuan; Daniel Volland; Sven Kirschner; Marina Uzelac; Gary Nichol; Agnieszka Nowak-Krol; Michael Ingleson
|
Organic Chemistry; Organic Synthesis and Reactions; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-11-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619d184d7848057fce9802df/original/enhanced-n-directed-electrophilic-c-h-borylation-generates-bn-5-and-6-helicenes-with-improved-photophysical-properties.pdf
|
63f5dc711d2d184063ec191f
|
10.26434/chemrxiv-2023-wt5rf
|
From CO2 to CS2: Mechanistic mapping of cooperative (CS2/CO2)/epoxide ring-opening copolymerisation catalysis
|
The placement of main group functionalities within the polymer main chain represents a strategy to access a wide catalogue of materials but is limited by poor understanding of the catalyst selection criteria and polymerisation mechanism when moving down the periodic table. Here we study a series of new heterobimetallic CO2 and CS2/epoxide copolymerisation catalysts which allow for a comparative mechanistic understanding of two ROCOP processes. We reveal that the distinct roles each metal plays are preserved from CO2 to CS2 maintaining activity and selectivity across copolymerisations. Experimental and computational studies show that CS2/epoxide copolymerisation can be understood as a series of structurally related insertion events which are interlinked by a central O/S scrambling reaction at the propagating chain end. This facilitates the synthesis of new CO2/CS2/epoxide derived terpolymers with improved degradability over the parent CO2/epoxide copolymers at low levels of sulfur incorporation.
|
Alex Plajer; Jenny Stephan; Merlin Stühler; Susanne Rupf; Samuel Neal
|
Inorganic Chemistry; Catalysis; Polymer Science
|
CC BY 4.0
|
CHEMRXIV
|
2023-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f5dc711d2d184063ec191f/original/from-co2-to-cs2-mechanistic-mapping-of-cooperative-cs2-co2-epoxide-ring-opening-copolymerisation-catalysis.pdf
|
60c740fa9abda2cefdf8bdc0
|
10.26434/chemrxiv.7446014.v2
|
Mapping Binary Copolymer Property Space with Neural Networks
|
The extremely large number of
unique polymer compositions that can be achieved through copolymerisation makes
it an
attractive strategy for tuning their optoelectronic
properties. However, this same attribute also makes it challenging to explore
the resulting property space and understand the range of properties that can be
realised. In an effort to enable the rapid exploration of this
space in the case of binary copolymers, we train a neural network using a
tiered data generation strategy to accurately predict the optical and
electronic properties of 350,000 binary copolymers that are, in principle,
synthesizable from their dihalogen monomers via Yamamoto, or Suzuki-Miyaura and
Stille coupling after one-step functionalisation. By extracting general features
of this property space that would otherwise be obscured in smaller datasets, we
identify simple models that effectively relate the properties of these
copolymers to the homopolymers of their constituent monomers, and challenge
common ideas behind copolymer design. We find that binary
copolymerisation does not appear to allow access to regions of the
optoelectronic property space that are not already sampled by the homopolymers,
although conceptually allows for more fine-grained property control. Using
the large volume of data available, we test the hypothesis that
copolymerisation of ‘donor’ and ‘acceptor’ monomers can result in copolymers
with a lower optical gap than their related homopolymers. Overall, despite the
prevalence of this concept in the literature, we observe that this phenomenon is
relatively rare, and propose conditions that greatly enhance the likelihood of
its experimental realisation. Finally, through a ‘topographical’ analysis of
the co-polymer property space, we show how this large volume of data can be
used to identify dominant monomers in specific regions of property space that
may be amenable to a variety of applications, such as organic photovoltaics,
light emitting diodes, and thermoelectrics.
<div>
<div>
<div>
<p>
</p>
</div>
</div>
</div>
|
Liam Wilbraham; Seb Sprick; Kim Jelfs; Martijn Zwijnenburg
|
Optical Materials; Organic Polymers; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740fa9abda2cefdf8bdc0/original/mapping-binary-copolymer-property-space-with-neural-networks.pdf
|
60df275ce924192f37e1d912
|
10.26434/chemrxiv-2021-pv941
|
Using collocation and solutions for a sum-of-product potential to compute
vibrational energy levels for general potentials
|
It is easier to compute a vibrational spectrum when the potential energy surface (PES) is a sum-ofproducts
(SOP). Many popular computational methods work only if the PES is a SOP. However, the most
accurate PESs are not SOPs. We propose using collocation and solutions of the Schrödinger equation with
a SOP PES to compute solutions on a corresponding general PES. This makes it possible to account for
coupling and anharmonicity omitted from the SOP PES. We find that correcting energy levels computed on
a SOP PES with collocation reduces differences with exact energy levels by about two orders of magnitude.
|
Jesse Simmons; Tucker Carrington
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60df275ce924192f37e1d912/original/using-collocation-and-solutions-for-a-sum-of-product-potential-to-compute-vibrational-energy-levels-for-general-potentials.pdf
|
66daf5d612ff75c3a194e6cd
|
10.26434/chemrxiv-2024-vtmqd
|
A bench-stable fluorophosphine nickel(0) complex and its catalytic application
|
We herein present a bench-stable fluorophosphine-based nickel(0) complex [Ni(PFPh2)4] (1), which is highly stable in air and water. This complex does not only incorporate a nickel centre in the zero-oxidation state, but also includes fluorophosphine ligands. Since these ligands typically tend to disproportionation in solution, they represent a vastly underexplored ligand class. [Ni(PFPh2)4] can be obtained from a one-pot reaction of [Ni(MeCN)4](BF4)2 with Ph2P(=O)–PPh2, involving a unique in-situ reduction of Ni(II) to Ni(0) and the simultaneous fluorination by the BF4– anion. The application of [Ni(PFPh2)4] as highly stable Ni(0) pre-catalyst in combination with additional phosphine ligands, such as dppf (1,1'-bis(diphenylphosphino)ferrocene) in Suzuki-Miyaura coupling reactions uncovers its high catalytic activity, which is greatly superior to the conventional Ni(0) source [Ni(COD)2]. A remarkable catalytic activity is achieved through the combination of 1 and dppf after a light-induced activation of the complex.
|
Franziska Flecken; Arjun Neyyathala; Toni Grell; Schirin Hanf
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66daf5d612ff75c3a194e6cd/original/a-bench-stable-fluorophosphine-nickel-0-complex-and-its-catalytic-application.pdf
|
62c1063d9ca5bb065fefdd00
|
10.26434/chemrxiv-2022-09wr7
|
Oxyl Character and Methane Hydroxylation Mechanism in Heterometallic M(O)Co3O4 Cubanes (M = Cr, Mn, Fe, Mo, Tc, Ru, Rh)
|
C–H activation in alkanes poses a major challenge in chemistry due to the inert character of this bond, manifesting the necessity of improved catalysts. Although various metal–oxo complexes are known to facilitate alkane hydroxylation, probing the mechanistic nature of the reaction is difficult due to the extremely fast rebound of the radical intermediate in the postulated oxygen-rebound pathway. Automated reaction mechanism discovery methods, such as the artificial force induced reaction (AFIR) method, enable the efficient exploration of both expected and unexpected reaction pathways, revealing the reaction mechanism. Here, we employed this approach combined with density-functional theory (DFT) to investigate the structure and reactivity of heterometallic cubane complexes similar to the oxygen-evolving complex of photosystem II. For a series of M(O)Co3O4 cubanes, where M(O) is a terminal oxo with M = Cr, Mn, Fe, Mo, Tc, Ru and Rh, we first computed the stability of the possible spin states and the radical (i.e., oxyl) character of the M(O) moiety as a measure of their potential activity in the catalytic hydroxylation of alkanes. DFT calculations on these reactions promoted by Ru(O)Co3O4 and Fe(O)Co3O4 suggest that the latter promotes the hydroxylation of methane with a rate-determining H-abstraction barrier of 24.6 kcal mol-1. The moderate height of this barrier, together with the low cost and low toxicity of iron and cobalt, suggest that the Fe(O)Co3O4 cubane is a promising candidate for the catalytic oxidation of methane to methanol. AFIR calculations showed that the oxygen-rebound pathway yields the lowest-energy profile, thus validating this mechanism for the hydroxylation of alkanes by heterometallic cubanes. Furthermore, unexpected intermediates in which the methyl radical couples with either the metal center or the bridging-oxo ligands were also observed.
|
Bastian Skjelstad; Trygve Helgaker; Satoshi Maeda; David Balcells
|
Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c1063d9ca5bb065fefdd00/original/oxyl-character-and-methane-hydroxylation-mechanism-in-heterometallic-m-o-co3o4-cubanes-m-cr-mn-fe-mo-tc-ru-rh.pdf
|
6697b7bac9c6a5c07a8793b5
|
10.26434/chemrxiv-2024-4m97l
|
Sugar characteristics of honey from Abu Dhabi (United Arab Emirates) market
|
Honey is a natural sweetening agent having concentrated solution of sugars. The sugar composition and percentage ratio are valuable quality parameters as some of the physiochemical properties like hygroscopicity, granulation, viscosity is influenced by the composition of sugars. Honey samples from the retail markets in the Emirate of Abu Dhabi were utilized to determine fructose, glucose, and sucrose values due to their dominance in the nectars having profound impact in determining the honey quality. The sum of reducing sugar content was in the range of 27% to 87% while sucrose content was between 5 to 37%. About 33% of the samples failed to comply with standard threshold of glucose and fructose. The samples having higher sucrose content exhibited decreased glucose and fructose levels. In conclusion, the commercially available honey samples require rigorous scrutiny and monitoring due to higher levels of quality non-compliance in accordance with local standards.
|
Abdullah Siddiqui; Khuloud Khalfan Altaleei; Ahmed Awadh Hatem Al Muharrami; Ali Usama Lashari; Premanandh Jagadeesan
|
Analytical Chemistry; Agriculture and Food Chemistry; Analytical Chemistry - General; Separation Science; Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6697b7bac9c6a5c07a8793b5/original/sugar-characteristics-of-honey-from-abu-dhabi-united-arab-emirates-market.pdf
|
62bb4105f51939ae3e771354
|
10.26434/chemrxiv-2022-2bkqk
|
Synthesis and styrene copolymerization of novel methyl and oxy ring-disubstituted tert-butyl phenylcyanoacrylates
|
Novel ring-disubstituted tert-butyl phenylcyanoacrylates, RPhCH=C(CN)CO2C(CH3)3, where R is 2,5-dimethyl, 3,4-dimethyl, 2,3-dimethoxy, 2,5-dimethoxy, 3,5-dimethoxy, 4-methoxy-2-methyl, 4-methoxy-3-methyl, 3-ethoxy-4-methoxy, 3-ethoxy-4-hydroxy, 3-ethoxy-2-hydroxy, 3-benzyloxy-4-methoxy, 4-benzyloxy-3-methoxy, 2,3-(methylenedioxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and tret-butyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation at 70C. The compositions of the copolymers were calculated from nitrogen analysis.
|
Lena K. Abu-Safieh; Christopher J. Ahrens; Sabina Kalata; Tessa Lusis; Emily Melink; Gabriela Petrova; Anusha N. Rao; Allison J. Rawson; Kayla R. Serafini; Shivani S. Shah; Kaitlyn E. Shelley; Maya R. Skowronski; Maria Tkachuk; Fernanda N. Vivas; Brooke A. Weitzel; Sara M. Schjerven; Nicholas M. Tassone; Gregory B. Kharas
|
Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers
|
CC BY 4.0
|
CHEMRXIV
|
2022-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bb4105f51939ae3e771354/original/synthesis-and-styrene-copolymerization-of-novel-methyl-and-oxy-ring-disubstituted-tert-butyl-phenylcyanoacrylates.pdf
|
6390e8ac44ccbc311c11dd03
|
10.26434/chemrxiv-2022-359ch
|
A Comprehensive Empirical–Computational Study of Diverse Het-eroarene Stacking under Physiological Conditions
|
Heteroaromatic stacking interactions help stabilize protein tertiary structure and are important in drug binding, supramolecu-lar chemistry, and materials science. Although diverse computational and experimental approaches have been utilized to study these interactions, a broadly useful protein–ligand model system has yet to emerge, despite laudable efforts by Diederich and co-workers in this vein. Here we studied thirty synthetic ligands that present diverse heteroarene probes for stacking between symmetry-related tyrosine residues at the dimer interface of procaspase-6. We demonstrate crystallograph-ically that stacking geometries are highly conserved across the ligand test set and show with high-accuracy computations that differences in ligand binding free energies are primarily attributable to the relative strength of the stacking interactions. The empirical results are discussed in light of recent computational studies of these interactions, including the effects of torsional strain, heteroarene tautomeric state, and co-axial orientation of stacking groups. Overall, this study provides an extensive dataset of empirical and high-level computed binding energies in a versatile new protein–ligand system highly amenable to studies of other intermolecular interactions.
|
Stacie Canan; Takaya Togo; Linh Tram; Laura Denton; Xochina ElHilali-Pollard; Jun Gu; Jinglei Jiang; Chenglei Liu; Yan Zhao; Yanlong Zhao; Yingzhe Zheng; Yunping Zheng; Jingjing Yang; Michelle Arkin; Panpan Fan; Deqian Sun; Steven Wheeler; Adam Renslo
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Physical Organic Chemistry; Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6390e8ac44ccbc311c11dd03/original/a-comprehensive-empirical-computational-study-of-diverse-het-eroarene-stacking-under-physiological-conditions.pdf
|
6481fb42e64f843f41824a97
|
10.26434/chemrxiv-2022-h0r79-v2
|
Formation and Characterisation of
Polymetallic Rings in vacuo
|
Understanding the (dis)assembly mechanisms of large metallosupramolecules is critical in their design, stability and diverse applications. Yet this task is difficult because of the inherent complexity of the structures, with many potential pathways of combining (or separating) the constituent building blocks. Here, we use collision-induced dissociation mass spectrometry to study the disassembly of heterometallic complexes, which have attracted interest due to their potential properties as new materials. Collisional activation leads to the formation of a series of previously unknown smaller ring products and we characterise their geometry using ion mobility. Specifically, the disassembly of both {CrxCu2} hourglass structures (x = 10, 12) and of a {Cr12Gd4} cluster shows the formation of rare closed, heptametallic species namely {Cr6Cu}, {Cr5Cu2} and {Cr5Gd2} as dominant products, as well as other closed ions like {Cr5Cu}, {Cr10Cu}, {Cr12Cu}, {Cr10}, {Cr12}, and {Cr6Gd2}. The collision cross section of cyclic products and precursors has a linear correlation with ion mass, a relationship that does not hold for acyclic systems. Thus, ion mobility mass spectrometry can determine whether a candidate polymetallic complex exists as a closed or open structure. As these rings are non-trivial to synthesize individually in solution, we propose the presented workflow as a means to identify and characterise feasible target molecules.
|
Niklas Geue; Grigore Timco; George Whitehead; Eric McInnes; Neil Burton; Richard Winpenny; Perdita Barran
|
Inorganic Chemistry; Analytical Chemistry; Organometallic Chemistry; Mass Spectrometry; Organometallic Compounds; Supramolecular Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6481fb42e64f843f41824a97/original/formation-and-characterisation-of-polymetallic-rings-in-vacuo.pdf
|
65c1623366c13817290a6104
|
10.26434/chemrxiv-2024-pz1tk
|
Molecularly Shielded, On-Demand, Ultrasound-Cured Polymer Networks
|
Networks formed from polymers can range from soft hydrogels to ultrahard protective coatings, making them useful for a wide range of applications from cell culture to highly bonded adhesives. Polymer networks are commonly crosslinked via heat or high energy light, and recently mechanical force has also been used to induce the formation of crosslinks in pre-existing networks. Here, we demonstrate a new strategy to use mechanical deformation and ultrasound to induce liquid-to-solid crosslinking. We synthesized graft copolymers with large poly(ethylene glycol) (PEG) side-chains acting as molecular shielding groups to protect otherwise highly reactive epoxide group. Solutions of highly shielded polymers could remain as a liquid solution when left undisturbed , and we could initiate gelation of these solutions with ultrasound in 20 seconds. These ultrasound-sensitive polymers are particularly useful in light and heat sensitive applications, and where precise control over the gelation time is required.
|
Adrian Lorenzana; Hsu Shwe Yee Naing; John Klier; Shelly Peyton
|
Polymer Science; Polymer brushes
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c1623366c13817290a6104/original/molecularly-shielded-on-demand-ultrasound-cured-polymer-networks.pdf
|
60c751cc469df4cbe7f44a8c
|
10.26434/chemrxiv.13160996.v2
|
Squeezing out the Catalysts: The Disulphide Bond Exchange in Aryl Disulphides at High Hydrostatic Pressure
|
Exchange of the disulphide bond is a prominent example
of equilibrium reactions. Therefore, the wide library of disulphide exchange
reactions requires the application of catalysts, such as reducing agents,
strong bases, ultraviolet light, or ultrasounds to stimulate higher conversion
yields. We employed the pressure between 100 and 400 MPa, for promoting the exchange
reactions between various homodimeric aryl disulphides and for optimized
conditions obtained 100 % yields and pure single-crystal form of the heterodimer.
