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6591ccd39138d23161e8e853 | 10.26434/chemrxiv-2024-whvl8 | Direct visualization of chemical transport in solid-state chemical reactions by time-of-flight secondary ion mass spectrometry | Systematic control and design of solid-state chemical reactions is required for modifying materials properties and in novel synthesis. Understanding chemical dynamics at the nanoscale is therefore essential to reveal the key reactive pathways. Herein, we combine focused ion beam-scanning electron microscopy (FIB-SEM) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) to track the migration of sodium from a borate coating to the oxide scale during in situ hot corrosion testing. We map the changing distribution of chemical elements and compounds from 50 to 850 °C to reveal how sodium diffusion induces corrosion. The results are validated by in situ X-ray diffraction and post-mortem TOF-SIMS. We additionally retrieve the through-solid sodium diffusion rate by fitting measurements to a Fickian diffusion model. This study presents a step-change in analysing microscopic diffusion mechanics with high chemical sensitivity and selectivity, a widespread analytical challenge that underpins the defining rates and mechanisms of solid-state reactions. | Sang T. Pham; Kiet Tieu; Chao Sun; Shanhong Wan; Sean Collins | Materials Science; Analytical Chemistry; Nanoscience; Coating Materials; Mass Spectrometry; Microscopy | CC BY 4.0 | CHEMRXIV | 2024-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6591ccd39138d23161e8e853/original/direct-visualization-of-chemical-transport-in-solid-state-chemical-reactions-by-time-of-flight-secondary-ion-mass-spectrometry.pdf |
64db7a7369bfb8925af78eea | 10.26434/chemrxiv-2023-4x3gr-v2 | Data Efficient and Stability Indicated Sampling
for Developing Reactive Machine Learning
Potential to Achieve Ultra-long Simulation in
Lithium Metal Batteries | Modelling the formation of solid-liquid interphase (SEI) is challenging as its strict
requirement with both simulation accuracy and length. Machine learning potential
(MLP) based molecular dynamics (MD) simulation is expected to play a role in this
field while currently its use is hindered by sampling efficiency and simulation stability.
In this work, we tackle the two challenges together. We propose the stability-indicatedsampling (SIS) algorithm for efficiently sampling training data using physical information (temperature). Unlike previous strategies, our method does not need prior
knowledge of reaction networks or training multiple MLPs for uncertainty estimation.
Compared with the recent proposed methods HAIR and DP-GEN, our approach gives
significant improvement of sampling efficiency with less requirements with the initial
training data, to realize > 10 ns MLPMD simulation using ab initio MD (AIMD)
trajectory of just a few ps. We introduce the concept underlying instability consistency by showing the accuracy of reaction mechanisms and radial distribution function (RDF) can be improved by SIS-MLPMD, although their information is not explicitly
used in our sampling decision. Furthermore, we show that long-time MLPMD simulation of Lithium metal battery (LMB) can not only reproduce some well-known SEI
components including LiF, Li2O, LiOH, LiS and the incomplete N-S breaking in highconcentration systems, but also ionic aggregation structures of LiF, which is not shown
in our AIMD training data but matches previous results of electrochemical impedance
spectroscopy. Our work is expected to help accelerate future investigations, especially
for studying long-time (≥ ns scale) reaction dynamics in interfacial problems. | Longkun Xu; Wei Shao; Haishun Jin; Qiang Wang | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64db7a7369bfb8925af78eea/original/data-efficient-and-stability-indicated-sampling-for-developing-reactive-machine-learning-potential-to-achieve-ultra-long-simulation-in-lithium-metal-batteries.pdf |
679351406dde43c9082aee59 | 10.26434/chemrxiv-2025-kbdl0 | On the Performance of the Bethe-Salpeter Equation for Electronic Excitations in First-Row Transition Metal Complexes | The performance of the BSE@GW approach has been systematically tested on a series of first-row transition metal complexes. Special attention was paid to the in- terplay between metal-centered (MC) and charge transfer (CT) transitions and their ordering in the excited singlet and triplet state manifolds. Here, the commonly used time-dependent density functional theory reaches its limits and in particular shows a strong dependence on the exchange-correlation functional. In contrast, the present BSE@GW UV-VIS spectra show a good agreement with experimental results as far as the absorption spectra and their assignment are concerned. This is achieved in- dependently of the exchange-correlation functional underlying the initial guess of the GW iteration. These conclusions are drawn on the basis of an investigation of a test set including nearly pure MC transitions in triazacyclononane with different metal centers and mixed MC-CT transitions in Fe(II) complexes with different numbers of N-heterocyclic carbene ligands. Furthermore, important aspects of the calculations such as the dependence on the ground state equilibrium geometry or the influence of the Tamm-Dancoff approximation are highlighted. | Florian Bogdain; Oliver Kuehn | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679351406dde43c9082aee59/original/on-the-performance-of-the-bethe-salpeter-equation-for-electronic-excitations-in-first-row-transition-metal-complexes.pdf |
64db27bd4a3f7d0c0d322e40 | 10.26434/chemrxiv-2023-h67fz | Kinetics of N2 Release from Diazo Compounds: A Combined Machine Learning-Density Functional Theory Study | Diazo compounds are commonly employed as carbene precursors in carbene transfer reactions during a variety of functionalization procedures. Release of N2 gas from diazo compounds may lead to carbene formation, and the ease of this dissociation is highly dependent on the characteristics of the substituents located in the vicinity of the diazo moiety. A quantum mechanical density functional theory assisted by machine learning was used to investigate the relationship between the chemical features of diazo compounds and the activation energy required for the N2 dissociation. Our results suggest that diazo molecules possessing a higher positive partial charge on the carbene carbon and more negative charge on the terminal nitrogen, encounter a lower energy barrier. A more positive C charge decreases the π-donor ability of the carbene lone pair to the π∗ orbital of N2 , while the more negative N charge is a result of a weak interaction between N2 lone pair and vacant p orbital of the carbene. The findings of this study can pave the way for molecular engineering for the purpose of carbene generation which serves as a crucial intermediate for many chemical transformations in synthetic chemistry. | Kaveh Farshadfar; Arsalan Hashemi; Reza Khakpour; Kari Laasonen | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64db27bd4a3f7d0c0d322e40/original/kinetics-of-n2-release-from-diazo-compounds-a-combined-machine-learning-density-functional-theory-study.pdf |
667adfa2c9c6a5c07a5c9ec4 | 10.26434/chemrxiv-2024-p6grv | Nanowire Morphology Control in Sb Metal-derived Antimony Selenide Photocathodes for Solar Water Splitting | We report a facile method to enhance the photoelectrochemical (PEC) performance of Sb2Se3 photocathodes by controlling the growth of bilayer Sb2Se3 consisting of vertically oriented nanorods on a compact Sb2Se3 layer. Sb2Se3 thin films with controllable nanorod diameters were achieved by manipulating the substrate temperature during metallic Sb thin film deposition. The lower temperature-derived Sb2Se3 photocathode, with a larger nanorod diameter (202 ± 48 nm), demonstrated a photocurrent density of -15.2 mA cm−2 at 0 VRHE and an onset potential of 0.21 VRHE. In contrast, the higher temperature-derived Sb2Se3 photocathode, with a smaller nanorod diameter (124 ± 28 nm), exhibited an improved photocurrent density of -22.1 mA cm−2 at 0 VRHE and an onset potential of 0.31 VRHE. The enhanced PEC performance is attributed to reduced charge recombination facilitated by a shorter charge transport path in the [hk0] direction. This study highlights the significance of morphology control in optimizing Sb2Se3 photocathodes, providing insights for future material and device design. | Zhenbin Wang; Yongping Gan; Erin Service; Pardis Adams; Thomas Moehl; Wenzhe Niu; David Tilley | Catalysis; Electrocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667adfa2c9c6a5c07a5c9ec4/original/nanowire-morphology-control-in-sb-metal-derived-antimony-selenide-photocathodes-for-solar-water-splitting.pdf |
661c9e3c21291e5d1dd980e6 | 10.26434/chemrxiv-2024-lbn4r | Molecular Docking Simulation to Predict Inhibitors Against Zinc Transporters | Zinc is one of the essential elements required by our body for normal functioning. This zinc concentration inside the cell is maintained by a particular type of protein called zinc transporter (ZnT). These transporters actively transport zinc ions outside the cells and playplay an important role in diabetes. ZnT is present in the pancreatic β cells plasma membrane, and , and overexpression of ZnT results in a high insulin secretion in the body and results in a decrease in the glucose concentration in the body (hypoglycemia). Therefore, regulating the zinc concentration inside the cell can help in regulating the cells can help in regulating insulin secretion and can potentially control diabetes. In the current work, we have utilized molecular docking simulations to screen 5249 chemical compounds that can bind and inhibit these proteins. The Zinc20 database was used to download the 3D structure of the ligands. Based on our studies, we have predicted five chemical compounds (ligands) that bind strongly to the periplasmic opening of the ZnT. The binding of these ligands to the opening of the ZnT will impede zinc transport, helping in regulating insulin secretion and contributing to diabetes management. In addition, based on the physical properties of the ligands, all of them show strong interactions and drug-likeliness. Understanding the mechanism of inhibitor binding will shed light on treating diseases like diabetes. | Irene Batta; Gaurav Sharma | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661c9e3c21291e5d1dd980e6/original/molecular-docking-simulation-to-predict-inhibitors-against-zinc-transporters.pdf |
61f2a7e463acba59d11bdfdf | 10.26434/chemrxiv-2022-6k895 | Facile and Low-Waste Self-Digitization of Samples by Oil-Triggered, Template-Confined Dewetting on a Networked Microwell Array | In this work, we present a simple, straightforward, and robust method for spontaneously digitizing samples into an array of dis-crete volumes. The method is based on an oil-triggered, template-confined dewetting phenomenon. To realize the dewetting-induced sample digitization, an aqueous sample is firstly infused into a networked microwell array (NMA) through a predegassing-based self-pumping mechanism, and then an immiscible oil phase is applied over the surface of NMA chip to induce the templated dewetting. Due to a periodic interfacial tension heterogeneity, such dewetting ruptures the sample at the thinnest parts (i.e., con-nection channels) and spontaneously splits the sample into droplets in individual microwells. Without requiring any complex pump-ing or valving systems, this method can discretize a sample into tens of thousands of addressable droplets in a matter of minutes with nearly 98% usage. To demonstrate the utility and universality of this self-digitization method, we exploited it to discretize samples into 40,233 wells for digital PCR assay, digital quantification of bacteria, and self-assembly of spherical colloidal photonic crystals. We believe this facile technique will be useful in a broad range of applications where partitioning of samples into a large number of small individual volumes is required. | Nankun Xiong; Anyan Wang; Tengbao Xie; Tianbao Hu; Qiang Chen; Qiang Zhao; Gang Li | Analytical Chemistry; High-throughput Screening | CC BY NC 4.0 | CHEMRXIV | 2022-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f2a7e463acba59d11bdfdf/original/facile-and-low-waste-self-digitization-of-samples-by-oil-triggered-template-confined-dewetting-on-a-networked-microwell-array.pdf |
67c884186dde43c9089e5c08 | 10.26434/chemrxiv-2025-z9424 | Scalable Synthesis of MXene Nanoscrolls | MXenes are a promising class of 2D carbides and nitrides known for their high electrical conductivity, hydrophilicity, mechanical strength, and unique optoelectronic properties, leading to numerous applications. However, their scalable synthesis in a 1D morphology, such as MXene nanotubes or scrolls, has not been demonstrated yet. This work presents a versatile and scalable method for manufacturing MXene scrolls, including Ti2CTx, Ti3C2Tx, Ti3CNTx, V2CTx, Nb2CTx, and Ta4C3Tx. We demonstrate high-yield production of up to 45 wt% of MAX phase precursor and precise control over scrolls’ alignment and morphology. Properties of scrolls differ from 2D flakes; e.g., a freestanding film made of scrolled Nb2CTx presents a transition to superconducting state below 5.2 K. Films of MXene scrolls exhibit 3 times lower density and enhanced mass transport compared to flakes, resulting in an improved performance in supercapacitor electrodes and humidity sensors. The dispersion of the scrolls in water behaves like an electrorheological fluid. Aligning scrolls in an electric field allows for circuit switching between electrically insulating and conductive states. These scrolls can be assembled into vertically aligned MXene forests, fibers, and other architectures. The availability of 1D MXene scroll offers exciting opportunities in many fields. | Teng Zhang; Benjamin Chacon; Danzhen Zhang; Aidan Cotton; Yihui Zhang; Yuan Zhang; Stefano Ippolito; Francesca Urban; Tetiana Parker; Lingyi Bi; Kateryna Shevchuk; Kyle Matthews; Eric A. Stach; Yury Gogotsi | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c884186dde43c9089e5c08/original/scalable-synthesis-of-m-xene-nanoscrolls.pdf |
60c73efe702a9b6172189e6a | 10.26434/chemrxiv.7195817.v1 | Emergence of Selectivity in Inherently Nonselective Gold Nanoparticles Through Preferential Breaking of Interparticle Interactions | <p>We
demonstrate a fundamentally unique identification strategy to impart
selectivity to a traditionally and inherently nonselective
carboxylate-functionalized gold-nanoparticles ([-] AuNPs), without the aid of
any analyte specific ligands. The
common practice is to use the ability of divalent ions to trigger the
aggregation process in a kinetically trapped dispersed solution of [-] AuNPs.
Aggregation of NPs being a thermodynamically favourable process will result in
a uniform and nonselective turn-off response from most of the strongly binding
divalent ions. Our approach is to use the abilities of various divalent ions to
break a thermodynamically stable inter-nanoparticle precipitates containing [+]
and [-] AuNPs (<i>nanoionic precipitates</i>),
as the means of identification. Importantly both [+] and [-] AuNPs,
independently, were ‘blind’ in terms of selectivity towards divalent ions.
