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657a291c7acf130c322941d6 | 10.26434/chemrxiv-2023-dwlf1-v2 | Tuning Potential Functions to Host–Guest Binding Data | Software to more rapidly and accurately predict protein--ligand binding affinities is of high interest for early-stage drug discovery, and physics-based methods are among the most widely used technologies for this purpose. The accuracy of these methods depends critically on the accuracy of the potential functions they use. Potential functions are typically trained against a combination of quantum chemical and experimental data. However, although binding affinities are among the most important quantities to predict, experimental binding affinities have not to date been integrated into the experimental dataset used to train potential functions. In recent years, the use of host--guest complexes as simple and tractable models of binding thermodynamics has gained popularity due to their small size and simplicity, relative to protein--ligand systems. Host--guest complexes can also avoid ambiguities that arise in protein--ligand systems, such as uncertain protonation states. Thus, experimental host--guest binding data are an appealing additional data type to integrate into the experimental dataset used to optimize potential functions. Here, we report the extension of the Open Force Field Evaluator framework to enable the systematic calculation of host--guest binding free energies and their gradients with respect to force field parameters, coupled with the curation of 126 host--guest complexes with available experimental binding free energies. As an initial application of this novel infrastructure, we optimized generalized Born (GB) cavity radii for the OBC2 GB implicit solvent model against experimental data for 36 host--guest systems. This refitting led to a dramatic improvement in accuracy for both the training set and a separate test set with 90 additional host--guest systems. The optimized radii also showed encouraging transferability from host--guest systems to 59 protein-ligand systems. However, the new radii are significantly smaller than the baseline radii and lead to excessively favorable hydration free energies (HFE). Thus, users of the OBC2 GB model currently may choose between GB cavity radii that yield more accurate binding affinities or GB cavity radii that yield more accurate HFEs. We suspect that achieving good accuracy on both will require more far-reaching adjustments to the GB model. We note that binding free energy calculations using the OBC2 model in OpenMM gain about a 10x speedup relative to corresponding explicit solvent calculations, suggesting a future role for implicit solvent absolute binding free energy (ABFE) calculations in virtual compound screening. This study proves the principle of using host--guest systems to train potential functions that are transferrable to protein--ligand systems, and provides an infrastructure that enables a range of applications. | Jeffry Setiadi; Simon Boothroyd; David Slochower; David Dotson; Matthew Thompson; Jeffrey Wagner; Lee-Ping Wang; Michael K. Gilson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657a291c7acf130c322941d6/original/tuning-potential-functions-to-host-guest-binding-data.pdf |
62f2999542ddf53111b52651 | 10.26434/chemrxiv-2022-ddfzp | Directed Evolution of a Fe(II)- and α-Ketoglutarate-Dependent Dioxygenase for Site-Selective Azidation of Unactivated Aliphatic C-H Bonds | Fe(II)- and α-ketoglutarate-dependent halogenases and oxygenases can catalyze site-selective functionalization of C-H bonds via a variety of C-X bond forming reactions. Achieving high chemoselectivity for functionalization using non-native functional groups remains rare, however, particularly for non-native substrates. The current study shows that directed evolution can be used to engineer variants of an engineered dioxygenase, SadX, that address this challenge. Site-selective azidation of succinylated amino acids and a succinylated amine was achieved using variants with improved azidation yield and selectivity on a probe substrate as a result of mutations throughout the SadX structure. The installed azide group was reduced to a primary amine, and the succinyl group required for azidation was enzymatically cleaved to provide the corresponding amine. These results provide a promising starting point for evolving additional SadX variants with activity on structurally distinct substrates and for enabling enzymatic C-H functionalization with other non-native functional groups. | Christian A. Gomez; Dibyendu Mondal; Qian Du; Natalie Chan; Jared C. Lewis | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f2999542ddf53111b52651/original/directed-evolution-of-a-fe-ii-and-ketoglutarate-dependent-dioxygenase-for-site-selective-azidation-of-unactivated-aliphatic-c-h-bonds.pdf |
66505b6d21291e5d1d263a13 | 10.26434/chemrxiv-2024-sr5dc | Ordered Transfer from 3D-oriented MOF Superstructures to Polymeric Films: Microfabrication, Enhanced Chemical Stability, and Anisotropic Fluorescent Patterns | Films and patterns of 3D-oriented metal-organic frameworks (MOFs) afford well-ordered pore structures extending across centimeter-scale areas. These macroscopic domains of aligned pores are pivotal to enhance diffusion along specific pathways and orient functional guests. The anisotropic properties emerging from this alignment are beneficial for applications in ion conductivity and photonics. However, the structure of 3D-oriented MOF films and patterns can rapidly degrade under humid and acidic conditions. Thus, more durable 3D-ordered porous systems are desired for practical applications. Here, oriented porous polymer films and patterns are prepared by using heteroepitaxially oriented N3-functionalized MOF films as precursor materials. The film fabrication protocol utilizes an azide–alkyne cycloaddition on the Cu2(AzBPDC)2DABCO MOF. The micropatterning protocol exploits the X-ray sensitivity of azide groups in Cu2(AzBPDC)2DABCO, enabling selective degradation in the irradiated areas. The masked regions of the MOF film retain their N3-functionality, allowing for subsequent cross-linking through azide-alkyne coupling. Subsequent acidic treatment removes the Cu ions from the MOF, yielding porous polymer micro-patterns. The polymer has high chemical stability and shows an anisotropic fluorescent response. The use of 3D-oriented MOF systems as precursors for the fabrication of oriented porous polymers will facilitate the progress of optical components for photonic applications. | Lea A. Brandner; Benedetta Marmiroli; Mercedes Linares-Moreau; Mariano Barella; Behnaz Abbasgholi-NA; Miriam de J. Velásquez-Hernández; Kate L. Flint; Simone Dal Zilio; Guillermo P. Acuna; Heimo Wolinski; Christian J. Doonan; Paolo Falcaro | Materials Science; Coating Materials; Optical Materials; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66505b6d21291e5d1d263a13/original/ordered-transfer-from-3d-oriented-mof-superstructures-to-polymeric-films-microfabrication-enhanced-chemical-stability-and-anisotropic-fluorescent-patterns.pdf |
648939c0be16ad5c57e5fc34 | 10.26434/chemrxiv-2023-v9nc6 | Osmotic Energy Conversion in Deep-Sea Hydrothermal Vents | Selective ion transport through nanochannels plays a crucial role in osmotic energy conversion in cellular systems. We show that this cell-essential process occurs in a submarine hydrothermal vent (HV) precipitate derived from a serpentine-hosted geological environment. Plate-like layered nanocrystals are aligned on the nano to millimeter scale, forming confined nanochannels in the HV precipitate. The nanochannels with surface charges function as a cation- and anion-selective ion transport membrane, allowing the precipitates to convert ionic gradients of Na+, K+, H+, and Cl- into electrical energy. Our findings suggest that osmotic energy conversion can occur spontaneously and widely through geological processes, offering valuable insights into the establishment of electrochemically coupled ion transport in early life as well as the creation of self-organized structures in engineering fields. | Hye-Eun Lee; Tomoyo Okumura; Hideshi Ooka; Kiyohiro Adachi; Takaaki Hikima; Kunio Hirata; Yoshiaki Kawano; Hiroaki Matsuura; Masaki Yamamoto; Masahiro Yamamoto; Akira Yamaguchi; Ji-Eun Lee; Ki Tae Nam; Yasuhiko Ohara; Daisuke Hashizume; Shawn McGlynn; Ryuhei Nakamura | Physical Chemistry; Materials Science; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648939c0be16ad5c57e5fc34/original/osmotic-energy-conversion-in-deep-sea-hydrothermal-vents.pdf |
60c74e79337d6c2794e27fa6 | 10.26434/chemrxiv.12751361.v1 | In Silico Docking Analysis Revealed the Potential of Phytochemicals Present in Phyllanthus Amarus and Andrographis Paniculata, Used in Ayurveda Medicine in Inhibiting SARS-CoV-2 | No therapeutics and vaccines
are available against SARS-CoV-2 at present. In the current study we have made an attempt to provide preliminary
evidences for interaction of 35 phytochemicals from two plants (<i>Phyllanthus amarus </i>and <i>Andrographis paniculata</i> used in Ayurveda<i>)</i> with SARS-CoV-2 proteins (S protein,
3CLpro, PLpro and RdRp) through <i>in silico</i>
docking analysis. The docking was performed with the aid of AutoDock Vina and ADME and other pharmacokinetic properties were predicted using SWISSADME and admetSAR | Shridhar Hiremath; Vinay Kumar H D; Nandan M; Mantesh M; Shankarappa K S; Venkataravanappa V; Jahir Basha C R; C N Lakshminarayana Reddy | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e79337d6c2794e27fa6/original/in-silico-docking-analysis-revealed-the-potential-of-phytochemicals-present-in-phyllanthus-amarus-and-andrographis-paniculata-used-in-ayurveda-medicine-in-inhibiting-sars-co-v-2.pdf |
668bda5fc9c6a5c07aa78742 | 10.26434/chemrxiv-2024-42f7k | “Fruity” Dye-based Fluorescent Nanoparticles (dFONs): A Fully Organic Counterpart of Alloy and Core-Shell Metallic Nanoparticles. Tuning Topology to Maximize Nano-interfacial Promoted Fluorescence Enhancement | Engineered nanomaterials are a blooming field of research among which luminescent nanoparticles are becoming major players for biological applications. While inorganic and hybrid organic-inorganic nanoparticles greatly dominate the field, research on all-organic nanoparticles is gaining momentum thanks to the versatility and tunability offered by advances in synthesis especially in polymer science but also by molecular engineering. Following this less travelled route, in the present work we demonstrate how to achieve ultra-bright dye-based Fluorescent Organic Nanoparticles (dFONs) mimicking metallic nanoparticles; i.e. core-shell and alloy type dFONs. Their design relies on the smart association of organic constituents that combine structural similarity, finely tuned electronic and photophysical properties for efficient Förster Resonance Energy Transfer if confined into close proximity. Strikingly, these nano-constructions show unique optical properties. First, both core-shell and alloy dFONs show highly efficient energy harvesting and giant absorption thanks to ultimate molecular confinement of a large number of strongly absorbing dyes. Second, we demonstrate for the first time that we can maximize the nano-interfacial emission enhancement (NIEE) effect by tuning the topology of core-shell type dFONs. Finally bioimaging experiments demonstrate that core-shell dFONs are internalized into COS7 cells and retain their specific emissive properties in these cells. | Eleonore Kurek; Morgane Rosendale; Jean-Baptiste Verlhac; Sébastien Marais; Jonathan Daniel; Mireille Blanchard-Desce | Physical Chemistry; Nanoscience; Plasmonic and Photonic Structures and Devices; Self-Assembly; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668bda5fc9c6a5c07aa78742/original/fruity-dye-based-fluorescent-nanoparticles-d-fo-ns-a-fully-organic-counterpart-of-alloy-and-core-shell-metallic-nanoparticles-tuning-topology-to-maximize-nano-interfacial-promoted-fluorescence-enhancement.pdf |
60c73f69567dfe2471ec39fb | 10.26434/chemrxiv.7379396.v1 | Catalytic Asymmetric Allylation of Aldehydes with Alkenes Mediated by Organophotoredox and Chiral Chromium Hybrid Catalysis | A hybrid system accomplishing cooperativity between an organophotoredox acridinium catalyst and a chiral chromium<br />complex catalyst was developed, enabling the unprecedented exploitation of unactivated hydrocarbon alkenes as precursors to chiral allylchromium nucleophiles for the asymmetric allylation of aldehydes. The reaction proceeded under visible light irradiation at room temperature and with high functional group tolerance, affording the corresponding homoallylic alcohols with up to >20/1 diastereomeric ratio and 99% ee. The addition of Mg(ClO4)2 elicited profound enhancement of both reactivity and enantioselectivity. | Harunobu Mitsunuma; Shun Tanabe; Hiromu Fuse; Kei Ohkubo; Motomu Kanai | Organic Synthesis and Reactions; Photochemistry (Org.); Stereochemistry; Organocatalysis; Photocatalysis; Redox Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f69567dfe2471ec39fb/original/catalytic-asymmetric-allylation-of-aldehydes-with-alkenes-mediated-by-organophotoredox-and-chiral-chromium-hybrid-catalysis.pdf |
63b6a2c41699ca1ce5e44f33 | 10.26434/chemrxiv-2022-0r6qr-v2 | Synergistic effects of marine pollutants and microplastics on the destabilization of lipid bilayers | The increasing production of plastic worldwide results in increasing amounts of plastic waste dumped into the oceans. Plastic waste is fragmenting into smaller pieces up to micro and nanoplastics, which may cross physiological barriers and affect the functions of living organisms. Microplastics can travel with rain and clouds; they are present in soil, snow-capped mountains, and even in the organs and blood of human beings. The potential health implications of microplastics in living organisms raise concerns and are intensively investigated. Recently, we reported the effect of mechanical stretching of microplastics on a lipid bilayer. By combining experimental and theoretical approaches, we have shown that microplastic particles adsorbed on lipid membranes increase membrane stress even at low particle concentrations. In this manuscript, we demonstrate the synergetic effect of marine pollutants on the mechanical interaction induced by microplastics. For this purpose, bare microplastics are incubated in seawater containing marine pollutants. We show that pollutants, such as chemical solvents, significantly increase the mechanical stretching induced by microplastics. In turn, microplastics can be viewed as vectors for solvent molecules, facilitating their penetration into the core of lipid membranes and thus strongly affecting their biophysical properties. | jean baptiste fleury; Vladimir A. Baulin | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b6a2c41699ca1ce5e44f33/original/synergistic-effects-of-marine-pollutants-and-microplastics-on-the-destabilization-of-lipid-bilayers.pdf |
