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67d9484d6dde43c9083d4dde | 10.26434/chemrxiv-2025-qchjl | MASSISTANT: A Deep Learning Model for De Novo Molecular Structure Prediction from EI‑MS Spectra via SELFIES Encoding | Gas chromatography coupled with electron impact mass spectrometry (GC‑EI‑MS) is a widely used analytical technique for identifying volatile and semi‑volatile compounds in applications ranging from pharmaceutical research to material science. However, since not every molecule is included in EI‑MS databases, scientists often have to identify unknown chromatographic peaks solely from their EI‑MS spectra. This manual interpretation is time-consuming and depends heavily on expert knowledge, often leading to ambiguous or inconclusive results. In this work, we introduce MASSISTANT, a novel deep learning model that directly predicts de novo molecular structures from low‑resolution EI‑MS spectra using SELFIES encoding. Trained on compounds with molecular weights below 600 Da, MASSISTANT’s performance is sensitive to dataset curation; while training on the full NIST dataset (180k spectra) yields approximately 10% exact predictions, a more focused, chemically homogeneous subset boosts this rate to as high as 54% (Tanimoto score = 1). These results highlight the capability of deep neural networks to capture complex fragmentation patterns and generate chemically valid structures, offering mass spectrometry scientists a powerful tool to enhance the interpretation and elucidation of whole molecular structures but also substructures, and functional groups in GC‑EI‑MS analyses. | John Mommers; Lazar Barta; Marcin Pietrasik; Anna Wilbik | Theoretical and Computational Chemistry; Analytical Chemistry; Mass Spectrometry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d9484d6dde43c9083d4dde/original/massistant-a-deep-learning-model-for-de-novo-molecular-structure-prediction-from-ei-ms-spectra-via-selfies-encoding.pdf |
659cdad09138d2316180749a | 10.26434/chemrxiv-2024-r461c | Implications of Efficient and Selective NO and NO2 Detection via Surface Functionalized h-B2S2 Monolayer | The advent of two-dimensional (2D) materials has ushered in a novel era in materials science, owing to
their unique physical and chemical features. The boron-sulfide (B2S2) monolayer is a promising new addition to MoS2-like 2D material with a lighter element, boron (B), having similar valence electrons between Mo and B2 pair. In the present study, we have functionalized the h-phase boron sulfide monolayer by introducing an oxygen atom called Oh-B2S2 and elucidating the structural properties, stabilities, and electronic characteristics of this modified configuration. The charge carrier mobility of the system was found to be 790 × 102 cm2 V-1 s-1, which is much higher than the mobility of the MoS2 monolayer (200 cm2 V-1 s-1). The potential application of the 2D Oh-B2S2 monolayer in the realm of gas sensing was evaluated using a combination of density functional theory (DFT), ab initio molecular dynamics (AIMD), and non-equilibrium Green’s function (NEGF) based simulations. Our results imply that Oh-B2S2 monolayer outperform graphene and MoS2 in NO and NO2 selective sensing with higher adsorption energies (-0.56 and -0.16 eV) and charge transfer values (0.34 and 0.13 e). Further, the current-voltage characteristics show that the Oh-B2S2 monolayer may selectively detect NO and NO2 gases after a bias of 1.4 V, making a boron-based gas-sensing device a greater possibility in future nanoelectronics. | Upasana Nath; Manabendra Sarma | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659cdad09138d2316180749a/original/implications-of-efficient-and-selective-no-and-no2-detection-via-surface-functionalized-h-b2s2-monolayer.pdf |
67701bf081d2151a02331a2e | 10.26434/chemrxiv-2024-5rhzp | A stable and reversable zinc-ion microbattery from a printed gel-electrolyte and a carbon-zinc formulation | Aqueous zinc ion batteries (ZIBs) are attracting increasing attention due to their low cost, earth abundance and safety. So far, they have been regarded as a promising battery system for large scale grid applications, and here we demonstrate prospects of their use to power portable devices. We have fabricated fully 3D printed and rechargeable ZIB with interdigitated geometry capable to power a commercial sensor for days. A full battery was assembled using aqueous and scalable formulations with a printed anode based on zinc powder and carbon black, a printed colloidal electrolyte and a printed MnO2 cathode. The anode withstands more than 500h of galvanostatic plating/stripping with a low overpotential of ~32.2 mV and the ZIB displays a capacity of ~1.3 mAh/cm² and a capacity retention of ~66% after 100 cycles. Finally, we show how this battery can power a Bluetooth proximity sensor for more than 3 days of continuous operation | Stefano Tagliaferri; Goli Nagaraju; Maria Sokolikovaa ; Haoyu Bai; Caiwu Liang; Ifan Stephens; Cecilia Mattevi | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67701bf081d2151a02331a2e/original/a-stable-and-reversable-zinc-ion-microbattery-from-a-printed-gel-electrolyte-and-a-carbon-zinc-formulation.pdf |
623110685c8dae0980eb14fb | 10.26434/chemrxiv-2022-ph8qc | Phytochemistry, Biological Activities, Therapeutic Potential, and Socio-economic Value of Caper (Capparis spinosa L.) | Capparis spinosa L., known as caper, is an aromatic plant growing in most of the Mediterranean basin and some parts in the west of Asia. C. spinosa L. has been utilized as a medicinal plant for quite a long time in conventional phytomedicine. Polyphenols and numerous bioactive chemicals extracted from C. spinosa L. display various therapeutic properties that have made this plant a target for further research as a health promoter. This review is meant to systematically summarize the traditional uses, the phytochemical composition of C. spinosa L., and the diverse pharmacological activities, as well as the synthetic routes to derivatives of some identified chemical components for the improvement of biological activities and enhancement of pharmacokinetic profiles. This review also addresses the benefits of C. spinosa L. in adapting to climate change and the socio-economic value that C. spinosa L. brings to the rural economies of many countries. | Ayoub Kdimy; Meryem El Yadini; Abdelkarim Guaâdaoui; Ilhame Bourais; Souad El Hajjaji; Hoang Le | Biological and Medicinal Chemistry; Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623110685c8dae0980eb14fb/original/phytochemistry-biological-activities-therapeutic-potential-and-socio-economic-value-of-caper-capparis-spinosa-l.pdf |
6584ccdc9138d23161386ab0 | 10.26434/chemrxiv-2023-m92gz | DFT Studies of Cubane [4Fe-4S]2+/3+ Clusters: J-Aggregates of FeS Tetramers | Iron sulfur clusters are essential cofactors of numerous proteins that play many important biological roles due to their unique reactivity—a product of their geometry, oxidation, and spin states. The geometry of the iron sulfur clusters of [4Fe-4S]2+ and [4Fe-4S]3+ in various spin states was investigated using density functional theory (DFT). Geometry optimizations and vibrational frequency calculations were carried out on these clusters using the B3LYP functional and the 6-311+G(d,p) basis set. The most stable spin state for the [4Fe-4S]2+ cluster was found to be the 19-et, an antisymmetric structure. The most stable spin state for the [4Fe-4S]3+ cluster was found to be the 20-et, also an antisymmetric structure. Interestingly, these cubane clusters consist of J aggregates of four species of FeS and FeS+. The breakage of a monomer FeS from a [4Fe-4S] cluster under different environments may be responsible for the observations of noncubane [4Fe-4S] clusters. Furthermore, with increased spin state, the positive and negative charges on the iron and sulfur increased and decreased, respectively, and the structure of cubane [4Fe-4S]2+ cluster evolves from the structure with a Fe tetramer as core and S as ligands to J-aggregate of FeS and to a homogeneous [4Fe-4S]2+ cluster. | Peshala Jayamaha; Grayson Venus; Cat Nimmo; Riya Krishnan; Zafeiria Nikolaidi; Zahid Siraj; Lichang Wang | Physical Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6584ccdc9138d23161386ab0/original/dft-studies-of-cubane-4fe-4s-2-3-clusters-j-aggregates-of-fe-s-tetramers.pdf |
60c746e7bb8c1a2b933da981 | 10.26434/chemrxiv.11428155.v1 | Effective Hamiltonians Derived from Equation-of-Motion Coupled-Cluster Wave-Functions: Theory and Application to the Hubbard and Heisenberg Hamiltonians | Effective Hamiltonians, which are commonly used for fitting experimental observables, provide a coarse-grained representation of exact many-electron states obtained in quantum chemistry calculations; however, the mapping between the two is not trivial. In this contribution, we apply Bloch’s formalism to equation-of-motion coupled-cluster (EOM-CC) wave functions to rigorously derive effective Hamiltonians in the Bloch’s and des Cloizeaux’s forms. We report the key equations and illustrate the theory by examples of systems with electronic states of covalent and ionic characters. We show that the Hubbard and Heisenberg Hamiltonians are extracted directly from the so-obtained effective Hamiltonians. By making quantitative connections between many-body states and simple models, the approach also facilitates the analysis of the correlated wave functions. Artifacts affecting the quality of electronic structure calculations such as spin contamination are also discussed.<br /> | Pavel Pokhilko; Anna I. Krylov | Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746e7bb8c1a2b933da981/original/effective-hamiltonians-derived-from-equation-of-motion-coupled-cluster-wave-functions-theory-and-application-to-the-hubbard-and-heisenberg-hamiltonians.pdf |
619e1890802991036ef0e346 | 10.26434/chemrxiv-2021-73w0p | Kernel Charge Equilibration: Efficient and Accurate Prediction of Molecular Dipole Moments with a Machine-Learning Enhanced Electron Density Model | State-of-the-art machine learning (ML) interatomic potentials use local representations of atomic environments to ensure linear scaling and size-extensivity. This implies a neglect of long-range interactions, most prominently related to electrostatics. To overcome this limitation, we herein present a ML framework for predicting charge distributions and their interactions termed kernel Charge Equilibration (kQEq). This model is based on classical charge equilibration models like QEq, expanded with an environment dependent electronegativity. In contrast to previously reported neural network models with a similar concept, kQEq takes advantage of the linearity of both QEq and Kernel Ridge Regression to obtain a closed-form linear algebra expression for training the models. Furthermore, we avoid the ambiguity of charge partitioning schemes by using dipole moments as reference data. As a first application, we show that kQEq can be used to generate accurate and highly data-efficient models for molecular dipole moments. | Carsten Staacke; Simon Wengert; Christian Kunkel; Gábor Csányi; Karsten Reuter; Johannes T. Margraf | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2021-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619e1890802991036ef0e346/original/kernel-charge-equilibration-efficient-and-accurate-prediction-of-molecular-dipole-moments-with-a-machine-learning-enhanced-electron-density-model.pdf |
60c73ea00f50dbe18b3956c3 | 10.26434/chemrxiv.7076816.v1 | A First-Principles Computational Comparison of the Aqueous Anatase TiO2 (001) Interface and the Disordered, Fluorinated TiO2 Interface | Chemical doping and other surface modifications have been used to engineer the bulk properties of materials, but their influence on the surface structure and consequently the surface chemistry are often unknown. Previous work has been successful in fluorinating anatase TiO<sub>2</sub> with charge balance achieved via the introduction of Ti vacancies rather than the reduction of Ti. Our work here investigates the interface between this fluorinated titanate with cationic vacancies and a<br />monolayer of water via density functional theory based molecular dynamics. We compute the projected density of states for only those atoms at the interface and for those states that fall within 1eV of the Fermi energy for various steps throughout the simulation, and we determine that the<br />variation in this representation of the density of states serves as a reasonable tool to anticipate where surfaces are most likely to be reactive. In particular, we conclude that water dissociation at the surface is the main mechanism that influences the anatase (001) surface whereas the change in<br />the density of states at the surface of the fluorinated structure is influenced primarily through the adsorption of water molecules at the surface. | Kyle Reeves; Damien Dambournet; Christel Laberty-Robert; Rodolphe Vuilleumier; Mathieu Salanne | Theory - Computational; Photocatalysis; Interfaces; Quantum Mechanics; Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ea00f50dbe18b3956c3/original/a-first-principles-computational-comparison-of-the-aqueous-anatase-ti-o2-001-interface-and-the-disordered-fluorinated-ti-o2-interface.pdf |
60c755630f50db52c2397ec8 | 10.26434/chemrxiv.13289354.v2 | Standardized Stirring for Small Scale Surveys | Stirring rates in
heterogeneous catalytic reactions have an effect on reaction rates. When
conducting small-scale surveys using a single central stir plate, reaction
vessels in different positions experience slightly different levels and
patterns of agitation. We probed this effect by running the same reaction 40
times, varying the stir rate (fast/slow) and the vial position using two 3D
printed vial holders. We found variability of conversion (measured mass
spectrometrically) to be approximately two times higher for vials placed at
different distances, but the effect was relatively small and could be minimized
by using a high stir rate. For those experimenters wishing to completely
eliminate differential stirring as a cause for variation in results, the 3D
printed circular array we designed is recommended over a conventional
rectangular array. | Isaac Omari; Mathias Paul; J Scott McIndoe | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755630f50db52c2397ec8/original/standardized-stirring-for-small-scale-surveys.pdf |
6434e8b80784a63aeee99b46 | 10.26434/chemrxiv-2023-gcwqn | Controlling intramolecular and intermolecular electronic coupling of radical ligands in a series of cobaltoviologen complexes | Controlling electronic coupling between two or more redox sites is of interest for tuning the electronic properties of molecules and materials. While classic mixed-valence (MV) systems are highly tunable, e.g., via the modular organic bridges connecting the redox sites, metal-bridged MV systems are difficult to control because the electronics of the metal cannot usually be altered independently of redox-active moieties embedded in its ligands. Herein, we overcome this limitation by varying the donor strengths of ancillary ligands in a series of cobalt complexes without directly perturbing the electronics of viologen-like redox sites bridged by the cobalt ions. The cobaltoviologens [1X-Co]n+ feature four 4-X-pyridyl donor groups (X = CO2Me, Cl, H, Me, OMe, NMe2) that provide gradual tuning of the electronics of the bridging CoII centers, while a related complex [2-Co]n+ with NHC donors supports exclusively CoIII states even upon reduction of the viologen ligands. Electrochemistry and IVCT band analysis reveal that the MV states of these complexes have electronic structures ranging from fully localized ([2-Co]4+; Robin-Day Class I) to fully delocalized ([1CO2Me-Co]3+; Class III) descriptions, demonstrating unprecedented control over electronic coupling without changing the identity of the redox sites or bridging metal. Additionally, single-crystal XRD characterization of the homovalent complexes [1H-Co]2+ and [1H-Zn]2+ revealed radical-pairing interactions between the viologen ligands of adjacent complexes, representing a type of through-space electronic coupling commonly observed for organic viologen radicals but never before seen in metalloviologens. The extended solid-state packing of these complexes produces 3D networks of radical π-stacking interactions that impart unexpected mechanical flexibility to these crystals. | Brice J. O. Kessler; Iram F. Mansoor; Derek I. Wozniak; Thomas J. Emge; Mark C. Lipke | Inorganic Chemistry; Organometallic Chemistry; Electrochemistry; Ligand Design; Materials Chemistry; Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2023-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6434e8b80784a63aeee99b46/original/controlling-intramolecular-and-intermolecular-electronic-coupling-of-radical-ligands-in-a-series-of-cobaltoviologen-complexes.pdf |
60c746ea0f50db5d533964ff | 10.26434/chemrxiv.11413122.v1 | Stiff-Stilbene Ligands Target G-Quadruplex DNA and Exhibit Selective Anticancer and Antiparasitic Activity | <p>G-quadruplex nucleic acid structures have long been studied as potential anticancer targets while their potential in antiparasitic therapy has only recently been recognized but barely explored. Herein we report the synthesis, biophysical characterization and <i>in vitro </i>screening of a series of stiff-stilbene G4 binding ligands featuring differing electronics, side-chain chemistries and molecular geometries. The ligands display selectivity for G4 DNA over duplex DNA and exhibit nanomolar toxicity against <i>Trypasanoma brucei </i>and HeLa cancer cells whist remaining up to two orders of magnitude less toxic to non-tumoral mammalian cell line MRC5. Our study demonstrates that stiff-stilbenes show exciting potential as the basis of selective anticancer and antiparasitic therapies. In order to achieve the most efficient G4 recognition the scaffold must possess the optimal electronics and substitution pattern and correct molecular geometry. <br /></p> | Michael O'Hagan; pablo Peñalver; Rosina S. L. Gibson; Juan Carlos Morales; M. Carmen Galan | Bioorganic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ea0f50db5d533964ff/original/stiff-stilbene-ligands-target-g-quadruplex-dna-and-exhibit-selective-anticancer-and-antiparasitic-activity.pdf |