Remarkably, a hybrid-system composed of such nonselective nanoparticles was
able to discriminate between the hard-to-distinguish pair of Pb<sup>2+</sup>
and Cd<sup>2+</sup> ions. The rationale is that only the strongest of strongly
binding ions will be able to break the interactions between the NP precipitates
(thermodynamically stable state) and re-disperse them back in solution
(kinetically trapped state). This is in stark contrast with the conventional
idea of forming an interaction between NPs and divalent ions, with the help of
analyte-specific ligands.</p> | Anish Rao; Govind Sasi Kumar; Soumendu Roy; Ajesh T. R.; Gayathri Devatha; Pramod Pillai | Aggregates and Assemblies; Nanostructured Materials - Nanoscience; Physical and Chemical Properties; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73efe702a9b6172189e6a/original/emergence-of-selectivity-in-inherently-nonselective-gold-nanoparticles-through-preferential-breaking-of-interparticle-interactions.pdf |
60c7409e469df4c709f42c58 | 10.26434/chemrxiv.7410659.v2 | Cofactor Analogues as Active Site Probes in Lysine Acetyltransferases | Here we present the synthesis of two functional cofactor-based chemical probes and their usage as mechanistic tools in a broadly applica-ble assay platform for histone acetyltransferases (HATs). In this platform, a fluorescence polarization (FP) based binding assay was combined with biolayer interferometry (BLI) competition analysis and a FP competition activity immunoassay to enable easy, reliable, and pro-found evaluation of ligands that target the KAT cofactor binding site. | Roman P. Simon; Tobias Rumpf; Vaida Linkuvienė; Daumantas Matulis; Asifa Akhtar; Manfred Jung | Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7409e469df4c709f42c58/original/cofactor-analogues-as-active-site-probes-in-lysine-acetyltransferases.pdf |
619b002cb039f2003aafe2e7 | 10.26434/chemrxiv-2021-r5gb6 | Metal-Free Polymerizations of Microencapsulated Activated Alkynes for Autonomous Damage Visualization of Polymers | The development of autonomous materials with desired performance and built-in visualizable sensing units is of great academic and industrial significance. Although a wide range of damage indication methods have been reported, the “turn-on” sensing mechanism by damaging events based on microcapsule systems, especially those relying on chemical reactions to elicit a chromogenic response, are still very limited. Herein, a facile and metal-free polymerization route with an interesting reaction-induced coloration effect is demonstrated. Under the catalysis of 1,4-diazabicyclo[2.2.2]octane (DABCO), the polymerizations of difunctional or trifunctional activated alkynes proceed very quickly at 0 oC in air. A series of polymers composed of stereoregular enyne structure (major unit) and divinyl ether structure (minor unit) are obtained. Both the catalyst and monomers are colorless while the polymerized products are deep-colored. This process can be applied for the damage visualization of polymers using the microencapsulation technique. Microcapsules containing the reactive alkyne monomer are prepared and mixed in a DABCO-dispersed polymer film. The mechanical damage of this composite film can be readily visualized once the reaction is initiated from the ruptured microcapsules. Moreover, the newly formed polymer automatically sealed the cracks with an additional protection function. | Ting Han; Shusheng Chen; Xinnan Wang; Xinyao Fu; Haifei Wen; Zaiyu Wang; Dong Wang; Anjun Qin; Jinglei Yang; Ben Zhong Tang | Polymer Science; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619b002cb039f2003aafe2e7/original/metal-free-polymerizations-of-microencapsulated-activated-alkynes-for-autonomous-damage-visualization-of-polymers.pdf |
60c756ba4c8919ca22ad48af | 10.26434/chemrxiv.14292161.v1 | Nano- and Mesoscale Structures of Amorphous Calcium Carbonate Indicate Nanoscale Assembly Processes | <div>Here, we approach the issue
of ACC ultrastructure by applying a method for determining atomically resolved structures of
amorphous materials using Monte Carlo simulations constrained by both X-ray and
neutron scattering data. This structural analysis approach allows us to develop
a detailed model for ACC at the atomic level. Our findings reveal that synthetic
ACC, rapidly precipitated at high pH, consists of two-nanometer sized units
containing a high degree of near range order similar to partially disordered
nano-crystals. Small-angle scattering analyses show a multi-scale hierarchical
organisation of the structure, supportive of a multi-step colloid self-assembly
process. Computer simulations and high-resolution transmission electron
microscopy show that the mesostructure of ACC resembles that of a glassy gel
with crystalline material in domains. Our findings support the formation of ACC
by a nanoparticle aggregation process that likely starts from prenucleation
clusters in solution.</div> | Simon M. Clark; Bruno Colas; Dorrit E. Jacob; Jӧrg Neuefeind; Hsiu-Wen Wang; Katherine L. Page; Alan K. Soper; Philipp I. Schodder; Patrick Duchstein; Benjamin Apeleo Zubiri; Tadahiro Yokosawa; Vitaliy Pipich; Dirk Zahn; Erdmann Spiecker; Stephan E. Wolf | Bioinorganic Chemistry; Main Group Chemistry (Inorg.); Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756ba4c8919ca22ad48af/original/nano-and-mesoscale-structures-of-amorphous-calcium-carbonate-indicate-nanoscale-assembly-processes.pdf |
60c751ae4c891969f8ad3ff8 | 10.26434/chemrxiv.13203887.v1 | Mikania Mikrantha Leaf Extract Mediated Biogenic Synthesis of Magnetic Iron Oxide Nanoparticles: Characterization and Its Antimicrobial Activity Study | <p>With an aim to introduce a new highly
potent antimicrobial nanoparticles using an environment-friendly route, he
present work reports the green synthesis of iron oxide nanoparticles (Fe<sub>3</sub>O<sub>4</sub>NPs)
utilizing <i>Mikania mikrantha</i> leaf
extract and its application as efficient antimicrobial agent. The green Fe<sub>3</sub>O<sub>4</sub>NPs
have been described by X-beam diffraction (XRD), Ultraviolet-Visible (UV-Vis) spectroscopy,
Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM) and
Fourier Transform-Infra Red (FT-IR) investigation. The TEM image shows the
rhomboidal Fe<sub>3</sub>O<sub>4</sub>NPs with average mean sizes 20.27 nm. The
FT-IR investigation proved Fe<sub>3</sub>O<sub>4</sub>NPs have been balanced
out through the associations of steroids, terpenoids, flavonoids, phenyl
propanoids, phenolic acids and proteins present in the leaf extract. The
synthesized Fe<sub>3</sub>O<sub>4</sub>NPs shows a very high antibacterial and
antifungal property against 5 bacterial strains such as <i>Bacillus cereus,
Acinetobacter johnsonii, Pseudomonas aeruginosa, Achromobacter spanius </i>and <i>Chromobacterium
pseudoviolaceum</i> strain, and 4 fungal strains (<i>Aspergillus niger, Penicillium citirinum, Fusarium oxysporium</i>, and <i>Candida albicans</i>). The green synthesized
iron oxide nanoparticles can interfere metabolic activities of microorganisms
which determine its antimicrobial properties and could bring a promising
application in the fields of medicine. </p> | Aayushi Biswas; Vanlalveni Chhangte; R. Lalfakzuala; Soumitra Nath; Samuel Lalthazuala Rokhum | Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751ae4c891969f8ad3ff8/original/mikania-mikrantha-leaf-extract-mediated-biogenic-synthesis-of-magnetic-iron-oxide-nanoparticles-characterization-and-its-antimicrobial-activity-study.pdf |
65e602d59138d23161a78e3f | 10.26434/chemrxiv-2024-610nl | Dark State Concentration Dependent
Emission and Dynamics of CdSe Nanoplatelet
Exciton-Polaritons | The recent surge of interest in polaritons has prompted fundamental questions about
the role of dark states in strong light-matter coupling phenomena. Here, we systematically
vary the relative number of dark state polaritons by controlling the number of
stacked CdSe nanoplatelets confined in a Fabry-Pérot cavity. We find the emission spectrum
to change significantly with an increasing number of nanoplatelets, with a gradual
shift of the dominant emission intensity from the lower polariton branch to a manifold
of dark states. Through accompanying calculations based on a kinetic model, this shift is rationalized by an entropic trapping of excitations by the dark state manifold, while
a weak dark state dispersion due to local disorder explains their non-zero emission. Our
results point towards the relevance of the dark state concentration to the optical and
dynamical properties of cavity-embedded quantum emitters with ramifications for Bose-
Einstein condensate formation, polariton lasing, polariton-based quantum transduction
schemes, and polariton chemistry. | Woo Je Chang; Hongfei Zeng; Connor Terry Weatherly; Justin Provazza; Pufan Liu; Emily Weiss; Nathaniel Stern; Roel Tempelaar | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e602d59138d23161a78e3f/original/dark-state-concentration-dependent-emission-and-dynamics-of-cd-se-nanoplatelet-exciton-polaritons.pdf |
65e001119138d231614a1a1d | 10.26434/chemrxiv-2024-lnxl9 | Effect of Temperature on Surfactant Adsorption
at the Liquid-Liquid Interface: Insights from
Molecular Dynamics Simulations | Much is known about the effect of surfactants on the heterogeneity of liquid-liquid
interfaces, but interfacial properties are sensitive to temperature. The relationship
between temperature, surfactant adsorption, and interface structure has not yet been
a major research topic. In this work, the effect of temperature on the interfacial
structure of the tri-n-butyl phosphate saturated water/octane was investigated through
molecular dynamics simulations. We compared the differences in interfacial tension
curves of water/organic systems with and without surfactants at different temperatures,
focusing on the effects of temperature on surfactant adsorption, interfacial stability,
hydrogen bond network, and water extraction. We found the temperature dependence
of interfacial protrusion formation and provided a molecular-level understanding of how
protrusions promote subsequent water extraction processes. | Lei Li; Zhu Liu | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e001119138d231614a1a1d/original/effect-of-temperature-on-surfactant-adsorption-at-the-liquid-liquid-interface-insights-from-molecular-dynamics-simulations.pdf |
62e09bbaed926e486aa770df | 10.26434/chemrxiv-2022-kqbhw | Deprotonation from Diphenylsilane with Organosilyllithium Agents | In contrast to their carbon analogs, there are only a few reports on deprotonation from silanes. This is because the normal polarization of a Si-H bond is Si(delta+)-H(delta-), while that of a C-H bond is C(delta-)-H(delta+). From a bond orbital perspective, a sigma*CH orbital has greater expansion on hydrogen, while a sigma*SiH orbital has greater expansion on Si. Thus, the lone pair of a base mainly attacks hydrogen of a C-H bond for deprotonation, but adds to the silicon atom of a Si-H bond. Previous reports showed that the assistance of negative hyperconjugation between the lone pair of the silyl anion and sigma* orbitals on silyl substituent(s) or an intramolecular chelating group (a pincer ligand) is necessary for deprotonation from silanes. In fact, Kira et al. found that treatment of diphenylsilane with t-butyllithium or LDA resulted in nucleophilic substitution, not deprotonation, only to eliminate a hydride as a leaving group. Recently, we developed a silicon-homologation reaction by a deprotonation-nucleophilic substitution sequence. In that reaction, we assumed that dispro-portionation led to alkoxysilyllithium or a silenoid species generated in situ. We expected that a disproportionation approach could be applied to the deprotonation of monosilanes, such as diphenylsilane. Here we report the first successful approach to the deprotonation of monosilanes with no intramolecular chelation. | Atsushi Takamori; Shoki Ito; Yuji Naruse | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Inorg.); Organometallic Compounds; Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e09bbaed926e486aa770df/original/deprotonation-from-diphenylsilane-with-organosilyllithium-agents.pdf |
6797a2aa81d2151a022a7270 | 10.26434/chemrxiv-2025-t1x54 | Photoreactors Manufactured from 3D-Printed (Photo-) Catalytic Materials | This study demonstrates the successful fabrication of 3D-printed, photoactive reactor components utilizing a TiO2-polypropylene composite filament. The reactor components were employed in the photocatalytic reduction of nitrobenzene and the photocatalyzed synthesis of quinaldine. The reactor inserts were subjected to hydrodynamic and reactive characterization. Furthermore, the viability of employing a solid acid as an alternative to a homogeneous acid catalyst was demonstrated for the photocatalytic synthesis of quinaldine. It was determined that the immobilization of the solid acid not only affects the activity but also the selectivity of the reaction. The immobilization of catalysts obviates the necessity for downstream separation and allows for the modification of reactor designs to achieve optimal reaction performance. The selected rapid prototyping approach facilitated the acceleration of development cycles, and the use of multiple parts comprising different chemically active components enabled the tailoring of (photo)chemical reactors, ultimately paving the way for the development of multi-functional reactors for cascade reactions with high performance and selectivities. | Fabian Guba; Jana Timm; Hong Thu Duong; Aneta Pashkova; Jonathan Zacharias Bloh; Roland Marschall; Dirk Ziegenbalg | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6797a2aa81d2151a022a7270/original/photoreactors-manufactured-from-3d-printed-photo-catalytic-materials.pdf |
60c750b69abda20410f8daa9 | 10.26434/chemrxiv.13072910.v1 | Tunable Eg Orbital Occupancy in Heusler Compounds for Oxygen Evolution Reaction | Heusler compounds have great potential in electrocatalysis due to their
mechanical robustness, metallic conductivity, and wide tunability in
the electronic structure and element compositions. This study reports the first
application of Co<sub>2</sub><i>YZ</i> type Heusler
compounds as electrocatalysts towards oxygen evolution reaction (OER). A range
of Co<sub>2</sub><i>YZ</i> crystals was
synthesized through the arc-melting method and the <i>e</i><sub>g</sub> orbital filling of Co was precisely regulated by
varying <i>Y</i> and <i>Z</i> sites of the compound. A strong correlation between the <i>e</i><sub>g</sub>
orbital filling of reactive Co sites and OER activity was found on Co<sub>2</sub>MnZ
compounds (Z = Ti, Al, V, and Ga) whereby higher catalytic current was achieved
with <i>e</i><sub>g</sub> orbital filling
approaching to unity. A similar trend of <i>e</i><sub>g</sub>
orbital filling on the reactivity of cobalt sites was also observed for other
set of Heusler compounds (Co<sub>2</sub>V<i>Z</i>,
<i>Z</i> = Sn and Ga). This work
demonstrates proof of concept of application of Heusler compounds as a new
class of OER electrocatalyst and the influence of the manipulation of the spin
orbitals on their catalytic performances. | Mingquan Yu; Guowei Li; Chenguang Fu; Enke Liu; Kaustuv Manna; Eko Budiyanto; Claudia Felser; Harun Tüysüz | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b69abda20410f8daa9/original/tunable-eg-orbital-occupancy-in-heusler-compounds-for-oxygen-evolution-reaction.pdf |
6640d66f21291e5d1d12ccb0 | 10.26434/chemrxiv-2024-7hgts | New sulfenate sources for double pallado-catalyzed cross-coupling reaction: application in symmetrical biarylsulfoxides synthesis, and evidence of TADF properties. | Tetrahydro-4H-thiopyran-4-one 1-oxide 1 and sulfinyl-di-tert-butylpropionate 2 were reported as sources of bis-sulfenate anion and applied in a double pallado-catalyzed cross-coupling reaction for the synthesis of symmetrical biarylsulfoxides, tolerating a large array of electronic properties and bulkiness. The photophysical properties of a biarylsulfoxide have been explored, demonstrating an unreported TADF phenomenon on sulfoxide-containing scaffolds. | Valentin Magné; Iulia Cretoiu; Sonia Mallet-Ladeira; Eddy Maerten; David Madec | Physical Chemistry; Catalysis; Homogeneous Catalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6640d66f21291e5d1d12ccb0/original/new-sulfenate-sources-for-double-pallado-catalyzed-cross-coupling-reaction-application-in-symmetrical-biarylsulfoxides-synthesis-and-evidence-of-tadf-properties.pdf |
60c7546c469df4f006f44f41 | 10.26434/chemrxiv.13615421.v2 | Benchmarking Graph Neural Networks for Materials Chemistry | Graph neural networks (GNNs) have received intense interest as a rapidly expanding class of
machine learning models remarkably well-suited for materials applications. To date, a number of
successful GNNs have been proposed and demonstrated for systems ranging from crystal stability
to electronic property prediction and to surface chemistry and heterogeneous catalysis. However,
a consistent benchmark of these models remains lacking, hindering the development and consistent
evaluation of new models in the materials field. Here, we present a workflow and testing platform,
MatDeepLearn, for quickly and reproducibly assessing and comparing GNNs and other machine
learning models. We use this platform to optimize and evaluate a selection of top performing
GNNs on several representative datasets in computational materials chemistry. From our
investigations we note the importance of hyperparameter selection and find roughly similar
performances for the top models once optimized. We identify several strengths in GNNs over
conventional models in cases with compositionally diverse datasets and in its overall flexibility
with respect to inputs, due to learned rather than defined representations. Meanwhile several
weaknesses of GNNs are also observed including high data requirements, and suggestions for
further improvement for applications in materials chemistry are proposed. | Victor Fung; Jiaxin Zhang; Eric Juarez; Bobby Sumpter | Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7546c469df4f006f44f41/original/benchmarking-graph-neural-networks-for-materials-chemistry.pdf |
6733fec97be152b1d0e30f18 | 10.26434/chemrxiv-2024-dlx0q | Phosphoryl-Deoxygenated Access to Cationic Phosphacycles Enabled by Intramolecular SEAr process of Pentavalent Phosphorus Cations | Achieving a direct functionalization of phosphine oxides through the cleavage of the inert P=O double bond remains a formidable challenge in phosphorus chemistry. Herein, we reported a metal-free catalytic electrophilic aromatic substitution (SEAr) phosphacyclization, effectively transforming phosphine oxides into valuable cationic phosphacycles by introducing a powerful nucleofugality (-OTf) to promote the SEAr process via a formal P(v)-dication transition-state. Meanwhile, the theoretically calculated results indicate that the splitting P─OTf bond is pivotal to trigger the SEAr reaction of P(v)-cationic species. Moreover, the kinetic studies also verify that the generated acid (HOTf) would facilitate the nucleofugality leaving from the cationic P-center to accelerate the cyclization. In addition, we investigated their photophysical and electrochemical properties of some typical phosphacycles, which implied the fused di-cationic phosphacyles could be a class of potential optical function molecules. Summarily, this work not only extends the application boundary of phosphine oxides but also paves a way for effectively preparing various mono/di/tri-cationic phosphacycles. | Huang Haiyang; Longgen Sun; Zhichao Mei; Jiang Bai; Chao Chen; Mengyao You; Yanli Wu; Haixin Ding; Qiang Xiao | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6733fec97be152b1d0e30f18/original/phosphoryl-deoxygenated-access-to-cationic-phosphacycles-enabled-by-intramolecular-se-ar-process-of-pentavalent-phosphorus-cations.pdf |
67cb86856dde43c908fc2c0c | 10.26434/chemrxiv-2024-hxgnv-v2 | Teaching the concepts of Donnan potential and liquid-junction potential by evaluating homemade pH and ion-sensitive probes constructed using commercial ion-exchange membranes and reference electrodes | Transport of ions across semipermeable membranes, like ion-exchange membranes, and salt bridges, like porous frits, can each results in electric potential differences that are sensed in most electrochemical experiments. While often neglected by electrochemists, these electric potential differences can significantly impact the interpretation of experimental results. To assist in comprehension of these concepts, which are pertinent to the electrochemistry of many aqueous chemical systems, we designed, implemented, and evaluated a several-hours-long hands-on laboratory activity that we performed with undergraduate and graduate students in electroanalytical chemistry courses. The activity requires that students construct a simple two-compartment electrochemical cell from inexpensive and readily available disposable plastic cuvettes, commercially available polymeric ion-exchange membranes, two nominally identical reference electrodes placed in liquid electrolytes that wet each side of the membrane, and a voltmeter or a potentiostat to measure the open-circuit potential between the reference electrodes, i.e. the cell potential. Using commercially available reference electrodes, each consisting of a wire (e.g. Ag/AgCl) immersed in a fritted tube containing an aqueous electrolyte, measured open-circuit potentials report on the magnitude of both Donnan and liquid-junction electric potential differences. These electric potentials are dictated by the composition of ions in each electrolyte, through interactions with the ion-exchange membrane and porous frits at the tip of each reference electrode. When a cation-exchange membrane separates aqueous solutions consisting of different concentrations of hydrochloric acid (HCl) or potassium hydroxide (KOH), the cell responds like a pH or pK probe, respectively, because the membrane interfaces are more sensitive to the activity of H+ and K+ over Cl– and OH–, respectively. Analogously, when an anion-exchange membrane is used, the cell should respond like a pCl or pOH probe, respectively, because the membrane interfaces are more sensitive to the respective activity of Cl– and OH– over H+ and K+. When the solutions contain large concentrations of multiple types of ions, measured open-circuit potentials typically deviate from values dominated by Donnan potential differences and are instead dominated by liquid-junction-like effects where electric potentials within and across ion-exchange membranes form due to differences in permeabilities of the ions. When reference electrodes consist of wires immersed directly into the aqueous electrolytes that wet the membranes, and not in fritted tubes, measured open-circuit potentials also include contributions from the chemical potential of redox-active species that are present in the aqueous electrolytes as Nernst potentials. While this hands-on laboratory activity is suitable for most upper-level undergraduate students in physical science and engineering disciplines, the concepts of Donnan electric potential, liquid-junction electric potential, and species chemical potential are advanced enough to educate graduate students and senior researchers alike. Student feedback obtained using surveys given before and after the laboratory activity provides additional guidance to instructors who plan to implement our activity. | William Gaieck; Anni Zhang; Ashley Sabatose; Madison Ngo; Eric Schwartz; William White; Simon Luo; Leanna Schulte; Yixian Wang; Shane Ardo | Analytical Chemistry; Polymer Science; Chemical Education; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cb86856dde43c908fc2c0c/original/teaching-the-concepts-of-donnan-potential-and-liquid-junction-potential-by-evaluating-homemade-p-h-and-ion-sensitive-probes-constructed-using-commercial-ion-exchange-membranes-and-reference-electrodes.pdf |
