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664cc2cf418a5379b0e2a778 | 10.26434/chemrxiv-2024-jkvxr | Selective copper-mediated cross-coupling of pyroglutamate post-translational modifications | Pyroglutamate is a cyclic N-terminal posttranslational modifica-tion that occurs in both proteins and peptide hormones. The prevalence and biological roles of pyroglutamate are little under-stood, in part due to limited tools to identify, quantify, and ma-nipulate its pyrrolidinone structure. Selective modification of pyroglutamate residues in complex polypeptides may provide unique tools to better understand its biological roles, and to al-low late-stage diversification of biologically active pyrogluta-mate-containing sequences. This work describes a copper-catalyzed N–H cross-coupling of unprotected peptides that is selective for N-terminal pyroglutamate residues. The reaction is operationally simple under mild conditions, and tolerates almost all canonical residues. Mechanistic studies point to a key role for a multidentate copper-binding mode of the extended polypeptide structure in delivering the observed reactivity. The reaction al-lows direct labeling and identification of a pyroglutamate hormone present in porcine intestinal extracts. | Yuxuan Ding; Yuecheng Jiang; Nicolas Serrat; Zachary Ball | Biological and Medicinal Chemistry; Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Bioorganometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664cc2cf418a5379b0e2a778/original/selective-copper-mediated-cross-coupling-of-pyroglutamate-post-translational-modifications.pdf |
65dcb08d66c1381729975125 | 10.26434/chemrxiv-2023-6rng3-v2 | emle-engine: a flexible electrostatic machine learning embedding package for multiscale molecular dynamics simulations | We present in this work the emle-engine package (https://github.com/chemle/emle-engine) – the implementation of a new machine learning embedding scheme for hybrid machine learning potential / molecular mechanics (ML/MM) dynamics simulations. The package is based on an embedding scheme that uses a physics-based model of the electronic density and induction with a handful of tuneable parameters derived from in vacuo properties of the subsystem to be embedded. This scheme is completely independent of the in vacuo potential and requires only the positions of the atoms of the machine learning subsystem and the positions and partial charges of the molecular mechanics environment. These characteristics allow emle-engine to be employed in existing QM/MM software. We demonstrate that the implemented electrostatic machine learning embedding scheme (named EMLE) is stable in enhanced-sampling molecular dynamics simulations. Through calculation of free energy surfaces of alanine dipeptide in water with two different ML options for the in vacuo potential and three embedding models, we test the performance of EMLE. When compared to the reference DFT/MM surface, the EMLE embedding is clearly superior to the MM one based on fixed partial charges. The configurational dependence of the electronic density and the inclusion of the induction energy introduced by the EMLE model leads to a systematic reduction in the average error of the free energy surface when compared to MM embedding. By enabling usage of EMLE embedding in practical ML/MM simulations, emle-enline will make it possible to accurately model systems and processes that feature significant variations in the charge distribution of the ML subsystem and/or the interacting environment. | Kirill Zinovjev; Lester Hedges; Rubén Montagud Andreu; Christopher Woods; Iñaki Tuñón; Marc W. van der Kamp | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dcb08d66c1381729975125/original/emle-engine-a-flexible-electrostatic-machine-learning-embedding-package-for-multiscale-molecular-dynamics-simulations.pdf |
648c6985be16ad5c57059d5e | 10.26434/chemrxiv-2023-pkb1n | Electrochemical Gold-Catalyzed 1,2-Difunctionalization of C–C Multiple Bonds | Herein, we disclose the first report of 1,2-difunctionalization of C-C multiple bonds using electrochemical redox gold catalysis. By adopting the electrochemical strategy, the inherent π-activation and cross-coupling reactivity of gold catalysis are harnessed to develop the oxy-alkynylation of allenoates under external-oxidant-free conditions. Detailed mechanistic investigations such as 31P NMR, control experiments, mass studies, and cyclic voltammetric (CV) analysis have been performed to support the proposed reaction mechanism. | Anil Kumar; Khyati Shukla; Salman Ahsan; Amit Paul; Nitin T. Patil | Organic Chemistry; Catalysis; Organometallic Chemistry; Electrocatalysis; Homogeneous Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648c6985be16ad5c57059d5e/original/electrochemical-gold-catalyzed-1-2-difunctionalization-of-c-c-multiple-bonds.pdf |
60c74479337d6ca83fe26de8 | 10.26434/chemrxiv.9828515.v1 | Acceleration vs Accuracy: Influence of Basis Set Quality on the Mechanism and Dynamics Predicted by Ab Initio Molecular Dynamics | <p>Ab initio molecular
dynamics (AIMD) is an indispensable tool for understanding the mechanistic
details of externally-energy mediated chemical reactions. In this work, we show
that the predicted thermodynamic and catalytic properties of certain reactions
using AIMD simulations critically depend on the quality of the employed basis
set. To this end, we have examined the reactants and products of the water-gas
shift reaction (viz., CO, CO<sub>2</sub>, H<sub>2</sub>, and H<sub>2</sub>O)
and studied their interaction with the ZnO(101̄0) surface using density
functional theory (DFT) and Born Oppenheimer Molecular Dynamics (BOMD) simulations.
By merely increasing the quality of the basis, from double zeta (commonly used
in most calculations of these systems) to triple zeta, we surprisingly find
that the reaction outcome of an H<sub>2</sub>O molecule colliding with a ZnO
surface pre-covered with carbon monoxide gives qualitatively different results.
These surprising results are shown to be robust with similar trends that are
also obtained with other software packages. Furthermore, we show that the
calculated adsorption energies can vary by as much as 380 meV (which is an
order of magnitude larger than room temperature) by simply changing the basis
set. Using electron density difference maps, we present mechanistic insight
into the origin of these changes. Finally, we propose a simple diagnostic test
that uses a single-point binding energy calculation to estimate the impact of
basis-set quality, which can be used before carrying out a
computationally-expensive BOMD simulation.</p> | Sharma Yamijala; Zulfikhar A. Ali; Bryan Wong | Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Homogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Physical and Chemical Processes; Quantum Mechanics; Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74479337d6ca83fe26de8/original/acceleration-vs-accuracy-influence-of-basis-set-quality-on-the-mechanism-and-dynamics-predicted-by-ab-initio-molecular-dynamics.pdf |
60c74a35567dfe7b0bec4d1b | 10.26434/chemrxiv.12156462.v1 | Mechanistic Molecular Motion of Transition-Metal Mediated Beta-Hydride Transfer: Quasiclassical Trajectories Reveal Dynamically Ballistic, Dynamically Unrelaxed, Two Step, and Concerted Mechanisms | <div>The transfer of a -hydrogen from a metal-alkyl group to ethylene is a fundamental</div><div>organometallic transformation. Previously proposed mechanisms for this transformation involve either a</div><div>two-step -hydrogen elimination and migratory insertion sequence with a metal hydride intermediate</div><div>or a one-step concerted pathway. Here, we report density functional theory (DFT) quasiclassical direct</div><div>dynamics trajectories that reveal new dynamical mechanisms for the -hydrogen transfer of</div><div>[Cp*RhIII(Et)(ethylene)]</div><div>Despite the DFT energy landscape showing a two-step mechanism with a Rh-H</div><div>intermediate, quasiclassical trajectories commencing from the -hydrogen elimination transition state</div><div>revealed complete dynamical skipping of this intermediate. The skipping occurred either extremely fast</div><div>(typically <100 femtoseconds (fs)) through a dynamically ballistic mechanism or slower through a</div><div>dynamically unrelaxed mechanism. Consistent with trajectories begun at the transition state, all</div><div>trajectories initiated at the Rh-H intermediate show continuation along the reaction coordinate. All of</div><div>these trajectory outcomes are consistent with the Rh-H intermediate <1 kcal/mol stabilized relative to</div><div>the -hydrogen elimination and migratory insertion transition states. For Co, which on the energy</div><div>landscape is a one-step concerted mechanism, trajectories showed extremely fast traversing of the</div><div>transition-state zone (<50 fs), and this concerted mechanism is dynamically different than the Rh</div><div>ballistic mechanism. In contrast to Rh, for Ir, in addition to dynamically ballistic and unrelaxed</div><div>mechanisms, trajectories also stopped at the Ir-H intermediate. This is consistent with an Ir-H</div><div>intermediate that is stabilized by ~3 kcal/mol relative to the -hydrogen elimination and migratory</div><div>insertion transition states. Overall, comparison of Rh to Co and Ir provides understanding of the</div><div>relationship between the energy surface shape and resulting dynamical mechanisms of an</div><div>organometallic transformation.</div> | Josh Wheeler; Ryan Carlsen; Daniel Ess | Bond Activation; Catalysis; Theory - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a35567dfe7b0bec4d1b/original/mechanistic-molecular-motion-of-transition-metal-mediated-beta-hydride-transfer-quasiclassical-trajectories-reveal-dynamically-ballistic-dynamically-unrelaxed-two-step-and-concerted-mechanisms.pdf |
666567bd12188379d8b17259 | 10.26434/chemrxiv-2024-9z422 | Exploiting Decarbonylation and Dehydrogenation of Forma-mides for the Synthesis of Ureas, Polyureas, and Poly(urea-urethanes) | Urea derivatives, polyureas, and poly(urea-urethanes) are materials of great interest. However, their current methods of syn-thesis involve toxic feedstock - isocyanate and phosgene gas. There is a significant interest in developing alternative meth-odologies for their synthesis from safer feedstock. We report here new methods for the synthesis of urea derivatives, polyure-as, and polyurea(urethane) using a ruthenium pincer catalyst. In this approach, urea derivatives and polyureas are synthesized from the self-coupling of formamides and diformamides, respectively, whereas polyurea(urethanes) are synthesized from the coupling of diformamides and diols. CO and H2 gases are eliminated in all these processes. Decarbonylation of formamides using such organometallic catalysts has not been reported before and therefore mechanistic insights have been provided using experiments and DFT computation to shed light on pathways of these processes. | James Luk; Alister Goodfellow; Nachiket More; Michael Buehl; Amit Kumar | Catalysis; Polymer Science; Organic Polymers; Polymerization (Polymers); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666567bd12188379d8b17259/original/exploiting-decarbonylation-and-dehydrogenation-of-forma-mides-for-the-synthesis-of-ureas-polyureas-and-poly-urea-urethanes.pdf |
63165c30173b5d734ef2a452 | 10.26434/chemrxiv-2022-88x2b-v2 | Computational study of the intercalation of NO2 between bilayer MoTe2 | Transition-metal dichalcogenide (TMD) layers have been a subject of widespread interest as chemical sensors with their sensitivity selectively enhanced depending on the number of layers. The effect has been linked to possible intercalation of species such as nitrogen dioxide (NO2). However, whether intercalation helps or even occurs remains speculative. Hence, this work investigates, employing density functional theory (DFT) calculations, the intercalation of NO2 between bilayers of molybdenum ditelluride (MoTe2), its energy, and the impact on charge transfer. The effects are confronted with the intercalation of nitrogen molecules (N2) and the equivalent adsorption of both species. The results show that the intercalation of NO2 can be energetically favorable for <0.4, 1.5–3.0, and >4.0 molecules/nm2 and that at low coverage, the molecule-sheet interactions are too weak to facilitate sufficient interlayer expansion, and thus the molecules dissociate. The dissociation and non-dissociative intercalation of NO2 enhance the per molecule charge transfer by 1110% and 256%, respectively, relative to adsorption. Hence, in all favorable cases, the intercalation should significantly enhance the response of the system. Furthermore, the results suggest that the evacuation of NO2 should be feasible, allowing MoTe2 recovery. In contrast, N2 intercalation is unfavorable, illustrating the selectivity of the process. | Maciej Jan Szary | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Nanostructured Materials - Materials; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63165c30173b5d734ef2a452/original/computational-study-of-the-intercalation-of-no2-between-bilayer-mo-te2.pdf |
60c74ab0337d6c6ddee2795f | 10.26434/chemrxiv.12240746.v1 | Synthesis of Highly Enantioenriched Sulfonimidoyl Fluorides and Sulfonimidamides by Stereospecific SuFEx Reaction | Sulfonimidamides present exciting opportunities as chiral isosteres of sulfonamides, with potential for additional directional interactions. Here we present the first modular enantioselective synthesis of sulfonimidamides, including the first stereoselective synthesis of enantioenriched sulfonimidoyl fluorides, and studies on their reactivity. A new route to sulfonimidoyl fluorides is presented from solid bench-stable, NBoc-sulfinamide salt building blocks. Enantioenriched arylsulfonimidoyl fluorides are shown to be readily racemized by fluoride ions. Conditions are developed which trap fluoride, and enable the stereospecific reaction of sulfonimidoyl fluorides with primary and secondary amines (100% es) generating sulfonimidamides with up to 99% ee. Aryl and alkyl sulfonimidoyl fluoride reagents are suitable for mild late stage functionalization reactions, exemplified by coupling with a selection of complex amines in marketed drugs. | Stephanie Greed; Edward L. Briggs; Fahima Idiris; Andrew J. P. White; Ulrich Lücking; James Bull | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ab0337d6c6ddee2795f/original/synthesis-of-highly-enantioenriched-sulfonimidoyl-fluorides-and-sulfonimidamides-by-stereospecific-su-f-ex-reaction.pdf |
62ca444b516311a81919e6b2 | 10.26434/chemrxiv-2022-grc1b | High-quality AB bilayer graphene films by direct solar-thermal chemical vapor deposition | Mass production of graphene by plasma or thermal chemical vapor deposition consumes much energy with potentially adverse effects on the environment. This work reports the use of a high-flux solar simulator that approximates the sun's spectrum and a cold-wall chemical vapor deposition reactor to demonstrate a renewable energy process for graphene growth. Synthesis of high-quality (I_{D}/I_{G} = 0.13) AB-stacked bilayer graphene with greater than 90% coverage is achieved on commercial polycrystalline copper in a one-step process and short time of 5 min. The graphene exhibits large grain sizes of at least 20 micron with spatial uniformity over a large area up to 20 mm in radius. The transmissivity and sheet resistance of the graphene films fall in the ranges of 92.8-95.3% and 2-4 kOhm/sq. Thus, direct solar capture provides a compelling option for graphene synthesis that can potentially decrease fabrication costs and environmental pollution. | Abdalla Alghfeli; Timothy Fisher | Nanoscience; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ca444b516311a81919e6b2/original/high-quality-ab-bilayer-graphene-films-by-direct-solar-thermal-chemical-vapor-deposition.pdf |
60c744fc0f50db15063961d0 | 10.26434/chemrxiv.9941867.v1 | A Novel Aza-Nazarov Cyclization of Quinazolinonyl Enones: A Facile Access to CRing Substituted Vasicinones and Luotonins | Our pre-print titled " A Novel Aza-Nazarov Cyclization of Quinazolinonyl Enones: A Facile Access to C-Ring Substituted Vasicinones and Luotonins" describes:· design and development of a novel variant of aza-Nazarov reaction of quinazolinonyl enones as a methodology to access pyrroloquinazolinones (14 examples)· identification of reaction conditions to achieve two types of pyrroloquinazolinones i.e., linear vs angular, through the intrinsic divergence built in to the enones· detailed computational investigation of the mechanism of this novel cyclization· application in diastereoselctive synthesis of C-ring substituted vasicinones (14 analogues)· application in synthesis of C-ring substituted luotonins (14 analogues)<br /> | Sivappa Rasapalli; Vamshisammeta Reddy Sammeta; Zachary F Murphy; Yanchang Huang; Jeffrey A Boerth; James A Golen; Sergey N Savinov | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fc0f50db15063961d0/original/a-novel-aza-nazarov-cyclization-of-quinazolinonyl-enones-a-facile-access-to-c-ring-substituted-vasicinones-and-luotonins.pdf |
60c758a7842e659173db488f | 10.26434/chemrxiv.14572050.v1 | De Novo Design with Deep Generative Models Based on 3D Similarity Scoring | <p>We have demonstrated the utility of a 3D shape and
pharmacophore similarity scoring component in molecular design with a deep
generative model trained with reinforcement learning. Using Dopamine receptor
type 2 (DRD2) as an example and its antagonist haloperidol <b>1</b> as a
starting point in a ligand based design context, we have shown in a
retrospective study that a 3D similarity enabled generative model can discover
new leads in the absence of any other information. It can be efficiently used for scaffold
hopping and generation of novel series. 3D similarity based models were
compared against 2D QSAR based, indicating a significant degree of
orthogonality of the generated outputs and with the former having a more
diverse output. In addition, when the two scoring components are combined
together for training of the generative model, it results in more efficient
exploration of desirable chemical space compared to the individual components. </p> | Kostas Papadopoulos; Kathryn A. Giblin; Jon Paul Janet; Atanas Patronov; Ola Engkvist | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758a7842e659173db488f/original/de-novo-design-with-deep-generative-models-based-on-3d-similarity-scoring.pdf |
668fc32dc9c6a5c07af6baaa | 10.26434/chemrxiv-2024-g3vzg | Targeting the NOT9 subunit of the CCR4-NOT complex inhibits mRNA deadenylation | The removal of poly(A) tail from mRNA sequences reduces their stability and translational activity. The deadenylation process is mainly regulated by the CCR4-NOT complex for which potent chemical inhibitors are rare. The subunit NOT9 binds various RNA binding proteins (RBPs) which recruit mRNA in a sequence-specific manner to the CCR4-NOT complex to promote their deadenylation. Several of these RBPs interact with NOT9 through an evolutionary conserved (C)NOT9 binding motif (CBM) which we used as a starting point for inhibitor design. A potent hydrocarbon stapled peptide (NIP-2) with a 60 nM binding affinity for NOT9 was identified and able to inhibit the deadenylation activity of the CCR4-NOT complex on poly(A) RNA in vitro. A co-crystal structure of NIP-2 bound to NOT9 was obtained and allowed further optimization of the peptide through point mutation which led to a variant with high cell permeability. The optimized NIP-2-H27A-N3 was able to increase the poly(A) tail length of target mRNAs by inhibiting the deadenylation activity of the CCR4-NOT complex in cells demonstrating the feasibility of increasing mRNA stability using deadenylation inhibitors. | Sunit Pal; Ilja Gordijenko; Stefan Schmeing; Somarghya Biswas; Yasemin Akbulut; Raphael Gasper; Peter 't Hart | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668fc32dc9c6a5c07af6baaa/original/targeting-the-not9-subunit-of-the-ccr4-not-complex-inhibits-m-rna-deadenylation.pdf |
60c749d49abda2d1fcf8ccf9 | 10.26434/chemrxiv.12115638.v1 | Computational Approach Revealed Potential Affinity of Antiasthmatics Against Receptor Binding Domain of 2019n-Cov Spike Glycoprotein | The novel COVID-19 pandemic is now a health threat, with a deep-felt impact worldwide. The new coronavirus 2019 (2019 n-Cov) binds to host human receptors through Receptor Binding Domain RBD of Spike glycoprotein (S), making it a prominent drug target. The present study aims to identify new potential hits that can inhibit the S protein using in silico approaches. Several natural and synthetics compounds (antiasthmatics, Antiviral, Antimalarial, Antibacterial, Anti-Inflammatory, cyclic peptide, and cyclic bis) were screened by molecular docking using AutoDock Vina. Additionally, we tested calcitriol and three known drugs (Azithromycin, HydroxyChloroquine, and Chloroquine ) against the spike protein to found if they have any direct interaction.<br />Our finding consists of 4 potential synthetic compounds from PubChem database, known for their antiasthmatic effects, that show highly binding energies each (-8.6 kcal/mol, 7.7kcal/mol, -7.2 kcal/mol and -7.0 kcal/mol). Another 5 natural compounds from the South African natural sources database (SANCDB) that bind to RBD of Spike with significant energy each: (Marchantin C with -7.3 kcal/mol, Riccardin C with -7.0 kcal/mol, Digitoxigenin-glucoside with -6.9 kcal/mol, D-Friedoolean-14-en-oic acid with -6.8 kcal/mol and, Spongotine A with -6.7 kcal/mol). The FaF-Drugs server was used to evaluate the drug-like properties of the identified compounds. Additionally, Calcitriol, Azithromycin, and HydroxyChloroquine have an appreciable binding affinity to 2019-nCoV S, suggesting a possible mechanism of action. Using in silico approaches like molecular docking and pharmacokinetic properties, we showed new potential inhibitors. Our findings need further analysis, and chemical design for more effective derivatives of these compounds speculated to disrupt the viral recognition of host receptors. | LAMIAE ELKHATTABI; Hicham Charoute; Rachid Saile; Abdelhamid Barakat | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d49abda2d1fcf8ccf9/original/computational-approach-revealed-potential-affinity-of-antiasthmatics-against-receptor-binding-domain-of-2019n-cov-spike-glycoprotein.pdf |
60c75344842e65ac6edb3f16 | 10.26434/chemrxiv.13347317.v2 | Assessment of Sauvignon Blanc Aroma and Quality Gradings Based on Static Headspace-Gas Chromatography-Ion Mobility Spectrometry (SHS-GC-IMS): Merging Analytical Chemistry with Machine Learning | <div>In this paper, we report on the application of the static headspace-gas chromatography-ion mobility spectrometry (SHS-GC-IMS) instrument in the field of wine aroma analysis and its potential in constructing a prediction model for the quality gradings of wines. The easy-to-operate, cost effective SHS-GC-IMS instrument was innovatively used for a non-targeted search for volatile compounds in Sauvignon Blanc wine, with the identification of volatiles seldom before reported. The wine aroma profile acquired by the instrument was organically and innovatively combined with advanced classification models, inspired by the computer science community, to produce high classification accuracy in terms of wine quality gradings. Useful insights were also extracted by using advanced interpretation methods on complex models to learn the important volatiles correlated with wine quality grading.</div> | Wenyao Zhu; Frank Benkwitz; Paul Kilmartin | Analytical Apparatus; Chemoinformatics; Food | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75344842e65ac6edb3f16/original/assessment-of-sauvignon-blanc-aroma-and-quality-gradings-based-on-static-headspace-gas-chromatography-ion-mobility-spectrometry-shs-gc-ims-merging-analytical-chemistry-with-machine-learning.pdf |
670d44cccec5d6c14220f196 | 10.26434/chemrxiv-2024-l6llg | Melt electrowriting of amorphous solid dispersions: influence of drug and plasticizer on rheology and printing performance | Drug loaded microfiber scaffolds have potential for sublingual drug delivery due to their fast dissolution time and tunable porosity. Such microfiber scaffolds can be prepared by melt electrowriting (MEW), wherein a polymer melt is electrostatically drawn out of a syringe onto a computer controlled moving collector. The fabrication of such scaffolds via MEW has previously been shown for a polymer with a glass transition temperature (Tg) just above room temperature, making handling challenging. For this reason, ABA triblock copolymers bearing poly(2-oxazoline) and poly(2-oxazine) with slightly higher Tg were synthesized and their processability into drug loaded microfiber scaffolds was assessed. Additionally, plasticizers commonly used in drug products were added to decrease the fabrication temperature. The aim was to investigate the influence of plasticizers on the melt viscosity and printability to expand the polymer platform for the preparation of drug loaded microfiber scaffolds.