6511f29ab927619fe7cf85b1 | 10.26434/chemrxiv-2023-ct37g | Unraveling Luminescence Quenching Mechanism in Strong and Weak Quantum-Confined CsPbBr3 Triggered by Triarylamine-Based Hole Transport Layers | Luminescence quenching by hole transport layers (HTLs) is one of the major issues in developing efficient perovskite light-emitting diodes (PeLEDs); particularly, it is more prominent in blue LEDs. Often, various interfacial layers are used to overcome this issue. However, the origin of such quenching and the type of interactions between perovskites and HTLs are still ambiguous. Here, we present a systematic investigation of the luminescence quenching of CsPbBr3 by a commonly employed hole transport polymer, Poly(9,9-dioctylfluorene-alt-N-(4-sec-butylphenyl)-diphenylamine) (TFB) in LEDs. Strong and weak quantum-confined CsPbBr3 (nanoplatelets (NPLs)/nanocrystals (NCs)) are rationally selected to study the quenching mechanism by considering the differences in their morphology, energy level alignments, and quantum confinement. The steady-state and time-resolved Stern-Volmer plots unravel the dominance of dynamic and static quenching at lower and higher concentrations of TFB, respectively, with maximum quenching efficiency of 98 %. The quenching rate in NCs is faster than in NPLs owing to their longer PL lifetimes and weak quantum confinement. The ultrafast transient absorption results support these dynamics and rule out the involvement of Forster or Dexter energy transfer. Finally, the 1D 1H and 2D NOESY NMR study confirms the exchange of native ligands at the NCs surface with TFB, leading to dark CsPbBr3-TFB ensemble formation accountable for luminescence quenching. This highlights the critical role of the triarylamine functional group on TFB (which is also the backbone of many HTLs) in the quenching process. These results shed light on the underlying reasons for the luminescence quenching in PeLEDs and will help to choose the interfacial layers rationally for developing efficient LEDs. | Anuraj S Kshirsagar; Katherine A Koch; Ajay Ram Srimath Kandada; Mahesh K Gangishetty | Nanoscience; Energy; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6511f29ab927619fe7cf85b1/original/unraveling-luminescence-quenching-mechanism-in-strong-and-weak-quantum-confined-cs-pb-br3-triggered-by-triarylamine-based-hole-transport-layers.pdf |
67c95ef96dde43c908b72d34 | 10.26434/chemrxiv-2025-q2pz8 | Nickel-Photocatalytic Decarboxylative Oxidation of Mandelic Acids | Selective oxidation of α-hydroxy acids, particularly Mandelic acids, was achieved by merging Nickel and photoredox catalysis. This approach enables the discrete formation of aldehydes and ketones without observable overoxidation. By decoupling the decarboxylation and alcohol oxidation/dehydrogenation steps, the reaction proceeds under free-radical conditions to afford prod- ucts in high-yield. The method described is scalable and holds the potential for broadening the scope of metallaphotoredox catalysis in coupled oxidation processes. | Ning Wei; Sebastian B. Beil | Organic Chemistry; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c95ef96dde43c908b72d34/original/nickel-photocatalytic-decarboxylative-oxidation-of-mandelic-acids.pdf |
636c7089b588507d0045f283 | 10.26434/chemrxiv-2022-xv98l | NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems | NUPACK is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems serving the needs of researchers in the fields of nucleic acid nanotechnology, molecular programming, synthetic biology, and across the life sciences. NUPACK algorithms are unique in treating complex and test tube ensembles containing arbitrary numbers of interacting strand species, providing crucial tools for capturing concentration effects essential to analyzing and designing the intermolecular interactions that are a hallmark of these fields. The all-new NUPACK web app (nupack.org) has been re-architected for the cloud, leveraging a cluster that scales dynamically in response to user demand to enable rapid job submission and result inspection even at times of peak user demand. The web app exploits the all-new NUPACK 4 scientific code base as its backend, offering enhanced physical models (coaxial and dangle stacking subensembles), dramatic speedups (20-120x for test tube analysis), and increased scalability for large complexes. NUPACK 4 algorithms can also be run locally using the all-new NUPACK Python module. | Mark E. Fornace; Jining Huang; Cody T. Newman; Nicholas J. Porubsky; Marshall B. Pierce; Niles A. Pierce | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636c7089b588507d0045f283/original/nupack-analysis-and-design-of-nucleic-acid-structures-devices-and-systems.pdf |
60c740a49abda23ab1f8bd31 | 10.26434/chemrxiv.7312070.v3 | Synthesis of High Molecular Weight Chitosan from Chitin by Mechanochemistry and Aging | Chitosan
can be obtained from the deacetylation of chitin. This process is however
difficult and usually accompanied by depolymerization, affording low molecular
weight chitosan. We report a novel path, relying on a combination of
mechanochemitry and aging, to afford high molecular weight chitosan with
minimal use of energy and solvent. This method is versatile and applicable to a
number of chitin sources, including crude crustaceans and insect shells,
yielding deacetylation up to 98% and remarkably high molecular weights. Chitin
deacetylation was measured by magic angle spinning nuclear magnetic resonance
and molecular weight by viscometry. This process affords chitosan in a safer
fashion and with less materials and energy usage than the classic hydrothermal
one. | Thomas Di Nardo; Caroline Hadad; Albert Nguyen Van Nhien; Audrey Moores | Biopolymers; Polymer chains; Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a49abda23ab1f8bd31/original/synthesis-of-high-molecular-weight-chitosan-from-chitin-by-mechanochemistry-and-aging.pdf |
612e912d6563690c121edf02 | 10.26434/chemrxiv-2021-q7n34 | An S-Shaped Double Helicene Showing both Multi-Resonance Thermally Activated Delayed Fluorescence and Circularly Polarized Luminescence | We present the first example of a multi-resonant thermally activated delayed fluorescent (MR-TADF) helicene, Hel-DiDiKTa. This S-shaped double helicene exhibits sky-blue emission, a singlet-triplet energy gap, EST, of 0.15 eV and narrow emission at a peak maximum of 473 nm with a full-width at half-maximum of 44 nm in toluene. The MR-TADF character is confirmed by the small degree of positive solvatochromism and temperature-dependent increase in intensity of the delayed emission. The chiroptical properties of the separated enantiomers are similar to other large helicenes with comparable dissymmetry values, but with the added benefit of MR-TADF. Thus, this study further strengthens the burgeoning area of chiral TADF emitters for use in cutting-edge optoelectronic and photocatalytic molecules and materials. | John Dos Santos; Dianming Sun; Juan Moreno-Naranjo; David Hall; Francesco Zinna; Seán Ryan; Wenda Shi; Tomas Matulaitis; David Cordes; Alexandra Slawin; David Beljonne; Stuart Warriner; Yoann Olivier; Eli Zysman-Colman; Matthew Fuchter | Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Stereochemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e912d6563690c121edf02/original/an-s-shaped-double-helicene-showing-both-multi-resonance-thermally-activated-delayed-fluorescence-and-circularly-polarized-luminescence.pdf |
61232ed2ded28ab922866adb | 10.26434/chemrxiv-2021-4t24p-v2 | Comparing Transfer Learning to Feature Optimization in Microstructure Classification | Human analysis of research data is slow and inefficient. In recent years machine learning tools have advanced our capability to perform tasks normally carried out by humans, such as image segmentation and classification. In this work, we seek to further improve binary classification models for high throughput identification of different microstructural morphologies. We utilize a dataset with limited observations (133 dendritic structures, 444 non-dendritic) and employ data augmentation via rotation and translation to enhance the dataset six-fold. Then, transfer learning is carried out using pre-trained networks VGG16, InceptionV3, and Xception achieving only moderate F1 scores (0.801 to 0.822). We hypothesize that feature engineering could yield better results than transfer learning alone. To test this, we employ a new nature-inspired feature optimization algorithm, the Binary Red Deer Algorithm (BRDA), to carry out binary classification and observe F1 scores above 0.93. | Debanshu Banerjee; Taylor D. Sparks | Materials Science; Alloys; Imaging Agents; Materials Processing | CC BY NC 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61232ed2ded28ab922866adb/original/comparing-transfer-learning-to-feature-optimization-in-microstructure-classification.pdf |
657b52b466c13817292f2f20 | 10.26434/chemrxiv-2023-5l8mq | Pincer-ligated Iridium Complexes with Low-Field Ancillary Ligands:
Complexes of (iPrPCP)IrCl2 and Comparison with (iPrPCP)IrHCl
| Pincer-ligated iridium complexes have been widely developed, and (pincer)Ir(III) complexes, particularly five-coordinate, are central to their chemistry. Such complexes typically bear two formally anionic ligands in addition to the pincer ligand itself. Yet despite the prevalence of halides as anionic ligands in transition metal chemistry there are relatively few examples in which both of these ancillary anionic ligands are halides or even other monodentate low-field anions. We report a study of the fragment (iPrPCP)IrCl2 (iPrPCP = 3-2,6-C6H3(CH2PiPr2)), and adducts thereof. These species are found to be thermodynamically disfavored relative to the corresponding hydridohalides. For example, DFT calculations and experiment indicate that one Ir-Cl bond of (iPrPCP)IrCl2 complexes will undergo reaction with H2 to give the (iPrPCP)IrHCl or an adduct thereof. In the presence of aqueous HCl, (iPrPCP)IrCl2 adds a chloride ion to give an unusual example of an anionic transition metal complex ((iPrPCP)IrCl3–) with a Zundel cation (H5O2+). (iPrPCP)IrCl2 is not stable as a monomer at room temperature but exists in solution as a mixture of clusters which can add various small molecules. DFT calculations indicate that dimerization of (iPrPCP)IrCl2 is more favorable than dimerization of (iPrPCP)IrHCl, in accord with its observed tendency to form clusters. | Ashish Parihar; Thomas J. Emge ; Alan S. Goldman | Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Coordination Chemistry (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657b52b466c13817292f2f20/original/pincer-ligated-iridium-complexes-with-low-field-ancillary-ligands-complexes-of-i-pr-pcp-ir-cl2-and-comparison-with-i-pr-pcp-ir-h-cl.pdf |
60c753ac337d6c4487e288b8 | 10.26434/chemrxiv.13524296.v1 | Biotin as a Reactive Handle to Selectively Label Proteins and DNA with Small Molecules | <p>Here we report the reaction between biotin and azide-labelled oxaziridine reagents in aqueous conditions at room temperature. This method, which we call biotin redox-activated chemical tagging (BioReACT), achieves efficient and stable labelling of proteins with oxaziridine reagents. We functionally validate the method by generating an antibody-drug conjugate and numerous flow-cytometry reagents. Finally, we conjugate a functional click handle to a biotinylated oligonucleotide. These studies show that the biotin–oxaziridine reaction is a powerful approach for the efficient synthesis of stable protein and DNA bioconjugates.</p> | Adam Cotton; James Wells; Ian Seiple | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753ac337d6c4487e288b8/original/biotin-as-a-reactive-handle-to-selectively-label-proteins-and-dna-with-small-molecules.pdf |
60d5dac767d491730895e6f5 | 10.26434/chemrxiv-2021-4x9sf | Structural insight into an atomic layer deposition (ALD) grown Al2O3 layer on Ni/SiO2: impact on catalytic activity and stability in dry reforming of methane | The development of stable Ni-based dry reforming of methane (DRM) catalysts is a key challenge owing to the high operating temperatures of the process and the propensity of Ni for promoting carbon deposition. In this work, Al2O3-coated Ni/SiO2 catalysts have been developed by employing atomic layer deposition (ALD). The structure of the catalyst at each individual preparation step was characterized in detail through a combination of in situ XAS-XRD, ex situ 27Al NMR and Raman spectroscopy. Specifically, in the calcination step, the ALD-grown Al2O3 layer reacts with the SiO2 support and Ni, forming aluminosilicate and NiAl2O4. The Al2O3-coated Ni/SiO2 catalyst exhibits an improved stability for DRM when compared to the benchmark Ni/SiO2 and Ni/Al2O3 catalysts. In situ XAS-XRD during DRM together with ex situ Raman spectroscopy and TEM of the spent catalysts confirm that the ALD-grown Al2O3 layer suppresses the sintering of Ni, in turn reducing also coke formation significantly. In addition, the formation of an amorphous aluminosilicate phase by the reaction of the ALD-grown Al2O3 layer with the SiO2 support inhibited catalysts deactivation via NiAl2O4 formation, in contrast to the reference Ni/Al2O3 system. The in-depth structural characterization of the catalysts provided an insight into the structural dynamics of the ALD-grown Al2O3 layer, which reacts both with the support and the active metal, allowing to rationalize the high stability of the catalyst under the harsh DRM conditions. | Kim Sungmin ; Armutlulu Andac; Wei-Chih Liao; Davood Hosseini; Dragos Stoian; Zixuan Chen; Paula Abdala; Christophe Copéret; Christoph Rüdiger Müller | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d5dac767d491730895e6f5/original/structural-insight-into-an-atomic-layer-deposition-ald-grown-al2o3-layer-on-ni-si-o2-impact-on-catalytic-activity-and-stability-in-dry-reforming-of-methane.pdf |
61b465e7535d6304fe98d632 | 10.26434/chemrxiv-2021-j78m4 | Highly luminescent hetero-ligand MOF nanocrystals with engineered massive Stokes shift for photonic applications. | A high efficiency emission with a massive Stokes shift is obtained by fluorescent conjugated acene building blocks arranged in nanocrystals. The two ligands of equal molecular length and connectivity, yet complementary electronic properties, are co-assembled by zirconium oxy-hydroxy clusters, generating highly crystalline hetero-MOF nanoparticles The fast diffusion of singlet molecular excitons in the framework, coupled with the fine matching of ligands absorption and emission properties, enables to achieve an ultrafast activation of the low energy emission by diffusion-mediated non-radiative energy transfer in the 100 ps time scale, by using a low amount of co-ligands. This allow to obtain MOF nanocrystals with a fluorescence quantum efficiency of ̴ 70% and an actual Stokes shift as large as 750 meV. This large Stokes shift suppresses the reabsorption of fast emission issues in bulk devices, pivotal for a plethora of applications in photonics and photon managing spacing from solar technologies, imaging, and detection of high energy radiation. These features allowed to realize a prototypal fast nanocomposite scintillator that shows an enhanced performance with respect to the homo-ligand nanocrystals, achieving benchmark. values which compete with those of some inorganic and organic commercial systems. | Jacopo Perego; Charl Bezuidenhout; Irene Villa; Francesca Cova; Roberta Crapanzano; Isabel Frank; Fiammetta Pagano; Nicolaus Kratochwill; Etiennette Auffray; Silvia Bracco; Anna Vedda; Christophe Dujardin; Piero Sozzani; Francesco Meinardi; Angiolina Comotti; Angelo Monguzzi | Physical Chemistry; Materials Science; Nanoscience; Composites; Hybrid Organic-Inorganic Materials; Radiation | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b465e7535d6304fe98d632/original/highly-luminescent-hetero-ligand-mof-nanocrystals-with-engineered-massive-stokes-shift-for-photonic-applications.pdf |
657ec7fae9ebbb4db918cc93 | 10.26434/chemrxiv-2023-7t1fx | Blue Light-Induced 1,2-Aminochlorination of Olefins using Dichlorocarbamates | Activation of N,N-dichlorocarbamates with blue light facilitates a direct 1,2-aminochlorination of unactivated olefins to yield 1,2-chloro-N-Cl-carbamates under ambient conditions. Mechanistic studies suggest that N,N-dichlorocarbmates undergo a photochemical excitation to yield a neutral nitrogen-centered radical, which rapidly reacts with olefins in an anti-Markovnikov fashion. Using the method, a range of functionally diverse substrates are successfully aminochlorinated to yield the corresponding 1,2-chloro-N-Cl compounds. | Sini Irvankoski; Michael Davenport; Daniel Ess; Juha Siitonen | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657ec7fae9ebbb4db918cc93/original/blue-light-induced-1-2-aminochlorination-of-olefins-using-dichlorocarbamates.pdf |
659e951ce9ebbb4db9d9019f | 10.26434/chemrxiv-2023-6nqn3-v2 | Endergonic synthesis driven by chemical fuelling | Spontaneous chemical reactions proceed energetically downhill to either a local or global
minimum, limiting possible transformations to those that are exergonic. Endergonic reactions
do not proceed spontaneously and require an input of energy. Light has been used to drive a
number of deracemisations and thermodynamically unfavourable bond-forming reactions, but
is restricted to substrates that can absorb, directly or indirectly, energy provided by photons.
In contrast, anabolism involves energetically uphill transformations powered by chemical fuels.