The reactions were performed in a diamond-anvil cell, as well as in a hydraulic
piston-and-cylinder press, and the products were characterized by X-ray
diffraction, mass and NMR spectroscopy. <br />
|
Szymon Sobczak; Paulina Ratajczyk; Andrzej Katrusiak
|
Combinatorial Chemistry; Physical Organic Chemistry; Chemical Kinetics; Physical and Chemical Processes; Physical and Chemical Properties; Self-Assembly; Solution Chemistry; Thermodynamics (Physical Chem.); Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751cc469df4cbe7f44a8c/original/squeezing-out-the-catalysts-the-disulphide-bond-exchange-in-aryl-disulphides-at-high-hydrostatic-pressure.pdf
|
65d5ca4c9138d23161a03af5
|
10.26434/chemrxiv-2024-nzc9j
|
Remote control of anion binding by CH-based receptors
|
We show that the substitution of tetra(benzimidazole)resorcin[4]arenes with electron withdrawing groups on the upper rim enhances anion binding at the opposite edge by more than three orders of magnitude. Moreover, selective anion binding at either the OH/NH or CH binding sites is demonstrated.
|
Paulina Jurek; Marek Szymański; Agnieszka Szumna
|
Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d5ca4c9138d23161a03af5/original/remote-control-of-anion-binding-by-ch-based-receptors.pdf
|
6785fcb56dde43c908703e05
|
10.26434/chemrxiv-2024-pz39d-v2
|
Diverging Reaction Pathways and Key Intermediates in Ethylene Forming Enzyme
|
Ethylene-forming enzyme (EFE) is a non-heme iron (II)- and 2-oxoglutarate-(Fe(II)/2OG)-dependent oxygenase that exhibits distinct catalytic activity. While most Fe(II)/2OG-dependent oxygenases catalyze the substrate hydroxylation accompanied by the decarboxylation of the 2OG cosubstrate to succinate, EFE primarily converts the 2OG into CO2 and ethylene. Experimental studies suggest that the reaction mechanism of EFE does not involve the Fe(IV)=O (ferryl) intermediate central in the consensus mechanism for hydroxylation in Fe(II)/2OG-dependent oxygenases, and the ethylene-forming reaction pathway diverges early in the catalytic cycle after binding molecular oxygen. In this paper, we employ a multifaceted approach, including molecular dynamics, quantum mechanics and molecular mechanics methods, theoretical Mössbauer spectroscopy, and the analysis of the intrinsic electric field exerted by the protein environment, to examine possible reaction pathways for ethylene formation and hydroxylation in EFE. Our study reveals a new reaction pathway with a low energy barrier via the formation of Fe(II)-pyrocarbonates, which is different from all previously proposed reaction mechanisms. Based on our results, we introduce a revised reaction mechanism for the ethylene formation in the EFE that is consistent with the available experimental data. This work also provides new insights into both the first and second branchpoints of the ethylene-forming pathway that can be useful in EFE modifications aimed at shifting the product yield in the EF reaction.
|
Chao Wang; Elvira Sayfutyarova
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6785fcb56dde43c908703e05/original/diverging-reaction-pathways-and-key-intermediates-in-ethylene-forming-enzyme.pdf
|
67525c1b5a82cea2fa2227b7
|
10.26434/chemrxiv-2024-mjgbr
|
Heavily Polluted Tijuana River Drives Regional Air Quality Crisis
|
Toxic industrial chemicals and untreated sewage have polluted the Tijuana River for decades, recently causing over 1,000 consecutive days of California beach closures. In the summer of 2024, wastewater flows surged to millions of gallons per day despite no rain, enhancing water-to-air hydrogen sulfide (H2S) transfer at a turbulent hotspot. High wastewater flows and low winds led to nighttime H₂S peaks, reaching 4,500 parts-per-billion (ppb)—exceeding typical urban levels of 1 ppb. H₂S levels and community malodor reports were strongly correlated (r = 0.92), validating long-dismissed community voices and highlighting an environmental injustice issue. This study demonstrates that poor water quality can significantly impact air quality—though rarely included in air quality models and health assessments—with widespread implications as polluted waterways increase globally.
|
Benjamin Rico; Kelley Barsanti; William Porter; Paula Stigler Granados; Kimberly Prather
|
Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Environmental Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67525c1b5a82cea2fa2227b7/original/heavily-polluted-tijuana-river-drives-regional-air-quality-crisis.pdf
|
65b8fa6de9ebbb4db948f689
|
10.26434/chemrxiv-2023-rxm8h-v2
|
Towards dual light control of a catalytically-driven chemical reaction cycle
|
Chemically-fueled chemical reaction networks (CRNs) are key in controlling dissipative self-assembly. Having catalysts gating fuel consumption for both the activation and deactivation chemistry of (assembly-prone) monomers and controlling the catalytic activity with an external stimulus would provide better control over where, when, and how long self-assembled structures can form. Here we achieve light control over monomer activation and subsequent assembly into supramolecular fibers, and partial light control over deactivation and fiber disassembly. Activation proceeds via photoredox catalysis under visible light, whereas deactivation is achieved by organometallic catalysis that relies on a photocaged pre-fuel activated by ultraviolet light. Overall, we show how supramolecular fibers can be formed by visible light and how their destruction is accelerated by ultraviolet light.
|
Jorge S. Valera; Álvaro López-Acosta; Thomas Hermans
|
Materials Science; Polymer Science; Aggregates and Assemblies
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b8fa6de9ebbb4db948f689/original/towards-dual-light-control-of-a-catalytically-driven-chemical-reaction-cycle.pdf
|
67c5700efa469535b9ba11e1
|
10.26434/chemrxiv-2025-3ndrr
|
Investigating the Stability of Individual Carboxylate Rich Alicyclic Molecules Under Simulated Environmental Irradiation and Microbial Incubation Conditions
|
Understanding environmental dissolved organic matter (DOM) relies on the development of methods capable of navigating its inherent complexity. Although analytical techniques have continually advanced, leading to improved insight for both bulk and fractionated DOM, the fate of individual compound classes remains nearly impossible to track with current technology. Previously, we reported the synthesis of carboxylate rich alicyclic molecule (CRAM) compounds that shared more similar analytical features with DOM than previously available standards. Here, we adopt an alternative approach to the conventional use of DOM as a bulk material, by taking our synthesized CRAM compounds and subjecting them to simulated solar irradiation and microbial incubation experiments alongside an additional curated set of purchased molecules with chosen biological or chemical relevance. Irradiation experiments typically showed that compounds bearing only carboxylic acids and/or alcohols on a saturated carbon backbone were the most resistant to photochemical degradation, but also that some compounds with CRAM-like formulas and chemical functionality were notably more stable in the presence of DOM. Within microbial incubations, all of our synthesized CRAMs were entirely stable after 8-months in various aquatic settings. These sets of experiments provide support for the proposed stability of CRAM within the environment, as well as providing a platform from which a more diverse set of molecules can be used to assist in probing the stability of DOM.
|
Alexander Craig; Mahsa Norouzi; Paul Löffler; Foon Yin Lai; Rim Mtibaà; Eva Breyer; Federico Baltar; Lindon W. K. Moodie; Jeffrey A. Hawkes
|
Earth, Space, and Environmental Chemistry; Geochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c5700efa469535b9ba11e1/original/investigating-the-stability-of-individual-carboxylate-rich-alicyclic-molecules-under-simulated-environmental-irradiation-and-microbial-incubation-conditions.pdf
|
643ce5dd73c6563f140499bf
|
10.26434/chemrxiv-2023-47vhg
|
A Combined Spectroscopic and Computational Investigation on the Solvent-to-Chromophore Excited-State Proton Transfer in the 2,2’-Pyridylbenzimidazole-Methanol Complex
|
This article demonstrated experimental proof of excited state ‘solvent-to-chromophore’ proton transfer (ESPT) in the isolated gas phase PBI (2,2'-pyridylbenzimidazole)-CH3OH complex, aided by computational calculation. The binary complexes of PBI with CH3OH/CH3OD were produced in a supersonic jet-cooled molecular beam and the energy barrier of the photo-excited process was determined using resonant two-colour two-photon ionization spectroscopy (R2PI). The ESPT process in the PBI-CH3OH complex was confirmed by the disappearance of the Franck-Condon active vibrational transitions above 0_0^0+390 cm-1. In the PBI-CH3OD complex, the reappearance of the Franck-Condon till 0_0^0+800 cm-1 confirmed the elevation of the ESPT barrier upon isotopic substitution due to the lowering of the zero-point vibrational energy. The ESPT energy barrier in PBI-CH3OH was bracketed as 410±20 cm-1 (4.91±0.23 kJ mol-1) by comparing the spectra of PBI-CH3OH and PBI-CH3OD. The solvent-to-chromophore proton transfer was confirmed based on the significantly decreased quantum tunnelling of the solvent proton in the PBI-CH3OD complex. The computational investigation resulted in an energy barrier of 6.0 kJ mol-1 for the ESPT reaction in the PBI-CH3OH complex, showing excellent agreement with the experimental value. Overall, the excited state reaction progressed through an intersection of ππ* and nπ* states before being deactivated to the ground state via internal conversion. The present investigation reveals a novel reaction pathway on the deactivation mechanism of the photo-excited N-containing biomolecules in the presence of protic-solvents.
|
surajit maity; Ramesh Jarupula; saurabh khodia; Shabeeb Md.
|
Physical Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643ce5dd73c6563f140499bf/original/a-combined-spectroscopic-and-computational-investigation-on-the-solvent-to-chromophore-excited-state-proton-transfer-in-the-2-2-pyridylbenzimidazole-methanol-complex.pdf
|
677e9caa6dde43c908bbd8f0
|
10.26434/chemrxiv-2024-bm3lv-v2
|
peptidy: A light-weight Python library for peptide representation in machine learning
|
In this work, we introduce peptidy -- a lightweight Python library that facilitates converting peptides (expressed as aminoacid sequences) to numerical representations suited to machine learning. peptidy is free from external dependencies, integrates seamlessly into modern Python environments, and supports a range of encoding strategies suitable for both predictive and generative machine learning approaches. Additionally, peptidy supports peptides with post-translational modifications, such as phosphorylation, acetylation, and methylation, thereby extending the functionality of existing Python packages for peptides and proteins. peptidy is freely available with a permissive license on GitHub at the following URL: https://github.com/molML/peptidy
|
Rıza Özçelik; Laura van Weesep; Sarah de Ruiter; Francesca Grisoni
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677e9caa6dde43c908bbd8f0/original/peptidy-a-light-weight-python-library-for-peptide-representation-in-machine-learning.pdf
|
63fd981b32cd591f1297b767
|
10.26434/chemrxiv-2023-x7zgc
|
Mg-doped SrTiO3 Photocatalyst with Ag-Co Cocatalyst for Enhanced Selective Conversion of CO2 to CO Using H2O as the Electron Donor
|
Photocatalytic conversion of CO2 by H2O is a promising method for solving energy and environmental problems. In this context, efficient photocatalysts that facilitate the selective conversion of CO2 to the value-added chemical CO are essential. In this study, for the first time in the literature, we used an Mg-doped SrTiO3 photocatalyst (Mg-SrTiO3) for the photocatalytic conversion of CO2 to CO using H2O as the electron donor under monochromatic UV-light irradiation at 365 nm. Compared to pristine SrTiO3, Mg-SrTiO3, which is prepared via a flux method, exhibited dramatically enhanced conversion of CO2 to CO in the presence of Ag-Co cocatalyst. Moreover, the selectivity toward CO evolution was greater than 99%, indicating suppression of the unnecessary and competitive H2 evolution. Scanning electron microscopy of Mg-SrTiO3 revealed edge-shaved cubic particles, which were correlated to the anisotropic distribution of photogenerated electrons and holes and the consequent enhancement of photocatalytic activity. Furthermore, the Mg-doping temperature and amount used to prepare Mg-SrTiO3 influenced the substitution of Ti4+ sites in the bulk of SrTiO3 by Mg2+, thereby affecting the CO evolution. The apparent quantum efficiency of optimal Mg-SrTiO3 in the photocatalytic conversion of CO2 was determined to be 0.05%.
|
Takechi NAKAMOTO; Shoji IGUCHI; Shimpei NANIWA; Tsunehiro TANAKA; Kentaro TERAMURA
|
Catalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fd981b32cd591f1297b767/original/mg-doped-sr-ti-o3-photocatalyst-with-ag-co-cocatalyst-for-enhanced-selective-conversion-of-co2-to-co-using-h2o-as-the-electron-donor.pdf
|
67a24711fa469535b90c272c
|
10.26434/chemrxiv-2025-8xp04
|
IR-Bot: an autonomous robotic system for real-time chemical mixture analysis via infrared spectroscopy and machine learning
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Rapid and accurate quantification of chemical mixtures is vital in autonomous chemical experimentation, which can serve as real-time feedback that guides decision-making and reduces resource consumption. Here, we present IR-Bot, an intelligent system that integrates robotic automation, infrared (IR) spectroscopy, quantum chemical simulations, and machine learning (ML) to enable autonomous, real-time mixture analysis. The autonomy is driven by a newly developed large-language-model-based IR Agent, working alongside a multi-agent robotic system to orchestrate theoretical IR calculations, experimental data acquisition, and ML-driven interpretation. Central to IR-Bot is the Alignment-Prediction approach: experimental spectra are aligned with simulated references, and a pre-trained prediction model then provides composition estimates. This fusion of pre-training, alignment, and prediction yields accurate, interpretable results for both binary and ternary mixtures, as demonstrated via a Suzuki coupling reaction. Moreover, IR-Bot’s explainable ML framework uncovers the specific vibrational modes guiding its predictions, offering deeper insights into fundamental chemical behaviour. By enabling rapid, reliable, and autonomous composition analysis, IR-Bot paves the way for a new generation of data-driven laboratory workflows capable of dynamic decision-making and real-time modification of experimental conditions.
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Xiaoyu Yue; Tao Song; Jiaqi Cao; Xiaolong Zhang; Shuo Feng; Weiwei Shang; Jun Jiang; Linjiang Chen
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Theoretical and Computational Chemistry; Analytical Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
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CC BY NC ND 4.0
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CHEMRXIV
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2025-02-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a24711fa469535b90c272c/original/ir-bot-an-autonomous-robotic-system-for-real-time-chemical-mixture-analysis-via-infrared-spectroscopy-and-machine-learning.pdf
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628aa2795d9485538bcb0b22
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10.26434/chemrxiv-2022-ls3rp
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An approach for the pore-centred description of adsorption in hierarchical porous materials
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Analysis of pore size distributions based on crystalline representations of metal-organic frameworks (MOFs) featuring hierarchical pore systems, DUT-32, DUT-75, UMCM-1 and NU-1000, is presented here and leveraged to understand gas adsorption in these unique pore structures.
Statistical analysis was used to effectively partition the pore space into distinct regions labelled by the pore size.
This pore description was used to discover how adsorbates are located, with respect to the different pores, during simulations of argon adsorption at 87K.
To further examine adsorption behaviour, a method of clustering the pore environments to locate the centre of the pore was developed.
These pore centres were employed to observe the distribution of gas within the pore, describing adsorbate positions during filling events from the unique perspective of the pore centre.
The methods presented here provide unsurpassed information about pore structure and adsorption properties that cannot be obtained with currently available methods and are now ready to apply to new materials to uncover new adsorption processes.
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Jack Evans
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Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Statistical Mechanics; Thermodynamics (Physical Chem.); Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2022-05-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628aa2795d9485538bcb0b22/original/an-approach-for-the-pore-centred-description-of-adsorption-in-hierarchical-porous-materials.pdf
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63aaebe116e9a844b6368f14
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10.26434/chemrxiv-2022-k208v
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Stable Ketenyl Anions via Ligand Exchange at an Anionic Carbon as Powerful Synthons
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A (phosphino)diazomethyl anion salt 1 ([[P]−CN2][K(18-C-6)(THF)]) ([P] = [(CH2)(NDipp)]2P; 18-C-6 = 18-crown-6) behaves as a (phosphino)carbyne anion-dinitrogen adduct ([P]−C−←:N2). Under an atmosphere of carbon monoxide (CO), 1 undergoes a facile N2/CO ligand exchange reaction giving (phosphino)ketenyl anion salt [[P]−CCO][K(18-C-6)] 2. Oxidation of 2 with elemental Se affords (selenophosphoryl)ketenyl anion salt ([P](Se)−CCO][K(18-C-6)]) 3. These ketenyl anions feature a strongly bent geometry at the P-bound carbon and this carbon atom is highly nucleophilic. The electronic structure of 2 is examined by theoretical studies. Reactivity investigations demonstrate 2 as a versatile synthon for derivatives of ketene, enolate, acrylate and acrylimidate moieties.
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Rui Wei; Xin-Feng Wang; David Ruiz; Liu Leo Liu
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Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.)