Temperature dependent melt rheology measurements of the polymers and their mixtures revealed a drop in viscosity by one order of magnitude by the addition of triethyl citrate and ethylene glycol, respectively. Addition of the model drug indomethacin led to a further decrease in viscosity. Even though the drug loaded samples were printable with and without the addition of triethyl citrate, better fiber stacking and therefore improved printing results were obtained with the plasticizer added. However, the addition of the plasticizer did alter the dissolution profile for some of the polymer samples, leading to longer dissolution times or lower drug release compared to the samples without plasticizer, which makes it difficult to predict the influence of the plasticizer on the dissolution profile. | Larissa Keßler; Robert Luxenhofer | Materials Science; Polymer Science; Materials Processing; Polymer blends; Polymer scaffolds | CC BY 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d44cccec5d6c14220f196/original/melt-electrowriting-of-amorphous-solid-dispersions-influence-of-drug-and-plasticizer-on-rheology-and-printing-performance.pdf |
612e3d9465db1efdc1a9055b | 10.26434/chemrxiv-2021-x328s-v2 | Exploring the Effects of Methylation on the CID of Protonated Lysine: A Combined Experimental and Computational Approach | We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced dissociation of L-lysine-H$^+$ and its side-chain methylated analogues, $N_\epsilon$-Methyl-L-lysine-H$^+$ (\methylLysH{1}), $N_\epsilon$,$N_\epsilon$-Dimethyl-L-lysine-H$^+$ (\methylLysH{2}), and $N_\epsilon$,$N_\epsilon$,$N_\epsilon$-Trimethyl-L-lysine-H$^+$ (\methylLysH{3}). The major pathways observed in the experimental measurements were \mz 130 and 84, with the former dominant at low collision energies and the latter at intermediate to high collision energies. The \mz 130 peak corresponds to loss of N(CH$_3$)$_n$H$_{3-n}$ while \mz 84 has the additional loss of H$_2$CO$_2$ likely in the form of H$_2$O+CO. Within the time frame of the direct dynamics simulations, \mz 130 and 101 were the most populous peaks, with the latter identified as an intermediate to \mz 84. The simulations allowed for the determination of several reaction pathways that result in these products. A graph theory analysis enabled the elucidation of the significant structures that compose each peak. Methylation results in the preferential loss of the side-chain amide group and a reduction of cyclic structures within the \mz 84 peak population in simulations. | Kenneth Lucas; Amy Chen; Megan Schubmehl; Kristopher J. Kolonko; George L. Barnes | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e3d9465db1efdc1a9055b/original/exploring-the-effects-of-methylation-on-the-cid-of-protonated-lysine-a-combined-experimental-and-computational-approach.pdf |
65ef2070e9ebbb4db9745ff1 | 10.26434/chemrxiv-2024-n9mcb | Influence of Chloride and Electrolyte Stability on Anode Passivation Layer Formation and its Dissolution in Mg Batteries Revealed by operando EQCM-D | Rechargeable magnesium batteries are promising for future energy storage. However, among other challenges, their practical application is hindered by low coulombic efficiencies of magnesium plating and stripping. Fundamental processes such as the formation, structure, and stability of passivation layers and the influence of different electrolyte components on them are still not fully understood. Here, we gain unique insights into the initial Mg plating and stripping cycles by comparing Mg bis(trifluoromethanesulfonyl)imide (Mg(TFSI)2)- and Mg tetrakis(hexafluoroisopropyloxy)borate (Mg[B(hfip)4]2)-based electrolytes, each with and without MgCl2, on gold electrodes by highly sensitive operando electrochemical quartz crystal microbalance with dissipation monitoring (EQCM-D), applying hydrodynamic spectroscopy. With the stable Mg[B(hfip)4]2-based electrolytes, highly efficient and interphase-free cycling is possible and passivation layers are attributed to electrolyte contaminants. These are forming and degrading during the so-called conditioning process. With the more reactive Mg(TFSI)2 based electrolyte, thick passivation layers with small pores are growing during cycling. We demonstrate that the addition of chloride lowers the amount of passivated Mg deposits in these electrolytes and accelerates the currentless dissolution of the passivation layer. This has a positive effect since we observe the most efficient cycling and uniform deposition when no interphase is present on the electrode. | Benjamin W. Schick; Viktor Vanoppen; Matthias Uhl; Matthias Kruck; Sibylle Riedel; Zhirong Zhao-Karger; Erik J. Berg; Xu Hou; Timo Jacob | Physical Chemistry; Materials Science; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ef2070e9ebbb4db9745ff1/original/influence-of-chloride-and-electrolyte-stability-on-anode-passivation-layer-formation-and-its-dissolution-in-mg-batteries-revealed-by-operando-eqcm-d.pdf |
6204bc19cbb4f4daeebbd8d0 | 10.26434/chemrxiv-2022-9078r | Spectroscopic investigations, DFT calculations, molecular docking and MD simulations of 3-[(4-Carboxyphenyl) carbamoyl]-4-hydroxy-2-oxo-1, 2-dihydroxy quinoline-6-carboxylic acid. | By FT-IR, FT-Raman and DFT computations spectral characterization of 3-[(4-Carboxyphenyl) carbamoyl]-4-hydroxy-2-oxo-1, 2-dihydroxy quinoline-6-carboxylic acid was performed. Computational calculations were done using B3LYP/6-31G(d’) basis set. Vibrational assignments of wavenumbers were performed on the basis of potential energy distribution. Donor acceptor interactions were evaluated using NBO analysis. To foresee the important reactive sites of the title compound we combined DFT calculations and molecular dynamics (MD) and visualized the ALIE and Fukui functions. Sensitive nature of the compound towards autoxidation and degradation in the presence of water was investigated by the calculation of BDE and RDF. By molecular docking the compound forms a stable complex with ubiquinol-cytochrome–c reductase inhibitor. | P. K. Ranjith; Angel Ignatious; C. Yohannan Panicker; B. Sureshkumar; Stevan Armakovic; Sanja. J. Armakovic; C. Van Alsenoy; P. L. ANTO | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6204bc19cbb4f4daeebbd8d0/original/spectroscopic-investigations-dft-calculations-molecular-docking-and-md-simulations-of-3-4-carboxyphenyl-carbamoyl-4-hydroxy-2-oxo-1-2-dihydroxy-quinoline-6-carboxylic-acid.pdf |
64d79e7e4a3f7d0c0d0e171d | 10.26434/chemrxiv-2023-s6wvk | Interplay between Growth Mechanism, Materials Chemistry, and Band Gap Characteristics in Sputtered Thin Films of Chalcogenide Perovskite BaZrS3 | The prototypical chalcogenide perovskite BaZrS3, with its direct band gap, exceptionally strong light-harvesting ability and good carrier transport properties, provides fundamental prerequisites for a promising photovoltaic material. This inspired synthesis of BaZrS3 in the form of thin films, using sputtering and rapid thermal processing, aimed at device fabrication for future optoelectronic applications. Using a combination of long- and short-range structural information from x-ray absorption spectroscopy (XAS) and x-ray diffraction (XRD), we have elucidated how, starting from a random network of Ba, Zr, S atoms, thermal treatment induces crystallization and growth of BaZrS3 and explained its impact on observed PL properties. We also provide an electronic structure description and confirm the surface material chemistry using a combination of depth-dependent Photoelectron Spectroscopy (PES) using Hard X-ray (HAXPES) and traditional Al Kα radiation. From the knowledge of the optical band gap of BaZrS3 thin films, synthesized at an optimal temperature of 900°C, and our estimation of the valence band edge position with respect to the Fermi level, one may conclude that these semiconductor films are intrinsic in nature with a slight n-type character. A detailed understanding of the growth mechanism and electronic structure of BaZrS3 thin films helps pave the way for their use in photovoltaics. | Soham Mukherjee; Stefania Riva; Corrado Comparotto; Fredrik O. L. Johansson; Gabriel J. Man; Dibya Phuyal; Konstantin Simonov; Justus Just; Konstantin Klementiev; Sergei Butorin; Jonathan Scragg; Håkan Rensmo | Materials Science; Energy; Thin Films; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d79e7e4a3f7d0c0d0e171d/original/interplay-between-growth-mechanism-materials-chemistry-and-band-gap-characteristics-in-sputtered-thin-films-of-chalcogenide-perovskite-ba-zr-s3.pdf |
668ac1e301103d79c54c0fe3 | 10.26434/chemrxiv-2024-b5532 | Excitonic Approach for Nonadiabatic Dynamics: Extending Beyond the Frenkel Exciton Model | We report the formulation and implementation of an extended Frenkel exciton model (EFEM) designed for simulating the dynamics of multichromophoric systems, taking into account of the possible presence of inter-chromophore charge transfer states, as well as other states in which two chromophores are simultaneously excited. Our approach involves constructing a Hamiltonian based on calculations performed on monomers and selected dimers within the multichromophoric aggregate. The nonadiabatic molecular dynamics is addressed using a surface hopping approach, while the electronic wavefunctions and energies required for constructing the EFEM are computed utilizing the semiempirical floating occupation molecular orbitals-configuration interaction (FOMO-CI) electronic structure method. However, our approach can in principle be adapted to ab initio methods. To validate our method, we simulate the singlet fission process in a trimer of 2,5-bis(fluorene-9 ylidene)-2,5-dihydrothiophene (ThBF) molecules, embedded in their crystal environment, comparing the results of the EFEM to the standard "supermolecule" approach. | Eduarda Sangiogo Gil; Andrea Giustini; Davide Accomasso; Giovanni Granucci | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668ac1e301103d79c54c0fe3/original/excitonic-approach-for-nonadiabatic-dynamics-extending-beyond-the-frenkel-exciton-model.pdf |
60c74562842e65794ddb260e | 10.26434/chemrxiv.10009007.v1 | Chemically Induced Splay Nematic Phase with Micron Scale Periodicity | <p>Nematic liquid crystals lack positional order of their
constituent molecules, which share an average orientational order only. Modulated
nematic liquid crystal phases also lack positional order, but possess a
periodic variation in this direction of average orientation. In the recently discovered splay nematic (N<sub>S</sub>)
phase the average orientational order is augmented with a periodic splay
deformation of orientation perpendicular to the director. In this communication
we report the first example of a splay nematic phase which is chemically
induced by mixing two materials, neither of which exhibit the N<sub>S</sub>
phase. The splay-nematic phase is identified based on its optical textures,
X-ray scattering patterns, and small enthalpy of the associated phase
transition. We measure the splay periodicity optically, finding it to be ~ 9 μm.
This unexpected generation of the splay-nematic phase through binary mixtures offers
a new route to materials which exhibit this phase which complements ongoing
studies into structure-property relationships and could accelerate the
development of technologies utilising this remarkable polar nematic variant.</p> | Perri Connor; Richard Mandle | Liquid Crystals | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74562842e65794ddb260e/original/chemically-induced-splay-nematic-phase-with-micron-scale-periodicity.pdf |
67154907cec5d6c142b702d2 | 10.26434/chemrxiv-2024-w71ss | Advancing non-atom-centered basis methods for more accurate interaction energies: benchmarks and large-scale applications | Recent advances in local electron correlation approaches enable the relatively routine access to CCSD(T) [that is coupled cluster (CC) with single, double, and perturbative triple excitations] computations for molecules of a hundred or more atoms. Here, approaching their complete basis set (CBS) limit becomes more challenging due to extensive basis set superposition errors, often necessitating the use of large atomic orbital (AO) basis sets with diffuse functions. Here, we study a potential remedy in the form of non-atom-centered or floating orbitals (FOs). FOs are still rarely employed even for small molecules due to the practical complication of defining their position, number, exponents, etc. The most frequently used FO method thus simply places a single FO center with a large number of FOs toward the middle of non-covalent dimers, however, a single FO center for larger complexes can soon become insufficient. A recent alternative uses a grid of FO centers around the monomers with a single s function per center, which is currently only applicable for H, C, N, and O atoms.
Here, we build on the above advantages and mitigated some drawbacks of previous FO approaches by using a layer of FO centers and 4–9 FOs/center for each monomer.
Thus, a double layer of FOs are placed between the interacting subsystems. When extending the double-ζ AO basis with this double layer of FOs, the quality of conventional augmented double-ζ or conventional triple-ζ AO bases can be reached or surpassed with less orbitals, leading to few tenths of a kcal/mol basis set errors for
medium-sized dimers. This good performance extends to larger molecules (showed here up to 72 atoms), as efficient local natural orbital (LNO) CCSD(T) computations with only double-ζ AO and 4 FOs/center FO bases matches our LNO-CCSD(T)/CBS reference within ca. 0.1 kcal/mol. These developments introduce FO methods to the accurate modeling of large molecular complexes without limitations to atom types by further accelerating efficient correlation calculations, like LNO-CCSD(T). | Balázs Lőrincz; Péter Nagy | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67154907cec5d6c142b702d2/original/advancing-non-atom-centered-basis-methods-for-more-accurate-interaction-energies-benchmarks-and-large-scale-applications.pdf |
621ffc5491a2e6fceae2b5ab | 10.26434/chemrxiv-2022-n5jqd | Basis Set Dependence of Optical Rotation Calculations with Different Choices of Gauge | In this work, the basis set dependence of optical rotation (OR) calculations is examined for various choices of gauge/level of theory. The OR is calculated for a set of 50 molecules using B3LYP and CAM-B3LYP, and 17 molecules using coupled cluster with single and double ex- citations (CCSD). The calculations employ the correlation-consistent basis sets, aug-cc-pVζZ with ζ = D, T, Q. An inverse-power extrapolation formula is then utilized to obtain OR values at the complete basis set (CBS) limit. We investigate the basis set convergence for these methods and three choices of gauge: length gauge (with gauge-including atomic orbitals, LG(GIAOs), for DFT), the origin-invariant length gauge [LG(OI)], and the modified velocity gauge (MVG). The results show that all methods converge smoothly to the CBS limit and that the LG(OI) approach has a slightly faster convergence rate than the other choices of gauge. While the DFT methods reach gauge invariance at the CBS limit, CCSD does not. The significant difference between the MVG and LG(OI) results at the CBS limit, 26%, indicates that CCSD is not quite at convergence in the description of electron correlation for this property. On the other hand, gauge invariance at the CBS limit for DFT does not lead to the same OR values for the two density functionals, which is also due to electron correlation incompleteness. A limited comparison to gas-phase experimental OR values for the DFT methods shows that CAM-B3LYP seems more accurate than B3LYP. Overall, this study shows that the LG(OI) approach with the aug-cc-pVTZ basis set for DFT, and with the CBS(DT) extrapolation for CCSD, provides a good cost/accuracy balance. | Taylor Parsons; Ty Balduf; James Cheeseman; Marco Caricato | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621ffc5491a2e6fceae2b5ab/original/basis-set-dependence-of-optical-rotation-calculations-with-different-choices-of-gauge.pdf |
661398d921291e5d1d5d6155 | 10.26434/chemrxiv-2024-6zb16 | Aged and obscured wildfire smoke associated with downwind health risks | Fine-mode particulate matter (PM2.5) is a highly detrimental air pollutant produced in large quantities from wildfires, which are increasing with climate change. Leveraging advanced chemical measurements in conjunction with source apportionment and health risk assessments, we quantified the stark pollution enhancements during Canadian wildfire smoke transport to New York City at its peak over June 6-9, 2023. Interestingly, we also observed lower-intensity, but frequent, multi-day wildfire smoke episodes during May-June 2023, which risk exposure misclassification as generic aged organic PM2.5 given its extensive chemical transformations during 1-6+ days of transport. This smoke-related organic PM2.5 showed significant associations with asthma exacerbations, and estimates of in-lung oxidative stress demonstrate the health risks of increasingly-frequent smoke episodes and potential enhancements with chemical aging. Avoiding underestimated contributions of aged biomass burning PM2.5, especially outside of peak pollution episodes, necessitates real-time chemically-resolved monitoring to enable next-generation health studies, models, and policy under far-reaching wildfire impacts. | Taekyu Joo; Mitchell J. Rogers; Catelynn Soong; Tori Hass-Mitchell; Seulkee Heo; Michelle L. Bell; Nga L. Ng; Drew R. Gentner | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661398d921291e5d1d5d6155/original/aged-and-obscured-wildfire-smoke-associated-with-downwind-health-risks.pdf |
671d43b098c8527d9e7aa1cb | 10.26434/chemrxiv-2024-hck8q | Solvatochromic dyes increase the sensitivity of
nanosensors | Organic dyes can be chemically tailored to bind specific molecules and act as molecular sensors or probes. However, they bleach and most of them fluoresce in the UV-Vis range. In contrast, nanomaterials such as single-wall carbon nanotubes (SWCNTs) fluoresce in the near infrared (NIR) tissue transparency window and are extremely stable. Here, we combine solvatochromic dyes with SWCNTs to create molecular sensors and increase their sensitivity. We find that the dyes trans-4-[4-(Dimethylamino)styryl]-1-methylpyridinium iodide (t-DSMI) and Reichardt´s dye (Betaine 30) increase the fluorescence responses of DNA-modified SWCNTs to target analytes. With t-DSMI the fluorescence of (GC)15-SWCNT decreases 4 times more to pH compared to the SWCNT itself. Betaine 30 also boosts the sensitivity of T20-SWCNT for the lipid linoleic acid (LA) more than 2-fold. A kinetic model shows that not the affinity for the analyte, but mainly the fluorescence change is increased by the presence of the solvatochromic dyes. This approach provides a flexible design framework to increase the sensitivity of SWCNTs-based biosensors and combines the best of two worlds.