64ea86343fdae147fae56906 | 10.26434/chemrxiv-2023-hvjxn | Electrochemical capture and conversion of CO2 into syngas | For waste CO2 to be electrolytically converted into higher-value chemicals and fuels, electrolyzers that drive the CO2 reduction reaction need to be integrated with upstream CO2 capture units. However, this has not yet been demonstrated because of the large operational gap for the capture and conversion steps. Here, we report a coupled carbon reactor that captures and converts CO2 into syngas with a 1.7:1 ratio of H2 to CO. The resulting syngas can be utilized in the production of a wide range of valuable chemicals. This CCR uses a packed bed absorption column (“capture unit”) to react alkaline aqueous solution enriched in K2CO3(aq) with CO2 to form bicarbonate enriched solutions (“reactive carbon solutions”). These reactive carbon solutions are then fed into an electrochemical reactor (“bicarbonate electrolyzer”) to form CO(g) and OH– product. This alkaline product is then passed through a gas-liquid separator (“separator”) and recycled back to the capture unit for further reaction with CO2(g). These collective elements close the full loop for CO2 capture and conversion. An electrochemically inert CO2 capture promoter (glycine) was used to better match the CO2 capture rates in the absorption column to the OH– production rates in the electrolyzer, thereby producing CO at steady-state without intervention. We demonstrate that the CCR captures and converts CO2 from simulated flue gas (20% CO2; 80% N2) into CO with a Faradaic efficiency of 30% at 100 mA cm–2 for 30 hours of operation. | Yongwook Kim; Eric W. Lees; Chaitanya Donde; Christopher E.B. Waizenegger; Grace L. Simpson; Akshi Valji; Curtis P. Berlinguette | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ea86343fdae147fae56906/original/electrochemical-capture-and-conversion-of-co2-into-syngas.pdf |
64a581d7ba3e99daef8fedc2 | 10.26434/chemrxiv-2023-4z4n0 | Methanol on the rocks: Green rust transformation promotes the oxidation of methane | Shared coordination geometries between metal ions within reactive minerals and enzymatic metal cofactors hints at mechanistic and possibly evolutionary homology between particular abiotic chemical mineralogies and biological metabolism. The octahedral coordination of reactive Fe2+/3+ minerals such as green rusts, endemic to anoxic sediments and the early Earth’s oceans, mirrors the di-iron reaction center of soluble methane monooxygenase (sMMO), responsible for methane oxidation in methanotrophy. We show that methane oxidation occurs in tandem with the oxidation of green rust to lepidocrocite and magnetite, mimicking radical mediated methane oxidation found in sMMO to yield not only methanol but also halogenated hydrocarbons in the presence of seawater. This naturally occurring geochemical pathway for CH4 oxidation elucidates a previously unidentified carbon cycling mechanism in modern and ancient environments and reveals clues into mineral-mediated reactions in the synthesis of organic compounds necessary for the emergence of life. | Orion Farr; Nil Gaudu; Gregoire Danger; Michael Russell; Daniel Ferry; Wolfgang Nitschke ; Simon Duval | Materials Science; Catalysis; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a581d7ba3e99daef8fedc2/original/methanol-on-the-rocks-green-rust-transformation-promotes-the-oxidation-of-methane.pdf |
60c73e14337d6c0442e262a0 | 10.26434/chemrxiv.6383213.v1 | The Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore | <a></a><a>Docking of a
protein-DNA complex onto a nanopore can provide ample observation time for a detailed
inspection of the complex, enabling collection of biophysical data for
detection, identification, and characterization of the biomolecules. While
docking of a protein-DNA complex onto a biological nanopore has enabled analytic
applications of nanopores including DNA sequencing, the application of the same
principle to solid-state nanopores is tempered by poor understanding of the
docking process. Here, we elucidate the behaviour of individual protein-DNA
complexes docked onto a solid-state nanopore by monitoring the nanopore ionic
current. </a><a>Repeat docking of monovalent streptavidin-DNA
complexes is found to produce ionic current blockades that fluctuate between
discrete levels within the same current blockade. </a>We elucidate the roles of the protein plug and
the DNA tether in the docking process, finding the docking configurations to
determine the multitude of the current blockade levels whereas the frequency of
the current level switching to be determined by the interactions between the molecules
and the solid-state membrane. Finally, we prove the feasibility of using the
nanopore docking principle for single molecule sensing using solid-state
nanopores by detecting conformational changes of a tethered DNA molecule from a
random coil to an i-motif states. | Xin Shi; Qiao Li; Rui Gao; Wei Si; Shao-Chuang Liu; Aleksei Aksimentiev; Yi-Tao Long | Analytical Chemistry - General; Biochemical Analysis; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e14337d6c0442e262a0/original/the-dynamics-of-a-molecular-plug-docked-onto-a-solid-state-nanopore.pdf |
60c75775337d6c6feae29025 | 10.26434/chemrxiv.14403302.v1 | Stereospecific, Ligand-Free Synthesis of All-Carbon Quaternary Stereocenters from Tertiary Benzylic Carboxylates | Nickel-catalyzed, stereospecific cross-couplings via activation of secondary C–O bonds has been well
developed in the past few years. Meanwhile, stereospecific
cross-couplings of tertiary electrophiles have been rarely explored. Herein, we describe a nickel-catalyzed, ligand-free Suzuki-Miyaura vinylation, using easily prepared, highly enantioenriched tertiary benzylic carboxylates to install all-carbon
quaternary stereocenters in high yields and ee’s. In addition to
allowing stereospecific vinylation of these substrates for the
first time, this method overcomes the longstanding requirement for a naphthyl group on the benzylic carboxylate<br /> | Jianyu Xu; Sarah Pound; Corey Basch; Alana Duke; Mary Watson | Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75775337d6c6feae29025/original/stereospecific-ligand-free-synthesis-of-all-carbon-quaternary-stereocenters-from-tertiary-benzylic-carboxylates.pdf |
60c753b09abda28896f8e012 | 10.26434/chemrxiv.13480374.v1 | Reaction of Bis(pinacolato)diboron with H-Si(100): The Pursuit of On-surface Hydrosilane Borylation Reactions | On-surface solution phase chemical reactions, which are inherently
amenable to scale-up, provide a pathway towards overcoming challenges
present in gas phase processes for ultradoping of Si, a process that
introduces unprecedented concentration of dopant. Ultradoping, which can
only be achieved with a direct chemical bond between dopant and Si,
fundamentally changes the electronic properties of Si, making it a
promising next-generation electronic material. Traditional processes for
solvent-based chemical functionalization attach species to the Si
surface through carbon or oxygen linkers, which limits activated dopant
density. This prevents solution phase chemistry from being useful for
applications involving ultradoped Si. Recent work has focused on forming
a direct on-surface Si-dopant bond to provide a scalable ultra-doping
pathway. In this work, we expand upon that goal by demonstrating that
well-known homogeneous chemistries can be usefully applied to surface
reactions for ultradoping Si. By adapting a hydrosilane borylation
reaction used to synthesize silyl boranes into a surface chemistry
reaction, we successfully incorporate 1.3e14 cm<sup>-2 </sup>B using
scalable on-surface solvent based chemistry. This density is high enough
to produce the overlap of dopant wavefunctions required for achieving
unprecedented conductivity in Si. Using computational studies, performed
with the assumption that catalyst interaction was negligible, we
predict the reaction straightforwardly occurs through a Si-B bond.
However, with extensive experimental characterization including infrared
spectroscopy, x-ray photoelectron spectroscopy, and secondary ion mass
spectroscopy we elucidate cross-reactivity between the substrate, B<sub>2</sub>Pin<sub>2</sub> and catalyst. The reaction complexity indicates that radical initiating catalysts are not benign in surface chemistry systems. | Esther Frederick; Igor Kolesnichenko; Quinn Campbell; Luis Fabián Peña; Angelica Benavidez; Evan Anderson; David Wheeler; Shashank Misra | Nanodevices; Computational Chemistry and Modeling; Interfaces; Self-Assembly; Solution Chemistry; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753b09abda28896f8e012/original/reaction-of-bis-pinacolato-diboron-with-h-si-100-the-pursuit-of-on-surface-hydrosilane-borylation-reactions.pdf |
61a3635bdff1ccd2f6354fb9 | 10.26434/chemrxiv-2021-48dn4 | Organoarsenic probes to study proteins by NMR spectroscopy | Arsenical probes enable structural studies of proteins. We report the first organoarsenic probes for nuclear magnetic resonance (NMR) spectroscopy to study proteins in solutions. These probes can be attached to irregular loop regions. A lanthanide-binding tag induces sizable pseudocontact shifts in protein NMR spectra of a magnitude never observed for small paramagnetic probes before. | Mithun Mahawaththa; Henry Orton; Ibidolapo Adekoya; Thomas Huber; Gottfried Otting; Christoph Nitsche | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a3635bdff1ccd2f6354fb9/original/organoarsenic-probes-to-study-proteins-by-nmr-spectroscopy.pdf |
61202150e65e2dfb741cbcb1 | 10.26434/chemrxiv-2021-889ms | Direct and Catalytic C-Glycosylation of Arenes: Expeditious Synthesis of the Remdesivir Nucleoside | Since early 2020, scientists have strived to find an effective solution to fight SARS-CoV-2, especially by developing reliable vaccines that inhibit the spread of the disease and repurposing drugs for combatting its effects on the human body. The antiviral prodrug remdesivir is still the most widely used therapeutic during the early stage of the infection. However, the current synthetic routes rely on the use of protecting groups, air-sensitive reagents, and cryogenic conditions, impeding the cost-efficient supply to patients. We therefore focused on the development of a straightforward, direct addition of (hetero)arenes to unprotected sugars. Here we report a silylium-catalyzed and completely stereoselective C-glycosidation that initially yields the open-chain polyols, which can be selectively cyclized to provide either the kinetic alpha-furanose or the thermodynamically favored beta-anomer. The method significantly expedites the synthesis of remdesivir precursor GS-441524 after subsequent Mn-catalyzed C–H oxidation and deoxycyanation. | Carla Obradors; Benjamin Mitschke; Miles H. Aukland; Markus Leutzsch; Oleg Grossmann; Sebastian Brunen; Sebastian A. Schwengers; Benjamin List | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61202150e65e2dfb741cbcb1/original/direct-and-catalytic-c-glycosylation-of-arenes-expeditious-synthesis-of-the-remdesivir-nucleoside.pdf |
63e71696fcfb27a31f91283f | 10.26434/chemrxiv-2023-m1pwh | Pressure/thermo-induced hypsochromic-shifted and enhanced luminescence based on carbazole emitter | Most organic mechanochromic luminogens show bathochromic-shifted and quenched emission with increasing pressure. Design of turn-on mechanochromic material with hypsochromic-shifted luminescence is still a challenge. Herein, a novel emitter (namely DCzPy) was prepared through lab-synthesized carbazole to study its stimuli-responsive luminescence. The crystalline powders of DCzPy emitted blue-green fluorescence at 490 nm. Upon gently grinding, the fluorescence intensity of DCzPy was dramatically enhanced with a hypsochromic-shift by 33 nm. Further heavily grinding, its emission wavelength returned to 490 nm. Powder X-ray diffraction patterns indicated that such behaviors were attributed to the solid-state morphology transition from crystal-to-crystal. Interestingly, a large bathochromic-shifted and weakened fluorescence was achieved under isotropic compression. Moreover, thermo-responsive behavior of DCzPy was studied in the film to find that its emission turned from green to blue as temperature elevated. Given the thermo-induced fluorescence switching of DCzPy, a 2D code was fabricated for information anti-counterfeiting. | Jun-Cheng Yang; Zhiyuan Fu; Huili Ma; Tao Wang; Qiuying Li; Kai Wang; Lin Wu; Pu Chen; Hai-Tao Feng; Ben Zhong Tang | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e71696fcfb27a31f91283f/original/pressure-thermo-induced-hypsochromic-shifted-and-enhanced-luminescence-based-on-carbazole-emitter.pdf |
62a9ba2ae00d4e12cd2b576b | 10.26434/chemrxiv-2022-hlkgf | Stereoselective three-step one-pot cascade combining amino- and biocatalysis to access chiral γ-nitro alcohols | The combination of small molecule catalysis and enzyme catalysis represents an underexploited area of research with huge potential in asymmetric synthetic chemistry due to both compatibility in reaction conditions and complementary reactivity. In this manuscript, we describe the telescopic synthesis of chiral nitro alcohols starting from commercially available benzaldehyde derivatives via the one-pot three-step chemoenzymatic cascade combination of a Wittig reaction, chiral thiourea-catalysed asymmetric conjugate addition, and a ketoreductase-mediated reduction to access the corresponding target compounds in moderate to excellent overall isolated yields (36-80%) and high diastereomeric and enantiomeric ratios (up to >97:3). This represents the first example of the combination of an organocatalysed asymmetric conjugate addition via iminium ion activation and a bioreduction step catalysed by ketoreductases. | Christian Ascaso-Alegre; Raquel P. Herrera; Juan Mangas-Sanchez | Organic Chemistry; Catalysis; Biocatalysis; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a9ba2ae00d4e12cd2b576b/original/stereoselective-three-step-one-pot-cascade-combining-amino-and-biocatalysis-to-access-chiral-nitro-alcohols.pdf |