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CC BY NC ND 4.0
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CHEMRXIV
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2022-12-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63aaebe116e9a844b6368f14/original/stable-ketenyl-anions-via-ligand-exchange-at-an-anionic-carbon-as-powerful-synthons.pdf
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6763388ffa469535b9039fb8
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10.26434/chemrxiv-2024-5bf6f
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Spectroelectrochemistry with Hydrogen-Doped Indium Oxide Electrodes Monitors Electron and Hole Injection into PbS Quantum Dots
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We combine potential-modulated absorption spectroscopy with working electrodes made of hydrogen-doped indium oxide on glass to study the electrochemically induced changes to the infrared absorption of ethanedithiol-crosslinked PbS quantum dot thin films. We demonstrate an electrochemical window of -1.5 V to 1 V vs. ferrocene/ferrocenium as well as a spectral window of 800 nm – 1900 nm, and we show how these ranges can be fine-tuned by tailoring the composition of the working electrode. We find evidence for the successful injection of electrons and holes into the quantum dots to a comparable degree. This enables us to locate the absolute positions of the band edges and the Fermi level for PbS quantum dots with different diameters, monitor how the band edge positions depend on the diameter and show a correlation between the position of the Fermi level with the appearance of in-gap states. We discuss the specific advantages of the technique presented here for monitoring the redox behaviour of IR-active quantum dots, detail the experimental challenges and devise strategies for their mitigation.
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Sophia Westendorf; shangjing Li; Patrick Michel; Bin Hu; Marcus Scheele
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Physical Chemistry; Materials Science; Nanostructured Materials - Materials; Electrochemistry - Mechanisms, Theory & Study
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CC BY 4.0
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CHEMRXIV
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2024-12-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6763388ffa469535b9039fb8/original/spectroelectrochemistry-with-hydrogen-doped-indium-oxide-electrodes-monitors-electron-and-hole-injection-into-pb-s-quantum-dots.pdf
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60c750740f50db66bc39757a
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10.26434/chemrxiv.13043156.v1
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Why Conventional Design Rules for C–H Activation Fail for Open-Shell Transition-Metal Catalysts
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The design of selective and active C–H activation catalysts for direct methane-to-methanol conversion is challenging. Bioinspired complexes that form high valent metal-oxo intermediates capable of hydrogen abstraction and rebound hydroxylation are promising candidates. This promise has made them a target for computational high-throughput screening, typically simplified through the use of linear free energy relationships (LFERs). However, their mid-row transition-metal centers have numerous accessible spin and oxidation states that increase the combinatorial scale of design efforts. Here, we carry out a computational design screen of over 2,500 mid-row 3<i>d</i> transition-metal complexes with four metals in numerous spin and oxidation states. We demonstrate the importance of spin/oxidation state in dictating design principles, limiting the generalization of strategies derived for widely studied high-spin Fe(II) catalysts to other metals or spin/oxidation states. Combined assessment of the effect of ligand field tuning on reaction step energetics and on the identity of the ground state allows us to propose refined design strategies for spin-allowed methane-to-methanol catalysis. We observed weak coupling of energetics and design principles between reaction steps (e.g., oxo-formation vs methanol release), meaning that LFERs do not generalize across our larger catalyst set. To rationalize relative reactivity in known catalysts, we instead compute independent reaction energies and propose strategies for further improvements in catalyst design.
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Aditya Nandy; Heather Kulik
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High-throughput Screening; Computational Chemistry and Modeling; Theory - Computational; Homogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2020-10-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750740f50db66bc39757a/original/why-conventional-design-rules-for-c-h-activation-fail-for-open-shell-transition-metal-catalysts.pdf
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61a17e2cf93ad3164fb585f3
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10.26434/chemrxiv-2021-72ghc
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Modulating Photo- and Radioluminescence in Tb(III) Cluster-Based Metal–Organic Frameworks
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Luminescent metal–organic frameworks (MOFs) are of interest for sensing, theranostics, dosimetry, and other applications. The use of lanthanoids in MOF metal nodes allows for intrinsic met-al-based luminescence. In this work, a facile route for modulat-ing the photoluminescent and radioluminescent properties of Tb(III)-based MOFs is reported. By using Tb(III)-cluster nodes as X-ray attenuators, and organic linkers with varying excited state energies as sensitizers, MOFs with metal-based, linker-based, and metal+linker-based photo- and radioluminescence are reported.
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Zvart Ajoyan; Gabrielle A. Mandl; P. Rafael Donnarumma; Victor Quezada-Novoa; Hudson A. Bicalho; Hatem M. Titi; John A. Capobianco; Ashlee J. Howarth
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Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.); Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2021-11-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a17e2cf93ad3164fb585f3/original/modulating-photo-and-radioluminescence-in-tb-iii-cluster-based-metal-organic-frameworks.pdf
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66abb9bac9c6a5c07abacb00
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10.26434/chemrxiv-2024-067sp
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Computational characterization of the DAD photoisomerization: Functionalization, protonation and solvation effects.
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Photoswitches are becoming increasingly popular in pharmacology due to the possibility of modifying their activity with light. Hence, it is crucial to understand the photophysics of these compounds to identify promising light-activated drugs. We focused our study on DAD, an azobenzene derivative that, according to a previous experimental investigation, can restore visual function in blind mice due to trans-cis photoisomerization upon light absorption. With the present computational study, we aim to characterize the absorption spectrum of DAD, and to understand its photoisomerization mechanism by means of conformational search analysis, quantum mechanical (QM) and hybrid QM/continuum calculations, and classical molecular dynamics simulations. Moreover, we explored the effect of the derivation (DAD vs azobenzene), the protonation (DAD vs DADH22+, the two possible protonation states) and the solvation effects (vacuum vs water) on the photoisomerization. Similarly to azobenzene, we showed that the photoisomerization of both protonation states of DAD begin with the population of the bright S2 state. Then, it crosses to the S1 surface and relaxes along the rotation of the azo dihedral to a S1/S0 crossing point. The latter is close to a transition state that connects the trans and cis geometries on the ground state. Finally, our results suggested that amino derivation, non-protonation and water solvation could improve the quantum yield of the photoisomerization.
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Lucía López-Pacios; Juan J. Nogueira; Lara Martínez-Fernández
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2024-08-02
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66abb9bac9c6a5c07abacb00/original/computational-characterization-of-the-dad-photoisomerization-functionalization-protonation-and-solvation-effects.pdf
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624c577f804882e535045c53
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10.26434/chemrxiv-2022-pbj0d
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Synthesis and styrene copolymerization of benzyloxy, methylphenyl, acetoxy, acetyl, cyano, and amino ring-substituted 2-methoxyethyl phenylcyanoacrylates
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Novel ring-substituted 2-methoxyethyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH2OCH3 (where R is 2-benzyloxy, 3-benzyloxy, 4-benzyloxy, 3-(4-methylphenyl), 4-(4-methylphenyl), 4-acetoxy, 2-acetyl, 3-acetyl, 4-acetamido, 2-cyano, 3-cyano, 4-cyano, 4-dimethylamino, 4-diethylamino) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and 2-methoxyethyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis.
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Matthew A. Baily; Kristina M. Bell; Nidal N. Boutros; Terece K. Brown; Anjali N. Chudgar; Hannah C. Deutmeyer; Natalie Esh; Emily I. Gardner; Zachary J. Gembara; Gabe T. Inoshita; Ivan Karparov; Andres S. Lafuente; Patrick T. Watkins; Leticia Zepeda; Sara M. Rocus; William S. Schjerven; Gregory B. Kharas
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Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers
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CC BY 4.0
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CHEMRXIV
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2022-04-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624c577f804882e535045c53/original/synthesis-and-styrene-copolymerization-of-benzyloxy-methylphenyl-acetoxy-acetyl-cyano-and-amino-ring-substituted-2-methoxyethyl-phenylcyanoacrylates.pdf
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60ef3f40338e924d870b191c
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10.26434/chemrxiv-2021-bjvn9
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Diamond Membrane Production: The Critical Role of Radicals in the Non-Contact Electrochemical Etching of sp2 Carbon
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Sub-micrometre single crystal diamond membranes are of huge importance for next generation optical, quantum and electronic device applications. Electrochemical etching has proven a critical step in the production of such membranes. Etching is used to selectively remove a very thin layer of sub-surface sp2 bonded carbon, prepared by ion implantation in bulk diamond, releasing the diamond membrane. Due to the nanosized dimensions, etching is carried out using non-contact electrochemistry in low conductivity solutions (bipolar arrangement) which whilst effective, results in extremely slow etch rates. In this work, a new method of non-contact electrochemical etching is presented which uses high conductivity, high concentration, fully dissociated aqueous electrolytes. Careful choice of the electrolyte anion results in significant improvements in the sp2 carbon etch rate. In particular, we show both chloride and sulfate electrolytes increase etch rates significantly (up to ×40 for sulfate) compared to the current state-of-the-art. Electron paramagnetic resonance experiments, recorded after the electrode potential has been switched off, reveal sizeable hydroxyl radical concentrations at timescales > 10^7 longer than their lifetime (< microsecond). These measurements highlight the importance of electrochemically initiated, solution chemistry radical generation and regeneration pathways in high concentration sulfate and chloride solutions for nano-etching applications.
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Josh Tully; Emily Braxton; Sam Cobb; Ben Breeze; Matthew Markham; Mark Newton; Paramaconi Rodriguez; Julie Macpherson
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Analytical Chemistry; Electrochemical Analysis; Materials Chemistry
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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/60ef3f40338e924d870b191c/original/diamond-membrane-production-the-critical-role-of-radicals-in-the-non-contact-electrochemical-etching-of-sp2-carbon.pdf
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6266bdd8ef2adec7233ca55a
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10.26434/chemrxiv-2022-r7fgp
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Benchmark of Density Functional Theory Methods for the Study of Organic Polysulfides
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Elemental sulfur is often used in organic synthesis as its low cost and high abundance make it a highly desirable source of sulfur atoms. However, sulfur’s unpredictable catenation behavior poses challenges to its widespread usage due to difficulties in designing new reactions that can account for its multifaceted reactivity. In order to accurately model sulfur’s mechanisms using computational approaches, it is necessary to identify Density Functional Theory (DFT) methods that are accurate on these systems. This study benchmarks 12 well-known DFT functionals that include local, non-local, and hybrid methods against DLPNO-CCSD(T)/aug-cc-pV(Q+d)Z // MP2/aug-cc-pV(T+d)Z/SMD(MeCN) for the accurate treatment of organic polysulfides, taking cyanide as a nucleophile. Our benchmarking results indicate that the M06-2X and B3LYP-D3(BJ) density functionals are the most accurate for calculating reaction energies, while local functionals performed the worst. For activation energies, MN15, MN15-L, M06-2X, and ωB97X-D are the most accurate. Our analysis of structural parameters shows that all functionals perform well for ground state optimizations except B97D3, while MN15-L and M06-2X performed best for transition structure optimizations. Overall, the four hybrid functionals MN15, M06-2X, ωB97X-D and B3LYP-D3(BJ) appear adequate for studying the reaction mechanisms of polysulfides.
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Jyoti Sharma; Pier Alexandre Champagne
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Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2022-04-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6266bdd8ef2adec7233ca55a/original/benchmark-of-density-functional-theory-methods-for-the-study-of-organic-polysulfides.pdf
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60c74bbdbdbb89f935a39638
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10.26434/chemrxiv.12173640.v2
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Epitaxial GaN using Ga(NMe2)3 and NH3 Plasma by Atomic Layer Deposition
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<div>Low temperature deposition of high-quality epitaxial GaN is crucial for its integration in</div><div>electronic applications. Chemical vapor deposition at approximately 800 °C using SiC with an</div><div>AlN buffer layer or nitridized sapphire as substrates is used to facilitate the GaN growth. Here,</div><div>we present a low temperature atomic layer deposition (ALD) process using</div><div>tris(dimethylamido)gallium(III) with NH3 plasma. The ALD process shows self-limiting</div><div>behaviour between 130-250 °C with a growth rate of 1.4 Å/cycle. The GaN films produced were</div><div>crystalline on Si(100) at all deposition temperatures with a near stochiometric Ga/N ratio with</div><div>low carbon and oxygen impurities. When GaN was deposited on 4H-SiC, the films grew</div><div>epitaxially without the need for an AlN buffer layer, which has never been reported before. The bandgap of the GaN films was measured to be ~3.42 eV and the fermi level showed that the GaN was unintentionally n-type doped. This study shows the potential of ALD for GaN-based</div><div>electronic devices.</div>
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Polla Rouf; Nathan J O'Brien; Sydney C. Buttera; Ivan Martinovic; Babak Bakhit; Erik Martinsson; Justinas Palisaitis; Chih-Wei Hsu; Henrik Pedersen
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Thin Films; Nanostructured Materials - Nanoscience; Ligands (Inorg.); Main Group Chemistry (Inorg.); Organometallic Compounds; Main Group Chemistry (Organomet.); Interfaces; Surface; Crystallography
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CC BY 4.0
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CHEMRXIV
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2020-05-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bbdbdbb89f935a39638/original/epitaxial-ga-n-using-ga-n-me2-3-and-nh3-plasma-by-atomic-layer-deposition.pdf
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67bf4c126dde43c9089a4899
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10.26434/chemrxiv-2025-pbv33
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A Molecular Donor-Acceptor System to Induce and Visualize Proton Transfer Across Biomolecules
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Proton transfer (PT) is at the heart of fundamental natural biochemical reactions, e.g. in bioenergetics, where proteins are the main proton mediators. PT between two specific points requires a change in the proton motive force via alteration of acid-base properties. Nature solved this problem primarily by modulating the protein structure during the PT process. Here, we introduce a light-triggered proton donor-bridge-acceptor approach for inducing and visualizing directional PT in biosystems, specifically peptides. To do so, we synthesize unnatural amino acids containing a light-triggered proton donor and acceptor and place them at the ends of peptide bridges that differ in their amino acid composition while creating a giant ΔpKa* gradient between them upon photoexcitation. Ultrafast optical spectroscopies allow for visualization of the PT process across the donor-bridge-acceptor system and extraction of the PT kinetics. Our results reveal the importance of side chains, peptide structure, and environment in promoting PT. We show that helical structures can promote PT even with hydrophobic side chains, whereas titratable oxo-amino-acids can promote PT via their side chains even in an aprotic environment. Our strategy for inducing and visualizing the PT process across any desired pathway can be extended to various peptide systems and into proteins, thus opening a new field of research.
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Ramesh Nandi; Ganga Vamisetti; Samim Sardar; Diego Florio; Tomasz Pieńko; Fabian Glaser; Cosimo D’Andrea; Giulio Cerullo; Franco Camargo; Nadav Amdursky
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Physical Chemistry; Biophysical Chemistry; Chemical Kinetics
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CC BY 4.0
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CHEMRXIV
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2025-03-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bf4c126dde43c9089a4899/original/a-molecular-donor-acceptor-system-to-induce-and-visualize-proton-transfer-across-biomolecules.pdf
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6585aa7566c1381729cba561
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10.26434/chemrxiv-2023-3cc3c
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The isoelectric point of metal oxide films formed by anodization
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The surface charge of metal oxides is an important property that significantly contributes to a wide range of phenomena, including adsorption, catalysis and material science. The surface charge can be predicted by determining the isoelectric point (IEP) of a material and the pH of a solution. Although there have been several studies about the IEP of metal oxide (nano)particles, only few of them have reported the IEP of metal oxide films. The IEP of various compact metal oxide films such as TiO2, Nb2O5, WO3, ZrO2, NiO and Al2O3 formed via electrochemical anodization was determined in this project using the streaming potential technique. Nanostructured TiO2 and NiO were additionally produced using a single-step anodization technique and their IEPs were compared with the compact ones. The surface morphology and wettability of the oxides were studied by scanning electron microscopy (SEM) and contact angle (CA) measurements. X - ray powder diffraction (XRD) and X - Ray photoelectron spectroscopy (XPS) measurements were carried out to detect the elemental composition and phase analysis. The IEPs of compact anodic oxides are deviating from their nanoparticular and atomic layer deposited (ALD) counterparts. When comparing compact and nanostructured anodic oxides, the latter show even higher IEPs, emphasizing the dependency of the IEP on the method of oxide production.
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Aydan Yadigarli; Patrick Hartwich; Gabriel Onyenso; Torsten Kowald; Merve Kübra Aktan; Annabel Bream; Manuela S. Killian
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Analytical Chemistry; Nanoscience; Materials Chemistry
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CC BY NC 4.0
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CHEMRXIV
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2023-12-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6585aa7566c1381729cba561/original/the-isoelectric-point-of-metal-oxide-films-formed-by-anodization.pdf
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6672af4a01103d79c590136b
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10.26434/chemrxiv-2024-9j0xs-v2
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Mild and Scalable Conditions for the Solvothermal Synthesis of Imine-Linked Covalent Organic Frameworks
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A convenient method was developed that allows for the synthesis of highly crystalline and porous imine-linked covalent organic frameworks (COFs) in hours. The use of an apolar solvent in combination with a precise amount of water and acetic acid was crucial to obtain materials of optimal quality. Twelve different COFs could be produced under the same reaction conditions, using a green solvent mixture of n-butanol, acetic acid and water at 70 °C for 16 hours with stirring. The crystallinity of the COFs produced in this manner is similar or better than that obtained by traditional solvothermal synthesis. The method could be easily scaled to synthesize over ten grams of COF in one batch. Optical microscopy, FTIR spectroscopy and in situ Raman spectroscopy gave insight in the role of the solvent on the aggregation of COF nanosheets and the resulting crystallinity, porosity and robustness of the material.