| Chen Ma; Tanuja Kistwal; Bjoern F. Hill; Krisztian Neutsch; Sebastian Kruss | Physical Chemistry; Materials Science; Nanoscience; Carbon-based Materials; Dyes and Chromophores; Nanostructured Materials - Nanoscience | CC BY NC 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671d43b098c8527d9e7aa1cb/original/solvatochromic-dyes-increase-the-sensitivity-of-nanosensors.pdf |
60c73e580f50dbd2c9395646 | 10.26434/chemrxiv.6895646.v1 | The Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning | <div>Here we report PPB2 as a target prediction tool assigning targets to a query molecule based on ChEMBL data. PPB2 computes ligand similarities using molecular fingerprints encoding composition (MQN), molecular shape and pharmacophores (Xfp), and substructures (ECfp4), and features an unprecedented combination of nearest neighbor (NN) searches and Naïve Bayes (NB) machine learning, together with simple NN searches, NB and Deep Neural Network (DNN) machine learning models as further options. Although NN(ECfp4) gives the best results in terms of recall in a 10-fold cross-validation study, combining NN searches with NB machine learning provides superior precision statistics, as well as better results in a case study predicting off-targets of a recently reported TRPV6 calcium channel inhibitor, illustrating the value of this combined approach. PPB2 is available to assess possible off-targets of small molecule drug-like compounds by public access at ppb2.gdb.tools.</div> | Mahendra Awale; Jean-Louis Reymond | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e580f50dbd2c9395646/original/the-polypharmacology-browser-ppb2-target-prediction-combining-nearest-neighbors-with-machine-learning.pdf |
675c4ea2f9980725cff6d18d | 10.26434/chemrxiv-2024-rmq24 | Electrochemical Pedagogy | Reinvigoration of electrochemical education is important for the support of decarbonised economies and net zero climate change targets. Here, explicit instruction and fuel cell engineering are used to exemplify electrochemical science as a platform for teaching a variety of interdisciplinary concepts while addressing common misconceptions related to potentials. One-way analysis of variance of keyword data is consistent with students that struggle to connect overpotentials to the spatial dependence of the electrochemical potential, chemical potential and electric potential. | Agatha Dutton; James Ramwell; Charles Osarinmwian | Chemical Education | CC BY 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c4ea2f9980725cff6d18d/original/electrochemical-pedagogy.pdf |
64794d1be64f843f412dc6fc | 10.26434/chemrxiv-2023-gq0w8-v2 | Effect of velocity on the clogging of particles in water-saturated porous media using the CFDDEM | The clogging of particles in a slurry passing through a porous medium is mainly affected by the ratio of the particle diameter to the pore throat size of the medium. A previous study showed that the Stokes number and the particle concentration affect particle clogging and retention. Therefore, in this study, the effects of fluid velocity on particle clogging were investigated by analyzing the particle transport and retention in a homogeneous porous medium. The fluid-particle two-phase flow in a porous medium was simulated using the computational fluid dynamicsdiscrete element method. The results showed that increasing the fluid velocity of particles such that the Stokes number was almost equal to 1 increased the separation efficiency of particles. Further increasing the fluid velocity reduced the residence time, which reduced the separation efficiency of the particles. | Dan Sun | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64794d1be64f843f412dc6fc/original/effect-of-velocity-on-the-clogging-of-particles-in-water-saturated-porous-media-using-the-cfddem.pdf |
64d1118d4a3f7d0c0dc33b6b | 10.26434/chemrxiv-2023-glvvh | Rapid Alternating Polarity as a Unique Tool for Synthetic Electrochemistry | Electrosynthesis, driven by renewable energy, is a powerful method for accessing useful chemical reactivity in a sustainable fashion. Typically, electrochemical reactions have been carried out using direct current (DC), where electrons flow in a single direction. In contrast, utilization of alternating current (AC) has been largely unexplored in synthetic electrochemistry despite its wide applications in our daily life. This could stem from a historical perception regarding the lack of unique reactivity/selectivity that would result from using such a waveform, as well as the absence of readily available instrumentation to remove the engineering barrier for mass adoption. A breakthrough in this area is the introduction of rapid alternating polarity (rAP), which alternates the polarity of an electrode in the millisecond timescale. This mode of current delivery, now implemented in the widely employed potentiostat, ElectraSyn2.0, enables access to unique reactivity and selectivity in organic synthesis that are challenging or currently impossible to achieve by any known method (chemical or electrochemical). The remarkable chemoselectivity and simplicity of rAP open new vistas in modern synthetic electrochemistry. | Yu Kawamata; Phil Baran | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d1118d4a3f7d0c0dc33b6b/original/rapid-alternating-polarity-as-a-unique-tool-for-synthetic-electrochemistry.pdf |
624da9173b5f995787cffc89 | 10.26434/chemrxiv-2022-q2603 | Light-Induced Control of Voltage Gated Ion Channels | Voltage gated ion channels are transmembrane proteins responsible for the generation and propagation of action potentials in excitable cells. They are key targets in receptor pharmacology, since the simple actions of opening and closing their pore with different kinetics or conductivity have been associated with a large number of channelopaties. Crystal structures of ion channels became available only in the last decades and, in combination with mutagenesis data, allowed the identification of drugs able to modulate ion conduction. However, most of the traditional modulators are not selective and present adverse side effects. Photopharmacology is establishing a new approach to overcome the problem of selectivity often present in voltage gated ion channels due to highly conserved binding regions among channels of the same subfamily. In this review, we describe the central pore region of Voltage gated sodium and potassium channels from a structural and pharmacological perspective, characterizing the binding mode of natural toxins and synthetic compounds able to physically occlude ion conduction. In addition, a bridge is created between classical pharmacology and photopharmacology, describing the approaches aimed to control the activity of voltage gated ion channels by photosensitive drugs. | Vito F. Palmisano; Nuria Anguita-Ortiz; Shirin Faraji; Juan Jose Nogueira | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Chemical Biology; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624da9173b5f995787cffc89/original/light-induced-control-of-voltage-gated-ion-channels.pdf |
648cb993be16ad5c57083dc4 | 10.26434/chemrxiv-2023-r3sxg | Catalyzing the (3+2) Cycloaddition of Neutral TACs: Towards a Generalization of the CuAAC Reactivity Principles | The introduction of the copper-catalyzed azide-alkyne coupling (CuAAC) to 1,3-dipolar cycloadditions was pivotal to their popularization in synthetic chemistry and to their application to multiple other domains of science. The reaction rate enhancement observed when coinage metal acetylide intermediates are involved in the cyclization process greatly expanded the structural and conditional range in which (3+2) cycloadditions may take place with terminal alkynes. Herein we report that comparable rate enhancements, in nature and level, can be observed in the intramolecular (3+2) cycloaddition of terminal alkynes with “neutral” three-atom components (TACs), specifically alkynyl sulfides. Through careful observations amidst reaction optimization, experimental and DFT mechanistic studies, a pathway involving a proton-coupled cyclometallation key step is proposed. The sets of catalytic conditions that have been developed allow to overcome several scope limitations previously presented by the thermally promoted (3+2) cycloaddition of “neutral” TACs, thus expanding their synthetic and applicative potential. | Dominic Campeau; Alice Pommainville; Mila Gorodnichy; Fabien Gagosz | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648cb993be16ad5c57083dc4/original/catalyzing-the-3-2-cycloaddition-of-neutral-ta-cs-towards-a-generalization-of-the-cu-aac-reactivity-principles.pdf |
6585b25c66c1381729cbe411 | 10.26434/chemrxiv-2023-wc7sq-v2 | The Final Stereogenic Unit of [2]Rotaxanes: Type 2 Geometric Isomers | Mechanical stereochemistry arises when the interlocking of stereochemically trivial covalent subcomponents results in a stereochemical complex object. Although this general concept was identified in 1961, the stereochemical description of these molecules is still under development, with new mechanical stereoisomers identified recently. Here we present a simple analysis of rotaxane and catenane stereochemistry that allowed us to identify the final missing simple mechanical stereogenic unit, an overlooked form of rotaxane geometric isomerism, and demonstrate its stereoselective synthesis. | Andrea Savoini; Peter Gallagher; Abed Saady; Stephen Goldup | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2023-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6585b25c66c1381729cbe411/original/the-final-stereogenic-unit-of-2-rotaxanes-type-2-geometric-isomers.pdf |
66461c1991aefa6ce128b64a | 10.26434/chemrxiv-2024-5td92 | Preserving Precise Choreography of Bonds in Stereoretentive Olefin Metathesis: New Type of Ligand Allows High Z-Selectivity Even at Elevated Temperature | The Z-alkene geometry is prevalent in various chemical compounds, including numerous building blocks, fine chemicals, and natural products. Unfortunately, established Mo, W, and Ru Z‑selective catalysts lose their selectivity at high temperatures required for industrial processes like reactive distillation, which limits their synthetic applications. To address this issue, we developed a catalyst capable of providing Z-alkenes with high selectivity under harsh conditions. Our research revealed a novel dithiolate ligand that, stabilised by resonance, delivers high selectivity at temperatures up to 150 °C in concentrated mixtures. This distinguishes the dithioquinoxaline complex from existing Z-selective catalysts. Notably, this unique trait does not compromise the new catalyst’s usability under classical conditions, matching the activity of known stereoretentive catalysts. Density Functional Theory (DFT) calculations were employed to understand the reaction mechanism and selectivity, and to investigate the poisoning that the catalyst may undergo and how it competes with catalytic activity. Furthermore, the new quinoxaline-based catalyst enables the valorisation of bio-sourced alkene feedstocks and the production of agricultural sex pheromones for pest control. | Łukasz Grzesiński; Maryana Nadirova; Jannick Guschlbauer; Artur Brotons-Rufes; Albert Poater; Anna Kajetanowicz; Karol Grela | Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66461c1991aefa6ce128b64a/original/preserving-precise-choreography-of-bonds-in-stereoretentive-olefin-metathesis-new-type-of-ligand-allows-high-z-selectivity-even-at-elevated-temperature.pdf |
6584706e9138d23161344704 | 10.26434/chemrxiv-2023-kk029 | Computational Insights into the Thermophysical, Conformational and Electronic Properties of Diketopyrrolopyrrole and Isoindigo Based Semiconducting Polymers | Semiconducting polymers, driving the leading edge of organic electronics and emerging soft technologies, feature a range of key attributes including broad solubility for large-scale solution deposition and charge transport properties comparable to amorphous silicon. The optoelectronic and thermomechanical properties of these π-conjugated materials are fully controllable and tunable through synthetic design, continuously improving organic electronics; however, although semiconducting polymers offer multiple functionalization sites for derivatization, synthetic optimization can be time-consuming and costly. Additionally, minor structural changes, such as altering one carbon in the polymer sidechains or the nature of an aryl group in the repeating unit, can significantly affect their electronic or mechanical properties, positively or negatively. To accelerate and enhance the development of semiconducting materials and to predict their properties before synthesis, computational chemistry serves as a valuable tool. Recent advancements in computing power and algorithm availability have made this increasingly feasible. In this work, we investigate and determine key thermomechanical properties, including glass transition temperatures and persistence lengths, of high-performance donor-acceptor conjugated polymers based on diketopyrrolopyrrole and isoindigo using in silico methods. This study not only provides insights into the molecular mechanisms underlying trends in thermomechanical properties, but also discusses the limitations and advantages of the computational methods. Overall, our work demonstrates that computational methods are an effective and powerful tool for identifying potential design targets and for understanding and rationalizing trends in semiconducting polymers and related emerging electronic devices. | Maryam Kosar; Abd Al-Aziz Abu-Saleh; Angela Awada; Susanna Vu; Simon Rondeau-Gagné; John Trant | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Conducting polymers; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6584706e9138d23161344704/original/computational-insights-into-the-thermophysical-conformational-and-electronic-properties-of-diketopyrrolopyrrole-and-isoindigo-based-semiconducting-polymers.pdf |
64caa178dfabaf06ff98668f | 10.26434/chemrxiv-2023-zg0vh | Quinone-mediated hydrogen anode for non-aqueous reductive electrosynthesis | Electrochemical synthesis can provide more sustainable routes to industrial chemicals. Electrosynthetic oxidations often may be performed "reagent-free", generating H2 derived from the substrate as the sole byproduct at the counter electrode. Electrosynthetic reductions, however, require an external source of electrons. Sacrificial metal anodes are commonly used for small-scale applications, but more sustainable options are needed at large scale. Anodic water oxidation is an especially appealing option, but many reductions require anhydrous, air-free reaction conditions. This constraint motivates the growing interest in the electrochemical hydrogen oxidation reaction (HOR) under non-aqueous conditions. Here, we report a mediated H2 anode that achieves indirect electrochemical oxidation of H2 by pairing thermal catalytic hydrogenation of an anthraquinone mediator with electrochemical oxidation of the anthrahydroquinone. This quinone-mediated H2 anode is used to support nickel-catalyzed cross-electrophile coupling (XEC), a reaction class gaining widespread adoption within the pharmaceutical industry. Initial validation of this method in small-scale batch reactions is followed by adaptation to a recirculating flow reactor that enables hectogram-scale synthesis of a pharmaceutical intermediate. The mediated H2 anode technology disclosed here offers a general strategy to support H2-driven electrosynthetic reductions. | Jack Twilton; Mathew Johnson; Vinayak Sidana; Mareena C. Franke; Cecilia Bottecchia; Dan Lehnherr; François Lévesque; Spring M. M. Knapp; Luning Wang; James B. Gerken; Cynthia M. Hong; Thomas P. Vickery; Mark D. Weisel; Neil A. Strotman; Daniel J. Weix; Thatcher W. Root; Shannon S. Stahl | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Pharmaceutical Industry; Electrocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64caa178dfabaf06ff98668f/original/quinone-mediated-hydrogen-anode-for-non-aqueous-reductive-electrosynthesis.pdf |
654138eea8b423585aa97396 | 10.26434/chemrxiv-2023-tlztb | A Portrait of the Chromophore as a Young System. Quantum-Derived Force Field Unraveling Solvent Reorganization Upon Optical Excitation of Cyclocurcumin Derivatives | The study of fast non-equilibrium solvent relaxation in organic chromophores is still challenging for molecular modeling and simulation approaches, and is often overlooked, even in the case of non-adiabatic dynamics simulations. Yet, especially in the case of photoswitches, the interaction with the environment can strongly modulate the photophysical outcomes. To unravel such a delicate interplay, in the present contribution we resorted to a mixed quantum-classical approach, based on quantum mechanically derived force fields. The main task is to rationalize the solvent reorganization pathways in chromophores derived from cyclocurcumin, suitable for light-activated chemotherapy to destabilize cellular lipid membranes. The accurate and reliable decryption delivered by the quantum-derived force fields points to important differences in the solvent reorganization, which further justify the different photo-isomerization quantum yields. | Raul Losantos ; Giacomo Prampolini; Antonio Monari | Physical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654138eea8b423585aa97396/original/a-portrait-of-the-chromophore-as-a-young-system-quantum-derived-force-field-unraveling-solvent-reorganization-upon-optical-excitation-of-cyclocurcumin-derivatives.pdf |
64424133e4bbbe4bbf00d01f | 10.26434/chemrxiv-2023-97kbq | Insights into the Mechanism and Regioselectivity of Palladium-Catalyzed Arylation of α,β-Unsaturated Ketones | Transition-metal catalyzed coupling reactions of carbonyl compounds using simple chemical feedstocks have become a cornerstone of modern synthetic organic chemistry. The mechanisms and origins for ligand-controlled palladium-catalyzed regioselective α- and γ-arylation of α,β-unsaturated ketones with aryl halides have been investigated by density functional theory (DFT) calculations. Computational results have confirmed our proposed catalytic cycle, which includes four steps: oxidative addition, transmetallation, deprotonation/protonation, and reductive elimination. The Heck-type mechanism for α-arylation of α,β-unsaturated ketones is proved to be less feasible due to the high energy barrier for the insertion step. While reductive elimination is the rate-determining step (RDS), the critical process responsible for the regioselectivity depends upon the direction of protonation step, where the base function as a proton shuttle to facilitate H migration. Distortion/interaction analysis, natural bond orbital (NBO) analysis, and bur-ied volume calculations indicate that the regioselectivity is primarily controlled by the steric hindrance at the region of the ligand close to the enone. The indole ring of the phosphine ligand lay upward or downward, varying the space crowding in the region, thus leading to different protonation products followed by corresponding reductive elimination. The phenomenon of [1,5]-H trans-fer discovered in the γ-arylation of β-alkoxy cyclohexenones is also well rationalized by the proton shuttle model. | Jinbo Luo; Xiaoxi Su; Zhizheng Chen; Shuanglin Qu | Theoretical and Computational Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64424133e4bbbe4bbf00d01f/original/insights-into-the-mechanism-and-regioselectivity-of-palladium-catalyzed-arylation-of-unsaturated-ketones.pdf |
6749fefb7be152b1d061fbcc | 10.26434/chemrxiv-2024-snvfr | Temperature Behavior of Intermolecular Interactions in Ionic Liquids | Room-temperature ionic liquids (RTIL) represent a versatile class of chemical systems, comprised only of oppositely charged species, whose bulk properties can be fine-tuned by adjusting molecular structures and, consequently, intermolecular interactions. Understanding the intricate dynamics between the two ionic species can aid the rational design of RTIL as electrolytes facilitating electron- or proton-transfer reactions useful for energy applications. Here, we investigate the temperature dependency of the intermolecular interactions via magnetization transfer between oppositely charged ions by means of 1H-19F heteronuclear Overhauser effect spectroscopy (HOESY) for two ionic liquids, namely [BMIM][BF4] and [BMIM][PF6]. We find that cross-relaxation rates vary significantly over a rather small temperature range, crossing the null point and changing sign. Other NMR observables such as chemical shifts, scalar couplings or auto-relaxation rates are less affected by temperature, making intermolecular Overhauser transfer a sensitive tool to study the dynamics and especially intermolecular interactions in RTILs. Molecular Dynamics (MD) simulations on neat RTILs systems were performed to identify the origin of the observed behavior. Good agreement between simulated and experimental cross-relaxation rates was found at different temperatures. On this basis, we could attribute the observed temperature behavior to the modulation of dynamic properties rather than coordination changes of RTILs. Specifically, it is the change in relative diffusion coefficients that describes the temperature behavior of internuclear interactions, rather than the distance of closest approach. This information underscores the versatility and high thermal stability of ionic liquids. | Oscar Gao; Florin Teleanu; Kelsey Marr; Alexej Jerschow | Physical Chemistry; Quantum Mechanics; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6749fefb7be152b1d061fbcc/original/temperature-behavior-of-intermolecular-interactions-in-ionic-liquids.pdf |
