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60c7402c9abda2f152f8bc23 | 10.26434/chemrxiv.7660409.v1 | What Accounts for the Different Function in Photolyases and Cryptochromes: A Computational Study of Critical Events in the Protein Active Site | In the current work, we present a combination of various classical and quantum computational protocols to unveil the molecular mechanism of FAD protonation in <i>E. coli</i> photolyase and its mutant. A direct comparison to our previous study on the plant cryptochrome clearly shows the great influence of the electrostatic environment and the flexibility of the FAD pocket on the proton transfer mechanism. Additionally, we propose a proton transfer pathway for WT E. coli photolyase consistent with experimental observations. Taken together, our results and previous experimental data provide a comprehensive picture about the functional differentiation in the cryptochrome-photolyase family. | Daniel Holub; Thilo Mast; Tomáš Kubař; Marcus Elstner; Natacha Gillet | Biochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7402c9abda2f152f8bc23/original/what-accounts-for-the-different-function-in-photolyases-and-cryptochromes-a-computational-study-of-critical-events-in-the-protein-active-site.pdf |
6706f895cec5d6c142b8f756 | 10.26434/chemrxiv-2024-8kfcb | Polariton Spectra under the Collective Coupling Regime. I. Efficient Simulation of Linear Spectra and Quantum Dynamics | We outline two general theoretical techniques to simulate polariton quantum dynamics and optical spectra under the collective coupling regimes described by a Holestein-Tavis-Cummings (HTC) model Hamiltonian. The first one takes the advantage of sparsity of the HTC Hamiltonian, which allows one to reduce the cost of acting polariton Hamiltonian onto a state vector to the linear order of the number of states, instead of the quadratic order. The second one is applying the well-known Chebyshev series expansion approach for quantum dynamics propagation and applying them to simulate the polariton dynamics in the HTC system, allowing one to use a much larger time step for propagation and only requires a few recursive operations of the Polariton Hamiltonian acting on state vectors. These two theoretical approaches are general and can be applied to any trajectory-based non-adiabatic quantum dynamics methods. We apply these two techniques with our previously developed Lindblad-Partially Linearized Density Matrix (L-PLDM) approach to simulating the linear absorption spectra of the HTC model system, with both inhomogeneous site energy disorder as well as dipolar orientational disorders. Our numerical results agree well with the previous analytic and numerical work. | Elious Mondal; Nickolas Vamivakas; Steven Cundiff; Todd Krauss; Pengfei Huo | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706f895cec5d6c142b8f756/original/polariton-spectra-under-the-collective-coupling-regime-i-efficient-simulation-of-linear-spectra-and-quantum-dynamics.pdf |
636e4c618e0d359e1e1722c2 | 10.26434/chemrxiv-2022-j7gb1-v2 | DoE-It-Yourself: A Case Study for Implementing Design of Experiments into Nanoparticle Synthesis | Predictable and repeatable outcome is a major issue in nanoparticle synthesis. Traditionally, a one-factor-at-a-time (OFAT) method is relied upon to investigate and optimise synthetic processes; however, this method is inefficient and often misleading. Design of experiments (DoE), in contrast, can provide a greater amount of information in fewer experiments and lends itself to more reproducible results. Nevertheless, DoE techniques are only used by a relatively low number of practitioners in nanoparticle research. Here, we provide a step-by-step tutorial for the synthesis of oleylamine-capped gold nanoparticles (AuNPs). Through the use of DoE, we are able to achieve a marked reduction in dispersity and develop a model for detailed control over the mean diameter of the nanoparticle populations. Principles of the case study presented herein are applicable and should serve for facile implementation of DoE to other synthetic routes. | Niamh Mac Fhionnlaoich; Ye Yang; Runzhang Qi; Federico Galvanin; Stefan Guldin | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636e4c618e0d359e1e1722c2/original/do-e-it-yourself-a-case-study-for-implementing-design-of-experiments-into-nanoparticle-synthesis.pdf |
6785152f6dde43c90856f8c4 | 10.26434/chemrxiv-2025-3k58h | Structural Elucidation of Na2/3NiO2, A Dynamically Stabilised Cathode Phase with Ni Charge- and Na Vacancy- Ordering | NaNiO2 (NNO) has been investigated as a promising sodium-ion battery (NIB) cathode material, but it is limited by degradation-induced capacity fade. On desodiation, NNO forms multiple phases with large superstructures due in part to Na+-ion vacancy ordering, however, their structures are unknown. Here, we report a structural solution to the Na2/3NiO2 (P/3) de-sodiated phase using combined Rietveld refinement of high-resolution synchrotron X-ray (SXRD) and neutron diffraction (NPD) data, magnetic susceptibility, and 23Na solid-state nuclear magnetic resonance (ssNMR) spectroscopy. Our experimental results are compared to Ab Initio Molecular Dynamics (AIMD) simulations, which indicate multiple low-energy structures that are dynamically populated. We observe a combination of competing effects which contribute to the resultant dynamic nature of the structure, including honeycomb ordering of mixed-valence Ni, orbital-ordering of Jahn-Teller (JT) distorted Ni3+, and zigzag Na+/vacancy ordering. Our work provides evidence of the multiple contributions to the structures of de-sodiated Na2/3NiO2, along with a framework for investigating the other unsolved de-sodiated structures. This work may also inform understanding of the Jahn-Teller evolution in other nickel-rich lithium and sodium ion cathodes, such as LiNiO2. | James Mark Alexander Steele; Annalena R Genreith-Schriever; Joshua D Bocarsly; Liam Agostino Vincenzo Nagle-Cocco; Farheen N Sayed; Marie Juramy; Christopher A O'Keefe; Fabio Orlandi; Pascal Manuel; Siân E Dutton; Clare P Grey | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6785152f6dde43c90856f8c4/original/structural-elucidation-of-na2-3ni-o2-a-dynamically-stabilised-cathode-phase-with-ni-charge-and-na-vacancy-ordering.pdf |
60c74133842e654b3ddb1e4b | 10.26434/chemrxiv.7992239.v1 | Multi-modal Cell Labelling for Quantification and Optimization of Stem Cell Delivery to Orthotopic Breast Tumors | Stem cells have been utilized as anti-cancer agents due to their ability to home to and integrate within tumors. Methods to augment stem cell homing to tumors are being investigated with the goal of enhancing treatment efficacy. However, it is currently not possible to evaluate both cell localization and cell viability after engraftment, hindering optimization of therapy. In this study, luciferase expressing human adipocyte derived stem cells (ADSCs) were labelled with superparamagnetic iron oxide nanoparticles (SPIONs) conjugated to Indium-111 to produce cells with tri-modal imaging capabilities. ADSCs were administered intravenously (IV) or intracardially (IC) to mice bearing 4T1 orthotopic breast tumors. Cell fate was monitored serially using bioluminescence imaging (BLI) as a measure of cell viability, magnetic resonance imaging (MRI) for cell localization and single photon emission computer tomography (SPECT) for cell quantification. BLI/MRI/SPECT imaging revealed differences in whole body cell distribution between injection routes. BLI showed the presence of viable ADSCs within tumors as early as 1-hour post IC injection compared to 3 days post IV injection. SPECT data showed the percentage of ADSCs within tumors to be 2-fold higher after IC than IV at 5-hour post injection. Whereas, MRI confirmed the localization of SPION labelled cells in tumors after IC injection but not IV. Finally, histological analysis was used to validate engraftment of ADSC within tumor tissue. These findings demonstrate that multi-modal imaging can be used to evaluate the efficiency of stem cell delivery to tumors and that IC cell administration is more effective for tumor targeting.<br /> | May Zaw Thin; Robin Bofinger; Tomas D. Kostelec; John Connell; P. Stephen Patrick; Helen Allan; Helen C. Hailes; Alethea B. Tabor; Mark F. Lythgoe; Daniel J. Stuckey; Tammy L. Kalber | Imaging Agents; Nanostructured Materials - Materials; Imaging; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74133842e654b3ddb1e4b/original/multi-modal-cell-labelling-for-quantification-and-optimization-of-stem-cell-delivery-to-orthotopic-breast-tumors.pdf |
60c745429abda2cf74f8c524 | 10.26434/chemrxiv.10002785.v1 | Direct Observation of Chain Lengths and Conformations in Oligofluorene Distributions from Controlled Polymerization by Double Electron-Electron Resonance | Synthetic polymers are mixtures of different length chains, and their chain length and chain conformation is often experimentally characterized by ensemble averages. We demonstrate that Double-Electron-Electron-Resonance (DEER) spectroscopy can reveal the chain length distribution, and chain conformation and flexibility of the individual n-mers in oligo-(9,9-dioctylfluorene) from controlled Suzuki-Miyaura Coupling Polymerization (cSMCP). The required spin-labeled chain ends were introduced efficiently via a TEMPO-substituted initiator and chain terminating agent, respectively, with an in situ catalyst system. Individual precise chain length oligomers as reference materials were obtained by a stepwise approach. Chain length distribution, chain conformation and flexibility can also be accessed within poly(fluorene) nanoparticles. | Dennis Bücker; Annika Sickinger; Julian D. Ruiz Perez; Manuel Oestringer; Stefan Mecking; Malte Drescher | Oligomers; Conducting polymers; Nanostructured Materials - Nanoscience; Polymers; Computational Chemistry and Modeling; Polymerization (Organomet.); Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745429abda2cf74f8c524/original/direct-observation-of-chain-lengths-and-conformations-in-oligofluorene-distributions-from-controlled-polymerization-by-double-electron-electron-resonance.pdf |
67045df812ff75c3a1c471b3 | 10.26434/chemrxiv-2024-j2dtm | Thermally Driven Dynamic Behaviours in Polymeric Vesicles as Biomimetic Synthetic Cell Systems | Synthetic cells have emerged as a promising tool for understanding cellular processes and developing novel biotechnological applications. In this study, we engineer dynamic and biomimetic behaviours in polymersomes, aiming to create synthetic cells that mimic key biological functions. These vesicles exhibit a temperature-driven fusogenic property, enabling the transformation of nanoscale vesicles into microsized sponge-like polymeric droplets. These droplets, rich in membrane content, can act as synthetic cells analogues with the capability for controlled cargo release. Moreover, the thermoresponsive nature of our polymersomes makes them versatile components for the construction of lipid-based synthetic cells, allowing for controllable cargo release and dynamic organelle-like functionalities. We also demonstrate that the microscale polymer droplets possess biomimetic properties including contractility, a behaviour typically observed in biological systems. By modulating the temperature, it is possible to induce these contractile behaviours as well as other functions, including controlled fusion and efficient bacteria capture. | Matthew E. Allen; Yeyang Sun; Chi Long Chan; Oscar Ces; Yuval Elani; Claudia Contini | Physical Chemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67045df812ff75c3a1c471b3/original/thermally-driven-dynamic-behaviours-in-polymeric-vesicles-as-biomimetic-synthetic-cell-systems.pdf |
60c743b4567dfe19e0ec415a | 10.26434/chemrxiv.9569840.v1 | Preparation, Characterization, and Application of a Lipophilic Coated Exfoliated Egyptian Blue for Near-Infrared Luminescent Latent Fingermark Detection | A simple technique is described to create nanoscale near-infrared luminescent Egyptian Blue pigment particles with lipophilic surfaces for latent fingermark detection. An exfoliated Egyptian blue powder coated with cetrimonium bromide was prepared using a simple, one-pot process. Particle size and surface coatings were characterized using scanning electron and atomic force microscopies, dynamic light scattering, and infrared and luminescence spectroscopies. This new fingermark dusting powder presented more contrast compared to uncoated Egyptian blue of comparable particle size as well as commercial visible light fluorescent (Blitz Red) and near infrared luminescent (fpNatural1) powders in the detection of aged fingermarks on model surfaces. The coated Egyptian blue pigment presents a cost-effective fingermark dusting powder that reveals high contrast latent fingermarks with simple, inexpensive photography equipment. <br /><br /> | Sorour Shahbazi; John Goodpaster; Gregory Smith; Thomas Becker; Simon W. Lewis | Nanostructured Materials - Materials; Imaging; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b4567dfe19e0ec415a/original/preparation-characterization-and-application-of-a-lipophilic-coated-exfoliated-egyptian-blue-for-near-infrared-luminescent-latent-fingermark-detection.pdf |
60c74793702a9b550a18adfe | 10.26434/chemrxiv.10312529.v2 | Synthesis, Modular Composition, and Electrochemical Properties of Lamellar Iron SulfidesSynthesis, Modular Composition, and Electrochemical Properties of Lamellar Iron Sulfides | Transition metal chalcogenides with layered structures have emerged as promising materials for energy storage, catalysis, and electronics, among other areas. We have identified a new layered phase of iron sulfide containing interlayer solvated cations. We present an optimized synthesis for the Li+-containing material from an Fe(III) xanthate complex. Structure and composition data indicate the material consists of poorly-ordered iron sulfide layers separated by solvated cations. The lamellar spacing in these materials can be tuned by changing the identity of the cation. Furthermore, the lamellar spacing can also be reversibly tuned by the degree of solvation of the material. The material is electrically conductive and can serve as a pseudocapacitor with comparable performance to commercial materials such as MnO<sub>2</sub>. Furthermore, these materials also show promise as lithium or sodium ion battery cathodes with good capacity and reversibility. | Noah E. Horwitz; Elena V. Shevchenko; Jehee Park; Eungje Lee; Jiaze Xie; Alexander S. Filatov; John Anderson | Multilayers; Nanostructured Materials - Materials; Electrochemistry; Solid State Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74793702a9b550a18adfe/original/synthesis-modular-composition-and-electrochemical-properties-of-lamellar-iron-sulfides-synthesis-modular-composition-and-electrochemical-properties-of-lamellar-iron-sulfides.pdf |
60c7477f0f50dbc3083965f4 | 10.26434/chemrxiv.11684367.v1 | Variance of Atomic Coordinates as a Dynamical Metric to Distinguish Proteins and Protein-Protein Interactions in Molecular Dynamics Simulations | <b><i>In
this manuscript, </i>we introduce the Cumulative Variance of Coordinate
Fluctuations (CVCF) along atomistic MD trajectories, as a dynamical metric to
examine protein dynamics and sampling convergence in MD simulations.</b> Using model 1D and 2D PES, we first show that
CVCF, which traces over the fluctuations of protein atoms as a function of
sampling coordinate (time in MD simulations), captures both local and global
equilibria to distinguish the underlying PES of proteins. For both model PES and protein trajectories,
we compare the information content present in CVCF traces with that obtained
using other measures proposed in literature to reveal conditions under which a
consistent interpretation of data can be obtained. <b>Importantly, we show that
independent of convergence to either local or global equilibrium, the values
and features of protein CVCF can provide a comparative assessment of the
ruggedness and curvature of the underlying PES sampled by proteins along MD
trajectories.</b> Trends in CVCF therefore enable us to compare features of the
PES across multiple protein systems using MD simulations. We demonstrate some
of the attractive features of a CVCF based analysis on multi-microsecond (ms) MD trajectories of structurally homologous
ubiquitin family proteins which present a particularly striking example in
nature wherein sequence changes and complexation which do not lead to prominent
structural changes bring about dramatic functional consequences. | Sanjoy Paul; Sri Rama Koti Ainavarapu; Ravindra Venkatramani | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7477f0f50dbc3083965f4/original/variance-of-atomic-coordinates-as-a-dynamical-metric-to-distinguish-proteins-and-protein-protein-interactions-in-molecular-dynamics-simulations.pdf |
635e18b755a081080bcb0bae | 10.26434/chemrxiv-2022-rk11z | A Concise Total Synthesis of (±)-Stepharine and (±)-Pronuciferine | We herein report a concise total synthesis of (±)-stepharine and (±)-pronuciferine using readily available reagents as the starting materials. This synthesis features a three-component Catellani reaction/Au-catalyzed 6-exo-dig cyclization for the assembly of 1-methylene-THIQ scaffold and an oxidative dearomatization for constructing spiro-cyclohexadienone scaffold. | Ruiming Chen; Shihu Jia; Yuning Man; Hong-Gang Cheng; Qianghui Zhou | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635e18b755a081080bcb0bae/original/a-concise-total-synthesis-of-stepharine-and-pronuciferine.pdf |
6598076d66c1381729c7b852 | 10.26434/chemrxiv-2024-d506k-v2 | Preparation and characterization of transferable encapsulated dye-sensitized solar cells | The increasing demand for sustainable energy as a means to combat the impact of climate change is addressed via a novel concept in the present work. Herein, the development of encapsulated dye-sensitized solar cells, canonically “solar capsules”, for photovoltaic applications on alternative surfaces, such as facades, is presented. The solar capsule assembly houses all components necessary for photovoltaic energy conversion, enclosed within a semiconductor nanotubular array, making them truly unique in their construction. This capsule-style unit enables an easy transfer and draft onto a wide range of materials and surfaces for photovoltaic functionalization and applications. This type of dye-sensitized solar cell typically consists of transferred solar capsules and two additional electrodes. The design and construction of solar capsules have high economic viability as they can seamlessly be up-scaled using commercially established techniques such as anodization and subsequent functionalization. This work demonstrates a working model of such a capsule by fabricating TiO2 nanotubes that are functionalized via facile dip- and spin-coating techniques in a wet lab at ambient conditions. These prototype solar capsules are characterized in bulk and are thoroughly investigated at the nanoscale for information on the chemical distribution of the constituents, as they may be influenced during the manufacturing process. | Patrick Hartwich; Swathi Naidu Vakamulla Raghu; Maurice Müller; Christian Pritzel; Peter Haring Bolívar; Manuela S. Killian | Materials Science; Nanoscience; Energy; Nanostructured Materials - Materials; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6598076d66c1381729c7b852/original/preparation-and-characterization-of-transferable-encapsulated-dye-sensitized-solar-cells.pdf |
62682db7103388056afb812d | 10.26434/chemrxiv-2022-20m2q-v2 | Conical shape fluctuations determine the
rate of ion-evaporation and the emitted cluster-size distribution from multiple-charged droplets | The ion-evaporation mechanism (IEM) is perceived to be a major pathway for disintegration of multi-ion charged droplets found in atmospheric and sprayed aerosols.