Here we report on the transduction of energy from an artificial chemical fuel to drive a
thermodynamically unfavourable Diels–Alder reaction. Carboxylic acid catalysed
carbodiimide-to-urea formation is chemically orthogonal to the reaction of the diene and
dienophile, but transiently brings the functional groups into close proximity, causing the
otherwise prohibited cycloaddition to proceed in modest yield (15% after two fuelling cycles)
and with high levels of regio- (>99%) and stereoselectivity (92:8 exo:endo). Kinetic asymmetry
in the fuelling cycle ratchets the Diels–Alder reaction away from the equilibrium distribution of
the Diels–Alder:retro-Diels–Alder products. The driving of the endergonic reaction occurs
through a ratchet mechanism (an energy or information ratchet, depending on the synthetic
protocol), reminiscent of how molecular machines directionally bias motion. Ratcheting
synthesis has the potential to expand the synthetic chemistry toolbox, offering new paradigms
in reactivity, complexity and control. | Enzo Olivieri; James M. Gallagher; Alexander Betts; Toufic W. Mrad; David A. Leigh | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659e951ce9ebbb4db9d9019f/original/endergonic-synthesis-driven-by-chemical-fuelling.pdf |
653628e02431cc1dac57c9c2 | 10.26434/chemrxiv-2023-0fp1b | Nucleoside Phosphorylases Make N7-Xanthosine, the “Non-native” Regioisomer of Xanthosine | Modern, highly evolved, nucleoside-processing enzymes are known to exhibit perfect regioselectivity over the glycosylation of purine nucleobases at N9. We herein report an exception to this paradigm. Wild-type nucleoside phosphorylases also furnish N7- xanthosine, the “non-native” ribosylation regioisomer of xanthosine. This unusual nucleoside possesses several atypical physicochemical properties such as redshifted absorption spectra, a high equilibrium constant of phosphorolysis and low acidity. Ultimately, the biosynthesis of this previously unknown natural product illustrates how even highly evolved, essential enzymes from the primary metabolism are imperfect catalysts. | Sarah Westarp; Felix Brandt; Lena Neumair; Christina Betz; Amin Dagane; Sebastian Kemper; Christoph R. Jacob; Peter Neubauer; Anke Kurreck; Felix Kaspar | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Natural Products; Biochemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653628e02431cc1dac57c9c2/original/nucleoside-phosphorylases-make-n7-xanthosine-the-non-native-regioisomer-of-xanthosine.pdf |
66903c485101a2ffa81d75e1 | 10.26434/chemrxiv-2024-hp230 | Cooperative hydrogenation catalysis at a constrained gallylene-nickel(0) interface | The discovery of unique mechanisms in 3d metal catalysis is of paramount importance in utilising these Earth-abundant metals in place of scarce precious metals. Inspired by the Horiuti-Polanyi mechanism at play in heterogenous hydrogenation catalysts, we describe a bimetallic molecular catalyst which can selectively semi-hydrogenate alkynes via a ligand-to-substrate hydride transfer mechanism. This mimics established heterogeneous mechanisms in which remote surface-bound hydride ligands undergo a similar reactive process. This is achieved through the development of a chelate-constrained gallium(I) ligand, which operates in concert with nickel(0) to (reversibly) cleave H2, generating a [GaNi] 1,2-dihydride complex, found to be the resting state in the catalytic process. This discovery takes steps towards utilising non-innocent low-valent group 13 centres in effective cooperative catalysis, opening new mechanistic pathways which may aid in employing Earth-abundant metals in key catalytic transformations. | Till Kalkuhl; Israel Fernández; Terrance Hadlington | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66903c485101a2ffa81d75e1/original/cooperative-hydrogenation-catalysis-at-a-constrained-gallylene-nickel-0-interface.pdf |
6352afdeecdad55d48e71510 | 10.26434/chemrxiv-2022-3xsrn | Electrochemical nucleic acid-based sensors for detection of E. coli and Shiga toxin-producing E. coli (STEC) – Review of the recent developments | Escherichia coli (E. coli) are a group of bacteria, which are a natural part of the intestinal flora of warm-blooded animals, including humans. Most E. coli are non-pathogenic and are essential for the normal function of a healthy intestine, however, certain types such as Shiga toxin-producing E. coli (STEC) is a foodborne pathogen that can cause a life-threatening illness. Development of point-of-care (POC), rapid detection devices for E. coli have high importance from a food safety point of view. The most suitable way to distinguish between generic E. coli and STEC is by using nucleic acid-based detection, focusing on the virulence factors. Electrochemical sensors based on nucleic acid recognition have attracted much attention in recent years for use in pathogenic bacteria detection. This review has summarised nucleic acid-based sensors for the detection of generic E. coli and STEC since 2015. First, the sequences of the genes used as recognition probes are discussed and compared to the most recent research regarding the specific detection of general E. coli and STEC. Subsequently, the collected literature regarding nucleic acid-based sensors was described and discussed. The traditional sensors were divided into four categories such as gold, ITO, carbon-based electrodes, and those using magnetic particles. Finally, we summarised the future trends in nucleic acid-based sensor development for E. coli and STEC including some examples of fully integrated devices | Luiza Wasiewska; Ian Seymour; Vuslat Juska; Kaye Burgess; Geraldine Duffy; Alan O'Riordan | Analytical Chemistry; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6352afdeecdad55d48e71510/original/electrochemical-nucleic-acid-based-sensors-for-detection-of-e-coli-and-shiga-toxin-producing-e-coli-stec-review-of-the-recent-developments.pdf |
60c742694c89199adead2454 | 10.26434/chemrxiv.8267450.v1 | Study of Structural & Magnetic Properties of CoN Thin Films | Precise determination of structure of CoN has been achieved combining x-ray diffraction, x-ray absorption spectroscopy measurements and theoretical simulations both at Co and N K-edges and magnetization measurements.<br /> | Mukul Gupta; Yogesh Kumar; Nidhi Pandey; Akhil Tayal; Wolfgang Caliebe; Jochen Stahn | Alloys; Catalysts; Magnetic Materials; Materials Processing; Nanostructured Materials - Materials; Thin Films; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742694c89199adead2454/original/study-of-structural-magnetic-properties-of-co-n-thin-films.pdf |
622b70980350dd67f4d45a66 | 10.26434/chemrxiv-2022-2ljhn | Synthesis and styrene copolymerization of novel difluoro and chlorofluoro ring-disubstituted isobutyl phenylcyanoacrylates | Novel difluoro and chlorofluoro ring-disubstituted isobutyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH(CH3)2 (where R is 2,3-difluoro, 2,4-difluoro, 2,6-difluoro, 3,4-difluoro, 3,5-difluoro, 2-chloro-4-fluoro, 2-chloro-6-fluoro, 3-chloro-2-fluoro, 3-chloro-4-fluoro, 4-chloro-3-fluoro) were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-disubstituted benzaldehydes and isobutyl cyanoacetate and characterized by CHN analysis, IR, 1H and 13C NMR. The acrylates were copolymerized with styrene in solution with radical initiation at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Christopher D. Ahlers; Aisha A. Ahmed; Umamah Alam; Alima A. Sajwani; Megan V. Salloum; Makayla A. Schneider; Heysel M. Serra; Richard C. Tanawath; Gabriella L. Triolo; Marisol Velazquez; Sara Rocus; William Schjerven; Gregory Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622b70980350dd67f4d45a66/original/synthesis-and-styrene-copolymerization-of-novel-difluoro-and-chlorofluoro-ring-disubstituted-isobutyl-phenylcyanoacrylates.pdf |
639cef0404902abb3c05cc20 | 10.26434/chemrxiv-2022-njntj | An outer membrane-inspired polymer coating protects and endows E. coli with novel functionalities | A bio-inspired membrane made of Pluronic® L-121 is produced around E. coli thanks to the simple co-extrusion of bacteria and polymer vesicles. The block copolymer-coated bacteria can withstand a variety of harsh shocks, e.g. temperature, pressure, osmolarity and chemical agents. The polymer membrane also makes the bacteria resistant against enzymatic digestion and enables them to degrade toxic compounds, improving their performance as whole-cell biocatalysts. Moreover, the polymer membrane acts as a new region for surface modification. Being decorated with α-amylase or lysozyme, the cells are endowed with the ability to digest starch, or self-predatory bacteria are created. Thus, without any genetic engineering, the phenotype of encapsulated bacteria is changed, as they become sturdier and gain novel metabolic functionalities. | Andrea Belluati; Iain Harley; Ingo Lieberwirth; Nico Bruns | Polymer Science; Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639cef0404902abb3c05cc20/original/an-outer-membrane-inspired-polymer-coating-protects-and-endows-e-coli-with-novel-functionalities.pdf |
60c74703337d6c68d9e2726b | 10.26434/chemrxiv.9913865.v2 | Molecular Generation Targeting Desired Electronic Properties via Deep Generative Models | <p>The chemical space for novel electronic donor-acceptor oligomers with targeted properties was explored using deep generative models and transfer learning. A General Recurrent Neural Network model was trained from the ChEMBL database to generate chemically valid SMILES strings. The parameters of the General Recurrent Neural Network were fine-tuned via transfer learning using the electronic donor-acceptor database from the Computational Material Repository to generate novel donor-acceptor oligomers. Six different transfer learning models were developed with different subsets of the donor-acceptor database as training sets. We concluded that electronic properties such as HOMO-LUMO gaps and dipole moments of the training sets can be learned using the SMILES representation with deep generative models, and that the chemical space of the training sets can be efficiently explored. This approach identified approximately 1700 new molecules that have promising electronic properties (HOMO-LUMO gap <2 eV and dipole moment <2 Debye), 6-times more than in the original database. Amongst the molecular transformations, the deep generative model has learned how to produce novel molecules by trading off between selected atomic substitutions (such as halogenation or methylation) and molecular features such as the spatial extension of the oligomer. The method can be extended as a plausible source of new chemical combinations to effectively explore the chemical space for targeted properties.</p> | Qi Yuan; Alejandro Santana-Bonilla; Martijn Zwijnenburg; Kim Jelfs | Optical Materials; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74703337d6c68d9e2726b/original/molecular-generation-targeting-desired-electronic-properties-via-deep-generative-models.pdf |
64188037aad2a62ca10f591f | 10.26434/chemrxiv-2022-3rmd9-v2 | Viologen Hydrothermal Synthesis and Structure-Property Relationships for Redox Flow Battery Optimization | Aqueous organic redox flow batteries (AORFBs) are an emerging technology for fire safe grid energy storage systems with sustainable material feedstocks. Yet, designing organic redox molecules with the desired solubility, viscosity, permeability, formal potential, kinetics, and stability while remaining synthetically scalable is challenging. Herein, we demonstrate the adaptability of a single-step, high-yield hydrothermal reaction for nine viologen chloride salts. New empirical insights are gleaned into fundamental structure-property relationships for multi-objective optimization. A new asymmetric Dex-DiOH-Vi derivative showcased the ability to achieve an enhanced solubility of 2.7 M with minimal tradeoff in membrane permeability. With a record viologen cycling volumetric capacity (67 Ah∙L-1 anolyte theoretical), Dex-DiOH-Vi exhibited 14-days of stable cycling performance in anolyte-limiting AORFB with no crossover or chemical degradation. This work highlights the importance of designing efficient synthetic approaches of organic redox species for molecular engineering high-performance flow battery electrolytes. | Patrick Sullivan; HongHao Liu; Xiu-Liang Lv; Song Jin; Wenjie Li; Dawei Feng | Organic Chemistry; Energy; Organic Compounds and Functional Groups; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64188037aad2a62ca10f591f/original/viologen-hydrothermal-synthesis-and-structure-property-relationships-for-redox-flow-battery-optimization.pdf |
651b32e5a69febde9e1d257a | 10.26434/chemrxiv-2023-3v8sh | Thermosensitive Polymer Prodrug Nanoparticles Prepared by an All-Aqueous Nanoprecipitation Process and Application to Combination Therapy | Despite their great versatility and ease of functionalization, most polymer-based nanocarriers intended for use in drug delivery often face serious limitations that can prevent their clinical translation, such as uncontrolled drug release and off-target toxicity, which mainly originate from the burst release phenomenon. In addition, residual solvents from the formulation process can induce toxicity, alter the physico-chemical and biological properties and can strongly impair further pharmaceutical development. To address these issues, we report polymer prodrug nanoparticles, which are prepared without organic solvents via an all-aqueous formulation process, and provide sustained drug release. This was achieved by the “drug-initiated” synthesis of well-defined copolymer prodrugs exhibiting a lower critical solution temperature (LCST) and based on the anticancer drug gemcitabine (Gem). After screening for different structural parameters, prodrugs based on amphiphilic diblock copolymers were formulated into stable nanoparticles by all-aqueous nanoprecipitation, with rather narrow particle size distribution and average diameters in the 50–80 nm range. They exhibited sustained Gem release in human serum and acetate buffer, rapid cellular uptake and significant cytotoxicity on A549 and Mia PaCa-2 cancer cells. We also demonstrated the versatility of this approach by formulating Gem-based polymer prodrug nanoparticles loaded with doxorubicin (Dox) for combination therapy. The dual-drug nanoparticles exhibited sustained release of Gem in human serum and acidic release of Dox under accelerated pathophysiological conditions. Importantly, they also induced a synergistic effect on triple-negative breast cancer line MDA-MB-231, which is a relevant cell line to this combination. | Léa Guerassimoff; Marianne Ferrere; Simon Van Herck; Samy Dehissi; Valérie Nicolas; Bruno G. De Geest; Julien Nicolas | Polymer Science; Drug delivery systems; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651b32e5a69febde9e1d257a/original/thermosensitive-polymer-prodrug-nanoparticles-prepared-by-an-all-aqueous-nanoprecipitation-process-and-application-to-combination-therapy.pdf |
61b284180e35ebcbb19bba3b | 10.26434/chemrxiv-2021-hdg10 | An Electric Field–Based Approach for Quantifying Volumes and Radii of Chemically Affected Space | Chemical shape and size play a critical role in chemistry. The van der Waal (vdW) radii, a familiar manifold used to quantify size by assuming overlapping spheres, provides rapid estimates of size in atoms, molecules, and materials. However, the vdW method may be too rigid to describe highly polarized systems and chemical systems that stray from spherical atomistic environments. To deal with these exotic chemistries, numerous alternate methods based on electron density have been presented. While each boasts inherent generality, all define the size of a chemical system, in one way or another, by its electron density. Herein, we revisit the timeless problem of assessing sizes of atoms and molecules, instead through examination of the electric field produced by them. While conceptually different than nuclei-centered methods like that of van der Waal, the field assesses chemically affected volumes. This approac | Austin Mroz; Joshua Davis; Christopher Hendon | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b284180e35ebcbb19bba3b/original/an-electric-field-based-approach-for-quantifying-volumes-and-radii-of-chemically-affected-space.pdf |
62ffa66d0187d9a262996f80 | 10.26434/chemrxiv-2022-06vz9 | Divalent 2-(4-Hydroxyphenyl)benzothiazole Bifunctional Chelators for 64Cu PET Imaging in Alzheimer’s Disease | Herein we report a new series of divalent 2-(4-hydroxyphenyl)benzothiazole bifunctional chelators (BFCs) with high affinity for amyloid β aggregates and favorable lipophilicity for blood-brain barrier (BBB) penetration. The addition of an alkyl carboxylate ester pendant arm offers high binding affinity towards Cu(II). The novel BFCs form stable 64Cu-radiolabeled complexes and exhibit promising partition coefficient (log D) values of 1.05-1.85. Among the five compounds tested, the 64Cu-YW-15 complex exhibits significant staining of amyloid β plaques in ex vivo autoradiography studies. In addition, biodistribution studies show that 64Cu-YW-15-Me exhibits elevated brain uptake (0.89 ± 0.25 %ID/g) in transgenic AD versus wild type mice. | Liviu Mirica; Karna Terpstra; Yujue Wang; Truc Huynh; Nilantha Bandara; Hong Jun Cho; Buck Rogers | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ffa66d0187d9a262996f80/original/divalent-2-4-hydroxyphenyl-benzothiazole-bifunctional-chelators-for-64cu-pet-imaging-in-alzheimer-s-disease.pdf |
60c740a20f50dba75b395991 | 10.26434/chemrxiv.7771493.v1 | Electrochemically Driven, Ni-Catalyzed Aryl Amination: Scope, Mechanism, and Applications | <div>
<div>
<div>
<p>C–N cross-coupling is one of the most valuable and widespread transformations in organic synthesis. Largely dominated by Pd- and Cu-based catalytic systems, it has proven to be a staple transformation for those in both academia and industry. The
current study presents the development and mechanistic understanding of an electrochemically driven, Ni-catalyzed method for
achieving this reaction of high strategic importance. Through a series of electrochemical, computational, kinetic, and empirical experiments the key mechanistic features of this reaction have been unraveled, leading to a second generation set of conditions that is
applicable to a broad range of aryl halides and amine nucleophiles, including complex examples on oligopeptides, medicinally-relevant heterocycles, natural products, and sugars. Full disclosure of the current limitations as well as procedures for both batch and
flow scale-ups (100 gram) are also described.
</p>
</div>
</div>
</div> | Yu Kawamata; Julien Vantourout; David
P. Hickey; Peng Bai; Longrui Chen; Qinglong Hou; Wenhua Qiao; Koushik Barman; Martin
A. Edwards; Alberto F. Garrido-Castro; Justine
N. deGruyter; Hugh Nakamura; Kyle W. Knouse; Chuanguang Qin; Khalyd J. Clay; Denghui Bao; Chao Li; Jeremy T. Starr; Carmen N. Garcia-Irizarry; Neal Sach; Henry S. White; Matthew Neurock; Shelley D. Minteer; Phil Baran | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a20f50dba75b395991/original/electrochemically-driven-ni-catalyzed-aryl-amination-scope-mechanism-and-applications.pdf |
60c73e52f96a00a701285ec2 | 10.26434/chemrxiv.6802454.v1 | Symmetrically Backfolded Molecules Emulating the Self-Similar Features of Sierpinski Triangle | <p>Novel branching motif in hierarchical self-similar
molecules: we present an under-explored class of molecules featuring striking
geometric resemblance to the famous fractal of Sierpinski triangle. Unlike
the more traditional, starburst dendrimers,
the centripetal-shaped Sierpinski molecules feature side branches symmetrically
bent away from the growth direction of the main branch, thus contrasting the
natural-tree shape. Molecule G3 exhibits three distinct levels of structural
hierachy comprising the primary, secondary and tertiary branches, while the
smaller G2 contains only features of the 1<sup>st</sup> and 2<sup>nd</sup>
orders. In spite of the much larger conjugated backbone of G3, its UV-vis absorption
remains little shifted in wavelength compared to G2, while the emission of G3 is
curiously blue-shifted by over 50 nm from that of G2.</p> | Yan-Qiong Sun; Ran Xiao; Jun He; Matthias Zeller; Wai-Yeung Wong; Zhengtao Xu | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e52f96a00a701285ec2/original/symmetrically-backfolded-molecules-emulating-the-self-similar-features-of-sierpinski-triangle.pdf |
60c74b80bdbb89341aa395ea | 10.26434/chemrxiv.12286727.v2 | Neuraldecipher - Reverse-Engineering ECFP Fingerprints to Their Molecular Structures | <p>Protecting molecular structures from disclosure against external parties is of great relevance for industrial and private associations, such as pharmaceutical companies. Within the framework of external collaborations, it is common to exchange datasets by encoding the molecular structures into descriptors. Molecular fingerprints such as the extended-connectivity fingerprints are frequently used for such an exchange, because they typically perform well on quantitative structure-activity relationship tasks. </p><p>ECFPs are often considered to be non-invertible due to the way they are computed.</p><p>In this paper, we present a reverse-engineering method to deduce the molecular structure given revealed ECFPs. Our method includes the <i>Neuraldecipher</i>, a neural network model that predicts a compact vector representation of compounds, given ECFPs. We then utilize another pre-trained model to retrieve the molecular structure as SMILES representation. We demonstrate that our method is able to reconstruct molecular structures to some extent, and improves, when ECFPs with larger fingerprint sizes are revealed. For example, given ECFP count vectors of length 4096, we are able to correctly deduce around 60% of molecular structures on a validation set (112K unique samples) with our method.</p> | Tuan Le; Robin Winter; Frank Noé; Djork-Arné Clevert | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b80bdbb89341aa395ea/original/neuraldecipher-reverse-engineering-ecfp-fingerprints-to-their-molecular-structures.pdf |