64e9fdb43fdae147fade7222 | 10.26434/chemrxiv-2023-xpc5s | A Porphyrin-Based Molecular Cage Guided by Designed Local-Electric Field Is Highly Selective and Efficient | The present work outlines a general methodology for designing efficient catalytic machineries that can easily be tweaked to meet the demands of the target reactions. This work utilizes a principle of the designed local electric field (LEF) as the driver for an efficient catalyst. It is demonstrated that by tweaking the LEF, we can catalyze the desired hydroxylation products with enantioselectivity that can be changed at will. Using computation tools, we caged a synthetic analog of heme porphyrin (HM1) and investigated the pharmaceutically relevant conversion of Tetralin to Tetralol, inside the modified supramolecular cage. The QM/MM calculations demonstrate a resulting catalytic efficiency with virtually absolute Pro-R selectivity for the tetralin hydroxylation. Our calculations show that the LEF of the supramolecular cage and HM1 exerts a strong electric field along the Fe—O reaction axis, which is the main driving force for enhanced reactivity. At the same time, the supramolecular cage applies a lateral LEF that regulates the enantioselectivity. We further demonstrate that swapping the charged/polar substitution in the supramolecular cage switches the lateral LEF which changes the enantioselectivity of hydroxylation from R to S. | Shakir Ali Siddiqui; Sason Shaik; Surajit Kalita; Kshatresh Dubey | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e9fdb43fdae147fade7222/original/a-porphyrin-based-molecular-cage-guided-by-designed-local-electric-field-is-highly-selective-and-efficient.pdf |
635a8535ca86b83fdbc5cfa1 | 10.26434/chemrxiv-2022-8h843-v2 | Hydration Structure of Na+ and K+ Ions in Solution Predicted by Data-Driven Many-Body Potentials | The hydration structure of Na+ and K+ ions in solution is systematically investigated using a hierarchy of molecular models that progressively include more accurate representations of many-body interactions. We found that a conventional empirical pairwise additive force field that is commonly used in biomolecular simulations is unable to reproduce the extended X-ray absorption fine structure (EXAFS) spectra for both ions. In contrast, progressive inclusion of many-body effects rigorously derived from the many-body expansion of the energy allows the MB-nrg potential energy functions (PEFs) to achieve nearly quantitative agreement with the experimental EXAFS spectra, thus enabling the development of a molecular-level picture of the hydration structure of both Na+ and K+ in solution. Since the MB-nrg PEFs have already been shown to accurately describe isomeric equilibria and vibrational spectra of small ion–water clusters in the gas phase, the present study demonstrates that the MB-nrg PEFs effectively represent the long-sought-after models able to correctly predict the properties of ionic aqueous systems from the gas to the liquid phase, which has so far remained elusive. | Debbie Zhuang; Marc Riera; Ruihan Zhou; Alexander Deary; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Physical and Chemical Properties; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635a8535ca86b83fdbc5cfa1/original/hydration-structure-of-na-and-k-ions-in-solution-predicted-by-data-driven-many-body-potentials.pdf |
6764032b6dde43c9089c9ea6 | 10.26434/chemrxiv-2024-njrjh-v2 | Identifying Key Properties that Drive Redox Mediator Activity in Lactiplantibacillus plantarum | Lactiplantibacillus plantarum is known to utilize exogenous small molecule quinone mediators to perform extracellular electron transfer (EET), allowing it to produce a detectable current in a bioelectrochemical system (BES). Utilization of quinone mediators by L. plantarum requires a type-II NADH dehydrogenase (Ndh2), however structural variations in the core of 1,4-naphthoquinone EET mediators has shown to yield significantly different current outputs. Herein, we assembled a library of 40 quinone-based EET mediators to probe the important physicochemical properties and biochemical interactions responsible for Ndh2-dependent EET in L. plantarum. The library was designed with inspiration from naturally-occurring metabolites, and assembly was focused on structural modifications that diversified polarity, reduction potential, and predicted free energy of binding to Ndh2 (ΔGcomp), as these properties are hypothesized to drive EET activity. In general, Ndh2-dependent EET activity in an iron(III) nanoparticle reduction assay significantly correlates to the mediator's polarity and ΔGcomp. Five mediators were analyzed in BESs with L. plantarum and each generated Ndh2-dependent current over background signal. Importantly, an amine containing mediator yielded incredibly stable current output over the course of the experiment (up to 5 days). These findings improve our understanding of structure-activity relationships for quinone-mediated EET and provide stable mediators for bioelectronic sensing applications. | Benjamin T. Blackburn; Robyn A. C. Alba; Vladimir O. Porokhin; Rong Cai; Arden Hatch; Soha Hassoun; Caroline M. Ajo-Franklin; Emily Mevers | Biological and Medicinal Chemistry; Organic Chemistry; Energy; Natural Products; Organic Synthesis and Reactions; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6764032b6dde43c9089c9ea6/original/identifying-key-properties-that-drive-redox-mediator-activity-in-lactiplantibacillus-plantarum.pdf |
652d78df8bab5d20557bd047 | 10.26434/chemrxiv-2023-f1qhq | Triplet Upconversion Under Ambient Conditions Enables Digital Light Processing 3D Printing | The rapid photochemical conversion of materials from liquid to solid (i.e., curing) has enabled the fabrication of modern plastics used in microelectronics, dentistry, and medicine. However, industrialized photocurables remain restricted to unimolecular bond homolysis reactions (Type I photoinitiations) that are driven by high-energy UV light. This narrow mechanistic scope both challenges the production of high-resolution objects and restricts the materials that can be produced using emergent manufacturing technologies (e.g., 3D printing). Herein, we develop a photosystem based on triplet-triplet annihilation upconversion (TTA-UC) that efficiently drives a Type I photocuring process using green light at low power density (<10 mW/cm2) and in the presence of ambient oxygen. This system also exhibits a superlinear dependence of its cure depth on light exposure intensity, which enhances spatial resolution. This enables for the first-time integration of TTA-UC in an inexpensive, rapid, and high-resolution manufacturing process, digital light processing (DLP) 3D printing. Moreover, relative to traditional Type I and Type II (photoredox) strategies, the present TTA-UC photoinitiation method results in improved cure depth confinement and resin shelf-stability. This report provides a user-friendly avenue to utilize TTA-UC in ambient photochemical processes and paves the way towards fabrication of next generation plastics with improved geometric precision and functionality. | Connor O'Dea; Jussi Isokuortti; Emma Comer; Sean Roberts; Zachariah Page | Polymer Science; Polymerization (Polymers); Polymerization kinetics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652d78df8bab5d20557bd047/original/triplet-upconversion-under-ambient-conditions-enables-digital-light-processing-3d-printing.pdf |
66d86ef3cec5d6c1421d593e | 10.26434/chemrxiv-2024-xlpxn-v2 | Plasmonic microgel actuation induced by diffractively excited modes | Light-driven soft actuators at the microscale have gained significant interest owing to their flexible and contactless manipulation of small objects. However, a major challenge in this field is the limited number of control parameters for deformation, resulting in relatively simple actuation modes. To achieve complex deformable actuators, it is crucial to increase the number of control parameters. We investigated the deformation of PNIPAM microgels induced by diffractively excited plasmons, chosen for their high controllability. Upon irradiation with 830-nm light, the microgel rapidly shrank by 53% in width, followed by a return to its original state. The photothermal conversion efficiency using Au gratings was estimated to be 88 times higher than that of non-plasmonic Au thin films. This enhanced deformation was tunable by controlling not only the polarization angle of the excitation light but also the grating area. The deformation of the grating with an area of 30 um^2 was four times greater than that with an area of 15 um^2, despite the entire irradiated spot being confined within each grating area due to the superposition of the plasmonic waves. | Hiroaki Nishiyama; Wataru Tabata; Haruka Matsumoto; Shun Odashima; Shion Narushima | Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d86ef3cec5d6c1421d593e/original/plasmonic-microgel-actuation-induced-by-diffractively-excited-modes.pdf |
66370a0721291e5d1d731cce | 10.26434/chemrxiv-2024-7k052 | Modular MPS3-Based Frameworks for Superionic Conduction of Monovalent and Multivalent Ions | Next-generation batteries based on more sustainable working ions could offer improved performance, safety, and capacity over lithium-ion batteries, while also decreasing the cost. Development of next-generation battery technology using "beyond-Li" mobile ions is limited, in part, due to a lack of understanding of solid state conduction of these ions. Next-generation mobile ions tend to have relatively low mobility in solids due to: (1) larger ionic radii (Na+, K+, Ca2+), which limit the accessible migration pathways, and/or (2) higher charge densities (Mg2+, Zn2+, Al3+, which result in strong electrostatic interactions within the solid. Here, we introduce ligand-coordinated ions into MPS3-based solid host crystals (M = Mn, Cd) to simultaneously increase the size of the bottlenecks within the migration pathway and screen the charge-dense ions. We employ X-ray diffraction, thermogravimetric analysis, inductively coupled plasma mass spectrometry, scanning electron microscopy, energy dispersive X-ray spectroscopy, solid state magic angle spinning nuclear magnetic resonance spectroscopy, pulsed field gradient nuclear magnetic resonance spectroscopy, density functional theory quantum mechanics, and electrochemical impedance spectroscopy to probe the ionic mobility, structural and chemical changes in the MPS3 materials after ion exchange.
We show that the inclusion of coordinating ligands enables ambient temperature superionic conductivity of various next-generation mobile ions in an electronically-insulating MPS3-based solid. These ion-intercalated MPS3-based frameworks not only enable deeper understanding of ligand-coordination in solid state ionic conduction, but could potentially serve as a universal solid state electrolyte for various next-generation battery chemistries. | Zachery W. B. Iton; Zion Irving-Singh; Song-Jong Hwang; Amit Bhattacharya; Sammy Shaker; Tridip Das; Raphaële J. Clément; William A. Goddard; Kimberly A. See | Materials Science; Inorganic Chemistry; Electrochemistry; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66370a0721291e5d1d731cce/original/modular-mps3-based-frameworks-for-superionic-conduction-of-monovalent-and-multivalent-ions.pdf |
60c741a2842e653c08db1ef2 | 10.26434/chemrxiv.7422815.v2 | The Nature of Chemisorbed CO2 in Zeolite A | Formation of CO<sub>3</sub><sup>2-</sup> and HCO<sub>3</sub><sup>-</sup>
species without participation of the framework oxygen atoms upon chemisorption
of CO<sub>2</sub> in zeolite |Na<sub>12</sub>|-A is revealed. The transfer of O
and H atoms is very likely to have proceeded via the involvement of residual H<sub>2</sub>O
or acid groups. A combined study by solid-state <sup>13</sup>C MAS NMR, quantum
chemical calculations, and <i>in situ</i> IR
spectroscopy showed that the chemisorption mainly occurred by the formation of
HCO<sub>3</sub><sup>-</sup>. However, at a low surface coverage of physisorbed
and acidic CO<sub>2</sub>, a significant fraction of the HCO<sub>3</sub><sup>-</sup>
was deprotonated and transformed into CO<sub>3</sub><sup>2-</sup>. We expect
that similar chemisorption of CO<sub>2</sub> would occur for low-silica
zeolites and other basic silicates of interest for the capture of CO<sub>2</sub>
from gas mixtures. | Przemyslaw Rzepka; Zoltán Bacsik; Andrew J. Pell; Niklas Hedin; Aleksander Jaworski | Separation Science; Solid State Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a2842e653c08db1ef2/original/the-nature-of-chemisorbed-co2-in-zeolite-a.pdf |
60c746b7bdbb89165aa38c54 | 10.26434/chemrxiv.11369646.v1 | Efficient Multi-Configurational Wavefunction Method with Dynamical Correlation Using Non-Orthogonal Configuration Interaction Singles and Doubles (NOCISD) | <div>It is well known that inclusion of dynamical correlation is needed in order to reach quantitative agreement with experiment for molecular systems with multi-reference character. In this work, we start from a non-orthogonal configuration interaction (NOCI) framework that accounts for the static correlation and incorporate dynamical correlation by including singles and doubles excitations out of each reference determinant resulting in a NOCISD wavefunction. The equations defining the NOCISD wavefunction commonly require the solution a poorly condition generalized eigenvalue problem, which we avoid by projecting the equations to a small dimension space defined by the CISD eigenvectors of each reference determinant. We show that NOCISD results are in good qualitative agreement with other state-of-the-art method for challenging problems such as the electron transfer in the ethylene dimer radical cation and LiF, as well as the description of the Jahn-Teller distortion in the cyclopentadienyl and nitrogen trioxide radicals.</div> | Jacob Nite; Carlos A. Jimenez-Hoyos | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746b7bdbb89165aa38c54/original/efficient-multi-configurational-wavefunction-method-with-dynamical-correlation-using-non-orthogonal-configuration-interaction-singles-and-doubles-nocisd.pdf |
60c757b74c891947bcad4a73 | 10.26434/chemrxiv.14452797.v1 | Genetic Engineering of Chromobacterium Vaccinii DSM 25150 for Improved Production of FR900359 | <p></p><p><a></a>The depsipeptide FR900359 has been first described in
literature in 1988 (Fujioka <i>et al</i>, 1988) to be isolated from a methanol extract of the
whole plant of <i>Ardisia crenata</i>. FR900359
can be isolated from the leaves of <i>A. crenata</i>,
but the very low quantities and the complex matrix prevent access to sufficient
amounts of FR900359 to enable drug development efforts and potential commercial
manufacturing. Almost two decades later, it has been discovered that FR900359 is
in fact produced by a strictly obligate bacterial endosymbiont, <i>Candidatus</i> <i>Burkholderia crenata</i>, of the plant <i>Ardisia crenata</i> (Carlier <i>et al</i>, 2016). This study identified
also the DNA sequence of the biosynthetic gene cluster (BGC) of FR900359. In
order to identify alternative and scalable methods for production of FR900359,
a genome mining effort on bacterial genomes from both public sequence databases
and genome sequences generated from internal efforts at Novartis was initiated.
Translated amino acid sequences of the FR900359‑BGC from <i>Candidatus B. crenata</i> were used as query sequence. While the query
of public sequence databases did not return highly similar sequences, a gene cluster
with very high homology in translated amino acid sequence and identical
prediction of protein functions was discovered in the genome of <i>Chromobacterium vaccinii</i> DSM 25150,
which had been sequenced internally at Novartis. Here we describe the genetic engineering
of <i>Chromobacterium vaccinii</i> DSM 25150
resulting in mutants that exhibit improved production of FR900359 and improved
characteristics concerning downstream processing and purification.</p><p></p> | Dominik Pistorius; Kathrin Buntin; Caroline Bouquet; Etienne Richard; Eric Weber; Séverine Wollbrett | Natural Products; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757b74c891947bcad4a73/original/genetic-engineering-of-chromobacterium-vaccinii-dsm-25150-for-improved-production-of-fr900359.pdf |
678a7728fa469535b9688c35 | 10.26434/chemrxiv-2024-d2455-v2 | Non-Aromatic Fluorescence from Single α-Helical Peptides | We describe the first systematic analysis of NAF-emitting peptides in solution and show that short peptides derived from zwitterionic single α-helices (SAHs), formed exclusively by non-aromatic lysine and glutamic acid residues, are UV-active and luminescent at near-UV wavelengths in solution (λexc = 320 nm; λem ≈ 420 nm). We also show that their emission depends on the α helical folding, which favors intramolecular through-space interactions between the Lys/Glu side chains and that conservative mutations, such as the replacement of Lys by Orn or Arg, strongly influence the NAF emission. | Carmen González-González; Roi Lopez-Blanco; Juan A. González-Vera; Sara D’Ingiullo; David Bouzada; Manuel Melle-Franco; Angel Orte; M. Eugenio Vazquez | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a7728fa469535b9688c35/original/non-aromatic-fluorescence-from-single-helical-peptides.pdf |
631770a8be03b2837cec3c3a | 10.26434/chemrxiv-2022-2p1qb | Multi-particle orientational correlations are responsible for the nonlinear dielectric effect: Analysis of temperature-dependent measurements for glycerol | The nonlinear dielectric effect (NDE) is traditionally viewed as originating from saturation of the response of individual dipoles in a strong electric field. This mean-field view, mathematically described by the Langevin saturation function, predicts enhanced dielectric saturation at lower temperatures. In contrast, recent experiments for glycerol have shown a sharp increase of the NDE with increasing temperature. The NDE is a sum of a term representing binary correlations of dipolar orientations and terms referring to three- and four-particle orientational correlations. Analysis of experimental data shows that the contribution of three- and four-particle correlations strongly increases at elevated temperatures. The mean-field picture of dielectric saturation as the origin of the NDE is inconsistent with observations. A positive NDE (increment of the field-dependent dielectric constant) is predicted for low-concentration solutions of polar molecules in nonpolar solvents. The dependence of the NDE on the concentration of the polar component is polynomial. | Dmitry Matyushov | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Physical and Chemical Processes; Statistical Mechanics; Transport phenomena (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631770a8be03b2837cec3c3a/original/multi-particle-orientational-correlations-are-responsible-for-the-nonlinear-dielectric-effect-analysis-of-temperature-dependent-measurements-for-glycerol.pdf |
60c74d65842e655f38db346d | 10.26434/chemrxiv.12580031.v2 | Synergistic Effects of Carbon Dots and Palladium Nanoparticles Enhances the Sonocatalytic Performance for Rhodamine B Degradation in the Absence of Light | Carbon dot (CD) and palladium nanoparticles (Pd NPs) composites are semiconducting materials having tremendous applications in catalysis with suitable bandgap. However, their combination with suitable polymer matrix in sono-photo-catalysis has not been explored. Herein, we have synthesized and characterized a new nano-hybrid catalyst from polyamide cross-linked CD-polymer and subsequent deposition of Pd NPs. Sonocatalytic activity of 99% rhodamine B dye-degradation was achieved in mere 5 minutes (min) under dark. Model catalyst replacing CD with benzene and other control studies revealed that synergistic effects of CD and Pd NPs enhances the sonocatalytic activity of nano-hybrid catalyst. Interestingly, visible light did not influence the activity significantly. While mechanistic investigations suggest that generation of reactive oxygen species on the surface of CD-polymer initiated by ultrasound which further facilitated by Pd NPs is the key for remarkable catalytic activity (rate constant 0.99 min<sup>-1</sup>). Recyclable heterogeneous catalyst under ambient conditions are promising for the utility of exploring sono-assisted dark-catalysis for several avenues. | Abdul Selim; Sharanjeet Kaur; Arif Hassan Dar; Shaifali Sartaliya; Govindasamy Jayamurugan | Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d65842e655f38db346d/original/synergistic-effects-of-carbon-dots-and-palladium-nanoparticles-enhances-the-sonocatalytic-performance-for-rhodamine-b-degradation-in-the-absence-of-light.pdf |
672caf667be152b1d0522d3d | 10.26434/chemrxiv-2024-pvk9d-v2 | Machine Learning Approaches for Determining Molecular Packing of Organic Semiconductors: Toward Accurate Crystal Structure Prediction | Organic semiconductors (OSCs) with π-electron skeletons (π-cores) have garnered significant attention. The development of innovative molecules with high carrier mobility necessitates strategic molecular design.