65e5fd9b9138d23161a743ee | 10.26434/chemrxiv-2024-8w4zb | Proximity Biosensor Assay for PROTAC Ternary Complex Analysis | Ternary complexes, consisting of two proteins connected by small molecules like PROTACs or molecular glues pose new challenges for the analysis of molecular interactions, because they depend not only on binary affinities, but are orchestrated by cooperativity and avidity effects. Here, we introduce a proximity binding assay for the simultaneous measurement of binary and ternary interaction kinetics on a biosensor surface. Target proteins and ubiquitin E3 ligase substrate receptors are tethered to mobile swivel arms of a Y-shaped DNA scaffold, which presents them in close proximity to PROTAC analytes flown across the sensor. PROTAC-induced ternary complex formation is measured by fluorescence energy transfer (FRET), while binary interactions are detected by fluorescence quenching. The assay is applied to cereblon (CRBN) and von Hippel-Lindau (VHL) as E3 ligase substrate receptors, a range of compounds including AT1, MZ1, dBETs, and ARV-825 as PROTACs, and the two bromodomains of Brd2, Brd3, Brd4, and BrdT proteins as targets. Automated workflows enable the measurement of 384 real-time sensorgrams in a single run using picomo-lar sample quantities. Ternary and binary binding kinetics and proximity-mediated binding enhancements are analyzed. Ternary complex stability is shown to arise from a dynamic interplay of associations and dissociations, suggesting that proximity assays can be utilized to identify weak interactions. The insights into proximity-mediated binding kinetics can enable the development of PROTACs and molecular glues with improved properties for targeted protein degradation. | Irene Ponzo; Alice Solda; Charlotte Crowe; Goran Dahl; Stefan Geschwindner; Alessio Ciulli; Ulrich Rant | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; High-throughput Screening; Biophysics; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e5fd9b9138d23161a743ee/original/proximity-biosensor-assay-for-protac-ternary-complex-analysis.pdf |
6453b77307c3f02937343ecd | 10.26434/chemrxiv-2023-xl3vr | Biomass to energy: A machine learning model for optimum gasification pathways | Biomass is a highly versatile renewable resource for decarbonizing energy systems. Gasification is a promising conversion technology that can transform biomass into multiple energy carriers to produce heat, electricity, biofuels, or chemicals. At present, identifying the best gasification route for a given biomass relies on trial and error, time-consuming experimentation that, given the wide range of biomass feedstocks available, slows down the deployment of the technology. Here we develop a supervised machine-learning model to find the optimal application of a particular biomass in gasification processes. Our model can select the suitable gasification pathway from the characteristics of the biomass, and also identify the optimal operating conditions for a selected application of the produced gas. In addition, with this model, we can obtain insights into the relationships between biomass properties and gasification results, leading to a better understanding of the process. A relevant aspect of this work is that these results rely on a relatively small dataset, representative of those typically collected by research groups using different types of gasifiers worldwide. This study opens the path for future integration of such data, which would allow addressing the complexity of biomass and conversion process simultaneously. With this work, we aim to increase the flexibility of biomass gasification processes and promote the development of bioenergy technologies, considered crucial in the energy transition context. | María Victoria Gil; Kevin Maik Jablonka; Susana García; Covadonga Pevida; Berend Smit | Energy; Chemical Engineering and Industrial Chemistry; Fuels - Energy Science | CC BY NC 4.0 | CHEMRXIV | 2023-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6453b77307c3f02937343ecd/original/biomass-to-energy-a-machine-learning-model-for-optimum-gasification-pathways.pdf |
63295dbee61502116b1f1e5a | 10.26434/chemrxiv-2022-dhvjf | Investigation of Structure, Ionic Conductivity and
Electrochemical Stability of Halogen-substitution in solid-state
ion conductor Li3YBrxCl6-x | The materials Li3YX6 (X = Cl, Br) are Li-ion conductors to be used as solid electrolytes in all
solid-state batteries. Solid electrolytes ideally have high ionic conductivity and
(electro)chemical compatibility with the electrodes. It was proven that introducing Br to
Li3YCl6 increases ionic conductivity, but, according to thermodynamic calculations, should
also reduce oxidative stability. In this paper, the trade-off between ionic conductivity and
electrochemical stability in Li3YBrxCl6-x (x = 0 – 6) is investigated. The results show that, while
Br-rich materials are more conductive (5.36 10-3 S/cm at 30°C for x = 4.5), the oxidative
stability is lower (3V compared to 3.5V). Small Br content (x = 1.5) doesn’t affect oxidative
stability but substantially increases ionic conductivity compared to pristine Li3YCl6 (2.1
compared to 0.049 10-3 S/cm at 30°C). This work highlights that optimization of substitutions
in the anion-framework provide prolific and rational avenues for tailoring the properties of
solid electrolytes. | Eveline van der Maas; Wenxuan Zhao; Zhu Zheng; Theodosios Famprikis; Michel Thijs; Steven Parnell; Swapna Ganapathy; Marnix Wagemaker | Materials Science; Energy; Ceramics; Composites; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63295dbee61502116b1f1e5a/original/investigation-of-structure-ionic-conductivity-and-electrochemical-stability-of-halogen-substitution-in-solid-state-ion-conductor-li3y-brx-cl6-x.pdf |
6762bd166dde43c90882d019 | 10.26434/chemrxiv-2024-pvdl1 | Emergence of the Robeson bound in non-equilibrium molecular dynamics simulations | Theoretical understanding of multicomponent transport processes in polymer membranes at the molecular level remains a significant scientific challenge due to the high computational cost and poor reproducibility of non-equilibrium molecular simulation methods, aiming at replicating experimental conditions and gradient-driven processes. In this study, we employ Dual Control Volume Molecular Dynamics (DCVMD) with fully atomistic, microsecond-scale simulations to elucidate gas separation mechanisms in porous polymer membranes. Using PIM-PI-8 as a case study, we develop a comprehensive workflow that includes sensitivity analysis and calculations of key transport and structural characteristics of the model membranes. This approach allows us to thoroughly characterize the uncertainties inherent in non-equilibrium simulations and explore the challenges associated with making quantitative predictions using this method. Expanding our analysis to a family of PIM polymers, our simulations successfully replicate several experimentally observed trends. These include a linear correlation between permeability and fractional free volume, as well as the relationship between perm-selectivity and sorption selectivity. Most importantly, we demonstrate that trade-offs between perm-selectivity and permeability emerge in non-equilibrium molecular simulations, qualitatively capturing one of the key patterns in experiments, known as the Robeson upper bound. | Tianmu Yuan; Ronaldo Giro; Mathias B. Steiner; Hsianghan Hsu; Lev Sarkisov | Theoretical and Computational Chemistry; Polymer Science; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762bd166dde43c90882d019/original/emergence-of-the-robeson-bound-in-non-equilibrium-molecular-dynamics-simulations.pdf |
60c74ed2702a9be34c18ba71 | 10.26434/chemrxiv.12799787.v1 | Site Selective C-H Functionalization of Mitragyna Alkaloids Reveals a Molecular Switch for Tuning Opioid Receptor Signaling Efficacy | <p>Mitragynine is the most abundant alkaloid component of the psychoactive plant material “kratom”, which according to numerous anecdotal reports shows efficacy in self-medication for pain syndromes, depression, anxiety, and substance use disorders. We developed a new synthetic method for selective functionalization of the unexplored C11 position of the mitragynine scaffold (C6 position in indole numbering) via the use of an indole-ethylene glycol adduct and subsequent iridium-catalyzed borylation. We discovered that C11 represents a key locant for fine-tuning opioid receptor signaling efficacy. In the 7-hydroxymitragynine (7OH) series, the high efficacy parent compound was transformed to an equipotent low efficacy agonist by introducing a fluorine substituent in this position (11-F-7OH), as demonstrated in vitro at both mouse and human mu opioid receptors (mMOR/hMOR) and in vivo in mouse analgesia tests after systemic administration. Low efficacy opioid agonists are of high interest as candidates for generating safer opioid medications with mitigated adverse effects.</p> | Srijita Bhowmik; Juraj Galeta; Vaclav Havel; Melissa Nelson; Abdelfattah Faouzi; Benjamin Bechand; Tomas Fiala; Amanda Hunkele; Andrew Kruegel; Susruta Majumdar; Jonathan A. Javitch,; Dalibor Sames | Organic Synthesis and Reactions; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2020-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ed2702a9be34c18ba71/original/site-selective-c-h-functionalization-of-mitragyna-alkaloids-reveals-a-molecular-switch-for-tuning-opioid-receptor-signaling-efficacy.pdf |
66cd7ff9a4e53c4876bdf1b9 | 10.26434/chemrxiv-2024-vd18g | Tunable High-Temperature Afterglow through Recombination of Thermally Released Excitons | Developing smart materials with tunable high-temperature afterglow (HTA) luminescence remains a formidable challenge. This study presents a metal-free doping system using boric acid as matrix and polycyclic aromatic hydrocarbons as dopants. This composition achieves dynamically tunable afterglow combining a bright blue HTA lasting for over ten seconds even at 150℃ and an ultra-long yellow room-temperature phosphorescence (RTP) below 110℃. The observed HTA is attributed to the electron-hole recombination within the dopant molecules. Heating stimuli release the trapped electrons from oxygen vacancies formed by boric acid. The planarity of dopants is investigated playing a pivotal role in modulating Dexter electron transfer (ET) for capturing released electrons by dopants and thereby affecting the overall performance of tunable HTA. This work provides an efficient and universal doping strategy to engineer tunable HTA through the synergistic action of thermally releasing electrons, Dexter ET and electron-hole recombination. | Ping Jiang; Bingbing Ding; Jiayi Yao; Lei Zhou; Zhenyi He; Zizhao Huang; Chenjia Yin; He Tian; Xiang Ma | Physical Chemistry; Photochemistry (Physical Chem.); Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cd7ff9a4e53c4876bdf1b9/original/tunable-high-temperature-afterglow-through-recombination-of-thermally-released-excitons.pdf |
618b779dda150690dd9cc86b | 10.26434/chemrxiv-2021-rpkq9 | Insight into the Gd–Pt Bond: Slow Magnetic Relaxation of a Heterometallic Gd–Pt Complex | Lanthanide (Ln) compounds are common research targets in the field of magnetism and optics. Their properties arise from the electron localized in the f-orbital. Moreover, the effect of the covalency between lanthanide and ligands on magnetism attracted significant attention. We provided insight into the Gd–Pt bond (of the heterometallic Ln-Pt complexes: {[Pt(PhSAc)4]Ln[(PhSAc)4Pt]} NEt4·2DMF (Ln = Y(0), La(1), Gd(2); PhSAc = thiobenzoate, NEt4 = tetraethylammonium)); single-crystal polarized X-ray absorption near edge structure (XANES) reveal the electronic states around metal ion, where spectra of Gd-LIII edges show the Gd–Pt direction has the highest covalency (less ionic) around Gd ion in 2. In addition, calculating natural bonding (NBO) analysis, natural population analysis (NPA), LOL, and atoms in molecules (AIM), ab initio calculations reveal the role of metallic and organic ligands in the electronic and magnetic properties of Ln complexes. The slow magnetization relaxation of the Gd complex, which has not been reported previously in the Pt–Gd–Pt system, was observed up to 45K, the highest temperature reported to date among isolated Gd-complexes. | Takefumi Yoshida; Ahmed Shabana; Haitao Zhang; David Chukwuma Izuogu; Tetsu Sato; Kentaro Fuku; Hitoshi Abe; Yoji Horii; Goulven Cosquer; Norihisa Hoshino; Tomoyuki Akutagawa; Alex J. W. Thom; Shinya Takaishi; Masahiro Yamashita | Inorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY 4.0 | CHEMRXIV | 2021-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618b779dda150690dd9cc86b/original/insight-into-the-gd-pt-bond-slow-magnetic-relaxation-of-a-heterometallic-gd-pt-complex.pdf |
6794e25c81d2151a02ed6ea5 | 10.26434/chemrxiv-2024-mzs7b-v2 | A Deep Generative Model for the Inverse Design of Transition Metal Ligands and Complexes | Deep generative models yielding transition metal complexes (TMCs) remain scarce despite the key role of these compounds in industrial catalytic processes, anticancer therapies, and energy transformations. Compared to drug discovery within the chemical space of organic molecules, TMCs pose further challenges including the encoding of chemical bonds of higher complexity and the need to optimize multiple properties. In this work, we developed a junction tree variational autoencoder (JT-VAE) for the inverse design of transition metal ligands and complexes. After implementing a SMILES-based encoding of the metal–ligand bonds, the model was trained with the tmQMg-L ligand library, allowing for the generation of thousands of novel, highly diverse monodentate (κ1) and bidentate (κ2) ligands. The generated ligands were labeled with two target properties of the associated homoleptic square planar iridium TMCs: the HOMO-LUMO gap (ϵ) and the metal charge (qIr), both computed with a DFT method. These properties were used to implement a conditional JT-VAE model that generated ligands from a prompt, with the single- or dual-objective of optimizing either or both the ϵ and qIr properties. A similar model was implemented to condition the generation of metal ligands by their solubility and steric bulk. The JT-VAE models were able to navigate the central and extreme regions of these bidimensional property spaces, allowing for chemical interpretation after decoding their stepwise optimization. These optimizations also had an impact on other chemical properties of interest, including ligand dissociation energies and oxidative addition barriers. | Magnus Strandgaard; Trond Linjordet; Hannes Kneiding; Arron Burnage; Ainara Nova; Jan Halborg Jensen; David Balcells | Theoretical and Computational Chemistry; Physical Chemistry; Organometallic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6794e25c81d2151a02ed6ea5/original/a-deep-generative-model-for-the-inverse-design-of-transition-metal-ligands-and-complexes.pdf |
663b800b21291e5d1dc3e7ca | 10.26434/chemrxiv-2024-8tgr2 | Positional information-based morphogenesis of surfactant droplet swarms emerging from competition between local and global Marangoni effects. | Positional information is proposed as a key element in morphogenesis, where cells differentiate based on their position in an external morphogen gradient. Here, we demonstrate the position-dependent differentiation of floating surfactant droplets as they self-organize in a pH gradient, using the Marangoni effect to translate gradients of surface-active molecules into motion. We start with a field of surfactant microliter-droplets floating on water, that upon the release of surfactant drive local, outbound Marangoni flows and myelin filament growth. Next, we introduce a competing surfactant based on a hydrolysable amide, which is more surface active than the myelin surfactant and thereby inhibits the local Marangoni flows and myelin growth from the droplets. Upon introducing a pH gradient, the amide surfactant hydrolyses in the acidic region, so that the local Marangoni flows and myelin growth are reestablished. The resulting combination of local and global surface tension gradients produces a region of myelin-growing droplets and a region where myelin-growth is suppressed, separated by a wave front of closely packed droplets – featuring an organization that is reminiscent to the ‘French flag’-patterns emerging from concentration gradients in morphogenesis. | Pieter de Visser; Mink Neeleman; Pim Dankloff; Max Derks; Peter Korevaar | Physical Chemistry; Interfaces; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663b800b21291e5d1dc3e7ca/original/positional-information-based-morphogenesis-of-surfactant-droplet-swarms-emerging-from-competition-between-local-and-global-marangoni-effects.pdf |
60c744870f50db338c39610c | 10.26434/chemrxiv.9859103.v1 | Thioether-Facilitated Iridium-Catalyzed Hydrosilylation of Steric 1,1-Disubstituted Olefins | <p>One facile and efficient strategy for the hydrosilylation of steric 1,1-disubstituted
terminal alkenes is demonstrated. Investigations on substrate scope and control
experiments revealed the necessity of thioether in promoting this process under
a simple iridium catalysis system. This convenient and feasible method is
expected to be useful in the synthesis of sulfur-containing organosilicon
polymers with different side-chains.</p><p><br /></p> | Shengtao Ding | Organic Synthesis and Reactions; Polymerization (Organomet.); Reaction (Organomet.) | CC BY 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744870f50db338c39610c/original/thioether-facilitated-iridium-catalyzed-hydrosilylation-of-steric-1-1-disubstituted-olefins.pdf |
60c73f9dbb8c1a62e83d9bc1 | 10.26434/chemrxiv.7295903.v2 | Identifying Structure-Property Relationships through SMILES Syntax Analysis With Self-Attention Mechanism | <p>Recognizing
substructures and their relations embedded in a molecular structure
representation is a key process for <a></a><a>structure-activity</a>
or structure-property relationship (SAR/SPR) studies. A molecular structure can
be either explicitly represented as a connection table (CT) or linear notation,
such as SMILES, which is a language describing the connectivity of atoms in the
molecular structure. Conventional SAR/SPR approaches rely on partitioning the
CT into a set of predefined substructures as structural descriptors. In this
work, we propose a new method to identifying SAR/SPR through linear notation
(for example, SMILES) syntax analysis with self-attention mechanism, an
interpretable deep learning architecture. The method has been evaluated by
predicting chemical property, toxicology, and bioactivity
from experimental data sets. Our results demonstrate that the method yields superior performance
comparing with state-of-the-art methods. Moreover, the method can produce
chemically interpretable results, which can be used for
a chemist to design, and synthesize the activity/property improved compounds.</p> | Shuangjia Zheng; Xin Yan; Yuedong Yang; Jun Xu | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2018-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9dbb8c1a62e83d9bc1/original/identifying-structure-property-relationships-through-smiles-syntax-analysis-with-self-attention-mechanism.pdf |
6344bbe9975e94b3959c50f3 | 10.26434/chemrxiv-2022-bwvzj | Nannochloropsis Algae Biocathodes Improve Cathodic Energy Losses in Two-Chamber Microbial Fuel Cells | Microbial fuel cells (MFCs) are currently being researched as alternative energy sources with promising applications in wastewater treatment. However, in two-chamber designs, cathodic oxygen reduction is slow and limits MFC voltage. Biocathodes, cathodes containing microorganisms, show great promise for improving MFC performance. This study investigated how the microalgae Nannochloropsis affects cathodic oxygen reduction via a thermodynamic analysis of energy losses. Voltage, cathode pH, and cathode pO2 (partial pressure of oxygen) were measured in experimental MFCs containing Nannochloropsis biocathodes and compared to controls containing distilled water or abiotic algae media catahodes. Isolated Nanochloropsis cultures were also assayed. Under open circuit conditions, cathodic energy losses in experimental MFCs were 15% (p = 0.038597) and 19% (p = 0.042435) lower than distilled water and algae media controls, respectively. Experimental MFCs produced 73% higher power at 37% higher current density than distilled water MFCs. While the pH and pO2 of isolated Nannochloropsis cultures increased linearly each day, these measurements were constant in experimental MFC cathodes. This result suggests that participation in oxygen reduction reactions induces a change in Nannochloropsis metabolism, leading to reduced oxygen production and limiting pH changes. Taken together, this work presents a promising new type of two-chambered MFC with lower energy losses and greater power production that can also maintain a constant cathode pH and reveals a new behavior of Nannochloropsis algae in response to oxygen reduction reactions in such MFCs. | Sahand Adibnia; Kevin George | Energy; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6344bbe9975e94b3959c50f3/original/nannochloropsis-algae-biocathodes-improve-cathodic-energy-losses-in-two-chamber-microbial-fuel-cells.pdf |
614d12afb1d4a6427292792f | 10.26434/chemrxiv-2021-cf4rr | Data-driven design of bi-selective OSDAs for intergrowth zeolites | Zeolites are inorganic materials with wide industrial applications due to their topological diversity. Tailoring confinement effects in zeolite pores, for instance by crystallizing intergrown frameworks, can improve their catalytic and transport properties, but controlling zeolite crystallization often relies on heuristics. In this work, we use computational simulations and data mining to design organic structure-directing agents (OSDAs) to favor the synthesis of intergrown zeolites. First, we propose design principles to identify OSDAs which are selective towards both end members of the disordered structure. Then, we mine a database of hundreds of thousands of zeolite-OSDA pairs and downselect OSDA candidates to synthesize known intergrowth zeolites such as CHA/AFX, MTT/TON, and BEC/ISV. The computationally designed OSDAs balance phase competition metrics and shape selectivity towards the frameworks, thus bypassing expensive dual-OSDA approaches typically used in the synthesis of intergrowths. Finally, we propose potential OSDAs to obtain hypothesized disordered frameworks such as AEI/SAV. This work may accelerate zeolite discovery through data-driven synthesis optimization and design. | Daniel Schwalbe-Koda; Avelino Corma; Yuriy Román-Leshkov; Manuel Moliner; Rafael Gómez-Bombarelli | Theoretical and Computational Chemistry; Materials Science; Catalysis; Catalysts; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2021-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614d12afb1d4a6427292792f/original/data-driven-design-of-bi-selective-osd-as-for-intergrowth-zeolites.pdf |