64dbf9214a3f7d0c0d3bbe76 | 10.26434/chemrxiv-2023-zcrr5 | Modular Total Synthesis of the 5/5-Spirocyclic Spiroindimicins | Total syntheses of the 5/5-spirocyclic indoline alkaloids spiroindimicins B, C, D, E, F, and G have been achieved via a modular approach. Our route features direct coupling of halogenated pyrrolemetal and isatin partners, Suzuki coupling to append the indole unit, Lewis acid-mediated spirocyclization, and divergent functionalization to various family members. These syntheses are concise (6–7 steps from commercial materials), scalable, and highly amenable to analogue synthesis. Further studies of the antiparasitic properties of this class have revealed promising activity against T. brucei for certain congeners. Together with our prior approach to 6/5-family members, our work constitutes a synthetic solution to all known spiroindimicin natural products. | Ankush Banerjee; Tiffany Brisco; Sneha Ray; Arani Datta; Xiaoyu Zhang; Zhen Zhang; Alexander Busse; Hanspeter Niederstrasser; Krissty Sumida; Bruce Posner; Dawn Wetzel; Margaret Phillips; Myles Smith | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Natural Products; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dbf9214a3f7d0c0d3bbe76/original/modular-total-synthesis-of-the-5-5-spirocyclic-spiroindimicins.pdf |
66fee12bcec5d6c1420fd056 | 10.26434/chemrxiv-2024-dzkc1 | The Role of Hydration and Amino Acid Interactions on the Ion Permeation Mechanism in the hNaV 1.5 Channel | This study explores the ion selectivity and conduction mechanisms of the hNaV 1.5 sodium channel using classical molecular dynamics simulations under an externally applied electric field. Our findings reveal distinct conduction mechanisms for Na+ and K+, primarily driven by differences in their hydration states when they diffuse close to the channel’s selective filter (DEKA) and extracellular ring (EEDD). The Na+ ions undergo partial dehydration in the EEDD region, followed by a rehydration step in the DEKA ring, resulting in longer retention times and a deeper free energy minimum compared to K+. Conversely, the K+ ions exhibit a continuous dehydration process, facilitating a smoother passage through these key regions. These results indicate that ion selectivity and conductance are primarily governed by solvation dynamics, which in turn depends on the interactions with key charged residues within the channel. Addi- tionally, we show that the delicate energetic balance between the interactions of the ions with the protein residues and with their solvation shells during the dehydration and re-hydration processes is not properly captured by the force field. As a consequence, the selectivity of the channel is not well described, indicating that more accurate com- putational models must be applied to simulate ion conduction through eukaryotic NaV channels. | Nuria Anguita-Ortiz; Juan J. Nogueira | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fee12bcec5d6c1420fd056/original/the-role-of-hydration-and-amino-acid-interactions-on-the-ion-permeation-mechanism-in-the-h-na-v-1-5-channel.pdf |
60c74171bdbb89149da38361 | 10.26434/chemrxiv.8053385.v1 | Solid-like Ordering of Imidazolium-Based Ionic Liquids at Rough Nanostructured Oxidized Silicon Surfaces | The investigation of ionic liquids (ILs) confined in a solid porous matrix is of particular interest considering that these substances are increasingly used as electrolyte in devices employing nanostructured nanoporous materials for the electrodes. Furthermore, the confinement of the ILs into a porous matrix would allow overcoming the difficulties of its packaging, leakage and portability. In order to support applications, a deeper understanding of the interaction of ILs with the nanoporous solid material and its increased interface is required.<br />In this work, we report on the modification of morphological and mechanical properties of the imidazolium-based [Bmim][NTf2] ionic liquid upon surface confinement on a cluster-assembled nanostructured rough oxidized silicon (ns-SiOx) surface. An atomic force microscopy investigation revealed that upon the interaction with the ns-SiOx film, [Bmim][NTf2] locally rearranges into ordered, layered, stiff and poorly conducting solid-like domains, coexisting with, and embedded into, the liquid IL film. The observed interfacial layering of [Bmim][NTf2] deposited on ns-SiOx suggests that the behavior of the IL-electrode interface in photoelectrochemical devices employing nanostructured nanoporous materials can be far more complex than expected under the hypothesis of an IL-based electrolyte in the stable liquid phase. The observed effects reported in this work could in principle take place also inside the bulk nanoporous matrix, where they could be further amplified by the extreme spatial confinement. | francesca borghi; Paolo Milani; Alessandro Podestà | Thin Films; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74171bdbb89149da38361/original/solid-like-ordering-of-imidazolium-based-ionic-liquids-at-rough-nanostructured-oxidized-silicon-surfaces.pdf |
64948c82a2c387fa9ac5c1ce | 10.26434/chemrxiv-2023-czt1p-v3 | Characterization of a High Throughput Approach for Large Scale Retention Measurement in Liquid Chromatography | Many contemporary challenges in liquid chromatography - such as the need for “smarter” method development tools, and deeper understanding of chromatographic phenomena - could be addressed more efficiently and effectively with larger volumes of experimental retention data than are available. The paucity of publicly accessible, high-quality measurements needed for the development of retention models and simulation tools has largely been due to the high cost in time and resources associated with traditional retention measurement approaches. Recently we described an approach to improve the throughput of such measurements by using very short columns (typically 5 mm), while maintaining measurement accuracy. In this paper we present a perspective on the characteristics of a dataset containing about 13,000 retention measurements obtained using this approach, and describe a different sample introduction method that is better suited to this application than the approach we used in prior work. The dataset comprises results for 35 different small molecules, nine different stationary phases, and several mobile phase compositions for each analyte/phase combination. During the acquisition of these data, we have interspersed repeated measurements of a small number of compounds for quality control purposes. The data from these measurements not only enable detection of outliers but also assessment of the repeatability and reproducibility of retention measurements over time. For retention factors greater than 1, the mean relative standard deviation (RSD) of replicate (typically n=5) measurements is 0.4%, and the standard deviation of RSDs is 0.4%. Most differences between selectivity values measured six months apart for 15 non-ionogenic compounds were in the range of +/- 1%, indicating good reproducibility. A critically important observation from these analyses is that selectivity defined as retention of a given analyte relative to the retention of a reference compound (kx/kref) is a much more consistent measure of retention over a time span of months compared to the retention factor alone. While this work and dataset also highlight the importance of stationary phase stability over time for achieving reliable retention measurements, we are nevertheless optimistic that this approach will enable the compilation of large databases (>> 10,000 measurements) of retention values over long time periods (years), which can in turn be leveraged to address some of the most important contemporary challenges in liquid chromatography. All the data discussed in the manuscript are provided as Supplemental Information. | Trevor Kempen; Tina Dahlseid; Thomas Lauer; Alexandru Florea; Isabella Aase; Nathan Cole-Dai; Simerjit Kaur; Caroline Southworth; Kathleen Grube; Jos Bhandari; Maria Sylvester; Ryan Schimek; Bob Pirok; Sarah Rutan; Dwight Stoll | Analytical Chemistry; Separation Science | CC BY NC 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64948c82a2c387fa9ac5c1ce/original/characterization-of-a-high-throughput-approach-for-large-scale-retention-measurement-in-liquid-chromatography.pdf |
67df10e4fa469535b9381a9c | 10.26434/chemrxiv-2025-zzfqj-v2 | Colloidal Monolayers with Short-Range Attractions and Dipolar Repulsions | This study investigates the structure and phase behavior of monolayers composed of model colloids that exhibit both short-range attractions and long-range repulsions. The model is motivated by recent experiments of hard-sphere-like microspheres that effectively interact via depletion attractions and dynamically tunable dipolar repulsions. Brownian dynamics simulations, grand canonical Monte Carlo methods, and approximate thermodynamic models are combined to investigate how the model's equilibrium and kinetically accessible solid and cluster fluid states depend on the relative strengths of the attractive and repulsive interactions. The results may help guide the understanding and design of quasi-two-dimensional colloidal assemblies with magnetic field tunable interactions. | Chieh-Chih George Yeh; Harold W. Hatch; Adithya N. Sreenivasan; Bhuvnesh Bharti; Vincent K. Shen; Zachary M. Sherman; Thomas M. Truskett | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Aggregates and Assemblies; Magnetic Materials; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67df10e4fa469535b9381a9c/original/colloidal-monolayers-with-short-range-attractions-and-dipolar-repulsions.pdf |
6732c8c3f9980725cfe85123 | 10.26434/chemrxiv-2024-6mlkx | Structural Insights into the Mechanism of a Vanadium-Dependent Bromoperoxidase Enabled by High-Resolution Cryo-EM | Vanadium-dependent haloperoxidases (VHPOs) are a uniquely robust class of enzymes capable of performing electrophilic halogenation of organic substrates. Despite their emerging biotechnological significance, the precise catalytic and halide-selection mechanisms of VHPOs under native conditions remains largely unexamined. Herein, we leverage single-particle cryogenic transmission electron microscopy (cryo-EM) to provide insight into the catalytic mechanism of the vanadium-dependent bromoperoxidase from Corallina pilulifera (CpVBPO) under catalytically relevant conditions. Specifically, we have collected the first set of high-resolution cryo-EM structures of CpVBPO in four catalytically relevant states including binding to phosphate, orthovanadate, orthovanadate and bromide, and orthovanadate and hydrogen peroxide. The collected structures, resolved at 2.2 to 3.2 Å, reveal deviations from previously reported X-ray diffraction (XRD) structures, particularly in the geometry of the vanadate cofactor and key residue interactions in the active site. Our findings suggest a trigonal planar, metavanadate-like geometry for the vanadate cofactor in the resting state, contradicting the commonly proposed orthovanadate geometry containing an apical hydroxo ligand. Furthermore, the dynamic roles of residues Asp335 and Leu337 in halide specificity in the catalytic cycle are proposed through observed conformational changes upon bromide binding. Using pKa calculations and structural analyses, a mechanism for generating hypobromous acid, mediated by His487, is presented. This study not only refines the structural and mechanistic understanding of CpVBPO, but also demonstrates the capabilities of cryo-EM to capture native-like enzyme structures under catalytically relevant conditions, offering a more informative approach for investigating the mechanistic features of VHPOs. | Logan Z. Hessefort; Dewight R. Williams; Kyle F. Biegasiewicz | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6732c8c3f9980725cfe85123/original/structural-insights-into-the-mechanism-of-a-vanadium-dependent-bromoperoxidase-enabled-by-high-resolution-cryo-em.pdf |
60c74a920f50db887e396aa9 | 10.26434/chemrxiv.12220109.v1 | Tandem Photoredox Catalysis: Enabling Carbonylative Amidation of Aryl and Alkylhalides | <p>We report a new visible light-mediated carbonylative amidation of aryl, heteroaryl and alkyl halides. A tandem catalytic cycle of [Ir(ppy)<sub>2</sub>(dtb-bpy)]<sup>+</sup> generates a potent iridium photoreductant via a second catalytic cycle in the presence of DIPEA which productively engages aryl bromides, iodides and even chlorides as well as primary, secondary and tertiary alkyl iodides. The versatility of the in-situ generated catalyst is illustrated by compatibility with aliphatic and aromatic amines, high functional group tolerance and the late-stage amidation of complex natural products. </p> | José Augusto Forni; NENAD MICIC; Timothy Connell; GEETHIKA WERAGODA; Anastasios Polyzos | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a920f50db887e396aa9/original/tandem-photoredox-catalysis-enabling-carbonylative-amidation-of-aryl-and-alkylhalides.pdf |
639ab1baa2da4b6517046193 | 10.26434/chemrxiv-2022-xb3h9 | Gaussian Process Regression (GPR) Method for the Prediction of Rate Coefficients of Gas-phase Reactions in Chemical Ionization Mass Spectrometry | Reaction kinetics of chemical ionization mass spectrometry (CI-MS) based ion-molecule reactions is an important component in the quantification of trace-level volatile organic compounds (VOCs). The rate coefficients of such CI-MS reactions are predicted using the Gaussian process regression (GPR) machine learning method from the dipole moment, polarizability, and molecular weight of the molecules, mitigating experimental complexity in CI-MS rate coefficient estimation. GPR can make
predictions combining prior knowledge (kernel function) which is considered the heart of the GPR model and provide uncertainty measures over predictions. A suitable kernel combination with proper tuning of parameters can make the Gaussian process
more robust and powerful. Various kernel combinations, such as kernel addition and multiplication, are tested in the GPR prediction of rates. A blend of radial basis function (RBF), white noise, and squared exponential kernel performs better, and the predicted rates are in close agreement with the experimental rates. GPR provides an alternative to the capture collision rates and can be useful when there are no experimental data available and/or the available data contain large uncertainty in the rate coefficients. | MANJEET BHATIA | Theoretical and Computational Chemistry; Analytical Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639ab1baa2da4b6517046193/original/gaussian-process-regression-gpr-method-for-the-prediction-of-rate-coefficients-of-gas-phase-reactions-in-chemical-ionization-mass-spectrometry.pdf |
67449ef5f9980725cfd6213c | 10.26434/chemrxiv-2024-0zw8l | Energy transfer photoproximity labelling in live cells using
an organic cofactor | Photocatalytic proximity labelling has recently emerged as a powerful tool to resolve a wide variety of biomolecular and cellular interactions. While the use of high-resolution probe species, such as diazirines, enables cell-surface protein labelling with nanometre precision by generating highly reactive intermediates, intracellular applications are limited either by the intrinsic toxicity of frequently employed photocatalysts or lower resolution when long-lived reactive intermediates are used. In this work, we describe the discovery and application of an organic flavin cofactor
derivative, deazaflavin, capable of diazirine activation to form carbenes through triplet energy transfer and offers unparalleled biocompatibility. We demonstrate deazaflavin-diazirine energy transfer labelling (DarT-labelling) not only allows for targeted extracellular scenarios using antibody conjugates but, most importantly, for intracellular interactome mapping of cellpenetrating peptides (CPPs). We successfully mapped the localisation of two popular polyarginine CPPs and identified potential key membrane interactors. Furthermore, we showed the applicability of DarT-labelling over extended time by mapping the intracellular trafficking of a stable cyclic derivative to reveal its eventual exocytosis from the cell. We envision DarT-labelling has the unmet potential to enable detailed profiling of intracellular dynamics across diverse biological systems with unprecedented spatiotemporal control. | Leander Crocker; Jan Vincent V. Arafiles; Judith M. Müchler; Max Ruwolt; Kristin Kemnitz-Hassanin; Kilian Roßmann; Christian E. Stieger; Fan Liu; Christian P. R. Hackenberger | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67449ef5f9980725cfd6213c/original/energy-transfer-photoproximity-labelling-in-live-cells-using-an-organic-cofactor.pdf |
60c7414a702a9b02c618a210 | 10.26434/chemrxiv.8010302.v1 | High-Affinity Alkynyl Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT) | <div>
<div>
<div>
<div>
<p>In this work, structure-based rational design led to the development of potent and selective alkynyl bisubstrate inhibitors of NNMT. The reported nicotinamide-SAM conjugate (named <b>NS1</b>) features an alkyne as a key
design element that closely mimics the linear, 180° transition state geometry found in the NNMT-catalyzed SAM
→ NAM (nicotinamide) methyl transfer reaction. NS1 was synthesized as a single enantiomer and diastereomer in 14 steps and
found to be a high-affinity, subnanomolar NNMT inhibitor. An X-ray co-crystal structure and structure-activity
relationship (SAR) study revealed the unique ability of an alkynyl linker to span the methyl transfer tunnel of
NNMT with ideal shape complementarity. The compounds reported in this work represent the most potent and
selective NNMT inhibitors reported to date. The rational design principle described herein could potentially be
extended to other methyltransferase enzymes.
</p>
</div>
</div>
</div>
</div> | Rocco Policarpo; Ludovic Decultot; Elizabeth May; Petr Kuzmič; Samuel Carlson; Danny Huang; Vincent Chu; Brandon Wright; Saravanakumar Dhakshinamoorthy; Aimo Kannt; Shilpa Rani; Sreekanth Dittakavi; Joseph Panarese; Rachelle Gaudet; Matthew Shair | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7414a702a9b02c618a210/original/high-affinity-alkynyl-bisubstrate-inhibitors-of-nicotinamide-n-methyltransferase-nnmt.pdf |
60c7588e469df41959f456b3 | 10.26434/chemrxiv.14560860.v1 | Multichromophore Molecular Design for Efficient Thermally Activated Delayed Fluorescence Emitters with Near-Unity Photoluminescence Quantum Yields | Three multichromophore thermally activated delayed fluorescence (TADF) molecules, <b><i>p</i>-di2CzPN</b>, <b><i>m</i>-di2CzPN</b>, and<b> 1,3,5-tri2CzPN</b>, were synthesized and characterized. These molecules were designed by connecting the TADF moiety 4,5-di(9<i>H</i>-carbazol-9-yl)phthalonitrile (<b>2CzPN</b>) to different positions of a central benzene ring scaffold. Three highly soluble emitters all exhibited near quantitative photoluminescence quantum yields (<i></i><sub>PL</sub>) in toluene. High <i></i><sub>PL</sub>s were also achieved in doped films, 59% and 70% for <b><i>p</i>-di2CzPN</b> and <b><i>m</i>-di2CzPN</b> in 10 wt% DPEPO doped films, respectively, and 54% for <b>1,3,5-tri2CzPN</b> in 20 wt% doped CBP film. The rate constant of reverse intersystem crossing (<i>k</i><sub>RISC</sub>) for <b><i>p</i>-di2CzPN</b> and <b><i>m</i>-di2CzPN</b> in DPEPO films reached 1.1 × 10<sup>5</sup> s<sup>−1</sup> and 0.7 × 10<sup>5</sup> s<sup>−1</sup>, respectively, and <i>k</i><sub>RISC</sub> for <b>1,3,5-tri2CzPN</b> in CBP film reached 1.7 × 10<sup>5</sup> s<sup>−1</sup>. A solution-processed organic light-emitting diode based on <b>1,3,5-tri2CzPN </b>exhibited a sky-blue emission with CIE coordinate of (0.22, 0.44), and achieved a maximum external quantum efficiency of 7.1%. | Dongyang Chen; Yu Kusakabe; Yongxia Ren; Dianming Sun; P Rajamalli; Yoshimasa Wada; Katsuaki Suzuki; Hironori Kaji; Eli Zysman-Colman | Organic Compounds and Functional Groups; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7588e469df41959f456b3/original/multichromophore-molecular-design-for-efficient-thermally-activated-delayed-fluorescence-emitters-with-near-unity-photoluminescence-quantum-yields.pdf |
6523ae48bda59ceb9a295311 | 10.26434/chemrxiv-2023-wh8tn | NIR fluorophores clinically assessed for fluorescence guided surgery | The term “fluorescence” was first proposed nearly two centuries ago, yet its application in Medicine
has a relatively brief history of only 70 years. Nowadays, as fluorescence was gradually approaching
into more medicine studies, fluorescence image-guided surgery has become the new arena for this
technology. It allows surgeons to real-time visualize the target structure intraoperatively to increase
the efficacy of surgical tissue resection and meanwhile avoid unnecessary radical treatment during
open surgery, laparoscopy, thoracoscopy, or endoscopes. In this review, we introduce the concept of
near-infrared fluorescence imaging for cancer surgery, review the clinical trial literature to date,
outline the key issues pertaining to imaging system and contrast agent optimization, discuss
limitations and leverage, and provide a framework for making the technology available for the routine
care of cancer patients in the near future. | Yuan Ge; Donal O'Shea | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6523ae48bda59ceb9a295311/original/nir-fluorophores-clinically-assessed-for-fluorescence-guided-surgery.pdf |
60c747809abda2efa5f8c8f6 | 10.26434/chemrxiv.11687100.v1 | Cyclic Ion Mobility – Collision Activation Experiments Elucidate Protein Behaviour in the Gas-Phase | <i>Elucidating the properties of intrinsically disordered
proteins (IDPs) and unfolded and partially folded states of globular proteins
is challenging owing to their heterogeneous and dynamic nature. Protein
unfolding and misfolding is a key feature of a broad range of debilitating diseases,
whilst the conformational propensities of intrinsically disordered proteins can
play a significant role in modulating their activity, and the properties of
unfolded states of globular proteins modulates their stability and tendency to
aggregate. Ion mobility-mass spectrometry (IM-MS) is a powerful method for interrogating
these systems, however limits in resolution and the difficulty in probing the
energetics of interconversions amongst heterogeneous ensembles are major
issues. Herein, using a quadrupole/cyclic-IM/ time-of-flight MS instrument, we show
how the combination of precursor mass selection, mobility selection (IM<sup>n</sup>)
and collisional activation (CA) allows the elucidation of complicated gas-phase
dynamic behavior. The methodology employed is general and is demonstrated using
a classic model globular protein, cytochrome C, and an aggregation-prone IDP, amylin.
CA allows investigations of protein
conformational dynamics and unfolding in the gas-phase for heterogeneous
mixtures, whilst the additional precursor mass selection capability provides
high resolution and selectivity, facilitating more in-depth investigation.