60c75169702a9b200018bf3a | 10.26434/chemrxiv.13120139.v2 | Correlating Experiment and Theory for Electron Paramagnetic Resonance and Substrate Binding in a Lytic Polysaccharide Monooxygenase | <div>Lytic polysaccharide monooxygenases (LPMOs) are enzymes that binds polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between LPMO and polysaccharide is key to the mechanism and recent investigations have established structure-function relationships for this binding, employing hyperfine coupling constants (HFCs) from EPR spectroscopy. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have been supported with parameters cal-</div><div>culated with density functional theory. Yet, calculated HFCs are extremely sensitive</div><div>to the employed computational setup. Using the LPMO Ls(AA9)A, we here quantify</div><div>the importance of several choices in the computational setup, ranging from the use</div><div>of specialized basis, the underlying structures, and the employed exchange–correlation</div><div>functional. We compare our results to both X-ray structures and experiment (EPR spectra) for Ls(AA9)A as well as to recent experimental/theoretical results for another</div><div>(AA10) family of LPMOs.</div> | Yusuf A. Theibich; Stephan P. A. Sauer; Erik Hedegård; Leila Lo Leggio | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75169702a9b200018bf3a/original/correlating-experiment-and-theory-for-electron-paramagnetic-resonance-and-substrate-binding-in-a-lytic-polysaccharide-monooxygenase.pdf |
64de089401042bc1cc32d988 | 10.26434/chemrxiv-2023-8nlsb | Dual-Locked Macrocyclic “Turn-On” Drug for Selective and Traceless Release in Cancer Cells | Drug safety and efficacy due to premature drug release in the bloodstream and poor biodistribution remain challenging issues despite seminal advances in the field. To circumvent these limitations, we report a directed-macrocylization as a dual lock for camptothecin (CPT), a small molecule anticancer drug. In this way, the activity is “locked” within the cyclic structure by the redox responsive disulfide and pH-responsive boronic acid-salicylhydroxamate and turned on only in the presence of acidic pH and glutathione through traceless release. Notably the dual-responsive CPT is more active (100-fold) compared to the non-cleavable (closed) analogue. We further include bioorthogonal handle in the cyclic backbone for subsequent functionalization to generate cell-targeting peptide-macrocyclic and protein-macrocyclic CPTs for targeted, traceless drug release in triple negative metastatic breast cancer cells to inhibit cell growth in the low nanomolar concentration. | Dominik Schauenburg; Léa N. C. Rochet; Bingjie Gao; Darijan Schüler; Jaime A.S. Coelho; David Y.W. Ng; Vijay Chudasama; Seah Ling Kuan; Tanja Weil | Biological and Medicinal Chemistry; Organic Chemistry; Nanoscience; Organic Synthesis and Reactions; Biochemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64de089401042bc1cc32d988/original/dual-locked-macrocyclic-turn-on-drug-for-selective-and-traceless-release-in-cancer-cells.pdf |
63078eb7f9e99c49ec8995af | 10.26434/chemrxiv-2022-hpktf | Modular TEMPO Dimerization for Water-in-Catholyte Flow Batteries with Extreme Energy Density, Power, and Stability | Aqueous organic redox flow batteries (AORFBs) hold great promise for safe, sustainable, and cost-effective grid energy storage. However, developing catholyte redox molecules with desired energy density, power, and stability simultaneously has long been a critical challenge for AORFBs. Here, we report a novel class of ionic liquid mimicking TEMPO dimers (i-TEMPODs) that can be produced by our newly developed building block assembly synthetic platform. By systematically investigating 21 derivatives, we reveal i-TEMPODs have optimized size and charge that is compatible with highly conductive membrane and can form a “water-in-catholyte” (WiC) state. The tight coordination dynamics with water molecules deliver extreme solubility with promoted electrochemical stability at highly positive potentials. Leveraging these advances, we identify a champion molecule and demonstrate record overall AORFB performance in energy density (47.3 Wh/L), power density (0.325 W/cm2), and stability (no apparent capacity decay after 96 days) with low-cost and scalable chemistry. | Xiuliang Lv; Patrick Sullivan; Wenjie Li; Hui-Chun Fu; Ryan Jacobs; Chih-Jung Chen; Dane Morgan; Song Jin; Dawei Feng | Organic Chemistry; Energy; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63078eb7f9e99c49ec8995af/original/modular-tempo-dimerization-for-water-in-catholyte-flow-batteries-with-extreme-energy-density-power-and-stability.pdf |
620e57f14e899e3dc451327b | 10.26434/chemrxiv-2022-q2txr | Organolithium Gels – Simple Easily Divided Delivery Vehicles for Highly Reactive Species | Organolithium reagents are a vital tool in modern organic chemistry allowing the synthesis of new carbon-carbon bonds. However, due to the high reactivity of organolithiums, the use of low temperatures, inert atmospheres and strictly dried solvents are usually necessary. Here, we report a new encapsulating method for the stabilisation of the sensitive organolithium reagents, PhLi and BuLi (n-BuLi), within a low-cost hexatriacontane (C36H74) organogel. The use of this technology is showcased in nucleophilic addition reactions under ambient conditions, low-temperature bromine-lithium exchange and CH functionalisation reactions. The gel significantly enhances the stability of these organolithiums, allows simple handling, delivery and storage, and enables reproducible reagent portioning. The use of gels as easily divided delivery vehicles for hazardous organometallic reagents has the potential to revolutionise this area of synthetic chemistry, making these powerful reactions safer and more accessible to non-specialist researchers, enabling the more widespread use of these common synthetic methods. | Petr Slavik; Peter O'Brien; David Smith | Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e57f14e899e3dc451327b/original/organolithium-gels-simple-easily-divided-delivery-vehicles-for-highly-reactive-species.pdf |
6631a30691aefa6ce1d99a89 | 10.26434/chemrxiv-2024-48m91-v2 | Assessment of Anharmonicities in Clusters: Developing and Validating a Minimum-Information Partition Function | Precise thermodynamic calculations are essential for understanding the dynamics of cluster systems and new particle formation. However, the widely employed harmonic statistical mechanical approach often falls short in terms of accuracy. In this study, we present an improved statistical model that incorporates vibrational anharmonicity via a novel partition function that requires only one additional system-specific input parameter. In addition to considering vibrational aspects, we also account for anharmonicity related to the configurational space. The role of anharmonicities is thoroughly examined in the case of general clusters, where the complete sets of conformers, mechanically stable spatial arrangements, are known up to clusters composed of 14 monomers. By performing consistent Monte Carlo simulations on these systems, we benchmark the statistical model's efficacy in reproducing key thermodynamic properties (formation free energy and potential energy) in the classical limit. The model exhibits exceptional alignment with simulations, accurately reproducing free energies within a precision of 2kT and reliably capturing cluster melting temperatures. Furthermore, we demonstrate the significance and applicability of the model by reproducing thermodynamic barriers in homogeneous gas-phase nucleation of larger clusters. The transferability of our developed approach extends to more complex molecular systems and bears relevance for atmospheric multicomponent clusters, in particular. | Roope Halonen | Theoretical and Computational Chemistry; Physical Chemistry; Clusters; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6631a30691aefa6ce1d99a89/original/assessment-of-anharmonicities-in-clusters-developing-and-validating-a-minimum-information-partition-function.pdf |
668e5df1c9c6a5c07add1315 | 10.26434/chemrxiv-2024-b3sm2 | Programmable Merged-Net Porphyrinic Metal-Organic Frameworks for Water sorption | Porous materials have attracted considerable interest as water sorbents due to their potential in a broad range of water sorption-related applications. Metal-organic frameworks (MOFs) are particularly notable for their high porosity and tunability. However, their limited hydrolytic stability often results in pore collapse, which significantly hinders their water sorption performance. To address this issue, an innovative design strategy based on reticular chemistry is essential to enhance structural stability and ensuring efficient water sorption. Herein, we introduce a novel synthetic approach for constructing a merged-net MOF structure using metallolinkers. Specifically, we employed a porphyrin linker to successfully synthesize a porphyrin-based merged-net MOF, UPF-5. This MOF demonstrates significantly enhanced hydrolytic stability and improved water sorption performance while maintaining high pore volume. Additionally, the structure of UPF-5 allows for the modification of accessible Zr6 nodes, enabling control over the pore environments and fine-tuning the water sorption properties. This programmable synthetic strategy for porphyrin-based merged-net MOFs not only significantly enhances the structural stability for practical applications, including water sorption, but also advances reticular chemistry by discovering unprecedented topologies in MOF chemistry. | Junghye Lee; Dajin Park; Eunji Jin; Soochan Lee; Jinhyu Lee; Hyunchul Oh; Wonyoung Choe | Materials Science; Inorganic Chemistry; Nanostructured Materials - Materials; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668e5df1c9c6a5c07add1315/original/programmable-merged-net-porphyrinic-metal-organic-frameworks-for-water-sorption.pdf |
6196d2e6b039f27e4eaa4bcb | 10.26434/chemrxiv-2021-0l1jl | Conversion of Electrochemically Deposited Aragonite Crystallites to Perovskite through In Situ Ion Exchange | The unique and broadly applicable optoelectronic properties of metal-halide perovskite materials are determined by structural dimensionality. Conversion of scaffold supported carbonate salts to perovskite with microstructure retention has previously been shown to act as a gateway to unique morphologies. In the present work, calcium carbonate microstructures are electrochemically deposited on a transparent conducting oxide substrate. Through a series of ion-exchange reactions the microstructures are decorated with a layer of surface localized perovskite nanocrystals, indicating that this ion exchange process occurs at the microstructure surface. Throughout the conversion process, electron microscopy confirms that the microstructures retain their overall morphology while cubic perovskite nanocrystals exhibiting characteristic photoluminescence and photoblinking are formed at the interface. This work confirms a synthetic pathway in which perovskites can be made in shapes previously inaccessible, which may lead to enhanced optoelectronic properties. | William Leal; Caroline Bergeron; Tyler Rutherford; Marek Majewski | Inorganic Chemistry; Minerals | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6196d2e6b039f27e4eaa4bcb/original/conversion-of-electrochemically-deposited-aragonite-crystallites-to-perovskite-through-in-situ-ion-exchange.pdf |
6747ae0e5a82cea2fa2e918d | 10.26434/chemrxiv-2024-czb89 | Multilamellar Hyaluronic Acid-B-Poly(Lactic Acid) Polymersomes For Pathology-Responsive MRI Enhancement | This study introduces a biocompatible, stimuli-responsive imaging and therapeutic delivery system using ultrasmall iron oxide nanoparticles (USPIONs) encapsulated within hyaluronic acid-b-poly(lactic acid) (HA-PLA) polymersome membrane and a model protein bovine serum albumin in the core. These multilamellar vesicles exhibit enhanced T2-weighted MRI contrast, achieving a relaxivity 3-fold higher than existing agents. The polymersomes demonstrate acid- and enzyme-triggered degradation, enabling controlled release and measurable contrast changes in pathological environments. Preliminary in vivo and postmortem studies confirm their strong imaging performance, high biocompatibility, and targeted response to enzymatic, acidic microenvironments, paving the way for theranostic applications in disease diagnosis and treatment monitoring. | Dorian Foster; Naisha Shah; Alaura Cakley; Ronald Beyers; Jessica Larsen | Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6747ae0e5a82cea2fa2e918d/original/multilamellar-hyaluronic-acid-b-poly-lactic-acid-polymersomes-for-pathology-responsive-mri-enhancement.pdf |
6720727183f22e421480e9d0 | 10.26434/chemrxiv-2024-1xlvq-v2 | Influence of hole transport and thermal reactions in photo-driven water oxidation kinetics on crystalline TiO2 | The requirement that photogenerated holes accumulate to drive the rate limiting step is thought to cause slow water oxidation by TiO2 to form O2, however detailed kinetics studies that directly establish the connection between photoabsorption and surface reactions have not been reported. In this work, we use physically realistic kinetics models of photo-driven water oxidation on TiO2 to evaluate how hole generation, bulk diffusion, surface mobility and reaction are coupled. The calculations show that hole formation and diffusion in the bulk crystal dominate O2 formation at low light intensity, resulting in an apparent high order dependence of the O2 production rate on holes. As light intensity increases, the water splitting reaction becomes nearly independent of hole concentrations because of a buildup of intermediates that can only react thermally. Although it is believed that high hole mobility is a requirement for hole accumulation, a comparison of predicted to observed surface species indicates that immobilized holes dominate surface reactivity. The primary surface reaction sites are predicted to involve oxygen atoms that bridge two Ti atoms, supplied with OH formed by water dissociation on Ti sites. Because of the similarity among photocatalytic water oxidation mechanisms on diverse metal oxide semiconductors, which have generally low hole mobilities, the findings from this work may be relevant to them as well. If so, manipulations of hole mobility and accelerating the rate of thermal steps may provide a general pathway for improving water oxidation efficiency. | Pan Wang; Gabriel Benitez; Frances Houle | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Photocatalysis; Chemical Kinetics | CC BY 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720727183f22e421480e9d0/original/influence-of-hole-transport-and-thermal-reactions-in-photo-driven-water-oxidation-kinetics-on-crystalline-ti-o2.pdf |
636426afac45c77f8ca44b07 | 10.26434/chemrxiv-2022-4ml8d | Tuning Ether Motifs in Polymer Membranes for