However, the precise mechanism of IEM and the effect of the nature of the ions in the emitted cluster-size
distribution have not yet been established despite its broad
use in mass spectrometry and atmospheric chemistry over past half century. Here we present a systematic study of the emitted ion-cluster distribution in relation to
their spatial distribution in the parent droplet using
atomistic modeling. It is found that in the parent droplet,
multiple kosmotropic and weakly polarizable chaotropic ions (Cs+) are buried deeper within the droplet than
polarizable chaotropic ions (Cl-, I-). This differentiation in the ion location is only captured
by a polarizable model. It is demonstrated that the emitted cluster-size distribution is determined by
dynamic conical deformations and not by the equilibrium
ion-depth within the parent droplet as the IEM models assume. Critical factors that determine the cluster-size distribution such as the charge sign asymmetry that
have not been considered in models and in experiments are presented. We argue that the existing IEM analytical models do not establish a clear difference between IEM and Rayleigh fission. We propose a shift in the existing view for IEM from the equilibrium properties of the
parent droplet to the chemistry in the conical shape fluctuations that serve as the centers
for ion-emission. Consequently, chemistry in the conical fluctuations may also be a key element to explain charge states of macromolecules in mass spectrometry
and may have potential applications in catalysis due to the electric field in the conical region. | Victor Kwan; Styliani Consta | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Clusters; Solution Chemistry; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62682db7103388056afb812d/original/conical-shape-fluctuations-determine-the-rate-of-ion-evaporation-and-the-emitted-cluster-size-distribution-from-multiple-charged-droplets.pdf |
60c756ee337d6c726be28f3b | 10.26434/chemrxiv.14345384.v1 | A Topological Stitching Strategy for Biocompatible Wet Adhesion Using Mussel-Inspired Polyurethane | The biomedical and surgical applications of hydrogels demand effective methods to adhere hydrogels to diverse substrates including living tissues. Here we present a mussel mimetic polyurethane as topological suture material for tough adhesion of hydrogels by introducing catechol moieties into polymer chains. Solution of the stitching polyurethane can be injected onto the surface of a hydrogel, followed by diffusing spontaneously into the hydrogel, then get triggered by oxidant for in situ gelation. Oxidative cross-linkage of catechol-modified polyurethane after penetration into hydrogels or living tissues could establish enough covalently entangled networks to afford desired adhesion strength. The mussel mimetic polyurethane demonstrates excellent adhesion strength of hydrogels to universal substrates including inorganics, polymers, and biomaterials, with no requirements for specific functional groups or chemical modification. The adhesion energy achieved by the topological stitching strategy can reach up to 350 J/m<sup>2</sup>. Moreover, the stitching polymer shows good biocompatibility and the potential for debonding under the catalysis of elastase. This work will possibly become a promising strategy candidate for adhesion in wet environments. | Buyun Chen; Kun Lei; Dandan Zhu; Chongchong Yang; Chengyuan Sun; Wei Xiao; Zhen Zheng; Xinling Wang | Biocompatible Materials; Biodegradable Materials; Coating Materials; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756ee337d6c726be28f3b/original/a-topological-stitching-strategy-for-biocompatible-wet-adhesion-using-mussel-inspired-polyurethane.pdf |
66ed83cf12ff75c3a1ee501a | 10.26434/chemrxiv-2024-hsq64 | Nanostructured and recyclable palladium catalysts for hydrogenation of nitroarenes | This work reported the preparation of nanostructured palladium (Pd)-based catalysts that consisted of a magnetic core covered by a layer of functionalized mesoporous silica with Pd nanoparticles grown in situ within the porous channels (Fe3O4@mSiO2-Pd). The optimum Fe3O4@mSiO2-Pd with fine size and uniformly dispersed Pd nanoparticles was obtained on the amino (-NH2) functionalized magnetic mesoporous silica support with Na2PdCl4 as the Pd source. The performance of the synthesized Fe3O4@mSiO2-Pd was evaluated in the catalytic reduction of nitroarenes in aqueous solution with H2(g) as a reducing agent under ambient pressure and temperature. Compared with commercial Pd/SiO2, Fe3O4@mSiO2-Pd exhibited significantly improved reactivity in the reduction of various nitroarenes, which were completely reduced to the corresponding aminoarenes. The enhanced performance of Fe3O4@mSiO2-Pd may be attributed to the formation of small and well dispersed Pd nanoparticles within the confined support and the enhanced accessibility of reactive Pd sites within the mesoporous structure. Furthermore, the Fe3O4@mSiO2-Pd catalyst also showed excellent reusability and could be easily collected by an external magnetic field. Results suggested that the synthesized Fe3O4@mSiO2-Pd can be an effective and sustainable catalyst for hydrogenation of nitro-containing compounds. | Xiaopeng Min; Yin Wang | Catalysis; Earth, Space, and Environmental Chemistry; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ed83cf12ff75c3a1ee501a/original/nanostructured-and-recyclable-palladium-catalysts-for-hydrogenation-of-nitroarenes.pdf |
60c75932bdbb897c8fa3aee5 | 10.26434/chemrxiv.7791146.v5 | On the Thermodynamic Control of Ring Opening of 4-Substituted 1,3,3-Tris-Carbethoxycyclobutene and the Role of the C-3 Substituent in Masking the Kinetic Torquoselectivity. An alternate reaction pathway | <p>The predominant transformations of 4-methyl- and 4-phenyl-1,3,3-<i>tris</i>-carbethoxycyclobutenes
to s-<i>trans</i>,<i>trans</i>-1,1,3-<i>tris</i>-carbethoxy-4-methyl- and s-<i>trans</i>,<i>trans</i>-1,1,3-<i>tris</i>-carbethoxy-4-phenyl-1,3-butadienes,
respectively, are discussed to proceed through pathways entailing heterolytic
cleavage of the s<sub>C3C4</sub> bond rather than the usual conrotatory ring
opening following the rules of torquoselectivity. The adventitious or in situ
generated halogen acid from CDCl<sub>3</sub> catalyzes the reaction by
protonation of the geminal ester group to weaken s<sub>C3C4</sub> bond and allow its S<sub>N</sub>2
cleavage by chloride ion. This is followed by cisoid<b>→</b>transoid isomerization
and loss of the elements of halogen acid to form the products. In the Lewis
acid-catalyzed reaction of 4-phenyl-1,3,3-<i>tris</i>-carbethoxycyclobutene in
CH<sub>2</sub>Cl<sub>2</sub>, coordination of Lewis acid with the geminal ester
group is followed by heterolytic cleavage of the s<sub>C3C4</sub> bond. The resultant
species subsequently undergoes cisoid<b>→</b>transoid isomerization before losing the Lewis
acid to form the products.<br /></p> | Veejendra Yadav; Dasari L V K Prasad; Arpita Yadav; Maddali L N Rao | Stereochemistry; Computational Chemistry and Modeling; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75932bdbb897c8fa3aee5/original/on-the-thermodynamic-control-of-ring-opening-of-4-substituted-1-3-3-tris-carbethoxycyclobutene-and-the-role-of-the-c-3-substituent-in-masking-the-kinetic-torquoselectivity-an-alternate-reaction-pathway.pdf |
66ffe5f312ff75c3a1664c22 | 10.26434/chemrxiv-2024-9g3qz | Enantioselective Energy Transfer-Enabled Cyclization using a Privileged Al-Salen Photocatalyst | Chiral catalysts that can engage multiple substrates, via distinct activation modes, to deliver enantioenriched products with high levels of fidelity are often described as “privileged”. Antipodal to enzymatic specificity, this generality enables the reactivity - selectivity divide in ground state landscapes to be effectively reconciled. Achieving this latitude in excited state paradigms remains a frontier, and efforts to identify privileged chiral photocatalysts are currently a core area of research. Aluminum salen complexes are emergent contenders on account of their well-defined photophysical properties and competence in photo-induced single electron transfer processes: this has recently been leveraged in the deracemization of cyclopropyl ketones. To expand the activation repertoire of Al-salen photocatalysts, an unprecedented enantioselective energy transfer (EnT) catalysis-enabled photocyclization of acrylanilides has been developed. This operationally simple strategy allows reactivity and enantioselectivity to be simultaneously regulated by an inexpensive, commercial chiral Al-salen complex upon irradiation at λ = 400 nm: this allows diverse cyclic products to be forged with high levels of enantioselectivity (up to 96:4 e.r.). Establishing this dichotomy in excited state activation modes serves to consolidate the privileged status of chiral Al-salen complexes in enantioselective photocatalysts and to complement their ubiquity in ground-state regimes. | Julia Soika; Carina Onneken; Thorben Wiegmann; Tobias Morack; Leander Lindfeld; Marian Hebenbrock; Christian Mück-Lichtenfeld; Johannes Neugebauer; Ryan Gilmour | Organic Chemistry; Catalysis; Physical Organic Chemistry; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ffe5f312ff75c3a1664c22/original/enantioselective-energy-transfer-enabled-cyclization-using-a-privileged-al-salen-photocatalyst.pdf |
653868bf87198ede0735c04c | 10.26434/chemrxiv-2023-cllnd | Rh(III)-Catalyzed N-Amino-Directed C-H Coupling with 3-Methyleneoxetan-2-Ones for 1,2-Dihydroquinoline-3-Carboxylic Acid Synthesis | Polarity analysis is important for the deduction of organic reactivity but is largely restricted in the static polarity analysis regime. Dynamic polarity analysis is proposed herein as an expansive tool for quest into both static polarity and transient polarity, allowing the revelation of an augmented pool of reactivity patterns. Through this analysis formalism, polarity matching has been established for Rh(III)-catalyzed N-amino-directed C-H coupling with 3-methyleneoxetan-2-ones providing efficient access to 1,2-dihydroquinoline-3-carboxylic acids. The identified reaction, by virtue of the internal oxidative mechanism, showcases a mild reaction condition (room temperature), a short reaction time (2 h), and a generally high product yield. Taken together, the integration of static and dynamic polarity analysis creates a unified foundational framework for reactivity deduction and reactivity classification, in both organic and organometallic chemistry. | Renpeng Zhou; Shuaixin Fan; Lili Fang; Benfa Chu; Jin Zhu | Organic Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653868bf87198ede0735c04c/original/rh-iii-catalyzed-n-amino-directed-c-h-coupling-with-3-methyleneoxetan-2-ones-for-1-2-dihydroquinoline-3-carboxylic-acid-synthesis.pdf |
60c753874c89191afdad434a | 10.26434/chemrxiv.13506678.v1 | Synthesis of the C19–C30 Bis-THF Fragment of Iriomoteolide-13a via Stepwise SN2 Cyclization and Intramolecular syn-Oxypalladation | The C19–C30 bis-THF fragment of the proposed structure of
iriomoteolide-13a has been synthesized. The w-mesyloxy-substituted stereotetrad
possessing three continuous hydroxy groups was generated by <i>anti</i>-aldol reaction and asymmetric
dihydroxylation (AD). Upon heating in pyridine the stereotetrad underwent an S<sub>N</sub>2
cyclization to form the C19–C22
THF ring. It was followed by an intramolecular <i>syn</i>-oxypalladation of the C28 chiral allylic alcohol to give the
C23–C26
THF ring. | Hui Zhao; Kai Gao; Haichen Ma; Tsz Chun Yip; Wei-Min Dai | Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC 4.0 | CHEMRXIV | 2020-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753874c89191afdad434a/original/synthesis-of-the-c19-c30-bis-thf-fragment-of-iriomoteolide-13a-via-stepwise-sn2-cyclization-and-intramolecular-syn-oxypalladation.pdf |
6787666581d2151a02362d85 | 10.26434/chemrxiv-2025-41b4m | Switchable SuFEx linker chemistry for efficient coupling of alcohols, thiols, and selenols with O-/N-nucleophiles | Highly efficient linkage of readily available nucleophilic building blocks under mild conditions is essential for the synthesis of drug discovery and materials, yet it remains challenging due to the often unavoidable tendency of homo-coupling side reactions using traditional linkers. In this study, we present a versatile switchable SuFEx linker chemistry, exemplified by ESF, which enables highly efficient and selective coupling of thiols, alcohols, and selenols with O-/N-nucleophiles. This strategy harnesses the unique reactivity of the sulfonyl fluoride group in ESF, which can be “switched on” through noncovalent intramolecular interactions with chalcogen atoms, thereby facilitating subsequent SuFEx reactions and enabling the highly selective linkage of two distinct nucleophilic building blocks. | Minlong Wang; Jiaman Hou; Lingxia Chen; Xinshu Qin; Xuan Li; Ruoqing Peng; Lin Li; Chao Wang; Xiaohe Zhang; Jie An | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6787666581d2151a02362d85/original/switchable-su-f-ex-linker-chemistry-for-efficient-coupling-of-alcohols-thiols-and-selenols-with-o-n-nucleophiles.pdf |
60c74333bdbb8954baa385fd | 10.26434/chemrxiv.8980574.v1 | Multivalent Cluster Nanomolecules for Inhibiting Protein-Protein Interactions | Multivalent protein-protein interactions serve central roles in many essential biological processes, ranging from cell signaling and adhesion to pathogen recognition. Uncovering the rules that govern these intricate interactions is important not only to basic biology and chemistry, but also to the applied sciences where researchers are interested in developing molecules to promote or inhibit these interactions. Here we report the synthesis and application of atomically precise inorganic cluster nanomolecules consisting of an inorganic core and a covalently linked densely packed layer of saccharides. These hybrid agents are stable under biologically relevant conditions and exhibit multivalent binding capabilities, which enable us to study the complex interactions between glycosylated structures and a dendritic cell lectin receptor. Importantly, we find that subtle changes in the molecular structure lead to significant differences in the nanomolecule’s protein binding properties. Furthermore, we demonstrate an example of using these hybrid nanomolecules to effectively inhibit protein-protein interactions in a human cell line. Ultimately, this work reveals an intricate interplay between the structural design of multivalent agents and their biological activities toward protein surfaces. | Elaine A. Qian; Yanxiao Han; Marco Messina; Heather D. Maynard; Petr Král; Alexander Spokoyny | Nanostructured Materials - Nanoscience; Bioinorganic Chemistry; Main Group Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Bioengineering and Biotechnology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74333bdbb8954baa385fd/original/multivalent-cluster-nanomolecules-for-inhibiting-protein-protein-interactions.pdf |
6499f7cf6e1c4c986b62a5e9 | 10.26434/chemrxiv-2023-rlnx4 | Transmembrane Transport of Phosphate by a Strapped Calix[4]pyrrole
| Synthetic anion receptors are increasingly explored for the transport of anions across lipid membranes because of their potential therapeutic applications. A considerable amount of research focuses on the transport of chloride whereas the transmembrane transport of inorganic phosphate has not been reported to date, despite the biological relevance of this anion. Here we present a calix[4]pyrrole with a bisurea strap that functions as a receptor and transporter for H2PO4–, relying on the formation of 8 hydrogen bonds and efficient encapsulation of the anion. Using a phosphate-sensitive lanthanide probe and 31P NMR spectroscopy, we demonstrate that this receptor can transport phosphate into vesicles by H2PO4−/Cl− antiport, H2PO4− uniport, and Cs+/H2PO4− sym-port mechanisms. This first example of inorganic phosphate transport by a neutral receptor opens perspectives for the future devel-opment of transporters for various biological phosphates. | Alessio Cataldo; Karolis Norvaisa; Lau Halgreen; Samantha Bodman; Kristin Bartik; Stephen J. Butler; Hennie Valkenier | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2023-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6499f7cf6e1c4c986b62a5e9/original/transmembrane-transport-of-phosphate-by-a-strapped-calix-4-pyrrole.pdf |
616907558b620d615a4ff7c2 | 10.26434/chemrxiv-2021-bwg91 | New Insights on the Self-Assembly of Bio-sourced Block Copolymer MH-b-PS in Aqueous Solutions: Nanocorals, Cubosomes & Nanocubes | Polymer self-assembly in solution still constitutes a simple methodology for the preparation of elegant yet sophisticated nanomaterials. This work aims at presenting how the fine tuning of the experimental parameters of the nanoprecipitation process can lead to a variety of novel morphologies ranging from nanocorals through cubosomes to nanocubes. A carbohydrate dibloc copolymer with a simple and linear structure MH1.2k-b-PS2.3 has been used as a model to illustrate the formation of these new self-assemblies. This is the first time that nanocube morphology has been generated using this type of bio-sourced co-polymer in aqueous solution and at room temperature.
| Yomen Atassi; Redouane Borsali | Materials Science; Polymer Science; Nanoscience; Nanostructured Materials - Materials; Biopolymers; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616907558b620d615a4ff7c2/original/new-insights-on-the-self-assembly-of-bio-sourced-block-copolymer-mh-b-ps-in-aqueous-solutions-nanocorals-cubosomes-nanocubes.pdf |
63feb251937392db3d3e8651 | 10.26434/chemrxiv-2023-tcdgw | Calculating vibrational excited state absorptions with excited state constrained minimized energy surfaces | The modeling and interpretation of vibrational spectra are crucial for studying reaction dynamics using vibrational spectroscopy. Previous theoretical developments have mainly focused on fundamental vibrational transitions. In this study, we present a new method that uses excited state constrained minimized energy surfaces (CMES) to describe vibrational excited state absorptions. The excited state CMESs are obtained similarly to the previous ground state CMES development in our group but with additional wave function orthogonality constraints. Using a series of model systems, including the harmonic oscillator, Morse potential,
double-well potential, and quartic potential, we demonstrate that this new procedure provides good estimations of the transition frequencies for vibrational excited state absorptions. The results are significantly better than those obtained from harmonic approximations using conventional potential energy surfaces. | Yiwen Wang; Zehua Chen; Yang Yang | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63feb251937392db3d3e8651/original/calculating-vibrational-excited-state-absorptions-with-excited-state-constrained-minimized-energy-surfaces.pdf |
670d8a47cec5d6c142269a6b | 10.26434/chemrxiv-2024-qcb4h | Photoisomerization Dynamics of Azo-Escitalopram Using Surface Hopping and a Semiempirical Method | The photoisomerization dynamics of azoescitalopram, a synthetic photoswitchable inhibitor of the human serotonin transporter, is investigated in both gas-phase and water. We use the trajectory surface hopping method, as implemented in SHARC, interfaced with the semiempirical Floating Occupation Molecular Orbitals-Configuration Interaction (FOMO-CI) electronic structure method to calculate on-the fly energies, forces and couplings. The inclusion of explicit water molecules is enabled using a quantum mechanics/molecular mechanics (QM/MM) framework. We find that the photoisomerization quantum yield of trans-azoescitalopram is wavelength and environment dependent, with n→π* excitation yielding higher quantum yields than π→π* excitation. Additionally, we observe the formation of two distinct cis-isomers during photoisomerization from the most thermodynamically stable trans-isomer, with formation rates influenced by both the excitation window and surrounding environment. Longer excited-state lifetimes are found than those reported for azobenzene, suggesting that the escitalopram moiety contributes to these extended lifetimes and slower torsional motions. | Hans Georg Gallmetzer; Eduarda Sangiogo Gil; Leticia González | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d8a47cec5d6c142269a6b/original/photoisomerization-dynamics-of-azo-escitalopram-using-surface-hopping-and-a-semiempirical-method.pdf |
63a4b0bb518c16196c353c2b | 10.26434/chemrxiv-2022-7wdbg | Influence of the Excitation Wavelength on First Order Hyperpolarizabilities and Optimal Gap Tuning of Range Separated Hybrid Functionals | In this study, we compute the hyperpolarizability of the nitroaniline isomers, para-nitroaniline (pNA), ortho-nitroaniline (oNA), and meta-nitroaniline (mNA), by density functional theory (DFT), including with optimally tuned range separated hybrid (RSH) functionals. By utilizing the nitroanilines hyperpolarizability trend based on charge transfer (pNA>oNA>mNA), we can uncover how the excitation wavelength affects the prediction of the hyperpolarizabilities in both on and off resonant regimes, and optimal gap tuning of RSH functionals. In non-resonant regions, with reference to CCSD/aug-cc-pVDZ and experimental studies, we find that some computational approaches do not always reproduce the nitroanilines trend at specific excitation wavelengths. For example, RSH functionals require optimal gap tuning to reproduce the trend. In resonant regions, we find that the damped response theory predicts that the trend is maintained at the two-photon absorption, however, it breaks near the one photon pole. This suggests that the underlying charge transfer characteristics are undermined in the one-photon pole which in comparison to the two-state model suggests that this is due to the presence of other electronic states in some of the isomers. Furthermore, we find that cases where optimal gap tuning is ineffective (pathological behavior) are dependent on the excitation wavelength. | Shyam Parshotam; Julianne M. Gibbs; Alex Brown | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Optics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a4b0bb518c16196c353c2b/original/influence-of-the-excitation-wavelength-on-first-order-hyperpolarizabilities-and-optimal-gap-tuning-of-range-separated-hybrid-functionals.pdf |
666c52c6c9c6a5c07a7864af | 10.26434/chemrxiv-2024-4rz2q | Bidentate Phosphine Ligand Impacts on Previously Inaccessible 5-Membered N-Heteroaryne Formation and Functionalization | 5-Membered N-heteroarynes have long been considered synthetically inaccessible; however, we recently reported the use of a bisphosphine-ligated nickel center to stabilize and enable the formation of these otherwise unobtainable intermediates. Moti-vated by this success, we were compelled to study the role of the ancillary phosphine in aryne formation and reactivity. Here-in, a set four bidentate phosphine ligands with altered phosphine substituents and backbone length are interrogated for their competence as ancillary ligands for 5-membered N-heteroaryne formation. We determined that ligands with phenyl phosphine substituents or linker lengths longer than three carbons were unsuitable for this purpose, while ligands having alkyl phos-phine substituents and one, two, or three carbon linkers allowed for successful aryne formation. Reactivity studies using 2-PyZnBr as a nucleophilic coupling partner revealed intriguing regioselectivity enhancement (up to >20:1 r.r.) when utilizing ligands with altered linker lengths. We hypothesize that regioselectivity can be traced back to structural differences between these Ni-aryne complexes, as evidenced by crystallographic characterization. | Erin Plasek; Roman Belli; Douglas Kavaguti; Courtney Roberts | Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666c52c6c9c6a5c07a7864af/original/bidentate-phosphine-ligand-impacts-on-previously-inaccessible-5-membered-n-heteroaryne-formation-and-functionalization.pdf |
60c74747469df450e5f437cd | 10.26434/chemrxiv.11560188.v1 | Comparative structural analysis of 20S proteasome ortholog protein complexes by native mass spectrometry | <p>Ortholog protein complexes are responsible for equivalent functions
in different organisms. However, during evolution, each organism adapts to meet
its physiological needs and the environmental challenges imposed by its niche.