Understanding protein dynamics in the gas-phase will allow greater insight into
protein behaviour and allow application of gas-phase techniques to clinically
relevant systems. </i> | Charles Eldrid; Jakub Ujma; Hannah Britt; Tristan Cragnolini; Symeon Kalfas; Dale Cooper-Shepherd; nick tomczyk; Kevin Giles; mike morris; Rehana Akter; Daniel Raleigh; Konstantinos Thalassinos | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747809abda2efa5f8c8f6/original/cyclic-ion-mobility-collision-activation-experiments-elucidate-protein-behaviour-in-the-gas-phase.pdf |
674ae05b7be152b1d0771f15 | 10.26434/chemrxiv-2024-1m0q7 | Design, Synthesis and Photophysical properties of an Iridium(III) complex bearing an Indolo[3,2,1-jk]carbazole-decorated NHC ligand | The synthesis and characterization of a novel blue-green emitting neutral heteroleptic iridium(III) complex Ir(dFppy)2(iCzmi) (PL = 505 nm in MeCN) is reported. This represents the first example of an NHC ligand bearing an indolo-[3,2,1-jk]carbazolyl (iCz) unit, and the first use of an iCz containing ligand as the ancillary ligand in a heteroleptic Iridium(III) complex. The influence of the iCz moiety on the photophysical properties of Ir(dFppy)2(iCzmi) is explored by comparing its properties with those of the reference emitter – Ir(dFppy)2(pmi). Both complexes show similar photophysical properties, which are rationalized in terms of a detailed computational study. | Máire Griffin; Campbell Mackenzie; Eli Zysman-Colman | Inorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674ae05b7be152b1d0771f15/original/design-synthesis-and-photophysical-properties-of-an-iridium-iii-complex-bearing-an-indolo-3-2-1-jk-carbazole-decorated-nhc-ligand.pdf |
60c745b8702a9b0bca18aa6f | 10.26434/chemrxiv.10118324.v1 | Structure and Stability of Cun Clusters (N = 1-4) Adsorbed on Stoichiometric and Defective 2D MoS2 | <div>Layered materials, such as MoS2, are being intensely studied due to their interesting properties and wide variety of potential applications. These materials are also interesting as supports for low dimensional metals for catalysis, while recent work has shown increased interest in using 2D materials in the electronics industry as a Cu diffusion barrier in semiconductor device interconnects. The interaction between different metal structures and MoS2 monolayers is therefore of significant importance and first principle simulations can probe aspects of this interaction not easily accessible to experiment. Previous theoretical studies have focused particularly on the adsorption of a range of metallic elements, including first row transition metals, as well as Ag and Au. However, most studies have examined single atom adsorption or adsorb nanoparticles of noble metals. This means there is a knowledge gap in terms of thin film nucleation on 2D materials. To begin addressing this issue, we present in this paper a first principles density functional theory (DFT) study of the adsorption of small Cu_n structures, where n = 1-4, on 2D MoS2 as a model system. We find on a perfect MoS2 monolayer that a single Cu atom prefers an adsorption site above the Mo atom. With increasing nanocluster size the nanocluster binds more strongly when Cu atoms adsorb atop the S atom. Stability is driven by the number of Cu-Cu interactions and the distance between adsorption sites, with no obvious preference towards 2D or 3D structures. The introduction of a single S vacancy in the monolayer enhances copper binding energy, although some Cu_n nanoclusters are actually unstable. The effect of the vacancy is localised around the vacancy site. Finally on both the pristine and defective MoS2 monolayer, the density of states analysis shows that the adsorption of Cu introduces new electronic states as a result of partial Cu oxidation, but the metallic character of Cu nanoclusters is preserved. </div><div><br /></div> | Cara-Lena Nies; Michael Nolan | Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745b8702a9b0bca18aa6f/original/structure-and-stability-of-cun-clusters-n-1-4-adsorbed-on-stoichiometric-and-defective-2d-mo-s2.pdf |
677e9542fa469535b9325efb | 10.26434/chemrxiv-2025-mx3fh | HSADab2025: AI-powered Modelling of Human Serum Albumin | Human serum albumin (HSA) as the most prevalent protein constitutes ~60% of the protein mass. In this work, we augment our previously released HSA database (HSADab) via the incorporation of AI-powered modelling. The constructed webserver www.hsadab.cn enables instant prediction of HSA binding affinities for drug-like molecules through various machine-learning predictors, hosts the most comprehensive affinity and structure banks containing all HSA-relevant data published so far, and contains a complete set of deep-learning assisted docking structures for molecules presented in the database. We additionally present comprehensive analyses on the protein conformational space, docking performance and AlphaFold modelling, and further open source the most robust fingerprints-based model in the GitHub repository https://github.com/proszxppp/HSADab. | Lei Zheng; Xiaohui Wang; Xiao Liu; Mao Wang; John Zeng Hui Zhang; Zuo-yuan Zhang; Zhaoxi Sun | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677e9542fa469535b9325efb/original/hsa-dab2025-ai-powered-modelling-of-human-serum-albumin.pdf |
64ef1c29dd1a73847fd28284 | 10.26434/chemrxiv-2023-mvvbx | Open-shell Magnetic States in Alternant and Non-alternant Nanographenes: Conceptions and Misconceptions | In contrast to alternant nanographenes (NGRs), in non-alternant NGRs no “sublattice structure” can be defined associated with significant conceptual and computational simplifications. This leads to some fundamental differences between the two. We uncover here the broken electron-hole symmetry in non-alternant NGRs as one fundamental difference closely related to distorted Dirac points (cones) and their diradical open-shell character. We also show by higher level calculations beyond common DFT that the alternant series of peri-acenes (bisanthene, peri-tetracene, peri-pentacene, … etc.), contrary to opposite reports in the literature, have clearly closed singlet ground states, in contrast to their non-alternant isomers based on Stone-Wales (SW) defects. This is experimentally supported by sub-molecularly resolved STM images. The misconceptions in the literature are due to insufficient correlation. For non-alternant NGRs/GNRs with antiaromatic rings the driving force for open-shell states and distorted Dirac points (involving localized electrons and delocalized holes) is antiaromaticity, which is a sufficient but not always necessary condition. This is in juxtaposition to the aromaticity of the alternant isomers with closed shell states. Thus, in both cases sublattice problems lead to open shell magnetic states; ferromagnetic in cases of sublattice imbalance (e.g. triangulenes), antiferromagnetic for non-sublattice cases (e.g. SW3x2, SW4x2), and non-magnetic (diamagnetic) for balanced sublattices (e.g. AGNRs). Obviously, similar results are expected for larger NGRs/GNRs obtained by concatenation of such SW-motifs. | Aristides Zdetsis | Theoretical and Computational Chemistry; Physical Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ef1c29dd1a73847fd28284/original/open-shell-magnetic-states-in-alternant-and-non-alternant-nanographenes-conceptions-and-misconceptions.pdf |
6223c901011b58ede7beadba | 10.26434/chemrxiv-2022-f30sm | 7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries are Potent and Selective Inhibitors of DNA Methyltransferase 1 | Inhibitors of epigenetic writers such as DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug and probe discovery. There are many small molecules tested as inhibitors of DNMTs but, overall, they do not have potent enzymatic inhibition. Chemical companies are developing focused libraries for epigenetic targets to advance probe and drug discovery. Based on a knowledge-based approach, herein, we report the identification of two quinazoline-based derivatives identified in focused libraries with nanomolar inhibition of DNMT1 (30 and 81 nM), more potent than the positive control S-adenosylhomocysteine. The two compounds had low micromolar activity of DNMT3A and did not inhibit DNMT3B. The quinazolines reported in this work have low cell toxicity and are potent inhibitors of the epigenetic target writer G9a at the enzymatic and cellular levels. Molecular modeling helped rationalize the enzymatic inhibitory activity at the molecular level of the two compounds against DNMT1 and DNMT3A. The quinazoline-based compounds are attractive as novel potent inhibitors of DNMTs and as dual and selective epigenetic agents targeting two families of epigenetic writers. | José L. Medina-Franco; Edgar López-López; Liliam P. Martínez-Fernández | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6223c901011b58ede7beadba/original/7-aminoalkoxy-quinazolines-from-epigenetic-focused-libraries-are-potent-and-selective-inhibitors-of-dna-methyltransferase-1.pdf |
64e1c0e1694bf1540caa4eae | 10.26434/chemrxiv-2023-0hndv | CoeffNet: Predicting activation barriers through a chemically-interpretable, equivariant and physically constrained graph neural network | Activation barriers of elementary reactions are essential to predict molecular reaction mechanisms and kinetics. However, computing these energy barriers by identifying transition states with electronic structure methods (e.g., density functional theory) can be time-consuming and computationally expensive. In this work, we introduce CoeffNet, an equivariant graph neural network that predicts activation barriers using coefficients of a frontier molecular orbital (such as the highest occupied molecular orbital) of reactant and product complexes as graph node features. We show that using coefficients as features offer several advantages, such as chemical interpretability and physical constraints on the network’s behaviour and numerical range. Model outputs are either activation barriers or coefficients of the chosen molecular orbital of the transition state; the latter quantity allows us to interpret the results of the neural network through chemical intuition. We test CoeffNet on a dataset of SN2 reactions as a proof-of-concept and show that the activation barriers are predicted with a mean absolute error of less than 0.025 eV. The highest occupied molecular orbital of the transition state is visualized and the distribution of the orbital densities of the transition states is described for a few prototype SN2 reactions. | Sudarshan Vijay; Maxwell Venetos; Evan Spotte-Smith; Aaron Kaplan; Mingjian Wen; Kristin Persson | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Chemical Kinetics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e1c0e1694bf1540caa4eae/original/coeff-net-predicting-activation-barriers-through-a-chemically-interpretable-equivariant-and-physically-constrained-graph-neural-network.pdf |
6395973a7b7c914a5fecf20e | 10.26434/chemrxiv-2022-24hdp | Simultaneous Tracing of Protein Vicinal Dithiols in Live Cells Using an “Off-on” Fluorescent Probe | Vicinal dithiol-containing proteins (VDPs) are of considerable importance due to their role in regulating cellular functions through the reversible dithiol/disulfide inter-conversion reaction. However, there are currently no effective tools for the simultaneous tracing of endogenous VDPs in live cells. Here, we report an “off-on” fluorescent probe (RhQ) for the selective detection of VDPs and illustrate its utility for the long-term tracing of protein vicinal dithiols with simultaneous fluorescence imaging in various cell lines. Importantly, our study provides the first-time valuable insight into the localization of VDPs in whole cells, dynamically visualizing that presence of cell-surface protein vicinal dithiols in MCF-7 cells. Interestingly, some functional cell-surface VDPs have been reported for MCF-7 cells using proteomic analysis. Furthermore, the gradually released fluorescence from RhQ after its interaction with VDPs provides an overall picture of the cellular protein vicinal dithiol profile for different cell lines. This technology shows great promise as a visualization tool for revealing the role of cellular protein vicinal dithiols, especially VDPs on the cell-surface, and stimulating the design of VDP related drug candidates and vectors. | Tongxia Jin; Luling Wu; Ti Jia; Rongrong Zhao; Chusen Huang; Mengfang Tang; Weiping Zhu; Yufang Xu; Tony James; Xuhong Qian | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6395973a7b7c914a5fecf20e/original/simultaneous-tracing-of-protein-vicinal-dithiols-in-live-cells-using-an-off-on-fluorescent-probe.pdf |
6508922db338ec988ab6d696 | 10.26434/chemrxiv-2023-tjzr4-v2 | Machine Learning-Augmented Docking. 1. CYP inhibition prediction | significant portion of the oxidative metabolism carried out by the human body is accomplished by six cytochrome P450 (CYP) enzymes. The binding of small molecules to these enzymes affects drug activity and half-life. Additionally, the inhibition or induction of a CYP isoform by a drug can lead to drug-drug interactions, which in turn can lead to toxicity. To predict CYP inhibition, a variety of computational methods have been used, with docking methods being less accurate than machine learning (ML) methods. However, the latter methods are sensitive to training data and show reduced accuracy on test sets outside of the chemical space represented in the training set. In contrast, docking methods do not have this generalization issue and allow for visual analysis. We hypothesize that combining ML methods with docking can improve CYP inhibition predictions. To test this hypothesis, we pair our in-house docking program FITTED with several ML techniques to investigate the accuracy and transferability of this hybrid methodology, which we term ML-augmented docking. We find that ML-augmented docking can significantly improve the accuracy of docking software while consistently surpassing the performance of ligand-only models. Additionally, we show that ML-augmented docking is more generalizable than machine learning models trained on ligand-only data. The open-source code created for this project can be found at https://github.com/MoitessierLab/ML-augmented-docking-CYP-inhibition | Benjamin Weiser; Jérôme Genzling; Mihai Burai Patrascu; Ophélie Rostaing; Nicolas Moitessier | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6508922db338ec988ab6d696/original/machine-learning-augmented-docking-1-cyp-inhibition-prediction.pdf |
64c7aed1658ec5f7e57cf4d8 | 10.26434/chemrxiv-2023-q0j0l | Systematic exploration of accessible topologies of cage molecules via minimalistic models | Cages are macrocyclic structures with an intrinsic internal cavity that support applications in separations, sensing and catalysis. These materials can be synthesised via self-assembly of organic or metal-organic building blocks. Their bottom-up synthesis and the diversity in building block chemistry allows for fine-tuning of their shape and properties toward a target property. However, it is not straightforward to predict the outcome of self-assembly, and, thus, the structures that are practically accessible during synthesis. Indeed, such a prediction becomes more difficult as problems related to the flexibility of the building blocks or increased combinatorics lead to a higher level of complexity and increased computational costs. Molecular models, and their coarse-graining into simplified representations, may be very useful to this end. Here, we develop a minimalistic toy model of cage-like molecules to explore the stable space of different cage topologies based on a few fundamental geometric building block parameters. Our results capture, despite the simplifications of the model, known geometrical design rules in synthetic cage molecules and uncover the role of building block coordination number and preorganisation on the stability of cage topologies. This leads to a large-scale and systematic exploration of design principles, generating data that we expect could be analysed through expandable approaches toward the rational design of self-assembled porous architectures. | Andrew Tarzia; Emma H. Wolpert; Kim E. Jelfs; Giovanni M. Pavan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c7aed1658ec5f7e57cf4d8/original/systematic-exploration-of-accessible-topologies-of-cage-molecules-via-minimalistic-models.pdf |
6654d90391aefa6ce12299e2 | 10.26434/chemrxiv-2024-vgtk2-v2 | Investigating lipid transporter protein and lipid interactions using variable temperature electrospray
ionization, ultraviolet photodissociation mass spectrometry, and collision cross section analysis | Gram-negative bacteria develop and exhibit resistance to antibiotics owing to their highly
asymmetric outer membrane maintained by a group of six proteins comprising the Mla (maintenance of
lipid asymmetry) pathway. Here we investigate the lipid binding preferences of one Mla protein, MlaC,
which transports lipids through the periplasm. We used ultraviolet photodissociation (UVPD) to identify
and characterize modifications of lipids endogenously bound to MlaC expressed in three different bacteria
strains. UVPD was also used to localize lipid binding to MlaC residues 130-140, consistent with the crystal
structure reported for lipid-bound MlaC. The impact of removing the bound lipid from MlaC on its
structure was monitored based on collision cross section measurements, revealing that the protein
unfolded prior to release of the lipid. The lipid selectivity of MlaC was evaluated based on titrimetric
experiments, indicating that MlaC bound lipids in various classes (sphingolipids, glycerophospholipids,
fatty acids) as long as they possessed no more than two acyl chains. | Virginia James; Bradley Voss ; Amanda Helms; M. Stephen Trent; Jennifer Brodbelt | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6654d90391aefa6ce12299e2/original/investigating-lipid-transporter-protein-and-lipid-interactions-using-variable-temperature-electrospray-ionization-ultraviolet-photodissociation-mass-spectrometry-and-collision-cross-section-analysis.pdf |
66c3da87a4e53c4876e45945 | 10.26434/chemrxiv-2023-dks4g-v4 | Efficient Method for Twist-Averaged Coupled Cluster Calculation of Gap Energy: Bulk Study of Stannic Oxide | We study the gap energy of the semiconducting oxide SnO2 through ab-initio calculations including both DFT and coupled cluster methods. The effectiveness of twist-averaging in reducing finite-size errors is evaluated across different functionals. We report an overestimation of gap energy when applying finite-size scaling at the thermodynamic limit in equation-of-motion (EOM) CCSD calculations. To mitigate one-body and many-body errors, we integrate twist averaging with a post-processing correction mechanism, comparing finite-size and infinite-size DFT calculations using hybrid functionals. While inspired by the Kwee, Zhang, and Krakauer (KZK) approach, our method is tailored to hybrid functionals for a more accurate treatment of exchange-correlation effects. Our approach ensures that the many-body interactions are accurately reflected in the estimated gap for an infinite system. We introduce unique single twist angles that yield cost- effective and accurate energies, in comparison to full twist averaging in the EOM-CCSD calculations. Applying this approach to SnO2, we calculate a fundamental gap of 3.46 eV, closely matching the 3.59 eV gap obtained from two-photon spectroscopy experiments, thereby demonstrating the accuracy of this method. | Maliheh Shaban Tameh; Wayne L. Gladfelter; Jason D. Goodpaster | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c3da87a4e53c4876e45945/original/efficient-method-for-twist-averaged-coupled-cluster-calculation-of-gap-energy-bulk-study-of-stannic-oxide.pdf |
674f79b15a82cea2fadf40a3 | 10.26434/chemrxiv-2024-t87k5 | Rapid Functionalization of Polycarbonates and Polyurethanes via Organocatalyzed SNAr | Robust methodologies for polymer post-synthesis functionalization enable preparation of new high-performance material scaffolds with uniquely tailored properties. Here, we demonstrate that polycarbonates containing pendant fluoroarene groups provide a convenient handle for incorporation of different functional thiols into the polymer backbone via organocatalytic nucleophilic aromatic substitution using silyl-protected thiols. This transformation proceeds under mild conditions can be performed in a single-pot immediately following polymerization or on purified substrates in a second step. In both cases, the transformation is typically complete within 5 minutes. Overall, the methodology presented herein enables a more convergent approach for development of functional high-performance materials. | Eddy Wei Ping Tan; Yi Yan Yang; James Hedrick; Nathaniel Park | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674f79b15a82cea2fadf40a3/original/rapid-functionalization-of-polycarbonates-and-polyurethanes-via-organocatalyzed-sn-ar.pdf |