CO2 Separation | Polymer membranes are an attractive, energy efficient alternative to traditional unit operations for gas separation. Polyethers have been leading membrane materials for CO2 separation due to their unique ether oxygen moiety that exhibits affinity towards CO2. We systematically study the effect of an ether-oxygen moiety on solubility using perturbed-chain statistical associating fluid theory equation of state calculations and on diffusivity using molecular dynamics simulations for CO2 separation. We investigate five different polymer materials with varying oxygen content, including commonly used polymers such as poly(ethylene oxide) as well as polymers with higher ether-oxygen content. Our results show that increasing the ether-oxygen moiety in the polymer membrane significantly increases the CO2/N2 solubility selectivity. Of the studied materials, polyoxymethylene has the highest oxygen to carbon ratio, and it has the highest CO2/N2 solubility selectivity. Molecular dynamics simulations indicates CO2/N2 diffusivity selectivity increases with increasing ether-oxygen content in the polymer, although the individual gas diffusion slows down. Moreover, we find that increasing the temperature increases the gas diffusion; however, the polymers lose their selective interactions with CO2, thus resulting in lower selectivity. We demonstrate that the ether-oxygen is a key functional group controlling the CO2/N2 solubility selectivity of polymer membranes. | Yasemin Basdogan; Zhen-Gang Wang | Theoretical and Computational Chemistry; Polymer Science; Chemical Engineering and Industrial Chemistry; Organic Polymers; Computational Chemistry and Modeling; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636426afac45c77f8ca44b07/original/tuning-ether-motifs-in-polymer-membranes-for-co2-separation.pdf |
62c74ec8332f0222b0dfb729 | 10.26434/chemrxiv-2022-k4dkg | Prototyping styles accelerate hardware development | Hardware-based startups risk having longer times-to-market, deterring investment in critical fields such as cleantech, medical devices, and automation. We interviewed 55 leaders at hardware startups, mapped their development timelines, and found prototyping to be the longest development step (median of 19 weeks per prototype) regardless of prototype complexity or iteration. Qualitative interview analysis reveals the prototyping team’s choice of development style is a major factor affecting timeline. We define two development styles: natural and structured, typified by free-form exploration and rule-based execution, respectively. On average, natural development takes 35% less time than structured, and is thus preferred for early iterations, but adopting structure at strategic points is needed for timely commercialization. Critical points of transition to a structured style include adding new team members or engaging external partners, which demand clear communication and expectations. When pivoting to a new product or market, returning to a natural style is beneficial. | Erin Looney; Andre Buscariolli; Maria Yang; Geoffrey Raymond; Tonio Buonassisi; I. Marius Peters | Energy | CC BY 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c74ec8332f0222b0dfb729/original/prototyping-styles-accelerate-hardware-development.pdf |
670d0855cec5d6c1421b0757 | 10.26434/chemrxiv-2024-dnm6n | Metal-free electrochemical hydrogenation of activated alkenes by N-doped carbons | Electrochemically-driven organic reactions offer a greener alternative to traditional catalytic methods, which often require harsh conditions. A good example is electrochemical hydrogenation that can be performed under ambient conditions using water as a proton source. To date, commercial (noble) metal electrodes have been used, with less attention given to the development of effective and sustainable electrode materials for these applications. Nitrogendoped carbons (NDCs) have been extensively used in electrocatalysis and energy storage; however, their potential in organic electrosynthesis remains unexplored. In this study, we synthesized a nanoporous NDC derived from 7,7,8,8-tetracyanoquinodimethane via the saltmelt method and applied it to the electrochemical hydrogenation of maleic acid to succinic acid. The NDC exhibited exceptional electrochemical performance, showing an onset potential 0.2 V lower than that of previously reported metal electrodes, along with nearly 100% faradaic efficiency. The SA yield rates were comparable or superior to those achieved by other catalytic methods, while operating under milder conditions and without the use of noble metal catalyst. Moreover, by tuning the potential and electrolyte acidity, the reaction could be driven toward electron-less isomerization to fumaric acid, induced by electrochemical potential. | Anastasios Orestis Grammenos; Rémi F. André; Mahima Kamra; Markus Antonietti; Mateusz Odziomek | Materials Science; Catalysis; Carbon-based Materials; Nanostructured Materials - Materials; Electrocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d0855cec5d6c1421b0757/original/metal-free-electrochemical-hydrogenation-of-activated-alkenes-by-n-doped-carbons.pdf |
60c754a10f50db0c68397d65 | 10.26434/chemrxiv.13696483.v1 | Using the Mechanical Bond to Tune the Performance of a Thermally Activated Delayed Fluorescence Emitter | We report the characterization of rotaxanes based on a carbazole–benzophenone thermally activated delayed fluorescence luminophore. We find that the mechanical bond leads to an improvement in key photophysical properties of the emitter, notably an increase in photoluminescence quantum yield and a decrease in the energy difference between singlet and triplet states, as well as fine tuning of the emission wavelength, a feat that is difficult to achieve when using covalently bound substituents. Computational simulations, supported by X-ray crystallography, suggest that this tuning of properties occurs due to weak interactions between the axle and the macrocycle that are enforced by the mechanical bond. This work highlights the benefits of using the mechanical bond to refine existing luminophores, providing a new avenue for emitter optimization that can ultimately increase the performance of these molecules. | P Rajamalli; Federica Rizzi; Wenbo Li; Michael Jinks; Abhishek Gupta; Beth Laidlaw; Ifor Samuel; Thomas Penfold; Stephen Goldup; Eli Zysman-Colman | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754a10f50db0c68397d65/original/using-the-mechanical-bond-to-tune-the-performance-of-a-thermally-activated-delayed-fluorescence-emitter.pdf |
664e445891aefa6ce1ba11ee | 10.26434/chemrxiv-2024-3v2m9 | DETERMINATION OF ADSORPTION OF BLUE DYE USING SUGARCANE BAGASSE IN AN AQEOUS SOLUTION | This research provides valuable insights into using raw sugarcane bagasse (SB) as an adsorbent for dye removal from wastewater. Various activation and modification methods for SB were explored, including physical, chemical, and biological treatments, as well as composite formation and grafting. The study examined the effects of different optimization conditions on the adsorption process, such as adsorbent dosage, initial dye concentration, pH, and contact time. Key findings include an equilibrium contact time of 30 minutes for methylene blue dye, resulting in an 86% removal rate. The optimal pH for dye removal was identified as pH 6, achieving an 84% removal rate. The study also found that the optimum dye concentration for removal was 10 ppm, with a 70% removal rate, and the optimal adsorbent dosage was 0.4g, resulting in an 81% removal rate. These results demonstrate the effectiveness of raw sugarcane bagasse in adsorbing methylene blue dye under specific conditions, highlighting its potential as a low-cost and efficient adsorbent for wastewater treatment. | Manasseh Tachia Bwankwot ; Emmanuel Kambai Duniya; Nafisa LawaL | Materials Science; Catalysis; Analytical Chemistry; Dyes and Chromophores; Analytical Chemistry - General; Base Catalysis | CC BY 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664e445891aefa6ce1ba11ee/original/determination-of-adsorption-of-blue-dye-using-sugarcane-bagasse-in-an-aqeous-solution.pdf |
671ec62f98c8527d9e8f469f | 10.26434/chemrxiv-2024-sp5gg | Kinetic Resolution of Ferrocenyl Halides via Palladium/Chiral Norbornene
Cooperative Catalysis | The development of efficient general strategy for construction of structurally diverse
planar chiral ferrocenes has been attracting widespread attention in organic synthesis. Herein we
report enantioselective kinetic resolution (KR) of ferrocenyl halides via palladium/chiral
norbornene (Pd/NBE*) cooperative catalysis. Using simple aryl iodides and olefins as the resolution
reagents, we achieved good selective zero-order KR reaction and obtained a wide range of chiral
ferrocenyl halide and chiral ferrocenylphosphine oxide product with good to excellent
enantioselectivities (selectivity factor up to 49). The C–I bond in the recovered ferrocenyl iodide
can be efficiently converted into other functional groups, which providing a general strategy for the
diversified synthesis of planar chiral ferrocene. The chiral ferrocene phosphine ligand derived from
KR product was proved to be an efficient chiral ligand in Cu catalyzed asymmetric [3 + 2]
cyclization. | Lan Zhou; Dan Ye; Huimin Li; Yabin Zhang; Qianghui Zhou; Hong-Gang Cheng | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Catalysis; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671ec62f98c8527d9e8f469f/original/kinetic-resolution-of-ferrocenyl-halides-via-palladium-chiral-norbornene-cooperative-catalysis.pdf |
60c754f6f96a0066f3288760 | 10.26434/chemrxiv.13623155.v2 | Total Synthesis of Ritterazine B | <a></a>The first total synthesis of the cytotoxic alkaloid ritterazine B is reported. The synthesis features a unified approach to both steroid subunits, employing a titanium-mediated propargylation reaction to achieve divergence from a common precursor. Other key steps include gold-catalyzed cycloisomerizations that install both spiroketals, and late stage C–H oxidation to incorporate the C7<a></a><a>′</a> alcohol.<br /> | Yasuaki Nakayama; Michael Maser; Tatsuya Okita; Anton V. Dubrovskiy; Taryn L. Campbell; Sarah Reisman | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754f6f96a0066f3288760/original/total-synthesis-of-ritterazine-b.pdf |
634eea8fa2c7901b254c5ccc | 10.26434/chemrxiv-2022-754cx-v3 | Charge-transfer-to-solvent states provide a sensitive spectroscopic probe of the local solvent structure around anions | This computational study characterizes charge-transfer-to-solvent (CTTS) states of aqueous thiocyanate anion using equation-of-motion coupled-cluster methods combined with electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. Equilibrium sampling was carried out using classical molecular dynamics (MD) with standard force-fields and QM/MM ab initio molecular dynamics (AIMD) using density functional theory. The two calculations yield significantly different local structure around solvated SCN−. Because of the diffuse character of CTTS states, they are very sensitive to the local structure of solvent around the solute and its dynamic fluctuations. Owing to this sensitivity, the spectra computed using MD and AIMD based snapshots differ considerably. This sensitivity suggests that the spectroscopy exploiting CTTS transitions can provide an experimental handle for assessing the quality of force-fields and density functionals. By combining CTTS-based spectroscopies with reliable theoretical modeling, detailed microscopic information of the solvent structure can be obtained. We present a robust computational protocol for modeling spectra of solvated anions and emphasize the use of an ab initio characterization of individual electronic transitions as CTTS or local excitations.
| Ronit Sarangi; Kaushik Nanda; Anna I. Krylov | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634eea8fa2c7901b254c5ccc/original/charge-transfer-to-solvent-states-provide-a-sensitive-spectroscopic-probe-of-the-local-solvent-structure-around-anions.pdf |
60c743f7bb8c1ac0353da424 | 10.26434/chemrxiv.7742882.v2 | Poly(Boc-acryloyl hydrazide): The importance of temperature and RAFT agent degradation on its preparation | <p>Poly(acryloyl hydrazide) is a versatile polymer scaffold readily functionalised through post-polymerisation modification with aldehydes to yield polymers for biological applications. However, its polymerisation is affected by nucleophilic degradation of the RAFT agent that leads to early termination, an issue often overlooked in the polymerisation of primary acrylamides. Here we report the effect of temperature on the RAFT polymerisation of N’-(<i>tert</i>-butoxycarbonyl)acryloyl hydrazide (<b>1</b>) and demonstrate that by carefully selecting this polymerisation temperature, a balance between rate of polymerisation and rate of degradation of the RAFT agent can be achieved. This way a greater control over the polymerisation process is achieved, allowing the synthesis of Boc-protected poly(acryloyl hydrazide) with higher degrees of polymerisation than those achieved previously, while still maintaining low dispersities. We believe our results should be of importance to those working on the RAFT polymerization of primary and secondary (meth)acrylamides and monomers with nucleophilic moieties. </p> | Oliver Creese; Pavan Adoni; Guanlong Su; Andrey
V. Romanyuk; Paco Fernandez-Trillo | Polymerization (Polymers); Polymerization kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f7bb8c1ac0353da424/original/poly-boc-acryloyl-hydrazide-the-importance-of-temperature-and-raft-agent-degradation-on-its-preparation.pdf |
665ba2d5418a5379b0dd81a0 | 10.26434/chemrxiv-2024-f0zz5-v2 | Alzheimer's Disease: Exploring the Landscape of Cognitive Decline | Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, memory loss, and impaired daily functioning. The pathology of AD is marked by the accumulation of amyloid-beta plaques and tau protein tangles in brain, along with neuroinflammation and synaptic dysfunction. Genetic factors, such as mutations in APP, PSEN1, and PSEN2 genes, as well as APOE ε4 allele, contribute to increased risk of acquiring AD. Currently available treatments provide symptomatic relief but do not halt disease progression. Research efforts are focused on developing disease-modifying therapies that target the underlying pathological mechanisms of AD. Advances in identification and validation of reliable biomarkers for AD hold great promise for enhancing early diagnosis, monitoring disease progression, and assessing treatment response in clinical practice, in effort to alleviate the burden of this devastating disease.