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Andreas Laemont; Gilles Matthys; Roy Lavendomme; Pascal Van Der Voort
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Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2024-06-19
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6672af4a01103d79c590136b/original/mild-and-scalable-conditions-for-the-solvothermal-synthesis-of-imine-linked-covalent-organic-frameworks.pdf
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651db85fbda59ceb9adff313
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10.26434/chemrxiv-2023-s7s1t
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Simulating the Excited-State Dynamics of Polaritons with Ab Initio Multiple Spawning
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Over the last decade, there has been a growth of interest in polaritonic chemistry, where the formation of hybrid light-matter states (polaritons) can alter the course of photochemical reactions. These hybrid states are created by strong coupling between molecules and photons in resonant optical cavities and can even occur in the absence of light when the molecule is strongly coupled with the electromagnetic fluctuations of the vacuum field. We present a first-principles model to simulate nonadiabatic dynamics of such polaritonic states inside optical cavities by leveraging graphical processing units (GPUs). Our first implementation of this model is specialized for a single molecule coupled to a single photon mode confined inside the optical cavity, but with any number of excited states computed using complete active space configuration interaction (CASCI) and a Jaynes-Cummings type Hamiltonian. Using this model, we have simulated the excited-state dynamics of a single salicylideneaniline (SA) molecule strongly coupled to a cavity photon with the ab initio multiple spawning (AIMS) method. We demonstrate how the branching ratios of the photo-deactivation pathways for this molecule can be manipulated by coupling to the cavity. We also show how one can stop the photoreaction from happening inside an optical cavity. Finally, we also investigate cavity-based control of the ordering of two excited states (one optically bright and the other optically dark) inside a cavity for a set of molecules where the dark and bright states are close in energy.
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Bhaskar Rana; Edward G. Hohenstein; Todd J. Martínez
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Theoretical and Computational Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2023-10-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651db85fbda59ceb9adff313/original/simulating-the-excited-state-dynamics-of-polaritons-with-ab-initio-multiple-spawning.pdf
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66d32469f3f4b05290bb759a
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10.26434/chemrxiv-2024-8p0nj
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Nitriles as multipurpose reagents for the synthesis of sultams and sultons (review article)
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In this review, we discuss the use of the nitrile function in the synthesis of cyclic sulfonamides (sultams), an important class of antibiotics The cyano group is a versatile building block in sultam synthesis. It can form the sultam and sulton skeleton or activate adjacent positions. Commonly, the nitrile group undergoes the CSIC reaction, acting as an electrophilic center attacked by a carbanion, forming enamines. Nitriles also facilitate α-position substitutions through alkylation or cyclization and activate unsaturated bonds in various cycloadditions. Literature indicates the nitrile group, as a methyleneamine precursor, shows promise for sultam synthesis. This method could efficiently produce spirocyclic sultams with applications in chemistry and biology.
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Maksym Kovalov; Bohdan Vashchenko
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Organic Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-09-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d32469f3f4b05290bb759a/original/nitriles-as-multipurpose-reagents-for-the-synthesis-of-sultams-and-sultons-review-article.pdf
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619210da2e10adae4f47533e
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10.26434/chemrxiv-2021-tqjwg
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The syntheses, structures and spectroelectrochemical properties of 6-oxo-verdazyl derivatives bearing surface anchoring groups
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A series of 6-oxo verdazyl radicals functionalised at the 1- and 5-positions by methyl, thiomethyl and iodo groups were synthesised using conventional strategies. Facile Sonogashira cross-coupling reactions of terminal alkynes with the diiodo analogue were used for synthetic elaboration of the verdazyl core structure with π-conjugated ethynyl groups. The radicals were characterised by EPR spectroscopy, single-crystal X-ray diffraction, cyclic voltammetry and optical spectroscopy. The chemically and electrochemically reversible oxidation and reduction of these radicals within a convenient redox window permitted further studies on the closed-shell cationic and anionic forms using spectroelectrochemical methods, supported by (TD-)DFT calculations.
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Varshini Kumar; Jian-Zhong Wu; Martyna Judd; Elodie Rousset; Marcus Korb; Stephen Moggach; Nicholas Cox; Paul Low
|
Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-11-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619210da2e10adae4f47533e/original/the-syntheses-structures-and-spectroelectrochemical-properties-of-6-oxo-verdazyl-derivatives-bearing-surface-anchoring-groups.pdf
|
63d481a110cb6a55f3e93203
|
10.26434/chemrxiv-2023-6fdms
|
Highly Robust Multilamellar Lipid Vesicles Generated through Intervesicular Self-assembly Mediated by Hydrolyzed Collagen Peptides
|
Despite the advantages of lipid vesicles for drug and gene delivery, structural instability limits their practical applications and requires strictly regulated conditions for transport and storage. Chemical crosslinking and in situ polymerization have been suggested to increase the membrane rigidity and dispersion stability of lipid vesicles. However, such chemically modified lipids sacrifice the dynamic nature of lipid vesicles and obfuscate their in vivo metabolic fates. Here we present highly robust multilamellar lipid vesicles through the self-assembly of pre-formed, cationic large unilamellar vesicles (LUVs) with hydrolyzed collagen peptides (HCPs). The cationic LUVs undergo vesicle-to-vesicle attachment and structural reorganization through polyionic complexation with HCPs, resulting in the formation of multilamellar collagen-lipid vesicles (MCLVs). The resulting MCLVs exhibit excellent structural stability against variations in pH and ionic strength and the addition of surfactants. Particularly, the MCLVs maintain their structural stability against repeated freeze-thaw stresses, proving the excellent stabilization effect of HCPs on lipid lamellar structures. This work provides a practically attractive technique for the simple and quick fabrication of structurally robust lipid nanovesicles without covalent crosslinkers, organic solvents, and specialized instruments.
|
Bon Il Koo; Rafia Tasnim Rahman; Jihui Jang; Dong Jae Lee; Jun Bae Lee; Yoon Sung Nam
|
Nanoscience; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d481a110cb6a55f3e93203/original/highly-robust-multilamellar-lipid-vesicles-generated-through-intervesicular-self-assembly-mediated-by-hydrolyzed-collagen-peptides.pdf
|
60c747480f50db6690396594
|
10.26434/chemrxiv.10567097.v1
|
Design of Potent Mincle Signalling Agonists Based on an Alkyl b- Glucoside Template
|
The innate immune receptor Mincle senses lipid-based molecules derived from pathogens, commensals and altered self. Based on emerging structure-activity relationships we design simple alkyl 6-<i>O</i>-acyl-b-D-glucosides that are effective agonists of Mincle and signal with potency on par with the prototypical ligand trehalose dimycolate.
|
DYLAN SMITH; Yuki Hosono; Masahiro Nagata; Sho Yamasaki; Spencer Williams
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747480f50db6690396594/original/design-of-potent-mincle-signalling-agonists-based-on-an-alkyl-b-glucoside-template.pdf
|
67dd600dfa469535b91a39df
|
10.26434/chemrxiv-2025-gfq94
|
Theoretical simulation of the molecular structure of a free cyclopentadiene monomer: anticipating the GED experiment
|
In this study, we performed a quantum chemical (QC) study of the geometry and vibrational spectra of a free cyclopentadiene CPD molecule, with the aim of (i) comparing geometric parameters obtained using various theoretical approaches, (ii) comparing force fields and vibrational frequencies, and (iii) modeling the radial distribution functions for a planned gas-phase electron diffraction (GED) experiment to determine geometric and vibrational parameters of the free CPD molecule with precision, in accordance with modern requirements and using up-to-date experimental techniques and structural analysis of the results of electron diffraction.
|
Valeriya Mukhina; Alexey Eroshin; Ilya Navarkin; Sergey Shlykov
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd600dfa469535b91a39df/original/theoretical-simulation-of-the-molecular-structure-of-a-free-cyclopentadiene-monomer-anticipating-the-ged-experiment.pdf
|
60c74ff3702a9be04418bc8c
|
10.26434/chemrxiv.12967109.v1
|
New Light on Old Fingermarks: The Detection of Historic Latent Fingermarks on Old Paper Documents Using 1,2-Indanedione/zinc
|
This study explores trends in the effectiveness of 1,2-indandione/zinc chloride (IND/Zn) for visualizing latent fingermarks on paper substrates of various ages. Preliminary investigation of contemporaneous documents showed that high quality fingermarks could be deposited through incidental handling, although smudging and overlapping were evident. IND/Zn was then applied to incidentally handled documents up to 80 years old and successfully developed potentially identifiable fingermarks, significantly increasing the established timescale for fingermark detection with amino acid sensitive reagents. The results indicate that IND/Zn remains effective over longer periods than has been previously demonstrated, although a comparison between documents of different ages suggest that progressive diffusion of the target amino acids occurs over time, affecting the proportion of potentially identifiable marks.The findings of this study reinforce the applicability of IND/Zn for the detection of historic latent fingermarks on old paper documents.
|
Jemmy T. Bouzin; Jason Merendino; Stephen M. Bleay; Georgina Sauzier; Simon W. Lewis
|
Analytical Chemistry - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ff3702a9be04418bc8c/original/new-light-on-old-fingermarks-the-detection-of-historic-latent-fingermarks-on-old-paper-documents-using-1-2-indanedione-zinc.pdf
|
678fc1f06dde43c9088c2599
|
10.26434/chemrxiv-2025-65fz5
|
Stereocontrol in Reductive Aminases through Steric Modification of Residues Around Substrate and Cofactor Binding Pockets
|
Enzymatic reductive amination catalysed by imine reductases (IREDs) and reductive aminases (RedAms) provides green, stereoselective, and direct access to 2° and 3° chiral amines. Given existing interests in exploiting RedAms for commercial-scale synthesis of active pharmaceutical ingredients, developing efficient enantiodivergent RedAm systems would boost biocatalysis prospects in early drug discovery. To develop adaptable enantiodivergent RedAm systems, residues/motifs that can serve as handles for stereocontrol in this enzyme family need to be identified.
In this work, we have identified residues at both the cofactor and substrate binding pockets in a fungal reductive aminase (MaRedAm) and a bacterial imine reductase (AoIRED) that allow stereocontrol through steric modification of the side chains. In MaRedAm, steric bulk removal as in W33A and R35A at the cofactor binding pocket improved (R)-selectivity towards the synthesis (R)-rasagiline with up to 95% e.e., whereas W211A mutation at the substrate binding pocket inverted the selectivity of MaRedAm to yield (S)-rasagiline (42% e.e.). Similarly, varying steric bulk at N241 in AoIRED achieved enantiodivergency as N241L/H/F/Y variants produce (S)-configured 1-methyl-1,2,3,4,-tetrahydroisoquinoline (92->99% e.e. compared to 85% e.e. (S) achieved by the wild-type), whereas N241A/S/C mutations yield the (R)-configured amine (up 40% e.e.).
Atomistic insights obtained from molecular dynamics (MD) simulations revealed that steric modulation at the cofactor binding pocket (as in MaRedAM W33A and W35A) causes the reorganisation and downsizing of the active site. In contrast, the W211A mutation at the substrate binding pocket showed this pocket opening up to allow flexibility for the rotation of the substrate. Our work lays an important foundation for speedy rational engineering of stereoselectivity in IREDs/RedAms.
|
Jake Gooderham; Beatrice-Maria Zabava; David Aleku; Julie Vignot; Zuoye Xie; Ruth Bradshaw Allen; Mario Prejanò; Godwin Aleku
|
Organic Chemistry; Catalysis; Biocatalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678fc1f06dde43c9088c2599/original/stereocontrol-in-reductive-aminases-through-steric-modification-of-residues-around-substrate-and-cofactor-binding-pockets.pdf
|
676a9c4bfa469535b9a3b14b
|
10.26434/chemrxiv-2024-g1pcp-v2
|
A Simplified Model of Iterative Compound Optimization
|
This paper presents a simplified model of iterative compound optimization in drug/agrochemical discovery. Compounds are represented as binary strings, with project evolution simulated through random bit changes. The model reproduces key statistical features of real projects, including activity distributions and time-series characteristics. This framework enables statistical simulation of compound optimization, potentially aiding project planning and resource estimation.
|
John Delaney
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676a9c4bfa469535b9a3b14b/original/a-simplified-model-of-iterative-compound-optimization.pdf
|
60c75934bdbb896eeea3aef4
|
10.26434/chemrxiv.14035625.v2
|
Alternating substrate/ligand-metal coordination enables a low-energy pathway for C-O bond cleavage in the electrocatalytic reduction of carbon dioxide
|
Molecular electrocatalysts for CO<sub>2</sub>-to-CO conversion often operate at large overpotentials, the cleavage of C-O bond in the intermediate largely contributing to this phenomenon. Additional Lewis acids have been shown to aid in weakening the C-O bond. We herein present computational and experimental evidence, with ruthenium polypyridyl based CO<sub>2</sub> reduction electrocatalysts, for a mechanistic route that involves one metal center acting as both Lewis base and Lewis acid at different stages of the catalytic cycle. The Lewis basic character of Ru is seen in the initial nucleophilic attack at CO<sub>2</sub> to form [<b>Ru</b>-CO<sub>2</sub>]<sup>0</sup>, while its Lewis acid character allows the formation of a 5-membered metallacyclic intermediate, [<b>Ru</b>-CO<sub>2</sub>CO<sub>2</sub>]<sup>0,c</sup>, by intramolecular cyclization of a linear [<b>Ru</b>-CO<sub>2</sub>CO<sub>2</sub>]<sup>0</sup> species that is formed from [<b>Ru</b>-CO<sub>2</sub>]<sup>0</sup> and a second equivalent of CO<sub>2</sub>. [<b>Ru</b>-CO<sub>2</sub>CO<sub>2</sub>]<sup>0,c</sup> is crucial for energy-conserving turnover, as it allows for a third reduction at a more positive potential than that of the starting complex <b>Ru</b><sup>2+</sup>. The calculated activation barrier for C-O bond cleavage in [<b>Ru</b>-CO<sub>2</sub>CO<sub>2</sub>]<sup>-1,c</sup> is dramatically decreased to 10.5 kcal mol<sup>-1</sup> from 60 kcal mol<sup>-1</sup>, the latter required for C-O bond cleavage in the linear intermediate [<b>Ru</b>-CO<sub>2</sub>CO<sub>2</sub>]<sup>0</sup>. The intermediates are characterized experimentally by FT-IR and <sup>13</sup>C NMR spectroscopy during electrocatalytic turnover and are corroborated by density functional theory (DFT).<br />
|
Hemlata Agarwala; Xiaoyu Chen; Julien R. Lyonnet; Ben A Johnson; Mårten Ahlquist; Sascha Ott
|
Coordination Chemistry (Inorg.); Electrochemistry; Inorganic Acid/Base Chemistry; Kinetics and Mechanism - Inorganic Reactions; Ligands (Inorg.); Organometallic Compounds; Small Molecule Activation (Inorg.); Spectroscopy (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.); Electrocatalysis; Homogeneous Catalysis; Bond Activation; Catalysis; Coordination Chemistry (Organomet.); Electrochemistry - Organometallic; Kinetics and Mechanism - Organometallic Reactions; Ligand Design; Ligands (Organomet.); Small Molecule Activation (Organomet.); Spectroscopy (Organomet.); Theory - Organometallic; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75934bdbb896eeea3aef4/original/alternating-substrate-ligand-metal-coordination-enables-a-low-energy-pathway-for-c-o-bond-cleavage-in-the-electrocatalytic-reduction-of-carbon-dioxide.pdf
|
6464d3e7a32ceeff2dcb84ce
|
10.26434/chemrxiv-2023-8jlq8
|
Glucose Oxidase Loading in Ordered Porous Aluminosilicates: Exploring the Potential of Surface Modification for Electrochemical Glucose Sensing
|
Enzymatic electrochemical sensors have become the leading glucose detection technology due to their rapid response, affordability, portability, selectivity, and sensitivity. However, the performance of these sensors is highly dependent on the surface properties of the electrode material used to store glucose oxidase and its ability to retain enzymatic activity under variable environmental conditions. Mesoporous thin films have recently attracted considerable attention as promising candidates for storing enzymes while preserving their activity owing. Herein, we systematically compare pathways for the immobilization of glucose oxidase (GOx) and their effectiveness in electrochemical glucose sensing, following modification protocols that lead to electrostatic attraction (amino functionalization), covalent bonding (aldehyde functionalization) and electrostatic repulsion (oxygen plasma treatment) of the ordered porous aluminosilicate-coated electrodes. By direct comparison using a quartz crystal microbalance, we demonstrate that glucose oxidase can be loaded in a nanoarchitecture with a pore size of ~50 nm and pore interconnections of ~35 nm using the native aluminosilicate surface, as well as after amino or aldehyde surface modification, while oxygen plasma exposure of the native surface inhibits glucose oxidase loading. Despite a variety of routes for enzyme loading, quantitative electrochemical glucose sensing between 0-20 mM was only possible when the porous surface was functionalized with amino groups, which we relate to the role of surface chemistry in accessing the underlying substrate. Our results highlight the impact of rational surface modification on electrochemical biosensing performance and demonstrate the potential of tailoring porous nanoarchitecture surfaces for biosensing applications.