This selection pressure leads to
structural diversity in protein complexes, which are often difficult to specify,
especially in the absence of high-resolution structures. Here, we describe a multi-level
experimental approach based on native mass spectrometry (MS) tools for elucidating
the structural preservation and variations among highly related protein
complexes. The 20S proteasome, an essential protein degradation machinery,
served as our model system, wherein we examined five complexes isolated from
different organisms. We show that throughout evolution, from the <i>T.
acidophilum</i> archaeal prokaryotic complex to the eukaryotic 20S proteasomes in
yeast (<i>S. cerevisiae</i>) and mammals (rat - <i>R.</i> <i>norvegicus</i>,
rabbit - <i>O. cuniculus</i> and human - HEK293 cells), the proteasome
increased both in size and stability. Native Ms structural signatures of the
rat and rabbit 20S proteasomes, which heretofore lacked high-resolution
three-dimensional structures, highly resembled that of the human complex.
Using cryo-electron microscopy single-particle analysis we were
able to obtain a high-resolution structure of the rat 20S proteasome, allowing
us to validate the MS-based results. Our study also revealed that the yeast
complex, and not those in mammals, was the largest in size, and displayed the
greatest degree of kinetic stability. Moreover, we also identified a new proteoform
of the <a></a><a>PSMA7 </a>subunit that resides within the rat and rabbit
complexes, which to our knowledge have not been previously described. Altogether,
our strategy enables elucidation of the unique structural properties of protein
complexes that are highly similar to one another, a framework that is valid not
only to ortholog protein complexes, but also for other highly related protein
assemblies. </p> | Shay Vimer; Gili Ben Nissan; David Morgenstern; Fanindra Kumar-Deshmukh; Caley Polkinghorn; Royston S. Quintyn; YuryV. Vasli'ev; Joseph S. Beckman; Nadav Elad; Vicki Wysocki; Michal Sharon | Biochemistry | CC BY NC 4.0 | CHEMRXIV | 2020-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74747469df450e5f437cd/original/comparative-structural-analysis-of-20s-proteasome-ortholog-protein-complexes-by-native-mass-spectrometry.pdf |
60c74cc5f96a00586e28783a | 10.26434/chemrxiv.12526592.v1 | Genetic Algorithm-Based Docking of Potent Inhibitors Against SARS-CoV-2 Main Protease: A Comparison Between Natural Products and Synthetic Drugs. | <p>The Severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) has caused coronavirus disease-2019 (COVID-19)
pandemic. Despite the intensive research currently, there are no therapeutics
and vaccines available. As the main protease (M<sup>Pro</sup>) plays a vital
role in SARS-CoV-2, it is an attractive drug target. Herein we report,
potential inhibitors form natural products and synthetic drugs against M<sup>Pro</sup>. In detail, we studied the interaction of
inhibitors (Curcumin, Theaflavin, Deserpidine, Betulinic acid, Sinigrin, Emodin,
Leptodactylone, Synthetic drugs, Lopinavir, Ritonavir, Indinavir, Amprenavir, Darunavir,
Nelfinavir, Remdesivir, Saquinavir, Sivelestat, Galidesivir, and Favipiravir) with
the catalytic site of M<sup>Pro</sup>. Lastly, ADME (Absorption, Distribution,
Metabolism, and Excretion) properties of Natural products and synthetic drugs
are explored. We identified eight potential inhibitors against M<sup>Pro</sup>.
<b></b></p> | Pragadeeshwara Rao R; Tinku Basu | Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cc5f96a00586e28783a/original/genetic-algorithm-based-docking-of-potent-inhibitors-against-sars-co-v-2-main-protease-a-comparison-between-natural-products-and-synthetic-drugs.pdf |
60c73e75337d6cc315e26344 | 10.26434/chemrxiv.5993011.v2 | A Simple Algorithm for Despiking Raman Spectra | Raman Spectroscopy is a widely used analytical technique, favoured when molecular specificity with minimal sample preparation is required.<br />The majority of Raman instruments use charge-coupled device (CCD) detectors, these are susceptible to cosmic rays and as such multiple spurious spikes can occur in the measurement. These spikes are problematic as they may hinder subsequent analysis, particularly if multivariate data analysis is required. In this work we present a new algorithm to remove these spikes from spectra after acquisition. Specifically we use calculation of modified <i>Z</i> scores to locate spikes followed by a simple moving average filter to remove them. The algorithm is very simple and its execution is essentially instantaneous, resulting in spike-free spectra with minimal distortion of actual Raman data. The presented algorithm represents an improvement on existing spike removal methods by utilising simple, easy to understand mathematical concepts, making it ideal for experts and non-experts alike. <br /> | Darren Whitaker; Kevin Hayes | Chemoinformatics; Spectroscopy (Anal. Chem.); Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e75337d6cc315e26344/original/a-simple-algorithm-for-despiking-raman-spectra.pdf |
62e61ef17f3aa6334ffefa72 | 10.26434/chemrxiv-2022-rp7kd | Large Changes in Hydricity as a Function of Charge and Not Metal in (PNP)M-H (De)hydrogenation Catalysts That Undergo Metal-Ligand Cooperativity | Pincer-ligated catalysts that can undergo metal-ligand cooperativity (MLC), whereby H2 is heterolytically cleaved (with proton transfer to the ligand and hydride transfer to the metal), have emerged as potent catalysts for the hydrogenation of CO2 and organic carbonyls. Despite the plethora of systems developed that differ in metal/ligand identity, no studies establish how variation of the metal impacts the pertinent thermochemical properties of the catalyst, namely the equilibrium with H2, the hydricity of the resulting hydride, and the acidity of the ligand. These parameters can impact the kinetics, scope, and mechanism of catalysis and hence should be established. Herein, we describe how changing the metal (Co, Fe, Mn, Ru) and charge (neutral vs. anionic) impacts these parameters in a series of PNP-ligated catalysts (PNP = 2,6-bis[(di-tert-butylphosphino)methyl]pyridine). A linear correlation between hydricity and ligand pKa (when bound to the metal) is found, indicating that the two parameters are not independent of one another. This trend holds across four metals, two charges, and two different types of ligand (amine/amide and aromatization/dearomatization). Moreover, the effect of ligand deprotonation on the hydricity of (PNP)(CO)(H)Fe-H and (PNP)(CO)(H)Ru-H is assessed. It is determined that deprotonation to give anionic hydride species enhances the hydricity by ~ 16.5 kcal·mol-1 across three metals. Taken together, this work suggests that the metal identity has little effect on the thermodynamic parameters for PNP-ligated systems that undergo MLC via (de)aromatization, whilst the effect of charge is significant; moreover, ion-pairing allows for further tuning of the hydricity values. The ramifications of these findings for catalysis are discussed. | Kevin Schlenker; Lillee Casselman; Ryan VanderLinden; Caroline Saouma | Inorganic Chemistry; Catalysis; Organometallic Compounds; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e61ef17f3aa6334ffefa72/original/large-changes-in-hydricity-as-a-function-of-charge-and-not-metal-in-pnp-m-h-de-hydrogenation-catalysts-that-undergo-metal-ligand-cooperativity.pdf |
63da0a27ab681c2c9d266be2 | 10.26434/chemrxiv-2023-jkhx3-v2 | Synthesis, Structure, and Reactivity of a Gallylene Derivative Bearing a Phenalenyl-Based Ligand | Phenalenyl-based N,N-bidentate ligand-stabilized monovalent gallium(I) 1 was synthesized and characterized. Compound 1 promotes the oxidative addition of I-I, Si-Cl, C-I, and S-S bonds and oxidative cyclization with various Pi-components. Compound 1 can also coordinate to a tungsten complex to form a gallium-tungsten bond. | Takuya Kodama; Nijito Mukai; Mamoru Tobisu | Organic Chemistry; Inorganic Chemistry; Main Group Chemistry (Inorg.); Reaction (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da0a27ab681c2c9d266be2/original/synthesis-structure-and-reactivity-of-a-gallylene-derivative-bearing-a-phenalenyl-based-ligand.pdf |
626e24a46c989c0492cc5b83 | 10.26434/chemrxiv-2022-5mjrb | Cell-sized asymmetric phospholipid–amphiphilic protein vesicles with growth, fission, and molecule transportation | Lipid vesicles, which mimic cell membranes in structure and components, have been widely used to study the origin of life and artificial cell construction. A different approach to developing cell-mimicking systems focuses on the formation of protein- or polypeptide-based vesicles. However, micro-sized vesicles that are similar in membrane dynamics to the cell and that reconstitute membrane proteins are difficult to form. In this study, we generated cell-sized asymmetric phospholipid–amphiphilic protein (oleosin) vesicles that allow the reconstitution of membrane proteins and the growth and fission of vesicles. These vesicles are composed of a lipid membrane on the outer leaflet and an oleosin membrane on the inner leaflet. Further, we elucidated a mechanism for the growth and fission of cell-sized asymmetric phospholipid–oleosin vesicles by feeding phospholipid micelles. Our asymmetric phospholipid–oleosin vesicles with advantages of the lipid leaflet and the protein leaflet will potentially promote understanding of cellular biochemistry and synthetic biology. | Masato Suzuki; Koki Kamiya | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626e24a46c989c0492cc5b83/original/cell-sized-asymmetric-phospholipid-amphiphilic-protein-vesicles-with-growth-fission-and-molecule-transportation.pdf |
655e01c1cf8b3c3cd7dcdc13 | 10.26434/chemrxiv-2023-pcbrw | Towards quantum informed atom pairs | In the following research, a new modification of traditional atom pairs is studied. The atom pairs are enriched with values originating from quantum chemistry calculations. Random forest machine learning algorithm is applied in modelling 10 different properties and biological activities based on different molecular representations and evaluated in repeated cross-validation. The predictive power of modified atom pairs - quantum atom pairs are compared to the predictive powers of traditional molecular representations known and widely applied in cheminformatics. Root mean squared error, $R^2$, the area under the receiver operation curve and balanced accuracy are used to evaluate the predictive power of applied molecular representations. The research shows that while performing regression tasks, the quantum atom pairs provide better fitting to the data than their precursors. | Bartłomiej Fliszkiewicz; Marcin Sajdak | Theoretical and Computational Chemistry; Machine Learning; Quantum Computing; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655e01c1cf8b3c3cd7dcdc13/original/towards-quantum-informed-atom-pairs.pdf |
6762ff9c81d2151a022114f1 | 10.26434/chemrxiv-2024-mwlg6 | Efficient discovery of new medicine formulations using a semi-self-driven robotic formulator | We present the discovery of new medicine formulations using a semi-self-driven robotic formulator. Solubilising drugs is a significant challenge in the pharmaceutical industry, with the majority of active molecules in development for therapies being poorly soluble. The discovery of high solubility drug formulations, required for efficacious medicines, is a highly complex challenge involving the mixing of active molecules with excipients in thousands of potential combinations. We have developed a self-driving laboratory process for the production, assessment, and optimisation of solubility of liquid formulations suitable for injectable medicines, and apply it to the example molecule curcumin. In a series of loops driven by Bayesian optimisation our system discovered 7 lead formulations with high solubility (> 10mg/mL) after sampling only 256 out of 7776 potential formulations (~3%) in only a few days. Our workflow involves the generation of a seed sample set determined by clustering, followed by subsequent formulation optimisation performed by a liquid handling robot. Beyond presenting an efficient workflow for the optimisation and discovery of new liquid formulations, this work forms the basis for a more generalised optimisation workflow that could be applied to any formulation problem in the future, including those where no prior information is known. | Helena Ros; Michael Cook; David Shorthouse | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762ff9c81d2151a022114f1/original/efficient-discovery-of-new-medicine-formulations-using-a-semi-self-driven-robotic-formulator.pdf |
60d1d520c6229597361a786a | 10.26434/chemrxiv-2021-95v7d | Photogearing – A Concept for Translation of Precise Motions at the Nanoscale | Molecular gearing systems allow the integration of multiple motions in a correlated fashion, to translate motions from one locality to another and to change their speed and direction. However, currently no powerful concepts exist to implement active driving of gearing motions at the molecular scale. Herein, we present a light-fueled molecular gearing system and evidence its superiority over passive thermally activated gearing. Translation of a 180° rotation into a 120° rotation is achieved while at the same time the direction of the rotation axis is shifted by 120°. Within such photogearing process, precise motions at the nanoscale can be shifted in direction and decelerated similar to macroscopic bevel-gear operations in an energy consuming way – a necessary prerequisite to employ gearing as an active component in future integrated nanomachinery. | Aaron Gerwien; Frederik Gnannt; Peter Mayer; Henry Dube | Physical Chemistry; Organic Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d1d520c6229597361a786a/original/photogearing-a-concept-for-translation-of-precise-motions-at-the-nanoscale.pdf |
6377ed773551195158386693 | 10.26434/chemrxiv-2022-jmztm | Facilitating Flip-Flop: How Small-Molecule Structure Influences Interactions with Living Bacterial Membranes | The first barrier a small molecule must overcome before trespassing into a living cell is the lipid bilayer surrounding the intracellular content. It is imperative, therefore, to understand how the structure of a small molecule influences its fate in this region. Through the use of second harmonic generation (SHG), we show how the differing degrees of ionic headgroups, conjugated system, and branched hydrocarbon tail disparities of a series of four styryl dye molecules influence the propensity to `flip-flop' or to be further organized in the outer leaflet by the membrane. We show here that initial adsorption experiments match previous studies on model systems, however, more complex dynamics are observed over time. Aside from probe molecule structure, these dynamics also vary between cell species and can deviate from trends reported based on model membranes. Specifically, we show here that the membrane composition is revealed to be an important factor to consider for headgroup-mediated dynamics. Overall, the findings presented here on how structural variability of small molecules impacts their initial adsorption and eventual destinations within membranes in the context of living cells could have practical applications in antibiotic and drug adjuvant design. | Marea J. Blake; Hannah B. Castillo; Anna E. Curtis; Tessa R. Calhoun | Physical Chemistry; Biophysical Chemistry; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6377ed773551195158386693/original/facilitating-flip-flop-how-small-molecule-structure-influences-interactions-with-living-bacterial-membranes.pdf |
63770021207981dc442b6e63 | 10.26434/chemrxiv-2022-xmp4x | A computer simulation-based study on the intervention of active ingredients of Mongolian medicine into the S-protein of SARS-CoV-2-associated variant Omicron | Abstract
BACKGROUND: Omicron VOC (BF.7) is a variant of SARS-CoV-2 that is currently spreading globally as a dominant strain. BF.7 is more infectious than existing Omicron variants, and to date there are no specific therapeutic agents for this variant.
METHODS: The active compounds were collected by TCMSP, ETCM database and literature mining method, and the targets of the compounds were searched by Swiss Target Prediction and SUPERPRED database, while the targets of Omiron virus were collected by DisGeNET and GEO database, and then the intersecting targets were compared and analyzed. In this study, Swiss-Model was applied to construct the Spike RBD structure of Omicron variant BF.7 by replacing mutant amino acids into the Native Spike (S) structure, and the structural changes of Native S were compared. The four active compounds screened were docked with Omicron S protein and Omicron S-hACE2 complexes. To evaluate the structural stability of the complexes in a physiological environment, we also performed molecular dynamics simulations of the docked complexes and compared them to the control drug, chloroquine. The affinity of ligands and protein complexes was determined by free energy analysis using the MM-PBSA algorithm, and the structural changes of S proteins in combination with ligands were evaluated.
RESULTS: A total of 12 mongolic medicines were screened and 310 active ingredient predictions were made, with a total of 55 genes overlapping with Omicron variants and 14 targets with the largest differences being conserved. Once these 14 targets were mapped to the active ingredients of 12 mongolic herbs, four more precise active ingredients were filtered out. Of these four phytochemicals, Berberine was the most potent inhibitor of Omicron S protein. In addition, molecular docking simulations revealed that Berberine can bind stably to Omicron S protein and the Omicron S-hACE2 complex. Using molecular dynamics simulations, Berberine was shown to be able to form a stable complex with Omicron S in a physiological environment with better results than the control drug chloroquine. Free energy analysis by the MM-PBSA algorithm and evaluation of S protein structural changes following ligand binding also demonstrated a higher affinity of Berberine for Omicron S compared to the other small molecule compounds.