66dff59751558a15ef92ea01 | 10.26434/chemrxiv-2024-sm1lp | Bimetallic Synergy in Ru−Pt Alloy Catalyst for Polyethylene Hydrogenolysis | Hydrogenolysis of low-density polyethylene (LDPE) under low pressure of H2 has been accomplished with a Ru−Pt bimetallic alloy catalyst. Using Ru5Pt1/CeO2 (atomic ratio of Ru to Pt is 5:1) as a catalyst, LDPE was efficiently converted (99% conversion) to gas and liquid hydrocarbons under 5 bar of H2 at 200 °C. This is contrastive to the 55% conversion with Ru/CeO2 and <1% conversion with Pt/CeO2 under the same reaction conditions. Mechanistic studies suggested that the higher activity of Ru5Pt1/CeO2 can be attributed to the synergistic effect of Ru (cleavage of C−C bond) and Pt (acceleration of Ru−alkyl hydrogenation step) on the catalyst surface. | Yukari Yamazaki; Xiongjie Jin; Weihan Sun; Katsutoshi Nomoto; Kohei Takahashi; Hiroki Miura; Tetsuya Shishido; Akira Nakayama; Kyoko Nozaki | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dff59751558a15ef92ea01/original/bimetallic-synergy-in-ru-pt-alloy-catalyst-for-polyethylene-hydrogenolysis.pdf |
67dd4bb26dde43c908b99958 | 10.26434/chemrxiv-2025-5sc2b-v2 | Synthesis and Optical Properties of Single Crystalline Phosphors Gd3In2Ga3O12:RE3+ (RE = Nd3+ and Ho3+) Grown via the Optical Float Zone Method | The continuous development of innovative optical materials with lanthanoid ions as activators has emerged as a modern sector of materials chemistry. Our experience with the fabrication of single crystals with the optical float zone has motivated us to investigate the luminescence of Nd3+ and Ho3+ ions in the garnets (Gd3-xREx)In2Ga3O12 (RE = Nd and Ho, x = 0; 0.15 and 0.30). Upon usage of an Ar/O2 (80:20 ratio) atmosphere and application of an auxiliary pressure (6 bar) to suppress In2O3 evaporation, single crystalline domain sizes in the order of ~ 6 x 6 x 1 mm³ obtained. Structural analysis confirmed the formation of a cubic garnet phase with space group Ia3 ̅d, with the substituents incorporated in accordance with Vegard’s law. Backscattered electron imaging and energy-dispersive X-ray spectroscopy were conducted, demonstrating a homogeneous elemental distribution within the crystals. Photoluminescence studies were carried out, revealing the characteristic narrow-line 4fn→4fn transitions of Nd3+ and Ho3+, with decay times in the sub-millisecond range, suggesting non-negligible cross-relaxation effects were present. Despite this, the large nearest-neighbour Gd–Gd distance (3.88 Å) in Gd3In2Ga3O12 and the low phonon cutoff energy (~700 cm 1) were found to limit cross-relaxation pathways, preserving significant photoluminescence brightness. These results highlighted the potential of Gd3In2Ga3O12:RE3+ single crystals as promising candidates for advanced optical applications. | Hasan YILMAZ; Gülsüm Kinik; Masahiko Isobe; Pascal Puphal; Markus Suta; Oliver Clemens | Materials Science; Optical Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd4bb26dde43c908b99958/original/synthesis-and-optical-properties-of-single-crystalline-phosphors-gd3in2ga3o12-re3-re-nd3-and-ho3-grown-via-the-optical-float-zone-method.pdf |
60c73ed9337d6c07bde2641b | 10.26434/chemrxiv.7130801.v1 | Catalytic Carbonyl-Olefin Metathesis of Aliphatic Ketones: Iron(III) HomoDimers as Lewis Acidic Superelectrophiles | <div>Catalytic carbonyl-olefin metathesis reactions have recently been developed as a powerful tool for carbon-carbon bond</div><div>formation. However, currently available synthetic protocols rely exclusively on aryl ketone substrates while the corresponding aliphatic analogs remain elusive. We herein report the development of Lewis acid-catalyzed carbonyl-olefin ring-closing metathesis reactions for aliphatic ketones. Mechanistic investigations are consistent with a distinct mode of activation relying on the in situ formation of a homobimetallic singly-bridged iron(III)-dimer as the active catalytic species. These “superelectrophiles” function as more powerful Lewis acid catalysts that form upon association of individual iron(III)-monomers. While this mode of Lewis acid activation has previously been postulated to exist, it has not yet been applied in a catalytic setting. The insights presented are expected to enable further advancement in Lewis acid catalysis by building upon the activation principle of “superelectrophiles” and broaden the current scope of catalytic carbonyl-olefin metathesis reactions.</div> | Haley Albright; Paul S. Riehl; Christopher C. McAtee; Jolene P. Reid; Jacob R. Ludwig; Lindsey A. Karp; Paul M. Zimmerman; Matthew S. Sigman; Corinna S. Schindler | Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed9337d6c07bde2641b/original/catalytic-carbonyl-olefin-metathesis-of-aliphatic-ketones-iron-iii-homo-dimers-as-lewis-acidic-superelectrophiles.pdf |
65d3007c66c1381729f75595 | 10.26434/chemrxiv-2024-b444c-v2 | Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy | SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into its open state, wherein the catalytic cleft becomes fully exposed to its ligands. This study elucidates the dynamic properties of SHP2 structures across different states, with a focus on the effects of oncogenic mutation on two known binding sites of allosteric inhibitors. Through extensive modeling and simulations, we further identified an alternative allosteric binding pocket in solution structures. Additional analysis provides insights into the dynamics and stability of the potential site. In addition, multi-tier screening was deployed to identify potential binders targeting the potential site. Our efforts to identify a new allosteric site contribute to community-wide initiatives developing therapies using multiple allosteric inhibitors to target distinct pockets on SHP2, in the hope of potentially inhibiting or slowing tumor growth associated with SHP2. | Ashfaq Ur Rehman; Cizhang Zhao; Yongxian Wu; Qiang Zhu; Ray Luo | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d3007c66c1381729f75595/original/targeting-shp2-cryptic-allosteric-sites-for-effective-cancer-therapy.pdf |
6107e99a0321149c67b96db0 | 10.26434/chemrxiv-2021-668s4 | Identifying Nonadditive Contributions to the Hydrophobicity of Chemically Heterogeneous Surfaces via Dual-Loop Active Learning | Hydrophobic interactions drive numerous phenomena involving surfaces that are chemically heterogeneous at the nanoscale. Nonadditive contributions to the hydrophobicity of such surfaces depend on the chemical identities and spatial patterns of polar and nonpolar groups in ways that remain poorly understood. Here, we develop an active learning framework that utilizes molecular dynamics (MD) simulations, enhanced sampling, and a convolutional neural network to predict the hydration free energy (a thermodynamic descriptor of hydrophobicity) for nearly 200,000 chemically heterogeneous self-assembled monolayers (SAMs). Analysis of this data set reveals that SAMs with distinct polar groups exhibit substantial variations in hydrophobicity as a function of their composition and patterning, but the clustering of nonpolar groups is a common signature of highly hydrophobic patterns. Further MD analysis relates such clustering to the perturbation of interfacial water structure. These results provide new insight into the influence of chemical heterogeneity on hydrophobicity via quantitative analysis of a large set of surfaces, enabled by the active learning approach. | Atharva Kelkar; Bradley Dallin; Reid Van Lehn | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Interfaces; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2021-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6107e99a0321149c67b96db0/original/identifying-nonadditive-contributions-to-the-hydrophobicity-of-chemically-heterogeneous-surfaces-via-dual-loop-active-learning.pdf |
64661fbff2112b41e9c1a6c5 | 10.26434/chemrxiv-2023-bg0x0 | Palladium-Catalyzed Coupling of Amides and Cyclopropanols for the Synthesis of γ-Diketones | A palladium catalytic method has been developed for the coupling of amides and cyclopropanols to γ-diketones. Heteroatom ligand exchange and heteroatom-to-carbon ligation mode switch provide the mechanistic basis for avoiding the use of any stoichiometric organometallic reagent and base. The molecular cross-coupling reactivity can be programmed through the adjustment of structural context surrounding the amide N-atom, enabling the establishment of a set of reactivity order chemistry. With chemistry set, a collection of transformations with defined (especially quantitative) reactivity relations, as the fundamental synthetic planning unit, a synthetic programming strategy, set chemistry, can be envisioned. The γ-diketone synthesis can be further elaborated into an alkyl-alkyl coupling protocol, furnishing an alternative surrogate synthetic scheme for this to-a-certain-extent challenging reaction. | Lili Fang; Shuqi Jia; Shuaixin Fan; Jin Zhu | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64661fbff2112b41e9c1a6c5/original/palladium-catalyzed-coupling-of-amides-and-cyclopropanols-for-the-synthesis-of-diketones.pdf |
67158479b91c6e99719e42d5 | 10.26434/chemrxiv-2024-4gs2l | Nitro and nitritosilanes: Do they and can they exist? | NITROSILANES ARE UNKNOWN, MUCH LIKE THE NITRO ANALOGUES OF MOST METALLOIDS. THEIR NITRITE ISOMERS ARE BETTER KNOWN AND EVEN USED AS REAGENTS. STILL, MOST STUDIES ON NITRITOSILANES FOCUS ON REACTIVITIES AND THERE REMAINS SOME DOUBT ON THEIR IDENTITY. IN THIS CONTRIBUTION, WE VERIFY COMPUTATIONALLY WHETHER NITROSILANES CAN EXIST AND OBTAIN FULL SPECTROSCOPIC CONFIRMATION OF THE EXISTENCE OF NITRITOSILANES, THUS RECTIFYING PREVIOUSLY-REPORTED INTERPRETATIONS. | Houari Dahmani; Lara Harter; Louis-Philippe Poulin; Charles-Émile Fecteau; Paul A. Johnson; Guillaume Bélanger-Chabot | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67158479b91c6e99719e42d5/original/nitro-and-nitritosilanes-do-they-and-can-they-exist.pdf |
62b1ce2958b3d6777258aa44 | 10.26434/chemrxiv-2022-cz2x9-v2 | A Robust and Efficient Propane Dehydrogenation Catalyst from Unexpectedly Segregated Pt2Mn Nanoparticles | The increasing demand for short chain olefins like propene for plastics production and the availability of shale gas make the development of highly performing propane dehydrogenation (PDH) catalysts, robust towards industrially applied harsh regeneration conditions, a highly important field of research. A combination of surface organometallic chemistry (SOMC) and thermolytic molecular precursor (TMP) approach was used to prepare a nanometric, bimetallic Pt-Mn mate-rial (3 wt% Pt, 1.3 wt% Mn) supported on silica via consecutive grafting of a Mn and Pt precursor on surface OH groups present on the support surface, followed by a treatment under a H2 flow at high temperature. The material exhibits a 70% fraction of the overall Mn as MnII single sites on the support surface; the remaining Mn is incorporated in segregated Pt2Mn nanoparticles. The material shows great performance in PDH reaction with a low deactivation rate. In particular, it shows outstanding robustness during repeated regeneration cycles, with conversion and selectivity stabilizing at ca. 37% and 98%, respectively. Notably, a material with a lower Pt loading of only 0.05 wt% shows an outstanding catalytic per-formance – initial productivity of 4523 gC3H6/gPt h and an extremely low kd of 0.003 h-1 under a partial pressure of H2 – ranging among the highest reported productivities. A combined in situ XAS, STEM, EPR and metadynamics at the DFT level study could show that the strong interaction between the MnII decorated support and the unexpectedly segregated Pt2Mn particles is most likely responsible for the outstanding performance of the investigated materials. | Lukas Rochlitz; Quentin Pessemesse; Jörg W. A. Fischer; Daniel Klose; Adam H. Clark; Milivoj Plodinec; Gunnar Jeschke; Pierre-Adrien Payard; Christophe Copéret | Materials Science; Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2022-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b1ce2958b3d6777258aa44/original/a-robust-and-efficient-propane-dehydrogenation-catalyst-from-unexpectedly-segregated-pt2mn-nanoparticles.pdf |
60c7559bee301c42bac7b1d9 | 10.26434/chemrxiv.14135840.v1 | pH-Independent Heat Capacity Changes during Phosphorolysis Catalyzed by the Pyrimidine Nucleoside Phosphorylase from Geobacillus thermoglucosidasius | Enzyme-catalyzed reactions sometimes display curvature in their Eyring plots in the absence of denaturation, indicative of a change in activation heat capacity. However, pH and (de)protonation effects on this phenomenon have remained unexplored. Herein, we report a kinetic characterization of the thermophilic pyrimidine nucleoside phosphorylase from <i>Geobacillus thermoglucosidasius</i> across a two-dimensional working space covering 35 °C and 3 pH units with two substrates displaying different pK<sub>a</sub> values. Our analysis revealed the presence of a measurable activation heat capacity change in this reaction system, which showed no significant dependence on medium pH or substrate charge. Our results further describe the remarkable effects of a single halide substitution which has a minor influence on the heat capacity change but conveys a significant kinetic effect by lowering the activation enthalpy, causing a >10-fold rate increase. Collectively, our results present an important piece in the understanding of enzymatic systems across multidimensional working spaces where the choice of reaction condition can affect rate, affinity and thermodynamic phenomena independently of one another.<br /> | Felix Kaspar; Darian S. Wolff; Peter Neubauer; Anke Kurreck; Vickery Arcus | Biocatalysis | CC BY 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7559bee301c42bac7b1d9/original/p-h-independent-heat-capacity-changes-during-phosphorolysis-catalyzed-by-the-pyrimidine-nucleoside-phosphorylase-from-geobacillus-thermoglucosidasius.pdf |
60f17923105317856940f73c | 10.26434/chemrxiv-2021-057q7 | Immobilized Polythiophene-fullerene on Surfaces: Beyond Photovoltaics | Surfaces coated with polythiophene-fullerene, particularly poly(3-hexylthiophene)-Phenyl-C61-butyric acid methyl ester (P3HT-PCBM) emerged as a gold standard for fabrication of photovoltaic devices of bulk heterojunction type. Since, photocatalytic dye degradation has a similar initiation mechanism driven by electron-hole production under sunlight, the surface was used as a reusable photocatalytic "chip" to degrade polluting organic dyes. Detailed investigations were carried out on various factors affecting the efficacy | Debasis Samanta; Periyamuthu Ramar; B.V Aishwarya | Polymer Science; Polymer blends; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f17923105317856940f73c/original/immobilized-polythiophene-fullerene-on-surfaces-beyond-photovoltaics.pdf |
60c7513eee301c4a17c7aa23 | 10.26434/chemrxiv.13139846.v1 | Ligand-Programmed Consecutive Symmetry Break(s) in Nanoparticle Based Materials Showing Emergent Phenomena: Transitioning from Six-Fold to Three-Fold Symmetry in Anisotropic ZnO Colloids | The central promise of nanoparticle-based materials is that cooperative properties may emerge, when individual quantum dots are positioned on a periodic lattice. Yet, there are only few papers in literature reporting about such effects. Nevertheless, it is clear that the symmetry of the superlattice is decisive for the desired emergent phenomena. An interesting question is, how the symmetry of the initial monodisperse nanoparticles affects the structure of the colloidal crystal during self-assembly processes. For instance, particles with hexagonal cross-section show self-organization which is very similar to spherical colloids. Like-wise one would also expect that trigonal nanoparticles behave similar. Unfortunately, it is very hard to obtain monodisperse semiconductur colloids with trigonal shape, because this requires a symmetry break during morphogenesis of the nanocrystal. While such a symmetry-break is known in literature for structures attached to a solid substrate, it is shown here, colloidal synthesis of trigonal ZnO nanorods is successful, and the mechanism is elucidated by experimental and theoretical methods. 2D-superlattices formed by such particles with trigonal cross-section were compared to hexagonal analogues. It was found, there are distinct differences, which result in important differences in properties such as the formation of voids and also in optical properties. | Sebastian Theiss; Michael Voggel; Henning Kuper; Martin Hoermann; Ulrich Krings; Peter Baum; Jörg August Becker; Valentin Wittmann; Sebastian Polarz | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7513eee301c4a17c7aa23/original/ligand-programmed-consecutive-symmetry-break-s-in-nanoparticle-based-materials-showing-emergent-phenomena-transitioning-from-six-fold-to-three-fold-symmetry-in-anisotropic-zn-o-colloids.pdf |
637ef60ac567537f4a947782 | 10.26434/chemrxiv-2022-gjn1v | o-Nitrobenzyl oxime ethers enable photo-induced cyclization reac-tion to provide phenanthridines under aqueous conditions | In this paper, we describe a novel N–O photolysis of o-nitrobenzyl oxime ethers that enables the synthesis of phenanthridines via intramolecular cyclization reactions. Without the use of additional photocatalysts or photosensitizers, the process proceeds with an efficiency of up to 96% when exposed to near-visible light (405 nm) under aqueous circumstances. Through the photoinduced production of a fluorescent phenanthridine derivative in HeLa cells, biocompatibility of the reaction was demonstrated. This photoinduced cyclization reaction could be used as a different photochemical instrument to control biological processes by inducing the production of bioactive molecules. | Hidenori Okamura; Momoka Iida; Yui Kaneyama; Fumi Nagatsugi | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637ef60ac567537f4a947782/original/o-nitrobenzyl-oxime-ethers-enable-photo-induced-cyclization-reac-tion-to-provide-phenanthridines-under-aqueous-conditions.pdf |
60c73e80567dfe8d81ec3801 | 10.26434/chemrxiv.6990359.v1 | Mechanistic Studies of Cyclopentadienyl Ring-Slippage: A TRIR and DFT Study via Photolysis of (η1-C5Cl5)Mn(CO)5 | <div>Ring slip is among the most widely invoked ligand distortions in organometallic chemistry, yet very few ring slipped geometries have been directly characterized. Here we investigate the ultrafast photochemistry of (η1-C5Cl5)Mn(CO)5 to characterize the “reverse ring-slip” processes that result upon ligand dissociation from this complex in polar and nonpolar solvents. (η1- C5Cl5)Mn(CO)5 readily undergoes dicarbonyl-loss upon photoexcitation across a range of UV-excitation wavelengths, and the fac- ile ejection of a second-CO during the reverse ring-slip process is shown to occur due to a mechanism that relies on the enthalpy released during the reverse ring-slip. This mechanistic paradigm is potentially widespread in organometallic reactions involving changes in ligand hapticity, carrying implications for the expansive range of Cp-ligated organometallic complexes. Experiments in CH2Cl2 solution observe formation of a solvent-coordinated product upon coordination of CH2Cl2 to the monocarbonyl-loss spe- cies. An energetic barrier to solvent coordination is present due to the need for rearrangement of the ring geometry from a three- center M-C-Cl coordination to η1 coordination to accommodate the incoming solvent molecule. Density functional theory calculations are used to investigate the structures of the experimentally observed intermediates, as well as to explore the relevance of these experiments to analogous complexes containing the more commonly encountered Cp (C5H5) and Cp* (C5Me5) cyclopentadienyl ligands. </div><div><br /></div> | Justin Lomont; Son Nguyen; Charles Harris | Photochemistry (Org.); Computational Chemistry and Modeling; Kinetics and Mechanism - Organometallic Reactions; Ligand Design; Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e80567dfe8d81ec3801/original/mechanistic-studies-of-cyclopentadienyl-ring-slippage-a-trir-and-dft-study-via-photolysis-of-1-c5cl5-mn-co-5.pdf |