|
Maximiliano Jara Fornerod; Alberto Alvarez-Fernandez; Martyna Michalska; Ioannis Papakonstantinou; Stefan Guldin
|
Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6464d3e7a32ceeff2dcb84ce/original/glucose-oxidase-loading-in-ordered-porous-aluminosilicates-exploring-the-potential-of-surface-modification-for-electrochemical-glucose-sensing.pdf
|
60c743fa702a9b350e18a720
|
10.26434/chemrxiv.9731030.v1
|
Temperature-Induced Liquid Crystal Microdroplet Formation in a Partially Miscible Liquid Mixture
|
The controlled formation of microdroplets through temperature variation is an intriguing concept for binary liquid mixtures with a critical solution temperature. Here, we investigate this phenomenon for a blend of methanol (MeOH) and a thermotropic liquid crystal (LC) 4-Cyano-4’-pentylbiphenyl (5CB). A near-room-temperatureinduced phase separation leads to nucleation, growth and coalescence of mesogen-rich droplets. The size and number of the droplets is tunable on the microscopic scale by variation of temperature quench depth and cooling rate. Further cooling induces a phase transition to nematic droplets with radial configuration, well-defined sizes and stability over the course of an hour. This fully reversible process is an interesting material system with relevance in diagnostics, optoelectronics, materials templating and extraction processes.<br />
|
Mehzabin Patel; Anand N. Pallipurath Radhakrishnan; Ludovic Bescher; Elwin Hunter-Sellars; Benjamin Schmidt-Hansberg; Esther Amstad; Stuart Ibsen; Stefan Guldin
|
Aggregates and Assemblies; Liquid Crystals; Materials Processing
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743fa702a9b350e18a720/original/temperature-induced-liquid-crystal-microdroplet-formation-in-a-partially-miscible-liquid-mixture.pdf
|
643e53c71d262d40eaaf752b
|
10.26434/chemrxiv-2023-wjd4r
|
Zwitterionic Carbazole Ligands Enhance the Stability and Performance of Perovskite Nanocrystals in Light Emitting Diodes
|
We introduce a new carbazole-based zwitterionic ligand (DCzGPC) synthesized via Yamaguchi esterification which enhances the efficiency of lead halide perovskite (LHP) nanocrystals (NCs) in light emitting diodes (LED). A facile ligand exchange of the native ligand shell, monitored by nuclear magnetic resonance (NMR), ultraviolet-visible (UV-vis), and photoluminescence (PL) spectroscopy, enables more stable and efficient LHP NCs. The improved stability is demonstrated in solution and solid-state LEDs, where the NCs exhibit prolonged luminescence lifetimes and improved luminance, respectively. These results represent a promising strategy to enhance the stability of LHP NCs and to tune their optoelectronic properties for further application in LEDs or solar cells.
|
Christopher Kirsch; Tassilo Naujoks; Philipp Haizmann; Philipp Frech; Heiko Peisert; Thomas Chassé; Wolfgang Brütting; Marcus Scheele
|
Materials Science; Nanoscience; Nanostructured Materials - Materials; Optical Materials; Thin Films; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643e53c71d262d40eaaf752b/original/zwitterionic-carbazole-ligands-enhance-the-stability-and-performance-of-perovskite-nanocrystals-in-light-emitting-diodes.pdf
|
6310e8adbe03b27a97e71c42
|
10.26434/chemrxiv-2022-9wzgg
|
Biomimetic Photo-Switches Softening Model Lipid Membranes
|
We report the synthesis and characterization of a novel photo-switch based on biomimetic cyclocurcumin analogous and interacting with lipid bilayer, which can be used in the framework of oxygen-independent light induce therapy. More specifically, by using molecular dynamics simulations and free energy techniques, we show that the inclusion of hydrophobic substituents is needed to allow internalization in the lipid membrane. After having confirmed that the substituents do not preclude the efficient photoisomerization, we show that the chromophore is internalized in both lipid vesicles and monomolecular film, inducing their fluidification. The irradiation of the chromophore-loaded lipid aggregate modifies their properties due to the different organization of the two isomers. In particular a competition between a fast structural reorganization and a slower expulsion of the chromophore after isomerization can be observed. This report paves the way for future investigations in the optimization of biomimetic photoswitches potentially useful in modern light-induced therapeutic strategies
|
Jeremy Pecourneau ; Raul Losantos; Anastasiia Delova; Yann Bernhard; Stephane Parant ; Maxime Mourer; Andreea Pasc; Antonio Monari
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Interfaces
|
CC BY 4.0
|
CHEMRXIV
|
2022-09-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6310e8adbe03b27a97e71c42/original/biomimetic-photo-switches-softening-model-lipid-membranes.pdf
|
6618c4ab21291e5d1da9f3b6
|
10.26434/chemrxiv-2024-6lc2c
|
Gram-Scale Total Synthesis of Carbazomycins A–D
|
Gram-scale total synthesis of carbazomycins A–D is described. The total synthesis of carbazomycin A was achieved in 44% overall yield over six steps from symmetrical 5-chloro-1,2,3-trimethoxybenzene. The key aryne-mediated carbazole-formation and methylation steps provided the multiply substituted carbazole. The regioselective demethylation of the trimethoxycarbazole was performed using boron trichloride. Thereafter, the phenolic hydroxy group was converted into the methyl group to provide carbazomycin A. Subsequent installation of the methoxy group realized the total synthesis of carbazomycin D. Regioselective demethylation was performed using 1-dodecanethiol, effecting the conversions of carbazomycins A and D into carbazomycins B and C, respectively.
|
Yuxuan Feng; Atsunori Mori; Kentaro Okano
|
Organic Chemistry; Organometallic Chemistry; Natural Products; Organic Synthesis and Reactions; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6618c4ab21291e5d1da9f3b6/original/gram-scale-total-synthesis-of-carbazomycins-a-d.pdf
|
60c746c1bb8c1a2dea3da933
|
10.26434/chemrxiv.9738656.v3
|
Regioselective synthesis of 4-fluoro-1,5-substituted-1,2,3-triazoles from synthetic surrogates of 1-fluoroalkynes
|
Here, we show that 1-fluoronitroalkenes can serve as synthetic surrogates of 1-fluoroalkynes in [3+2] cycloaddition reactions with organic azides facilitated by a catalytic amount of trifloroacetic acid. This work provides the first regioselective method to access 4-fluoro-1,5-substituted-1,2,3-triazoles.
|
Sampad Jana; Sweta Adhikari; Michael Cox; Sudeshna Roy
|
Organic Synthesis and Reactions; Acid Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c1bb8c1a2dea3da933/original/regioselective-synthesis-of-4-fluoro-1-5-substituted-1-2-3-triazoles-from-synthetic-surrogates-of-1-fluoroalkynes.pdf
|
66444fc021291e5d1d529a2a
|
10.26434/chemrxiv-2024-wlprm
|
Concentration-Dependent Aggregation of Methylene Blue Acting as a Photoredox Catalyst
|
Hydroxylation reactions are important in biological processes and synthetic schemes. Many challenging hydroxylation reactions have been achieved using photoredox catalytic methods. For the oxidative hydroxylation of arylboronic acids, methylene blue has been used successfully as a photoredox catalyst to produce phenyl groups. Here we use broadband transient absorption spectroscopy to determine the mechanism of the photoredox catalytic reaction of methylene blue with phenylboronic acid in the presence of N,N-diisopropylethylamine. Our results show that the reaction proceeds through the triplet state of methylene blue in the presence of oxygen, generating superoxide radical anions. In addition, we observe dimerization of the methylene blue at typical catalytic loadings. As these dimers do not participate in the reaction, increasing the concentration of methylene blue is potentially detrimental to the overall yield.
|
Benjamin Thompson; Anshu Kumar; Vanessa Huxter
|
Physical Chemistry; Catalysis; Photocatalysis; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66444fc021291e5d1d529a2a/original/concentration-dependent-aggregation-of-methylene-blue-acting-as-a-photoredox-catalyst.pdf
|
659d4e979138d23161868aca
|
10.26434/chemrxiv-2024-20znb
|
Quality by Design Considerations for Drop-on-Demand Point-of-Care Pharmaceutical Manufacturing of Precision Medicine
|
Distributed and point-of-care (POC) manufacturing facilities enable an agile pharmaceutical production paradigm that can respond to localized needs, providing personalized and precision medicine. These capabilities are critical for narrow therapeutic index drugs and pediatric or geriatric dosing, among other specialized needs. Advanced additive manufacturing, 3D printing, and drop-on-demand (DoD) dispensing technologies have begun expanding into pharmaceutical production. We employed a quality by design (QbD) framework to identify critical quality attributes (CQAs), critical material attributes (CMAs), and critical process parameters (CPPs) of a pharmaceutical manufacturing framework that encompasses the production of active pharmaceutical ingredient (API) ‘inks’ at a centralized facility, which are distributed to POC sites for DoD dispensing into/onto delivery vehicles (e.g., orodispersible films, capsules, single liquid dose vials). QbD considerations and cause-and-effect analyses identified the dispensed API quantity and solid state form (CQAs), as well as nozzle diameter, system pressure channel, and number of drops dispensed (CPPs) for detailed investigation. Final assay quantification and content uniformity CQAs were measured from demonstrative levothyroxine sodium single-dose liquid vials of glycerin/water, meeting standard acceptance values. Each POC facility is unlikely to maintain full quality control laboratory capabilities, requiring development of appropriate atline or inline methods to ensure quality control. We developed control strategies, including, atline UV-Vis verification of the API ink prior to dispensing, inline drop counting during dispensing, intermediate atline dispensed volume checks, and offline batch confirmation by LC-MS/MS following production.
|
Thomas P Forbes; John Greg Gillen; William Feeney; Johnny Ho
|
Biological and Medicinal Chemistry; Materials Science; Analytical Chemistry; Analytical Apparatus; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659d4e979138d23161868aca/original/quality-by-design-considerations-for-drop-on-demand-point-of-care-pharmaceutical-manufacturing-of-precision-medicine.pdf
|
621ebb6bdaa4fb44167c6ac5
|
10.26434/chemrxiv-2022-zgh41
|
Grazing-Incidence Texture Tomography of a Patterned Organic Semiconductor Film
|
The use of grazing-incidence scattering methods for the characterization of 2D patterned organic thin
films is limited due to the elongated 1D footprint of the X-ray beam on the sample. However, this
characteristic feature can be turned into an advantage, when combined with tomographic
reconstruction. In this pilot study we show how the use of a chosen texture reflection and a diffuse
reflectivity signal can each provide 2D images of the deposits, simultaneously revealing the organic
film’s crystal orientation and the location of the metal electrodes.
|
Detlef Smilgies; Margaret Koker; Ruipeng Li; Leo Shaw; Zhenan Bao
|
Materials Science; Materials Processing; Thin Films
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621ebb6bdaa4fb44167c6ac5/original/grazing-incidence-texture-tomography-of-a-patterned-organic-semiconductor-film.pdf
|
60c74d86842e652baddb34b7
|
10.26434/chemrxiv.12631034.v1
|
Versatile Spectroelectrochemical Cell for in Situ Experiments: Development, Applications and Electrochemical Behavior
|
<p><b>Abstract:</b> (Photo)electrochemical processes are involved
in many fields of science and technology. The use of spectroscopic techniques
coupled to (photo)electrochemistry, are mandatory to get information about
interfacial processes on scale ranges from millimeters to the nanoscale. The
development of spectroelectrochemical cells (SEC) contribute to the progress of
the field of (photo)electrochemistry and its impact in science and technology.
Therefore, in this work, we describe in detail the development of a versatile
SEC that can be used for several <i>in situ</i>
techniques. We performed electrochemical and computational experiments to
analyze the response of our SEC as a function of the working electrode size,
position and distance to the window. We found that our SEC behaves as the
conventional cell when the electrode is far from the window. However, important
differences arise in the thin layer configuration. The computational
experiments suggest that to mitigate these problems, it is important to perform
<i>in situ</i> experiments in the thin layer configuration using electrodes as
small as possible.</p>
|
José L. Bott-Neto; Marta V.F. Rodrigues; Mariana C. Silva; Evaldo Batista Carneiro Neto; Gabriel Wosiak; Junior C. Mauricio; Ernesto C. Pereira; Santiago J. A. Figueroa; Pablo Fernández
|
Catalysts; Electrochemical Analysis; Computational Chemistry and Modeling; Electrocatalysis; Fuel Cells; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
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CHEMRXIV
|
2020-07-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d86842e652baddb34b7/original/versatile-spectroelectrochemical-cell-for-in-situ-experiments-development-applications-and-electrochemical-behavior.pdf
|
67c1d2776dde43c908df20c7
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10.26434/chemrxiv-2025-g7j3n-v2
|
The lysine deprotonation mechanism in a ubiquitin conjugating enzyme
|
Ubiquitination is a biochemical reaction in which a small protein, ubiquitin (Ub), is covalently linked to a lysine on a target protein. This type of post-translational modification can signal for protein degradation, DNA repair, or inflammation response. Ubiquitination is catalyzed by three families of enzymes: ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2), and ubiquitin ligases (E3). In this study, we focus on the chemical mechanism used by the E2 enzyme, Ubc13, which forms polyubiquitin chains by linking a substrate Ub to Lys63 on a target ubiquitin (Ub*). Initially, Ubc13 is covalently linked to the substrate Ub. Next, Lys63 in the Ub* is deprotonated, becomes an active nucleophile, and attacks the thioester bond in the Ubc13~Ub conjugate. The deprotonation mechanism is not well understood. There are two, conserved nearby residues that may act as conjugate bases (Asp119 on Ubc13 and Glu64 on Ub*.) It is also hypothesized that the active site environment suppresses the lysine's pKa, favoring deprotonated lysine. We test these hypotheses by simulating both WT and mutant Ubc13 with constant pH molecular dynamics (CpHMD), which allows titratable residues to change their protonation states. We use these simulations to monitor the protonation states and to generate titration curves of lysine 63. We found that the pKa of the lysine is highly dependent on its distance from the active site. Also, mutating Asp119 or Glu64 to Ala has little effect on the lysine pKa, indicating that neither residue acts as a generalized base. Finally, we note that mutating a structural residue (Asn79 to Ala) increases the lysine pKa, suggesting that alterations to the active site hydrogen bonding network can affect nucleophile activation.
|
Alexis J. Wathan; Nicole Deschene; Joseph Litz; Isaiah Sumner
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1d2776dde43c908df20c7/original/the-lysine-deprotonation-mechanism-in-a-ubiquitin-conjugating-enzyme.pdf
|
60c73d50bb8c1a80943d9722
|
10.26434/chemrxiv.5662351.v1
|
Structure and Stability of Molecular Crystals with Many Body Dispersion Inclusive Density Functional Tight Binding
|
<pre><p>Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semi-empirical electronic structure methods are computationally more efficient than their <i>ab initio </i>counterparts, allowing structure sampling with significant speed-ups. Here, we combine the Tkatchenko-Scheffler van-der-Waals method (TS) and the many body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) <i>via</i> a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speed-up of up to 3000 times compared to a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.