One critical property affecting the carrier mobility of π-conjugated OSCs is the molecular arrangement, particularly the two-dimensional (2D) molecular packing of the π-cores, such as π-stacking, herringbone (HB) packing, and brickwork (BW) packing.
These molecular packing structures, which are similar 2D packings, have not been theoretically predicted, leading chemists to design new OSC molecules based on empirical knowledge. Therefore, computational science and informatics are crucial for the strategic design of OSC molecules with unprecedented properties and functions.
In this study, we introduce a machine learning method to determine with high accuracy whether an OSC forms the HB packing, a 2D molecular packing known to enhance carrier mobility. We also present a computational method to predict the crystal structure of an OSC from its chemical structure using molecular mechanics (MM) calculations and molecular dynamics (MD) simulations, coupled with our proposed machine learning model to classify the type of 2D molecular packing. | Takuya Seki; Yudai Shinozaki; Ryosuke Ito; Shunsuke Sato; Jun Takeya; Toshihiro Okamoto; Go Watanabe | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672caf667be152b1d0522d3d/original/machine-learning-approaches-for-determining-molecular-packing-of-organic-semiconductors-toward-accurate-crystal-structure-prediction.pdf |
60c750cff96a007d89287edc | 10.26434/chemrxiv.13084430.v1 | Quantum Dots Ceramic Nano Membrane for Copper Mining Water Treatment, Turning Na2SO4 to NaOH and Pretreatment for Seawater Desalination | <p><a></a><a>This paper </a>reports on performance of ceramic nanofiltration membrane to treat copper mining water, waste salt recycling and purification of seawater. The ceramic filters have α-Al<sub>2</sub>O<sub>3</sub> flat-sheet supporter, with sintered TiO<sub>2</sub>, Fe<sub>2</sub>O<sub>3</sub>, or ZrO<sub>2</sub>nanoparticles as membrane on the surface of supporter. The membrane has photoluminescence phenomenon when irradiating with UV lamp. It indicates that they are quantum dots material, whose sizes may be between 2-10nm. The Nanofilter can remove more 90% contaminants from copper mining water. It shows good functional stability in the corrosive mining water. It is also able to turn Na<sub>2</sub>SO<sub>4</sub> to NaOH by adding Ca(OH)<sub>2</sub>. This provides a novel technology to reuse waste salt. The ceramic nanofilter can remove all suspended solid from seawater to ease the subsequent desalination of seawater with reserve osmosis membrane. </p> | Zhiqiang Wang; Tian Cheng Wang | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750cff96a007d89287edc/original/quantum-dots-ceramic-nano-membrane-for-copper-mining-water-treatment-turning-na2so4-to-na-oh-and-pretreatment-for-seawater-desalination.pdf |
66451702418a5379b061cdb5 | 10.26434/chemrxiv-2024-lpsvj | Parameterization of a Fluctuating Charge Model for Complexes Containing 3d Transition Metals | Metalloproteins widely exist in biology, playing pivotal roles in diverse life processes. Meanwhile, molecular dynamics (MD) simulations, which are driven by classical force fields, have emerged as indispensable tools in scientific research. Among the critical parameters within classical force fields are partial charges, which are traditionally derived from quantum mechanical (QM) calculations. However, QM calculations are often time-insensitive and prone to basis set dependence. Alternatively, fluctuating charge (FQ) models offer a promising avenue for partial charge derivation, boasting significant speed advantages conducive to large-scale screening. Building upon our previous work, which tailored an FQ model for zinc-containing complexes, we have extended this model to include additional 3d transition metals integral to the life sciences, namely chromium, manganese, iron, cobalt, and nickel. Employing CM5 charges as reference points for parameterization, our FQ model accurately reproduces partial charges for 3d metal complexes featuring biologically relevant ligands. Furthermore, by using atomic charges derived by our FQ model, MD simulations have been performed, and the results show excellent performance in simulating proteomic metal sites housing multiple metal ions. Specifically, our simulations accurately capture the behavior of a metalloprotein containing an iron-sulfur cluster and another containing a di-manganese metal site. These results showcase comparable performance to those of RESP charges. We anticipate that our study can accelerate the parameterization of atomic charges, thereby facilitating simulations of metalloproteins featuring 3d transition metals. | Luke Landry; Pengfei Li | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66451702418a5379b061cdb5/original/parameterization-of-a-fluctuating-charge-model-for-complexes-containing-3d-transition-metals.pdf |
62b482d98c5523ae9c1eeebc | 10.26434/chemrxiv-2022-n35w9-v3 | Ionic Multi-Resonant Thermally Activated Delayed Fluorescence Emitters for Light Emitting Electrochemical Cells | We designed and synthesized two new ionic thermally activated delayed fluorescent (TADF) emitters that are charged analogues of a known multiresonant TADF (MR-TADF) compound, DiKTa. The emission of the charged derivatives is red-shifted compared to the parent com-pound. For instance, DiKTa-OBuIm emits in the green (λPL = 499 nm, 1 wt% in mCP) while DiKTa-DPA-OBuIm emits in the red (λPL = 577 nm, 1 wt% in mCP). In 1 wt% mCP films, both emitters showed good photoluminescence quantum yields of 71% and 61%, and delayed life-times of 316.6 μs and 241.7 μs, respectively, for DiKTa-OBuIm and DiKTa-DPA-OBuIm, leading to reverse intersystem crossing rates of 2.85 × 103 s-1 and 3.04 × 103 s-1. Light-emitting electrochemical cells were prepared using both DiKTa-OBuIm and DiKTa-DPA-OBuIm as ac-tive emitters showing green (λmax = 534 nm) and red (λmax = 656 nm) emission, respectively. | Merve Karaman; Abhishek Kumar Gupta; Subeesh Madayanad Suresh; Tomas Matulaitis; Lorenzo Mardegan; Daniel Tordera; Henk Bolink; Sen Wu; Stuart Warriner; Ifor Samuel; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b482d98c5523ae9c1eeebc/original/ionic-multi-resonant-thermally-activated-delayed-fluorescence-emitters-for-light-emitting-electrochemical-cells.pdf |
66fae07912ff75c3a1f6faa8 | 10.26434/chemrxiv-2024-nw3nj | Graphene—Structure, and Synthesis Techniques: A Comprehensive | Graphene is a one-atom-thick layer of carbon atoms arranged in a two-dimensional honeycomb lattice. Graphene has attracted tremendous attention due to its exceptional mechanical, electrical, and thermal properties. Graphene was considered a ”wonder material” immediately after its discovery because it was deemed capa- ble of bringing drastic changes to many fields. This review gives a comprehensive overview of the atomic structure of graphene, its bonding, and the physical characteristics that have positioned this material as one of the most studied during the past two decades. Further, we discuss recent synthesis techniques including CVD and electrochemical exfoliation and detail the advantages and limitations of each with regard to scalable production. The following review further discusses the vast applications of graphene, from electronics to energy storage, involving production challenges and further improvements that could be achieved in the future. This collection is meant to serve as a starting point for researchers interested in the complications and opportunities brought about by graphene in today’s technologies. | NIZAR Ait Ben Lahcen | Materials Science; Nanoscience; Nanostructured Materials - Materials; Thin Films | CC BY 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fae07912ff75c3a1f6faa8/original/graphene-structure-and-synthesis-techniques-a-comprehensive.pdf |
675880ef085116a133f9a319 | 10.26434/chemrxiv-2024-dnkbx | Copper(II) cyclopeptides with ROS-mediated high cytotoxicity | We have synthesized two bipyridyl-based oligocationic cyclopeptides through solid phase peptide synthetic methods (SPPS) and studied their metal-binding, redox and biological properties in the presence of copper(II) ions in water media by several techniques. Remarkably, the studies performed indicate that, while the free cyclopeptides exhibit quite low or at most discrete cytotoxic properties, their Cu(II) derivatives show very high cytotoxic effects (an order of activity higher than cisplatin!) against different cancer cells lines, and, importantly, that the reason for this activity is that they can efficiently generate ROS within the cellular environment | Sonia Boga; David Bouzada; Roi Lopez-Blanco; Iria Salvadó; José Brea; María Isabel Loza; Silvia Mena; Gonzalo Guirado; Alice Santoro; Peter Faller; M. Eugenio Vázquez; Miguel Vázquez López | Biological and Medicinal Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675880ef085116a133f9a319/original/copper-ii-cyclopeptides-with-ros-mediated-high-cytotoxicity.pdf |
60c74806567dfe173bec4920 | 10.26434/chemrxiv.11839230.v1 | Improving Molecular Design by Stochastic Iterative Target Augmentation | Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient training data. In this paper, we propose a surprisingly effective self-training approach for iteratively creating additional molecular targets. We first pre-train the generative model together with a simple property predictor. The property predictor is then used as a likelihood model for filtering candidate structures from the generative model. Additional targets are iteratively produced and used in the course of stochastic EM iterations to maximize the log-likelihood that the candidate structures are accepted. A simple rejection (re-weighting) sampler suffices to draw posterior samples since the generative model is already reasonable after pre-training. We demonstrate significant gains over strong baselines for both unconditional and conditional molecular design. In particular, our approach outperforms the previous state-of-the-art in conditional molecular design by over 10% in absolute gain. | Kevin Yang; Wengong Jin; Kyle Swanson; Regina Barzilay; Tommi S Jaakkola | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74806567dfe173bec4920/original/improving-molecular-design-by-stochastic-iterative-target-augmentation.pdf |
60c74d70702a9b075618b85c | 10.26434/chemrxiv.12619883.v1 | High-Temperature-Induced Phase Transitions in Honeycomb Layered Oxides A2Ni2TeO6 (A = Na, K) | <p><b>Phase
transitions have been surmised as underlying factors behind the </b><b>exceptional electrochemical, ionic and magnetic
functionalities that have catapulted honeycomb layered oxides as superb functional
materials. As such, in this study (<i>short
communication</i>), we explore temperature elevation as an avenue for inducing
phase transitions in </b><b>h</b><b>oneycomb layered oxides adopting the composition </b><b><i>A</i></b><b><sub>2</sub></b><b><i>M</i></b><b><sub>2</sub></b><b>TeO<sub>6</sub>
(<i>A </i>= Li, Na, K; <i>M</i> =
(transition) metal). X-ray diffraction analyses indicate structural changes
occurring in Na<sub>2</sub>Ni<sub>2</sub>TeO<sub>6 </sub>hexagonal lattice
(centrosymmetric <i>P</i>6<sub>3</sub>/<i>mcm </i>→ accentric <i>P</i>6<sub>3</sub>(22) space group) with increase in temperature,
whilst in the potassium homologue (K<sub>2</sub>Ni<sub>2</sub>TeO<sub>6</sub>),
the phase transitions entail multiple changes in the lattice (from the initial
hexagonal → monoclinic (pseudo-orthorhombic) lattice at intermediate
temperatures) which reverts back to its initial hexagonal lattice with further
increase in temperatures. This study opens an alternative channel for
generating phase transition beside electrochemical alkali (re)insertion. </b><b></b></p> | Josef Rizell; Godwill Mbiti Kanyolo; Titus Masese; Yasmine Sassa; Zhen-Dong Huang | Ceramics; Multilayers; Electrochemistry; Energy Storage; Structure; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d70702a9b075618b85c/original/high-temperature-induced-phase-transitions-in-honeycomb-layered-oxides-a2ni2te-o6-a-na-k.pdf |
6758b0d6f9980725cfa85869 | 10.26434/chemrxiv-2024-d2cb2 | Synthesis, characterization and reactivity of a series of alkaline earth and rare earth iminophosphoranomethanide complexes | Herein we report the use of the methanide ligand {CH(SiMe3)P(Ph)2=NSiMe3}– (NPC-H) in the stabilization of alkaline earth and rare earth complexes. Protonolysis of the proligand with nBu2Mg or dibenzyl precursors [M(CH2Ph)2(THF)x] (M = Ca–Ba, Eu, Yb) afforded bis-methanide complexes [M(NPC-H)2(THF)x] (1-M·(THF)x; M = Mg, Eu, Yb, x = 0; M = Ca, x = 0, 1; M = Sr, x = 0, 2; M = Ba, x = 2). The same reaction protocol with SmⅡ afforded oxidation product [Sm(NPC-H)3] (2-Sm) reproducibly, which could also be obtained via salt metathesis reaction between [{K(NPC-H)}2] and SmI3(THF)3.5. This salt metathesis methodology was also extended to [REI3(THF)x] (RE = Y, La, Pr), affording tris-methanides, [RE(NPC-H)3] (2-RE; RE = Y, La, Pr). 1-M and 2-RE were characterized by multinuclear NMR, IR spectroscopy, elemental analysis, UV-vis-NIR spectroscopy and single crystal X-ray diffraction; additionally, reactivity of 1-Yb, 2-Y and 2-La as potential synthetic precursors was probed with HN(SiMe3)2 and HOC6H3tBu2-2,6. NMR studies of the 1-M family reveal some underlying changes in the M–C bond character and bonding parameters in the ligand. We also report the first 171Yb{1H} NMR chemical shift (1046.5 ppm) of an ytterbium complex with an iminophosphoranomethanide ligand. Finally, the electronic structure of 1-Eu was studied by means of electron paramagnetic resonance and ab initio calculations. | Matthew Stevens; Yu Liu; Rebecca Hawker; Luis Lezama; Daniel Reta; Fabrizio Ortu | Inorganic Chemistry; Lanthanides and Actinides; Main Group Chemistry (Inorg.); Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6758b0d6f9980725cfa85869/original/synthesis-characterization-and-reactivity-of-a-series-of-alkaline-earth-and-rare-earth-iminophosphoranomethanide-complexes.pdf |
66cf047020ac769e5f1a29d2 | 10.26434/chemrxiv-2024-vs03b | Au-Catalyzed Unusual Aerobic Dehydrogenative Aromatization to m-Phenylenediamine Derivatives via Product Selectivity Control | m-Disubstituted arenes are important in various fields but difficult to be directly synthesized by the classical methods in the case of two electron-donating substituents due to the o,p-orientation. Dehydrogenative aromatization from non-aromatic cyclohexenone motifs and nucleophiles via 1,2- and 1,4-addition to produce m-disubstituted arenes is promising as the novel process overcoming the intrinsic problems derived from using aromatic compounds as the substrates; however, there are no reports on tandem (one-step) synthesis via simultaneous 1,2- and 1,4-addition or m-phenylenediamine derivative synthesis via dehydrogenative aromatization because of the quite difficult product selectivity control. Here, by utilizing unique dehydrogenation catalysis of CeO2-supported Au nanoparticles, we have developed tandem aerobic oxidation to various m-phenylenediamine derivatives via selective dehydrogenative aromatization from cyclohexenone motifs and secondary amines. In addition, the product selectivity switch to enaminones or N,N-disubstituted anilines was also achieved by tuning reaction conditions. | Heizo Kimura; Takafumi Yatabe; Kazuya Yamaguchi | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cf047020ac769e5f1a29d2/original/au-catalyzed-unusual-aerobic-dehydrogenative-aromatization-to-m-phenylenediamine-derivatives-via-product-selectivity-control.pdf |
64a2905bba3e99daef6f87fd | 10.26434/chemrxiv-2023-6p49m | Multiscale Mechanochemical Modeling of Spiropyran-Merocyanine Isomerization in Linear PMMA Polymers | Mechanochemical reactions in functional polymers occur when mechanical forces cause labile bonds, e.g., in mechanophores, to break. While it is known that these reactions require a critical amount of force, the structure of the polymer network strongly affects the efficiency of force transduction. Experimentally it is challenging to track the force transmission along the polymer backbone. Despite the availability of quantum mechanochemical tools, the information on force transmission from the bulk to a local scale is still limited. Here we introduce a multiscale mechanochemical model that establishes a connection between bulk deformation and mechanophore activation. This is achieved by combining the quantum mechanical (QM) COnstrained Geometries simulate External Force (COGEF) method with cost-efficient molecular mechanical (MM) simulations. Based on a new parameterization of the well-known Spiropyran-Merocyanine (SP-MC) isomerization under stretching forces, we simulate mechanophore activation inside a realistic poly(methyl methacrylate) (PMMA) network at different strain rates and loading modes. The results are discussed in terms of stress-strain behavior of the system, influence of temperature and mechanochemical activity. The developed multiscale simulation model paves the way for further investigations on more complex mechanophore-doped polymer networks, subjected to external load. | Sourabh Kumar; Baris Demir; Lucio Colombi Ciacchi; Tim Neudecker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a2905bba3e99daef6f87fd/original/multiscale-mechanochemical-modeling-of-spiropyran-merocyanine-isomerization-in-linear-pmma-polymers.pdf |
612891ca65db1eb5cea56804 | 10.26434/chemrxiv-2021-r0xdb | Mechanochemical Grignard Reactions with Gaseous CO2 and Sodium Methyl Carbonate | Grignard reactions invert the intrinsic electrophilic reactivity of organohalides to form C–C bonds with other electrophiles. With carbon dioxide (CO2) as electrophile carboxylic acids can be prepared. Although scattered examples of mechanochemical reactions with CO2 have been reported, its synthetic application as C1-synthon has remained underexplored. Here, we developed a one-pot three-step protocol for the preparation of Grignard reagents from organobromides in a ball mill and their subsequent reaction with gaseous CO2 or sodium methyl carbonate to provide aryl and alkyl carboxylic acids in up to 82% yield. Noteworthy are the short reaction times and the significantly reduced solvent amount [2.0 equiv. for liquid assisted grinding (LAG) conditions]. Unexpectedly, aryl bromides with methoxy substituents lead to symmetric ketones as major products. | Victoria Pfennig; Romina Villella; Julia Nikodemus; Carsten Bolm | Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612891ca65db1eb5cea56804/original/mechanochemical-grignard-reactions-with-gaseous-co2-and-sodium-methyl-carbonate.pdf |
66635c55409abc0345e357d2 | 10.26434/chemrxiv-2024-5837l | In silico exploration of pyrocannabinoid interactions with key protein targets | Cannabinoids, particularly those derived from cannabis, have attracted considerable attention in recent years for their therapeutic potential in treating various diseases and ailments. In this study, we identified cannabinoid byproducts that result from the combustion of cannabidiol (CBD) - henceforth referred to as pyrocannabinoids - and employed molecular docking simulations to investigate their interactions with key protein targets implicated in different physiological processes. Specifically, we focused on peroxisome proliferator-activated receptor gamma (PPAR-γ), p21-activated kinase 1 (PAK1), CB1, CB2, and GPR119 proteins, elucidating the binding modes and affinities of pyrocannabinoid byproducts to these receptors. This investigation was done in collaboration with Real Isolates LLC. Our findings revealed diverse ligand-protein interactions, with some pyrocannabinoids displaying favorable binding energies and stable ligand-protein complexes. However, variations in binding affinities across different proteins underscored the complex pharmacological profiles of the pyrocannabinoids. Furthermore, the prediction of adsorption, distribution, metabolism, excretion and toxicity (ADMET) properties highlighted both promising and concerning aspects of cannabinoid pharmacokinetics, emphasizing the need for thorough preclinical evaluation. Additionally, our investigation into potential metabolic sites using cytochrome P450 enzymes provided insights into cannabinoid metabolites. Overall, our study contributes to the understanding of pyrocannabinoid pharmacology and informs the rational design of pyrocannabinoid-based therapeutics. Further experimental validation is warranted to translate these findings into clinically relevant applications. | Giovanni Ramirez; Tesfay Tesfatsion; Monica Pittiglio; Kyle Ray; Andrew Westerkamp; Westley Cruces | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66635c55409abc0345e357d2/original/in-silico-exploration-of-pyrocannabinoid-interactions-with-key-protein-targets.pdf |