CONCLUSION: Berberine was found to have the most substantial inhibitory potential against Omicron VOC (BF.7) S protein and could be further investigated and developed as a potential inhibitor of Omicron.
| Lidao Bao; Jiuwang Yu; Mr Morigentu; Xuhong Tian; Chenxu Zhai; Jiu Jin; Xiaodong Zhang; Fengchun Wang; Zhaoxin Yang; Jiahui Qin; Mila Na; Wenchen Liu; Yihao Xiao; Rigui Ye; Liang Zhang; Lan Wu | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63770021207981dc442b6e63/original/a-computer-simulation-based-study-on-the-intervention-of-active-ingredients-of-mongolian-medicine-into-the-s-protein-of-sars-co-v-2-associated-variant-omicron.pdf |
670ea22051558a15ef2ae23e | 10.26434/chemrxiv-2024-qn66k | High-purity single-molecule modification of carbon nanotubes by stochastic distribution of DNA | Single-walled carbon nanotubes (SWCNTs) show promise for probing molecular interactions at single-molecule resolution, but precise and uniform surface modifications needed for single-molecule SWCNT applications remain challenging due to the stochastic nature of chemical reactions. This study presents a batch-scale synthesis and separation of single-molecule modified SWCNTs, leveraging the stochastic distribution of single-stranded DNA (ssDNA) on SWCNTs and biology-inspired separation strategies. Specifically, SWCNTs were dispersed with ssDNA mixed with a small fraction of decorated ssDNA (m-ssDNA). We developed a stochastic ssDNA-SWCNT binding model to predict the distribution of ssDNA and m-ssDNA on SWCNT at distinct mixing ratios and successfully implemented our model to produce SWCNT nanoparticles predominately containing only one m-ssDNA tag. These singly modified SWCNTs were isolated from unmodified SWCNTs using magnetic bead exploiting biotin-streptavidin interactions, achieving 0.05 μg yield at 0.25% m-ssDNA ratio, corresponding to 97.6% purity of singly modified populations. Finally, the single-molecule modification at the predicted m-ssDNA ratios was confirmed using a fluorophore as a model, enabling precise determination of SWCNT molar concentration. Ultimately, our approach provides a batch-scale method for incorporating a single molecular tag per SWCNT, supporting diverse future applications in SWCNT-based nanotechnologies. | Shoichi Nishitani; Zirun Liang; Deverin Smith; Markita P. Landry | Materials Science; Nanoscience; Carbon-based Materials; Optical Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670ea22051558a15ef2ae23e/original/high-purity-single-molecule-modification-of-carbon-nanotubes-by-stochastic-distribution-of-dna.pdf |
611db098b136d62ad30a5a1a | 10.26434/chemrxiv-2021-j5lrx | Electrochemical Fluorination of Vinyl Boronates Through Donor-Stabilized Vinyl Carbocation Intermediates | The electrochemical generation of vinyl carbocations from vinyl boronic esters and boronates is reported. Using easy-to-handle nucleophilic fluoride reagents, these intermediates are trapped to form fully substituted vinyl fluorides. Mech-anistic studies support the formation of dicoordinated car-bocations through sequential single-electron oxidation events. Notably, this electrochemical fluorination features fast reaction times and mild conditions. This transfor-mation provides a complementary method to access vinyl fluorides with simple fluoride salts such as TBAF. | Benjamin Wigman; Woojin Lee; Wenjing Wei; Ken Houk; Hosea Nelson | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Electrocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611db098b136d62ad30a5a1a/original/electrochemical-fluorination-of-vinyl-boronates-through-donor-stabilized-vinyl-carbocation-intermediates.pdf |
60c755eb337d6c77cfe28d3d | 10.26434/chemrxiv.14183039.v1 | Role of Electronic Excited State in Kinetics of the CH2OO + SO2 ! HCHO + SO3 Reaction | In this work, kinetics of the CH2OO + SO2 ! HCHO + SO3 reaction was studied by ring-polymer molecular dynamics (RPMD). To perform RPMD calculations, multi-reference configuration interaction (MRCI) was first carried out to compute data for constructing potential energy surface (PES) through a kernel regression method. On the basis of the present MRCI calculations, the statics multi-state mechanism involving the lowest-lying singlet excited state (denoted by S 1) was proposed, which is di?erent from the previously proposed mechanism with the lowest-lying triplet state (denoted by T1). Moreover, the present RPMD calculations predicted the rate coe?cient of 3:95?1011cm3 molecule1s1 at the room temperature (namely 298 K), agreeing with the previously reported experimental values. Finally, based on the present calculations, a probable dynamics mechanism was discussed, where the produced HCHO molecule was proposed to be in a vibrationally excited state. This needs further experimental and theoretical observation in the future.<br /> | Qingfei Song; Qiuyu Zhang; Qingyong Meng | Computational Chemistry and Modeling; Machine Learning; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755eb337d6c77cfe28d3d/original/role-of-electronic-excited-state-in-kinetics-of-the-ch2oo-so2-hcho-so3-reaction.pdf |
647c442abe16ad5c5773b09c | 10.26434/chemrxiv-2023-jg5x7 | Hydrogen Splitting at a Single PIII-Center and Its Use for Hydrogenation | Main-group compounds that can mimic the behavior of the transition-metal (TM) complexes are of great interest due to their potential in TM-free catalysis. Here, we report the synthesis, isolation and full characterization of the geometrically constrained phosphenium cation with the 2,6-bis(o-carborano)pyridine pincer-type ligand. A preliminary reactivity study showed that this cation is capable of activating H−H bond by a formal oxidative addition to PIII cationic center, which is unprecedented reactivity for PIII-centers, producing new dihydrophosphonium cation. Remarkably, this new phosphenium cation is capable of catalyzing the hydrogenation reactions of C=C double bonds and fused aromatic systems. | Deependra Bawari; Kuldeep Jaiswal; Donia Toami; Roman Dobrovetsky | Inorganic Chemistry; Catalysis; Main Group Chemistry (Inorg.); Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647c442abe16ad5c5773b09c/original/hydrogen-splitting-at-a-single-piii-center-and-its-use-for-hydrogenation.pdf |
665ee82491aefa6ce1c29414 | 10.26434/chemrxiv-2024-32rxx | ArtiSAN: Navigating the complexity of material structures with deep reinforcement learning | Finding low-energy atomic ordering in compositionally complex materials is one of the hardest problems in materials discovery, the solution of which can lead to breakthroughs in functional materials - from alloys to ceramics. In this work, we present the Artificial Structure Arranging Net (ArtiSAN) - a reinforcement learning agent utilizing graph representation that is trained to find low-energy atomic configurations of multicomponent systems through a series of atomic switch operations. ArtiSAN is trained on small alloy supercells ranging from binary to septenary. Strikingly, ArtiSAN generalizes to much larger systems of more than a thousand atoms, which are inaccessible with state-of-the-art methods due to the combinatorially larger search space. The performance of the current ArtiSAN agent is tested and deployed on several compositions that can be correlated with known experimental and high-fidelity computational structures. ArtiSAN demonstrates transfer across size and composition and finds physically meaningful structures using no energy evaluation calls once fully trained. While ArtiSAN will require further modifications to capture all variability in structure search, it is a remarkable step towards solving the structural part of the problem of disordered materials discovery. | Jonas Elsborg; Arghya Bhowmik | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665ee82491aefa6ce1c29414/original/arti-san-navigating-the-complexity-of-material-structures-with-deep-reinforcement-learning.pdf |
64957118853d501c0061a811 | 10.26434/chemrxiv-2023-09wpg-v2 | Legacy and Emerging Plasticizers and Stabilizers in PVC Floorings: Impacts of an Industrial Transition and Recycling | Hazardous chemicals in building and construction plastics can lead to significant indoor exposure, health risks, and contamination of recycled materials. We systematically sample new PVC floorings on the Swiss market (n=151). We conduct elemental analysis using XRF, targeted and sus-pect GC MS analysis of ortho phthalates and alternative plasticizers, and bioassay tests for cytotoxicity, oxidative stress, and endocrine, mutagenic, and genotoxic activities (for selected samples). Surprisingly, 16% of the samples contain regulated chemicals above 0.1 weight%, mainly lead and bis(2-ethylhexyl) phthalate (DEHP). Their presence is likely linked with the use of recycled PVC in new floorings, highlighting that uncontrolled recycling can delay the phase-out of hazardous chemicals. Furthermore, 29% of the samples contain ortho-phthalates besides DEHP (mainly diisononyl and diisodecyl phthalates, DiNP and DiDP) above 0.1 weight%, and 17% of the 85 tested samples cause certain adverse biological effects. Together, they make up an additional 35% of samples of potential concern. Moreover, both suspect screening and bioassay results indicate the presence of additional (potentially) hazardous substances, including emerging alternative plasticizers. Overall, our study highlights the urgent need for accelerating the phase-out of hazardous substances and enhancing transparency of chemical compositions in plastics to protect human and ecosystem health and enable the transition to a safe and sustainable circular economy. | Helene Wiesinger; Christophe Bleuler; Verena Christen; Philippe Favreau; Stefanie Hellweg; Miriam Langer; Roxane Pasquettaz; Andreas Schönborn; Zhanyun Wang | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Wastes; High-throughput Screening; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64957118853d501c0061a811/original/legacy-and-emerging-plasticizers-and-stabilizers-in-pvc-floorings-impacts-of-an-industrial-transition-and-recycling.pdf |
641e7f7291074bccd03ec8c3 | 10.26434/chemrxiv-2023-z2n4n | An Explicit-Implicit Hybrid Solvent Model for Grand Canonical Simulations of the Electrochemical Environment | The development of ab initio methods for atomistic simulations of the electrochemical environment is essential for obtaining a mechanistic understanding of the fundamental reactions. We propose here an explicit-implicit solvent model, SOLHYBRID, that enables grand-canonical ensemble simulations of the electrochemical environment with the popular Vienna Ab initio Simulation Package (VASP), extending its capabilities beyond the commonly used the implicit solvent model VASPSol. We further present a subroutine, TPOT, that allows control of the electrode potential, thereby enabling simulations at constant electrode potential to mimic the experimental electrochemical cell. We demonstrate the key points of our approach for the case of CO2 adsorption on Au(110) in the presence of K+ cation. | Duy Le | Theoretical and Computational Chemistry; Materials Science; Catalysis; Catalysts; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641e7f7291074bccd03ec8c3/original/an-explicit-implicit-hybrid-solvent-model-for-grand-canonical-simulations-of-the-electrochemical-environment.pdf |
63730be974b7b6d84cfdda35 | 10.26434/chemrxiv-2022-l798p | Periodic Law of Chemistry Overturns for Superheavy Elements | The Periodic Law is one of the greatest discoveries in human history. Chemical elements in the same group of the Periodic Table possess similar valence states and other physico-chemical properties. With the increase of atomic number Z, the relativistic effects become so strong that the super-heavy elements tend to exhibit properties notably different from their lighter congeners. Here we report that the traditionally mono- or di-valent heavy s-block elements (87Fr, 88Ra, 119E, 120E) exhibit unusual penta- or hexa-valency at ambient conditions. Due to common quantum-mechanical and relativity effects, some atomic-core electrons of the heaviest s-block elements become sufficiently activated for chemical bonding, so that they no longer behave as strictly low-valent alkali and alkaline-earth elements. The classic Periodic Law discovered by Mendeleev and others since the 1860s has thus broken down for such super-heavy elements and beyond. | Chang-Su Cao; Han-Shi Hu; W. H. Eugen Schwarz; Jun Li | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63730be974b7b6d84cfdda35/original/periodic-law-of-chemistry-overturns-for-superheavy-elements.pdf |
6360190f311072da4df75b09 | 10.26434/chemrxiv-2022-grlsr | WaterKit: thermodynamic profiling of protein hydration sites | Water desolvation is one of the key components of the free energy of binding of small molecules to their receptors. Thus, understanding the energetic balance of solvation and desolvation resulting from individual water molecules can be crucial when estimating ligand binding, especially when evaluating different molecules and poses as done in High-Throughput Virtual Screening (HTVS). Over the last decades, several methods were developed to tackle this problem, ranging from fast approximate methods (usually empirical functions using either discrete atom-atom pairwise interactions or continuum solvent models), to more computationally expensive and accurate ones mostly based on Molecular Dynamics (MD) simulations, such as Grid Inhomogeneous Solvation Theory (GIST) or Double Decoupling. On one hand, MD-based methods are prohibitive to use in HTVS to estimate the role of waters on the fly for each ligand. On the other hand, fast and approximate methods show unsatisfactory level of accuracy, with low agreement with results obtained with the more expensive methods. Here we introduce WaterKit, a new grid-based sampling method with explicit water molecules to calculate thermodynamic properties using the GIST method. Our results show that the discrete placement of water molecules is successful in reproducing the position of crystallographic waters with very high accuracy, as well as providing thermodynamic estimates with accuracy comparable to more expensive MD simulations. Unlike these methods, WaterKit can be used to analyze specific regions on the protein surface, (such as the binding site of a receptor), without having to hydrate and simulate the whole receptor structure. The results show the feasibility of a general and fast method to compute thermodynamic properties of water molecules, making it well suited to be integrated in high-throughput pipelines such as molecular docking. | Jerome Eberhardt; Stefano Forli | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6360190f311072da4df75b09/original/water-kit-thermodynamic-profiling-of-protein-hydration-sites.pdf |
63af00bddadddc3cc2a020c9 | 10.26434/chemrxiv-2023-xd0wv | Magnetic Interactions in a [Co(II)3Er(III)(OR)4] Model Cubane Through Forefront Multiconfigurational Methods | Strong electron correlation effects are one of the major challenges in modern quantum chemistry. Poly-nuclear transition metal clusters are peculiar examples of systems featuring such forms of electron correlation. Multi-reference strategies, often based on, but not limited to, the concept of complete active space, are adopted to accurately account for strong electron correlation, and to resolve their complex electronic structures. However, transition metal clusters already containing four magnetic centers with multiple unpaired electrons, make conventional active space based strategies prohibitively expensive, due to their unfavorable
scaling with the size of the active space.
In this work, forefront techniques, such as DMRG, FCIQMC and MCPDFT, are employed to overcome the computational limitation of conventional multi-reference approaches and to accurately investigate the magnetic interactions taking place in a [Co(II)3Er(III)(OR)4] model cubane water oxidation catalyst. Complete active spaces with up to 56 electrons in 56 orbitals have been constructed for the seven energetically lowest different spin states. Relative energies, local spin and spin-spin correlation values are reported, and provide crucial insights on the spin interactions for this model system, pivotal in the rationalization of the catalytic activity of this system in the water-splitting reaction. A ferromagnetic ground state is found with a very small, ∼ 50 cm−1, highest-to-lowest spin gap. Moreover, for the energetically lowest states, S=3–6, the three Co(II) sites exhibit parallel aligned spins, and for the lower states, S=0–2, two Co(II) sites retain strong parallel spin alignment. | Ruocheng Han; Sandra Luber; Giovanni Li Manni | Theoretical and Computational Chemistry; Materials Science; Organometallic Chemistry; Magnetic Materials; Theory - Computational; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63af00bddadddc3cc2a020c9/original/magnetic-interactions-in-a-co-ii-3er-iii-or-4-model-cubane-through-forefront-multiconfigurational-methods.pdf |
60c743b6ee301c26a5c79069 | 10.26434/chemrxiv.9630623.v1 | Selective Growth of Al2O3 on Size-Selected Platinum Clusters by Atomic Layer Deposition | In heterogeneous catalysis, atomic layer deposition (ALD) has been developed as a tool to stabilize and reduce carbon deposition on supported nanoparticles. Here, we discuss use of high vacuum ALD to deposit alumina films on size-selected, sub-nanometer Pt/SiO2 model catalysts. Mass-selected Pt24 clusters were deposited on oxidized Si(100), to form model Pt24/SiO2 catalysts with particles shown to be just under 1 nm, with multilayer three dimensional structure. Alternating exposures to trimethylaluminum and water vapor in an ultra-high vacuum chamber were used to grow alumina on the samples without exposing them to air. The samples were probed in situ using X-ray photoelectron spectroscopy (XPS), low-energy ion scattering spectroscopy (ISS), and CO temperature-programmed desorption (TPD). Additional samples were prepared for ex situ experiments using grazing incidence small angle x-ray scattering spectroscopy (GISAXS). Alumina growth is found to initiate at least 60 times more efficiently at the Pt24 cluster sites, compared to bare SiO2/Si, with a single ALD cycle depositing a full alumina layer on top of the clusters, with substantial additional alumina growth initiating on SiO2 sites surrounding the clusters. As a result, the clusters were completely passivated, with no exposed Pt binding sites. | Timothy J. Gorey; Yang Dai; Scott Anderson; Sungsik Lee; Sungwon Lee; Soenke Siefert; Randall Winans | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b6ee301c26a5c79069/original/selective-growth-of-al2o3-on-size-selected-platinum-clusters-by-atomic-layer-deposition.pdf |
65b728c466c1381729797f7f | 10.26434/chemrxiv-2024-0ns4m | Continuous flow production of bioactive ceria quantum dots: New paradigms to the effect of process parameters on surface oxygen vacancy tuning | Precisely monitored nucleation-growth kinetics for governing the size, surface chemistry, and sought-after attributes of quantum dots (QDs) for large-scale manufacturing remains a formidable challenge. This study evinces the importance of ultrafast mixing and high heating rates for rapid nucleation, particularly in synthesizing monodispersed QDs with enriched surface defects. Recently, cerium oxide (CeO2) nanostructures have gained prominence in antioxidant therapy owing to the co-existence of Ce3+ and Ce4+. However, current batch processes lack scalability, reproducibility, and control over the reaction kinetics, key for fine-tuning the surface defect-driven properties of CeO2 nanostructures. Addressing this knowledge gap, we demonstrate a unique, sustainable, continuous flow platform that allows simultaneous engineering of surface oxygen vacancies (VO●) and regulates the size of L arginine functionalized CeO2 QDs (VO●-rich L-arg-CeO2 QDs). Introduction of the helical coil reactor regulated by dean vortices yields monodispersed QDs with enhanced Ce3+/Ce4+ ratio and VO● at the surface. Through various experimental methodologies, we showed how adjusting temperature, flowrate, and pH enables achieving the desirable size (3 nm), thereby bestowing an optimal surface Ce3+ and VO● fractions, pivotal for size-dictated photo-response, physiochemical properties, and biofunctionality of the QDs. The abundant surface VO● (72%) entails narrowing of the band gap (~ 2.5 eV), resulting in unprecedented photothermal response (ΔT = 19.7±0.6°C) and photoluminescence, features not typically found in defect-free conventional CeO2 nanostructures. With a strategic combination of process parameters, the defect-rich material system displayed excellent biocompatibility (95.6%), and antioxidant efficacy on human keratinocyte (HaCaT) cells, and long-term stability (ζ = -29±1.5 mV) in suspensions, even after 120 days. This economical, high throughput continuous flow platform for fabricating biofunctionalized VO●-rich L-arg-CeO2 QDs outperforms conventional batch processes, opening numerous possibilities for lab-to-clinic translation in the fight against oxidative stress-related disorders. | Sayoni Sarkar; Rohit Srivastava; Ajit Kulkarni | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b728c466c1381729797f7f/original/continuous-flow-production-of-bioactive-ceria-quantum-dots-new-paradigms-to-the-effect-of-process-parameters-on-surface-oxygen-vacancy-tuning.pdf |
62cc5716252b216201e4a74e | 10.26434/chemrxiv-2022-p1p49 | The Potential Role of Addition Coupled Electron Transfer (ACET) in Single Atom Catalysis: The Hydrogen Transfer from Metalloporphyrin to Imine is an ACET | The formal hydrogen transfer from single atom catalyst to unsaturated compounds is of great interest in the catalysis research. With the hydrogen transfer from metalloporphyrin hydride (MPcH, M = Fe, Co) to imines as an example, we have shown that this reaction is an addition coupled electron transfer (ACET) reaction instead of a hydride transfer, by combining density functional theory (DFT), multireference calculations, intrinsic reaction coordinate analysis and substituent effect study. The ACET mechanism is universe in both low-polar solvent (dichloromethane) and high-polar protic solvent (2-propanal). The barrier versus Hammett substituent constant relationship under dichloromethane solvation features a volcano-like shape, in which both electron-withdrawing and electron-donating groups accelerates the reaction. While the structure-reactivity relationship cannot be rationalized by either substituent constant σp or the spin delocalization constant σJJ, it can be successfully explained by a theoretical model of ACET proposed by us for the first time in this work. This work shows that ACET may be ubiquitous in single atom catalyzed addition reactions. | Yumiao Ma; Aqeel A. Hussein | Physical Chemistry; Organic Chemistry; Catalysis; Organocatalysis; Chemical Kinetics; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cc5716252b216201e4a74e/original/the-potential-role-of-addition-coupled-electron-transfer-acet-in-single-atom-catalysis-the-hydrogen-transfer-from-metalloporphyrin-to-imine-is-an-acet.pdf |