614517a7aeaa6e8d3aef8841 | 10.26434/chemrxiv-2021-1kgg7 | Tuning the Dielectric Response in a Nanocomposite Material through Nanoparticle Morphology | The introduction of metal cluster dopants and molecular-scale inclusions in metal oxide matrices provides an opportunity for exploring new high-k solid-state dielectrics with tunable response. The quantum properties of molecular nanoparticles depend strongly on their size and shape, a characteristic that can be exploited in changing the response properties of a material, while the small nanoparticle size can help limit the usual issues of conduction and leakage. Here, we model the polarization of molecular-scale silver inclusions in magnesium oxide, using the Modern Theory of Polarization and Car-Parinello Molecular Dynamics (CPMD). Several trends are considered, including nanoparticle size, shape and orientation relative to the applied field. Dielectric permittivity enhancements of 30-100% were observed with inclusion sizes varying from 8 to 32 atoms, considering both rod-like and disk-like inclusions, with alignment either parallel or perpendicular to the external field. Currents calculated using the modern theory of polarization with periodic boundary conditions can experience box edge jumps due to the distortion of the matrix during the simulations - an approach for addressing these issues in CPMD calculations is outlined within. | Archita Adluri; Brett Henderson; Irina Paci | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Composites; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614517a7aeaa6e8d3aef8841/original/tuning-the-dielectric-response-in-a-nanocomposite-material-through-nanoparticle-morphology.pdf |
6170c0c145f1eeeb263466af | 10.26434/chemrxiv-2021-5c17l | NHCs and Visible Light Co-catalyzed 1,4-Sulfonylacylation of 1,3-Enynes for Tetrasubstituted Allenyl Ketones | The modulation of selectivity of highly reactive carbon radical cross-coupling for the construction of C-C bonds represents a challenging task in organic chemistry. N-Heterocyclic carbenes (NHCs) catalyzed radical transformations opened a new avenue for acyl radical cross-coupling chemistry. With this method, highly selective cross-coupling of acyl radical with alkyl radical for efficient construction of C-C bonds were succussfully realized. However, the cross-coupling reaction of acyl radical with vinyl radicals represents an uncharted domain. We herein describe NHCs and photocatalysis co-catalyzed radical 1,4-sulfonylacylation of 1,3-enynes, providing structurally diversified valuable tetrasubstituted allenyl ketones. Mechanistic studies indicated that ketyl radicals are formed from aroyl fluorides via oxidative quenching process of excited photocatalysis, allenyl radicals are generated from chemo specific sulfonyl radical addition to the 1,3-enynes, finally, unprecedented key allenyl and ketyl radical cross-coupling provides tetrasubstituted allenyl ketones. | Lihong Wang; Ruiyang Ma; Jiaqiong Sun; Guangfan Zheng; Qian Zhang | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6170c0c145f1eeeb263466af/original/nh-cs-and-visible-light-co-catalyzed-1-4-sulfonylacylation-of-1-3-enynes-for-tetrasubstituted-allenyl-ketones.pdf |
60c748a8f96a00d5212870d3 | 10.26434/chemrxiv.11954820.v1 | A Method for the Highly Accurate Quantification of Gas Streams by On-Line Chromatography | This paper presents a method for the quantification of gas streams from reactive systems using on-line gas chromatography. The method is based on the mathematical development of correlations between the quantities detected by a set comprised of a thermal conductivity detector, a methanizer, and a flame ionization detector. The method allows for a complete and physically meaningful quantification of the composition of gas streams.<br /> | Víctor Stivenson Sandoval-Bohorquez; Edwing Alexander Velasco-Rozo; Víctor Gabriel Baldovino Medrano | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748a8f96a00d5212870d3/original/a-method-for-the-highly-accurate-quantification-of-gas-streams-by-on-line-chromatography.pdf |
6796e705fa469535b9fb45f9 | 10.26434/chemrxiv-2025-n2x5j | Palladium-catalyzed enantioselective and stereospecific assembly of axially chiral alkylidenecyclobutanes via N-tosylhydrazone-based carbene couplings | Synthesis of axially chiral alkylidenecyclobutanes exists sustained challenges by virtue of the compatibility of an efficient asymmetric catalytic system and the meticulous retention of its inherent strained ring structure. We herein disclose an enantioselective carbene cross-coupling reaction of cyclobutanecarbaldehyde-derived N‑tosylhydrazones with organohalides enabled by a combination of palladium catalysis and the modified sulfinamide phosphine ligand (Sadphos). This reaction proof the concept that axial chirality can be constructed on a strained metal carbene intermediate precisely through a sequential process of enantio-determined migratory insertion and β-H elimination. A variety of alkylidenecyclobutanes with heteroatom-substituted stereocenter, tertiary carbon stereocenter, and all-carbon quaternary stereocenter for particular, can be synthesized collectively with excellent yields and high enantioselectivities. Both the two enantiomers can be obtained via selecting the corresponding either cis or trans hydrazone substrates in a stereospecific manner. The synthetic applications of this asymmetric carbene coupling reaction are further demonstrated by the access of enantioenriched free amine by hydrolysis smoothly (99% ee) and the downstream transformations to reach versatile nitrogen-containing heterocycles without any enantiopurity erosion (99% ee). | Xiaoqin Ning; Tonglin Zhao; Yulei Zhu; Bo Liu; Xufei Yan; Ying Xia | Organic Chemistry; Catalysis; Organometallic Chemistry; Stereochemistry; Catalysis; Ligand Design | CC BY 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6796e705fa469535b9fb45f9/original/palladium-catalyzed-enantioselective-and-stereospecific-assembly-of-axially-chiral-alkylidenecyclobutanes-via-n-tosylhydrazone-based-carbene-couplings.pdf |
634faf114b0af359bdcb6729 | 10.26434/chemrxiv-2022-xwz3x | Description of conformational ensembles of disordered proteins by residue-local probabilities | The study of proteins with intrinsically disordered regions (IDRs) has emerged as an active field of research due to their intriguing nature. Despite IDRs lack of a well-defined folded structure, they play important functional roles in the cell, following biological mechanisms different from those of the traditional structured proteins. Consequently, it has been necessary to re-design experimental and theoretical methods in order to face the challenges introduced by the dynamic nature of IDRs. In this work, we present an accurate and cost-effective method to study the conformational dynamics of IDRs based on the use of residue-local probabilistic expressions that characterize the conformational ensembles obtained from finite-temperature molecular dynamics (MD) simulations. It is shown that the good performance and the high convergence rates achieved with our method are independent of the IDR lengths, since the method takes advantage of the major influence of the identity and conformation of the nearest residue neighbors on the amino-acid conformational preferences to evaluate the IDR conformational ensembles. This allows us to characterize the conformational space of IDRs using a reduced number of probabilities which can be obtained from comparatively short MD simulations or experimental databases. To exemplify the usefulness of our approach, we present an application to directly detect Molecular Recognition Features (MoRFs) in a IDR domain of the protein p53, and to follow the time evolution of the thermodynamic magnitudes of this system during its exploration of the conformational space. | Adolfo Bastida; José Zúñiga; Beatriz Miguel; Miguel A. Soler | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634faf114b0af359bdcb6729/original/description-of-conformational-ensembles-of-disordered-proteins-by-residue-local-probabilities.pdf |
60c74786bdbb8913fda38e07 | 10.26434/chemrxiv.11625885.v1 | Predicting Binding from Screening Assays with Transformer Network Embeddings | Cheminformatics aims to assist in chemistry applications that depend on molecular interactions, structural characteristics, and functional properties. The arrival of deep learning and the abundance of easily accessible chemical data from repositories like PubChem have enabled advancements in computer-aided drug discovery. Virtual High-Throughput Screening (vHTS) is one such technique that integrates chemical domain knowledge to perform in silico biomolecular simulations, but prediction of binding affinity is restricted due to limited availability of ground-truth binding assay results. Here, text representations of 83,000,000 molecules are leveraged to enable single-target binding affinity prediction directly on the outcome of screening assays. The embedding of an end-to-end Transformer neural network, trained to encode the structural characteristics of a molecule via a text-based translation task, is repurposed through transfer learning to classify binding affinity to a single target. Classifiers trained on the embedding outperform those trained on SMILES strings for multiple tasks, receiving between 0.67-0.99 AUC. Visualization reveals organization of structural and functional properties in the learned embedding useful for binding prediction. The proposed model is suitable for parallel computing, enabling rapid screening as a complement to virtual screening techniques when limited data is available. | Paul Morris; Rachel St Clair; Elan Barenholtz; William Edward Hahn | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74786bdbb8913fda38e07/original/predicting-binding-from-screening-assays-with-transformer-network-embeddings.pdf |
65bfae4466c1381729f2714a | 10.26434/chemrxiv-2024-q8zhr | Self-assembled nanoscale upconversion POP composite for hypoxia relieving and enhanced chemotherapy in hepatocellular carcinoma | Uncontrolled proliferations and altered metabolism of cancer cells result an imbalance of nutrients as well as oxygen supply and persuade hypoxia. This hypoxia in turn activates the transcription gene HIF-1α which eventually upregulates the efflux transporter P-gp and induce MDR. Thus, hypoxia leads to resistance towards conventional therapy methods. Therefore, the fabrication of a nanoscale porous system enriched with upconversion nanoparticle to target the cancer cells, evade hypoxia and enhanced anticancer therapy is the key goal of this chapter. Herein, the upconversion nanoparticles are embedded with the nanoscale POP and further conjugated with targeting moiety and also with catalase molecule. The nanoscale POP embedded with UCNPs are generated in room temperature. Targeting ligand lactobionic acid is attached after polymer coating which effectively targets liver cancer cells. Then catalase is grafted effectively produces oxygen. The endogenously generated oxygen alleviates the hypoxia of the liver cancer cells. The drug and catalase-loaded composite exhibits more cytotoxicity in case of hypoxic liver cells than the normal cells by overcoming hypoxia and
downregulating the hypoxia inducible factors. | Poulami Mukherjee; Subhabrata Guha; Antara Ghosh; Korak Kar; Gaurav Das; Sumanta Kumar Sahu | Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bfae4466c1381729f2714a/original/self-assembled-nanoscale-upconversion-pop-composite-for-hypoxia-relieving-and-enhanced-chemotherapy-in-hepatocellular-carcinoma.pdf |
6137535c65db1e49dbaecb5b | 10.26434/chemrxiv-2021-1bhnc | New Application of Natural Language Processing（NLP）for Chemist Predicting Intermediate and Providing an Effective Direction for Mechanism Inference | Predicting and proposing the reaction mechanism, as well as speculating the reaction intermediates are great challenges among the development of modern organic chemistry. Herein, a model from Natural Language Processing (NLP) was firstly employed to learn and perform the task of intermediate prediction, which is served as a language translation task. Radical cascade cyclization is prevalently used in life science and pharmaceutical projects, while the regioselectivity of radical attack is difficult to predict. The model is trained on self-built dataset to tackle the challenge. And transfer learning was used to surmount the restriction of limited amounts of data. The NLP transformer model performs well with remarkable accuracy, providing an efficient instruction for mechanism understanding. Manual encoding of rules is not required, thus, providing a favorable tool towards solving the challenging problem of computational organic chemical mechanism inference. | Jiangcheng Xu; Yun Zhang; Jiale Han; Haoran Qiao; Chengyun zhang; Jing Tang; Shen Xi; Bin Sun; Silong Zhai; Xinqiao Wang; Yejian Wu; Weike Su; Hongliang Duan | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6137535c65db1e49dbaecb5b/original/new-application-of-natural-language-processing-nlp-for-chemist-predicting-intermediate-and-providing-an-effective-direction-for-mechanism-inference.pdf |
6328b86d084700d2fc817184 | 10.26434/chemrxiv-2022-mgp5n-v4 | Towards a mechanically-rechargeable solid fuel flow battery based on earth-abundant materials | Metal-air batteries are a promising energy storage solution, but materials limitations (e.g., metal passivation, low active material utilization) have stymied their adoption. We investigate a solid fuel flow battery (SFFB) architecture that combines the energy density of metal-air batteries with the modularity of redox flow batteries. Specifically, a metallic solid electrochemical fuel (SEF) is spatially separated from the anodic current collector; a dissolved redox mediator shuttles charge between the two, and an oxygen reduction cathode completes the circuit. This modification decouples power and energy system components while enabling mechanical recharging and mitigating the effects of non-uniform metal oxidation. We conduct an exploratory study showing that metallic SEFs can chemically reduce organic redox mediators repeatedly. We subsequently operate a proof-of-concept SFFB cell for ca. 25 days as an initial demonstration of technical feasibility. Overall, this work illustrates the potential of this storage concept and highlights scientific and engineering pathways to improvement. | Alexis M. Fenton, Jr.; Yasser Ashraf Gandomi; Christopher T. Mallia; Bertrand J. Neyhouse; M. Aba Kpeglo; William E. Exson; Charles Tai-Chieh Wan; Fikile R. Brushett | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6328b86d084700d2fc817184/original/towards-a-mechanically-rechargeable-solid-fuel-flow-battery-based-on-earth-abundant-materials.pdf |
67d2bf39fa469535b9126cf0 | 10.26434/chemrxiv-2025-7t50s | Mn-Catalyzed Regioselective Alkene Hydrosilylation: from Mecha-nism Investigation | The catalytic hydrosilylation of alkenes is a cornerstone process in the large-scale production of organosilicon compounds. As a sustainable alternative to precious metal catalysts, manganese-based systems such as Mn(CO)₅Br have gained signifi-cant attention due to their low cost and high availability. However, the catalytic mechanism in place is not completely un-derstood and several propositions have been described in the literature. To clarify this point, we employed a combined exper-imental and computational approach to elucidate the activation mechanism of Mn(CO)₅Br in the anti-Markovnikov hydrosi-lylation of alkenes. Our findings reveal that the initiation involves specific CO ligand dissociation and substrate coordina-tion to generate an active Mn(I) intermediate that facilitates the desired transformation via concerted 2-electrons organometal-lic pathways. | Ming-Yu CHEN; Antoine FROT; Anthony VIVIEN; Clément CAMP; Chloé THIEULEUX; Pierre-Adrien PAYARD; Marie-Eve L. PERRIN | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d2bf39fa469535b9126cf0/original/mn-catalyzed-regioselective-alkene-hydrosilylation-from-mecha-nism-investigation.pdf |
67b10fd781d2151a02a4ea8a | 10.26434/chemrxiv-2025-qj8f5 | Scalable, Convergent Total Synthesis of (+)-Saxitoxin and Related Natural Products | The urgent demand for innovative pain therapies is underscored by pain affecting 20% of the global population, costing the U.S. $600 billion annually, more than cancer, heart disease, and diabetes combined, with current treatments lacking in efficacy or causing severe side effects1 . Saxitoxin (STX, 1), a potent neurotoxin from shellfish, first isolated in 19572, offers immense pharmaceutical potential due to its interaction with voltage-gated sodium channels, promising long-term anesthesia for conditions like anal fissures3 and chronic headaches4. However, its deadly nature, with just 1 mg potentially lethal, and the complexity of its over 50 related toxins5, challenge its clinical use. Efforts to modify STX aim to reduce its systemic toxicity while enhancing selectivity, potentially revolutionizing pain management and detoxification strategies, while also providing insights into cellular electrical transmission6. Hundreds of synthetic studies towards this end have been disclosed thus far, yet a fully modular and scalable approach to the family remains elusive. Here we show how a tactical combination of radical retrosynthesis, biocatalysis, and C–H functionalization logic can be combined to solve this problem resulting in a scalable approach to the STX family in less than 10 steps including the first total synthesis of neosaxitoxin (neoSTX, 4), a hydroxylated naturally occurring STX analog previously under clinical investigation7 | Yinliang Guo; Yiheng Li; Sihan Chen; Oscar Poll; Yige Wu; Christopher Prier; Kai-Jiong Xiao; Phil Baran | Organic Chemistry; Natural Products | CC BY 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b10fd781d2151a02a4ea8a/original/scalable-convergent-total-synthesis-of-saxitoxin-and-related-natural-products.pdf |
67ab0d806dde43c9085fcb17 | 10.26434/chemrxiv-2025-0mftt | Novel synthetic phospholipids for the preparation of thiol-responsive liposomes | This study introduces novel thiol-sensitive liposomes using pyridazinedione-based synthetic phospholipids. These formulations are designed to achieve an optimal balance between stability and responsiveness under tumour-specific conditions, enabling triggered release. Characterisation reveals the importance of phospholipid type and chain length in optimising reactivity and stability. This platform shows promise for advancing cancer nanomedicine through precise, stimulus-responsive delivery systems. | Célest Mordechai Attiach; Mélanie Sebastien; Edouard Brosset-Heckel; Salvatore Cinquerrui; Antoine Maruani | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab0d806dde43c9085fcb17/original/novel-synthetic-phospholipids-for-the-preparation-of-thiol-responsive-liposomes.pdf |
65bcbfed9138d231614569fe | 10.26434/chemrxiv-2024-3b08x | Bio-inspired synthesis and profiling of a potent antiviral flavonol targeting the lipid exchanger OSBP | Hijacking host cell lipid homeostatic pathways is a hallmark of infection by RNA-positive viruses. A key protein exploited by these viruses to facilitate replication is the lipid exchanger Oxysterol-binding protein (OSBP), making it an attractive target for antiviral strategies. However, the known OSBP ligands are poorly selective, and those of natural origin, referred to as ORPphilins, exhibit pronounced cytotoxicity. Here, we describe macarangin B, a new racemic flavonoid isolated from a Vietnamese bushy tree. This compound features a rare hydroxy-hexahydroxanthene moiety that confers the ability to bind OSBP. Using a bio-inspired method, we performed the total synthesis of both (R, R, R) and (S, S, S) enantiomers, allowing us to examine their distinct interaction with OSBP, based on their unique optical properties. Together, experimental and computational approaches indicate that the (R, R, R) enantiomer has the highest affinity for OSBP. We show that replication of the health-threatening Flavivirus Zika virus in infected human cells is strongly reduced by treatment with (R, R, R)-macarangin B, which selectively targets OSBP. Importantly, both enantiomers exhibit significantly decreased cytotoxicity when compared to the previously characterized ORPphilins, positioning (R, R, R)-macarangin B as a promising lead for the development of a novel family of antivirals. | Gwenaëlle Jézéquel; Zoé Grimanelli; Carole Guimard; Joëlle Bigay; Juliano Haddad; Jérôme Bignon; Cécile Apel; Vincent Steinmetz; Laurie Askenatzis ; Hélène Levaïque; Clara Pradelli; Van Cuong Pham ; Thi May Huong Doan; Marc Litaudon; Romain Gautier; Chaker El Kalamouni; Bruno Antonny; Sandy Desrat; Bruno Mesmin; Fanny Roussi | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bcbfed9138d231614569fe/original/bio-inspired-synthesis-and-profiling-of-a-potent-antiviral-flavonol-targeting-the-lipid-exchanger-osbp.pdf |
64c2170bce23211b20a043ad | 10.26434/chemrxiv-2023-w5rhq-v2 | Oxidative coupling of biogas to ethylene over a trilobe-shaped Mn-Na2WO4/α-Al2O3 catalyst in a single-pellet reactor | The oxidative coupling of methane (OCM), which offers a direct route for converting methane into higher-value ethylene.