60c74e639abda28356f8d623 | 10.26434/chemrxiv.9947228.v4 | On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units | The thermo-structural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of defects in MOF structures during synthesis. In this paper, factors affecting the flexibility of MIL-101(Cr) half-secondary building units (half-SBUs) are evaluated in solution using enhanced sampling methods. In particular, entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs are calculated in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). This analysis leads to the observation that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, the role of enthalpy and entropy in the conformational rearrangement of an SBU is investigated in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. This analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units and highlights the significant impact they have on the relative stability of crystal-like and non-crystal-like conformers. | Loukas Kollias; David Cantu; Vassiliki-Alexandra Glezakou; Roger Rousseau; Matteo Salvalaglio | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e639abda28356f8d623/original/on-the-role-of-enthalpic-and-entropic-contributions-on-the-conformational-free-energy-landscape-of-mil-101-cr-structural-building-units.pdf |
64dbb04769bfb8925afa0d54 | 10.26434/chemrxiv-2023-j1bwd | Direct Decarboxylation of Trifluoroacetates Enabled by Iron Photocatalysis | Trifluoroacetates are the most abundant and accessible sources of trifluoromethyl groups, which are key components in pharmaceuticals and agrochemicals. The generation of trifluoromethyl reactive radicals from trifluoroacetates requires their decarboxylation, which is hampered by their high oxidation potential. This constitutes a major challenge for redox-based methods, because of the need to pair the redox potentials with trifluoroacetate. Here we report a strategy based on iron photocatalysis to promote the direct photodecarboxylation of trifluoroacetates that displays reactivity features that escape from redox limitations. Our synthetic design has enabled the use of trifluoroacetates for the trifluoromethylation of more easily oxidizable organic substrates, offering new opportunities for late-stage derivatization campaigns using chemical feedstocks, Earth-abundant catalysts, and visible-light. | Sara Fernandez-Garcia; Veronika O. Chantzakou; Francisco Julia-Hernandez | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dbb04769bfb8925afa0d54/original/direct-decarboxylation-of-trifluoroacetates-enabled-by-iron-photocatalysis.pdf |
652a845c45aaa5fdbbfe98a1 | 10.26434/chemrxiv-2023-3lv53 | Topology switch between AIE and ACQ: a balance of substituents | Intermolecular interactions appearing in solution, aggregates and solid state are known to affect the photophysical properties of fluorophores, leading either to emission quenching or to emission enhancement upon aggregation. The novel strategy for the aggregation-induced fluorescence change based upon the subtle balance of the intermolecular and intramolecular charge transfer in the benzothiazole derivatives is presented here, leading to the extremely bright aggregates of the compounds dark in solution or vice versa. The introduction of the two different mild substituents into the fluorophore core results in two regioisomers exhibiting the same crystal packing, but extremely different behavior upon aggregation. Such an approach opens a simple way of controlling the AIE/ACQ behavior of small molecules in the wide range of FQY values. | Patryk Rybczyński; Tadeusz Muzioł; Anna Kaczmarek-Kędziera; Borys Osmialowski | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.); Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652a845c45aaa5fdbbfe98a1/original/topology-switch-between-aie-and-acq-a-balance-of-substituents.pdf |
61ea283b6afbefe8726c20db | 10.26434/chemrxiv-2022-1fcdk | A Polarizable Cationic Dummy Metal Ion Model | A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is described for molecular dynamics simulations of ions in condensed phases. Polarization effects are introduced by the electronegativity equalization model (EEM) method where charges on the metal ion and its dummy atoms can respond to the environment. This approach allows us to enhance the original fixed charge CDA model where the charge distribution can adapt to the local solvent structure. To illustrate the new CDApol model, we examined properties of the Zn2+ ion in aqueous solution. Polarizable model and Lennard-Jones parameters were refined for an octahedrally coordinated Zn2+ CDA to reproduce thermodynamic and geometrical properties. Using this locally polarizable model, we were able to obtain the experimental hydration free energy, ion-oxygen distance and coordination number coupled with the standard 12-6 Lennard-Jones model. This model can be used in myriad other applications where local polarization and charge transfer is important. | Ali Rahnamoun; Kurt A. O'Hearn; Mehmet Cagri Kaymak; Zhen Li; Kenneth M. Merz, Jr.; Hasan Metin Aktulga | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ea283b6afbefe8726c20db/original/a-polarizable-cationic-dummy-metal-ion-model.pdf |
612de54f27d9066dee7a0a46 | 10.26434/chemrxiv-2021-cjw3m | A New Formula Assignment Algorithm for the Deuterium Labeled Ultrahigh-Resolution Mass Spectrometry: Implications to the Formation Mechanism of Halogenated Disinfection Byproducts | The ultrahigh-resolution mass spectrometry (UHR-MS) coupled with isotope labeling is of increasing attentions in elucidating the transform mechanisms of dissolved organic matter (DOM). However, there is a paucity of automated formula assignment algorithm applicable to halogenated disinfection byproducts (Xn-DBPs), particurally for iodinated organic compounds, and deuterated DOM . Herein, for the first time, we have developed a novel formula assignment algorithm based on deuterium-labeled UHR-MS, namely FTMSDeu, and the algorithm was applied to determine precursor molecules of Xn-DBPs and evaluate the relative contribution of electrophilic addition and electrophilic substitution reactions in Xn-DBPs formation according to the hydrogen/deuterium exchange of DOM molecules. Furthermore, tandem mass spectrometry with homologous-based network analysis was employed to validate the formula assignment accuracy (41%) of FTMSDeu for iodinated disinfection byproducts (In-DBPs). And the remaining In-DBPs compounds were assigned with the empirical rule of minimum number of non-oxygen heteratoms. The electrophilic substitution accounted for 82%-98%, 71%-89%, and 43%-45% of Xn-DBPs formation for Xn-DBPs containing chlorine, bromine, and iodine, respectively, manifesting the dominant role of electrophilic substitution in chlorine disinfection under conditions of low bromine and iodine concentrations. The absence of presumed Xn-DBPs precursors in some treatments in this study also suggests that Xn-DBPs formation include secondary reactions (e.g., oxidation, hydrolysis) in addition to electrophilic addition and/or substitution of halogens. These findings highlight the significance of isotopically labeled UHR-MS techniques in revealing the transformation of DOM in natural and engineered systems. | Qing-Long Fu; Manabu Fujii; Akari Watanabe; Eunsang Kwon | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612de54f27d9066dee7a0a46/original/a-new-formula-assignment-algorithm-for-the-deuterium-labeled-ultrahigh-resolution-mass-spectrometry-implications-to-the-formation-mechanism-of-halogenated-disinfection-byproducts.pdf |
6193b868b039f23729a6e889 | 10.26434/chemrxiv-2021-cvfhh | Eu- and Tb-adsorbed Si3N4 and Ge3N4:
Tuning the colours with one luminescent host
| Phosphor-converted white light-emitting diodes (pc-LEDs) are emerging as an indispensable solid-state light source for the next generation lighting industry and display systems due to their unique properties. Nitrides with their wide-ranging applicability due to their intriguing structural diversity, their auspicious chemical and physical properties represent an essential component in industrial and materials applications.
Here, we present the successful adsorption of Eu and Tb at the grain boundaries of bulk β-Si3N4 and β-Ge3N4 by a succeeding combustion synthesis. The adsorption of europium and terbium and the synergic combination of both resulted in intriguing luminescence properties of all compounds (red, green, orange and yellow). Especially the fact that one host can deliver different colours renders Eu,Tb-β-M3N4 (M= Si, Ge) as prospective chief components for future light emitting diodes (LEDs).
For the elucidation of the RE adsorption on the electronic properties of β-Si3N4 and β-Ge3N4, Mott-Schottky (MS) measurements were conducted for the bare and RE adsorbed samples. Further insight on the electronic structure of β-Si3N4 and β-Ge3N4 were obtained via density functional theory (DFT) computations.
| Cordula Braun; Liuda Mereacre; Zheng Chen; Adam Slabon; David Vincent; Xavier Rocquefelte; Jean-Francois Halet | Materials Science; Inorganic Chemistry; Optical Materials; Lanthanides and Actinides; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6193b868b039f23729a6e889/original/eu-and-tb-adsorbed-si3n4-and-ge3n4-tuning-the-colours-with-one-luminescent-host.pdf |
64fecb59b6ab98a41c3d9c0f | 10.26434/chemrxiv-2023-mq2p7 | Binding modes of the KRAS(G12C) inhibitors GDC-6036 and LY3537982 revealed by all atom molecular dynamics simulations | Almost 80 co-crystal structures of KRAS switch-II pocket (SII-P) targeting inhibitors are currently available in the RCSB Protein Data Bank. These publicly available structures are invaluable tools that have led to a more in-depth understanding of KRAS SII-P pocket, which is crucial for targeted drug design efforts. The binding modes (co-crystal structures) of two KRAS(G12C) inhibitors that have advanced to the clinical trials, GDC-6036 (divarasib) and LY3537982, are currently unavailable. Here, we reveal the putative binding modes of these two G12C inhibitors by utilizing the available structural data of analogous compounds and molecular dynamics (MD) simulations (total simulation time of 200 µs). Furthermore, we analyzed the energetical barrier related to their atropisomer interconversion by quantum mechanics (QM) calculations. Finally, biochemical assays supported our in silico observations, revealing remarkably high affinity for both inhibitors towards KRAS(G12C), which is, however, sacrificed by a co-mutation at Tyr96 (GDC-6036, LY3537982) or His95 (GDC-6036). | Renne Leini; Kari Kopra; Tatu Pantsar | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fecb59b6ab98a41c3d9c0f/original/binding-modes-of-the-kras-g12c-inhibitors-gdc-6036-and-ly3537982-revealed-by-all-atom-molecular-dynamics-simulations.pdf |
639c9b25ff46517bf92cf363 | 10.26434/chemrxiv-2022-l6d45-v2 | Green and Potent: A Waste-Free and Skin-Compatible CuI Coating on Flexible Substrates with Rapid Antiviral and Antimicrobial Kinetics | Infectious pathogens, such as SARS-CoV-2, can remain viable on common fabrics for days, which poses a significant risk of fomite transmission in the community. We herein report a green method to fabricate copper iodide (CuI) coating on flexible cotton fabrics, attaining highly potent antiviral and antimicrobial efficacy with rapid biocidal kinetics. Only water was used as the processing solvent for the in situ formation of CuI microparticles on the coating substrate, and the unconsumed reagents can be fully recovered and recycled, making it a sustainable, economically viable, and waste-free technology promising for industrial scale-up. More remarkably, in just 2 minutes, the coating is able to inactivate over 99.9% and 99.9999% of murine hepatitis coronavirus and bacteriophage P22 as models for the enveloped and non-enveloped viral species, respectively. It is also capable of eradicating various bacteria and fungus with 3.5 – 7.4 log reductions within 2 – 5 minutes. The coating’s robust durability and skin compatibility were also experimentally demonstrated, imparting a great potential to this simple yet powerful coating approach for real-world applications, especially in future infectious disease outbreaks like Covid-19. | Adrielle Xianwen Chen; Huan Yi Lau; Jye Yng Teo; Yanming Wang; Darryl Zhi Yong Choong; He-Kuan Luo; Yi Yan Yang; Ning Li | Materials Science; Chemical Engineering and Industrial Chemistry; Coating Materials; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639c9b25ff46517bf92cf363/original/green-and-potent-a-waste-free-and-skin-compatible-cu-i-coating-on-flexible-substrates-with-rapid-antiviral-and-antimicrobial-kinetics.pdf |
60c73fc9ee301c1615c78978 | 10.26434/chemrxiv.6987248.v4 | Microstructure determines water and salt permeation in commercial ion exchange membranes | Ion exchange membrane (IEM) performance in electrochemical processes such as fuel cells, redox flow batteries, or reverse electrodialysis (RED) is typically quantified through membrane selectivity and conductivity, which together determine the energy efficiency. However, water and co-ion transport (i.e., osmosis and salt diffusion / fuel crossover) also impact energy efficiency by allowing uncontrolled mixing of the electrolyte solutions to occur. For example, in RED with hypersaline water sources, uncontrolled mixing consumes 20-50% of the available mixing energy. Thus, in addition to high selectivity and high conductivity, it is desirable for IEMs to have low permeability to water and salt in order to minimize energy losses. Unfortunately, there is very little quantitative water and salt permeability information available for commercial IEMs, making it difficult to select the best membrane for a particular application. Accordingly, we measured the water and salt transport properties of 20 commercial IEMs and analyzed the relationships between permeability, diffusion and partitioning according to the solution-diffusion model. We found that water and salt permeance vary over several orders of magnitude among commercial IEMs, making some membranes better-suited than others to electrochemical processes that involve high salt concentrations and/or concentration gradients. Water and salt diffusion coefficients were found to be the principal factors contributing to the differences in permeance among commercial IEMs. We also observed that water and salt permeability were highly correlated to one another for all IEMs studied, regardless of polymer type or reinforcement. This finding suggests that transport of mobile salt in IEMs is governed by the microstructure of the membrane, and provides clear evidence that mobile salt does not interact strongly with polymer chains in highly-swollen IEMs. <br /> | Ryan Kingsbury; Shan Zhu; Sophie Flotron; Orlando Coronell | Polymer chains; Electrochemical Analysis; Transport Phenomena (Chem. Eng.); Energy Storage; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fc9ee301c1615c78978/original/microstructure-determines-water-and-salt-permeation-in-commercial-ion-exchange-membranes.pdf |
60c7418d842e65304ddb1ee3 | 10.26434/chemrxiv.8063654.v1 | Using Cost-Effective Density Functional Theory (DFT) to Calculate Equilibrium Isotopic Fractionation for Reactions Involving Large Organic Molecules | With an eye towards applications in environmental sciences, the factors impacting the accuracy of calculating equilibrium isotopic fractionation α are considered. α is calculated from the reduced partition function relation β via the vibrational frequencies. Density-fitting (DF, or resolution of the identity – RI) is a popular tool to help reduce the cost of DFT energy calculations, and its impact on the accuracy of calculating vibration frequencies was determined to be negligible provided one uses a sufficiently large auxiliary density-fitting basis set. Using a set of high-accuracy fractionations for a series of small molecules, the accuracy of several density-functional theory (DFT) exchange–correlation functionals in calculating β was considered. Based on these results, a selection of functionals was tested against two benchmark databases of isotopic fractionations that were generated, one for D/H fractionation (HEIF11) and one for heavy-atom fractionation (CNOEIF35). It was found that, with the def2-TZVP basis set, O3LYP had the lowest mean absolute deviation (21‰ and 3.9‰, respectively), but the GGA/meta-GGA functionals τHCTH<sub>D3BJ</sub>, τHCTH and HCTH have almost similar performances (22‰ and 4.1‰, respectively, for τHCTH<sub>D3BJ</sub>). In this work we provide a roadmap to predict for equilibrium isotopic fractionations of large organic molecules, and constrain their potential uncertainties. | Mark Iron; Jonathan Gropp | Environmental Science; Geochemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7418d842e65304ddb1ee3/original/using-cost-effective-density-functional-theory-dft-to-calculate-equilibrium-isotopic-fractionation-for-reactions-involving-large-organic-molecules.pdf |
67ac679c6dde43c9088b2842 | 10.26434/chemrxiv-2025-t5whw | Organic–inorganic hybrid solid lubricants based on 2D silver thiolate coordination polymers featuring precise interlayers | Layered solid lubricants, such as molybdenum disulfide, are widely used to reduce friction and wear at moving contact surfaces. However, their limited structural variety makes it challenging to tailor their lubrication properties for specific applications. This study demonstrated the potential of two-dimensional silver thiolate (AgSR) coordination polymers, which feature distinctive organic–inorganic lamellar crystal structures, as tunable solid lubricants based on the precise structural design. X-ray diffraction measurements showed that various AgSR compounds with linear alkylthiolato and para-substituted benzenethiolato ligands formed layered structures with high crystallinity. Ball-on-disk friction tests were performed on powder-supported specimens to assess the solid lubricating properties of AgSR. The AgSRupported specimens with alkylthiolato ligands demonstrated a coefficient of friction (COF) of approximately 0.1, considerably lower than that of the well-known layered materials, MoS2 and alkylammonium-intercalated mica. This exceptional lubricity of AgSR is likely attributed to their unique interlayer structures, which exhibit minimal interdigitation of alkyl chains. Scanning electron microscopy and energy-dispersive X-ray spectroscopy analyses of the worn surfaces of the AgSRupported specimens revealed that AgSR compounds create lubricating films on the sliding substrates. Furthermore, for a series of AgSR compounds featuring para-substituted benzenethiolato ligands, the COF values were highly affected by the functional groups at the para position, which affected their interlayer interactions. Strong interlayer interactions, such as hydrogen bonds, resulted in considerable increases in the COF to approximately 0.7, suggesting that the lubrication properties of AgSR are derived from the ease of cleavage in their layered crystal structures. These findings imply that AgSR offers considerable advantages over traditional inorganic layered materials for the tailored development of custom solid lubricants. | Ren Muramatsu; Hiroshi Eguchi; Kenji Nagata | Inorganic Chemistry; Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ac679c6dde43c9088b2842/original/organic-inorganic-hybrid-solid-lubricants-based-on-2d-silver-thiolate-coordination-polymers-featuring-precise-interlayers.pdf |
664de6a821291e5d1df74ac0 | 10.26434/chemrxiv-2024-bmk3w | Neural Template Extraction - Learning the Language of SMIRKS | Transformer-based models have been successful at learning the language of chemical reactions. Here we show that natural language processing can be well applied to learn and extract the rules describing chemical reactions. Compared to previous approaches in chemical language modelling, we show that the model can learn generalised patterns composed of atom types, properties, logical operators, and internally consistent mapping between the components. Furthermore, we show that without prior knowledge of the reaction’s atom mapping, the models achieve up to 76 % accuracy for the task of rule extraction. This paves the way for using chemical language models for writing the rules of chemistry for tasks such as synthesis planning. | Amol Thakkar; Teodoro Laino | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664de6a821291e5d1df74ac0/original/neural-template-extraction-learning-the-language-of-smirks.pdf |
60c757d0842e654c3bdb476f | 10.26434/chemrxiv.14465343.v1 | A High-k and Low Energy-disorder Spiro-nanopolymer Semiconductor | <p></p><p>Gridization become the rising toolbox of cross-scale chemistry
that update the organic pi-conjugated polymers into nano-polymers with a
nano-scale persistence length that offer the cornerstone to overcome the
molecular limitation for the high-performance fourth-generation semiconductors.