678852bdfa469535b934b1fb | 10.26434/chemrxiv-2025-rzg0w | Shackles Off: A Kilo Scale Synthesis of Rawal’s Diene | Despite superior reactivity compared to Danishefsky's diene, Rawal's diene suffered from low commercial availability, limited scalability, and obscure stability issues. Herein, we present an optimized, scalable synthetic protocol that achieves yields suitable for the diene’s semi-industrial production, with adjustments to reagent concentrations, reaction conditions, and isolation procedures to enhance the efficiency of the synthetic protocol. Complementing synthetic advancements, this work explores the diene's physicochemical stability under diverse storage conditions. Rigorous quality control methodologies exploiting NMR and IR spectroscopy facilitate precise monitoring of purity and degradation pathways, establishing robust analytical standards. Additionally, the work demonstrates the utility of Rawal's diene in multigram syntheses of 2-alkyl-2,3-dihydro-4H-pyran-4-ones, showcasing its applicability for medicinal chemistry purposes. The findings disclosed in the paper establish a foundation for the broader adoption and commercialization of Rawal's diene, enabling its integration into academic and industrial workflows. | Oleksii Shamrai; Ievgenii Iermolenko; Eugeniy Ostapchuk; Dmytro Leha; Evgenij Zarudnitskii; Serhiy Ryabukhin; Dmytro Volochnyuk | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678852bdfa469535b934b1fb/original/shackles-off-a-kilo-scale-synthesis-of-rawal-s-diene.pdf |
644fee676ee8e6b5ed6a51b6 | 10.26434/chemrxiv-2023-vv5cq | FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols using Active Learning | Significant improvements have been made in the past decade to methods that rapidly and accurately predict binding affinity through free energy perturbation (FEP) calculations. This has been driven by recent advances in small molecule force fields and sampling algorithms combined with the availability of low-cost parallel computing. Predictive accuracies of ~1 kcal mol-1 have been regularly achieved, which are sufficient to drive potency optimization in modern drug discovery campaigns. Despite the robustness of these FEP approaches across multiple target classes, there are invariably target systems that do not display expected performance with default FEP settings. Traditionally, these systems required labor-intensive manual protocol development to arrive at parameter settings that produce a predictive FEP model. Due to the a) relatively large parameter space to be explored, b) significant compute requirements, and c) limited understanding of how combinations of parameters can affect FEP performance, manual FEP protocol optimization can take weeks to months to complete, and often does not involve rigorous train-test set splits, resulting in potential overfitting. These manual FEP protocol development timelines do not coincide with tight drug discovery project timelines, essentially preventing the use of FEP calculations for these target systems. Here, we describe an automated workflow termed FEP Protocol Builder (FEP-PB) to rapidly generate accurate FEP protocols for systems that do not perform well with default settings. FEP-PB uses active learning to iteratively search the protocol parameter space to develop accurate FEP protocols. To validate this approach, we applied it to pharmaceutically relevant systems where default FEP settings could not produce predictive models. We demonstrate that FEP-PB can rapidly generate accurate FEP protocols for the previously challenging MCL1 system with limited human intervention. We also apply FEP-PB in a real-world drug discovery setting to generate an accurate FEP protocol for the p97 system. FEP-PB is able to generate a more accurate protocol than the expert user, rapidly validating p97 as amenable to free energy calculations. Additionally, through the active learning process, we are able to gain insight into which parameters are most important for a given system. These results suggest that FEP-PB is a robust tool that can aid in rapidly developing accurate FEP protocols and increasing the number of targets that are amenable to the technology. | Cesar de Oliveira; Karl Leswing; Shulu Feng; Rene Kanters; Robert Abel; Sathesh Bhat | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644fee676ee8e6b5ed6a51b6/original/fep-protocol-builder-optimization-of-free-energy-perturbation-protocols-using-active-learning.pdf |
662a83da21291e5d1db5267b | 10.26434/chemrxiv-2024-wkn1x | DNA G‑Quadruplexes in the genome of Trypanosoma cruzi as potential therapeutic targets for Chagas disease: dithienylethene ligands as effective antiparasitic agents | Chagas disease is caused by the parasite Trypanosoma cruzi and affects over 7 million people worldwide. The two actual treatments, Benznidazole (Bzn) and Nifurtimox, cause serious side effects due to their high toxicity leading to treatment abandonment by the patients. In this work, we propose DNA G-quadruplexes (G4) as potential therapeutic targets for this infectious disease. We have found 174 putative quadruplex forming sequences per 100,000 nucleotides in the genome of T. cruzi and confirmed G4 formation of three frequent motifs. We synthesized a family of 14 quadruplex ligands based in the dithienylethene (DTE) scaffold and demonstrated their binding to these identified G4 sequences. Several DTE derivatives exhibited micromolar activity against epimastigotes of four different strains of T. cruzi, in the same concentration range as Bzn. Compounds 3 and 4 presented remarkable activity against trypomastigotes, the active form in blood, of T. cruzi SOL strain (IC50 = 1.5-3.3 μM, SI =25-40.9), being around 40 times more active than Bzn and displaying much better selectivity indexes. | Manuel Pérez-Soto; Javier Ramos-Soriano; Pablo Peñalver; Efres Belmonte-Reche; Michael O'Hagan; Anne Cucchiarini; Jean-Louis Mergny; Carmen Galán; Manuel Carlos López-López; Carmen Thomas; Juan Carlos Morales | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a83da21291e5d1db5267b/original/dna-g-quadruplexes-in-the-genome-of-trypanosoma-cruzi-as-potential-therapeutic-targets-for-chagas-disease-dithienylethene-ligands-as-effective-antiparasitic-agents.pdf |
6580c2979138d23161fdb78a | 10.26434/chemrxiv-2023-7x71w | Instructor listening during lecture: A case from introductory chemistry | Part of learning science is practicing reasoning, but some of the most common approaches to science instruction offer students little opportunity to do that, especially in the whole-class setting of large-enrollment courses. We present and closely examine a single episode of instructor listening – an instructor deliberately adopting a stance, and establishing a classroom culture, in which students’ nascent efforts at disciplinary reasoning are elicited, made sense of, and integrated into the collective learning process – in a 140-student introductory chemistry class, as an exemplar of what such instruction can look like. We delineate five aspects of the focal episode that mark it as exemplary of a listening approach to instruction. And we consider concerns about and potential value of such an approach. | Lara Appleby; Julia Gouvea; Ira Caspari-Gnann; Roger Tobin; David Hammer | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6580c2979138d23161fdb78a/original/instructor-listening-during-lecture-a-case-from-introductory-chemistry.pdf |
66fc3e7812ff75c3a1143466 | 10.26434/chemrxiv-2024-4gtww | Influence of anticoagulant on the spectroscopic analysis of drying blood pools | Over the course of a few minutes, untreated whole blood undergoes a clotting cascade making forensic research that investigates “fresh” bloodletting events difficult. In bloodstain pattern analysis research, whole blood treated with anticoagulant is often used to prolong the usability of the blood and allow for transport and experimentation to simulate pattern formation using “fresh” clot-free blood. Anticoagulants bind to components of this cascade making them unavailable to participate in coagulation, preventing the formation of clots. In this work, we investigate the spectral implications of anticoagulant addition for time since deposition (TSD) estimation methods, particularly of larger volume blood pools. We characterized the differences in spectral profiles of blood pools with and without a citrate-based anticoagulant using visible absorbance spectroscopy, attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). Across all methods, notable spectral differences were observed, namely the red-shift in the Soret peak maxima (visible), delayed increase in the 1532 cm-1 peak (ATR-FTIR), and increased accessibility of iron (XPS) in pools treated with ACD-A. Principal component analysis and partial least squares discriminant analysis (PLS-DA) were used to further assess the variation in the visible absorbance and ATR-FTIR spectra over time. The blood pools differed most significantly in the first week following deposition due to the addition of the water in the anticoagulant, slowed desiccation, and lack of clotting in the treated blood pools. At timepoints exceeding one week following deposition, the spectral profiles of the pools regained similarity. In summary, the fluid choice, and particularly the inclusion of anticoagulant is an important consideration during experimental design and TSD estimation method development. | Erin Giroux; Iraklii Ebralidze; Theresa Stotesbury | Analytical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc3e7812ff75c3a1143466/original/influence-of-anticoagulant-on-the-spectroscopic-analysis-of-drying-blood-pools.pdf |
61cc18a45b23d434f10d5d2e | 10.26434/chemrxiv-2021-hp4nb-v2 | Towards AquaSun practical utilization: strong adhesion and lack of ecotoxicity of solar-driven antifouling sol-gel coating | The outcomes of adhesion and ecotoxicity tests carried out on metal specimens faithfully representing the surface of real ships, including the primer and tie coat layers typically applied on ship hull prior to deposition of the antifouling paint, show the practical applicability of "AquaSun" antifouling sol-gel coatings. Newly developed AquaSun coatings share superhydrophicity (contact angle >115) and exceptionally high scratch resistance (ASTM 5B). Coupled to the ecofriendly antifouling mechanism based on continuous H2O2 formation upon exposure to solar light and foul release due to low surface energy, these results open the route to the practical utilization of these novel marine coatings. | Rosaria Ciriminna; Cristina Scolaro; Antonino Scurria; Silvia Sfameni; Gabriella Di Carlo; Mario Pagliaro; Anna Maria Visco | Materials Science; Coating Materials | CC BY NC 4.0 | CHEMRXIV | 2021-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cc18a45b23d434f10d5d2e/original/towards-aqua-sun-practical-utilization-strong-adhesion-and-lack-of-ecotoxicity-of-solar-driven-antifouling-sol-gel-coating.pdf |
6450828c6ee8e6b5ed700c1a | 10.26434/chemrxiv-2023-334xx | Reductive C–O Silylation by Rhodium/Lanthanum Cooperative Catalysis | In the realm of synthetic organic chemistry, a transformation enabling access to high-value-added compounds from readily available starting materials is the most ideal. Cross-electrophile coupling (XEC) reactions, the coupling of two different electrophiles, are of great importance in terms of the variety and availability of electrophiles compared with common nucleophiles. Among various electrophiles, phenols and aryl ethers can be particularly useful aryl electrophiles owing to their low toxicity, robustness, and availability. However, XEC of phenols and aryl ethers remains elusive because it is generally challenging to distinguish between two electrophiles and selectively obtain cross-coupling products under harsh reaction conditions that are often required for the activation of the less reactive C–O bonds. Meanwhile, chlorosilanes are easily available and serve as silicon electrophiles to access the most known organosilicon compounds through coupling with organic nucleophiles. Considering the utility of organosilicon compounds as organic materials and building blocks for organic synthesis, the XEC of phenols and chlorosilanes can be a highly practical and useful transformation but has never been viable. Here we describe the XEC of phenol and alcohol derivatives with chlorosilanes by cooperative rhodium and lanthanum catalysis. This reaction allows a range of anisole derivatives as well as benzylic ethers, phenols, benzylic alcohols, allylic ethers, and allylic alcohols to be transformed into various organosilicon compounds in a single step. Mechanistic studies including kinetics, stoichiometric organometallic reactions, XAS, and theoretical calculations suggest a heterobimetallic complex bearing a Rh–Mg and/or Rh–La bond as a key catalytically active species. This method can be applied to the development of novel silicon- containing organic materials and drugs containing silicon as a carbon isostere. On the other hand, the XEC of phenol derivatives enables the use of biomass-derived resources as an alternative to petroleum to produce useful compounds in a sustainable manner. | Rin Seki; Hikaru Takaya; Yoshiaki Nakao | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6450828c6ee8e6b5ed700c1a/original/reductive-c-o-silylation-by-rhodium-lanthanum-cooperative-catalysis.pdf |
634f2185dfbd2bbe525b876a | 10.26434/chemrxiv-2022-82czl | ZINC-22 - A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery | Purchasable chemical space has grown rapidly into the tens of billions of molecules providing unprecedented opportunities for ligand discovery, but also straining the tools that might exploit these molecules at scale. We have therefore developed ZINC-22, a database of commercially accessible small molecules derived from multi-billion-scale make-on-demand libraries. The new database and tools enable analog searching in this vast new space via a facile GUI, CartBlanche, drawing on similarity methods that scale sub-linearly in the number of molecules. The new library also uses data organization methods enabling rapid lookup of molecules and their physical properties, including conformations, partial atomic charges, cLogP values, and solvation energies, all crucial for molecule docking, which had become slow with older database organizations in previous versions of ZINC. As the libraries have continued to grow, we have been interested if molecular diversity has suffered, for instance, because certain scaffolds have come to dominate via easy analoging. This has not occurred thus far, and chemical diversity continues to grow with database size, with a log increase in Bemis-Murcko scaffolds for every two logs increase in database size. Most new scaffolds come from compounds with the highest heavy atom count. Finally, we consider the implications for databases like ZINC as the libraries grow towards and beyond the trillion-molecule range. ZINC is freely available to everyone and may be accessed at cartblanche22.docking.org, via Globus, and in the Amazon AWS and Oracle OCI clouds. | Benjamin Tingle; Khanh Tang; Jose Castanon; John Gutierrez; Munkhzul Khurelbaatar; Chinzorig Dandarchuluun; Yurii Moroz; John Irwin | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634f2185dfbd2bbe525b876a/original/zinc-22-a-free-multi-billion-scale-database-of-tangible-compounds-for-ligand-discovery.pdf |
67a641a6fa469535b96bf3b2 | 10.26434/chemrxiv-2025-d9zv4 | Programmable Strategies for the Conversion of Aldehydes to Unsymmetrical (Deuterated) Diarylmethanes and Diarylketones | Diarylmethanes and diarylketones are important chemicals which feature in various materials and bioactive molecules; however, efficient divergent strategies for their synthesis are lacking. Now, in this study, we present an efficient and versatile method for synthesizing unsymmetrical diarylmethanes and diarylketones using only aldehydes and arenes as starting materials. This was successfully achieved through: (1) Regioselective Ar-H alkylation to synthesize benzhydryl-phosphonium salts via one-pot, four-component coupling reactions that utilize simple, commercially available reagents. (2) We demonstrated the utility of these phosphonium salt building blocks through chemoselective reductions or oxidations of the benzylic C–P bond, leading to unsymmetrical diarylmethanes and diarylketones, respectively. Notably, the reduction process enables the synthesis of fully deuterated benzylic diarylmethanes by utilizing D2O as a deuterium source. The products obtained serve as valuable building blocks and are produced in high yields. This new approach is straightforward, featuring simple setups that promise to facilitate novel transformations for applications in both academic and pharmaceutical research. | Vipin Gavit; Nicole Hanania; Nadim Eghbarieh; Israa Shioukhi; Ahmad Masarwa | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a641a6fa469535b96bf3b2/original/programmable-strategies-for-the-conversion-of-aldehydes-to-unsymmetrical-deuterated-diarylmethanes-and-diarylketones.pdf |
6786d7a76dde43c908899805 | 10.26434/chemrxiv-2025-ttctv | Bifunctional Tagging Through N-doped Ozonide for Charge Switch-ing and Isomeric Characterization of Glycerophospholipids Using Tandem Mass Spectrometry | Glycerophospholipids (GPLs) are structurally diverse and play essential roles in cellular structure, signaling, and metabolism. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) has been an effective approach for identifying GPLs. How-ever, this approach often fails to differentiate between isomeric lipids. In this work, we have introduced a novel bifunctional tag, nitrophenyl pyrazole, that can react with the double bonds in lipids to simultaneously achieve charge switching and dou-ble bond positional identification. Our results indicate that this approach not only enhances the ionization efficiency of GPLs in the negative mode but also effectively identifies them by providing detailed insights into the fatty acyl chain compositions and position of carbon-carbon bonds in tandem MS. We have applied the method to characterization of polar lipid extracts from complex biological samples without the requirement of authentic lipid reference standards. | Chia-Lung Tsai; Xi Chen; Ramidi Reddy; Xin Yan | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6786d7a76dde43c908899805/original/bifunctional-tagging-through-n-doped-ozonide-for-charge-switch-ing-and-isomeric-characterization-of-glycerophospholipids-using-tandem-mass-spectrometry.pdf |
645e537afb40f6b3ee7821d7 | 10.26434/chemrxiv-2023-4rv28 | Ligand-Controlled Diastereodivergency in Propargylic Alkylation of Vinylogous Aza-enamine: Construction of 1,3-Stereocenters | The first diastereodivergent propargylic alkylation reaction has been developed. This Cu(I)-catalyzed formal decarboxylative [4+2]-cycloaddition between ethynyl benzoxazinanone and vinylogous aza-enamine delivers tetrahydroquinoline derivatives, bearing 1,3-stereocenters. Access to each diastereomer of the product from the same set of starting materials is possible using either i-Pr-Pybox or BINAP as ligand under otherwise identical reaction conditions. This is the first application of vinylogous aza-enamines in a transition metal-catalyzed trans-formation and the first example of the creation of 1,3-stereocenters in a propargylic substitution reaction. Preliminary experiments with the aim to access each of the product stereoisomers showed promising enantioselectivities. | Suman Ghosh; Santanu Mukherjee | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645e537afb40f6b3ee7821d7/original/ligand-controlled-diastereodivergency-in-propargylic-alkylation-of-vinylogous-aza-enamine-construction-of-1-3-stereocenters.pdf |
60c746819abda28db5f8c762 | 10.26434/chemrxiv.11320373.v1 | Precharging Photon Upconversion: Interfacial Interactions in Solution-Processed Perovskite Upconversion Devices | <p>Recent advances in perovskite-sensitized photon upconversion via triplet-triplet annihilation (TTA) in rubrene have yielded several unanswered questions about the underlying mechanism and processes occurring at the interface. In particular, the near-infrared perovskite emission is not significantly quenched and a rapid reversible photobleach of the upconverted emission can be observed under fairly low excitation densities of 3.2 mW/cm2. In this contribution, we investigate the perovskite/organic interface in more detail and conclude that non-covalent interactions between the organic layer and perovskite result in surface trap passivation. In addition, band bending results in a charge space region at the perovskite/rubrene interface, which precharges the rubrene interface with holes. Upon initial illumination, electrons can rapidly transfer to the excited triplet state of rubrene, followed by efficient TTA upconversion. As the device is continuously illuminated, the precharged holes are consumed and a new equilibrium is reached, resulting in the previously investigated steady-state upconversion efficiency.</p> | Sarah Wieghold; Lea Nienhaus | Interfaces; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746819abda28db5f8c762/original/precharging-photon-upconversion-interfacial-interactions-in-solution-processed-perovskite-upconversion-devices.pdf |