62f779116948b9197ab69042 | 10.26434/chemrxiv-2022-9lc2p | Improved recovery of captured airborne bacteria and viruses with liquid-coated air filters | The COVID-19 pandemic has revealed the importance of the detection of airborne pathogens. Here, we present composite air filters featuring a bio-inspired liquid coating that facilitates the removal of captured aerosolized bacteria and viruses for further analysis. We tested three types of air filters: commercial polytetrafluoroethylene (PTFE), which is well-known for creating stable liquid coatings, commercial high-efficiency particulate air (HEPA) filters, which are widely used, and in-house manufactured cellulose nanofiber mats (CNFM), which are made from sustainable materials. All filters were coated with omniphobic fluorinated liquid to maximize release. We found that coating both the PTFE and HEPA filters with liquid improved the rate at which Escherichia coli was recovered using a physical removal process compared to uncoated controls. Notably, the coated HEPA filters also increased the total number of recovered cells by 57%. Coating the CNFM filters did not improve either the rate of release or total number of captured cells. The ability of the highest performance materials, the liquid-coated HEPA filters were next evaluated on their ability to facilitate the removal of pathogenic viruses via a chemical removal process. Recovery of infectious JC polyomavirus, a non-enveloped virus which attacks the central nervous system, was increased by 92% over uncoated controls; however, there was no significant difference in the total amount of RNA recovered compared to controls. In contrast, significantly more RNA was recovered for SARS-CoV-2, the airborne, enveloped virus which causes COVID-19, from liquid-coated filters. Although the amount of infectious SARS-CoV-2 recovered was 58% higher, these results were not significantly different from uncoated filters due to high variability. These results suggest that the efficient recovery of airborne pathogens from filters could improve air sampling efforts, enhancing biosurveillance and global pathogen early warning. | Daniel P Regan; ChunKi Fong; Avery CS Bond; Claudia Desjardins; Justin Hardcastle; Shao-Hsiang Hung; Andrew P Holmes; Jessica D Schiffman; Melissa S Maginnis; Caitlin Howell | Biological and Medicinal Chemistry; Materials Science; Coating Materials; Bioengineering and Biotechnology; Microbiology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f779116948b9197ab69042/original/improved-recovery-of-captured-airborne-bacteria-and-viruses-with-liquid-coated-air-filters.pdf |
60c7588f337d6c0ca5e29261 | 10.26434/chemrxiv.14562069.v1 | Barrier-Lowering Effects of Baird Antiaromaticity in Photoinduced Proton-Coupled Electron Transfer (PCET) Reactions | <p>Baird antiaromaticity plays a central role in the photochemistry of proton-coupled electron transfer (PCET) reactions. We recognize that many popular organic chromophores that catalyze photoinduced PCET reactions are Hückel aromatic in the ground state, but gain significant Baird antiaromatic character in the lowest ππ* state, having important barrier-lowering effects for electron transfer. Two examples, 1) the photolytic O–H bond dissociation of phenol and 2) solar water splitting in the pyridine-water complex, are discussed. Contrary to an assumed homolytic O–H bond dissociation, both reactions proceed through loss (and gain) of an electron in the π-system (i.e., antiaromaticity relief), followed by heterolytic cleavage of the polar O–H bond near barrierlessly. Nucleus-independent chemical shifts (NICS), ionization energies (IE), electron affinities (EA), and excited-state PCET energy profiles of selected [4<i>n</i>] and [4<i>n</i>+2] π-systems are presented.<br /></p> | Lucas Karas; Chia-Hua Wu; Judy Wu | Photochemistry (Org.); Physical Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7588f337d6c0ca5e29261/original/barrier-lowering-effects-of-baird-antiaromaticity-in-photoinduced-proton-coupled-electron-transfer-pcet-reactions.pdf |
674e31807be152b1d0bb5d56 | 10.26434/chemrxiv-2024-7b2j2-v2 | From Membrane Composition to Antimicrobial Strategies: Experimental and Computational Approaches to AMP Design and Selectivity | The United Nations have committed to end the epidemics of communicable diseases by 2030 (SDG Target 3.3). In contrast with this ambition, the rise of Multi Drug Resistant (MDR) and Pan Drug Resistant (PDR) bacteria poses a threat of a return to the pre-antibiotic era. It is of high priority to find new therapies that target the ESKAPEE group of pathogens and their drug-resistant strains. Antimicrobial peptides (AMPs) are an emerging class of antibiotics that hold promises of overcoming bacterial resistance by using both novel mechanisms of action as well as targeting already known pathways. The chemical space of AMPs is potentially huge and methodologies allowing the rational exploration of novel structures are highly needed. This review focuses on case studies that give novel insights about the mechanisms of action, resistance and selectivity of some relevant AMPs, exemplifying the importance of microscopic, computational and experimental tools. Particular focus will be devoted to bacterial membranes, and how AMPs can target them while sparing human plasma membranes, in order to become safer drugs. The lessons learned from the literature cases give directions towards the development of AMPs as drug products. | Paolo Rossetti; Marius Trollmann; Christina Wichmann; Thomas Gutsmann; Christian Eggeling; Rainer Böckmann | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674e31807be152b1d0bb5d56/original/from-membrane-composition-to-antimicrobial-strategies-experimental-and-computational-approaches-to-amp-design-and-selectivity.pdf |
60c747c7842e658ba6db2a1f | 10.26434/chemrxiv.11786196.v1 | Nitrile-Substituted 2-(Oxazolinyl)-Phenols: Minimalistic Excited-State Intramolecular Proton Transfer (ESIPT)-Based Fluorophores | Herein, we present minimalistic single-benzene, excited-state intramolecular proton transfer (ESIPT) based fluorophores as powerful solid state emitters. The very simple synthesis gave access to all four regioisomers of nitrile-substituted 2(oxazolinyl)phenols (MW = 216.1). In respect of their emission properties they can be divided into aggregation-induced emission enhancement (AIEE) luminophores (1-CN and 2-CN), dual state emission (DSE) emitters (3-CN) and aggregation-caused quenching (ACQ) fluorophores (4‐CN). Remarkably, with compound 1-CN we discovered a minimalistic ESIPT based fluorophore with extremely high quantum yield in the solid state ΦF = 87.3% at λem = 491 nm. Furthermore, quantum yields in solution were determined up to ΦF = 63.0%, combined with Stokes shifts up till 11.300 cm–1. Temperature dependent emission mapping, crystal structure analysis and time-dependent density functional theory (TDDFT) calculations gave deep insight into the origin of the emission properties.<br /> | Dominik Göbel; Daniel Duvinage; Tim Stauch; Boris Nachtsheim | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c7842e658ba6db2a1f/original/nitrile-substituted-2-oxazolinyl-phenols-minimalistic-excited-state-intramolecular-proton-transfer-esipt-based-fluorophores.pdf |
60c744f84c8919a4e8ad28d2 | 10.26434/chemrxiv.9828281.v2 | Thermodynamic Separation of 1-Butene from 2-Butene in Metal–Organic Frameworks with Open Metal Sites | Most C<sub>4</sub> hydrocarbons are obtained as
byproducts of ethylene production or oil refining, and complex and
energy-intensive separation schemes are required for their isolation.
Substantial industrial and academic effort has been expended to develop more cost-effective adsorbent- or membrane-based approaches to purify
commodity chemicals such as 1,3-butadiene, isobutene, and 1-butene, but the
very similar physical properties of these C<sub>4</sub> hydrocarbons makes this
a challenging task. Here, we examine the adsorption behavior of 1-butene, <i>cis</i>-2-butene and <i>trans</i>-2-butene in the metal–organic frameworks M<sub>2</sub>(dobdc)
(M = Mn, Fe, Co, Ni; dobdc<sup>2</sup><sup>−</sup> =
2,5-dioxidobenzene-1,4-dicarboxylate) and
M<sub>2</sub>(<i>m</i>-dobdc) (<i>m</i>-dobdc<sup>4</sup><sup>−</sup> =
4,6-dioxido-1,3-benzenedicarboxylate), which all contain
a high density of coordinatively-unsaturated M<sup>2+</sup> sites. We find that
both Co<sub>2</sub>(<i>m</i>-dobdc) and Ni<sub>2</sub>(<i>m</i>-dobdc) are able to separate 1-butene
from the 2-butene isomers, a critical industrial process that relies largely on
energetically demanding cryogenic distillation. The origin of 1-butene
selectivity is traced to the high charge density retained by the M<sup>2+</sup>
metal centers exposed within the M<sub>2</sub>(<i>m</i>-dobdc) structures, which results in a reversal of the <i>cis</i>-2-butene selectivity typically observed
at framework open metal sites. Selectivity for 1-butene adsorption under
multicomponent conditions is demonstrated for Ni<sub>2</sub>(<i>m</i>-dobdc) in both the gaseous and liquid phases via breakthrough and batch adsorption experiments. | Brandon Barnett; Surya Parker; Maria
V. Paley; Miguel I. Gonzalez; Naomi Biggins; Julia Oktawiec; Jeffrey R. Long | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744f84c8919a4e8ad28d2/original/thermodynamic-separation-of-1-butene-from-2-butene-in-metal-organic-frameworks-with-open-metal-sites.pdf |
60c73f5b567dfe603bec39bd | 10.26434/chemrxiv.7318871.v1 | Direct Carbon Isotope Exchange Through Decarboxylative Carboxylation | A two-step degradation-reconstruction approach to the carbon-14 radiolabeling of alkyl carboxylic acids is presented. Simple activation via redox-active ester formation was followed by nickel-mediated decarboxylative carboxylation to afford a range of complex compounds with ample isotopic incorporations for drug metabolism and pharmacokinetic studies. The practicality and operational simplicity of the protocol was demonstrated by its use in an industrial carbon-14 radiolabeling setting. | Cian Kingston; Michael Wallace; Alban J. Allentoff; Justine deGruyter; Jason Chen; Sharon Gong; Samuel Bonacorsi, Jr.; Phil Baran | Organic Synthesis and Reactions; Mass Spectrometry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5b567dfe603bec39bd/original/direct-carbon-isotope-exchange-through-decarboxylative-carboxylation.pdf |
60feaef40b093e510de39763 | 10.26434/chemrxiv-2021-lxsjk | Machine-learning photodynamics simulations uncover the role of substituent effects on the photochemical formation of cubanes | Photochemical [2+2]-photocycloadditions are used to efficiently access strained organic molecular architectures, storing solar energy in chemical bonds. Functionalized [3]-ladderenes have been shown to undergo [2+2]-photocycloadditions to afford cubanes, an energy-dense class of organic molecules. The substituents (e.g., methyl, trifluoromethyl, and cyclopropyl) affect the overall reactivities of these cubane precursors leading to a yield from 1% to 48%. We now integrate single and multireference calculations and our machine-learning-accelerated non-adiabatic molecular dynamics (ML-NAMD) to understand how substituents affect the mechanistic photodynamics of [2+2]-photocycloadditions. Our calculations show that steric clashes destabilize the 4π-electrocyclic ring-opening pathway and minimum energy conical intersections by 0.72–1.15 eV and reaction energies by 0.68–2.34 eV. In contrast, favorable dispersive interactions stabilize the [2+2]-photocycloaddition pathway, lower the conical intersection energies by 0.31–0.85 eV and cubane reaction energies by 0.03–0.82 eV. The 2 ps ML-NAMD trajectories reveal that closed-shell repulsions block a 6π-conrotatory electrocyclic ring-opening pathway with increasing steric bulk. 57% of the methyl-substituted [3]-ladderene trajectories proceed through the 6π-conrotatory electrocyclic ring-opening, whereas the trifluoromethyl- and cyclopropyl-substituted 3-ladderenes chemoselectively proceed through [2+2]-photocycloaddition pathways. The predicted cubane yields (H: 0.4% < CH3: 1% < CF3: 14% < cPr: 20%) match the experimental trend; these substituents pre-distort the reactants to resemble the conical intersection leading to cubane. | Jingbai Li; Rachel Stein; Daniel Adrion; Steven Lopez | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2021-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60feaef40b093e510de39763/original/machine-learning-photodynamics-simulations-uncover-the-role-of-substituent-effects-on-the-photochemical-formation-of-cubanes.pdf |
610967cf537d10720581604b | 10.26434/chemrxiv-2021-5stld | Natural products and potent analogs: Capacity to interrupt the Spike-human ACE2 complex, Protease, and RdRp targets of COVID-19 replication via molecular docking and MD Simulations | Looking at the severity of SARS-CoV-2 even after the approval of several vaccines like Covishield and Covaxin, there is a concern to find a fruitful remedy for treating infected people in the whole world to stop the spreading of this virus. In this piece of work, we systematically carried out the computational study of potent natural flavonoids Podocarflavone A and Rugosaflavonoid A and their analogs with many targets of COVID-19 such as main Protease (6LU7), S-protein and human ACE2 receptor Complex (6VW1), and RdRp (6M71), which are essential for the survival of nCov-19. MD simulations for 50ns were carried out in TIP3P to check their stability. Thermodynamic stability of the receptor-ligand complexes was evaluated with MMGBSA, and MMPBSA study. The Podocarflavone A and dihydrorugosaflavonoid analogs showed effective binding energy (DS -8.8 to -8.0 Kcal/mol) with S-protein and human ACE2 receptor Complex (6VW1), Protease (6LU7), and RdRp (6M71) of COVID-19. The comparative analysis with several standard antivirals such as remdesivir, oseltamivir, lopinavir, sofosbuvir, tenofovir, galidesivir, and favipiravir displayed that these natural analogs can be better antiviral for the COVID-19. This study demonstrated that halogenated Podocarflavone 2b (MMGBSA -40.93 Kcal/mol, MMPBSA -14.16 Kcal/mol) has comparable results with lopinavir (MMGBSA -43.15 Kcal/mol, MMPBSA -11.89 Kcal/mol). These compounds could be selected for wet-lab screening to develop as lead molecules in the initial infective stage with spike protein and replicative stage with RdRp of the n-Cov-19 virus. | Pratibha Srivastava; Ritu Mamgain; Garima Mishra; Manisha Kharade; Ninad Puranik | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610967cf537d10720581604b/original/natural-products-and-potent-analogs-capacity-to-interrupt-the-spike-human-ace2-complex-protease-and-rd-rp-targets-of-covid-19-replication-via-molecular-docking-and-md-simulations.pdf |
61d6ef267f1d67402d3d1d75 | 10.26434/chemrxiv-2022-0ddv4 | Arel – Investigating [Eu(H2O)9]3+ photophysics and creating a method to by-pass luminescence quantum yield determinations | Lanthanide luminescence has been treated separate from molecular photophysics, although the underlying phenomena are the same. As the optical transitions observed in the trivalent lanthanide ions are forbidden, they do belong to the group that molecular photophysics have yet to conquer, yet the experimental descriptors remains valid. Determining these have proven challenging as full control/knowledge of sample composition is a prerequisite. This has been achieved, and here the luminescence quantum yields (ϕlum), luminescence lifetimes (τobs), oscillator strengths (f ), and the rates of non-radiative (knr) and radiative (kr ≡ A) deactivation of [Eu(H2O)9]3+ was determined for the trigonal tricapped prismatic (TTP) coordination geometry. Further, it was shown that instead of a full photophysical characterization, it is possible to relate changes in transition probabilities to the relative parameter Arel, which does not require reference data. While Arel does not afford comparisons between experiments, it resolves emission intensity changes due to emitter properties—changes in A—from intensity changes due to environmental effects—changes in knr, and differences in the number of photons absorbed. When working with fluorescence this may seem trivial, when working with lanthanide luminescence it is not. | Nicolaj Kofod; Patrick Nawrocki; Thomas Just Sørensen | Physical Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d6ef267f1d67402d3d1d75/original/arel-investigating-eu-h2o-9-3-photophysics-and-creating-a-method-to-by-pass-luminescence-quantum-yield-determinations.pdf |
60c73fdc9abda243d2f8bb5f | 10.26434/chemrxiv.7497803.v1 | Easily-Prepared Hydroxy-Containing Receptors Recognise Anions in Aqueous Media | <div>Despite their readily availability, O–H groups have received relatively little attention as anion recognition motifs. Here, we report two simple hydroxy-containing anion receptors that are prepared in two facile steps followed by anion exchange, without the need for chromatographic purification at any stage. These receptors contain a pyridinium bis(amide) motif as well as hydroxyphenyl groups, and bind mono- and divalent anions in 9:1 CD3CN:D2O, showing a selectivity preference for sulfate. Notably, a “model” receptor that does not contain hydroxy groups shows only very weak sulfate binding in this competitive solvent mixture.</div> | Mahbod Morshedi; Stephanie Boer; Michael Thomas; Nicholas White | Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdc9abda243d2f8bb5f/original/easily-prepared-hydroxy-containing-receptors-recognise-anions-in-aqueous-media.pdf |
67a3997e81d2151a0249651e | 10.26434/chemrxiv-2025-30hr4 | Carbamate Directed peri-C–H Alkynylation: Application to the Synthesis of Zethrenes | The Rh(III)-catalyzed regioselective alkynylation of 1-naphtyl and 1-pyrenyl carbamates and related substrates with bromoacetylenes allows introducing regioselectively an alkyne in the peri position of readily available amino-substituted polycyclic aromatic hydrocarbons. We have applied this methodology for the synthesis of new vertically π-extended zethrene derivatives with two pyrene subunits. Further oxidative cyclodehydrogenation forms regioselectivity a hexabenzo[def,i,lm,qrs,v,yz]pyranthrene, which has been characterized by electron diffraction. | Xiaoqing Shao; Jordi Benet-Buchholz; Antonio Echavarren | Organic Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a3997e81d2151a0249651e/original/carbamate-directed-peri-c-h-alkynylation-application-to-the-synthesis-of-zethrenes.pdf |
66ff32fc51558a15effe7a96 | 10.26434/chemrxiv-2024-b25hm-v3 | Helical dinuclear 3d metal complexes with bis(bidentate) [S,N] ligands: synthesis, structural and computational studies | A diprotic bis(β-thioketoimine) ligand precursor featuring a flexible 4,4’-methylbis(aniline) linker, H22, was synthesised via treatment of the corresponding bis(β-ketoimine) with Lawesson’s reagent. Lithiation of H22 and coordination with one equivalent of d-block metal(II) chlorides MCl2(THF)x (M = Fe, Co and Zn) yielded a corresponding series of homoleptic dinuclear complexes, [M2(μ-2)2]. X-ray diffraction analysis reveals a tetrahedral geometry for the two metals and a double-stranded helicate structure arising from inter-strand face-face π-stacking. These interactions create a helical ‘twist’ of ca. 70°. Utilising a bulky mononucleating β-thioketoiminate ligand, [3]–, the analogous series of heteroleptic monometallic complexes, [M(3)2] (M = Fe, Co and Zn), were prepared and characterised by spectroscopic and analytical techniques. To the best of our knowledge, these are the first complexes of Fe, Co and Zn supported by a bidentate β-thioketoiminate ligand to be structurally characterised by X-ray diffraction. A comprehensive DFT study of all complexes reveals a stronger M–S bonding compared to M–N due to a higher degree of covalency. Solution magnetic studies and Natural Bonding Orbital calculations on the mono- and dinuclear iron and cobalt complexes are consistent with high-spin tetrahedral Fe(II) and Co(II) centres, and cyclic voltammetry reveals both oxidation and reduction processes are accessible. | Jamie Allen; Jörg Saßmannshausen; Kuldip Singh; Alexander F. R. Kilpatrick | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ff32fc51558a15effe7a96/original/helical-dinuclear-3d-metal-complexes-with-bis-bidentate-s-n-ligands-synthesis-structural-and-computational-studies.pdf |
60c742f1bb8c1ab6163da220 | 10.26434/chemrxiv.8853056.v1 | Ni-Catalyzed Conversion of Enol Triflates to Alkenyl Halides | A Ni-catalyzed halogenation of alkenyl triflates was developed that enables the synthesis of a broad range of alkenyl iodides, bromides, and chlorides under mild reaction conditions. The reaction utilizes inexpensive, bench stable Ni(OAc)<sub>2</sub>•4H<sub>2</sub>O as a pre-catalyst and proceeds at room temperature in the presence of sub-stoichiometric Zn and either cod or DMAP as a supporting ligand. | Julie Hofstra; Kelsey Poremba; Alex M. Shimazono; Sarah Reisman | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f1bb8c1ab6163da220/original/ni-catalyzed-conversion-of-enol-triflates-to-alkenyl-halides.pdf |
60c7504e567dfe2eb8ec583f | 10.26434/chemrxiv.12331019.v2 | An Efficient and Accurate Model for Water with an Improved Non-Bonded Potential | A molecular mechanical model for liquid water is developed that uses a physically-motivated potential to represent Pauli repulsion and dispersion instead of the standard Lennard-Jones potential. The model has three-atomic sites and a virtual site located on the ∠HOH bisector (i.e., a TIP4P-type model). Pauli-repulsive interactions are represented using a Buckingham-type exponential decay potential. Dispersion interactions are represented by both and terms. This higher order dispersion term has been neglected by most force fields. The ForceBalance code was used to define parameters that optimally reproduce the experimental physical properties of liquid water. The resulting model is in good agreement with the experimental density, dielectric constant, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, diffusion coefficient, and radial distribution function. A GPU-accelerated implementation of this improved non-bonded potential can be employed in OpenMM without modification by using the CustomNonBondedForce feature. Efficient and automated parameterization of these non-bonded potentials provides a rational strategy to define a new molecular mechanical force field that treats repulsion and dispersion interactions more rigorously without major modifications to existing simulation codes or a substantially larger computational cost. | Mohamad Mohebifar; Christopher Rowley | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7504e567dfe2eb8ec583f/original/an-efficient-and-accurate-model-for-water-with-an-improved-non-bonded-potential.pdf |
60c74462842e659dd2db2447 | 10.26434/chemrxiv.9784595.v1 | Pyrazolium Phase Change Materials for Solar-Thermal and Wind Energy Storage | Renewable energy has the ultimate capacity to
resolve the environmental and scarcity challenges of the world’s energy
supplies. However, both the utility of these sources and the economics of their
implementation are strongly limited by their intermittent nature; inexpensive
means of energy storage therefore needs to be part of the design. Distributed
thermal energy storage is surprisingly underdeveloped in this context, in part
due to the lack of advanced storage materials. Here, we describe a novel family
of thermal energy storage materials based on pyrazolium cation, that operate in
the 100-220°C temperature range, offering safe, inexpensive capacity, opening
new pathways for high efficiency collection and storage of both solar-thermal
energy, as well as excess wind power. We probe the molecular origins of the
high thermal energy storage capacity of these ionic materials and demonstrate
extended cycling that provides a basis for further scale up and development. | Karolina Matuszek; R. Vijayaraghavan; Craig Forsyth; Surianarayanan Mahadevan; Mega Kar; Douglas Macfarlane | Organic Synthesis and Reactions; Energy Storage; Crystallography; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74462842e659dd2db2447/original/pyrazolium-phase-change-materials-for-solar-thermal-and-wind-energy-storage.pdf |
6245659f3affe427bd3bc1aa | 10.26434/chemrxiv-2022-92xn2 | Applying Molecular Dynamics for the Search of New Frank-Kasper Phases of 4-aminopyridinium Chloride. | In a previous crystallographic study on 4-aminopyridinium chloride, Frank-Kasper (FK) phases were serendipitously produced for the first time in a small organic molecule, showing that a simple organic salt can crystallise as hydrate phases of extraordinary complexity. These results raised questions on the mechanisms of formation of such phases, for instance, whether they arise from a specific pre-organization in the liquid state, probably following a non-classical nucleation path and, most importantly, opened discussions on whether this family of structures can be extended.