In this paper, we analyze data from the CAS Content Collection to summarize the research progress in Alzheimer’s disease. We examine the publication landscape in effort to provide insights into current knowledge advances and developments. We also review the most discussed and emerging concepts and assess the strategies to combat the disease. We explore the genetic risk factors, pharmacological targets, and comorbid diseases. Finally, we inspect clinical applications of products against AD with their development pipelines and efforts for drug repurposing. The objective of this review is to provide a broad overview of the evolving landscape of current knowledge regarding AD, to outline challenges, and evaluate growth opportunities to further efforts in combating the disease. | Rumiana Tenchov; Janet Sasso; Qiongqiong Angela Zhou | Biological and Medicinal Chemistry; Biochemistry | CC BY 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665ba2d5418a5379b0dd81a0/original/alzheimer-s-disease-exploring-the-landscape-of-cognitive-decline.pdf |
6284eddc6cae1c51680e49fa | 10.26434/chemrxiv-2022-blkmp | Machine-Learning Prediction of the Computed Band Gaps of Double Perovskite Materials | Conventional electronic structure methods based on density functional theory (DFT) suffer from not only high computational cost that scales cubically with the number of electrons, but also limited accuracy arising from the approximations of the exchange-correlation functional. In particular, the latter issue is particularly severe for insulators and semiconductors, whose band gaps are systematically underestimated by DFT. Surrogate methods based on machine learning has garnered much attention as a viable alternative to bypass these limitations, especially in prediction of solid-state band gaps. Here, we construct a random forest regression model for band gaps of double perovskite materials, using a dataset of 1306 band gaps computed with the GLLBSC (Gritsenko, van Leeuwen, van Lenthe, and Baerends solid correlation) functional. Among the 20 physical features employed, we find that the bulk modulus, superconductivity temperature, and cation electronegativity exhibit the highest importance scores, consistent with the physics of the underlying electronic structure. Using the top 10 features, a model accuracy of 85.6% with a root mean square error of 0.64 eV is obtained, comparable to a previous study employing kernel ridge regression. Our results attest to the potential of machine learning regressions for rapid screening of promising candidate functional materials. | Junfei Zhang; Yueqi Li; Xinbo Zhou | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6284eddc6cae1c51680e49fa/original/machine-learning-prediction-of-the-computed-band-gaps-of-double-perovskite-materials.pdf |
642af545a029a26b4cda15f0 | 10.26434/chemrxiv-2023-r6njk | A Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding | In this work, we investigate the role of solvent in the binding reaction of p53 transactivation domain (TAD) peptide to its receptor MDM2. Previously, our group generated 831 μs of explicit-solvent aggregate molecular simulation trajectory data for the MDM2-p53 peptide binding reaction using large-scale distributed computing, and subsequently built a Markov State Model (MSM) of the binding reaction (Zhou et al. 2017). Here, we perform tICA anlaysis and construct an MSM using only solvent-based structural features, and find a remarkably similar landscape and implied timescales for the slowest motions. The solvent shells contributing most to the first tICA eigenvector are those centered on Lys24 and Thr18 of p53 TAD peptide in the range of 3–6 Å. Important solvent shells were visualized to reveal wetting and dewetting transitions along peptide-protein binding trajectories. Our results provide a solvent-centric view of the hydrophobic effect in action for a realistic peptide-protein binding scenario. | Robert Raddi; Vincent Voelz | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642af545a029a26b4cda15f0/original/a-markov-state-model-of-solvent-features-reveals-water-dynamics-in-protein-peptide-binding.pdf |
60c755c3842e658632db43b4 | 10.26434/chemrxiv.14153249.v1 | Exploring the Chemical Space of Protein Glycosylation in Noncovalent Protein Complexes: An Expedition Along Different Structural Levels of Human Chorionic Gonadotropin Employing Mass Spectrometry | Exploration of a highly glycosylated non-covalent protein comples by mass spectreometry is a challenging task due to isobarisicy of the majority of glycoforms. Integration of data from multiple structural levels (released glycan-glycopeptide-protein subunit-protein complex) by means of computational algorithms permits unraveling the hidden diversity of the human chorionic gonadotropin heterodimer, constituting the base for the study of complex glycosylated protein assemblies.<br /> | Maximilian Lebede; Fiammetta di Marco; Wolfgang Esser-Skala; René Hennig; Therese Wohlschlager; Christian G. Huber | Biochemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c3842e658632db43b4/original/exploring-the-chemical-space-of-protein-glycosylation-in-noncovalent-protein-complexes-an-expedition-along-different-structural-levels-of-human-chorionic-gonadotropin-employing-mass-spectrometry.pdf |
67a4ffb6fa469535b94a3ad9 | 10.26434/chemrxiv-2025-zhkrf | Democratizing self-driving labs through user-developed automation infrastructure | As self-driving labs become widely deployed in chemicals and materials research, interest in democratizing access to these platforms is growing. SDLs can be democratized by lowering their costs to increase accessibility and by creating systems that allow researchers to modify, extend, and share SDL tools to meet the needs of their science and contribute to the advancement of the SDL community. In particular, user-developed automation infrastructure is an important component of democratized SDL ecosystems. To advance community adoption of democratized SDL practices, we organized the “Democratizing Self-Driving Labs” workshop held at the 2024 Accelerate conference. As part of this workshop, the authors contributed to a demonstration of their user-developed automation infrastructure. 14 examples of custom built hardware, software, and workflows were shared. This workshop provided an opportunity for researchers to see user-developed infrastructure in action, learn about how they could integrate these projects into their work, and contribute to discussion about what is needed to advance the state of democratized SDLs. In this perspective, ten contributed examples of user-developed hardware and software from the workshop are highlighted. Despite a diverse array of projects, common motivations for pursuing user-developed infrastructure were cost savings and specification requirements that were unmet by commercially available products. Continuing to advance the state of user-developed automation infrastructure will require commitments to completing high-quality documentation for open-source hardware projects, pathways for materials researchers to learn hardware development skills, and more opportunities for researchers to share their infrastructure advancements, in addition to the scientific advancements that they enable. | Brenden Pelkie; Sterling Baird ; Eunice Aissi; Kenzo Aspuru-Takata; Yang Cao; Jin Hyun Chang; Kshitij Gambhir; Wm Salt Hale; Lucy Hao; Chance Hattrick; Jason Hein; Danli Luo; Owen Melville; Monique Ngan; Louie Lucas Bisgaard Nyeland; Nadya Peek; Maria Politi; Ethan Elliot Rajkumar; Alexander Siemenn; Blair Subbaraman; Sonya Vasquez; Jeffrey Watchorn; Wenyu Zhang; Rógvi Ziskason; Lilo Pozzo; Tonio Buonassisi; Tejs Vegge | Materials Science; Chemical Engineering and Industrial Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a4ffb6fa469535b94a3ad9/original/democratizing-self-driving-labs-through-user-developed-automation-infrastructure.pdf |
627c6514708767b79a4fadbb | 10.26434/chemrxiv-2022-6r93n | Base-Catalyzed Dehydrogenative Coupling of Formate Anions to Oxalates: Effect of Alkali Metal Cations | Herein, the influence of group 1 and 2 metal cations on base-catalyzed dehydrogenative coupling of formate to form oxalate is reported. Treatment of sodium formate with a various types of bases (group 1 and 2 metal carbonates or metal hydroxides) revealed that, compared with carbonate salts, group 1 metal hydroxides behaved as efficient bases for the formation of oxalate, in which cesium hydroxide (CsOH) showed the best catalytic activity. DFT calculation for the reaction mechanism suggested that its kinetic advantage was generated from not only an increase of basicity but also destabilization of the intermediate species due to Na/Cs mixed cation system. The effect of cations in formate salts were also discussed both experimentally and theoretically, in which the yield of oxalic acid depended on thermodynamic stability of both products (oxalate salts) and intermediates. | Atsushi Tahara; Aska Mori; Jun-ichiro Hayashi; Shinji Kudo | Theoretical and Computational Chemistry; Inorganic Chemistry; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627c6514708767b79a4fadbb/original/base-catalyzed-dehydrogenative-coupling-of-formate-anions-to-oxalates-effect-of-alkali-metal-cations.pdf |
66a4efbf5101a2ffa8373111 | 10.26434/chemrxiv-2024-zm3t1-v2 | Secondary Cationic Interaction Driven Substrate Ligand Affinity for Pd(II)-Catalyzed Enantioselective C-H Activation of Ferrocenyl Amines | Secondary amines as a directing group for C-H activation have limitations as they are prone to undergo oxidation,
allylic deamination, and β-hydride elimination. The fundamental challenge observed here is the competition between the desired C-H activation versus the vulnerable β-C-H bond of secondary amine when the substrate ligand affinity is not strong enough. Herein, a potential of axially chiral NOBINAc ligand is revealed to accelerate the enantioselective PdII-catalyzed C-H activation process of ferrocenyl secondary amines. Further, the secondary interaction of cesium cation with NOBINAc ligand and sulfonate group of secondary amine plays an impressive role in mitigating the potential threat of β-hydride elimination via an enhanced substrate ligand affinity. This approach resulted in enantioselective C-H activation,
intermolecular annulation, and alkenylation of ferrocenyl secondary amines with allenes and activated olefines, leading to ferrocene fused tetrahydropyridines and alkenylated ferrocenyl amines with up to 70% yields and 99:1 er. | Devendra Parganiha; Raviraj Ananda Thorat; Ashwini Dilip Dhumale; Yagya Dutt Upadhyay; Raushan Kumar Jha; Saravanan Raju; Sangit Kumar | Organic Chemistry; Catalysis; Organometallic Chemistry; Stereochemistry; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a4efbf5101a2ffa8373111/original/secondary-cationic-interaction-driven-substrate-ligand-affinity-for-pd-ii-catalyzed-enantioselective-c-h-activation-of-ferrocenyl-amines.pdf |
66ad4cf35101a2ffa8f54171 | 10.26434/chemrxiv-2024-r81c8-v2 | Linear Graphlet Models for Accurate and Interpretable Cheminformatics | Advances in machine learning have given rise to a plurality of data-driven methods for predicting chemical properties from molecular structure. For many decades, the cheminformatics field has relied heavily on structural fingerprinting, while in recent years much focus has shifted toward leveraging highly parameterized deep neural networks which usually maximize accuracy. Beyond accuracy, to be useful and trustworthy in scientific applications, machine learning techniques often need intuitive explanations for model predictions and uncertainty quantification techniques so a practitioner might know when a model is appropriate to apply to new data. Here we revisit graphlet histogram fingerprints and introduce several new elements. We show that linear models built on graphlet fingerprints attain accuracy that is competitive with the state of the art while retaining an explainability advantage over black-box approaches. We show how to produce precise explanations of predictions by exploiting the relationships between molecular graphlets and show that these explanations are consistent with chemical intuition, experimental measurements, and theoretical calculations. Finally, we show how to use the presence of unseen fragments in new molecules to adjust predictions and quantify uncertainty. | Michael Tynes; Michael G Taylor; Jan Janssen; Daniel J Burrill; Danny Perez; Ping Yang; Nicholas Lubbers | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ad4cf35101a2ffa8f54171/original/linear-graphlet-models-for-accurate-and-interpretable-cheminformatics.pdf |
60c755b6702a9ba95818c752 | 10.26434/chemrxiv.14140790.v1 | Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies | In silico screening of drug target interactions is a key part of the drug discovery process. Changes in the drug scaffold via contraction or expansion of rings, the breaking of rings and the introduction of cyclic structures from acyclic structures are commonly applied by medicinal chemists to improve binding affinity and enhance favorable properties of candidate compounds. These processes, commonly referred to as scaffold hopping, are challenging to model computationally. Although relative binding free energy (RBFE) calculations have shown success in predicting binding affinity changes caused by perturbing R-groups attached to a common scaffold, applications of RBFE calculations to modeling scaffold hopping are relatively limited. Scaffold hopping inevitably involves breaking and forming bond interactions of quadratic functional forms, which is highly challenging. A novel method for handling ring opening/closure/contraction/expansion and linker contraction/expansion is presented here. To the best of our knowledge, RBFE calculations on linker contraction/expansion have not been previously reported. The method uses auxiliary restraints to hold the atoms at the ends of a bond in place during the breaking and forming of the bonds. The broad applicability of the method was demonstrated by examining perturbations involving small molecule macrocycles and mutations of proline in proteins. High accuracy was obtained using the method for most of the perturbations studied. Unlike other methods that rely on λ-dependent functional forms for bond interactions, the method presented here can be employed using modern MD software without modification of codes or force field functions. | Junjie Zou; Zhipeng Li; Shuai Liu; Chunwang Peng; Dong Fang; Xiao Wan; Zhixiong Lin; Tai-Sung Lee; Daniel Raleigh; Mingjun Yang; Carlos Simmerling | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755b6702a9ba95818c752/original/scaffold-hopping-transformations-using-auxiliary-restraints-for-calculating-accurate-relative-binding-free-energies.pdf |