Despite the development of selective catalyst formulations, kinetic and reactor design studies have been hampered by a lack of data for truly isothermal, relevant. Because of exothermicity issues, the temperature of a fixed-bed reactor filled with Mn-Na2WO4/SiO2 catalysts show a sudden temperature run-away accompanied with a drastic loss of selectivity.
The objective of this study is to measure catalyst activity under relevant reaction conditions of pressure (3 bar), biogas composition (no dilution) and contact time, while keeping the process as isothermal as possible. To this aim, we have synthesized and shaped a trilobed Mn-Na2WO4/α-Al2O3 catalyst, which may be used as is at industrial scale, and measured its performance in a single-pellet reactor.
We found that the presence of CO2 does not degrade catalyst performance, even on long run, which should enable the use of a CO2-rich stream such as biogas. Actually, higher methane conversions have been obtained in the presence of CO2, likely due to a possible contribution of methane dry reforming reaction. We also noticed a slow catalyst activation over the first 100 hours while selectivity was kept constant.
| Valentin L'hospital; Jordan Guillemot; Rémi Beucher; Thomas Michon; Didier Bonnet; Yves Schuurman; David Farrusseng | Catalysis; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c2170bce23211b20a043ad/original/oxidative-coupling-of-biogas-to-ethylene-over-a-trilobe-shaped-mn-na2wo4-al2o3-catalyst-in-a-single-pellet-reactor.pdf |
65d476ea66c13817291051eb | 10.26434/chemrxiv-2024-r67mx | The interplay of solvation and polarization effects on ion pairing in nanoconfined electrolytes | The nature of ion-ion interactions in electrolytes confined to nanoscale pores has important implications for energy storage and separations technologies. However, the physical effects dictating the structure of nanoconfined electrolytes remain debated. Here we employ machine learning-based molecular dynamics simulations to investigate ion-ion interactions with density functional theory-level accuracy in a prototypical confined electrolyte, aqueous NaCl within graphene slit pores. We find that the free energy of ion pairing in highly confined electrolytes deviates substantially from that in bulk solutions, observing a decrease in contact ion pairing but an increase in solvent-separated ion pairing. These changes arise from an interplay of ion solvation effects and graphene's electronic structure. Notably, the behavior observed from our first-principles-level simulations is not reproduced even qualitatively with the classical force fields conventionally used to model these systems. The insight provided in this work opens new avenues for predicting and controlling the structure of nanoconfined electrolytes. | Kara Fong; Barbara Sumic; Niamh O'Neill; Christoph Schran; Clare Grey; Angelos Michaelides | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d476ea66c13817291051eb/original/the-interplay-of-solvation-and-polarization-effects-on-ion-pairing-in-nanoconfined-electrolytes.pdf |
60c74838f96a004c2228703e | 10.26434/chemrxiv.11862243.v1 | Advancement of Actinide Metal-Organic Framework Chemistry via Synthesis of Pu-UiO-66 | We report the synthesis and characterization of the first plutonium metal-organic framework (MOF). Pu-UiO-66 expands the established UiO-66 series, which includes transition-metal, lanthanide, and early actinide elements in the hexanuclear nodes. The thermal stability and porosity of Pu-UiO-66 were experimentally determined and multi-faceted computational methods were used to corroborate experimental values, examine inherent defects in the framework and decipher spectroscopic signatures. The crystallization of a plutonium chain side product provides direct evidence of the competition that occurs between modulator and linker in MOF syntheses. Ultimately, the synthesis of Pu-UiO-66 demonstrates adept control of Pu(IV) coordination under hydrolysis-prone conditions, provides an opportunity to extend trends across isostructural UiO-66 frameworks and serves as the foundation for future plutonium MOF chemistry. | Ashley Hastings; Debmalya Ray; WooSeok Jeong; Laura Gagliardi; Omar
K. Farha; Amy Hixon | Lanthanides and Actinides; Spectroscopy (Inorg.); Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74838f96a004c2228703e/original/advancement-of-actinide-metal-organic-framework-chemistry-via-synthesis-of-pu-ui-o-66.pdf |
60c749fbee301c10e1c79b75 | 10.26434/chemrxiv.11448177.v2 | Automated Extraction of Chemical Synthesis Actions from Experimental Procedures | <div>
<div>
<div>
<p>Experimental procedures for chemical synthesis are commonly reported in prose in
patents or in the scientific literature. The automatic extraction of the details necessary to reproduce and validate a synthesis in a chemical laboratory is quite often a
tedious task, requiring extensive human intervention. We present a method to convert
unstructured experimental procedures written in English to structured synthetic steps
(action sequences) reflecting all the operations needed to successfully conduct the corresponding chemical reactions. To achieve this, we design a set of synthesis actions with
predefined properties and a deep-learning sequence to sequence model based on the
transformer architecture to convert experimental procedures to action sequences. The
model is pretrained on vast amounts of data generated automatically with a custom
rule-based natural language processing approach and refined on a smaller set of manually annotated samples. Predictions on our test set resulted in a perfect (100%) match
of the action sequence for 60.8% of sentences, a 90% match for 71.3% of sentences, and
a 75% match for 82.4% of sentences.
</p>
</div>
</div>
</div> | Alain C. Vaucher; Federico Zipoli; Joppe Geluykens; Vishnu H Nair; Philippe Schwaller; Teodoro Laino | Organic Synthesis and Reactions; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749fbee301c10e1c79b75/original/automated-extraction-of-chemical-synthesis-actions-from-experimental-procedures.pdf |
64dcc261dfabaf06ff5dd656 | 10.26434/chemrxiv-2023-rq8c6 | Diphosphine Ligand-Enabled Ni-Catalyzed Chelate-Assisted Inner-Selective Migratory Hydroarylation of Alkenes | The precise control of the regioselectivity in the transition metal-catalyzed migratory hydrofunctionalization of alkenes remains a big challenge. With a transient ketimine directing group, the nickel-catalyzed migratory β-selective hydroarylation and hydroalkenylation of alkenyl ketones has been realized with aryl boronic acids using alkyl halide as the mild hydride source for the first time. The key to this success is the use of a diphosphine ligand, which is capable of the generation of a Ni(II)-H species in the presence of alkyl bromide, and enabling the efficient migratory insertion of alkene into Ni(II)-H species and the sequent rapid chain walking process. The present approach diminishes organosilanes reductant, tolerates a wide array of complex functionalities with excellent regioselective control. Moreover, this catalytic system could also be applied to the migratory hydroarylation of alkenyl azahetereoarenes, thus providing a general approach for the preparation of 1,2-aryl heteroaryl motifs with wide potential applications in pharmaceutical discovery. | Hua-Dong He; Ravi Chitrakar; Zhi-Wei Cao; Dao-Ming Wang; Peng-Gang Zhao; Yichen Wu; Yuan-Qing Xu; Zhong-Yan Cao; Peng Wang | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dcc261dfabaf06ff5dd656/original/diphosphine-ligand-enabled-ni-catalyzed-chelate-assisted-inner-selective-migratory-hydroarylation-of-alkenes.pdf |
6609c60066c13817295d64f5 | 10.26434/chemrxiv-2024-x7jwz | Core Binding Energy Calculations: A Scalable
Approach with Quantum Embedding based
EOM-CC Method | We investigate the use of density matrix embedding theory to facilitate the computation of core ionization energies (IP) of large molecules at the equation of motion
coupled-cluster singles doubles with perturbative triples (EOM-CCSD*) level in combination with the core-valence separation (CVS) approximation. The unembedded
IP-CVS-EOM-CCSD* method with a triple-ζ basis set produces ionization energies
within < 1 eV of experiment with a standard deviation of about 0.2 eV for the core65
dataset. The embedded variant contributes very little systematic error relative to the
unembedded method, with a mean unsigned error of 0.07 eV and a standard deviation
of about 0.1 eV, in exchange for accelerating the calculations by many orders of magnitude. By employing embedded EOM-CC methods, we computed the core-ionization
energies of uracil-hexamer, doped fullerene, and chlorophyll molecule, utilizing up to
∼4000 basis functions within < 1 eV from experimental values. Such calculations are
not currently possible with unembedded EOM-CC method. | Bhavnesh Jangid; Matthew R. Hermes; Laura Gagliardi | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6609c60066c13817295d64f5/original/core-binding-energy-calculations-a-scalable-approach-with-quantum-embedding-based-eom-cc-method.pdf |
6532eea8c3693ca993c20205 | 10.26434/chemrxiv-2023-ssnjl-v3 | Role of cationic organisation on water dynamics in saponite clays | Water dynamics impacts many phenomena from geosciences to biology, especiallly in confined environments. In the presence of charged interfaces, there are some ions the role of which with regards to the water dynamics is unclear. Here a synthetic saponite clay, which is oriented in a film, is used as confining medium in the bilayer state. It confines two water layers between negatively charged planes, the charge of which is compensated by sodium cations. Water dynamics is determined both parallel and perpendicular to the charged clay layers with Neutron Spin Echo (NSE). This technique gives access to long enough times and directly provides the intermediate scattering function that is calculated on the other hand by Molecular Dynamics (MD) simulations. These latter also enable the study of cations dynamics, not experimentally accessible on this time scale. The results point towards a huge role of these cations on the water dynamics, mainly through their local structure and localization between the charged confining planes. | Virginie Marry; Sébastien Le Crom; Eric Ferrage; Laurent Michot; Bela Farago; Alfred Delville; Emmanuelle DUBOIS | Physical Chemistry; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6532eea8c3693ca993c20205/original/role-of-cationic-organisation-on-water-dynamics-in-saponite-clays.pdf |
67d9961e6dde43c9084a2eeb | 10.26434/chemrxiv-2025-7mjjt | Birch-bark suberin-reconstructed polyester film as packaging materials | Fossil-based polymers dominate the packaging industry thanks to their performance and low cost. However, their negative impact on our biosphere demands a paradigm shift in the industry. Nature may provide an alternative in the form of suberin. Suberin is an amorphous polyester present in plants where it contributes to controlling the water and gas exchange with the environment. The bark is rich in suberin and it represents a large by-product of the forestry industry, hence, it is a potential source of renewable monomers for the synthesis of packaging materials. In this study, we demonstrated that un-refined suberin monomers, extracted from birch bark, could be exploited to synthesize a cross-linked polyester film through a standard melt-polycondensation and compression molding process. The polyester film resulted in being translucent while blocking UV radiation, and to have an elastomer-like behavior. The measured water vapor transmission rate was comparable to other polyesters, such as polylactide and polycaprolactone. Finally, the thermal gravimetric analysis showed the lack of any unreacted suberin monomers, suggesting food packaging as a potential application, where migration of monomers must be prevented. | Raffaele Perrotta; Isabella Kwan; Veerababu Polisetti; Monica Ek; Anna J. Svagan; Mikael S. Hedenqvist | Materials Science; Polymer Science; Thin Films; Polymerization (Polymers); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d9961e6dde43c9084a2eeb/original/birch-bark-suberin-reconstructed-polyester-film-as-packaging-materials.pdf |
60c7414b469df45591f42dea | 10.26434/chemrxiv.8015027.v1 | Iron Detection and Remediation with a Functionalized Porous Polymer Applied to Environmental Water Samples | <div>
<p>Iron is one of the most abundant
elements in the environment and in the human body. As an essential nutrient,
iron homeostasis is tightly regulated, and iron dysregulation is implicated in
numerous pathologies, including neuro-degenerative diseases, atherosclerosis,
and diabetes. Endogenous iron pool concentrations are directly linked to iron
ion uptake from environmental sources such as drinking water, providing
motivation for developing new technologies for assessing iron(II) and iron(III)
levels in water. However, conventional methods for measuring aqueous iron pools
remain laborious and costly and often require sophisticated equipment and/or
additional processing steps to remove the iron ions from the original
environmental source. We now report a simplified and accurate chemical platform
for capturing and quantifying the iron present in aqueous samples through use
of a post-synthetically modified porous aromatic framework (PAF). The
ether/thioether-functionalized network polymer, PAF-1-ET, exhibits high
selectivity for the uptake of iron(II) and iron(III) over other physiologically
and environmentally relevant metal ions. Mössbauer spectroscopy, XANES, and
EXAFS measurements provide evidence to support iron(III) coordination to
oxygen-based ligands within the material. The polymer is further successfully
employed to adsorb and remove iron ions from groundwater, including field
sources in West Bengal, India. Combined with an 8-hydroxyquinoline colorimetric
indicator, PAF-1-ET enables the simple and direct determination of the iron(II)
and iron(III) ion concentrations in these samples, providing a starting point
for the design and use of molecularly-functionalized porous materials for
potential dual detection and remediation applications.</p></div> | Sumin Lee; Adam Uliana; Mercedes Taylor; Khetpakorn Chakarawet; Siva Bandaru; Sheraz Gul; Jun Xu; Cheri Ackerman; Ruchira Chatterjee; Hiroyasu Furukawa; Jeffrey A. Reimer; Junko Yano; Ashok Gadgil; Gary Long; Fernande Grandjean; Jeffrey R. Long; Christopher Chang | Hydrology and Water Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7414b469df45591f42dea/original/iron-detection-and-remediation-with-a-functionalized-porous-polymer-applied-to-environmental-water-samples.pdf |
67351d6d5a82cea2fa0945cf | 10.26434/chemrxiv-2024-5p9fn | Polariton Spectra under the Collective Coupling Regime. II. 2D Non-linear Spectra | In our previous work [Ref.~\citenum{MondalJCP2024paper1}], we developed several efficient strategies to simulate exciton-polariton dynamics described by the Holestein-Tavis-Cummings (HTC) Hamiltonian under the collective coupling regime. Here, we incorporated these strategies into the previously developed $\mathcal{L}$-PLDM approach for simulating 2D Electronic Spectroscopy (2DES) spectra of exciton-polariton under the collective coupling regime. In particular, we apply the efficient quantum dynamics propagation scheme developed in Paper I to both the forward and the backward propagations in the PLDM, and develop an efficient important sampling scheme and GPU vectorization scheme that allow us to reduce the computational costs from $\mathcal{O}(\mathcal{K}^2)\mathcal{O}(T^3)$ to $\mathcal{O}(\mathcal{K}) \mathcal{O}(T^0)$ for the 2DES spectra simulation, where $\mathcal{K}$ is the number of states and $T$ is the number of time steps of propagation. We further simulated the 2DES spectra for an HTC Hamiltonian under the collective coupling regime and analyzed the signal from both rephasing and non-rephasing contributions of the ground state bleaching (GSB), excited state emission (ESA), and stimulated emission (SE) pathways. | M. Elious Mondal; A. 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 | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67351d6d5a82cea2fa0945cf/original/polariton-spectra-under-the-collective-coupling-regime-ii-2d-non-linear-spectra.pdf |
65d8804d66c138172953df14 | 10.26434/chemrxiv-2024-n4zhb | Development of analytic gradients for the Huzinaga quantum embedding method and its applications to large-scale hybrid and double hybrid DFT forces | The theory of analytic gradients is presented for the projector-based density functional theory (DFT) embedding approach utilizing the Huzinaga-equation. The advantages of the Huzinaga-equation-based formulation are demonstrated. In particular, it is shown that the projector employed does not appear in the Lagrangian, and the potential risk of numerical problems is avoided at the evaluation of the gradients. The efficient implementation of the analytic gradient theory is presented for the approaches where hybrid DFT, second-order Moller-Plesset perturbation theory (MP2), or double hybrid DFT is embedded in lower-level DFT environments. To demonstrate the applicability of the method and to gain insight into its accuracy, it is applied to equilibrium geometry optimizations, transition state searches, and potential energy surface scans. Our results show that bond lengths and angles converge rapidly with the size of the embedded system. While providing structural parameters close to high-level quality for the embedded atoms, the embedding approach has the potential to relax the coordinates of the environment as well. Our demonstrations on a 171-atom zeolite and a 570-atom protein system show that the Huzinaga-equation-based embedding can accelerate (double) hybrid gradient computations by an order of magnitude with sufficient active regions and enables affordable force evaluations or geometry optimizations for molecules of hundreds of atoms. | Jozsef Csoka; Bence Hegely; Peter Nagy; Mihaly Kallay | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d8804d66c138172953df14/original/development-of-analytic-gradients-for-the-huzinaga-quantum-embedding-method-and-its-applications-to-large-scale-hybrid-and-double-hybrid-dft-forces.pdf |
626d7aa7bdc9c250f2e8f229 | 10.26434/chemrxiv-2022-0mk48 | Lewis Acid Mediated Coupling of Silyloxyallylsilanes and Ortholactones: A Convergent, Fragment-Coupling Approach to Functionalized Spiroketals | A convergent, fragment-based coupling approach to the formation of spiroketals has been developed. This approach combines the spiroketal forming step with a fragment coupling utilizing ortholactones as double electrophiles with silyloxyallylsilanes. We also discoved a rapid and regioselective isomerization of the exo-cyclic sprioketals to their endo-cyclic forms. | Kate Marshall; Matthew Cook | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626d7aa7bdc9c250f2e8f229/original/lewis-acid-mediated-coupling-of-silyloxyallylsilanes-and-ortholactones-a-convergent-fragment-coupling-approach-to-functionalized-spiroketals.pdf |
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