Here we report the results from a classical molecular dynamics investigation aimed to give more insights on this matter. In particular, we modelled the thermal behaviour of an arbitrary FK phase of 4-aminopyridinium chloride prior the melting and after cooling the molten phase, exploring the mechanisms of dehydration of these phases and nucleation from the melt. The results, also confirmed by experiments, suggest that the dehydration of these phases can occur without dramatic changes in the crystal packing. This is also confirmed by simulating a stable anhydrous FK phase of 4-aminopyridinium chloride. Most importantly, molecular dynamics simulated by cooling the melt of this anhydrous phase, showed the formation of mainly two types of aggregates identical to those observed in the experimental crystal structures. These results confirm that other unknown FK structures might be obtained for our system, either from the melt or by dehydration of the known phases. Moreover, they provide further evidence that their crystallisation follows a non-classical path with a probable formation of two types of highly symmetric clusters that assemble into the solid-state only when the relative ratio of these reaches a threshold.
| Giacomo Saielli; Luca Fusaro; Nikolay Tumanov; Johan Wouters; Vieri Fusi; Riccardo Montis | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6245659f3affe427bd3bc1aa/original/applying-molecular-dynamics-for-the-search-of-new-frank-kasper-phases-of-4-aminopyridinium-chloride.pdf |
60c745bdbb8c1a212f3da723 | 10.26434/chemrxiv.10247528.v1 | Controlling Gas Selectivity in Molecular Porous Liquids by Tuning the Cage Window Size | Control
of pore window size is the standard approach for tuning gas selectivity in
porous solids. Here, we present the first example where this is translated into
a molecular porous liquid formed from organic cage molecules. Reduction of the
cage window size by chemical synthesis switches the selectivity from
Xe-selective to CH<sub>4</sub>-selective, which is understood using <sup>129</sup>Xe,
<sup>1</sup>H, and pulsed-field gradient NMR spectroscopy. | Benjamin Egleston; Konstantin V. Luzyanin; Michael C. Brand; Rob Clowes; Michael E. Briggs; Rebecca L. Greenaway; Andrew
I. Cooper | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745bdbb8c1a212f3da723/original/controlling-gas-selectivity-in-molecular-porous-liquids-by-tuning-the-cage-window-size.pdf |
66a70e565101a2ffa8768861 | 10.26434/chemrxiv-2024-fz37h-v3 | NGT: Generative AI with Synthesizability Guarantees Identifies Potent Inhibitors for a G-protein Associated Melanocortin Receptor in a Tera-scale vHTS Screen | Commercially available, synthesis-on-demand virtual libraries contain upwards of trillions of readily synthesizable compounds for drug discovery campaigns. These libraries are a critical resource for rapid cycles of in silico discovery, property optimization and in vitro validation. However, as these libraries continue to grow exponentially in size, traditional search strategies that scale linearly with the number of compounds encounter significant limitations. Here we present NeuralGenThesis (NGT), an efficient reinforcement learning approach to retrieving compounds from ultra-large libraries that satisfy a set of user-specified constraints. Our method first trains a generative model over a virtual library and subsequently trains a normalizing flow to learn a distribution over latent space that decodes constraint-satisfying compounds. NGT allows multiple constraints without dictating how molecular properties are calculated, enabling versatile searches within virtual libraries. When NGT learned a policy reporting on compound bioactivity for the melanocortin- 2 receptor (MC2R) it prospectively identified potent and selective inhibitors in a three trillion compound library. NGT offers a powerful and scalable solution for navigating ultra-large virtual libraries, accelerating drug discovery efforts. | Saulo de Oliveira; Aryan Pedawi; Victor Kenyon; Henry van den Bedem | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a70e565101a2ffa8768861/original/ngt-generative-ai-with-synthesizability-guarantees-identifies-potent-inhibitors-for-a-g-protein-associated-melanocortin-receptor-in-a-tera-scale-v-hts-screen.pdf |
60c745b8ee301c543bc79391 | 10.26434/chemrxiv.10119299.v1 | Generating Customized Compound Libraries for Drug Discovery with Machine Intelligence | <div>
<div>
<p>Generative machine learning models sample drug-like molecules from chemical space without the need for explicit design rules. A deep learning framework for customized compound library generation is presented, aiming to enrich and expand the pharmacologically relevant chemical space with new molecular entities ‘on demand’. This de novo design approach was used to generate molecules that combine features from bioactive synthetic compounds and natural products, which are a primary source of inspiration for drug discovery. The results show that the data-driven machine intelligence acquires implicit chemical knowledge and generates novel molecules with bespoke properties and structural diversity. The method is available as an open-access tool for medicinal and bioorganic chemistry.<br /></p>
</div>
</div> | Michael Moret; Lukas Friedrich; Francesca Grisoni; Daniel Merk; Gisbert Schneider | Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY 4.0 | CHEMRXIV | 2019-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745b8ee301c543bc79391/original/generating-customized-compound-libraries-for-drug-discovery-with-machine-intelligence.pdf |
64da6dd269bfb8925aee7d64 | 10.26434/chemrxiv-2023-bwkcd | Deprotonation of arenes with weak base: assessing and expanding the functional group compatibility of aryne chemistry | Arynes hold immense potential as reactive intermediates in organic synthesis as they engage in a diverse range of mechanistically distinct chemical reactions. However, the poor functional group compatibility of generating arynes or aryne precursors has stymied their widespread use. Here, we show that generating arynes can be both efficient and mild by deprotonating aryl(TMP)iodonium salts with potassium phosphate (TMP = 2,4,6-trimethoxyphenyl) and these conditions are uniquely compatible with acyclic diaryliodonium salts. We have also performed the first comparison of functional group compatibility by the method of additives across a range of reaction conditions, including the current state-of-the-art, to generate arynes. The scope of the reaction conditions includes sensitive functional groups such as benzylic halides, ketones, alcohols, and boronate esters that are not compatible with prior methods and charts a new course forward for aryne chemistry. | Bryan Metze; Riley Roberts; Aleksandra Nilova; David Stuart | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64da6dd269bfb8925aee7d64/original/deprotonation-of-arenes-with-weak-base-assessing-and-expanding-the-functional-group-compatibility-of-aryne-chemistry.pdf |
633e95ff2984c9cf8e7a2161 | 10.26434/chemrxiv-2022-3d8pk | Novel ultrahard sp2/sp3 hybrid carbon allotrope from crystal chemistry and first principles: body-centered tetragonal C6 ('neoglitter') | A novel ultrahard carbon allotrope, body-centered tetragonal C6 (space group I-4m2) presenting mixed sp2/sp3 carbon hybridizations is proposed by crystal chemistry approach and studied for the ground state structure and stability (both dynamic and mechanical) using density functional theory calculations. Given that C4 tetrahedra in-plane stacking with corner-sharing and connected out-of-plane with C–C trigonal carbon, a close relationship with so-called 'glitter', hypothetical dense carbon network devised ~30 years ago, is established, so we named the new allotrope 'neoglitter'. 'Neoglitter' is characterized by large bulk and shear moduli and very high hardness, and its metallic-like electronic structure is assigned mainly to the itinerant role of trigonal carbon π-electrons. | Samir F. Matar; Vladimir L. Solozhenko | Theoretical and Computational Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633e95ff2984c9cf8e7a2161/original/novel-ultrahard-sp2-sp3-hybrid-carbon-allotrope-from-crystal-chemistry-and-first-principles-body-centered-tetragonal-c6-neoglitter.pdf |
60c741a5469df449c6f42e62 | 10.26434/chemrxiv.8066282.v1 | Magnetic Anisotropy in Divalent Lanthanide Complexes | We report here high-level ab initio calculations for [LnO], Ln=Tb, Dy, Ho, which show that divalent lanthanides can exhibit equally strong magnetic anisotropy and magnetization blocking barriers. | Liviu Ungur; Liviu Chibotaru; Weibing Zhang; Almas Muhtadi | Lanthanides and Actinides; Magnetism; Theory - Inorganic; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a5469df449c6f42e62/original/magnetic-anisotropy-in-divalent-lanthanide-complexes.pdf |
6239922113d47881ab979bcc | 10.26434/chemrxiv-2022-7880k | Terpene Cyclase Mimicking Chlorine-Induced Polyene Cyclizations | Nature forges a plethora of structurally divers polyenes with high efficiency and selectivity in a single cyclization step from achiral precursor. Imitating this powerful strategy has been the subject of numerous synthetic efforts. While bromo- and iodocyclizations have recently been successfully implemented, chlorocyclizations have been scantly investigated. Here, we present a selective and generally applicable biomimetic concept on a direct chlorination-induced polyene cyclization by utilizing a confined HFIP-chlorenium network inspired by the enzymatic pocket of terpene cyclases. Chloro-iodanes proved to be superior as electrophilic chlorine source. Together with catalytic amounts of saccharine in HFIP, a manifold of different alkenes with various inter- and intramolecular nucleophiles were converted with high yields and selectivities (up to 78% yield and d.r. >95:5). The cyclization platform was even extended to several structurally challenging terpenes and terpenoid carbon frameworks. NMR experiments revealed attractive non-covalent interactions between the F-alcohol and the lactone moiety in chloro-iodanes that are probably facilitating the chlorocyclization. The present results mark another milestone in the biomimetic cyclization of polyenes, allowing direct and selective access to these powerful molecules. | Julia Binder; Tanja Gulder | Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6239922113d47881ab979bcc/original/terpene-cyclase-mimicking-chlorine-induced-polyene-cyclizations.pdf |
60c74742842e65902edb2940 | 10.26434/chemrxiv.11576904.v1 | Dehydra-Decyclization of 2-Methyltetrahydrofuran to Pentadienes on Boron-Containing Zeolites | Biomass-derived 2-methyltetrahydrofuran (2-MTHF) undergoes tandem ring-opening and dehydration (dehydra-decyclization) to linear pentadienes, namely 1,3-pentadiene and 1,4-pentadiene. It can also fragment to butenes and formaldehyde through a competing retro-Prins condensation pathway. Using detailed kinetic measurements of 2-MTHF dehydra-decyclization on zeolites with disparate acidities (boro- and alumino-silicates) and micropore environments (MFI, MWW, and BEA), weakly acidic borosilicates were shown to exhibit ca. 10-30% higher selectivity to dienes at about five-to-sixty times lower proton-normalized rates than aluminosilicates (453-573 K). Dehydra-decyclization site time yields (STYs) were invariant for aluminosilicates within the investigated frameworks, indicating the absence of pore-confinement influence. However, individual site-normalized reaction rates varied by almost an order of magnitude on borosilicates in the order MWW > MFI > BEA at a given temperature (523 K), indicating the different nature of active sites in these weak solid acids. The diene distribution remained far from equilibrium and was tuned towards the desirable conjugated diene (1,3-pentadiene) by facile isomerization of 1,4-pentadiene. This tuning capability was facilitated by high bed residence times, as well as the smaller micropore sizes among the considered zeolite frameworks. The suppression of competing pathways and promotion of 1,4-pentadiene isomerization events lead to a hitherto unreported ∼86% 1,3-pentadiene yield and an overall ∼ 89% combined linear C5 dienes’ yield at near quantitative (~98%) 2-MTHF conversion on the borosilicate B-MWW, without a significant reduction in diene selectivities for at least 80 hours time-on-stream under low space velocity (0.85 g reactant/g cat./h) and high temperature (658 K) conditions. Finally, starting with iso-conversion levels (ca. 21-26%) and using total turnover numbers (TONs) accrued over the entire catalyst lifetime as the stability criterion, borosilicates were demonstrated to be significantly more stable than aluminosilicates under reaction conditions (~3-6x higher TONs). | Gaurav Kumar; Dongxia Liu; Dandan Xu; Limin Ren; Michael Tsapatsis; Paul Dauenhauer | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74742842e65902edb2940/original/dehydra-decyclization-of-2-methyltetrahydrofuran-to-pentadienes-on-boron-containing-zeolites.pdf |
60c756a09abda2137df8e576 | 10.26434/chemrxiv.14285222.v1 | Quantum-Classical Simulation of Molecular Motors Driven Only by Light | <div><div><div><p>Molecular motors that exhibit controlled unidirectional rotation provide great prospects for many types of applications including nanorobotics. Existing rotational motors have two key components: photoisomerisation around a pi-bond followed by a thermally activated helical inversion; the latter being the rate-determining step. We propose an alternative molecular system, where the rotation is caused by the electronic coupling<br />of chromophores. This is used to engineer the excited state energy surface and achieve unidirectional rotation using light as the only input and avoid the slow thermal step, potentially leading to much faster operational speeds. To test the working principle we employ quantum-classical calculations to study the dynamics of such a system. We estimate that motors build on this principle should be able to work on a sub-nanosecond timescale for such a full rotation. We explore the parameter space of our model to guide the design of a molecule which can act as such motor.</p></div></div></div> | Atreya Majumdar; Thomas L.C. Jansen | Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756a09abda2137df8e576/original/quantum-classical-simulation-of-molecular-motors-driven-only-by-light.pdf |
630eb9ed0187d93b72a781e7 | 10.26434/chemrxiv-2022-94p6s | High Resolution Photoelectron Spectroscopy of the Acetyl Anion | High-resolution photoelectron spectra of cryogenically cooled acetyl anions (CH3CO¯) obtained using slow photoelectron velocity-map imaging are reported. The high resolution of the photoelectron spectrum yields a refined electron affinity of 0.4352 ± 0.0012 eV for the acetyl radical as well as the observation of new vibronic structure that is assigned based on ab initio calculations. Three vibrational frequencies of the neutral radical are measured to be 1047 ± 3 cm-1 (ν6), 834 ± 2 cm-1 (ν7), and 471 ± 1 cm-1 (ν8). This work represents the first experimental measurement of the ν6 frequency of the neutral. The measured electron affinity is used to calculate a refined value of 1641.35 ± 0.42 kJ mol 1 for the gas-phase acidity of acetaldehyde. Analysis of the photoelectron angular distributions provides insight into the character of the highest occupied molecular orbital of the anion, revealing a molecular orbital with strong d-character. Additionally, details of a new centroiding algorithm based on finite differences, which has the potential to decrease data acquisition times by an order of magnitude at no cost to accuracy, are provided. | Marty DeWitt; Mark Babin; Jascha Lau; Tonia Solomis; Daniel Neumark | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630eb9ed0187d93b72a781e7/original/high-resolution-photoelectron-spectroscopy-of-the-acetyl-anion.pdf |
60c759be0f50db42d839875e | 10.26434/chemrxiv.14726184.v1 | Looking Beyond Adsorption Energies to Understand Interactions at Surface Using Machine Learning | Abstract<br />Identifying factors that influence interactions at the surface is still an active area of research. In this study, we present the importance of analyzing bondlength activation, while interpreting Density Functional Theory (DFT) results, as yet another crucial indicator for catalytic activity. We studied the<br />adsorption of small molecules, such as O 2 , N 2 , CO, and CO 2 , on seven face-centered cubic (fcc) transition metal surfaces (M = Ag, Au, Cu, Ir, Rh, Pt, and Pd) and their commonly studied facets (100, 110, and 111). Through our DFT investigations, we highlight the absence of linear correlation between adsorption energies (E ads ) and bondlength activation (BL act ). Our study indicates the importance of evaluating both to develop a better understanding of adsorption at surfaces. We also developed a Machine Learning (ML) model trained on simple periodic table properties to predict both, E ads and BL act . Our ML model gives an accuracy of Mean Absolute Error (MAE) ∼ 0.2 eV for E ads predictions and 0.02 Å for BL act predictions. The systematic study of the ML features<br />that affect E ads and BL act further reinforces the importance of looking beyond adsorption energies to get a full picture of surface interactions with DFT.<br /> | Sheena Agarwal; Kavita Joshi; Sheena Agrawal | Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759be0f50db42d839875e/original/looking-beyond-adsorption-energies-to-understand-interactions-at-surface-using-machine-learning.pdf |