</p></pre>
|
Majid Mortazavi; Jan Gerit Brandenburg; Reinhard J. Maurer; Alexandre Tkatchenko
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-12-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d50bb8c1a80943d9722/original/structure-and-stability-of-molecular-crystals-with-many-body-dispersion-inclusive-density-functional-tight-binding.pdf
|
644631d983fa35f8f62ae646
|
10.26434/chemrxiv-2023-7phst-v2
|
Concerted local and nonlocal effects on tip-enhanced nonlinear plasmonics
|
We report critical impacts of local and nonlocal geometries of plasmonic tips on the broadband nonlinear optical responses in tip-substrate nanocavities. Using gold tips with varied geometries, we demonstrated for the first time that not only the nanometer-scale sharpness of tip apexes but also the micrometer-scale surface geometry of tip shafts directly affects the enhancement properties of second-harmonic generation over the visible-to-infrared wavelength range. Numerical simulations of plasmonic field in the tip-substrate nanocavities revealed concerted contributions from spatially nonlocal and local plasmonic modes. Micrometer-scale tip shafts enable the excitation of nonlocal plasmonic modes throughout the tip, enhancing near-to-mid-infrared incoming light. Subsequent radiation of visible-to-near-infrared second harmonics is predominantly boosted by localized plasmons at the nanogap. Based on the agreement between experiments and calculations, our results indicate the importance of nanometer- and micrometer-scale geometrical engineering of plasmonic tips and provide a firm basis for the understanding and fine manipulation of nonlinear optical phenomena in tip-substrate nanocavities.
|
Shota Takahashi; Atsunori Sakurai; Tatsuto Mochizuki; Toshiki Sugimoto
|
Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Optics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644631d983fa35f8f62ae646/original/concerted-local-and-nonlocal-effects-on-tip-enhanced-nonlinear-plasmonics.pdf
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60c751e40f50db823b397875
|
10.26434/chemrxiv.12956960.v2
|
Tuning the Performance of Aqueous Organic Redox Flow Batteries from First Principles
|
<div>Aqueous organic redox flow batteries have many appealing properties in the application of large-scale energy storage. The large chemical tunability of organic electrolytes shows great potential to improve the performance of flow batteries. Computational studies at the quantum-mechanics level are very useful to guide experiments, but in previous studies explicit water interactions and thermodynamic effects were ignored. Here, we applied the computational electrochemistry method based on ab initio molecular dynamics to calculate redox potentials of quinones and their derivatives. The calculated results are in excellent agreement with experimental data. We mixed side chains to tune their reduction potentials, and found that solvation interactions and entropy effects play a significant role in side-chain engineering. Based on our calculations, we proposed several high-performance negative and positive electrolytes. Our first-principles study paves the way towards the development of large-scale and sustainable electrical energy storage.</div>
|
Junting Yu; Tianshou Zhao; Ding Pan
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751e40f50db823b397875/original/tuning-the-performance-of-aqueous-organic-redox-flow-batteries-from-first-principles.pdf
|
60c74419f96a00bd14286906
|
10.26434/chemrxiv.9742688.v1
|
Reinvestigation of the Synthesis of "Covalent-Assembly" Type Probes for Fluoride Ion Detection. Identification of Novel 7-(Diethylamino)coumarins with Aggregation-Induced Emission Properties
|
An unprecedented C-3 functionalization of 4-(diethylamino)salicylaldehyde through a Friedel-Crafts type alkylation reaction has been discovered during the synthesis of "covalent-assembly"-based fluorescent probes for detection of fluoride ions. The resulting Friedel-Crafts adduct was successfully used for the preparation of two novel 8-substituted 7-(diethylamino)coumarin dyes. The photophysical study of these fluorophores has enabled us to highlight their remarkable aggregation-induced emission (AIE) properties characterized by a yellow-orange emission of aggregates in water. Therefore, 4-(tert butyldimethylsilyloxy)benzyl substituent was identified as a novel AIE-active moiety which could be seen as a possible alternative to popular tetraphenylethylene (TPE).
|
Valentin QUESNEAU; Benoît ROUBINET; Pierre-Yves RENARD; Anthony ROMIEU
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74419f96a00bd14286906/original/reinvestigation-of-the-synthesis-of-covalent-assembly-type-probes-for-fluoride-ion-detection-identification-of-novel-7-diethylamino-coumarins-with-aggregation-induced-emission-properties.pdf
|
65d708b6e9ebbb4db9f0869f
|
10.26434/chemrxiv-2024-n122g
|
Atomically precise inorganic helices with a programmable irrational twist
|
Helicity in atomic scale structures often arises from the precise ordering of cooperative intra- and inter-molecular bonding interactions. The exclusivity of these interactions to natural, organic, or molecular systems has limited the demonstration and understanding of helical motifs in densely packed solid-state lattices. Herein, we report that the ordering of Ga atoms in GaSeI, a representative crystal from an exfoliable class of atomically precise III-VI-VII 1D van der Waals (vdW) crystals, manifests the elusive Boerdijk-Coxeter (B-C) helix motif. B-C helicity is a rare non-repeating geometric pattern arising from the distinct face-sharing order of well-defined tetrahedra with adjacent vertices defined by an irrational rotational or twist angle, previously thought to only exist in macro- to molecular-scale structures but not at the atomic scale. Using InSeI and GaSeI as models, we show that the structural degree of freedom in a 1D vdW lattice generally allows for the systematic twisting of a tetrahelical lattice defined by a periodic 41 screw axis in InSeI to its infinitely extending B-C helix counterpart in GaSeI. Helical coordinate analysis of GaSeI reveals that the Ga atoms forming the [GaSe3I]∞ repeating motif display B-C helicity whereas Se and I atoms order as concentric tetrahelices that form B-C helix variants with systematically expanded helical radii. This discovery of ideal B-C helicity in optically active vdW lattices exfoliable down to single helix chains presents a distinctive materials platform towards understanding aperiodic helicity and chirality in low-dimensional solids, enabling new opportunities in designing well-defined solid state materials for quantum transport and long-range chirality-driven phenomena.
|
Dmitri Cordova; Kenneth Chua; Tyler Kerr; Toshihiro Aoki; David Knez; Grigorii Skorupskii; Diana Lopez; Joseph Ziller; Dmitry Fishman; Maxx Arguilla
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d708b6e9ebbb4db9f0869f/original/atomically-precise-inorganic-helices-with-a-programmable-irrational-twist.pdf
|
62d6408e81efd00c5ab1bcbc
|
10.26434/chemrxiv-2022-5t5ts
|
Uni-Dock: A GPU-Accelerated Docking Program Enables Ultra-Large Virtual Screening
|
Molecular docking, a structure-based virtual screening method, is a reliable tool to enrich bio-active molecules from molecular databases. With the expansion of the size of virtual libraries, the speed of existing molecular docking programs becomes less than adequate to meet the demand for screening ultra-large libraries containing tens of millions or billions of molecules. Here we propose Uni-Dock, a GPU-accelerated molecular docking program supporting various scoring functions including vina, vinardo, and ad4, which achieves more than 1000-fold speed-up with high accuracy compared with the AutoDock Vina single-CPU-core version, outperforming reported GPU-accelerated docking programs including AutoDock-GPU and Vina-GPU. Uni-Dock divides molecules into batches and simultaneously docks batches of molecules using hundreds of concurrent threads for each molecule. The data flow between GPU and CPU is optimized to eliminate CPU hotspots and maximize GPU utility. We demonstrate and analyze the improved performance of Uni-Dock on the CASF-2016 and DUD-E datasets and recommend three combinations of hyperparameters corresponding to different docking scenarios. To demonstrate Uni-Dock's capability on routinely screening ultra-large libraries, we performed hierarchical virtual screening experiments with Uni-Dock on Enamine Diverse REAL drug-like set containing 38.2 million molecules to a popular target KRAS G12D in 12 hours using 100 NVIDIA V100 GPUs.
|
Yuejiang Yu; Chun Cai; Zhengdan Zhu; Hang Zheng
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d6408e81efd00c5ab1bcbc/original/uni-dock-a-gpu-accelerated-docking-program-enables-ultra-large-virtual-screening.pdf
|
6694501b01103d79c505a035
|
10.26434/chemrxiv-2024-70rz1
|
Coiled Coil Peptide Tiles (CCPTs): Multivalent Peptide Macrocycles for Expanding the Coiled Coil Assembly Toolkit
|
As one of the most well-understood protein folds, coiled coils represent an attractive assembly directing motif for engineering modular and responsive bionanomaterials. Here, we expand the coiled coil assembly “toolkit” through unveiling the design and synthesis of novel, multivalent peptide macrocycles (96mers) that comprise multiple orthogonal coiled coil peptide domains. These fully synthetic constructs, termed coiled coil peptide tiles (CCPTs), are assembled using a convergent synthetic strategy via a combination of native chemical ligation and Sortase A-mediated cyclization. Circular dichroism (CD) studies reveal the increased helical stability associated with cyclization and subsequent coiled coil formation along CCPT edges. Size exclusion chromatography (SEC), analytical high-performance liquid chromatography (HPLC), and fluorescence quenching assays provide comprehensive biophysical characterization of various CCPT complexes and confirm the orthogonal co-localization between coiled coil domains within CCPTs and their designed on-target free peptide partners. Lastly, we employ molecular dynamic (MD) simulations, which provide molecular-level insights to experimental results, as a supporting method for understanding the structural dynamics of CCPTs and their complexes. MD analysis of the simulated CCPT architectures reveal the atomic-level interactions mediating their structure and stability and provide insights for guiding designs of future generations of CCPTs. The addition of CCPTs into the repertoire of coiled coil-based building blocks have the potential for expanding the coiled coil assembly landscape by unlocking new topologies through designable intermolecular interfaces.
|
Anthony Perez; Adekunle Adewole; Daphney Sihwa; Michael Colvin; Andrea Merg
|
Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Biochemistry; Bioengineering and Biotechnology; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6694501b01103d79c505a035/original/coiled-coil-peptide-tiles-ccp-ts-multivalent-peptide-macrocycles-for-expanding-the-coiled-coil-assembly-toolkit.pdf
|
66977ce9c9c6a5c07a83c9e6
|
10.26434/chemrxiv-2024-p4f1l
|
Large-scale parameter estimation for Crystal Structure Prediction. Part 1: Dataset, Methodology, and Implementation
|
Crystal Structure Prediction (CSP) seeks to identify all thermodynamically accessible solid forms of a given compound and, crucially, to establish the relative thermodynamic stability between different polymorphs. The conventional hierarchical CSP workflow suggests that no single energy model can fulfill the needs of all stages in the workflow, and energy models across a spectrum of fidelities and computational costs are required. Hybrid ab initio/empirical force-field (HAIEFF) models have demonstrated a good balance of these two factors, but the force-field component presents a major bottleneck for model accuracy. Existing parameter estimation tools for fitting this empirical component are inefficient and have severe limitations on the manageable problem size. This, combined with a lack of reliable reference data for parameter fitting, has resulted in developments in the force-field component of HAIEFF models having mostly stagnated. In this work, we address these barriers to progress. Firstly, we introduce a curated database of 755 organic crystal structures, obtained using high quality, solid-state DFT-D calculations, which provide a complete set of geometry and energy data. Comparisons to various theoretical and experimental data sources indicate that this database provides suitable diversity for parameter fitting. In tandem, we also put forward a new parameter estimation algorithm implemented as the CrystalEstimator program. Our tests demonstrate that CrystalEstimator is capable of efficiently handling large-scale parameter estimation problems, simultaneously fitting as many as 62 model parameters based on data from 445 structures. This problem size far exceeds any previously reported works related to CSP force-field parameterization. These developments form a strong foundation for all future work involving parameter estimation of transferable or tailor-made force-fields for HAIEFF models. This ultimately opens the way for significant improvements in the accuracy achieved by the HAIEFF models.
|
David Bowskill; Benjamin Tan; Adam Keates; Isaac Sugden; Claire Adjiman; Constantinos Pantelides
|
Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Crystallography – Organic
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66977ce9c9c6a5c07a83c9e6/original/large-scale-parameter-estimation-for-crystal-structure-prediction-part-1-dataset-methodology-and-implementation.pdf
|
62e3f5ba3cba7f9bc7398cab
|
10.26434/chemrxiv-2022-5b60v
|
Angular Orientation between the Cores of Magnetic Iron Oxide Nanoclusters Controls their Properties and Functions
|
Oriented attachment of nanobricks into hierarchical multi-scale structures such as inorganic nanoclusters is one of the crystallization mechanisms that has revolutionized the field of nano and materials science. Herein, we show that the mosaicity, which measures the misalignment of crystal plane orientation between the nanobricks, governs their magneto-optical properties as well as the magnetic heating functions of iron oxide nanoclusters. Thanks to high-temperature and time-resolved microfluidics, we were able to isolate and characterize (structure, properties, function) the different intermediates involved in the diverse steps of the nanocluster’s formation, to propose a detailed dynamical mechanism of their formation and establish a clear correlation between changes in mosaicity at the nanoscale and their resulting physical properties. Finally, we demonstrate that their magneto-optical properties can be described using simple molecular theories.
|
Ali Abou-Hassan; Enzo Bertuit; nicolas Menguy; claire wilhelm; anne-laure Rollet
|
Physical Chemistry; Materials Science; Nanoscience; Magnetic Materials; Nanostructured Materials - Nanoscience; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e3f5ba3cba7f9bc7398cab/original/angular-orientation-between-the-cores-of-magnetic-iron-oxide-nanoclusters-controls-their-properties-and-functions.pdf
|
65c85ccf66c1381729632630
|
10.26434/chemrxiv-2024-gspzt
|
Doxorubicin-Polysorbate 80 Conjugates: Targeting Effective and Sustained Delivery to the Brain
|
Targeting therapeutic agents to the brain to treat the central nervous system (CNS) diseases is a major challenge due to the blood-brain-barrier (BBB). In this study, an attempt was made to deliver a model drug such as doxorubicin (DOX) to the brain in a mice model through DOX-Polysorbate 80 (DOX-PS80) conjugates. DOX was successfully conjugated with the non-ionic surfactant Polysorbate 80 (PS80) by carbamate linkage and the conjugate was characterized by different spectroscopic techniques such as FTIR, UV-Visible and NMR. The DOX conjugation efficacy was found to be 43.69 ± 4.72 %. The in vitro cumulative release of DOX from the conjugates was found to be 4.9 ± 0.8 % in PBS of pH 7.3 and 3.9 ± 0.6 % in simulated cerebrospinal fluid (CSF) of pH 7.3 at the end of 10 days. In vitro BBB permeability assay was carried out using bEnd.3 cells and DOX-PS80 conjugate showed a 3-fold increase in BBB permeability compared to controls. In vitro cytotoxicity assay using U251 human glioblastoma cells showed an IC50 value of 38.10 µg/mL for DOX-PS80. Cell uptake studies revealed that DOX-PS80 was effectively taken up (90%) by the bEnd.3 and U251 cells and localized in cytoplasm at the end of 24 h. Tumor spheroid assay and in vivo experiments in Swiss albino mice demonstrated the possibility of DOX-PS80 conjugate crossing the BBB and delivering the drug molecules to the target site for treating CNS disorders.
|
Ram Prasad Sekar; Sruthi Sudheendran Leena; Ani Deepthi; Resmi A.N.; Jayasree S Ramapurath ; Jayakrishnan Athipettah
|
Biological and Medicinal Chemistry; Materials Science; Polymer Science; Controlled-Release Systems; Drug delivery systems; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c85ccf66c1381729632630/original/doxorubicin-polysorbate-80-conjugates-targeting-effective-and-sustained-delivery-to-the-brain.pdf
|
656ec531cf8b3c3cd7cfc85b
|
10.26434/chemrxiv-2023-n7t0x
|
An integrated ROS booster: Hydrogen sulfide-donating nanoclusters designed for multi-mode breast cancer treatment
|
Nanomaterial-assisted chemodynamic cancer therapy has received considerable attention in recent years. It outperforms other modalities for its unique pattern of reactive oxygen species (ROS) production via the non-exogenous stimulant. However, the treatment outcome is limited by the insufficient content of endogenous hydrogen peroxide (H2O2). Herein, a biodegradable H2S-releasing MnS@HA-DOX nanocluster (MnS@HA-DOX NC) was constructed by in situ biomineralization from hyaluronic acid, to amplify ROS cascade and boost Mn2+-based chemodynamic therapy (CDT). The acid-responsive NCs could quickly degrade after internalization into endo/lysosomes, releasing Mn2+, H2S gas, and anticancer drug doxorubicin (DOX). The Fenton-like reaction catalyzed by Mn2+ was amplified by both H2S and DOX, producing a mass of cytotoxic ·OH radicals. Through the combined action of gas therapy (GT), CDT, and chemotherapy, oxidative stress would be synergistically amplified, inducing irreversible DNA damage and cell cycle arrest, eventually resulting in cancer cell apoptosis.
|
Zixin Wang; Yuxuan Ge; Jiaqi Liu; Peiyunfeng Shi; Ruiyang Xue; Bin Hao; Yin Wang
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656ec531cf8b3c3cd7cfc85b/original/an-integrated-ros-booster-hydrogen-sulfide-donating-nanoclusters-designed-for-multi-mode-breast-cancer-treatment.pdf
|
60c7510abb8c1aba093dbbe6
|
10.26434/chemrxiv.13114625.v1
|
Chemoselective Union of Olefins, Organohalides and Redox-Active Esters Enables Regioselective Alkene Dialkylation
|
<div>Multicomponent catalytic processes that can generate multiple C(sp<sup>3</sup>)-C(sp<sup>3</sup>) bonds in a single step under mild conditions,particularly if the catalysts and substrates are inexpensive, are highly sought-after in chemistry research for complex molecule synthesis. Here, we disclose an efficient Ni-catalysed reductive protocol that chemoselectively merges alkenyl amides with two different</div><div>aliphatic electrophiles. Starting materials are readily accessible from stable and abundant feedstock and products are furnished in up to >98:2 regioisomeric ratios. The present strategy eliminates the use of sensitive organometallic reagents, tolerates a wide array of complex functionalities and enables regiodivergent addition of two primary alkyl groups bearing similar electronic and steric attributes across aliphatic C=C bonds with exquisite control of site selectivity. Utility is underscored by the concise synthesis of bioactive compounds and post-reaction functionalizations leading to structurally diverse scaffolds. DFT studies revealed that the regiochemical outcome originates from the orthogonal reactivity and chemoselectivity profiles of in situ-generated organonickel species.</div>
|
Tao Yang; Yi Jiang; Yixin Luo; Yu Lan; Ming Joo Koh
|
Organic Synthesis and Reactions; Homogeneous Catalysis; Theory - Organometallic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7510abb8c1aba093dbbe6/original/chemoselective-union-of-olefins-organohalides-and-redox-active-esters-enables-regioselective-alkene-dialkylation.pdf
|
64f487b1dd1a73847f16a828
|
10.26434/chemrxiv-2023-wp0wx
|
Efficient regio- and stereo-selective C-H bond hydroxylation of steroids using an engineered heme-thiolate peroxygenase biocatalyst
|
A crucial reaction in chemical synthesis is the activation of unactivated carbon-hydrogen bonds in complex molecules. We demonstrate the regio- and stereo-selective hydroxlation of the steroids progesterone and androstenedione using the peroxygenase activity of an engineered bacterial cytochrome P450 enzyme, CYP154C8. By replacing a single amino acid of the I-helix we change this monooxygenase enzyme into a peroxygenase, enabling the efficient and selective biocatalytic formation of the 16α-hydroxy steroid metabolite.