In this work, spiro-polygridization indeed exhibit the ultralong persistence
length of ~41 nm with the extraordinary semiconducting behaviors such as a hole
mobility of 3.94 × 10<sup>-3</sup> cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup> and
an ultralow energy disorder (<50 meV) as well as the high dielectric
constant (<i>k</i> = 8.43). Gridochemistry open a way to organic intelligent
multimedia facing organic intelligence.</p><p></p> | Dongqing Lin; Wenhua Zhang; Hang Yin; Haixia Hu; Chaoyang Dong; Yongxia Wang; Xinmiao Xie; Le Wang; Hongkai Hu; Yongxia Yan; Haifeng Ling; Jin’an Liu; Yue Qian; Lei Tang; Linghai Xie; Hao Zhang; He Zhang; Shasha Wang; Ying Wei; Xuefeng Guo; Dan Lu; Wei Huang | Carbon-based Materials; Nanostructured Materials - Materials; Optical Materials; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757d0842e654c3bdb476f/original/a-high-k-and-low-energy-disorder-spiro-nanopolymer-semiconductor.pdf |
60c75663bb8c1a525e3dc5fb | 10.26434/chemrxiv.14222261.v1 | Breaking the Upper Bound of Siloxane Uptake: Metal-Organic Frameworks as an Adsorbent Platform | Biogas, regarded as a promising renewable energy source, still needs to be upgraded. This calls for the removal of the most prominent contaminants, among others the octamethylcyclotetrasiloxane (D4) molecule. Herein, high throughput computational screening in tandem with synthesis and adsorption testing revealed the hydrophobic Zr-MOF PCN-777 as an optimal D4 adsorbent with record gravimetric (1.8 g/g) and volumetric (0.49 g/cm3) uptakes, alongside with a reversible and fast adsorption/desorption process, good cyclability and easy regeneration. This MOF was demonstrated to encompass an ideal combination of mesoporous cages and chemical functionality to enable an optimal packing of the siloxane molecules and their efficient removal while maintaining the process highly reversible thanks to moderately high host/guest interactions. This work highlights the efficacy of an integrated workflow for accelerating adsorbent selection for a desired application, spanning the entire pipeline from method validation to computational screening, synthesis and adsorption testing towards the identification of the optimal adsorbents.<br /> | Ezgi Gulcay; Paul Iacomi; Youngsang Ko; Jong-San Chang; Guillaume Rioland; Sabine Devautour-Vinot; Guillaume Maurin | Hybrid Organic-Inorganic Materials; Chemoinformatics - Computational Chemistry; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75663bb8c1a525e3dc5fb/original/breaking-the-upper-bound-of-siloxane-uptake-metal-organic-frameworks-as-an-adsorbent-platform.pdf |
63f6145b32cd591f12509aab | 10.26434/chemrxiv-2023-xs7p7 | Position of Gold Dictates the Photophysical and Photocatalytic Properties of Cu2O in Cu2O/Au Multicomponent Nanoparticles | Utilizing solar radiation for driving chemical reactions has been of great interest in the last decade. Although Cu2O nanocrystals as a low-cost, abundant, and tailorable photocatalyst are promising candidates to provide a platform for solar-driven applications, their photophysical properties are affected by the limited charge carrier mobility. This paper focuses on the more efficient utilization of the UV light-excited charge carriers in cuprous oxide by preparing different heterostructures with gold. While keeping the size, shape as well as overall composition of the heterostructures identical, the realization of the gold component is varied: either nanograins are created at the surface of the Cu2O nanooctahedra or nanorods are embedded in their interior. The effect of the morphology and the semiconductor-metal contact on the optical and photocatalytic properties is investigated in-detail by spectroscopy, spectrofluorometry, imaging techniques, X-ray diffractometry, and photoelectron spectroscopy extended with optical simulations and single-particle spectroscopy measurements. In terms of particle stability and photocatalytic activity, gold-decorated Cu2O nanooctahedra show superior properties. The comprehensive comparison of the multicomponent nanoparticles underlines the importance of the nanoscale design (including composition, morphology, and surface chemistry), which utilizes the photoexcited carriers in the semiconductor without injecting hot electrons from the metal. | Dávid Kovács; András Deák; György Z. Radnóczi; Zsolt E. Horváth; Attila Sulyok; Róbert Schiller; Ottó Czömpöly; Dániel Zámbó | Physical Chemistry; Materials Science; Nanoscience; Optical Materials; Nanostructured Materials - Nanoscience; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f6145b32cd591f12509aab/original/position-of-gold-dictates-the-photophysical-and-photocatalytic-properties-of-cu2o-in-cu2o-au-multicomponent-nanoparticles.pdf |
60d2ff53e21133c355e05f45 | 10.26434/chemrxiv-2021-t1817 | Carrier Protein-Free Chemo-Enzymatic Synthesis of Arylomycin A2 and Structural Characterization of the Cytochrome P450 AryC | The functional and structural evaluation of AryC, the cytochrome P450 performing biaryl coupling in biosynthetic arylomycin assembly, and its application in the chemo-enzymatic synthesis of arylomycin A2 is described. AryC efficiently converts free substrates without the requirement of any protein interaction partner, likely enabled by a strongly hydrophobic cavity at the surface of AryC pointing to the substrate tunnel. The resulting reactivity of AryC is unprecedented in cytochrome P450-mediated biaryl construction in non-ribosomal peptides, in which PCP-tethering so far was crucial both in vivo and in vitro. Our work thus provides a basis for the development of general biocatalytic platforms for the efficient biocatalytic synthesis of biaryl peptide antibiotics. | Hülya Aldemir; Shuangjie Shu; Francoise Schaefers; Hanna Hong; René Richarz; Sabrina Harteis; Manuel Einsiedler; Tobias M. Milzarek; Sabine Schneider; Tobias A. M. Gulder | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d2ff53e21133c355e05f45/original/carrier-protein-free-chemo-enzymatic-synthesis-of-arylomycin-a2-and-structural-characterization-of-the-cytochrome-p450-ary-c.pdf |
66b6662fc9c6a5c07aa8b740 | 10.26434/chemrxiv-2024-2cf6g-v3 | Structure-activity relationship of inositol thiophosphate analogs as allosteric activators of Clostridioides difficile toxin B | Clostridioides difficile is a bacterium that causes life-threatening intestinal infections. Infection symptoms are mediated by a toxin secreted by the bacterium. Toxin pathogenesis is modulated by the intracellular molecule, inositol-hexakisphosphate (IP6). IP6 binds to a cysteine protease domain (CPD) on the toxin, inducing auto-proteolysis, which liberates a virulence factor in the cell cytosol. We developed second-generation IP6 analogs designed to induce auto-proteolysis in the gut lumen, prior to toxin uptake, circumventing pathogenesis. We synthesized a panel of thiophosphate-/sulfate-containing IP6 analogs, and characterized their toxin binding affinity, auto-proteolysis induction and cation interactions. Our top candidate was soluble in extracellular cation concentrations, unlike IP6. The IP6 analogs were more negatively charged than IP6, which improved affinity and stabilization of the CPD, enhancing toxin auto-proteolysis. Our data illustrate the optimization of IP6 with thiophosphate biomimetics which are more capable of inducing toxin auto-proteolysis than the native ligand, warranting further studies in vivo. | Rebecca Cummer; Félix Grosjean; Raphaël Bolteau; Seyed Ehsan Vasegh; Simon Veyron; Liam Keogh; Jean-François Trempe; Bastien Castagner | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b6662fc9c6a5c07aa8b740/original/structure-activity-relationship-of-inositol-thiophosphate-analogs-as-allosteric-activators-of-clostridioides-difficile-toxin-b.pdf |
60c74607567dfea352ec4575 | 10.26434/chemrxiv.10325204.v1 | Titanium-Mediated Catalytic Hydrogenation of Monocyclic and Polycyclic Arenes | <p>Two electron-reduction of the Ti(IV) guanidinate complex (Im<sup>Dipp</sup>N)(<sup>Xyket</sup>guan)TiCl<sub>2</sub> gives (η<sup>6</sup>-Im<sup>Dipp</sup>N)(<sup>xyket</sup>guan)Ti (1<sup>intra</sup>) and (Im<sup>Dipp</sup>N)(<sup>Xyket</sup>guan)Ti(η<sup>6</sup>-C<sub>6</sub>H<sub>6</sub>) (1<sup>inter</sup>) (<sup>xyket</sup>guan = [(<sup>t</sup>BuC=N)C(NXylyl)<sub>2</sub>]<sup>-</sup>, Xylyl = 2,5-dimethylphenyl) in the absence or presence of benzene, respectively. These complexes have been found to hydrogenate monocyclic and polycyclic arenes under relatively mild conditions (150 psi, 80 °C) – the first example of catalytic, homogeneous arene hydrogenation with TON > 1 by a Group IV system.</p> | Alejandra Gomez-Torres; J. Rolando Aguilar-Calderón; Angela M. Encerrado-Manriquez; Maren Pink; Alejandro
J. Metta-Magaña; Wen-Yee Lee; Skye Fortier | Homogeneous Catalysis; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74607567dfea352ec4575/original/titanium-mediated-catalytic-hydrogenation-of-monocyclic-and-polycyclic-arenes.pdf |
60c747420f50db40dc396583 | 10.26434/chemrxiv.11558202.v1 | Effect of an Al(III) Complex on the Regio- and Stereoisomeric Formation of Bicyclic Organic Carbonates | Valorization of carbon dioxide into organic
molecules using catalytic approaches has witnessed an upsurge in recent years.
Here, the influence of an Al(III) aminotriphenolate complex on the regio- and
stereo-chemical features of the coupling between carbon dioxide and a cyclic
epoxy alcohol has been studied. Three distinct bicyclic carbonate products were
produced from a single starting material depending on the catalytic conditions.
The proposed carbonate configurations were examined by solution and solid phase
techniques including NMR spectroscopic and X-ray crystallographic analyses.
Control experiments combined with DFT calculations provide a rationale for the
distinct catalytic manifolds observed in the presence and absence of the
Al(III) complex. | Cristina Maquilón; Bart Limburg; Victor Laserna; Diego Garay-Ruiz; Joan González Fabra; Carles Bo; Marta Martinez Belmonte; Eduardo C. Escudero Adán; Arjan. W. Kleij | Stereochemistry; Kinetics and Mechanism - Inorganic Reactions; Organometallic Compounds; Base Catalysis; Homogeneous Catalysis; Organocatalysis; Catalysis; Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747420f50db40dc396583/original/effect-of-an-al-iii-complex-on-the-regio-and-stereoisomeric-formation-of-bicyclic-organic-carbonates.pdf |
64f427a6dd1a73847f11ec02 | 10.26434/chemrxiv-2023-0bwdp | Molecular Additives Improve Selectivity of CO2 Photoelectrochemical Reduction over Gold Nanoparticles on Gallium Nitride | Photoelectrochemical CO2 reduction (CO2R) is an appealing solution to convert carbon dioxide into higher-value products. However, CO2R in aqueous electrolytes suffers from poor selectivity due to the competitive hydrogen evolution reaction dominant on semiconductor surfaces in aqueous electrolytes. We demonstrate that functionalizing gold/p-type gallium nitride devices with a film derived from diphenyliodonium triflate suppresses hydrogen generation from 90% to 18%. As a result, we observe an increase in the Faradaic efficiency and partial current density for carbon monoxide by 50% and 3x, respectively. Furthermore, we demonstrate through optical absorption measurements that the molecular film employed herein, regardless of thickness, does not affect the photocathode’s light absorption and, therefore, photocurrent. Together, this study provides a rigorous platform to elucidate catalytic structure-property relationships to enable engineering of active, stable, and selective materials for photoelectrochemical CO2 reduction. | Aisulu Aitbekova; Nicholas Watkins; Matthias Richter; Phillip Jahelka; Jonas Peters; Theodor Agapie; Harry Atwater | Catalysis; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f427a6dd1a73847f11ec02/original/molecular-additives-improve-selectivity-of-co2-photoelectrochemical-reduction-over-gold-nanoparticles-on-gallium-nitride.pdf |
6254f72cef2ade1d4f2c53b1 | 10.26434/chemrxiv-2022-t31fm | Regioselective Boracarboxylation of α-Substituted Vinyl Arenes | An experimental study of the effect of CO2 pressure on the copper(I)-catalyzed boracarboxylation of α-substituted vinyl arenes is reported. Preliminary experiments using ICyCuCl catalyst (ICy = 1,3-bis(cyclohexyl)imidazol-2-ylidine) showed that boracarboxylation of tert-butylstyrene can be achieved in 30 minutes at modest CO2 pressure (3-6 atm) as opposed to 24-36 hours at atmospheric pressure. Due to increased substrate sterics that allowed catalytic reduction of CO2 to compete kinetically, boracarboxylation of a-methyl styrene, even at modest CO2 pressures, gave poor yields. Low CO2 pressure and SIMesCuCl catalyst (SIMes = 1,3-bis(2,4,6-trimethylphenyl)imidazol-4,5-dihydro-2-ylidine) provided moderate to good yields of an electronically and sterically diverse group of quaternary carboxylic acid products featuring a -boronic ester functional group. | Steven W. Knowlden; Brian V. Popp | Organometallic Chemistry; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6254f72cef2ade1d4f2c53b1/original/regioselective-boracarboxylation-of-substituted-vinyl-arenes.pdf |
6604816ae9ebbb4db9b5ddda | 10.26434/chemrxiv-2023-lnzvr-v2 | In silico screening of LRRK2 WDR domain inhibitors using deep docking and free energy simulations | The Critical Assessment of Computational Hit-Finding Experiments (CACHE) Challenge series is focused on identifying small molecule inhibitors of protein targets using computational methods. Each challenge contains two phases, hit-finding and follow-up optimization, each of which is followed by experimental validation of the computational predictions.. For the CACHE Challenge #1, the Leucine-Rich Repeat Kinase 2 (LRRK2) WD40 Repeat (WDR) domain was selected as the target for in silico hit-finding and optimization. Mutations in LRRK2 are the most common genetic cause of familial form of Parkinson's disease. The LRRK2 WDR domain is an understudied drug target with no known molecular inhibitors. Herein we detail the first phase of our winning submission to the CACHE Challenge #1. We developed a framework for the high-throughput structure-based virtual screening of a chemically diverse small molecule space. Hit identification was performed using the large-scale Deep Docking (DD) protocol followed by absolute binding free energy (ABFE) simulations. ABFEs were computed using an automated molecular dynamics (MD)-based thermodynamic integration (TI) approach. 4.1 billion ligands from Enamine REAL were screened with DD followed by ABFEs computed by MD TI for 793 ligands. 76 ligands were prioritized for experimental validation, with 59 compounds successfully synthesized and 5 compounds identified as hits, yielding a 8.5% hit rate. Our results demonstrate the efficacy of the combined DD and ABFE approaches for hit identification for a target with no previously known hits. This approach is widely applicable for the efficient screening of ultra-large chemical libraries as well as rigorous protein-ligand binding affinity estimation leveraging modern computational resources. | Evgeny Gutkin; Filipp Gusev; Francesco Gentile; Fuqiang Ban; S. Benjamin Koby; Chamali Narangoda; Olexandr Isayev; Artem Cherkasov; Maria G. Kurnikova | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6604816ae9ebbb4db9b5ddda/original/in-silico-screening-of-lrrk2-wdr-domain-inhibitors-using-deep-docking-and-free-energy-simulations.pdf |
652668e78bab5d20551ad1b7 | 10.26434/chemrxiv-2023-vcgnf | VOLTA: a tool for battery screening bridging the gap between virtual electrode materials and practical applications | We present a battery screening Python pipeline, VOLTA. It allows for a novel battery active material explorative workflow, prioritizing the cell level performance indicators, such as cell capacity and voltage profile. This is achieved by the construction of a starting dataset of both observed and virtual active materials from the Materials Project, the implementation of the physics-based ARTISTIC project pipeline for the assessment of practical electrode properties like porosity and thickness, and the coupling of the electrodes into virtual cells, whose figures of merit are calculated, like voltage and capacity. The screening can be conducted by applying filters to these cell-level properties, achieving an indirect selection of the most suitable active materials. The approach is validated through comparison to current commercial battery technology, and we demonstrate that VOLTA is able to identify promising electrode materials for high energy batteries, like the well-known LiCoO2, LiNiO2 and graphite. We also illustrate a case-study, where the pipeline is used to identify suitable low-voltage, realistic virtual batteries obtained by combining entries of the Materials Project battery database (a battery revealing type of task). | Antonio Carnevali; Rosa Palacin; Clare Grey; Alejandro A. Franco | Materials Science; Energy; Composites; Materials Processing; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652668e78bab5d20551ad1b7/original/volta-a-tool-for-battery-screening-bridging-the-gap-between-virtual-electrode-materials-and-practical-applications.pdf |
65d45aafe9ebbb4db9c3289d | 10.26434/chemrxiv-2024-bqh4x | A method for surface characterization using solid-state nuclear magnetic resonance spectroscopy demonstrated on nano-crystalline ZnO:Al | Nano-scale zinc-oxide doped with aluminium ZnO:Al is studied by different techniques targeting surface changes induced by the conditions at which ZnO:Al is used as support material in the catalysis of methanol. While it is well established, that a variety of 1H and 27Al resonances can be found by solid-state NMR for this material, it was not clear yet which signals are related to species located close to the surface of the material and which to species located in the bulk. To this end, a method is suggested which makes use of a paramagnetically impregnated material to suppress NMR signals close to particle surface in the blind-sphere around the paramagnetic metal atoms. It is shown that it is important to use conditions which guarantee a stable reference system relative to which it can be established whether the coating procedure is conserving the original structure or not. This method, called Paramagnetically Assisted Surface Peak Assignment (PASPA), helped to assign the 1H and 27Al NMR peaks to the bulk and the surface layer defined by the blind- sphere of the paramagnetic atoms. The assignment results are further corroborated by the results from heteronuclear 27Al{1H} dipolar dephasing experiments, which indicate the hydrogen atoms are preferentially located in the surface layer and not in the particle core. | Jan Konrad Wied; Benjamin Mockenhaupt; Ulrich Schürmann; Lorenz Kienle; Sebastian Mangelsen; Janin Glänzer; Vinicius Ribeiro Celinski; Malte Behrens; Jörn Schmedt auf der Günne | Inorganic Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Spectroscopy (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d45aafe9ebbb4db9c3289d/original/a-method-for-surface-characterization-using-solid-state-nuclear-magnetic-resonance-spectroscopy-demonstrated-on-nano-crystalline-zn-o-al.pdf |
60c75622842e65d4eadb445e | 10.26434/chemrxiv.14214479.v1 | Metal-Free Fenton-like Photocatalysts Based on Covalent Organic Frameworks | The Fenton reaction is one
of the most efficient and widely used advanced oxidation processes for
remediating the ever-growing water pollution. Metal-free photocatalysts for
Fenton-like reactions have gathered enormous scientific interest for their advantages
including board pH operation range and high stability. Herein, we demonstrate a
metal-free covalent organic framework (COF)-based
standalone photocatalyst with superior reactivity and reusability for
Fenton-like reactions at acid and neutral pH solutions, which can be attributed
to its large porosity, high density of the photoactive triazine moiety,
vertical π arrays formed by eclipsed layer stacking and the <i>β</i>‑ketoenamine
linkage. Our experiments showed that the photocatalyst can absorb visible light
effectively for activation of H<sub>2</sub>O<sub>2</sub>, producing abundant
reactive oxygen species including superoxide radical (O<sub>2</sub><sup>·-</sup>),
hydroxyl radical (<sup>·</sup>OH), and singlet oxygen (<sup>1</sup>O<sub>2</sub>)
for oxidizing organic pollutants. This work not only provides an efficient
metal-free photocatalyst for Fenton-like reactions, but also paves the way for
COFs towards advanced oxidation processes, opening up the possibilities to
their future applications in industry. | Qiaobo Liao; Can Ke; Dongni Wang; Yiying Zhang; Qingwen Han; Yifan Zhang; Kai Xi | Catalysts; Heterogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75622842e65d4eadb445e/original/metal-free-fenton-like-photocatalysts-based-on-covalent-organic-frameworks.pdf |
60c74fcd469df494c1f4476a | 10.26434/chemrxiv.12949274.v1 | Time-Resolved Study of Light-Induced Ground State Proton Transfer from Acid Medium to 4-Nitrophenolate | In the present work, we
study the transient laser-induced formation of 4-nitrophenolate (4-NPO<sup>-</sup>)
in the ground electronic state and subsequent proton transfer reaction with
acetic acid and water with numerical calculations and laser flash photolysis. We
employ the Debye-Smoluchowski spherically-symmetric diffusion model of photoacid
proton transfer to determine experimental conditions for studying thermally
activated chemical reactions in the ground electronic state. Numerically calculated
protonation and deprotonation probabilities for 4-NPO<sup>-</sup> and
4-nitrophenol (4-NPOH) in both ground and excited states showed the feasibility
of efficiently producing the ground state anion in the photoacid cycle. We
performed laser flash photolysis measurements of 4-NPOH to characterize the
photo-initiated ground state protonation and deprotonation rate constants of
4-NPO<sup>-</sup>/4-NPOH as a function of acetic acid, pH, temperature and
viscosity. Overall, the work presented here shows a simple way to study fast
competing bimolecular proton transfer reactions in non-equilibrium conditions
in the ground electronic state <i>(GSPT)</i>. | Leandro Scorsin; Leticia Martins; Haidi Fiedler; Faruk Nome; RENE NOME | Chemical Kinetics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fcd469df494c1f4476a/original/time-resolved-study-of-light-induced-ground-state-proton-transfer-from-acid-medium-to-4-nitrophenolate.pdf |
60c75336469df47313f44cf2 | 10.26434/chemrxiv.13426412.v1 | A Small Molecule – Protein Hybrid for Voltage Imaging via Quenching of Bioluminescence | <p>We report a small molecule enzyme pair for optical voltage
sensing via quenching of bioluminescence. This <u>Q</u>uenching <u>B</u>ioluminescent
V<u>olt</u>age Indicator, or Q-BOLT, pairs the dark absorbing,
voltage-sensitive dipicrylamine with membrane-localized bioluminescence from
the luciferase NanoLuc (NLuc). As a result, bioluminescence is quenched through
resonance energy transfer (QRET) as a function of membrane potential. Fusion of
HaloTag to NLuc creates a two-acceptor bioluminescence resonance energy
transfer (BRET) system when a tetramethylrhodamine (TMR) HaloTag ligand is
ligated to HaloTag. In this mode, Q-BOLT is capable of providing direct
visualization of changes in membrane potential in live cells via three distinct
readouts: change in QRET, BRET, and the ratio between bioluminescence emission
and BRET. Q-BOLT can provide up to a 29% change in bioluminescence (ΔBL/BL) and
>100% ΔBRET/BRET per 100 mV change in HEK 293T cells, without the need for
excitation light. In cardiac monolayers derived from human induced pluripotent
stem cells (hiPSC), Q-BOLT readily reports on membrane potential oscillations.