65022a9c99918fe537e6ced3 | 10.26434/chemrxiv-2023-lng5h | Redox Properties of Flavin in BLUF and LOV Photoreceptor Proteins from Hybrid QM/MM Molecular Dynamics Simulation | Flavins play an important role in many oxidation and reduction processes in bio- logical systems. For example, flavin adenine dinucleotide (FAD) and flavin mononu- cleotide (FMN) are common cofactors found in enzymatic proteins that use the special redox properties of these flavin molecules for their catalytic or photoactive functions. The redox potential of the flavin is strongly affected by its (protein) environment, however the underlying molecular interactions of this effect are still unknown. Using hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) simulation techniques, we have studied the redox properties of flavin in the gas phase, aqueous solution and two different protein environments, in particular a BLUF and a LOV photoreceptor domain. By mapping the changes in electrostatic potential and solvent structure, we gain insight in how specific polarization of the flavin by its environment tunes the re- duction potential. We find also that accurate calculation of the reduction potentials of these systems by using the hybrid QM/MM approach is hampered by a too limited sampling of the counter ion configurations and by artifacts at the QM/MM boundary. We make suggestions on how these issues can be overcome. | Murat Kılıç; Bernd Ensing | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65022a9c99918fe537e6ced3/original/redox-properties-of-flavin-in-bluf-and-lov-photoreceptor-proteins-from-hybrid-qm-mm-molecular-dynamics-simulation.pdf |
6769abaefa469535b993a264 | 10.26434/chemrxiv-2024-w770q | Revealing and Mitigating Crossover-Driven Side Reactions in Ferrocyanide-Based Redox Flow Batteries | There is an urgent need for new energy storage solutions that will support the decarbonization of the electricity grid. Aqueous organic redox flow batteries are low-cost, long-duration energy storage devices that are in the process of being commercialized for this application; however, their operational lifetime is limited by electrolyte decomposition and crossover. These degradation processes are generally studied separately, so the relationship between the two is poorly understood. Previously, it had been assumed that the main contribution to battery capacity fade was electrochemical degradation of the electrolytes. Using the on-line 1H NMR crossover characterization method we developed previously, we reveal the first evidence for crossover-driven side reactions in redox flow batteries. If the impact of these side reactions is not considered, it will lead to an underestimation of crossover and its impacts on battery lifetime. We further introduce simple ‘simulated-crossover’ experiments to identify anolyte-catholyte combinations where these processes are occurring. Using these simulated-crossover experiments, we find that crossover-driven side reactions can be mitigated by avoiding the use of anolytes with hydroxyl functional groups when using ferrocyanide electrolytes. These insights should be used to assist the design of new anolytes and catholytes, which will facilitate the development of longer-lasting redox flow batteries. | Emma Latchem; Thomas Kress; Muireann de h-Óra; Anqi Wang; Qilei Song; Alexander C Forse | Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6769abaefa469535b993a264/original/revealing-and-mitigating-crossover-driven-side-reactions-in-ferrocyanide-based-redox-flow-batteries.pdf |
649b888e6e1c4c986b73e535 | 10.26434/chemrxiv-2023-8t8kt-v4 | Discovering Chemically Novel, High-Temperature
Superconductors | One of the biggest unsolved problems in condensed
matter physics is what mechanism causes high-temperature superconductivity and if there is a material that can exhibit superconductivity at both room temperature and atmospheric pressure. Among the many important properties of a superconductor, the critical temperature (Tc) or transition temperature is the point at which a material transitions into a superconductive state. In this implementation, machine learning is used to predict
the critical temperatures of chemically unique compounds in an attempt to identify new chemically novel, high-temperature superconductors. The training data set (SuperCon) consists of known superconductors and their critical temperatures, and the testing data set (NOMAD) consists of around 700,000 novel chemical formulae. The chemical formulae in these data sets are first passed through a collection of rapid screening tools, SMACT, to check for chemical validity. Next, the DiSCoVeR algorithm is used to train on the SuperCon data to form a model, and then screens through batches of the formulae in the NOMAD data set. Having a combination of a chemical distance metric, density-aware dimensionality reduction, clustering, and a regression model, the DiSCoVeR algorithm serves as a tool to identify and assess these superconducting compositions [1]. This research and implementation resulted in the screening of
chemically novel compositions exhibiting critical temperatures upwards of 150 K, which correlates to superconductors in the cuprate class. This implementation demonstrates a process of performing machine learning-assisted superconductor screening (while exploring chemically distinct spaces) which can be utilized in the materials discovery process. | Colton C. Seegmiller; Sterling G. Baird; Hasan M. Sayeed; Taylor D. Sparks | Theoretical and Computational Chemistry; Materials Science; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649b888e6e1c4c986b73e535/original/discovering-chemically-novel-high-temperature-superconductors.pdf |
64edbafd3fdae147fa0f854b | 10.26434/chemrxiv-2023-144cn | Fabrication of Porphyrin Based Colorimetric Sensor for the Detection of Liver Cirrhosis Biomarker
| The early detection of liver cirrhosis biomarkers is crucial for timely medical intervention and improved patient outcomes. In this study, we present the fabrication of a novel colorimetric sensor based on porphyrin derivatives for the specific and sensitive detection of a prominent liver cirrhosis biomarker. The sensor design capitalizes on the unique optical properties of porphyrins, allowing for a rapid and visually detectable response upon biomarker binding. The synthesis and characterization of the porphyrin receptor are detailed, highlighting its structural and spectroscopic properties. The sensor's performance was evaluated using RGB analysis demonstrating exceptional selectivity and sensitivity towards the target biomarker. Importantly, the sensor's response mechanism is elucidated, shedding light on the underlying molecular interactions. The proposed porphyrin-based colorimetric sensor offers a promising avenue for the early diagnosis of liver cirrhosis, paving the way for point-of-care applications and enhancing disease management. | Anup Gurung; Rushmika Gurung; Priyanka Kumari; Thinley Bhutia; Promodh Poudyal; Gyaltsen Pradhan | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64edbafd3fdae147fa0f854b/original/fabrication-of-porphyrin-based-colorimetric-sensor-for-the-detection-of-liver-cirrhosis-biomarker.pdf |
6308705f11986ca74346921d | 10.26434/chemrxiv-2022-xd6cg | Mixology of MA1-xEAxPbI3 Hybrid Perovskites: Phase Transitions, Cation Dynamics and Photoluminescence | Mixing of molecular cations in hybrid lead halide perovskites is a highly effective approach to enhance stability and performance of the optoelectronic devices based on these compounds. In this work, we prepare and study novel mixed methylammonium (MA)-ethylammonium (EA) MA1-xEAxPbI3 (x < 0.4) hybrid perovskites. We use a suite of different techniques to determine the structural phase diagram, cation dynamics and photoluminescence properties of these compounds. Upon introduction of EA, we observe a gradual lowering of the phase transition temperatures indicating stabilization of the cubic phase. For mixing levels higher than 30%, we obtain a complete suppression of the low-temperature phase transition and formation of a new tetragonal phase with different symmetry. We use the broadband dielectric spectroscopy to study the dielectric response of the mixed compounds in an extensive frequency range, which allows us to distinguish and characterize three distinct dipolar relaxation processes related to the molecular cation dynamics. We observe that mixing increases the rotation barrier of the MA cations and tunes the dielectric permittivity values. For the highest mixing levels, we observe signatures of the dipolar glass phase formation. Our findings are supported by the density functional theory calculations. Our photoluminescence measurements reveal a small change of the band gap upon mixing indicating suitability of these compounds for optoelectronic applications. | Mantas Simenas; Sergejus Balciunas ; Anna Gagor ; Agnieszka Pieniazek ; Kasper Tolborg ; Martynas Kinka; Vytautas Klimavicius ; Sarunas Svirskas ; Vidmantas Kalendra ; Maciej Ptak ; Daria Szewczyk ; Artur Herman ; Robert Kudrawiec ; Adam Sieradzki ; Robertas Grigalaitis ; Aron Walsh ; Miroslaw Maczka; Juras Banys | Physical Chemistry; Inorganic Chemistry; Physical and Chemical Processes; Physical and Chemical Properties; Crystallography | CC BY NC 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6308705f11986ca74346921d/original/mixology-of-ma1-x-e-ax-pb-i3-hybrid-perovskites-phase-transitions-cation-dynamics-and-photoluminescence.pdf |
60c74b2aee301c3c2cc79dac | 10.26434/chemrxiv.12298559.v1 | Unsupervised Attention-Guided Atom-Mapping | Knowing how atoms rearrange during a chemical transformation is fundamental to numerous applications aiming to accelerate organic synthesis and molecular discovery. This labelling is known as atom-mapping and is an NP-hard problem. Current solutions use a combination of graph-theoretical approaches, heuristics, and rule-based systems. Unfortunately, the existing mappings and algorithms are often prone to errors and quality issues, which limit the effectiveness of supervised approaches. Self-supervised neural networks called Transformers, on the other hand, have recently shown tremendous potential when applied to textual representations of different domain-specific data, such as chemical reactions. Here we demonstrate that attention weights learned by a Transformer, without supervision or human labelling, encode atom rearrangement information between products and reactants. We build a chemically agnostic attention-guided reaction mapper that shows a remarkable performance in terms of accuracy and speed, even for strongly imbalanced reactions. Our work suggests that unannotated collections of chemical reactions contain all the relevant information to construct coherent sets of reaction rules. This finding provides the missing link between data-driven and rule-based approaches and will stimulate machine-assisted discovery in the chemical domain.<div><br /></div><div>Code is available at: https://github.com/rxn4chemistry/rxnmapper</div> | Philippe Schwaller; Benjamin Hoover; Jean-Louis Reymond; Hendrik Strobelt; Teodoro Laino | Organic Synthesis and Reactions; Chemoinformatics; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b2aee301c3c2cc79dac/original/unsupervised-attention-guided-atom-mapping.pdf |
6706e1e912ff75c3a1fd3519 | 10.26434/chemrxiv-2024-msd0q-v3 | Widespread misinterpretation of pKa terminology for zwitterionic compounds and its consequences | The acid dissociation constant (pK a), which quantifies the propensity for a solute to donate a proton to its solvent, is crucial for drug design and synthesis, environmental fate studies, chemical manufacturing, and many other fields. Unfortunately, the terminology used for describing acid base phenomena is inconsistent, causing large potential for misinterpretation. In this work, we examine a systematic confusion underlying the definition of “acidic” and “basic” pKa values for zwitterionic compounds. Due to this confusion, some pKa data is misrepresented in data repositories, including the widely- used and highly trusted ChEMBL Database. Such datasets are widely used to supply training data for pKa prediction models, and hence, confusion and errors in the data makes model performance worse. Herein, we discuss the intricacies of this issue. We make suggestions for describing acid-base phenomena, training pKa prediction models, and stewarding pKa datasets, given the high potential for confusion and potentially high impact of accurately describing acid-base phenomena. | Jonathan Zheng; Ivo Leito; William Green | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706e1e912ff75c3a1fd3519/original/widespread-misinterpretation-of-p-ka-terminology-for-zwitterionic-compounds-and-its-consequences.pdf |
655f59b15bc9fcb5c9354a43 | 10.26434/chemrxiv-2023-cs3wb | Molecular Similarity: Theory, Applications, and Perspectives | Molecular similarity pervades much of our understanding and rationalization of chemistry. This has become particularly evident in the current data-intensive era of chemical research, with similarity measures serving as the backbone of many Machine Learning (ML) supervised and unsupervised procedures. Here, we present a discussion on the role of molecular similarity in drug design, chemical space exploration, chemical “art” generation, molecular representations, and many more. We also discuss more recent topics in molecular similarity, like the ability to efficiently compare large molecular libraries. | Kenneth Lopez Perez; Juan Avellaneda Tamayo; Lexin Chen; Edgar Lopez Lopez; K. Euridice Juarez Mercado; Jose Luis Medina Franco; Ramon Miranda-Quintana | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655f59b15bc9fcb5c9354a43/original/molecular-similarity-theory-applications-and-perspectives.pdf |
65f3f4b1e9ebbb4db9be6918 | 10.26434/chemrxiv-2024-0g9h1 | Mechano-Adaptive Meta-Gels Through Synergistic Chemical and Physical Information-Processing | Global functional adaptation after local mechanical stimulation, as in mechanobiology and the mimosa plant, is fascinating and ubiquitous in nature. This is achieved by locally sensing mechanical deformation with precise thresholds, processing this information via biochemical circuits, followed by downstream actuation. The integration of such embodied intelligence allowing for mechano-to-chemo-to-function information-processing remains elusive in man-made systems. By merging the fields of chemical circuits and metamaterials, we introduce adaptive metamaterial hydrogels (meta-gels) that can accurately sense mechanical stimuli (local touch and global strain), transmit this information over long distances via reaction-diffusion signaling, and induce downstream mechanical strengthening by growing nanofibril networks, or soft robotic actuation through competitive swelling. All elements of the sensor-processor-actuator system are embedded in the device, functioning autonomously without external feeding reservoirs. Our concept enables designing advanced life-like materials systems that synergistically combine two worlds – chemical circuits for chemical information-processing and metamaterial unit cells for physical information-processing. | Brigitta Duzs; Oliver Skarsetz; Giorgio Fusi; Claudius Lupfer; Andreas Walther | Polymer Science; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f3f4b1e9ebbb4db9be6918/original/mechano-adaptive-meta-gels-through-synergistic-chemical-and-physical-information-processing.pdf |
6792fb6081d2151a02b55c28 | 10.26434/chemrxiv-2025-q68w5-v2 | Cultivating Success: Mentoring Experiences in the Honors Program (Chemistry) for Health Sciences at Community College | The pursuit of academic excellence is often marked by collaborative endeavors and supportive relationships. This study delves into the mentoring experiences within the Honors Program for Chemistry for Health Sciences at Community College. The research focused on students who completed classes in preparatory chemistry and Introductory General, Organic, and Biochemistry. Through qualitative exploration, this article unveils the multifaceted role of mentors and their impact on the academic and personal growth of participating students.
The study used a thorough approach involving talking to participants, watching what happens, and studying academic results. What I discovered shows that being mentored in the Honors Program truly helps students succeed. It creates a feeling of belonging, provides direction, and helps individuals develop skills. I looked at how mentoring plays out in both basic and more advanced chemistry classes, showing how it goes beyond just regular academic stuff.
I also talked about the difficulties students face while being mentored, which gave me ideas on how to make things better. In the end, I suggest some ways teachers, school leaders, and mentors can improve Honors Programs even more. I discussed the opportunity to create special support programs, particularly in chemical education, to make the learning experience more fulfilling.