624ff67946cd784a316113c3 | 10.26434/chemrxiv-2022-tncn2-v2 | Disinfectants Role in the Prevention of Spreading the COVID-19 and Other Infectious Diseases – The Need for Functional Polymers! | The spreading of coronavirus through droplets and aerosols of an infected person is a well-known mechanism. The main protection methods from this virus are using disinfectants/sanitizers, face masks, keeping social distance, and vaccination. With the rapid mutations of the virus accompanied by its features and contagions changing, new advanced functional materials development is highly needed. The usage of disinfectants/sanitizers in excess generates poisonous effects among the general public. Effective and simultaneously, human-friendly sanitizers or disinfectants are required to prevent the poisoning and the associated issues. They minimize the toxic effects of the currently available materials by rapid action, high potential, long-term stability, and excellent biocompatible nature. Here, we summarize the available antiviral materials, their features, and their limitations. We highlight the need to develop an arsenal of advanced functional antiviral polymers with intrinsic bioactive functionalities or released bioactive moieties in a controlled manner for rapid and long-term actions for current and future anticipated viral outbreaks. | Konda Reddy Kunduru; Neta Kutner; Eid Nassar-Marjiya; Merna Shaheen-Mualim; Luna Rizik; Shady Farah | Polymer Science; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624ff67946cd784a316113c3/original/disinfectants-role-in-the-prevention-of-spreading-the-covid-19-and-other-infectious-diseases-the-need-for-functional-polymers.pdf |
636928758e0d3584ec0f8e85 | 10.26434/chemrxiv-2022-lzzsp | Tautomerisation Mechanisms in the Adenine-Thymine Nucleobase Pair During DNA Strand Separation | The adenine-thymine tautomer (A*-T*) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A*-T* while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A*-T* as the DNA strands unzip and the hydrogen bonds between the bases stretch. Molecular Dynamics simulations reveal the timescales and dynamics of DNA strand separation and statistical ensemble of opening angles present in a biological environment. Our results demonstrate that the unwinding of DNA, an inherently out-of-equilibrium process facilitated by helicase, will change the energy landscape of the adenine-thymine tautomerisation reaction. We propose that DNA strand separation allows the stable tautomerisation of adenine-thymine, providing a feasible pathway for genetic point mutations via proton transfer between the A-T bases. | Benjamin King; Max Winokan; Paul Stevenson; Jim Al-Khalili; Louie Slocombe; Marco Sacchi | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636928758e0d3584ec0f8e85/original/tautomerisation-mechanisms-in-the-adenine-thymine-nucleobase-pair-during-dna-strand-separation.pdf |
60c7545c4c89190823ad44ef | 10.26434/chemrxiv.13653020.v1 | Adsorbed Xenon Propellant Storage: Are Nanoporous Materials Worth the Weight? | Xenon is used as a propellant for spacecraft. Conventionally, xenon is compressed to high pressures (75-300 bar) for bulk storage onboard the spacecraft. An adsorbed xenon storage system based on nanoporous materials (NPMs) could, potentially, (i) reduce the storage pressures, (ii) allow for thinner-walled and lighter pressure vessels, and (iii) if the NPM itself is sufficiently light, reduce the overall mass of the storage system and thus of the payload of the rocket launch.<br /><br />To investigate, we develop a simple mathematical model of an adsorbed xenon storage system by coupling a mechanical model for the pressure vessel and a thermodynamic model for the density of xenon adsorbed in the NPM. From the model, we derive the optimal storage pressure, tailored to each NPM, with the objective of minimizing the mass of the storage materials (walls of the pressure vessel + NPM) required to store the xenon. The model enables us to: (i) rank NPMs for adsorbed xenon propellant storage, (ii) compare adsorbed storage to the baseline of bulk storage, and (iii) understand what properties of NPMs are desirable for adsorbed xenon propellant storage.<br /><br />We use the model to evaluate several NPMs, mostly metal-organic frameworks (MOFs), for adsorbed xenon propellant storage at room temperature, using experimental xenon adsorption data as input. We find Ni-MOF-74 and MOF-505 outperform the traditional adsorbent, activated carbon. However, we find each optimized adsorbed xenon storage system is heavier than the optimized bulk storage system, owing dominantly to the large mass of the NPM itself. Our model suggests that, for a NPM to provide a lighter adsorbed xenon storage system compared to bulk storage, the saturation loading of xenon in the adsorbent must exceed ca. 94 mmol Xe/g adsorbent. | Melanie T. Huynh; Nickolas Gantzler; Samuel Hough; David Roundy; Praveen K. Thallapally; Cory M. Simon | Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2021-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7545c4c89190823ad44ef/original/adsorbed-xenon-propellant-storage-are-nanoporous-materials-worth-the-weight.pdf |
60c7459ebdbb89802fa38a6c | 10.26434/chemrxiv.10072475.v1 | High-Performance Iron-Based ORR Catalysts Synthesized via Chemical Vapor Deposition | A Fe-N-C catalyst was synthesized via chemical vapor deposition (CVD) of gas phase FeCl3 onto a metal organic framework (MOF)-derived N-doped carbon (N-C) substrate at 750 ℃. This catalyst exhibits an unprecedented current density of 0.033 mA·cm-2 at 0.90 ViR-free (IR-corrected) and 0.044 mA·cm-2 at 0.89 ViR-free in a H2-O2 proton exchange membrane fuel cell under 1.0 bar and 80 ℃ conditions. The exceptional ORR activity of this catalyst is attributed to the ultra-high density of the Fe(II)-N4 sites. The high density of Fe(II)-N4 sites is realized by CVD that allows for the ready formation of Fe(II)-N4 sites via direct incorporation of gas phase FeCl3 into microporous N-C defects at relatively low temperatures. At these low temperatures, the doped N and Fe(II)-N4 are better preserved as compared to those in previous Fe-N-C catalysts synthesized via pyrolysis of the mixture of Fe, N, and C precursors at 1000 ± 100 ℃.<br /> | Li Jiao; Jingkun Li; Lynne K. LaRochelle Richard; Thomas Stracensky; Ershuai Liu; Qiang Sun; Moulay-Tahar Sougrati; Zipeng Zhao; Fan Yang; Sichen Zhong; Hui Xu; Sanjeev Mukerjee; Yu Huang; Deborah J. Myers; Frédéric Jaouen; Qingying Jia | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7459ebdbb89802fa38a6c/original/high-performance-iron-based-orr-catalysts-synthesized-via-chemical-vapor-deposition.pdf |
65c0fd1c66c138172904ec4b | 10.26434/chemrxiv-2024-76mm4 | A Fast and Efficient MN-Approach for Reactivity of Natural Product Exploration in Plant Extract: Application to Diterpene Esters from Euphorbia dendroides | Natural products represent a rich source of bioactive compounds covering a large chemical space. Even if challenging, this diversity can be extended by applying chemical modifications. However, these studies require generally multigram amounts of isolated natural products and face frequent testing failures. To overcome this limitation, we propose a rapid and efficient approach that uses molecular networking (MN) to visualize new chemical diversity generated by simple chemical modifications of natural extract. Moreover, the strategy deployed enables the most appropriate reagents to be defined quickly upstream a reaction on a pure compound, in order to maximize chemical diversity. This methodology was applied to the latex extract of Euphorbia dendroides to follow the reactivity towards a series of acids and Lewis acids of three class of diterpene esters identified in this species: jatrophane, terracinolide, and phorbol. Through the molecular networking interpretation, in aim to illustrate our approach, two Lewis acids were selected for chemical modification on previously isolated jatrophane esters. Three rearranged compounds (3−5) were obtained when exposed to BF3.OEt2, showing that the most appropriate reagents can be selected by MN interpretation. | Mélissa Nothias-Esposito; Fanny Roussi; Julien Paolini; Marc Litaudon; Sandy Desrat | Organic Chemistry; Analytical Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c0fd1c66c138172904ec4b/original/a-fast-and-efficient-mn-approach-for-reactivity-of-natural-product-exploration-in-plant-extract-application-to-diterpene-esters-from-euphorbia-dendroides.pdf |
65fdc5519138d231610ba559 | 10.26434/chemrxiv-2024-r7bd9 | Comprehensive Untargeted Lipidomic Profiling of Third Generation Lentiviral Vectors and Packaging Cells | Lentiviral Vectors (LV) are emerging tools for genetic therapies and novel cancer treatments. While effective, LV-based therapies have extremely large costs associated with their manufacturing and delivery. LV technology descends from human immunodeficiency virus (HIV), whose lipid envelope has been previously measured and shown to have a direct impact on its transduction efficiency. We developed a rapid, robust, and sensitive untargeted lipidomics pipeline to analyze novel LV biotherapeutic products and demonstrate its utility on HEK 293T packaging cells and concentrated culture media containing LV. The impact of 48 hours of LV production on the lipidome of HEK 293T cells was measured and compared to the expression of Vesicular stomatitis virus G protein (VSV G) over the same timeframe. 151 lipids were identified in HEK 293T packaging cells, 84 of which had fold changes with FDR-corrected P<0.05 compared to HEK 293T treated with media. It was found that fold changes with FDR-adjusted P<0.05 after VSV G expression and LV production were highly correlated (R2=0.89). Concentrating LV in culture media led to the identification of 102 lipids, half of which being determined to be unique LV virion lipids after subtracting the media lipidome. Our approach can be readily used to study the lipid dynamics of large-scale LV production and be rapidly translated into targeted methods to quantify individual lipid components or applied to other viral vector platforms. | Joshua Roberts; Elena Godbout; Jocelyn Menard; Christopher Boddy; Jean-Simon Diallo; Jeffrey Smith | Analytical Chemistry; Biochemical Analysis; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fdc5519138d231610ba559/original/comprehensive-untargeted-lipidomic-profiling-of-third-generation-lentiviral-vectors-and-packaging-cells.pdf |
673173997be152b1d0aa2ae0 | 10.26434/chemrxiv-2024-dtjvk | All-graphite microchannel microbial fuel cells with high-power generation and conversion efficiency | In this work, we present a new “all-graphite” concept in microfluidic fuel cells, applied to microbial fuel cells (MFCs). The all-graphite microfluidic MFCs were fabricated by milling channels directly into the electrodes. Two such electrode channels were affixed face-to-face with separation by an ion exchange membrane to form a complete MFC. Three such MFCs were fabricated with simple straight channels having different channel heights and activated with pure culture anaerobic Geobacter sulfurreducens electroactive biofilm. After the proof-of-principle and correlation between the channel height and electroactive biofilm thickness, we demonstrated improvements on power and current outputs using a fourth design, which featured a high surface area provided by pillars. A high acetate conversion efficiency of more than 80% and low internal resistance of 1.2 kΩ were achieved using the pillar MFC. Additionally, a high-power density of 4.7 W m-2 was obtained with a straight channel MFC. | Linlin Liu; William Varroy; Marc-Antoine Bansept; Changhong Cao; Denis Boudreau; Jesse Greener | Energy; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673173997be152b1d0aa2ae0/original/all-graphite-microchannel-microbial-fuel-cells-with-high-power-generation-and-conversion-efficiency.pdf |
60c75281ee301c3277c7ac0c | 10.26434/chemrxiv.13299149.v1 | Novel Inhibitors of Eukaryotic Elongation Factor 2 Kinase: In Silico, Synthesis, and in Vitro Studies | <p>Eukaryotic elongation factor 2 kinase (eEF2K) is an unusual alpha
kinase whose expression is highly upregulated in various cancers and
contributes to tumor growth, metastasis, and progression. More importantly, expression
of eEF2K is associated with poor clinical outcome and shorter patient survival
triple negative breast cancer (TNBC). Therefore, eEF2K is an emerging molecular
target for development of novel targeted therapeutics and precision medicine in
solid cancers. However, currently potent,
and specific inhibitors of eEF2K are not available for clinical translation. In
the current study, we investigated the effects of various newly designed and
synthesized a series of compounds with coumarin scaffold substitutions in
inhibiting eEF2K activity using <i>in silico
</i>approaches and <i>in vitro </i>studies
in TNBC cells. We utilized an amide substitution at 3-position on the coumarin
ring with their pharmacologically active groups containing pyrrolidine,
piperidine, morpholine and piperazine groups with –(CH<sub>2</sub>)<sub>2</sub>– bridged for aliphatic amides. To evaluate
substituent effects on coumarin scaffold, boronic acid pinacol ester and
boronic acids on phenyl rings were investigated using <i>in silico</i> and <i>in vitro</i>
analyses. Due to their ability to form covalent binding to the target enzyme,
we investigated the effects of boron containing groups on functionalized
coumarin ring (3 compounds) and designed novel aliphatic and aromatic
derivatives of coumarin scaffolds (10 compounds) and phenyl ring with boron
groups <b>(</b>4 compounds<b>)</b>. <i>In
silico</i> analysis and molecular docking studies were performed using the
Glide/SP module of Maestro molecular modeling package. According to obtained
results, structure activity relationship (SAR) was carried out. Among the newly
designed, synthesized, and tested compounds, our <i>in vitro</i> findings revealed that several compounds displayed a
highly effective eEF2K inhibition at submicromolar concentration in<i> in vitro </i>breast cancer cells. In
conclusion, we identified novel eEF2K inhibitors as promising anticancer drug
substance candidates which should be further evaluated by <i>in vivo</i> studies, preclinical and clinical studies.</p><br /> | Ferah CÖMERT ÖNDER; Serdar DURDAĞI; Nermin Kahraman; Tuğçe Nur Uslu; Hakan Kandemir; Esen Bellur Atici; Bülent ÖZPOLAT; Mehmet AY | Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Biochemistry; Biophysics; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75281ee301c3277c7ac0c/original/novel-inhibitors-of-eukaryotic-elongation-factor-2-kinase-in-silico-synthesis-and-in-vitro-studies.pdf |
6555376cdbd7c8b54b56e002 | 10.26434/chemrxiv-2023-zd7mz | Probing the Actives Sites of Oxide Encapsulated Electrocatalysts with Controllable Oxygen Evolution Selectivity | Electrocatalysts encapsulated by nanoscopic overlayers can catalyze redox reactions at the outer surface of the overlayer or at the buried interface between the overlayer and the active catalyst, leading to complex behavior in the presence of two competing electrochemical reactions. This study investigated oxide encapsulated electrocatalysts (OECs) comprised of iridium (Ir) thin films coated with an ultrathin (2-10 nm thick) silicon oxide (SiOx) or titanium oxide (TiOx) overlayer. The performance of SiOx|Ir and TiOx|Ir thin film electrodes towards the oxygen evolution reaction (OER) and Fe(II)/Fe(III) redox reactions were evaluated. An improvement in selectivity towards the OER was observed for all OECs. Overlayer properties, namely ionic and electronic conductivity, were assessed using a combination of electroanalytical methods and molecular dynamics simulations. SiOx and TiO¬x overlayers were found to be permeable to H2O and O2 such that the OER can occur at the MOx|Ir (M = Ti, Si) buried interface, which was further supported with molecular dynamics simulations. In contrast, Fe(II)/Fe(III) redox reactions occur to the same degree irrespective of whether electrocatalysts are bare, have TiOx overlayers with thicknesses less than 4 nm, or have SiOx overlayers with thicknesses less than 2 nm. This observation is attributed to facile electronic transport between the buried interface and outer surface of the overlayer, as measured with through-plane conductivity and ionic permeability measurements of wetted overlayer materials. These findings reveal the influence of oxide overlayer properties on the activity and selectivity of OECs and suggest opportunities to tune these properties for a wide range of electrochemical reactions. | William D.H. Stinson; Robert S. Stinson; Jingjing Jin; Zejie Chen; Mingjie Xu; Fikret Aydin; Yinxian Wang; Marco F. Calegari Andrade; Xiaoqing Pan; Tuan Anh Pham; Katherine E. Hurst; Tadashi Ogitsu; Shane Ardo; Daniel V. Esposito | Catalysis; Nanoscience; Nanostructured Materials - Nanoscience; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6555376cdbd7c8b54b56e002/original/probing-the-actives-sites-of-oxide-encapsulated-electrocatalysts-with-controllable-oxygen-evolution-selectivity.pdf |
673ca19d7be152b1d09f8681 | 10.26434/chemrxiv-2024-66xzb | Comparison of PGSE NMR and ESI-MS Measurements on Methylaluminoxane | PGSE NMR and ESI-MS studies of different grades of hydrolytic MAO demonstrate that the average dimensions and anion distribution of MAO are correlated with one another, as revealed through studies of aging and gelation of a commercial formulation of MAO. Formulations featuring an anion distribution skewed to higher m/z ratios have significantly higher activator contents as measured by 1H NMR spectroscopy in otherwise very similar formulations. PSGE NMR studies in toluene vs. chlorobenzene media demonstrate that the average dimensions of MAO are largely unaffected by solvent polarity, though aggregation behavior is more pronounced in the more polar solvent. As for catalyst activation and ion-pair speciation, the situation in polar solvents is complicated by the formation of solvated cations (and anions) in chlorobenzene which dramatically lower dimensions. DFT studies of model aluminoxane structures in the size range for MAO featuring a variety of architectures, molar mass and Me3Al content reveal that a linear correlation between Dt, as measured by PGSE NMR, can be related to molar mass using simple relationships and estimates of molecular volume if suitable high molecular weight standards are available. There is a reasonable agreement in molar mass with available ESI-MS data, recognizing that MAO is not monodisperse. | Luca Rocchigiani; Scott Collins; J. Scott McIndoe; Mikko Linnolahti | Catalysis; Organometallic Chemistry; Polymer Science; Polymerization catalysts; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ca19d7be152b1d09f8681/original/comparison-of-pgse-nmr-and-esi-ms-measurements-on-methylaluminoxane.pdf |
60c74589337d6c4224e26fce | 10.26434/chemrxiv.9725120.v2 | Dynamic Structural Changes Accompany the Production of 2-Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase | 2,3-Dihydroxypropanesulfonate (DHPS) is a major sulfur species in the biosphere. One important route for the production of DHPS includes sulfoglycolytic catabolism of sulfoquinovose (SQ) through the Embden-Meyerhof-Parnas (sulfo-EMP) pathway. SQ is a sulfonated carbohydrate present in plant and cyanobacterial sulfolipids (sulfoquinovosyl diacylglyceride and its metabolites) and is biosynthesised globally at a rate of around 10 billion tonnes per annum. The final step in the bacterial sulfo-EMP pathway involves reduction of sulfolactaldehyde (SLA) to DHPS, catalysed by an NADH-dependent SLA reductase. On the basis of conserved sequence motifs, we assign SLA reductase to the β-hydroxyacid dehydrogenase (β-HAD) family, making it the first example of a β-HAD enzyme that acts on a sulfonic acid, rather than a carboxylic acid substrate. We report crystal structures of the SLA reductase YihU from E. coli K-12 in its apo and cofactor-bound states, as well as the ternary complex YihU•NADH•DHPS with the cofactor and product bound in the active site. Conformational flexibility observed in these structures, combined with kinetic studies, confirm a sequential mechanism and provide evidence for dynamic domain movements that occur during catalysis. The ternary complex structure reveals a conserved sulfonate pocket in SLA reductase that recognises the sulfonate oxygens through hydrogen bonding to Asn174, Ser178, and the backbone amide of Arg123, along with an ordered water molecule. This triad of residues distinguishes these enzymes from classical β-HADs that act on carboxylate substrates. A comparison of YihU crystal structures with close structural homologues within the β-HAD family highlights key differences in the overall domain organization and identifies a unique peptide sequence that is predictive of SLA reductase activity.<br /> | Mahima Sharma; Palika Abayakoon; James P. Lingford; Yi Jin; Ruwan Epa; Ethan
D. Goddard-Borger; Gideon J. Davies; Spencer Williams | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74589337d6c4224e26fce/original/dynamic-structural-changes-accompany-the-production-of-2-dihydroxypropanesulfonate-by-sulfolactaldehyde-reductase.pdf |
6309c436f07ee121c8f37e6f | 10.26434/chemrxiv-2022-62jn7 | A molecular switch via chemisorption of the Au6 cluster by cyclo [18] carbon: utilization of an external electric field | The Au6 cluster can produce a variety of adsorption conformation complexes with carbon materials by physical or chemical adsorption. Such complexes are potential molecular switches. The adsorption behavior of the newly reported pure carbon ring cyclo [18] carbon (C18) with transition metal Au6 clusters is investigated based on density functional theory (DFT). The results show that the complexes are chemically bonded and have two stable conformations. An applied electric field can achieve the interconversion of the two dominant conformations. Various wave function analyses showed that the formation of the complexes reduced the delocalization of the carbon ring π electrons, and there were significant differences in the electron transfer modes and infrared spectra of the two stable conformations. The formation of complexes reduces the intrinsic reactivity of both fragments and can play a role in stabilizing both C18 and Au6 clusters. This study has positive implications for revealing the microscopic nature of the chemical processes between metals and C18 in the transition region. | Long Li; Yanying Zheng | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6309c436f07ee121c8f37e6f/original/a-molecular-switch-via-chemisorption-of-the-au6-cluster-by-cyclo-18-carbon-utilization-of-an-external-electric-field.pdf |