Q-BOLT is the first example of a hybrid small molecule – protein voltage
indicator that does not require excitation light and may be useful in contexts
where excitation light is limiting.</p>
<p> </p> | Brittany Benlian; Pavel Klier; Kayli Martinez; Marie Schwinn; Thomas Kirkland; Evan Miller | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75336469df47313f44cf2/original/a-small-molecule-protein-hybrid-for-voltage-imaging-via-quenching-of-bioluminescence.pdf |
613f7489fc08e371f393864e | 10.26434/chemrxiv-2021-gwm9m-v2 | Performance comparison of r2SCAN and SCAN metaGGA density functionals for solid materials via an automated, high-throughput computational workflow | Computational materials discovery efforts utilize hundreds or thousands of density functional theory (DFT) calculations to predict material properties. Historically, such efforts have performed calculations at the generalized gradient approximation (GGA) level of theory due to its efficient compromise between accuracy and computational reliability. However, high-throughput calculations at the higher metaGGA level of theory are becoming feasible. The Strongly Constrainted and Appropriately Normed (SCAN) metaGGA functional offers superior accuracy to GGA across much of chemical space, making it appealing as a general-purpose metaGGA functional, but it suffers from numerical instabilities that impede it's use in high-throughput workflows. The recently-developed r2SCAN metaGGA functional promises accuracy similar to SCAN in addition to more robust numerical performance. However, its performance compared to SCAN has yet to be evaluated over a large group of solid materials.
In this work, we compared r2SCAN and SCAN predictions for key properties of approximately 6,000 solid materials using a newly-developed high-throughput computational workflow. We find that r2SCAN predicts formation energies more accurately than SCAN and PBEsol for both strongly- and weakly-bound materials and that r2SCAN predicts systematically larger lattice constants than SCAN. We also find that r2SCAN requires modestly fewer computational resources than SCAN and offers significantly more reliable convergence. Thus, our large-scale benchmark confirms that r2SCAN has delivered on its promises of numerical efficiency and accuracy, making it a preferred choice for high-throughput metaGGA calculations. | Ryan Kingsbury; Ayush Gupta; Christopher Bartel; Jason Munro; Shyam Dwaraknath; Matthew Horton; Kristin Persson | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613f7489fc08e371f393864e/original/performance-comparison-of-r2scan-and-scan-meta-gga-density-functionals-for-solid-materials-via-an-automated-high-throughput-computational-workflow.pdf |
66ea8d6fcec5d6c1426a17f9 | 10.26434/chemrxiv-2024-2d7wr | Hybrid synthesis of AMFC-derived amides using supported gold nanoparticles and acyl-coenzyme A ligases | By integrating different types of catalysts in the same system, hybrid catalysis emerges as an attractive and competitive approach. Within the framework of valorizing sustainably sourced bio-based products, we herein present a synthetic method for producing amides from alcohols and the bio-sourced 5-aminomethyl-2-furancarboxylic acid (AMFC). This approach utilizes supported gold metal nanoparticles as heterogeneous chemocatalysts, in conjunction with an acyl-coenzyme A ligase (ACL). By combining the actions of these catalysts, aliphatic mono- and di-alcohols are converted to the corresponding AMFC-derived amides with yields of up to 65% in aqueous buffer at 60 °C. This process requires only the addition of the enzyme and associated reactants in the same vessel for the second step in an one-pot/two-steps procedure. | Lucas Bisel; Aurélie Fossey-Jouenne; Richard Martin; Jonathan Bassut; Antoine Lancien; Louis Mouterde; Vivien Herrscher; Muriel Billamboz; Carine Vergne-Vaxelaire; Rénato Froidevaux; Anne Zaparucha; Egon Heuson | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Chemical Biology; Biocatalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ea8d6fcec5d6c1426a17f9/original/hybrid-synthesis-of-amfc-derived-amides-using-supported-gold-nanoparticles-and-acyl-coenzyme-a-ligases.pdf |
676cbe4681d2151a02ed9edc | 10.26434/chemrxiv-2024-zsjx5 | B2Pin2-Enabled Reductive Thioesterification of Aryl Triflates with Thiocarbonates | In this work, we demonstrate aryl thioester synthesis via an unprecedented B2Pin2-mediated reductive coupling of aryl triflates with thiocarbonates. This method demonstrates good to high efficiency for 2,6-disubstituted aryl substrates, which are thought to be challenging due to high steric hinderance. The practicality of this method was showcased by rapid thioesterification of triflates derived from pharmaceutical compounds such as Apixaban, Ezetimibe, and Ethinyl estradiol. This work may further invoke development of B2Pin2-mediated reductive C(sp2)-C(sp2) coupling under earth-abundant transition metal catalysis, avoiding otherwise use of Zn and Mn, which may present scalability and metal residue issues. | Houguang Shi; Fan Wu; Wei Zhu; Hong C. Shen; Honger Yao; Xiang Wang; Hegui Gong | Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676cbe4681d2151a02ed9edc/original/b2pin2-enabled-reductive-thioesterification-of-aryl-triflates-with-thiocarbonates.pdf |
64483673df78ec501561ba25 | 10.26434/chemrxiv-2023-tv7rp | Time-resolved in-situ nanoparticle size evolution during magnetron sputtering onto liquids | Aggregation and growth of silver nanoparticles (Ag NPs) occur both at the plasma-liquid interface and inside the silicone oil during and after the magnetron sputtering. Despite the same amount of deposited silver, the growth kinetics of Ag NPs in silicone oil vary at different deposition rates. Stirring helps to disaggregate the particle lumps. The Light Extinction Spectroscopy (LES) technique is employed for the first time to in-situ and real-time characterize the particle size distribution (PSD) during and after the sputtering of the silver atoms onto silicone oil, i.e., Sputtering onto Liquids (SoL) process. The effects of the deposition rate and the stirring speed on the PSDs are analyzed. Based on De Brouckere mean diameters, the size evolution of Ag NPs over time is monitored. Via the LES technique, Ag NPs bigger than 20 nm are detected, and the PSDs are shown to be poly-disperse, which is also supported by the ex-situ TEM measurements and in-situ time-resolved absorption spectra. At higher deposition rates, larger NPs are formed. Faster stirring does not substantially influence the final size but promotes the formation of smaller NPs (<20 nm). Low colloidal stability of Ag NPs in silicone oil is also observed. | Pinar Eneren; Anastasiya Sergievskaya; Yunus Tansu AKSOY; Polona Umek; Stephanos Konstantinidis; Maria Rosaria Vetrano | Nanoscience; Nanofluidics | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64483673df78ec501561ba25/original/time-resolved-in-situ-nanoparticle-size-evolution-during-magnetron-sputtering-onto-liquids.pdf |
60c74d08702a9b811118b7ae | 10.26434/chemrxiv.12582284.v1 | An Iron-Based Catalyst Enables The Enantioconvergent Synthesis of Chiral 1,1-Diarylalkanes Through a Suzuki-Miyaura Cross-Coupling Reaction | By using an iron-based catalyst, access to enantioenriched 1,1-diarylakanes was enabled through an enantioselective Suzuki-Miyaura crosscoupling reaction. The combination of a chiral cyanobis(oxazoline) ligand framework and 1,3,5-trimethoxybenzene additive were essential to afford high yields and enantioselectivities in cross-coupling reactions between unactivated aryl boronic esters and a variety of benzylic chlorides, including challenging ortho-substituted benzylic chloride substrates. Mechanistic investigations implicate a stereoconvergent pathway involving carbon-centered radical intermediates. | Chet Tyrol; Nang Yone; Connor Gallin; Jeffery Byers | Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d08702a9b811118b7ae/original/an-iron-based-catalyst-enables-the-enantioconvergent-synthesis-of-chiral-1-1-diarylalkanes-through-a-suzuki-miyaura-cross-coupling-reaction.pdf |
672a2e1e7be152b1d0104381 | 10.26434/chemrxiv-2024-xk9ts | Synthesis of Enantioenriched 2-((Hetera)cyclo)alkylchromanols and their Spirocyclic Analogs through Enzymatic Resolution | An efficient approach to the multigram synthesis of 2-((hetera)cyclo)alkylchromanols and their spirocyclic analogs based on enzymatic resolution is described. It is shown that enzymatic acylation could be used for the preparation of enantioenriched title compounds with primary alkyl substituents at the C-2 position. Meanwhile, enzymatic hydrolysis of the corresponding acetates was optimal for the synthesis of the target alcohols when significant steric hindrance is present, e.g., due to the -branching. The latter factor was demonstrated to be crucial for the enzymatic reaction rate in both cases. The synthetic utility of the obtained chiral alcohols was demonstrated through Mitsunobu configuration inversion, as well as by the preparation of the corresponding primary amines – valuable sp3-enriched building blocks for medicinal chemistry. | Oleksii Timokhin; Anastasiia Romanova; Viktoria Moskvina; Olexandr Kucher; Aleksandr Boiko; Anna Banasevych; Dmytro Durylin; Volodymyr Brovarets; Oleksandr Grygorenko | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a2e1e7be152b1d0104381/original/synthesis-of-enantioenriched-2-hetera-cyclo-alkylchromanols-and-their-spirocyclic-analogs-through-enzymatic-resolution.pdf |
65604ef5cf8b3c3cd7009e1f | 10.26434/chemrxiv-2023-sx61w | Generation of conformational ensembles of small molecules via Surrogate Model-Assisted Molecular Dynamics | The accurate prediction of thermodynamic properties is crucial in various fields such as drug discovery and materials design. This task relies on sampling from the underlying Boltzmann distribution, which is challenging using conventional approaches such as simulations. In this work, we introduce Surrogate Model-Assisted Molecular Dynamics (SMA-MD), a new procedure to sample the equilibrium ensemble of molecules. First, SMA-MD leverages Deep Generative Models to enhance the sampling of slow degrees of freedom. Subsequently, the generated ensemble undergoes statistical reweighting, followed by short simulations. Our empirical results show that SMA-MD generates more diverse and lower energy ensembles than conventional Molecular Dynamics simulations. Furthermore, we showcase the application of SMA-MD for the computation of thermodynamical properties by estimating implicit solvation free energies. | Juan Viguera Diez; Sara Romeo Atance; Ola Engkvist; Simon Olsson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65604ef5cf8b3c3cd7009e1f/original/generation-of-conformational-ensembles-of-small-molecules-via-surrogate-model-assisted-molecular-dynamics.pdf |
663ddf20418a5379b0ebd920 | 10.26434/chemrxiv-2024-h6dvb | Precision Molecular Engineering of Miniaturized Near-Infrared Fluorophores | Organic fluorophores with near-infrared (NIR) emissions and reduced molecular weights are crucial for advancing bioimaging and biosensing technologies. Traditional methods, such as conjugation expansion and heteroatom engineering, often fail to reduce fluorophore size without sacrificing NIR emission properties. Addressing this challenge, our study utilized computational screening and structure-property relationship analysis to establish comprehensive design principles for compact, single-benzene-based NIR fluorophores. These newly developed fluorophores not only exhibit emissions above 700 nm but also maintain molecular weights under 200 g/mol, approximately 25% of that of Cy7. Additionally, they display unique environmental sensitivity—non-emissive in aqueous solutions but highly emissive in lipid environments. This property significantly enhances their utility in live cell imaging by enabling wash-free applications. Our findings mark a substantial breakthrough in fluorophore engineering, paving the way for more efficient and adaptable imaging methodologies. | Rongrong Huang; Qinglong Qiao; Tianruo Shen; Xia Wu; Chao Wang; Nannan Ding; Weijie Chi; Huaming Sun; Zhaochao Xu; Yu Fang; Xiaogang Liu | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Physical and Chemical Properties; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663ddf20418a5379b0ebd920/original/precision-molecular-engineering-of-miniaturized-near-infrared-fluorophores.pdf |
61d42c62d1f6626fbe4f5ea2 | 10.26434/chemrxiv-2022-dp94p | Directed Evolution of a Ketone Synthase for Efficient and Highly Selective Functionalization of Internal Alkenes by Accessing Reactive Carbocation Intermediates
| The direct regioselective oxidation of internal alkenes to ketones could simplify synthetic routes and solve a longstanding challenge in synthesis. This reaction is of particular importance because ketones are predominant moieties in valuable products as well as crucial intermediates in synthesis. Here we report the directed evolution of a ketone synthase that oxidizes internal alkenes directly to ketones with several thousand turnovers. The evolved ketone synthase benefits from more than a dozen crucial mutations, most of them distal to the active site. Computational analysis reveals that all these mutations collaborate to facilitate the formation of a highly reactive carbocation intermediate by generating a confined, rigid and preorganized active site through an enhanced dynamical network. The evolved ketone synthase fully exploits a catalytic cycle that has largely eluded small molecule catalysis and consequently enables various challenging functionalization reactions of internal alkenes. This includes the first catalytic, enantioselective oxidation of internal alkenes to ketones, as well as the formal asymmetric hydration and hydroamination of unactivated internal alkenes in combination with other biocatalysts. | Sebastian Gergel; Jordi Soler; Alina Klein; Kai Schülke; Bernhard Hauer; Marc Garcia-Borràs; Stephan Hammer | Biological and Medicinal Chemistry; Catalysis; Biochemistry; Bioinformatics and Computational Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d42c62d1f6626fbe4f5ea2/original/directed-evolution-of-a-ketone-synthase-for-efficient-and-highly-selective-functionalization-of-internal-alkenes-by-accessing-reactive-carbocation-intermediates.pdf |
60c7575b842e65e9b1db4699 | 10.26434/chemrxiv.14397566.v1 | Radical Trifluoroacetylation of Alkenes Triggered by a Visible-Light-Promoted C−O Bond Fragmentation of Trifluoroacetic Anhydride | Trifluoromethyl ketones are not only found in drug like substances, but
are also considered as key synthons for the preparation of various fluorinated
heterocyclic molecules. Access to such trifluoromethyl ketone derivatives typically
requires the incorporation of the trifluoromethyl group, or a surrogate moiety,
at the beginning of a multi-step synthetic sequence. However, direct trifluoroacylation
of alkenes could potentially provide a highly efficient and straightforward
method for the synthesis of a,b-unsaturated trifluoromethyl ketones. Here we report a mild and
operationally simple trifluoroacylation strategy of olefines, that utilizes trifluoroacetic
anhydride as a low-cost and readily available reagent. This light-mediated
process is fundamentally different from conventional methodologies and occurs
through an trifluoroacyl radical mechanism promoted by a photocatalyst. Beyond
simple alkenes, this method allows for chemo- and regioselective
functionalization of small-molecule drugs and common pharmacophores. | Kun Zhang; David Rombach; Nicolas Yannick Nötel; Gunnar Jeschke; Dmitry Katayev | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7575b842e65e9b1db4699/original/radical-trifluoroacetylation-of-alkenes-triggered-by-a-visible-light-promoted-c-o-bond-fragmentation-of-trifluoroacetic-anhydride.pdf |
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