This research helped me, as a chemistry instructor, to better understand the problems that did not allow me to create productive collaboration between mentors and students. This study provides a nuanced perspective on how mentorship shapes the educational journeys of students in the dynamic field of chemical education. The lessons learned from this study will help me to find new strategies for cultivating success within the Honors program. | Olena Novobranova | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6792fb6081d2151a02b55c28/original/cultivating-success-mentoring-experiences-in-the-honors-program-chemistry-for-health-sciences-at-community-college.pdf |
60c754af842e656a47db41d0 | 10.26434/chemrxiv.13064225.v2 | Energy-Based Automatic Determination of Buffer Region in the Divide-and-Conquer Second-Order Møller-Plesset Perturbation Theory | In the linear-scaling divide-and-conquer (DC) electronic structure method, each subsystem is calculated together with the neighboring buffer region, the size of which affects the energy error introduced by the fragmentation in the DC method. The DC self-consistent field calculation utilizes a scheme to automatically determine the appropriate buffer region that is as compact as possible for reducing the computational time while maintaining acceptable accuracy (<i>J. Comput. Chem.</i> <b>2018</b>, <i>39</i>, 909). To extend the automatic determination scheme of the buffer region to the DC second-order Møller-Plesset perturbation (MP2) calculation, a scheme for estimating the subsystem MP2 correlation energy contribution from each atom in the buffer region is proposed. The estimation is based on the atomic orbital Laplace MP2 formalism. Based on this, an automatic buffer determination scheme for the DC-MP2 calculation is constructed and its performance for several types of systems is assessed. | Toshikazu Fujimori; Masato Kobayashi; Tetsuya Taketsugu | Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2021-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754af842e656a47db41d0/original/energy-based-automatic-determination-of-buffer-region-in-the-divide-and-conquer-second-order-m-ller-plesset-perturbation-theory.pdf |
6677ef3f01103d79c5eb3160 | 10.26434/chemrxiv-2024-0lrh8 | Repurposing a Fully-Reducing Polyketide Synthase for 2-Methyl Guerbet-like Lipid Production | In Nature, thousands of diverse and bioactive polyketides are assembled by a family of multifunctional, “assembly line” enzyme complexes called Polyketide Synthases (PKS). Since the late 20th century, there have been several attempts to decode, re-arrange and “re-programme” the PKS assembly line to generate valuable materials such as biofuels and platform chemicals. By mastering the biosynthetic logic underpinning PKSs, there exists the potential to develop these enzymes into scalable biocatalysts for sustainable chemical production. Here, the first module from Mycobacterium tuberculosis (Mt) PKS12 – an unorthodox, “modularly-iterative” PKS – was modified and repurposed towards the production of 2-methyl Guerbet lipids, which have wide applications in industry. We established a robust method for the recombinant expression and purification of this modified module (named [M1*]), and we demonstrated its synthetic utility in generating several 2-methyl Guerbet-like lipids (C13-C21). Furthermore, we studied and applied the promiscuous thioesterase (TE) activity of a neighbouring β-ketoacyl synthase (KS) to release [M1*]-bound condensation products in a one-pot biosynthetic cascade. Finally, by coupling the E. coli fatty acyl-CoA synthetase FadD to [M1*], we could generate our primary target compound – 2-methyltetradecanoic acid – from lauric acid, highlighting the potential to derive valuable lipids from inexpensive fatty acids. This work demonstrates the biosynthetic potential of [M1*] in generating industrially-useful Guerbet-like chemicals, whilst also contributing to the broader exploration and application of PKS modules for sustainable chemical manufacturing. | Michael Andrés Herrera; Stephen McColm; Louise-Marie Craigie; Joanna Simpson; Fraser Brown; David Clarke; Reuben Carr; Dominic Campopiano | Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6677ef3f01103d79c5eb3160/original/repurposing-a-fully-reducing-polyketide-synthase-for-2-methyl-guerbet-like-lipid-production.pdf |
672ea39c5a82cea2fa8986a0 | 10.26434/chemrxiv-2024-4jf0z | Computational Studies on the Functional and Structural Impact of Pathogenic Mutations in Enzymes | Enzymes are critical biological catalysts involved in maintaining the intricate balance of metabolic processes within living organisms. Mutations in enzymes can result in disruptions to their functionality, that may lead to a range of diseases. This review focuses on computational studies that investigate the effects of disease-associated mutations in various enzymes. Through molecular dynamics simulations, multiscale calculations, and machine learning approaches, computational studies provide detailed insights into how mutations impact enzyme structure, dynamics, and catalytic activity. This review emphasizes the increasing impact of computational simulations in understanding molecular mechanisms behind enzyme (dis)function by highlighting the application of key computational methodologies to selected enzyme examples, aiding in the prediction of mutation effects and the development of therapeutic strategies. | Upeksha C. Dissanayake; Arkanil Roy; Yazdan Maghsoud; Sarthi Polara; Tanay Debnath; G. Andrés Cisneros | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672ea39c5a82cea2fa8986a0/original/computational-studies-on-the-functional-and-structural-impact-of-pathogenic-mutations-in-enzymes.pdf |
653ad506a8b423585a4d9baf | 10.26434/chemrxiv-2023-jt226 | Chiral Carbene Zinc(II) Dithiolates: Efficient TADF Emitters Showing Circularly Polarized Luminescence | Luminescent metal complexes based on earth abundant elements are a valuable target to substitute 4d/5d transition metal complexes as triplet emitters in advanced photonic applications. Whereas Cu(I) complexes have been thoroughly investigated in the last two decades for this purpose, no structure-property-relationships for efficient luminescence involving triplet excited states from ZnII complexes are established. Herein, we report on the design of monomeric carbene zinc(II) dithiolates (CZT) featuring a donor-acceptor-motif that leads to highly efficient thermally activated delayed fluorescence (TADF) with for Zn(II) compounds unprecedented radiative rate constants k(TADF) = 1.2x10^6 s^-1 at 297 K. Our high-level DFT/MRCI calculations revealed that the relative orientation of the ligands involved in the ligand-to-ligand charge transfer (1/3^LLCT) states is paramount to control the TADF process. Specifically, a dihedral angle of 36-40° leads to very efficient reverse intersystem-crossing (rISC) on the order of 10^9 s^-1 due to spin–orbit coupling (SOC) mediated by the sulfur atoms in combination with a small E(S1-T1) of ca. 56 meV (calc. 20 meV). In addition, the chiral carbene ligand leads to the generation of circularly polarized luminescence (CPL) with high dissymmetry values g(lum) of up to 3.3x10^-2 in polystyrene (PS). | Mousree Mitra; Ondřej Mrózek; Markus Putscher; Jasper Guhl; Benjamin Hupp; Andrey Belyaev; Christel Marian; Andreas Steffen | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Compounds; Spectroscopy (Inorg.); Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653ad506a8b423585a4d9baf/original/chiral-carbene-zinc-ii-dithiolates-efficient-tadf-emitters-showing-circularly-polarized-luminescence.pdf |
660a2a069138d23161db0a91 | 10.26434/chemrxiv-2024-pvskd | A spreadsheet-based redox flow battery cell cycling model enabled by closed-form approximations | The complex interplay between numerous parasitic processes—voltage losses, crossover, decay—challenges interpretation of cycling characteristics in redox flow batteries (RFBs). Mathematical models offer a means to predict cell performance prior to testing and to interpret experimentally measured cycling data, however most implementations require extensive domain knowledge and computational resources. To address these challenges, we previously developed a computationally inexpensive zero-dimensional modeling approach by deriving analytical solutions to species mass balances during cell cycling. Here, we expand on this framework by deriving closed-form expressions for key performance metrics and comparing the accuracy of these simplifications to the complete analytical model. The resulting closed-form model streamlines the computational structure and allows for spreadsheet modeling of cell cycling behavior, which we highlight by developing a simulation package in Microsoft® Excel®. We then apply this model to analyze previously published experimental data from our group and others, highlighting its utility in numerous diagnostic configurations—bulk electrolysis, compositionally unbalanced symmetric cell cycling, and full cell cycling. Given the accessibility of this modeling toolkit, it has potential to be a widely deployable tool for RFB research, aiding in data interpretation, performance prediction, and electrochemistry education. | Bertrand Neyhouse; Fikile Brushett | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660a2a069138d23161db0a91/original/a-spreadsheet-based-redox-flow-battery-cell-cycling-model-enabled-by-closed-form-approximations.pdf |
63810ea20146ef496905eab8 | 10.26434/chemrxiv-2022-hfxtx | CO2-mineralization and carbonation reactor rig: design and validation for in situ neutron scattering experiments - Engineering and Lessons Learned | CO2 mineralization via aqueous Mg/Ca/Na-carbonate (MgCO3/CaCO3/Na2CO3) formation represents a huge opportunity for the utilization of captured CO2. However, large-scale mineralization is hindered by slow kinetics due to the highly hydrated character of the cations in aqueous solutions (Mg2+ in particular). Reaction conditions can be optimized to accelerate carbonation kinetics, for example by the inclusion of selected additives that promote competitive dehydration of Mg and subsequent agglomeration, nucleation and crystallization. Towards tracking mineralisation and these steps of the reaction, neutron scattering presents unprecedented advantages over traditional techniques for time-resolved in situ measurements. However, a setup providing continuous solution circulation to ensure reactant system homogeneity for industrially relevant CO2-mineralizsation was currently available for use on neutron beamlines. We therefore undertook the design, construction, testing and implementation of such a self-contained reactor rig for use on selected neutron beamlines at the ISIS Neutron and Muon Source (Chilton, UK). The design ensured robust attachment via suspension from the covering flange to stabilize the reactor assembly and all fittings, as well as facilitating precise alignment of the entire reactor and sample (test) cell with respect to beam dimension and direction. The assembly successfully accomplished the principal tasks of providing a continuous flow of the reaction mixture for homogeneity, quantitative control of CO2 flux into the mixture as well as temperature and pressure regulation throughout the reaction and measurements. The design is discussed, with emphasis placed on the reactor including its geometry, components and all technical specifications. Descriptions of the offbeamline bench tests, safety and functionality, as well as the installation on beamlines and trial experimental procedure are provided, together with representative raw neutron scattering results.
| Ali Mortazavi; Fu V. Song; Michael Michael Dudman; Michael J. Evans; Robert Copcutt; Giovanni Romanelli; Franz Demmel; David H. Farrar; Stewart F. Parker; Kun V. Tian; Devis Di Tommaso; Gregory A. Chass | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Physical and Chemical Processes; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63810ea20146ef496905eab8/original/co2-mineralization-and-carbonation-reactor-rig-design-and-validation-for-in-situ-neutron-scattering-experiments-engineering-and-lessons-learned.pdf |
62b31f5b7da6ce7eaa1b6e24 | 10.26434/chemrxiv-2022-l4vbd | Recent Advances in Multiple Heterohelicenes | Multiple heterohelicenes involing one or more heteroatoms in the helical backbone, in light of the importance of their spanning disciplines of the chemical and material sciences, have thus attracted significant interest from various research fields. In this review, we will specially concentrate on current progress in the chemistry of multiple heterohelicenes especially of those with boron, nitrogen, oxygen, silicon, or phosphorous atoms fused into the skeletons over the past decade (2012-2022). For each multiple heterohelicenes, their synthesis, structural features, electronic and chiroptical properties, as well as examples of their applications, are collected. | Jun-Jian Shen; Wen-Wen Yang | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b31f5b7da6ce7eaa1b6e24/original/recent-advances-in-multiple-heterohelicenes.pdf |
60c73f204c8919ccc9ad1f10 | 10.26434/chemrxiv.7149461.v2 | Impurities Limit the Capacitance of Carbon Based Supercapacitors | Supercapacitors cannot fulfill their potential as energy storage devices without substantially improving their comparatively low energy density. This requires improving their capacitance. Unfortunately, predicting the capacitance of the carbon-based materials that typically make up supercapacitor electrodes is difficult. For example, remarkably we lack a theoretical understanding of the capacitance of even the most basic example of a carbon electrode: highly oriented pyrolytic graphite. (HOPG) This material has a capacitance that is an order of magnitude lower than both standard metals and theoretical expectations. Here, we use new quantum mechanical calculations in combination with a critical analysis of the literature to demonstrate that the standard explanations of this unusually low capacitance are inadequate. We then demonstrate that a layer of hydrocarbon impurities which has recently been shown to form on graphite is the most plausible explanation. We develop a model of this effect which accounts for the penetration of solvent into the hydrocarbon layer as the voltage increases. This model explains the characteristic V shape of the capacitance as a function of voltage. Finally, we present evidence that this layer also forms and limits the capacitance in real supercapacitor materials such as activated carbon. Methods of modifying or removing this layer could therefore potentially lead to significant improvements in the capacitance of typical supercapacitors. | Timothy Duignan; Xiu Song Zhao | Carbon-based Materials; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f204c8919ccc9ad1f10/original/impurities-limit-the-capacitance-of-carbon-based-supercapacitors.pdf |
67b862bc6dde43c908d7b26e | 10.26434/chemrxiv-2025-gxj4r | Accelerated stochastic simulation of free radical polymerization through a hybrid algorithm | Stochastic Simulation Algorithms (SSA) are a cornerstone in simulating Free Radical Polymerization (FRP) due to their accuracy and reliability. However, computational inefficiency remains a challenge for large-scale and complex polymerization systems. This work introduces a novel stochastic simulation algorithm designed to significantly enhance computational efficiency while maintaining high accuracy. By streamlining simulation processes, the proposed algorithm reduces computational time and extends the scalability of stochastic methods. Beyond FRP, the algorithm is also applied to Degenerative Transfer (DT) systems as a demonstration of its versatility. These results showcase the algorithm's potential as a universal tool for accelerating stochastic simulations in polymer science, enabling deeper insights and broader applications across various polymerization processes. | Hang Yin; Yinghao Li; Wenxin Wang; Jing Lyu | Polymer Science; Chemical Engineering and Industrial Chemistry; Polymerization kinetics; Process Control | CC BY 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b862bc6dde43c908d7b26e/original/accelerated-stochastic-simulation-of-free-radical-polymerization-through-a-hybrid-algorithm.pdf |
67734989fa469535b94cef56 | 10.26434/chemrxiv-2025-m7hkl | Light-Driven Paramagnetic Tags for Efficient Pseudocontact Shifts Measurments in Protein NMR Spectroscopy | Pseudocontact shifts (PCS) values are essential for studies of protein structure and dynamics. However, structural calcu-lations typically require multiple tags or labeling at multiple sites, which can be both time-consuming and expensive. In this study, we demonstrate that two independent sets of PCS values can be obtained using an azobenzene-based paramag-netic probe. Upon photo-isomerization, the magnetic field around the protein is redistributed, resulting in a distinct NMR spectrum and enabling the acquisition of a new set of structural constraints. This light-driven spatial motion of the para-magnetic center eliminates the need for additional mutations or chemical activators to induce magnetic transitions, pav-ing the way for the development of tensor-switchable paramagnetic tags. | Zhaofei Chai; Qiong Wu; Kai Cheng; Weixuan Wang; Xiaoli Liu; Yujun Xie; Zhen Li; Ling Jiang; Conggang Li | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67734989fa469535b94cef56/original/light-driven-paramagnetic-tags-for-efficient-pseudocontact-shifts-measurments-in-protein-nmr-spectroscopy.pdf |
615daad6b564b6aee56e4315 | 10.26434/chemrxiv-2021-zd39r-v2 | Virtual screening of norbornadiene-based molecular solar thermal energy storage systems using a genetic algorithm | We present a computational methodology for the screening of a chemical space of 10²⁵ substituted norbornadiene molecules for promising kinetically stable molecular solar thermal (MOST) energy storage systems with high energy densities that absorb in the visible part of the solar spectrum. We use semiempirical tight-binding methods to
construct a dataset of nearly 34,000 molecules and train graph convolutional networks to predict energy densities, kinetic stability, and absorption spectra and then use the
models together with a genetic algorithm to search the chemical space for promising MOST energy storage systems. We identify 15 kinetically stable molecules, five of which have energy densities greater than 0.45 MJ/kg and the main conclusion of this study is that the largest energy density that can be obtained for a single norbornadiene moiety with the substituents considered here, while maintaining a long half-life and absorption in the visible spectrum, is around 0.55 MJ/kg. | Nicolai Ree; Mads Koerstz; Kurt V. Mikkelsen; Jan H. Jensen | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615daad6b564b6aee56e4315/original/virtual-screening-of-norbornadiene-based-molecular-solar-thermal-energy-storage-systems-using-a-genetic-algorithm.pdf |
622aa5a6702f04329eb7cee8 | 10.26434/chemrxiv-2022-pvwjn | General mechanism and mitigation for strong adhesion of frozen oil sands on solid substrates | Oil sands adhered on truck bed reduce transport capacity of the truck, require manual cleaning, and create hurdles for automated surface mining. Study on the adhesion properties of oil sands to solid substrates is important to minimize the fouling of substrates during mining operation. In this work, we study the influence of hydrophobicity and mechanical properties of the substrates on the adhesion strength of frozen oil sands. By using an adhesion force apparatus with temperature control, we measure the adhesion strength of both ice and frozen oil sands on six types of substrates with water contact angle from ∼20◦ to ∼130◦ and Young’s modulus from a few MPa to 300 GPa. A clear linear correlation between the adhesion strength of pure ice and that of frozen oil sands is observed. Furthermore, the adhesion strength increases with the load on the oil sands sample and reaches a plateau at ∼450 kPa. The maximum adhesion strength may be due to the limit of particle packing of oil sands. We also demonstrate that spray coating of anti-freezing liquids is effective for the mitigation of the adhesion of frozen oil sands. Substrates coated with various anti-freezing liquids showed undetectable oil sands adhesion strength at -20 ◦C with 0.06 MPa of load. The study on oil sands adhesion and potential fouling mitigation method may provide a potential solution to industries looking to reduce fouling of surfaces by frozen granular matter. | Qimeng Yang; Nikoo Moradpour; Jae Bem You; Dehui Wang; Boran Tian; Shaofeng Sun; Qi Liu; Xu Deng; Dan Daniel; Xuehua Zhang | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622aa5a6702f04329eb7cee8/original/general-mechanism-and-mitigation-for-strong-adhesion-of-frozen-oil-sands-on-solid-substrates.pdf |
6776ea28fa469535b991c521 | 10.26434/chemrxiv-2025-w2qn8 | LEGOLAS: a Machine Learning method for rapid and accurate predictions of protein NMR chemical shifts. | This work introduces LEGOLAS, a fully open source TorchANI-based neural network model designed to predict NMR chemical shifts for protein backbone atoms. LEGOLAS has been designed to be fast, and without loss of accuracy, as our model is able to predict backbone chemical shifts with root-mean-square errors of 2.69 ppm for N, 0.95 ppm for Ca, 1.40 ppm for Cb, 1.06 ppm for C’, 0.52 ppm for amide protons, and 0.29 ppm for H. The program predicts chemical shifts at least one order of magnitude faster than the widely utilized SHIFTX2 model. This breakthrough allows us to predict NMR chemical shifts for a very large number of input structures, such as frames from a molecular dynamics trajectory. In our simulation of the protein BBL from E. coli, we observe that averaging the chemical shift predictions for a set of frames of an MD trajectory substantially improves the agreement with experiment with respect of using a single frame of the dynamics. We also show that LEGOLAS can be successfully applied to the problem of recognizing the native states of a protein among a set of decoys. | Mikayla Darrows; Dimuthu Kodituwakku; Jinze Xue; Ignacio Pickering; Nicholas Terrel; Adrian Roitberg | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2025-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6776ea28fa469535b991c521/original/legolas-a-machine-learning-method-for-rapid-and-accurate-predictions-of-protein-nmr-chemical-shifts.pdf |
6301914b58843b1cd5974eb5 | 10.26434/chemrxiv-2022-l1r9s-v2 | Interpretable Machine Learning of Two-Photon Absorption | Molecules with strong two-photon absorption (TPA) are important in many advanced applications such as upconverted laser and photodynamic therapy, but their design is hampered by the high cost of experimental screening and accurate quantum chemical (QC) calculations. Here we perform a systematic study by collecting and analyzing with interpretable machine learning (ML) experimental TPA database with ca. 900 molecules. We uncovered that only very few molecular features are sufficient to explain the TPA magnitudes. The most important feature is conjugation length (rather than area as believed before) followed by features reflecting effects of donor and acceptor substitution and coplanarity. These features are used to create a very fast ML model with prediction errors of similar magnitude compared to experimental and affordable QC meth-ods errors. Our ML model has the potential for high-throughput screening as additionally validated with our new experimental measurements. | Yuming Su; Yiheng Dai; Yifan Zeng; Caiyun Wei; Yangtao Chen; Fuchun Ge; Peikun Zheng; Da Zhou; Pavlo O. Dral; Cheng Wang | Physical Chemistry; Materials Science; Dyes and Chromophores; Optical Materials; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6301914b58843b1cd5974eb5/original/interpretable-machine-learning-of-two-photon-absorption.pdf |