6678f5a25101a2ffa85a4e29 | 10.26434/chemrxiv-2024-0xr1z-v3 | Engineering Cryptand-like Coordination Sites in Multisite Metal Acyl-Organic Cages for Specific Recognition and Deep Purification of Radioactive Strontium(II) | Tailored design of organic linkers or metal nodes can implant desirable binding sites in metal-organic cages (MOCs), expanding the types of guests they can encapsulate. In this work, we propose a feasible method of engineering acyl-type metal nodes to endow MOCs with selective recognition ability towards metal ions without compromising structural robustness, and a novel uranyl-sealed multisite metal supramolecular cage (UOC) is synthesized as a prototype compound. In UOC, peroxide-bridged dimeric uranyl units create a well-defined cryptand-like cavity as a recognition site for efficient encapsulation of Sr2+ through precise size-matching effect. Bonding analysis of Sr@UOC reveals significant electrostatic interaction and orbital overlap between Sr 4d and O 2p, explaining the high binding strength. Hydrophobic cavities at both ends of UOC allow further co-inclusion of organic guests, facilitating the co-encapsulation of two different types of guest species. Inspired by UOC's strong binding affinity for Sr2+, it is employed as absorbents to capture low concentrations of Sr2+ in aqueous solutions. A removal rate of 99.9% for Sr2+ ions at an initial concentration as low as 0.01 mM is achieved, with a record high distribution coefficient (Kd) of 1.36×107 mL/g, demonstrating UOC’s potential for deep purification of trace amounts of radioactive 90Sr2+. | Wei Jin; Qun-yan Wu; Yan Lou; Zhi-wei Huang; Feng Liu; Bo-wen Hu; Ji-Pan Yu; Kong-Qiu Hu; Li-yong Yuan; Lei Mei; Wei-Qun Shi | Inorganic Chemistry; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6678f5a25101a2ffa85a4e29/original/engineering-cryptand-like-coordination-sites-in-multisite-metal-acyl-organic-cages-for-specific-recognition-and-deep-purification-of-radioactive-strontium-ii.pdf |
66058b149138d231618e1ea8 | 10.26434/chemrxiv-2024-jkhk9-v4 | Optimized Substrate Positioning Enables Switches in C–H Cleavage Site and Reaction Outcome in the Hydroxylation-Epoxidation Sequence Catalyzed by Hyoscyamine 6β-Hydroxylase | Hyoscyamine 6β-hydroxylase (H6H) is an Fe(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase that catalyzes the last two steps in the biosynthesis of scopolamine, a prolifically administered anti-nausea drug. After its namesake first reaction, H6H couples the newly installed C6-bonded oxygen to C7 to form the epoxide of scopolamine. Oxoiron(IV) (ferryl) intermediates initiate both reactions by cleaving C–H bonds, but it remains unclear how the enzyme switches target site and promotes (C6)O–C7 coupling in preference to C7 hydroxylation in the second step. In one possible epoxidation mechanism, the C6 oxygen would – analogously to mechanisms proposed for the Fe/2OG halogenases and, in a parallel study, N-acetylnorloline synthase (LolO) – coordinate as alkoxide to the C7–H-cleaving ferryl intermediate to enable alkoxyl coupling to the ensuing C7 radical. Here we provide structural and kinetic evidence that H6H instead exploits the distinct spatial dependencies of competitive C–H-cleavage (C6 vs C7) and C–O-coupling (oxygen rebound vs cyclization) steps to promote the two-step sequence without substrate coordination or repositioning for the epoxidation step. Structural comparisons of ferryl-mimicking vanadyl complexes of wild-type H6H and a variant that preferentially 7-hydroxylates instead of epoxidizing 6β-hydroxyhyoscyamine suggest that only a modest (~ 10°) shift in the Fe–O–H(C7) approach angle is sufficient to change the outcome. The observation that, in wild-type H6H, ²H₂O solvent also increases the C7-hydroxylation:epoxidation ratio by ~ 8-fold implies that the latter outcome requires cleavage of the alcohol O-H bond, which, unlike in the LolO oxacyclization, is not accomplished in advance of C–H cleavage. | Eliott Wenger; Ryan Martinie; Richiro Ushimaru; Christopher Pollock; Debangsu Sil; Aaron Li; Nhi Hoang; Gavin Palowitch; Brandt Graham; Irene Schaperdoth; Evan Burke; Ailiena Maggiolo; Wei-Chen Chang; Benjamin Allen; Carsten Krebs; Alexey Silakov; Amie Boal; J. Martin Bollinger Jr. | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66058b149138d231618e1ea8/original/optimized-substrate-positioning-enables-switches-in-c-h-cleavage-site-and-reaction-outcome-in-the-hydroxylation-epoxidation-sequence-catalyzed-by-hyoscyamine-6-hydroxylase.pdf |
65c2903e66c1381729198ee8 | 10.26434/chemrxiv-2023-8bfgm-v2 | Assessing the progress of the performance of
continuous monitoring solutions under
single-blind controlled testing protocol | Recent regulatory spotlight on continuous monitoring (CM) solutions and the rapid development of CM solutions has demanded the characterization of solutions performance through regular, rigorous testing using consensus test protocols. This study is the second known implementation of such protocol involving single-blind controlled testing of 9 CM solutions. Controlled releases of rates (6 to 7100) g CH4/h over durations (0.4 to 10.2) hours under wind speed range of (0.7 to 9.9) m/s were conducted for 11 weeks. Results showed that 4 solutions achieved method detection limits (DL90s) within tested emission rate range with all 4 solutions having both the lowest DL90s (3.9 [3.0, 5.5] kg CH4/h to 6.2 [3.7, 16.7] kg CH4/h) and false positive rates (6.9% to 13.2%) indicating efforts at balancing low sensitivity with low false positive rate. Quantification results showed wide individual estimate uncertainties with emissions underestimation and overestimation by factors up to > 14 and 42 respectively. Three solutions had > 80% of their estimates within a quantification factor of 3 for controlled releases in the ranges of (0.1 – 1] kg CH4/h and >1 kg CH4/h. Relative to the study by Bell et al., current solutions performance, as a group, generally improved primarily due to solutions from the study by Bell et al. that retested. This result highlights the importance of regular, quality testing to the advancement of CM solutions for effective emissions mitigation. | Chiemezie Ilonze; Ethan Emerson; Aidan Duggan; Daniel Zimmerle | Energy; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC 4.0 | CHEMRXIV | 2024-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c2903e66c1381729198ee8/original/assessing-the-progress-of-the-performance-of-continuous-monitoring-solutions-under-single-blind-controlled-testing-protocol.pdf |
63c76d035ab31382dfab46f7 | 10.26434/chemrxiv-2023-4hpzm | Sarglamides A–E, Indolidinoid-Monoterpenoid Hybrids with Anti-Neuroinflammatory Activity from a Sarcandra Species | Sarglamides A–E (1−5), representing the first example of heterodimers of a trans-N-cinnamoylindolidinoid and an α-phelladrene derivatives, were isolated from Sarcandra glabra subsp. brachystachys. Particularly, compounds 4 and 5 possess unprecedented cage-like 6/6/5/6/5- and 6/6/6/6/5-fused pentacyclic scaffolds, respectively. Their structures were established by spectroscopic analysis, X-ray crystallography, quantum chemical calculations, and chemical conversions. Plausible biosynthetic pathways of 1−5, involving the co-isolated enantiomers 6a and 6b were proposed. Compounds 3–7 showed inhibitory activity against lipopolysaccharide (LPS) induced inflammation in BV-2 microglial cells. | Bin Zhou; Qi Gong; Yan Fu; Jun-Su Zhou; Hai-Yan Zhang; Jian-Min Yue | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c76d035ab31382dfab46f7/original/sarglamides-a-e-indolidinoid-monoterpenoid-hybrids-with-anti-neuroinflammatory-activity-from-a-sarcandra-species.pdf |
60c754cf0f50db385a397dcf | 10.26434/chemrxiv.13721179.v1 | Stripping off of the Hydration Shells in the Double Layer Formation: Water Networks Matter | <div><br /></div><div><p>The double layer at the solid/electrolyte interface is a key concept in electrochemistry. Here, we present an experimental study combined with simulations, which provides a molecular picture of the double-layer formation in operando processes. By THz spectroscopy we are able to follow the stripping off of the cation/anion hydration shells for a NaCl electrolyte at the Au surface when decreasing/increasing the bias potential. While Na<sup>+</sup> is attracted toward the electrode already at the smallest applied negative potentials, stripping-off of the Cl<sup>-</sup> hydration shell is observed only at higher potential values. These phenomena are directly measured by in operando THz spectroscopy with ultra-bright synchrotron light as a source and rationalized by accompanying molecular-dynamics simulations and electronic-structure calculations. </p></div> | Serena Rosa Alfarano; Simone Pezzotti; Christopher Stein; Zhou Lin; federico sebastiani; Sarah Funke; Katja Mauelshagen; Claudius Hoberg; Inga kolling; Chun Yu Ma; T Ockelmann; G. Schwaab; Li Fu; JB brubach; roy pascale; Martin Head-Gordon; Marie-Pierre Gaigeot; Kristina Tschulik; martina havenith | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754cf0f50db385a397dcf/original/stripping-off-of-the-hydration-shells-in-the-double-layer-formation-water-networks-matter.pdf |
6407de9a6642bf8c8f2451cc | 10.26434/chemrxiv-2023-npdmn | Hydrodynamics Determine Tafel Slopes in Electrochemical CO2 Reduction on Copper | The hydrodynamics of electrochemical CO2 reduction (CO2R) systems is an insufficiently investigated area of research that has broad implications on catalyst activity and selectivity. While most previous reports are limited to laminar and CO2-sparged systems, herein we address a wide range of hydrodynamics via electrolyte recirculation systems. We find that increased hydrodynamics at the electrode surface results directly in changes to the ethylene and methane Tafel slopes, demonstrating that mass transport is on equal footing with catalyst active sites in determining reaction mechanisms and the ensuing product distribution. Mass transport is traditionally considered to be in the purview of systems-level engineering, yet the present work shows that CO2R mechanistic work must be considered in the context of the mass transport conditions. We extend our analysis to organic coatings, demonstrating that the films shield the active sites from variability in hydrodynamics and increase the residence time of CO so that it may be further reduced to desirable products. | Nicholas Watkins; Zachary Schiffer; Yungchieh Lai; Charles Musgrave III; Harry Atwater; William Goddard III; Theodor Agapie; Jonas Peters; John Gregoire | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Electrocatalysis; Heterogeneous Catalysis; Fuels - Energy Science | CC BY NC 4.0 | CHEMRXIV | 2023-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6407de9a6642bf8c8f2451cc/original/hydrodynamics-determine-tafel-slopes-in-electrochemical-co2-reduction-on-copper.pdf |
60c751a2702a9be88418bfaf | 10.26434/chemrxiv.13193771.v1 | A Facile Modular Addition Approach to Size Control in the Synthesis of Oxo Bridged Phosphazane Macrocycles | Inorganic macrocycles remain largely underdeveloped compared with their
organic counterparts due to the challenges involved in their synthesis. Among
them, cyclodiphosphazane macrocycles have shown to be promising candidates for
supramolecular chemistry applications. However, further developments have been
handicapped by the lack of synthetic routes to high-order cyclodiphosphazane
macrocycles. Here we report the synthesis of high-order oxygen-bridged
phosphazane macrocycles via a “3+n” (n= 1 and 3) condensation reaction
synthetic strategy using novel trimeric building blocks. Using this method, the
first-ever all-PIII high-order hexameric cyclodiphosphazane macrocycle was
isolated, displaying a larger macrocyclic cavity than comparable organic
crown-ether counterparts. Our approach demonstrates that increasing building
block complexity enables unprecedented rational control over macrocycle size. | Xiaoyan Shi; felix leon; Rakesh Ganguly; jesus diaz; Felipe Garcia | Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751a2702a9be88418bfaf/original/a-facile-modular-addition-approach-to-size-control-in-the-synthesis-of-oxo-bridged-phosphazane-macrocycles.pdf |
650ad8feed7d0eccc3e12b45 | 10.26434/chemrxiv-2023-69ns9 | Photoisomerization-Induced Melting and Spontaneous Crystallization in Acicular Star-Shaped Microcrystals | In recent years, significant advancements have occurred in the development of smart materials, particularly in creating molecular crystals that can convert light energy into mechanical work. In this study, we focus on the synthesis, characterization, and photomechanical behavior of a new molecule, bis(2,2,2-trifluoroethyl) (E)-2-(3-(anthracen-9-yl)allylidene)malonate (trans-ATF), which is capable of forming acicular star-shaped microcrystals resembling sea Urchins. These crystals are formed via the seeded growth method from aqueous surfactant solution. When these microcrystals are exposed to visible light while suspended in an aqueous medium, they undergo a process in which the tips of these microcrystals temporarily become liquid and move inward towards the center. This transformation is initiated by the photoisomerization of trans-ATF to cis-ATF when absorbing visible light. After this phase, the melted crystals quickly return to their solid state in less than a minute while maintaining a balance between the two different photoisomers of the ATF molecule. In the presence of suspended silica microspheres, the star-shaped trans-ATF microcrystals undergo a similar melting process induced by visible light. During this process, the melted branches capture and pull these suspended silica microspheres towards the center of the molten crystal structure. This leads to the silica microspheres becoming enclosed within the molten crystal, which then solidifies again | Kevin Lam; Imadul Islam; Ebrahim Bushnak; Raghad Al-Muzarie; Christopher Bardeen; Rabih Al-Kaysi | Organic Chemistry; Photochemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650ad8feed7d0eccc3e12b45/original/photoisomerization-induced-melting-and-spontaneous-crystallization-in-acicular-star-shaped-microcrystals.pdf |
6377032b3551192860377d5a | 10.26434/chemrxiv-2022-6xrws-v2 | Atomic scale mechanism of platinum catalyst
restructuring under a pressure of reactant gas | Heterogeneous catalysis is key for chemical transformations. Understanding how catalyst active sites dynamically evolve at the atomic scale under reaction conditions is a prerequisite for accurate determination of catalytic mechanisms and predictably developing catalysts. We combine in-situ time-dependent observation and machine learning-accelerated first-principle atomistic simulations to uncover the mechanism of restructuring of Pt catalysts under a pressure of carbon monoxide (CO). We show that a high CO coverage at a Pt step edge triggers the formation of atomic protrusions of low-coordination Pt atoms, which then detach from the step edge to create subnano-islands on the terraces, where undercoordinated sites are stabilized by the CO adsorbates. The fast and accurate machine learning potential is key to enable the exploration of ten of thousands of configurations for the CO covered restructuring catalyst. These studies open an avenue to achieve atom-scale understanding of structural dynamics of more complex metal nanoparticle catalysts under reaction. | Vaidish Sumaria; Luan Nguyen; Franklin (Feng) Tao; Philippe Sautet | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Machine Learning; Heterogeneous Catalysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6377032b3551192860377d5a/original/atomic-scale-mechanism-of-platinum-catalyst-restructuring-under-a-pressure-of-reactant-gas.pdf |
619e7276a1292345924ceab4 | 10.26434/chemrxiv-2021-vkqw0 | Expanding the scope of prenylated 1,2,3-triazoles as new antiparasitic drug candidates | We have previously shown that prenyl and aliphatic triazoles are interesting motifs to prepare new chemical entities for antiparasitic and antituberculosis drug development. In this opportunity a new series of prenyl-1,2,3-triazoles were prepared from isoprenyl azides and different alkynes looking for new antimalarial drug candidates. The compounds were prepared by copper(I) catalyzed dipolar cycloaddition of the isoprenyl azide equilibrium mixture providing exclusively 1,4-disubstituted 1,2,3-triazols in a regiospecific fashion. The complete collection of 64 compounds was tested on chloroquine -sensitive, Sierra Leone (D6), and the chloroquine-resistant, Indochina (W2), strains of Plasmodium falciparum and those compounds which were not previously reported were also tested against Leishmania donovani , the causative agent for visceral leishmaniasis. Thirteen analogs displayed antimalarial activity with IC50 below 10 uM, while the antileishmanial activity was less potent than the previously reported analogs. The cytotoxicity assay against Vero cells revealed that none of the compounds was cytotoxic up to concentrations of 4.75 ug/mL. Compounds 1o and 1r were identified as the most promising antimalarial drug leads with IC50 below 3.0 uM for both CQ-sensitive and resistant P. falciparum strains. Finally, a chemoinformatic in silico analysis was performed to evaluate physicochemical parameters, cytotoxicity risk and drug score. The validation of a bifunctional farnesyl/geranylgeranyl diphosphate synthase PfFPPS/GGPPS as the potential target of the antimalarial activity of selected analogs should be further investigated. | Renzo Carlucci; Gabriel Di Gresia; Babu Tekwani; Shabana Khan; Guillermo Labadie | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619e7276a1292345924ceab4/original/expanding-the-scope-of-prenylated-1-2-3-triazoles-as-new-antiparasitic-drug-candidates.pdf |
67d14b2281d2151a0218fbe0 | 10.26434/chemrxiv-2025-1v585 | Selective semi-hydrogenation of acetylene using a single-atom cobalt on carbon nitride photocatalyst with water as a proton source | Light-powered strategies for the semi-hydrogenation of acetylene to ethylene are rapidly emerging as sustainable alternatives to the traditional thermochemical processes. The development of a robust, selective, as well as recyclable, non-noble catalyst that can be powered by visible light to accomplish this important reaction using water as the proton source remains a key challenge. Here we report the first demonstration of cobalt single-atom catalysts anchored on carbon-nitride (Co-CN) as an all-in-one photocatalysts for the semi-hydrogenation reaction of acetylene to ethylene using water as the proton source and no organic solvents or hydrogenated organics, offering advantages over current hydrogenation technologies. Carbon nitride is a photoactive support that hosts the individual catalytic active sites of cobalt thus combining photosensitizer and cocatalyst in one unit, in line with first-principles modelling. Under visible light irradiation, Co-CN reduces acetylene to ethylene with stable activity for over 40 days of continuous operation and ≥99.9%, selectivity and provides means for coupling organic upgrading to produce valuable oxidation products. The heterogenous Co-CN can be easily recovered and reused repeatedly without loss of catalytic activity and structural integrity. Thereby, the reported hydrogenation photocatalyst overcomes the need of coupling a separate photosensitiser to a catalyst providing an integrated and recyclable platform, and using noble metal catalysts with an external H2 gas feed.
Thanks to these features, together with longevity and semi-hydrogenation selectivity, this system holds potential for practical implementation of light-driven acetylene reduction and for exploration of other non-noble metal single atom heterogenous photocatalysts to achieve this important transformation using water as the proton source. | Anna Fortunato; Daniele Perilli; Alexandru Dron; Verónica Celorrio; Goran Dražić; Luka Ðorđević; Laura Calvillo; Cristiana Di Valentin; Francesca Arcudi | Catalysis; Energy; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d14b2281d2151a0218fbe0/original/selective-semi-hydrogenation-of-acetylene-using-a-single-atom-cobalt-on-carbon-nitride-photocatalyst-with-water-as-a-proton-source.pdf |
60c73d97337d6c11ede261c6 | 10.26434/chemrxiv.6008222.v1 | Direct Assembly of Large Area Nanoparticle Arrays | We describe the fabrication of large area arrays of single nanoparticles using electrophoretic deposition. | Paul Mulvaney; HEYOU ZHANG; CALUM KINNEAR; Jasper Cadusch; TIMOTHY JAMES; ANN ROBERTS | Nanofabrication; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d97337d6c11ede261c6/original/direct-assembly-of-large-area-nanoparticle-arrays.pdf |
610e3d7345805d7d6b82855b | 10.26434/chemrxiv-2021-cmbr3 | Tuning diazonium modification of gold nanoparticles for fuel cell application | Products made from alcohol oxidation are very important and used in food industry, pharmaceuticals and dryers to name but a few. In this regard, precious metals such as gold operate in various shapes and sizes as effective catalysts for the oxidation of alcohols. In this work, 20 nm-sized gold nanoparticles were synthesized and modified with either 4-carboxybenzenediazonium tetrafluoroborate (AB) (single salt catalyst) or a mixture of the latter with 3,5-dimethylbenzenediazonium tetrafluoroborate (AB-DMB, double-salt catalyst). The relative concentrations of the diazonium salts were tuned in order to maintain the electrocatalytic property of the arylated gold nanoparticles in the electro-oxidation of ethanol. The physicochemical properties (size, aryl layer thickness and composition) and electrocatalytic performances of the capped gold nanoparticles (in single and double salt catalyst systems) were investigated by means of TEM, XPS, UV-visible, TGA-DTA and electrochemistry. The aryl capping layer thickness is below 1 nm when the total salt concentration was 510-5 M, without any significant loss of current compared to pure gold nanoparticles. For 1 μL of pristine or arylated Au NPs, coated on 0.07 cm² glassy carbon electrode disk, we achieved a low oxidation potential of 200 mV and high current ethanol oxidation peak intensity levelling off at ~80 μA for the single diazonium arylation. It is demonstrated that dilution of the carboxylic acid-functionalized diazonium is more important than mixing this compound with 3,5-dimethylbenzene diazonium salt at equal total concentration. The dual arylation strategy returned lower ethanol oxidation intensity likely due to hydrophic effect imparted by the 3,5-dimethylphenyl groups, thus hindring access of ethanol to the nanocatalyst surface.