60c73f58567dfe1575ec39b2 | 10.26434/chemrxiv.7297766.v1 | Structural Basis for Selectivity in Flavin-Dependent Monooxygenase-Catalyzed Oxidative Dearomatization | Herein, we disclose the structural basis for substrate binding in TropB, which performs a synthetically challenging asymmetric oxidative dearomatization reaction with exquisite site- and stereoselectivity across a range of substrates, providing a foundation for future protein engineering and reaction development efforts. Our hypothesis for substrate binding is informed by the first crystal structure of TropB and molecular dynamics simulations with the corresponding computational TropB model and is supported by experimental data. | Attabey Rodríguez Benítez; Sara Tweedy; Summer A. Baker Dockrey; April L. Lukowski; Troy Wymore; Dheeraj Khare; Charles L. Brooks III; Janet L. Smith; Alison Narayan | Biochemistry; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f58567dfe1575ec39b2/original/structural-basis-for-selectivity-in-flavin-dependent-monooxygenase-catalyzed-oxidative-dearomatization.pdf |
60c75065567dfec41fec5845 | 10.26434/chemrxiv.12401708.v2 | Experimental Evidence for a General Model of Modulated MOF Nanoparticle Growth | <p>Nanoparticles of metal-organic frameworks (nanoMOFs) boast superior properties compared to their bulk analogs, yet little is known about how common synthetic parameters dictate particle sizes. Here, we provide experimental evidence for the “seesaw” model of nanoMOF growth. Solution acidity, ligand excess, and reactant concentrations are decoupled and shown to form the key independent determinants of nanoMOF sizes, thereby validating the proposal that nanoMOFs arise from coupled equilibria involving ligand deprotonation and metal-ligand complexation. By achieving the first demonstration of a seesaw relationship between nanoMOF sizes and ligand excess, these results provide further proof of the model, as they required deliberate manipulation of relationships outlined by the model. Exploring the relative impacts of these parameters reveals that ligand excess has the greatest ability to decrease sizes, although low acidity and high concentrations can exhibit similar effects. As a complement to existing models of polymer formation and crystal growth, the seesaw model therefore offers a powerful tool for reliable control over nanoMOF sizes.</p> | Checkers R. Marshall; Sara Staudhammer; Carl Brozek | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75065567dfec41fec5845/original/experimental-evidence-for-a-general-model-of-modulated-mof-nanoparticle-growth.pdf |
61406e5890051e0a62f2f0f0 | 10.26434/chemrxiv-2021-bxpzz | Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids. | The lone-pair…π (lp…π) (deoxy)ribose…nucleobase stacking is a recurring structural motif in Z DNA and RNAs that is characterized by sub-van der Waals lp…π contacts (<3.0 Å). It is part of the structural signature of the CpG Z-steps in Z-DNA and r(UNCG) tetraloops. These nucleic acid structures are poorly behaving in molecular dynamics (MD) simulations. Although the exact origin of these issues remains unclear, a significant part of the problem might be due to an imbalanced description of non-bonded interactions including the characteristic lp…π stacking. To gain insights into the links between lp…π stacking and MD issues, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the non-bonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, U). Among other differences, we found that the AFF overestimates the DHDF D3 lp…π distances by ~0.1-0.2 Å while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule (AIM) polarizabilities and SAPT analysis, we inferred that the DHDF-D3 vs. AFF differences partly originate in the Lennard-Jones (LJ) parameters that are identical for nucleobase carbon atoms despite the presence/absence of connected electron withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp…π contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations. | Klaudia Mrazikova; Jiri Sponer; Vojtech Mlynsky; Pascal Auffinger; Holger Kruse | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61406e5890051e0a62f2f0f0/original/short-range-imbalances-in-the-amber-lennard-jones-potential-for-deoxy-ribose-nucleobase-lone-pair-contacts-in-nucleic-acids.pdf |
60c753b1bb8c1a0f0a3dc0cc | 10.26434/chemrxiv.13531010.v1 | Mechanochemical Transformation of Planar Polyarene to Curved Fused-Ring System: Solid-Phase Synthesis of Corannulene | This work demonstrates that mechanochemical forces can successfully transform a planar<br />polyarene into a curved geometry by creating new C-C bonds along the rim of the molecular structure.<br />In doing so, mechanochemistry does not require inert conditions or organic solvents and provide<br />better yields within shorter reaction times. This is illustrated in a 15-minute synthesis of corannulene,<br />a fragment of fullerene C60, in 66% yield through ball milling of planar tetrabromomethylfluoranthene<br />precursor under ambient conditions. Traditional solution and gas-phase synthetic pathways do not<br />compete with the practicality and efficiency offered by the mechanochemical synthesis, which now<br />opens up a new reaction space for inducing curvature at a molecular level. | Yong Teoh; Gabor Báti; Felipe Garcia; Mihaiela C. Stuparu | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753b1bb8c1a0f0a3dc0cc/original/mechanochemical-transformation-of-planar-polyarene-to-curved-fused-ring-system-solid-phase-synthesis-of-corannulene.pdf |
6625219e91aefa6ce107d12c | 10.26434/chemrxiv-2024-7cf61-v2 | Deciphering Spin-Activity Relationships of FeN4 Moieties Bridged in Halogenated MXenes for Oxy-gen Reduction | pin control of the FeN4 moieties is critical for enhancing the electrocatalytic oxygen reduction reaction (ORR). The relationship between the spin state transitions of the FeN4 moieties and ORR activity is complex and remains debatable due to the discrepancies between the theoretical models and experi-mental catalyst structures, along with potential misinterpreting the characterization data. In this study, we utilized Ti3C2Tx MXenes with various terminations (−I, −Br, −Cl, −F, and −O) integrated with iron phthalocyanine (FePc) to form model catalysts with defined FeN4-Tx-Ti structures; this enabled the pre-cise modulation of the FeN4 spin states, established a clear correlation between the intermediate spin states, and improved the ORR performance. Specifically, compared FePc with a 17.1% intermediate spin state, Ti3C2Brx/FePc with an 88.1% intermediate spin state exhibited superior electrochemical per-formance, showing an ORR half-wave potential of 0.94 V versus RHE and doubled power densities in Zn-air batteries (252.5 mW cm-2) and H2-O2 fuel cells (350.7 mW cm-2). Theoretical studies confirmed that the intermediate spin state led to electron filling in the antibonding orbital composed of the Fe 3dz2 and O2 π* orbitals, significantly improving the O2 activation and ORR activity. This research advances our understanding of the spin-related origins of catalytic activity and facilitates the design and optimiza-tion of advanced ORR catalysts. | Shuren Zhang; Genban Sun | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6625219e91aefa6ce107d12c/original/deciphering-spin-activity-relationships-of-fe-n4-moieties-bridged-in-halogenated-m-xenes-for-oxy-gen-reduction.pdf |
67d2d43f81d2151a023a418b | 10.26434/chemrxiv-2024-qmcz4-v2 | Conformational Pruning via the Permutation Invariant Root Mean Square Deviation of Atomic Positions | The Cartesian root-mean-square-deviation (RMSD) of atomic coordinates is fundamental for comparing three dimensional molecular structures, particularly in identifying and classifying molecular conformations. Since molecular properties are determined by the molecular conformation, pruning duplicates via a structural similarity metric like the RMSD will reduce redundant calculations and hence directly impact the cost of automated workflows in computational chemistry. However, the traditional RMSD metric struggles when dealing with local symmetry in molecules and atom permutation, often leading to inflated errors and computational inefficiency.
This work addresses these challenges by providing clear definitions for structural similarity within conformational ensembles and developing an efficient divide-and- conquer algorithm for their distinction. The proposed permutation invariant RMSD (iRMSD) approach efficiently overcomes challenges associated with symmetric molecules and multiple rotamers by incorporating a procedure that assigns canonical atom identities and optimizes the atom-to-atom assignment process. This procedure leads to significant reductions in computational complexity, making the method highly suit- able for rapid, large-scale conformational analysis and automated property prediction workflows, both by effective pruning of duplicate conformations and enabling cross-methodology ensemble comparison. | Philipp Pracht | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d2d43f81d2151a023a418b/original/conformational-pruning-via-the-permutation-invariant-root-mean-square-deviation-of-atomic-positions.pdf |
60c7422d9abda2db03f8bf8e | 10.26434/chemrxiv.8247803.v1 | Gold(I)-Catalyzed Stereoselective Cyclization of 1,3-Enyne Aldehydes by 1,3-Acyloxy Migration/Nazarov/Aldol Cascade | Stereoselective synthesis of
bicyclo[3.3.0]octenones from chiral 1,3 enyne aldehydes bearing propargylic
acetates is described. The method is based on a Au(I)-catalyzed domino sequence
with concomitant transfer of chirality involving 1,3-acyloxy migration followed
by Nazarov cyclization and an unprecedented aldol addition. The method furnishes
densely functionalized bicyclic structures in high yields, up to 97% ee, and
good diastereoselectivity. | Marco Brandstaetter; Nikolas Huwyler; Erick Carreira | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422d9abda2db03f8bf8e/original/gold-i-catalyzed-stereoselective-cyclization-of-1-3-enyne-aldehydes-by-1-3-acyloxy-migration-nazarov-aldol-cascade.pdf |
6226facfc3e9da3951843dd4 | 10.26434/chemrxiv-2022-rhj07 | Prediction Of QcrB Inhibition As A Measure Of Antitubercular Activity With Machine Learning Protocols. | Mycobacterium tuberculosis has been a challenging target with respect to developing interventional therapies. Over the years, several attempts at developing anti-tubercular agents have hit a dead-end due to the propensity of the tubercular bacilli to mutate rapidly. Recently, cytochrome bcc complex (QcrB) has shown some promise as a novel target of the tubercular bacilli; with Q203 being the first molecule acting on this target. In this paper, we report the deployment of several ML-based approaches to design molecules against QcrB. Machine Learning (ML) models were developed based on a large dataset of 350 molecules using three different sets of molecular features, i.e. MACCS keys, ECFP6 fingerprints and Mordred descriptors. Each feature set was trained on eight ML classifier algorithms and optimised to classify molecules accurately. Of the 24 models generated, the best performing model was one built with support vector machine and based on the ECFP6 feature set. A further screening of the known imidazopyridine amide inhibitors demonstrated that the model correctly classified the most potent molecules as actives. Thus validating the model for future applications. | Afreen Khan; Ketki Bhave; Sannidhi Poojary; Krishna Iyer; Santosh Nandan; Evans Coutinho | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6226facfc3e9da3951843dd4/original/prediction-of-qcr-b-inhibition-as-a-measure-of-antitubercular-activity-with-machine-learning-protocols.pdf |
62b6f9c60bba5d7a1c745c43 | 10.26434/chemrxiv-2021-tm4gl-v3 | Divalent benzimidazolium-based axles for self-reporting pseudorotaxanes | Mono and (bis)benzimidazoliums were evaluated both experimentally and computationally for their potential as pseudopolyrotaxane axle building blocks. Their aggregation and photophysical behavior, along with their potential to form a [2]pseudorotaxane with dibenzyl-24-crown-8, was studied through the synergistic application of 1D/2D and diffusion ordered NMR spectroscopy, mass spectrometry, ultraviolet-visible & fluorescence spectroscopy, and time-dependent density functional theory. Their photophysical behaviour was measured and modeled as a function of protonation state, solvent, and concentration. The axles show strong solvochromaticism and a very pronounced concentration-dependent optical profile, including self-quenching when a pseudorotaxane is formed. This axle with multiple recognition sites, has the potential to form pseudorotaxanes with tunable optical behavior. | S. Maryamdokht Taimoory; Xiao Yu; N. Kodiah Beyeh; John F. Trant | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Self-Assembly; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b6f9c60bba5d7a1c745c43/original/divalent-benzimidazolium-based-axles-for-self-reporting-pseudorotaxanes.pdf |