|
Jinia Akter; Eva Hayball; Stephen Bell
|
Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Biocatalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-09-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f487b1dd1a73847f16a828/original/efficient-regio-and-stereo-selective-c-h-bond-hydroxylation-of-steroids-using-an-engineered-heme-thiolate-peroxygenase-biocatalyst.pdf
|
645bfe08fb40f6b3ee5d903e
|
10.26434/chemrxiv-2023-g2rj1
|
In-situ Studies of Copper-based CO2 Reduction Electrocatalysts
by Scanning Transmission Soft X-ray Microscopy
|
A micro-fluidic enabled electrochemical device has been developed to investigate electrochemically active materials under reaction conditions using in-situ scanning transmission soft X-ray microscopy (STXM). In-situ STXM measurements at the Cu 2p edge were conducted on electro-deposited Cu catalysts under electrochemical CO2 reduction (CO2R) conditions. The study provides detailed, quantitative results about the changes in the morphology and chemical structure (oxidation state) of the catalyst particles as a function of applied electrode potentials. The initially electrochemically deposited Cu particles contain both Cu(0) and Cu(I). As an increasingly cathodic potential is applied, the Cu(I) species gradually converted to Cu(0) over the potential range of +0.4 to 0 V versus the reversible hydrogen electrode (VRHE). During this process, Cu(I) particles of various sizes are converted to metallic Cu at different reaction rates and at slightly different electrode potentials, indicating a degree of heterogeneity in the electrochemical response of discrete particles. At CO2R relevant potentials, only metallic Cu is observed, and the morphology of the particles is fairly stable within the spatial resolution limits of STXM (~ 40 nm). We also prepared a working electrode with relatively thick Cu-based electro-deposits. The spatially resolved chemical analysis by STXM identified that Cu-oxide species can persist under CO2R conditions, but only when the catalyst particles are electronically isolated from the working electrode and therefore are catalytically irrelevant. Thus, in-situ STXM is presented as a technique to gain advanced morphological and spatially-resolved chemical structure insight into electrochemically active materials, which was used to provide improved understanding regarding Cu electrodes under CO2 reaction conditions.
|
Chunyang Zhang; Haytham Eraky; Shunquan Tan; Adam Hitchcock; Drew Higgins
|
Physical Chemistry; Catalysis; Electrocatalysis; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645bfe08fb40f6b3ee5d903e/original/in-situ-studies-of-copper-based-co2-reduction-electrocatalysts-by-scanning-transmission-soft-x-ray-microscopy.pdf
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615b8777be10744e5492238e
|
10.26434/chemrxiv-2021-dr3mf
|
Machine Learning Guides Peptide Nucleic Acid Flow Synthesis and Sequence Design
|
Peptide nucleic acids (PNAs) are potential antisense therapies for genetic, acquired, and viral diseases. Efficiently selecting candidate PNA sequences for synthesis and evaluation from a genome containing hundreds to thousands of options can be challenging. To facilitate this process, we leverage here machine learning (ML) algorithms and automated synthesis technology to predict PNA synthesis efficiency and guide rational PNA sequence design. The training data was collected from individual fluorenylmethyloxycarbonyl (Fmoc) deprotection reactions performed on a fully automated PNA synthesizer. Our optimized ML model allows for 93% prediction accuracy and 0.97 Pearson’s r. The predicted synthesis scores were validated to be correlated with the experimental HPLC crude purities (correlation coefficient R2 = 0.95). Furthermore, we demonstrated a general applicability of ML through designing synthetically accessible antisense PNA sequences from 102,315 predicted candidates targeting exon 44 of the human dystrophin gene, SARS-CoV-2, HIV, as well as selected genes associated with cardiovascular diseases, type II diabetes, and various cancers. Collectively, ML provides an accurate prediction of PNA synthesis quality and serves as a useful computational tool for rational PNA sequence design.
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Chengxi Li; Genwei Zhang; Somesh Mohapatra; Alex Callahan; Andrei Loas; Rafael Gomez-Bombarelli; Bradley Pentelute
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Machine Learning
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CC BY NC ND 4.0
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CHEMRXIV
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2021-10-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615b8777be10744e5492238e/original/machine-learning-guides-peptide-nucleic-acid-flow-synthesis-and-sequence-design.pdf
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6511e45e60c37f4f767132de
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10.26434/chemrxiv-2023-kw0xn
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Total Synthesis of Dynobactin A
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The first total synthesis of the potent antimicrobial agent dynobactin A is disclosed. This synthesis capitalizes on the hidden symmetry present in this complex decapeptide by enlisting an aziridine ring opening strategy to access b-branched amino acids. Featuring a number of unique maneuvers to navigate inherently sensitive and epimerizable functional groups, this convergent approach proceeds in only 14 steps (LLS) from commercial materials and should facilitate the synthesis of numerous analogs for medicinal chemistry studies.
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Fabian Schneider; Yinliang Guo; You-Chen Lin; Kelly Eberle; Debora Chiodi; Jonathan Greene; Chenxin Lu; phil baran
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Organic Chemistry; Natural Products; Organic Synthesis and Reactions
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CC BY 4.0
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CHEMRXIV
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2023-09-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6511e45e60c37f4f767132de/original/total-synthesis-of-dynobactin-a.pdf
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643019ee736114c963130d96
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10.26434/chemrxiv-2023-0zv2f-v2
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De Novo Design of Molecules Towards Biased Properties via a Deep Generative Framework and Iterative Transfer Learning
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De Novo design of molecules with targeted properties represents a new frontier in molecule development. Despite enormous progress, two main challenges remain, i.e., (i) generation of novel molecules with targeted and quantifiable properties; (ii) generated molecules having property values beyond the range in the training dataset. To tackle these challenges, we propose a novel reinforced regressional and conditional generative adversarial network (RRCGAN) to generate chemically valid, small molecules with targeted heat capacity (Cv) values as a proof-of-concept study. As validated by DFT, ~80% of the generated samples have a relative error (RE) of < 20% of the targeted Cv values. To bias the generation of molecules with the Cv values beyond the range of the original training molecules, transfer learning was applied to iteratively retrain the RRCGAN model. After only two iterations of transfer learning, the mean Cv of the generated molecules increases to 44.0 cal/(mol·K) from the mean value of 31.6 cal/(mol·K) shown in the initial training dataset. This demonstrated computation methodology paves a new avenue to discovering small molecules with biased properties.
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Kianoosh Sattari; Dawei Li; Yunchao Xie; Olexandr Isayev; Jian Lin
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Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2023-04-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643019ee736114c963130d96/original/de-novo-design-of-molecules-towards-biased-properties-via-a-deep-generative-framework-and-iterative-transfer-learning.pdf
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65cacd82e9ebbb4db93771aa
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10.26434/chemrxiv-2024-w6vc4
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Efficient Capture and Release of the Rare-Earth Element Neodymium in Aqueous Solution by Recyclable Covalent Organic Frameworks
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Rare-earth elements (REEs) are present in a broad range of critical materials. The development of solid adsorbents for REE capture could enable the cost-effective recycling of REE-containing magnets and electronics. In this context, covalent organic frameworks (COFs) are promising candidates for REE adsorption due to their exceptionally high surface area. Despite having attractive physical properties, COFs are heavily underutilized for REE capture applications due to their limited lifecycle in aqueous acidic environments, as well as synthetic challenges associated with the incorporation of ligands suitable for REE capture. Here, we show how the Ugi multicomponent reaction can be leveraged to post-synthetically modify imine-based COFs for the introduction of diglycolic acid (DGA) moiety, a promising scaffold for REE capture. The adsorption capacity of the DGA-functionalized COF was found to be more than 40 times higher than that of the pristine imine COF precursor and more than three times higher than that of the next-best reported DGA-functionalized solid support. This rationally designed COF has appealing characteristics of high adsorption capacity, fast and efficient capture and release of the REE ions, and reliable recyclability, making it one of the most promising adsorbents for solid-liquid REE ion extractions reported to date.
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Puranjan Chatterjee; Alexander Volkov; Jiashan Mi; Minghui Niu; Simin Sun; Aaron J. Rossini; Levi M. Stanley; Wenyu Huang
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Organic Chemistry; Polymer Science; Supramolecular Chemistry (Org.); Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2024-02-14
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cacd82e9ebbb4db93771aa/original/efficient-capture-and-release-of-the-rare-earth-element-neodymium-in-aqueous-solution-by-recyclable-covalent-organic-frameworks.pdf
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660eb16b418a5379b00def1a
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10.26434/chemrxiv-2023-qpmzd-v2
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Theoretical Insights into the Reduction of Azurin Metal Site with Unnatural Amino Acid Substitutions
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Copper-containing proteins play crucial roles in biological systems. Azurin is a copper-containing protein which has a Type 1 copper site that facilitates electron transfer in the cytochrome chain. Previous research has highlighted the significant impact of mutations in the axial Met121 of the copper site on the reduction potential. However, the mechanism of this regulation has not been fully established. In this study, we employed theoretical modeling to investigate the reduction of the Type 1 copper site, focusing on how unnatural amino acid substitutions at Met121 influence its behavior. Our findings demonstrated a strong linear correlation between electrostatic interactions and the reduction potential of the copper site, which indicates that the perturbation of the reduction potential is primarily influenced by electrostatic interactions between the metal ion and the ligating atom. Furthermore, we found that CF/π and CF…H interactions could induce subtle changes in geometry and hence impact the electronic properties of the systems under study. In addition, our calculations suggest the coordination mode and ion-ligand distance could significantly impact the reduction potential of the copper site. Overall, this study offers valuable insights into the structural and electronic properties of the Type 1 copper site, which could potentially guide the design of future artificial catalysts.
|
Yang Wei; Pengfei Li
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2024-04-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660eb16b418a5379b00def1a/original/theoretical-insights-into-the-reduction-of-azurin-metal-site-with-unnatural-amino-acid-substitutions.pdf
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6546ae57c573f893f1d01ca3
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10.26434/chemrxiv-2023-vrdv6
|
Pendulum‐like Hemilability in a Ti‐based Frustrated Lewis Trio
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We describe the first experimental example of a theoretically predicted Frustrated Lewis Trio (FLT). A tetradentate PNNP ligand is used to stabilise a highly
electrophilic [TiCl3]+ fragment in a way that results in two equally long and frustrated Ti‐P bonds. A combined experimental and computational approach
revealed a distinct role of each Lewis basic phosphine in the heterolytic activation of chemical bonds. This dual functionality is characterised by a pendulumlike
hemilability, where one of the phosphines acts as a nucleophile while the other serves as a hemilabile ligand that dynamically tunes the Ti‐P distance
as a function of the required electron density at the Ti centre.
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Errikos Kounalis; Dylan van Tongeren; Stanislav Melnikov; Martin Lutz; Daniel L. J. Broere
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Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Frustrated Lewis Pairs; Bond Activation; Ligand Design
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CC BY NC 4.0
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CHEMRXIV
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2023-11-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6546ae57c573f893f1d01ca3/original/pendulum-like-hemilability-in-a-ti-based-frustrated-lewis-trio.pdf
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615d8156f718df1626d54e8c
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10.26434/chemrxiv-2021-gpllr-v2
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Hydrogen Bonding Networks Enable Brønsted Acid-Catalyzed Carbonyl-Olefin Metathesis
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Synthetic chemists have learned to mimic nature in using hydrogen bonds and other weak interactions to dictate the spatial arrangement of reaction substrates and to stabilize transition states to enable highly efficient and selective reactions. The activation of a catalyst molecule itself by hydrogen bonding networks, in order to enhance its catalytic activity to achieve a desired reaction outcome, is less explored in organic synthesis, despite being a commonly found phenomenon in nature. Herein, we show our investigation into this underexplored area by studying the promotion of carbonyl-olefin metathesis reactions by hydrogen bonding-assisted Brønsted acid catalysis, using hexafluoroisopropanol (HFIP) solvent in combination with para-toluenesulfonic acid (pTSA). Our experimental and computational mechanistic studies reveal not only an interesting role of HFIP solvent in assisting pTSA Brønsted acid catalyst, but also insightful knowledge about the current limitations of the carbonyl-olefin metathesis reaction.
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Tuong Anh To; Chao Pei; Rene Koenigs; Thanh Vinh Nguyen
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Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Organocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-10-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615d8156f718df1626d54e8c/original/hydrogen-bonding-networks-enable-br-nsted-acid-catalyzed-carbonyl-olefin-metathesis.pdf
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6538778087198ede07373f6e
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10.26434/chemrxiv-2023-cj7l3
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Divergence between local structure, dynamics and nucleation outcome in heterogeneous nucleation of close-packed crystals
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Heterogeneous crystal nucleation is the dominant mechanism of crystallization in most systems, yet its underlying physics remains an enigma. While emergent interfacial crystalline order precedes heterogeneous nucleation, its importance in the nucleation mechanism is unclear. Here, we use molecular dynamics simulations and path sampling techniques to demonstrate that crystalline order in its traditional sense is not predictive of the outcome of heterogeneous nucleation of close-packed crystals. Consequently, structure-based collective variables (CVs) that reliably describe homogeneous nucleation can be poor descriptors of heterogeneous nucleation. This divergence between structure and nucleation outcome is accompanied by an intriguing dynamical anomaly wherein low- coordinated crystalline particles outpace their liquid-like counterparts. Both these anomalies are morphologically associated with low-coordinated crystalline particles participating in bridges connecting crystalline domains. We also demonstrate that reliance on ineffective CVs yields a flawed comprehension of the nucleation mechanism by overestimating the face-centered cubic (FCC) content of crystalline nuclei in the systems and surfaces considered here. We use committor analysis, high-throughput screening, and machine learning to devise CV optimization strategies, and present suitable structural heuristics within the metastable fluid for CV pre-screening. Employing such optimized CVs is pivotal in properly characterizing the mechanism of heterogeneous nucleation in a wide variety of systems, including inorganic, metallic and colloidal systems.
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Tiago Domingues; Sarwar Hussain; Amir Haji-Akbari
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
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CC BY NC 4.0
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CHEMRXIV
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2023-10-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6538778087198ede07373f6e/original/divergence-between-local-structure-dynamics-and-nucleation-outcome-in-heterogeneous-nucleation-of-close-packed-crystals.pdf
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60c74bd9bb8c1a44883db2e1
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10.26434/chemrxiv.12290474.v2
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Helium Nanodroplet Isolation Spectroscopy in an Undergraduate Teaching Laboratory
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<div><p>A home-built helium
nanodroplet isolation spectrometer has been utilized by undergraduate students
in course-based experiments to investigate the rovibrational dynamics of small
molecules. Helium nanodroplets are well known to simplify the spectroscopy of
embedded molecules owing to their low temperature (0.4 K) and weakly
interacting nature. In the infrared spectral region, this results in a small
number of rotationally resolved lines that can often be collected and analyzed
in several lab periods. We demonstrate the advantages of using this technique
in an upper-level undergraduate chemistry course for which the laser spectroscopy
of helium solvated <sup>13</sup>C-labelled formic acid was investigated
for the first time.</p></div>
|
Paul Raston
|
Chemical Education - General
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-05-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bd9bb8c1a44883db2e1/original/helium-nanodroplet-isolation-spectroscopy-in-an-undergraduate-teaching-laboratory.pdf
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662a0a30418a5379b0aac183
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10.26434/chemrxiv-2024-959gm
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Short, Enantioselective Synthesis of Mevalonic Acid
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A new enantioselective synthesis of mevalonic acid that is short, flexible, scalable to gram amounts, and uses readily available starting materials is reported. Enantioselective homoallylic epoxidation of isoprenol followed by enantiomeric enrichment gave the key epoxide intermediate. Further reactions led to either racemic mevalonic acid in 74% yield over two steps or the individual (R)- or (S)-enantiomer on a gram scale in 51% overall yield and ≥99% ee over five linear steps.