This work demonstrates that arylated gold nanoparticles are unique nanocatalysts for ethanol oxidation reaction, with remarkable performances. This electrocatalytic performance of the nanoparticles was maintained through the use of finely tuned aryl capping layer. The strategy opens avenues for other arylated electrocatalysts and uses thereof. | Atieh Aghajani; Marie-Pierre Santoni; Peyman Mirzaei; Ahmed Mohamed; Mohamed CHEHIMI; Mohamed Jouini | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2021-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610e3d7345805d7d6b82855b/original/tuning-diazonium-modification-of-gold-nanoparticles-for-fuel-cell-application.pdf |
61d7739481f3fe2b4e9cda41 | 10.26434/chemrxiv-2022-twtjl | A new amino acid for improving permeability and solubility in macrocyclic peptides through side chain-to-backbone hydrogen bonding. | Despite the notoriously poor membrane permeability of peptides in general, many cyclic peptide natural products show high passive membrane permeability and potently inhibit a variety of “undruggable” intracellular targets. A major impediment to designing cyclic peptides with good permeability is the high desolvation energy associated with the peptide backbone amide NH groups. Strategies for mitigating the deleterious effect of the backbone NH group on permeability include N-methylation, steric occlusion, and the formation of intramolecular hydrogen bonds with backbone carbonyl oxygens, while there have been relatively few studies on the use of polar side chains to sequester backbone NH groups. We investigated the ability of N,N-pyrrolidinyl glutamine (Pye), whose side chain contains a powerful hydrogen bond accepting C=O amide group but no hydrogen bond donors, to sequester exposed backbone NH groups in a series of cyclic hexapeptide diastereomers. Analyses of partition coefficients, lipophilic permeability efficiencies (LPE), artificial and cell-based permeability assays revealed that specific Leu-to-Pye substitutions conferred dramatic improvements in aqueous solubility and permeability in a scaffold- and position-dependent manner. Introduction of the Pye residue thus offers a complementary tool, alongside traditional approaches, for improving membrane permeability and solubility in cyclic peptides. | Jaru Taechalertpaisarn; Satoshi Ono; Okimasa Okada; Timothy C. Johnstone; R. Scott Lokey | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d7739481f3fe2b4e9cda41/original/a-new-amino-acid-for-improving-permeability-and-solubility-in-macrocyclic-peptides-through-side-chain-to-backbone-hydrogen-bonding.pdf |
60c7424c0f50db490e395cab | 10.26434/chemrxiv.8248838.v1 | Opportunities and Challenges for Nanoparticle Synthesis using Continuous Flow Systems: A Magnetite Nanocluster Case Study | <div>In this study, we demonstrate a new high temperature flow synthesis system for magnetite nanoparticle clusters. We find that successful synthesis of nanoparticle clusters is dependent on residence time in the reaction chamber and linear flow speed. The long reaction times and elevated temperatures required, combined with the resulting slurry formed with successful magnetite nanocluster synthesis, made this reaction challenging to adapt to a flow system. However, proper design of a continuous flow synthesis platform and synthesis parameter control allows for the adoption of even difficult solvothermal synthesis processes. We discuss the importance of reaction pressure control and reaction duration for successful synthesis of magnetite nanoclusters and address opportunities and challenges associated with adopting solvothermal synthesis to continuous flow synthesis platforms.</div> | Erika Fong; Jinkyu Han; C. Cameron Cornell; Yong Han | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7424c0f50db490e395cab/original/opportunities-and-challenges-for-nanoparticle-synthesis-using-continuous-flow-systems-a-magnetite-nanocluster-case-study.pdf |
6378dd2456c6f4209873dd4e | 10.26434/chemrxiv-2022-h664m | Chiral-Induced Spin Selectivity and Non-equilibrium Spin Accumulation in Molecules and Interfaces: A First-Principles Study | Electrons moving through chiral molecules are selected according to their spin orientation and the helicity of the molecule, an effect known as chiral induced spin selectivity (CISS). The underlying physical mechanism is not yet completely understood. To help elucidate this mechanism, a non-equilibrium Green’s function method, combined with a Landauer approach and density functional theory, is applied to carbon helices contacted by gold electrodes, resulting in spin polarization of transmitted electrons. Interestingly, spin polarization is also observed in the non-equilibrium electronic structure of the junctions. While this spin polarization is small, its sign changes with the direction of current and with the handedness of the molecule. While these calculations were performed with a pure exchange-correlation functional, previous studies suggest that computationally more expensive hybrid functionals may lead to considerably larger spin polarization in the electronic structure. Thus, nonequilibrium spin polarization could be a key component in understanding the CISS mechanism. | Sumit Naskar; Vladimiro Mujica; Carmen Herrmann | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Theory - Computational; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6378dd2456c6f4209873dd4e/original/chiral-induced-spin-selectivity-and-non-equilibrium-spin-accumulation-in-molecules-and-interfaces-a-first-principles-study.pdf |
60c73d570f50db72bd3954a8 | 10.26434/chemrxiv.5782224.v1 | Toward Expanded Diversity of Host-Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives | Researchers developing software to predict the binding constants of small molecules for proteins have, in recent years, turned to host-guest systems as simple, computationally tractable model systems to test and improve these computational methods. However, taking full advantage of this strategy requires aqueous host-guest systems that probe a greater diversity of chemical interactions. Here, we advance the development of an experimental platform to generate such systems by building on the cyclodextrin (CD) class of hosts. The secondary face derivative mono-3-carboxypropionamido-β-cyclodextrin (CP-β-CD) was synthesized in a one-pot strategy with 87% yield, and proved to have much greater aqueous solubility than native β-CD. The complexation of anionic CP-β-CD with the cationic drug rimantadine hydrochloride was explored using one and two-dimensional nuclear magnetic resonance (NMR); NOESY analysis showed secondary face binding of the ammonium moiety of the guest, based on cross-correlations between the amic acid functionality and the side-chain of rimantadine. Isothermal titration calorimetry was furthermore used to determine the standard free energy and enthalpy for this binding reaction, and the results were compared with those of rimantadine with native β-CD. | Kathryn Kellett; Samuel A. Kantonen; Brendan M. Duggan; Michael K. Gilson | Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d570f50db72bd3954a8/original/toward-expanded-diversity-of-host-guest-interactions-via-synthesis-and-characterization-of-cyclodextrin-derivatives.pdf |
60c7583f702a9b85b218ccc2 | 10.26434/chemrxiv.14528625.v1 | Peptoid-Based Reprogrammable Template for Cell-Permeable Inhibitors of Protein–Protein Interactions | <div>
<div>
<div>
<p>The development of inhibitors of intracellular protein–protein interactions (PPIs) is of great significance
for drug discovery, but the generation of a cell-permeable molecule with high affinity to protein is
challenging. Oligo(N-substituted glycines) (oligo-NSGs), referred to as peptoids, are attractive as
potential intracellular PPI inhibitors owing to their high membrane permeability. However, their
intrinsically flexible backbones make the rational design of inhibitors difficult. Here, we propose a
peptoid-based rational approach to develop cell-permeable PPI inhibitors using oligo(N-substituted
alanines) (oligo-NSAs). The rigid structures of oligo-NSAs enable independent optimization of each
N-substituent to improve binding affinity and membrane permeability, while preserving the backbone
shape. A molecule with optimized N-substituents inhibited a target PPI in cells, which demonstrated the
utility of oligo-NSA as a reprogrammable template to develop intracellular PPI inhibitors.
</p>
</div>
</div>
</div> | Yasuhiro Fukuda; Marin Yokomine; Daisuke Kuroda; Kouhei Tsumoto; Jumpei Morimoto; Shinsuke Sando | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7583f702a9b85b218ccc2/original/peptoid-based-reprogrammable-template-for-cell-permeable-inhibitors-of-protein-protein-interactions.pdf |
62a21e04bb751904a5487692 | 10.26434/chemrxiv-2022-fxl2z | A Brief History of and Insight in the Choice of Sensitizers/Dyes for Dye Sensitized Solar Cells | In this review, a discussion on renewable sources of energy with clear focus on solar cell applications is presented. Especially, possible future directions for development of dye-sensitized solar cells (DSSCs) are discussed. Dye-sensitized solar cells have become an important topic of research due to its high importance in energy conversion. Current DSSCs are based on either metal dye sensitizers, metal-free organic dyes or natural dyes. They have been extensively studied due to their low cost, simple preparation methodology, low toxicity, and ease of production. Still there is a need to find more abundant DSSC materials that at same time exhibit long-term stability. Computational studies have been an important ally for developing/designing new dye sensitizers. They are reviewed here with a special emphasis on the benefit of such studies. The conceptual understanding of development and working principle of photoactive DSSC materials are the primary feature of the review followed by examples of studies on different dye sensitizers using scarce to abundant metal based dyes and metal free organic dyes with donor-π-acceptor geometries for both n- and p-type DSSCs. The proper choice of organic dyes including donor, spacer, or acceptor is discussed and a prospective on dual donor based dyes is presented. | Anik Sen; Miftahussurur Hamidi Putra; Abul Kalam Biswas; Anil Kumar Behera Behera; Axel Gross | Energy; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a21e04bb751904a5487692/original/a-brief-history-of-and-insight-in-the-choice-of-sensitizers-dyes-for-dye-sensitized-solar-cells.pdf |
623394aa21e2d026d8a7746a | 10.26434/chemrxiv-2022-85p09 | Bench-Stable Dinuclear Mn(I) Catalysts in E-selective Alkyne Semihydrogenation: A Mechanistic Investigation | Dinuclear complexes [Mn2(CO)8(µ-H)(µ-PR2)] (R = Ph, 1; R = iPr, 2) were synthesized and the role of phosphido substitu-ent in E-selective alkyne semi-hydrogenation (E-SASH) catalysis was examined. Using diphenylacetylene (dpa) as the sub-strate, 2 has improved efficiency over 1, achieving 75% conversion to stilbene (E/Z ≈ 8-15 depending on conditions) with remaining dpa converting into hexaphenylbenzene and hydrophosphinated alkene (hpa) byproducts. Investigation of the mechanism revealed rich coordination chemistry and insights into the active catalyst speciation. Having isolated each species individually, the different complexes 3-8 were independently subjected to catalytic conditions: only 2, 3, and 5 furnished product with similar conversions and E-selectivity and these complexes have similar dinuclear structures. Control reactions with Mn2(CO)10, HMn(CO)5, and [Mn(CO)4(µ-H)]3 resulted in no to very low conversions and these did not exhibit E-selectivity. When (cyclopropylethynyl)benzene was used instead of dpa, the inserted species 10 was obtained with cyclopro-pane ring intact, and treatment of 10 with H2 furnished the corresponding trans-(2-cyclopropylvinyl)benzene. In addition to other tests for radicals, these latter two results indicate a non-radical mechanism for E-SASH which is highly unusual for MnH catalysts. Finally, the reaction between 3 and H2 furnishes exclusively trans-stilbene. Combined with the fact that 2 and 3 are virtually inactive towards cis to trans alkene isomerization, a mechanism and origin of selectivity is proposed, one where dinuclear complexes play a critical role. | Preshit Abhyankar; Samantha MacMillan; David Lacy | Organometallic Chemistry; Catalysis; Coordination Chemistry (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2022-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623394aa21e2d026d8a7746a/original/bench-stable-dinuclear-mn-i-catalysts-in-e-selective-alkyne-semihydrogenation-a-mechanistic-investigation.pdf |
654e9ef6dbd7c8b54b08e13b | 10.26434/chemrxiv-2023-qjwlc | Dicationic Acridinium/Carbene Hybrids as Strongly Oxidizing Photocatalysts | A new design concept for organic, strongly oxidizing photocatalysts is described based upon dicationic acridinium/carbene hybrids. A highly modular synthesis of such hybrids is presented and the dications are utilized as novel, tailor-made photoredox catalysts in the direct oxidative C−N coupling. Under optimized conditions, benzene and even electron-deficient arenes can be oxidized and coupled with a range of N-heterocycles in high to excellent yields with a single low-energy photon per catalytic turnover, while commonly used acridinium photocatalysts are not able to perform the challenging oxidation step. In contrast to traditional photocatalysts, the here reported hybrid photocatalysts feature a reversible two-electron redox system with regular or inverted redox potentials for the two-electron transfer. The different oxidation states could be isolated and structurally characterized supported by NMR, EPR and X-ray analysis. Mechanistic experiments employing time-resolved emission and transient absorption spectroscopy unambiguously reveal the outstanding excited-state oxidation potential of our best-performing catalyst (+2.5 V vs. SCE) and they provide evidence for mechanistic key steps and intermediates. | Samaresh C. Sau; Matthias Schmitz; Chris Burdenski; Marcel Baumert; Patrick W. Antoni; Christoph Kerzig; Max Hansmann | Organic Chemistry; Catalysis; Photochemistry (Org.); Homogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654e9ef6dbd7c8b54b08e13b/original/dicationic-acridinium-carbene-hybrids-as-strongly-oxidizing-photocatalysts.pdf |
6583b5ace9ebbb4db9651e08 | 10.26434/chemrxiv-2023-14n8g | Probing the Interfacial Structure of Aqueous Surfactants
through Helium Atom Evaporation | Dissolved helium atoms evaporate from liquids in super-Maxwellian speed distributions because their interactions are too weak to enforce full thermal equilibration at the surface as they are "squeezed" out of solution. The excess speeds of these He atoms reflect their last interactions with solvent and solute molecules at the surfaces of water and other liquids. We extend this observation here by monitoring He atoms evaporating from salty water solutions coated with surfactants. These surface-active molecules span neutral, anionic, and cationic amphiphiles: butanol, 3-methyl-1-butanol, pentanol, pentanoic acid, pentanoate, tetrabutylammonium, benzyltrimethylammonium, hexyltrimethylammonium, and dodecyltrimethylammonium. The helium energy distributions, recorded in vacuum using a salty water microjet, reveal a sharp distinction between neutral and ionic surfactant monolayers. Helium atoms evaporate through neutral surfactant monolayers in speed distributions that are similar to a pure hydrocarbon, reflecting the common alkyl chains of both. In contrast, He atoms appear to evaporate through ionic surfactant layers in distributions that are closer to pure salty water. We speculate that the ionic surfactants distribute themselves more loosely and deeply through the top layers of the aqueous solution than do neutral surfactants, with gaps between the surfactants that may be filled with salty water. This difference is supported by prior molecular dynamics simulations and ion scattering measurements of surfactant solutions. | Xiao-Fei Gao; David Hood; Timothy Bertram; Gilbert Nathanson | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6583b5ace9ebbb4db9651e08/original/probing-the-interfacial-structure-of-aqueous-surfactants-through-helium-atom-evaporation.pdf |
62b5b14e5983a94a6f6d473f | 10.26434/chemrxiv-2022-zj065 | Targeted Cancer Phototherapy Using Phthalocyanine–Anticancer Drug Conjugates | Phototherapy, the use of light to selectively ablate cancerous tissue, is a compelling prospect. Phototherapy is divided into two major domains: photodynamic and photothermal, whereby photosensitizer irradiation generates reactive oxygen species or heat, respectively, to disrupt the cancer microenvironment. Phthalocyanines (Pcs) are prominent phototherapeutics due to their desirable optical properties and structural versatility. Targeting of Pc photosensitizers historically relied on the enhanced permeation and retention effect, but the weak specificity engendered by this approach has hindered bench-to-clinic translation. To improve specificity, antibody and peptide active-targeting groups have been employed to some effect. An alternative targeting method exploits the binding of anticancer drugs to direct the photosensitizer close to essential cellular components, allowing for precise, synergistic phototherapy. This Feature Article explores the use of Pc–drug conjugates as targeted anticancer phototherapeutic systems with examples of Pc–platin, Pc–kinase, and Pc–anthracycline conjugates discussed in detail. | Christopher Rennie; Robert Edkins | Biological and Medicinal Chemistry; Organic Chemistry; Inorganic Chemistry; Photochemistry (Org.); Coordination Chemistry (Inorg.); Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b5b14e5983a94a6f6d473f/original/targeted-cancer-phototherapy-using-phthalocyanine-anticancer-drug-conjugates.pdf |
620fd6154e899e2fc25291de | 10.26434/chemrxiv-2022-rsvdf | Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach | In the context of advanced hit-to-lead drug design based on atomistic Molecular Dynamics simulations, we propose a dual topology alchemical approach for calculating the relative binding free energy (RBFE) between two chemically distant compounds. The method (termed NE-RBFE) relies on the enhanced sampling of the end-states in bulk and in the bound state via Hamiltonian Replica Exchange, alchemically connected by a series of independent and fast nonequilibrium (NE) simulations. The technique has been implemented in a bi-directional fashion, applying the Crooks theorem to the NE work distributions for RBFE predictions. The dissipation of the NE process, negatively affecting accuracy, has been minimized by introducing a smooth regularization based on shifted electrostatic and Lennard-Jones non bonded potentials. As a challenging testbed, we have applied our method to the calculation of the RBFE’s in the recent host-guest SAMPL international contest, featuring a macrocyclic host with guests varying in the net charge, volume, and chemical fingerprints. Closure validation has been successfully verified in cycles involving compounds with disparate Tanimoto coefficient, volume, and net charge. NE-RBFE is specifically tailored for massively parallel facilities and can be used with little or no code modification on most of the popular software packages supporting nonequilibrium alchemical simulations such as Gromacs, Amber, NAMD, or OpenMM. The proposed methodology bypasses most of the entanglements and limitations of the standard single topology RBFE approach for strictly congeneric series based on free energy perturbation, such as slowly relaxing cavity water, sampling issues along the alchemical stratification, and the need for highly overlapping molecular fingerprints.
| Piero Procacci | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620fd6154e899e2fc25291de/original/relative-binding-free-energy-between-chemically-distant-compounds-using-a-bidirectional-nonequilibrium-approach.pdf |
634ae9511df688f2e0918737 | 10.26434/chemrxiv-2022-7123z | Analysis of Raman spectra with surface and nanocrystalline growth in carbon nitride thin films with nitrogen flow rate | Raman spectroscopy of amorphous hydrogenated carbon nitride (a-C: H: N) films deposited by PECVD respectively were studied. The three stage Ferrari Robertson model was used to explain the structural modifications taking place. A competition between the cluster size growth and clustering itself was identified. A graphene to graphane conversion leading to hydrogen storage possibility in the films has been discussed. Higher nitrogen concentration also led to smoothening of the films. The growth of nanocrystallites took place which was evident through XRD. | Ritambhara Dash; Pravanshu Mohanta; Arnab Bhattacharyya | Materials Science; Nanoscience; Carbon-based Materials; Coating Materials; Thin Films | CC BY 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634ae9511df688f2e0918737/original/analysis-of-raman-spectra-with-surface-and-nanocrystalline-growth-in-carbon-nitride-thin-films-with-nitrogen-flow-rate.pdf |
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