67210dcb7be152b1d02b4b05 | 10.26434/chemrxiv-2024-2q6l5 | AI4Green4Students: Promoting sustainable chemistry in undergraduate laboratories with an electronic lab notebook | AI4Green is an open-source, machine-learning-powered electronic laboratory notebook (ELN) developed by our research group to help chemists mitigate environmental impacts, particularly within the pharmaceutical sector. This study presents AI4Green4Students, a pedagogically adapted version designed to foster sustainable laboratory practices and encourage the use of digital tools within undergraduate laboratory teaching. The AI4Green4Students ELN includes features for sustainability assessment, data documentation, and analysis, aiming to equip students with skills for modern, sustainable laboratory practices. User feedback, gathered through questionnaires and interviews, informed the initial development and subsequent refinements of the application, enhancing its usability, efficiency, and functionality. Implementation in a Year 3 undergraduate chemistry lab project indicated improved adherence to sustainable practices, suggesting that the ELN supports the integration of sustainable chemistry into laboratory teaching. Future efforts will expand AI4Green4Students to include additional experiments to broaden its applicability across undergraduate chemistry courses, as well as integrate machine learning tools to enhance data analysis capabilities. | Peace Nwafor; Shason Gurung; Philip van Krimpen; Lenka Schnaubert; Katherine Jolley; Samantha Pearman-Kanza; Cerys Willoughby; Jonathan Hirst | Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67210dcb7be152b1d02b4b05/original/ai4green4students-promoting-sustainable-chemistry-in-undergraduate-laboratories-with-an-electronic-lab-notebook.pdf |
6160928da3d2c94eb1d037e2 | 10.26434/chemrxiv-2021-h5hhv | Optimization of a Pyrimidinone Series for Selective Inhibition of Ca2+/Calmodulin-Stimulated Adenylyl Cyclase 1 Activity for the Treatment of Chronic Pain | Adenylyl cyclase type 1 is an emerging target for the treatment of chronic pain that is downstream on the analgesic pathway from the traditional µ-opioid receptor. AC1 is expressed in the central nervous system and critical for signaling in pain sensitization. Behavioral studies have revealed AC1 knockout mice exhibit reduced behavioral pain sensitization responses similar to morphine administration. AC1, and a closely related isoform AC8, are also implicated to have a role in learning and memory signaling processes. However, reports suggest selectively targeting AC1 over AC8 may be a viable strategy to eliminate potential deleterious effects on learning and memory. Our team has carried out cellular screening for inhibitors of AC1 that yielded a pyrazolyl-pyrimidinone scaffold with potency comparable to previously published AC1 inhibitors, selectivity versus AC8, and improved drug-like physicochemical properties. Structure-activity relationship (SAR) studies produced 36 analogs that balanced improvements in potency with cellular IC50 values as low as 0.25 µM and selectivity versus AC8. Prioritized analogs were selective for AC1 compared to other AC isoforms and other common neurological targets. A representative analog was assessed for efficacy in a mouse model of inflammatory pain and displayed modest anti-allodynic effects. This series of compounds represents the most potent and selective inhibitors of Ca2+/Calmodulin-stimulated AC1 activity to date with reduced off-target liabilities and improved drug-like physicochemical properties making them promising lead compounds for the treatment of inflammatory pain. | Jason Scott; Monica Soto-Velasquez; Michael Hayes; Justin Lavigne; Heath Miller; Jatinder Kaur; Karin Ejendal; Val Watts; Daniel Flaherty | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6160928da3d2c94eb1d037e2/original/optimization-of-a-pyrimidinone-series-for-selective-inhibition-of-ca2-calmodulin-stimulated-adenylyl-cyclase-1-activity-for-the-treatment-of-chronic-pain.pdf |
60c741a1f96a00c65c28645c | 10.26434/chemrxiv.8068238.v1 | Electrochemical Impedance Spectroscopy as a Performance Indicator of Water Dissociation in Bipolar Membranes | Using electrochemical impedance spectroscopy (EIS), we observed the rate of water dissociation decrease in the presence of salt ions while also observing the diffusion and migration of these salt ions, showing a clear link between the peaks observed in EIS and ion crossover. In addition, we show how EIS can be used to in-situ monitor the stability and ageing of a BPM, revealing that degradation of the BPM is more prominent in extreme pH electrolyte pairs compared to non-extreme electrolyte pairs. The in-situ monitoring of the WDR and stability of a BPM are vital methods for adequate and consistent comparison of novel designs of BPM-based systems, where EIS allows for discriminating BPM characteristics from other components even during operation. <br /> | marijn blommaert; david vermaas; boaz izelaar; ben in't veen; wilson smith | Reaction Engineering; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.); Water Purification; Electrocatalysis; Redox Catalysis; Energy Storage; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a1f96a00c65c28645c/original/electrochemical-impedance-spectroscopy-as-a-performance-indicator-of-water-dissociation-in-bipolar-membranes.pdf |
64f1f013dd1a73847ff63bc8 | 10.26434/chemrxiv-2023-0q3fn | Gold-Catalyzed Alkenylation and Arylation of Phosphorothioates | Reported herein is the gold-catalyzed alkenylation and arylation of phosphorothioates using alkenyl and aryl iodides. The facile transmetalation between Ag-sulfur complex and Au(III) intermediate formed after oxidative addition is the key to the success of this transformation. This methodology operates under mild reaction conditions with catalyst loading as low as 1 mol%, thereby providing an efficient access to biologically active S-alkenyl and S-aryl phosphorothioates | Urvashi Urvashi; Sampoorna Mishra; Nitin T. Patil | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f1f013dd1a73847ff63bc8/original/gold-catalyzed-alkenylation-and-arylation-of-phosphorothioates.pdf |
60c754e6842e650aaedb4260 | 10.26434/chemrxiv.13830920.v1 | Thermochemical Aerobic Oxidation Catalysis in Water Proceeds via Coupled Electrochemical Half-Reactions | <div>
<p><b>Heterogeneous
aqueous-phase aerobic oxidations are an important emerging class of catalytic
transformations, particularly for upgrading next generation bio-derived
substrates. The mechanism of these reactions and the precise role of O<sub>2</sub>
in particular remains unclear. Herein, we test the hypothesis that
thermochemical aerobic oxidation proceeds via two coupled electrochemical
half-reactions for oxygen reduction and substrate oxidation. We collect</b><b> electrochemical and thermochemical data on common
noble metal catalysts under identical reaction/transport environments, and find
that the electrochemical polarization curves of the O<sub>2</sub> reduction and
the substrate oxidation half-reaction closely predict the mixed potential of
the catalyst measured <i>in operando</i>
during thermochemical catalysis across 13 diverse variables spanning </b><b>reaction
conditions, catalyst composition, reactant identity, and pH</b><b>. Additionally, we find that driving the oxidation
half-reaction reaction electrochemically in the absence of O<sub>2</sub> at the
mixed potential leads to very similar rates and selectivities as for the
thermochemical reaction in all cases examined. These findings strongly indicate
that the role of O<sub>2</sub> in thermochemical aerobic oxidation is solely as
an electron scavenger that provides an incipient electrochemical driving force
for substrate oxidation. These studies provide a </b><b>quantitative
and predictive link between thermochemical and electrochemical catalysis,
thereby enabling the rational design of new thermochemical liquid-phase aerobic
oxidation schemes by applying the principles of electrochemistry.</b></p>
</div>
<br /> | Jaeyune Ryu; Daniel Bregante; William C. Howland; Ryan P. Bisbey; Corey J. Kaminsky; Yogesh Surendranath | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754e6842e650aaedb4260/original/thermochemical-aerobic-oxidation-catalysis-in-water-proceeds-via-coupled-electrochemical-half-reactions.pdf |
60c745ceee301c7084c793df | 10.26434/chemrxiv.10275917.v1 | Infra-Red Assisted Synthesis of Prebiotic Glycine | <p>In the present study, we have shown for the first time
how glycine can be synthesized under prebiotic-like conditions using an
Infra-Red laser to trigger the reaction. In particular, we observed that in the
low-density conditions it can be obtained from simple ion-molecule reactions of
acetic acid and protonated hydroxylamine. This reaction, studied years ago in
more dense conditions [<i>J. Am. Chem. Soc.</i> <b>2007</b>, <i>129</i>, 9910-9917R], was the center of a controversy, since accurate
quantum chemistry calculations have shown that it is not barrierless [<i>Astrophys. J.</i> <b>2012</b>, <i>748</i>, 99] such that
a source of energy is needed. In space, and more in general in prebiotic
conditions (interstellar medium, comets, asteroids) temperature is very low but
the photon density can be important. Here we propose a way of synthesizing such
complex organic molecule in a very low-pressure environment (about 10<sup>-3</sup>
mbar). This way of forming complex
organic molecule is of relevance also beyond the prebiotic interest of finding
a scenario which was at the origin of the synthesis of such molecules. In fact our
work proposes a new way of assisting reactions using IR radiation. Only few
cases were found in which IR can trigger complex reactions (i.e. not simple
dissociations) while there is a clear interest of using such low-energy
radiation. This study will be at the basis of new researches devoted to find
other reactions which can be assisted by IR laser.</p> | Debora Scuderi; Ariel F. Perez-Mellor; Joël Lemaire; Suvasthika Indrajith; Jean-Xavier Bardaud; Antonio Largo; Yannick Jeanvoine; Riccardo Spezia | Clusters; Physical and Chemical Processes; Radiation; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745ceee301c7084c793df/original/infra-red-assisted-synthesis-of-prebiotic-glycine.pdf |
61256a9b9d6e6e78d674049f | 10.26434/chemrxiv-2021-tmg9m | Single–Ion Conducting Polymer Nanoparticles as Functional Fillers for Solid Electrolytes in Lithium Metal Batteries | Composite solid electrolytes including inorganic nanoparticles or nanofibers which improve the performance of polymer electrolytes due to their superior mechanical, ionic conductivity or lithium transference number are actively being searched for applications in lithium metal batteries. However, inorganic nanoparticles present limitations such as its tedious surface functionalization and agglomeration issues and poor homogeneity at high concentrations in polymer matrices. In this work, we report on polymer nanoparticles with lithium sulfonamide surface functionality (LiPNP) for application as electrolytes in lithium metal battery. The particles are prepared by semibatch emulsion polymerization, an easily up–scalable technique. LiPNPs are used to prepare two different families of particle reinforced solid electrolytes. When mixed with polyethylene oxide and lithium bis(trifluoromethane)sulfonimide (LiTFSI/PEO), the particles provoke a significant stiffening effect (E´ > 106 Pa vs. 105 Pa at 80 ºC) while retaining high ionic conductivity (σ = 6.6 × 10–4 S cm–1). Preliminary testing in LiFePO4 full cells, showed promising performance of the PEO nanocomposite electrolytes. By mixing the particles with propylene carbonate without any additional salt, we obtain true single ion conducting gel electrolytes as the lithium sulfonamide surface functionalities are the only sources of lithium ions in the system. The gel electrolytes are mechanically robust (up to G´ =106 Pa) and show ionic conductivity up to 10–4 S cm–1. Finally, the PC nanocomposite electrolytes were tested in symmetrical lithium cells. Our findings suggest that all–polymer nanoparticles could represent a new building block material for solid–state lithium metal battery applications. | Luca Porcarelli; Preston Sutton; Vera Bocharova; Robert Aguirresarobe; Haijin Zhu; Nicolas Goujon; Jose Leiza; Alexei Sokolov; Maria Forsyth; David Mecerreyes | Materials Science; Polymer Science; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61256a9b9d6e6e78d674049f/original/single-ion-conducting-polymer-nanoparticles-as-functional-fillers-for-solid-electrolytes-in-lithium-metal-batteries.pdf |
67b20fa96dde43c9082726a9 | 10.26434/chemrxiv-2024-h1x6w-v4 | Novel Evaluation of Hydrophobicity in Micropores of Nanostructured Metal-Organic Framework Materials from a Unified Isotherm Analysis | The fundamental, angstrofluidic features of confined water and corresponding observations of hydrophobicity in microporous materials are dictated by molecular and continuum level phenomena, directed by surface and nanostructural interactions and characterized by isosteric heat of adsorption and micropore size. These features are critical to addressing the water-energy nexus and are foundational to a wide range of technologies involving biological or energy storage applications. However basic metrics for assessment of these features are currently absent from fundamental analyses. Proposed herein is a novel metric that is demonstrably capable of relating hydrophobic and hydrophilic isotherm types. It is coherently coupled with characterization methodology which not only circumvents difficulties inherent in other analyses but also partitions surface from structural hydrophobicity and is uniquely delivered in a simple, rigorous, analytic form. Moreover, transitions from hydrophobic to hydrophilic behavior are uniquely captured by unified isotherm analysis which explicitly links nine distinct adsorption equilibrium models. Subsequent simplification for characterization of water adsorption in 26 ostensibly hydrophobic, microporous, Metal-Organic Framework (MOF) materials yields Ising-Model-Modified-Kelvin-Analysis (IMMKA). Embedded in the analysis are concepts of nanocapillarity and nanowetting which directly deliver estimates of contact angle and isosteric heat that are consistent with independent assessments. The findings herein broadly offer means to successfully capture interactions that underpin hydrophobic observations, discriminate foundational features of confined water and advance fundamental descriptions of angstrofluidic phenomena. | Steven William Rutherford | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Physical and Chemical Properties; Surface | CC BY NC 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b20fa96dde43c9082726a9/original/novel-evaluation-of-hydrophobicity-in-micropores-of-nanostructured-metal-organic-framework-materials-from-a-unified-isotherm-analysis.pdf |