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Ryan J. Oconnell; Nicholas J. Dolphin; Olaf Wiest; Paul Helquist
|
Organic Chemistry; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a0a30418a5379b0aac183/original/short-enantioselective-synthesis-of-mevalonic-acid.pdf
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671eda9e98c8527d9e911fea
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10.26434/chemrxiv-2024-gjplf-v2
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Facile, Stereoselective Preparation and Pd-catalyzed Suzuki-Miyaura Cross-coupling of Alkenyl Sulfoximine
|
Although numerous transition-metal catalyzed cross-coupling reactions of alkenyl electrophiles with a sulfur(VI) leaving group, mainly alkenyl sulfones, have been developed, most rely heavily on highly nucleophilic Grignard reagents, and the use of organoboron reagents remains challenging. We report herein facile preparation and the following Pd-catalyzed Suzuki-Miyaura cross-coupling reaction of alkenyl sulfoximine, a monoaza analog of sulfone. The condensation of alkyl sulfoximine with aldehydes, developed in this study, makes alkenyl sulfoximines more readily available. The resulting alkenes undergo an unprecedented oxidative addition of the C–S bond to the Pd center. This cross-coupling proceeds with retention of its original stereochemistry and provided alkenes bearing three different functionalities in a stereoselective fashion. DFT calculations highlight the critical role of boronic acid, rather than boronic ester, in facilitating this transformation.
|
Kosuke Yasui; Yuichiro Tomishima; Tomoya Miura; Ken Yamazaki; Koji Hirano
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671eda9e98c8527d9e911fea/original/facile-stereoselective-preparation-and-pd-catalyzed-suzuki-miyaura-cross-coupling-of-alkenyl-sulfoximine.pdf
|
63abee97e8047a4274f81b3c
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10.26434/chemrxiv-2022-8djs0
|
Regio- and Diastereoselective Synthesis of Unsymmetrical 1,4-Diketone-Derived (Z)-Monosilyl Enol Ethers via Siloxyallylpotassium Intermediates
|
This paper describes the regio- and diastereoselective synthesis of unsymmetrical 1,4-diketone-derived (Z)-monosilyl enol ethers from 1-arylallyloxysilanes and Weinreb amides using (trimethylsilyl)methylpotassium as a base. The metalation of 1-arylallyloxysilanes to generate siloxyallylpotassiums is the key step in this transformation. The products can be transformed into diverse α-monofunctionalized unsymmetrical 1,4-diketones.
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Shuto Okuda; Yutaka Narita; Rikuo Hayashi; Masahiro Sai
|
Organic Chemistry; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-12-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63abee97e8047a4274f81b3c/original/regio-and-diastereoselective-synthesis-of-unsymmetrical-1-4-diketone-derived-z-monosilyl-enol-ethers-via-siloxyallylpotassium-intermediates.pdf
|
66753e1401103d79c5c249f4
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10.26434/chemrxiv-2024-7x7z6-v3
|
The multifaceted role of water as an accelerator of the crosslinking reaction of isocyanate-free polyurethane networks
|
Polyhydroxyurethane (PHU) thermosets are the most promising isocyanate-free substitutes to polyurethane ones when targeting the main applications of the PU business (coatings, adhesives, foams). However, the curing of their solvent-free formulations at near room temperatures is often very slow and requires the utilization of organocatalysts, limiting the large-scale deployment of the technology. Herein, we study the impact of water, introduced as an additive (2 to 10 wt.%), on the crosslinking rate of common solvent-free thermosetting PHU formulations composed of a polycyclic carbonate and a diamine. Rheology measurements, using a multi-frequency approach, indicate that even very small amounts of water (< 5 wt.%) impressively shorten gel times, by up to 5 folds at 40 °C. The multi-frequency methodology highlights for the first time the strong interactions of water with the growing PHU network during the crosslinking reaction. It suggests that water breaks down the multiple intra-/inter-molecular H-bond interactions within the PHU clusters, consequently enhancing the molecular mobility and delaying the vitrification (hydroplasticization), both phenomena contributing to accelerate the crosslinking rate. On top of that, through a combination of model reactions and computational calculations, we demonstrate that water is an actual catalyst of the cyclic carbonate aminolysis. Eventually, thanks to its multifaceted role, water can efficiently substitute the organocatalysts (e.g. TBD, DBU) usually required to cure PHU formulations at near ambient temperature. This work demonstrates that the use of additive amounts of water in solvent-free formulations is a cost-effective, non-toxic, and robust solution to accelerate the production of PHU materials, free of any organocatalyst. It offers promising prospects for the deployment of PHU-based materials requiring mild processing conditions.
|
Florent Monie; Thomas Vidil; Etienne Grau; Bruno Grignard; Christophe Detrembleur; Henri Cramail
|
Catalysis; Polymer Science; Organic Polymers; Polymerization (Polymers); Polymerization kinetics; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66753e1401103d79c5c249f4/original/the-multifaceted-role-of-water-as-an-accelerator-of-the-crosslinking-reaction-of-isocyanate-free-polyurethane-networks.pdf
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60f80c97393cc942f64dfb03
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10.26434/chemrxiv-2021-kl62l
|
Solution additives promoting the onset of MgCO3 nucleation
|
Formed via aqueous carbonation of Mg2+ ions, the crystallization of magnesite (MgCO3) is a promising carbon capture and reuse technology, albeit limited by the slow precipitation of MgCO3. Although magnesite is naturally abundant, forming at low temperature conditions, its production is an energy-intensive process due to the temperatures required to prevent the formation of hydrated phases. The principle difficulty arises from the very strong Mg2+···H2O interaction, raising barriers to dehydration. Using atomistic simulations, we have investigated the influence of thirty additive anions (Xn–, n = 1–3), ranging from simple halides to more complex molecules, on the first two steps of MgCO3 aggregation from solution: Mg2+ dehydration and Mg2+∙∙∙CO32– pairing. We have computed the thermodynamic stability of solvent shared ion pairs, Mg2+···H2O···Xn–, and contact ion pairs, Mg2+···Xn–, with Mg2+ to reveal the propensity of solution additives to inhibit Mg2+∙∙∙CO32– formation. We have determined the stabilization of undercoordinated hydrated Mg2+ states with a vacant coordination site to which CO32– can bind, subsequently initiating MgCO3 nucleation or Mg2+ incorporation into the crystal lattice. Extensive molecular dynamics simulations of electrolyte solutions containing Na2CO3 with different sources of Mg2+, MgCl2, MgSO4 and Mg(CH3COO)2, further shows that the degree of dehydration of Mg2+ and the structure of prenucleation MgCO3 clusters changes depending on the type counterion. Through a fundamental understanding of the role of solution additives in the mechanism of Mg2+ dehydration, our computational study can rationalize previously reported experimental observation of the effect of solvation environments on the growth of magnesite. This understanding may contribute to identifying solution composition conditions that could promote the low-temperature CO2 conversion into MgCO3.
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Dimitrios Toroz; Fu Song; Amira Uddin; Gregory A. Chass; Devis Di Tommaso
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Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-07-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f80c97393cc942f64dfb03/original/solution-additives-promoting-the-onset-of-mg-co3-nucleation.pdf
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67b77d36fa469535b931afdc
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10.26434/chemrxiv-2025-752xn
|
AutoSIM: Redesigning and automating umbrella sampling for biomolecular conformational transitions
|
Umbrella sampling (US) is a widely used biased simulation technique to generate projections of free energy surfaces
(FES) of chemical and biomolecular processes along a reaction coordinate (RC). US results are sensitive to the choice and discretization of the RC along which bias is applied as well as simulation lengths. Furthermore, the combination and comparison of FES slices from multiple US runs remains poorly understood. Here, we address these issues through a redefined US scheme based on recent statistical insights in sampling equilibration and convergence of RCs. The scheme is implemented in an algorithm—AutoSIM—that automates US runs based on a non-equilibrated molecular dynamics (MD) trajectory initiated in the native state basin. AutoSIM can generate FES sections associated with functional conformational transitions in biomolecules independent of apriori information on RCs or even the final end state. We validate AutoSIM by comparing FES projections for alanine dipeptide and ubiquitin along the top Principal Components with those from brute-force unbiased simulations. Additionally, we apply AutoSIM to capture the energetics for large scale conformational transitions of HIV-1 protease between open and closed forms of the enzyme.
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Mitradip Das; Ravindra Venkatramani
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b77d36fa469535b931afdc/original/auto-sim-redesigning-and-automating-umbrella-sampling-for-biomolecular-conformational-transitions.pdf
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60c73fb2842e653cc7db1b69
|
10.26434/chemrxiv.7471388.v1
|
Synthesis of L-DOPA Based Melanins with Reproducible Physic-Chemical Properties
|
This report expands our ongoing research efforts
into the non-enzymatic synthesis of melanins. We have explored four different
methods for the synthesis of L-DOPA based melanins and evaluated the
reproducibility of some of their physic-chemical properties. The melanins were
synthesized through the addition of NaOH, tyrosinate or Fe<sup>2+</sup>/H<sub>2</sub>O<sub>2</sub>.
Two different approaches for the reactions involving Fe<sup>2+</sup> and H<sub>2</sub>O<sub>2</sub>
were tested: a) addition of H<sub>2</sub>O<sub>2</sub> spread out over multiple
days or b) addition of H<sub>2</sub>O<sub>2</sub> in one fraction at the start
of the reaction. The physic-chemical properties of the melanins explored involved:
1) retention on size exclusion chromatography column, 2) FT-IR spectroscopy, 3)
UV-Vis spectroscopy and 4) the capacity to reduce a redox dye,
dichlorophenolindophenol. Overall the results obtained indicated that 1) the
various synthesis methods lead to melanins with reproducible physic-chemical
properties, 2) that the melanins synthesized in the presence of Fe<sup>2+</sup>/H<sub>2</sub>O<sub>2</sub>
are distinctly different from the melanins synthesized in the presence of NaOH
or tyrosinate and 3) that no distinctly different melanins were generated when
comparing the two different synthesis approaches involving Fe<sup>2+</sup>/H<sub>2</sub>O<sub>2</sub>.
Only the melanins synthesized in the presence of Fe<sup>2+</sup>/H<sub>2</sub>O<sub>2</sub>
appeared to possess the capacity to reduce dichlorophenolindophenol.
|
Koen Vercruysse; Jayla Moore
|
Bioorganic Chemistry; Biochemistry; Chemical Biology; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-12-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fb2842e653cc7db1b69/original/synthesis-of-l-dopa-based-melanins-with-reproducible-physic-chemical-properties.pdf
|
677330bf6dde43c908d45029
|
10.26434/chemrxiv-2025-pnjg7
|
A Data-Driven Reaction Discovery Strategy Based on Large Language Models
|
The discovery of novel reactions and optimization of reaction conditions are fundamental challenges in organic synthesis, with significant implications for retrosynthetic analysis and condition selection. This work proposes a data-driven strategy for reaction discovery, integrating high-throughput experimentation (HTE) with insights derived from large language models (LLMs). By leveraging LLMs to process chemical information from extensive literature, the method enables hypothesis-driven design and experimental validation, minimizing reliance on serendipity.
Taking cross-electrophile coupling (XEC) as a case study, this research extracts key trends, substrate combinations, and reaction conditions from 520 relevant publications. The methodology identifies unexplored substrate pairs and designs reaction plates for HTE, facilitating systematic discovery. Additionally, the concept of directed evolution in chemical catalysis is explored, hypothesizing that catalytic conditions can evolve systematically based on structural and reactivity similarities.
The findings demonstrate the utility of combining LLMs with HTE for reaction discovery and catalysis research. This approach emphasizes methodology development, prioritizing the generation of hypotheses and protocols over isolated reaction discoveries, offering a scalable framework for advancing chemical innovation.
|
Jingyang Zhang
|
Organic Chemistry; Catalysis; Chemical Education; Homogeneous Catalysis; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677330bf6dde43c908d45029/original/a-data-driven-reaction-discovery-strategy-based-on-large-language-models.pdf
|
664d615191aefa6ce1a19d4a
|
10.26434/chemrxiv-2024-7pt1w
|
Elementary Exciton Processes of InP/ZnS Quantum Dots
Under Applied Pressure
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In colloidal quantum dots (QDs), excitons are confined within nanoscale dimensions, and the relaxation of hot electrons occurs through Auger cooling. The behavior of hot electrons is evident under ambient pressure. Nanocrystal characteristics, including their size, are key to determining hot electron behavior because they serve as the stage. Applying pressure to materials can effectively modify this stage by providing a means to reversibly control interatomic distances. Unlike the behavior in ambient conditions, the pressure-dependent behavior remains unclear. In this study, InP/ZnS QDs were synthesized, and their pressure-dependent ultrafast carrier dynamics were analyzed using fs-transient absorption spectroscopy. The hot electron relaxation remained nearly constant with pressure up to 3 GPa, suggesting constant interaction between electrons and holes. However, above this threshold, the hot electron relaxation was accelerated by trapping from higher excited states. This study contributes to establishing a fundamental understanding of the pressure-dependent behavior of hot electrons in QDs.
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Daichi Eguchi; Tomoko Kagayama; Katsuya Shimizu; Naoto Tamai
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Nanoscience
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CC BY NC ND 4.0
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CHEMRXIV
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2024-05-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664d615191aefa6ce1a19d4a/original/elementary-exciton-processes-of-in-p-zn-s-quantum-dots-under-applied-pressure.pdf
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633dbc93fee74e8fdd56e15f
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10.26434/chemrxiv-2022-m719x
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Fast Evaluation of the Adsorption Energy of
Organic Molecules on Metals via Graph
Neural Networks
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Modeling of solid-state material-molecule interfaces in heterogeneous catalysis requires the extensive evaluation of the energy of molecules on surfaces. Obtaining the binding energy of many configurations of large organic molecules requires a vast amount of computational time with density functional theory (DFT). Here, we use a graph neural network (GNN) to evaluate the adsorption energy of molecular species adsorbed on metallic surfaces. The GNN is trained on a set of C1–4 fragments including N, O, S heteroatoms and C6–10 aromatic rings. Compared to DFT, the GNN shows a mean absolute error (MAE) of 0.17 eV on the test set being 6 orders of magnitude faster. When applying the trained model with subsequent hyperparameter optimization to molecules of industrial interest (biomass, plastics and polyurethanes precursors) containing up to 22 carbon atoms, the prediction performance for the adsorption energy yields a MAE of 0.03 eV/(non-H atom). While the error for out-of-distribution molecules is higher, it is still within the acceptable limit for adsorption energies (0.05 eV/atom), confirming the viability of the approach. The proposed framework represents a potential tool for the fast screening of catalytic materials, as well as their inverse design, enabling the multi-scale modeling for systems that cannot be easily simulated by DFT.
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Sergio Pablo-García; Santiago Morandi; Rodrigo Alejandro Vargas-Hernández; Kjell Jorner; Núria López; Alán Aspuru-Guzik
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Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Artificial Intelligence; Heterogeneous Catalysis; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2022-10-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633dbc93fee74e8fdd56e15f/original/fast-evaluation-of-the-adsorption-energy-of-organic-molecules-on-metals-via-graph-neural-networks.pdf
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6451603627fccdb3ea62d46f
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10.26434/chemrxiv-2023-g56vc
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Upscaled laser synthesis of copper nanoparticles in acetone to correlate the surface modification of Nd-Fe-B feedstock properties with part properties after full melting and rapid solidification
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The possibilities of nanoadditivation to achieve finer, more equiaxed grains unlock huge potential for the application field of functional materials, e.g. Nd-Fe-B magnets, where the control of the microstructure and the composition is of significant importance. The surface modification of hard magnetic microparticles by non-magnetic nanoparticles (NPs) opens a novel field of research. Here, especially Cu NPs with low amounts of oxides are of high relevance as colloidal nano-additive material. To increase the productivity of surfactant-free, laser-generated Cu NPs, we performed a process parameter study via laser ablation in acetone aiming for the highest possible productivity, increasing the throughput of NP additivation on the surface of functional feedstock micro powders. By optimizing the process parameters of laser power, laser fluence, repetition rate, volume flow, and spot size, a productivity of 0.19 µg/J of Cu NPs in acetone was achieved. Then we investigated how a fine microstructure of the magnet powder MQP-S can be retained to some extent along the process chain, throughout the melting and resolidification process during suction casting. A loading series of Cu NP nanoadditivation on magnet micro powders of 0.1, 0.5, 1.0, and 2.5 wt.% was analyzed regarding magnetic properties and microstructure of the as-built part. Using full melting conditions of MQP-S by producing samples via suction casting modified with different amounts of Cu NP additions leads to finer grains, but increasing α-Fe content. Overall, the results enable higher production rates of Cu NPs in acetone and provide insights into the influence of NP-supporting characteristics on the properties of permanent magnet micro powders after full melting and resolidification.
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Philipp Gabriel; Jianing Liu; Franziska Staab; Rene Streubel; Matthias Miertz; Karsten Durst; Oliver Gutfleisch; Stephan Barcikowski; Anna Rosa Ziefuß
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Materials Science; Nanoscience; Magnetic Materials; Materials Processing; Nanostructured Materials - Materials
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CC BY NC ND 4.0
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CHEMRXIV
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2023-05-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6451603627fccdb3ea62d46f/original/upscaled-laser-synthesis-of-copper-nanoparticles-in-acetone-to-correlate-the-surface-modification-of-nd-fe-b-feedstock-properties-with-part-properties-after-full-melting-and-rapid-solidification.pdf
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