6526d20d45aaa5fdbbc92bdd | 10.26434/chemrxiv-2023-jvs7d | Liquid DNA coacervates form porous capsular hydrogels via viscoelastic phase separation on microdroplet interface | Liquid-liquid phase separation (LLPS) droplets of biopolymers are known as functional microdroplets in living cells and have recently been used to construct protocells and artificial cells. The formation of DNA coacervates (also referred to as DNA droplets) from branched DNA nanostructures and the control of their physical properties via DNA nanostructure design were demonstrated previously. For the construction of artificial cells or protocells, however, even though physical effects such as surface tension, wetting, and viscoelasticity are more important in a tiny (micrometer-sized), confined environment than in a bulk solution environment, they have not been explored yet. This study shows that a tiny, confined environment using a water-in-oil (W/O) microdroplet interface modulates the phase separation dynamics of DNA coacervates, leading to micrometer-sized porous capsular structures. The porous structures were produced via two types of viscoelastic phase separation (VPS) processes in DNA coacervates: (i) simple VPS and (ii) cluster-cluster aggregation after VPS. Finally, it was shown that environmental chemical stimulation can manipulate porous capsular DNA hydrogels extracted from W/O microdroplets. These results provide an approach for designing and fabricating artificial cells or protocells with complex structures and physicochemical properties. | Masamune Morita; Tetsuro Sakamoto; Shin-ichiro M. Nomura; Satoshi Murata; Miho Yanagisawa; Masahiro Takinoue | Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Biophysics; Interfaces | CC BY 4.0 | CHEMRXIV | 2023-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6526d20d45aaa5fdbbc92bdd/original/liquid-dna-coacervates-form-porous-capsular-hydrogels-via-viscoelastic-phase-separation-on-microdroplet-interface.pdf |
673fbe767be152b1d0413b8f | 10.26434/chemrxiv-2024-8g61h-v2 | In situ neutron reflectometry reveals the interfacial microenvironment driving electrochemical ammonia synthesis | Electrified interfaces are critical to the performance of energy systems and often demonstrate substantial complexity under operating conditions. Nanoscale understanding of the interfacial microenvironment, i.e., the solid electrolyte interphase (SEI), in lithium-mediated nitrogen reduction (Li-N2R) is key for realizing efficient ammonia (NH3) production. Herein, we have used time-resolved neutron reflectometry (NR) to observe SEI formation under Li-N2R conditions. We found that LiBF4-based electrolyte provided a substantially more well-defined SEI layer than previous SEI NR interrogation that used LiClO4, highlighting the underlying chemistry that dictates electrolyte design and enabling new NR-based studies. Using in situ neutron reflectometry, we found the LiBF4-derived SEI under Li-N2R conditions comprises a thick, diffuse outer layer and a thin, compact inner layer at low current cycling (<2 mA/cm2), revealing a structure which ex situ studies have not been able to probe. Increased current cycling and sustained current cycling led to the merge of the layers to a single-layer SEI. We used isotope contrast methods with d6-EtOH and d8-THF to drive time-resolved tracking of SEI growth at low current cycling, revealing that the proton donor modifies the inner layer, and the solvent modifies the outer layer. Li dendritic growth was observed in the absence of a proton donor. Neutron absorption also indicated the presence of boron in the SEI, underscoring the value of neutron-based interrogation. Our results inform Li-based systems and reaction microenvironments, and these methods can be applied broadly to interfacial energy technologies. | Valerie Anne Niemann; Mathieu Doucet; Peter Benedek; Niklas Henrik Deissler; Jon Bjarke Valbaek Mygind; Sang-Won Lee; Isabela Rios Amador; Wrayzene Willoughby; Ib Chorkendorff; Adam Nielander; William Tarpeh; Thomas Jaramillo | Materials Science; Catalysis; Energy; Nanostructured Materials - Materials; Thin Films; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673fbe767be152b1d0413b8f/original/in-situ-neutron-reflectometry-reveals-the-interfacial-microenvironment-driving-electrochemical-ammonia-synthesis.pdf |
65debf0766c1381729bb3947 | 10.26434/chemrxiv-2024-ljrdf | Immobilization of Liposomes into Porous Anodized Aluminum Oxide and Intact and On-demand Release by Ultrasonic Irradiation | Synthetic anionic liposomes represent useful models of extracellular vesicles for understanding their biological functions. Their integration into nanomaterials holds a great potential for various applications including drug delivery systems, separation techniques and containers. In this study, we report that porous anodized aluminum oxide (AAO) membranes serve as useful platforms for the integration of synthetic anionic liposomes. The examination using fluorophore (NBD)-labelled liposomes (average diameter, 122 nm) revealed that liposomes were successfully immobilized into AAO pores with no leakage for one week. We demonstrated that the immobilized liposomes could be released from AAO pores rapidly and on-demand by only one-minute ultrasonic irradiation while they did not leak spontaneously during storage in the buffer solution. Significantly, the released liposomes were found to be intact by scanning electron-assisted dielectric microscopy (SE-ADM) and spectroscopic techniques, with their size and morphology remaining unchanged compared to the liposomes before immobilization into AAO. Systematic analysis of a series of liposomes suggested that the immobilization of anionic liposomes proceeded though an ion-exchange mechanism. Intactness of released liposomes would be ascribed to the relatively weak attraction with the pore surface due to the electrostatic repulsion. The utilization of AAO membranes as beneficial platforms for integrating liposomes is anticipated to expedite the development of functional composite materials incorporating liposomes for drug delivery systems. | Masahiro Okada; Yusuke Sato; Toshihiko Ogura; Tetsuji Itoh; Seiichi Nishizawa | Physical Chemistry; Materials Science; Composites; Controlled-Release Systems; Physical and Chemical Properties; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65debf0766c1381729bb3947/original/immobilization-of-liposomes-into-porous-anodized-aluminum-oxide-and-intact-and-on-demand-release-by-ultrasonic-irradiation.pdf |
677b274c81d2151a020280ca | 10.26434/chemrxiv-2025-wbt2v | Label-Free Identification of Tumor Tissues by Coherent Nonlinear Vibrational Mode Imaging | We present vibrational sum-frequency generation (VSFG) microscopy as a new label-free chemical imaging technique for tumor identification. This method combines the chemical-bond selectivity of vibrational spectroscopy with coherent interference of second-order coherent nonlinear optics. Using a fast line-scanning VSFG microscope, we obtained hyperspectral VSFG images of collagen I from both lung tissues bearing metastatic tumors and in tumor-free ones, which reveal drastic different spectral signatures: tumor samples exhibit large NH stretch (NHS) and CH stretch (CHS) versus the CH2 symmetric stretch (CH2,Ss), compared to healthy controls. We then identified two key spectral signatures to distinguish metastatic tumor and tumor-free tissues: the intensity ratio of NHS/CH2,Ss and CHS/CH2,Ss modes. These signatures demonstrated high fidelity in distinguishing between tumors and normal tissue in both mouse and human lung samples. Theoretical modeling indicates that distinctive interferences of spectral peaks are sensitive to interfibrillar distances, at 130 of nanometer level. These findings suggest that collagen fibrils are more densely packed in tumors, corroborating the enhanced stiffness observed in tumor tissues. VSFG microscopy offers a highly selective, label-free chemical imaging characterization that preserves sample integrity, making it a valuable tool for oncology, pathology and fundamental biophysical research. | Bin Yang; Jianyu Ren; Chun-Chieh Yu; Zixuan Wang; Minghui Cao; Shizhen Emily Wang; Wei Xiong | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2025-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677b274c81d2151a020280ca/original/label-free-identification-of-tumor-tissues-by-coherent-nonlinear-vibrational-mode-imaging.pdf |
60c7495cbdbb895c81a39177 | 10.26434/chemrxiv.12055893.v1 | Synthetic Routes to Novel Fluorogenic Pyronins and Silicon Analogs with Far-Red Spectral Properties and Enhanced Aqueous Stability | Fluorogenic detection of reactive (bio)analytes is often achieved with "smart" probes, whose activation mechanism causes the release of aniline-based fluorophores. Indeed, the protection-deprotection of their primary amino is the simplest way to induce dramatic and valuable changes in spectral features of the fluorogenic reporter. In this context, and due to their small size and intrinsic hydrophilicity, we focused on pyronin dyes and related heteroatom analogs (i.e., formal derivatives of 3-imino-3H-xanthen-6-amine and its silicon analog) for their use as optically tunable aniline-based fluorophores. To overcome some severe limitations associated with the use of such fluorogenic scaffolds (i.e., poor aqueous stability and spectral features only in the green-yellow spectral range), the synthesis of novel unsymmetrical derivatives of (Si)-pyronins bearing a single bulky tertiary aniline (i.e., N-methylindoline and julolidine) was explored and presented in this Article. This structural alteration has been found to be beneficial to dramatically lower electrophilicity of the meso-position and to reach attractive fluorescence properties within the far-red spectral region. | Garance Dejouy; Kévin RENAULT; Ibai E. Valverde; Anthony ROMIEU | Organic Compounds and Functional Groups; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7495cbdbb895c81a39177/original/synthetic-routes-to-novel-fluorogenic-pyronins-and-silicon-analogs-with-far-red-spectral-properties-and-enhanced-aqueous-stability.pdf |
627a7cb16b12b6022e6d25f3 | 10.26434/chemrxiv-2022-208k9 | Synthesis and styrene copolymerization of novel bromo, chloro, fluoro, and iodo ring-substituted octyl phenylcyanoacrylates | Halogen ring-substituted octyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2(CH2)6CH3 (where R is 4-bromo, 2-chloro, 3-chloro, 4-chloro, 2-fluoro, 3-fluoro, 4-fluoro, 2-iodo, 3-iodo, 4-iodo) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and octyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Aleksandra D. Deren; Luke R. Bench; Daniyal Chaudhary; Antoinette M. Defrenza; Ava E. Devaney; Shayla M. Emmett; Kristen Folkes; Jigisha J. Gohel; Mylena G. de S. Sena Sena; Omair S. Hussain; Massie Jones; Sara M. Rocus; William S. Schjerven; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627a7cb16b12b6022e6d25f3/original/synthesis-and-styrene-copolymerization-of-novel-bromo-chloro-fluoro-and-iodo-ring-substituted-octyl-phenylcyanoacrylates.pdf |
67c6875afa469535b9d8b7fa | 10.26434/chemrxiv-2025-wxq8d | Concurrent processing of VQE-UCCSD calculations with the FMO scheme | The fragmentation-based method has attracted interest to reduce the computational cost for quantum computation of quantum chemistry. Previously (K. Sugisaki et al., J. Comput. Chem. 2024, 45, 2204), we reported the simulation results of the variational quantum eigensolver (VQE) of unitary coupled cluster singles and doubles (UCCSD) under the fragment molecular orbital (FMO) framework, where the influence of Trotter error was highlighted for (FH)3 and H2O-(FH)2 models. In this report, the concurrent processing for the fragment list is adapted with examples of Li(I)-(H2)n (n=4,6) clusters. VQE-UCCSD energies and timing data are presented to illuminate the issues of practical applications. | Hideo Doi; Kenji Sugisaki; Tatsuya Nakano; Takahiro Katagiri; Yuji Mochizuki | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c6875afa469535b9d8b7fa/original/concurrent-processing-of-vqe-uccsd-calculations-with-the-fmo-scheme.pdf |
60c75227bdbb89ac32a3a1ff | 10.26434/chemrxiv.13182590.v2 | Nickel-Catalyzed Site- and Stereoselective Reductive Alkylalkynylation of Alkynes | Development of a catalytic multicomponent reaction by orthogonal activation of readily available substrates for the streamlined difunctionalization of alkynes is a compelling objective in organic chemistry. Alkyne carboalkynylation, in particular, offers a direct entry to valuable 1,3-enynes with different substitution patterns. Here, we show that the synthesis of stereodefined 1,3-enynes featuring a trisubstituted olefin is achieved by merging alkynes, alkynyl bromides and redox-active <i>N</i>-(acyloxy)phthalimides through nickel-catalyzed reductive alkylalkynylation. Products are generated in up to 89% yield as single regio- and <i>E</i> isomers. Transformations are tolerant of diverse functional groups and the resulting 1,3-enynes are amenable to further elaboration to synthetically useful building blocks. With olefin-tethered <i>N</i>-(acyloxy)phthalimides, a cascade radical addition/cyclization/alkynylation process can be implemented to obtain 1,5-enynes. The present study underscores the crucial role of redox-active esters as superior alkyl group donors compared to haloalkanes in reductive alkyne dicarbofunctionalizations. | Yi Jiang; Jiaoting Pan; Tao Yang; Joel Jun Han Lim; Yu Zhao; Ming Joo Koh | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75227bdbb89ac32a3a1ff/original/nickel-catalyzed-site-and-stereoselective-reductive-alkylalkynylation-of-alkynes.pdf |
60c74fdd567dfe84f7ec5777 | 10.26434/chemrxiv.12110643.v2 | Enantiodivergent Non-Linear Effects in Asymmetric Catalysis | In this paper, we theoretically discuss the enantiodivergent product formation in asymmetric catalysis, a process in which the sign of the overall product enantiomer switches upon a change of catalyst concentration. The presented model is based on a catalytic system that consists of both discrete and dimeric aggregated metal complexes, in competition and in equilibrium. These concepts were then expanded to a non-enantiopure catalyst, giving rise to enantiodivergent non-linear effects – a special case of a hyperpositive non-linear effects where the product enantiomer’s sign switches upon a change of the catalyst enantiomeric excess. Different cases are considered allowing a discussion of the influence of the parameters governing both models. Finally, we present experimental results that support the enantiodivergence while varying the concentration of enantiopure catalyst or while varying the enantiomeric excess of the catalyst, using chiral N-methylephedrine as a ligand for the enantioselective addition of dimethylzinc to benzaldehyde. | Yannick Geiger; thierry achard; aline maisse-françois; Stephane Bellemin-Laponnaz | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fdd567dfe84f7ec5777/original/enantiodivergent-non-linear-effects-in-asymmetric-catalysis.pdf |
60c73e3abdbb89c181a37dc8 | 10.26434/chemrxiv.6721553.v1 | Biomimetic Extracellular Vesicles Embedded with Black Phosphorus for Molecular Recognition-Guided Biomineralization | Extracellular
vesicles (EVs) are involved in the regulation of cell physiological activity
and the reconstruction of extracellular environment. Matrix vesicles (MVs) are
a type of EVs, and they participate in the regulation of cell mineralization.
Herein, bioinspired MVs embedded with black phosphorus are functionalized with
cell-specific aptamer (denoted as Apt-bioinspired MVs) for stimulating
biomineralization. The aptamer can direct bioinspired MVs to targeted cells,
and the increasing concentration of inorganic phosphate originated from the
black phosphorus can facilitate cell biomineralization. The photothermal effect
of the Apt-bioinspired MVs also positively affects mineralization. In addition,
the Apt-bioinspired MVs display outstanding bone regeneration performance.
Considering the excellent behavior of the Apt-bioinspired MVs for promoting
biomineralization, our strategy provides a way of designing bionic tools for
studying the mechanisms of biological processes and advancing the development
of medical engineering.<br /> | Yingqian Wang; Xiaoxia Hu; Lingling Zhang; Chunli Zhu; Jie Wang; Yingxue Li; Yulan Wang; Can Wang; Yufeng Zhang; Quan Yuan | Biochemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e3abdbb89c181a37dc8/original/biomimetic-extracellular-vesicles-embedded-with-black-phosphorus-for-molecular-recognition-guided-biomineralization.pdf |
65366f20c3693ca993f107d7 | 10.26434/chemrxiv-2023-c2zz0 | Hierarchically Conductive Electrodes Unlock Stable and Scalable CO2 Electrolysis | Electrochemical CO2 reduction has emerged as a promising CO2 utilization technology, with Gas Diffusion Electrodes (GDEs) becoming the predominant architecture to maximize performance. GDEs must maintain robust hydrophobicity to prevent flooding, while also ensuring high conductivity to minimize ohmic losses. Intrinsic material tradeoffs have led to two main GDE architectures: carbon paper is highly conductive but floods easily; ePTFE is flooding resistant but non-conductive, limiting electrode sizes to just 5cm2. Here we demonstrate a Hierarchically Conductive GDE architecture (HCGDE) which overcomes these limitations by employing inter-woven microscale conductors within a hydrophobic ePTFE membrane. We develop a model which captures the spatial variability in voltage and product distribution on electrodes due to ohmic losses and use it to rationally design the HCGDE. The HCGDE architecture overcomes scaling limitations, achieving C2+ Faradaic efficiencies of ~75% for electrodes as large as 50cm2. Our approach can be broadly applied to scale any electrode, independent of catalyst chemistry and morphology. | Simon Rufer; Michael Nitzsche; Sanjay Garimella; Jack Lake; Kripa K. Varanasi | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65366f20c3693ca993f107d7/original/hierarchically-conductive-electrodes-unlock-stable-and-scalable-co2-electrolysis.pdf |
63adef0de9d0fd6c4b2dee98 | 10.26434/chemrxiv-2022-m0sht-v2 | A new computational tool for interpreting infrared spectra of molecular complexes | The popularity of the Infrared (IR) spectroscopy is due
to its high interpretive power. This study presents
a new computational tool for analyzing the IR spectra
of molecular complexes in terms of intermolecular
interaction energy components. In particular, the
proposed scheme enables to associate the changes in IR spectra occurring upon the complex formation with individual types of intermolecular interactions (electrostatic, exchange, induction, dispersion), thus providing a completely new insight into the relations between the spectral features and the nature of interactions in molecular complexes. To demonstrate its interpretive power, we analyze for selected vibrational modes which interaction types rule the IR intensity changes upon
the formation of two different types of complexes, namely π...π stacked (benzene...1,3,5-trifluorobenzene) and hydrogen-bonded (HCN...HNC) systems. The exemplary applications of the new scheme to these two molecular complexes revealed that the interplay of interaction
energy components governing their stability might be very different from that behind the IR intensity changes.
For example, in the case of the dispersion-bound π...π-type complex, dispersion contributions to the interaction
induced IR intensity of the selected modes are notably smaller than their first-order (electrostatic and exchange)
counterparts. | Alex Iglesias-Reguant; Heribert Reis; Miroslav Medved'; Josep M. Luis; Robert Zalesny | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63adef0de9d0fd6c4b2dee98/original/a-new-computational-tool-for-interpreting-infrared-spectra-of-molecular-complexes.pdf |
67a4c87681d2151a02616129 | 10.26434/chemrxiv-2025-133gp | Genie in a Bottle – Formation and Reactivity of an Elusive Monomeric Mn(IV)-Oxo Species Inside a Cavitand Pore | Metal-functionalized cavitands are promising platforms for mimicking the chemical environments of hydrophobic pockets in natural metalloenzymes. However, successfully combining the unique supramolecular capabilities of cavitand scaffolds, with the high reactivity of transition metal complexes, still remains a major challenge. In this study, we present a conceptually novel cavitand architecture featuring a coordinatively-unsaturated Mn(II) center embedded deep within its pore. This metallocavitand was employed to generate a Mn(IV)-oxo species inside a molecular cavity. This elusive intermediate was fully characterized spectroscopically (UV-vis, EPR, and HRMS) and – for the first time for a pseudo-octahedral Mn(IV)-oxo species – also by XRD. The experimental data was corroborated by detailed ab-initio/TDDFT calculations, confirming the Mn(IV)-oxo (rather than Mn(III)-oxyl) electronic character of this species. Reactivity and mechanistic studies, including monitoring the decay of this complex in various chlorinated solvents and its reactions with representative substrates, revealed that despite the steric protection provided by the cavitand scaffold, its Mn(IV)-oxo core remains highly reactive in both H atom abstraction (HAA) and O atom transfer (OAT) reactions. Moreover, this reactivity is subject to a high degree of steric control imposed by the cavitand framework capable of discriminating between potential substrate molecules based on their size and shape. This was further demonstrated by the regioselective oxidation of a bisphosphine substrate – emulating the regioselectivity of natural metalloenzymes. | Galon Green; Kamal Uddin Ansari; Thejasree Munikrishna; Sagi Ezov; Donia Shamali; Orit Cohen; Daphna Shimon; Yuri Tulchinsky | Organic Chemistry; Inorganic Chemistry; Catalysis; Supramolecular Chemistry (Org.); Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.) | CC BY 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a4c87681d2151a02616129/original/genie-in-a-bottle-formation-and-reactivity-of-an-elusive-monomeric-mn-iv-oxo-species-inside-a-cavitand-pore.pdf |
6784e11281d2151a02e2b015 | 10.26434/chemrxiv-2025-732st | Unveiling microbial single-cell growth dynamics under rapid periodic oxygen oscillations | Microbial metabolism and growth are tightly linked to oxygen (O2). Microbes experience fluctuating O2 levels in natural environments; however, our understanding of how cells respond to fluctuating O2 over various time scales remains limited, due to challenges in observing microbial growth at single-cell resolution under controlled O2 conditions and in linking individual cell growth with the specific O2 microenvironment. We performed time-resolved microbial growth analyses at single-cell resolution under a temporally controlled O2 supply. A multilayer microfluidic device was developed, featuring gas supply above a cultivation layer, separated by a thin membrane enabling efficient gas transfer. This platform enables microbial cultivation under constant, dynamic, and oscillating O2 conditions. Automated time-lapse microscopy and deep-learning-based image analysis provide access to
spatiotemporally resolved growth data at the single-cell level. O2 switching within tens of seconds, coupled with precise monitoring of the microenvironment, allows us to
accurately correlate cellular growth with local O2 concentrations. Growing Escherichia coli microcolonies subjected to varying O2 oscillation periods show distinct growth dynamics, characterized by response and recovery phases. The comprehensive growth data and insights gained from our unique platform are a crucial step forward to systematically study cell response and adaptation to fluctuating O2 environments at single-cell resolution. | Keitaro Kasahara; Johannes Seiffarth; Birgit Stute; Eric von Lieres; Thomas Drepper; Katharina Nöh; Dietrich Kohlheyer | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6784e11281d2151a02e2b015/original/unveiling-microbial-single-cell-growth-dynamics-under-rapid-periodic-oxygen-oscillations.pdf |
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