6571a08dcf8b3c3cd7026688 | 10.26434/chemrxiv-2023-0hc00 | The Mechanism of CO2 Electroreduction to Multi- carbon Products over Iron Phthalocyanine Single-Atom Catalyst | Carbon dioxide reduction reaction (CO2 RR) is a promising method for converting CO2 into value-added products. CO2 RR over single atom catalysts (SAC) is widely known to result in chemical compounds such as carbon monoxide and formic acid that contain only one carbon atom (C1). Indeed, at least two active sites are commonly believed to be required for C-C coupling to synthesize compounds such as ethanol and propylene (C2+ ) from CO2 . However, experimental evidence suggests that Iron Phthalocyanine (PcFe), which possesses only a single metal center, can produce a trace amount of C2+ products. To the best of our knowledge, the mechanism by which C2+ products are formed over a SAC such as PcFe is still unknown. Using density functional theory (DFT), we analyzed the mechanism of CO2 RR to C1 and C2+ products over PcFe. Due to the high concentration of bicarbonate at pH=7, CO2 RR competes with HCO3 – reduction. Our computations indicate, that bicarbonate reduction is significantly more favourable. However, the rate of this reaction is influenced by H3 O+ concentration. For the formation of C2+ products, our computations reveals that C-C coupling proceeds through the reaction between in-situ formed CO and PcFe("0")-CH2 or PcFe("-I")-CH2 intermediates. This reaction step is highly exergonic and requires only low activation energies of 0.44 eV and 0.24 eV for PcFe("0")-CH2 and PcFe("-I")-CH2 . The DFT results, in line with experimental evidence, suggest that C2+ compounds are produced over PcFe at low potentials whereas CH4 is still the main post-CO product. | Reza Khakpour; Kaveh Farshadfar; Si-Thanh Dong; Benedikt Lassalle-Kaiser; Kari Laasonen; Michael Busch | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6571a08dcf8b3c3cd7026688/original/the-mechanism-of-co2-electroreduction-to-multi-carbon-products-over-iron-phthalocyanine-single-atom-catalyst.pdf |
637440b121b45c6e2a1d0ec8 | 10.26434/chemrxiv-2022-cvjg7 | A machine learning q-RASPR approach for efficient predictions of the specific surface area of perovskites | In this study, the specific surface area of various perovskites was modeled using a novel quantitative read-across structure-property relationship (q-RASPR) approach, which clubs both Read-Across (RA) and quantitative structure-property relationship (QSPR) together. After optimization of the hyper-parameters, certain similarity-based error measures for each query compound were obtained. Clubbing some of these error-based measures with the previously selected features along with the Read-Across prediction function, a number of machine learning models were developed using Partial Least Squares (PLS), ridge regression (RR), linear support vector regression (LSVR), and random forest (RF) regression. Based on the external prediction quality and interpretability, the PLS model was selected as the best predictor which underscored the previously reported results. The finally selected model should efficiently predict specific surface areas of other perovskites for their use in photocatalysis. The new q-RASPR method also appears promising for the prediction of several other property endpoints of interest in materials science. | Arkaprava Banerjee; Agnieszka Gajewicz-Skretna; Kunal Roy | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637440b121b45c6e2a1d0ec8/original/a-machine-learning-q-raspr-approach-for-efficient-predictions-of-the-specific-surface-area-of-perovskites.pdf |
67bfcd3381d2151a023b0243 | 10.26434/chemrxiv-2025-4t8fh | Towards the Computational Design of Single Atom Alloys for Methane to Ethylene Conversion | Direct conversion of methane to value-added chemicals has been a longstanding challenge in leveraging abundant natural gas resources due to unfavorable C-H bond activation and coke formation. We recently evaluated stability and reactivity of single atom alloys (SAAs) formed by atomically doping 3d-5d transition metals on Cu(111) as catalysts for direct methane conversion to C2 hydrocarbons using density functional theory calculations. Here, to further develop catalyst design principles for this chemistry, we systematically evaluate kinetics of methane dehydrogenation and C-C coupling steps on ten promising Cu(111)-based SAAs and unearth descriptors that correlate with catalyst activity and selectivity. Our results show that ethylene formation is kinetically favored over ethane formation across all SAAs studied. Notably, catalytic activity of SAAs highly correlates with their selectivity for direct methane conversion to C2 products, highlighting the synergy between dopant and host metal in enhancing methane activation and preference towards C-C coupling. In addition, we identify C2H4 adsorption energy as an effective descriptor that guides the SAA reactivity for methane activation to ethylene. Combining all analyses, we discover that iridium dispersed on copper (Ir/Cu) SAA stands out as a highly active and selective catalyst for methane to ethylene conversion. These findings pave the way for high-throughput screening of a vast SAA chemical space for the chemistry of methane transformation. | Chengyu Zhou; Manish Kothakonda; Qing Zhao | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bfcd3381d2151a023b0243/original/towards-the-computational-design-of-single-atom-alloys-for-methane-to-ethylene-conversion.pdf |
60c746799abda263a4f8c73f | 10.26434/chemrxiv.11328347.v1 | Generalized Single Excitation Configuration Interaction: An Investigation into the Impact of the Inclusion of Non-Orthogonality on the Calculation of Core-Excited States | <div>In this paper, we investigate different non-orthogonal generalizations of the configuration interaction with single substitutions (CIS) method for the calculation of core-excited states. Fully non-orthogonal CIS (NOCIS) has been described previously for singlets and doublets and this paper reports the extension to triplet molecules. In addition to NOCIS, we present a novel method, 1C-NOCIS(1C-NOCIS), for open-shell molecules which is intermediate between NOCIS and the static exchange approximation (STEX). We explore this hierarchy of spin-pure methods for singlet, doublet, and triplet molecules and conclude that, while NOCIS provides the best results and preserves the spatial symmetry of the wavefunction, 1C-NOCIS retains much of the accuracy of NOCIS at a dramatically reduced cost. For molecules with closed-shell ground states, STEX and 1C-NOCIS are identical.</div> | Katherine J. Oosterbaan; Alec F. White; Diptarka Hait; Martin Head-Gordon | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746799abda263a4f8c73f/original/generalized-single-excitation-configuration-interaction-an-investigation-into-the-impact-of-the-inclusion-of-non-orthogonality-on-the-calculation-of-core-excited-states.pdf |
60c759bd0f50dbf8c0398740 | 10.26434/chemrxiv.14728206.v1 | Estimation of Binding Rates and Affinities from Multiensemble Markov Models and Ligand Decoupling | Accurate and efficient simulation of the thermodynamics and kinetics of protein-ligand interactions is crucial for computational drug discovery. Multiensemble Markov Model (MEMM) estimators can provide estimates of both binding rates and affinities from collections of short trajectories, but have not been systematically explored for situations when a ligand is decoupled through scaling of non-bonded interactions. In this work, we compare the performance of two MEMM approaches for estimating ligand binding affinities and rates: (1) the transition-based reweighting analysis method (TRAM) and (2) a Maximum Caliber (MaxCal) based method. As a test system, we construct a small host-guest system where the ligand is a single uncharged Lennard-Jones (LJ) particle, and the receptor is an 11-particle icosahedral pocket made from the same atom type. To realistically mimic a protein-ligand binding system, the LJ ε parameter was tuned, and the system placed in a periodic box with 860 TIP3P water molecules. A benchmark was performed using over 80 μs of unbiased simulation, and an 18-state Markov state model used to estimate reference binding affinities and rates. We then tested the performance of TRAM and MaxCal when challenged with limited data. Both TRAM and MaxCal approaches perform better than conventional MSMs, with TRAM showing better convergence and accuracy. We find that subsampling of trajectories to remove time correlation improves the accuracy of both TRAM and MaxCal, and that in most cases only a single biased ensemble to enhance sampled transitions is required to make accurate estimates. | Yunhui Ge; Vincent Voelz | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759bd0f50dbf8c0398740/original/estimation-of-binding-rates-and-affinities-from-multiensemble-markov-models-and-ligand-decoupling.pdf |
60c74e0b9abda20b8bf8d57d | 10.26434/chemrxiv.12690104.v1 | Data from Experiments on Bubbling Fluidization of Group B Glass Particles | <p>Bubbling fluidization experiments were performed in three
cylindrical columns having internal diameters of 2.5, 4 and 6 inches. Glass particles having a sauter mean diameter of 332 microns were
used, and the operating conditions were held constant in all the units.
Statistics of differential pressure and interface height are reported.</p> | Avinash Vaidheeswaran; Cheng Li; Huda Ashfaq; Xiongjun Wu; Steven Rowan; William Rogers | Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2020-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e0b9abda20b8bf8d57d/original/data-from-experiments-on-bubbling-fluidization-of-group-b-glass-particles.pdf |
60c7517c9abda25f30f8dc0b | 10.26434/chemrxiv.13173698.v1 | The Untargeted Capability of NMR Recognizes Adulterated Natural Products | Curcuma longa (turmeric) has a long ethnomedical background for common ailments, and Dietary
Supplements (DS) labelled as “Curcumin” (CDS) are a highly visible portion of today’s selfmedication market. Due to cost pressure, these CDS products are affected by economically
motivated adulteration with synthetic curcumin and are associated with unexpected toxicological
issues due to “residual” impurities. Using a combination of targeted and untargeted
(phyto)chemical analysis, this study investigated the botanical integrity of two commercial
“turmeric” CDS with vitamin and other additives that were associated with reported clinical cases
of hepatotoxicity. Analyzing multi-solvent extracts of the CDS by 100% quantitative 1H NMR
(qHNMR), alone and in combination with countercurrent separation (CCS), provided chemical
fingerprints that allowed both the targeted identification and quantification of declared components
and the untargeted recognition of adulteration. While confirming the presence of curcumin as a
major constituent, the universal detection capability of NMR identified significant residual
impurities. While the loss free nature of CCS captured a wide polarity range of declared and
unwanted chemical components and increased dynamic range, (q)HNMR determined their mass
proportions and chemical constitutions. The results demonstrate that NMR can recognize
undeclared constituents even if they represent a relatively minor gap in the mass balance of a DS
product. The chemical information associated with the missing 4.8% and 7.4% (m/m) in the two
commercial samples, exhibiting an otherwise adequate curcumin content of 95.2% and 92.6%,
pointed to a product integrity issue and adulteration with undeclared synthetic curcumin.
Impurities from synthesis are most plausibly the cause of the observed adverse clinical effects. The
study exemplifies how the simultaneously targeted and untargeted analytical principle of 100%
qHNMR method, performed with entry-level instrumentation (400 MHz), can enhance the safety
of DS by identifying adulterated, non-natural “natural” products<br /> | Seon Beom Kim; Jonathan Bisson; J. Brent Friesen; Luca Bucchini; Stefan Gafner; David
C. Lankin; Shao-Nong Chen; Guido Pauli; James McAlpine | Analytical Chemistry - General; Separation Science; Spectroscopy (Anal. Chem.) | CC BY 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7517c9abda25f30f8dc0b/original/the-untargeted-capability-of-nmr-recognizes-adulterated-natural-products.pdf |
650cbf01ed7d0eccc3fb0e64 | 10.26434/chemrxiv-2023-qfb1n-v2 | Elucidating the Competitive Adsorption of H2O and CO2 in CALF-20: New Insights for Enhanced Carbon Capture Metal-Organic Frameworks | In light of the pressing need for efficient carbon capture solutions, our study investigates the simultaneous adsorption of water (H2O) and carbon dioxide (CO2) as a function of relative humidity in CALF-20, a highly scalable and stable metal-organic framework (MOF). Advanced computer simulations reveal that, due to their similar interactions with the frame- work, H2O and CO2 molecules compete for the same binding sites, occupying similar void regions within the CALF-20 pores. This competition results in distinct thermodynamic and dynamical behavior of H2O and CO2 molecules, depending on whether one or both guest species are present. Notably, the presence of CO2 molecules forces the H2O molecules to form more connected hydrogen-bond networks within smaller regions, slowing water reorien- tation dynamics and decreasing water entropy. Conversely, the presence of water speeds up the reorientation of CO2 molecules, decreases CO2 entropy, and increases the propensity for CO2 to be adsorbed within the framework due to stronger water-mediated interactions. Due to the competition for the same void spaces, both H2O and CO2 molecules exhibit slower diffusion when molecules of the other guest species are present. These findings offer valuable strategies and insights to enhance the differential affinity of H2O and CO2 for MOFs specifically designed for carbon capture applications. | Ching-Hwa Ho; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650cbf01ed7d0eccc3fb0e64/original/elucidating-the-competitive-adsorption-of-h2o-and-co2-in-calf-20-new-insights-for-enhanced-carbon-capture-metal-organic-frameworks.pdf |
66c8b048a4e53c48765f6dfa | 10.26434/chemrxiv-2024-1skr0 | Expedited Aminoglutarimide C-N Cross-Coupling Enabled by High-Throughput Experimentation | A simple protocol for the direct Buchwald-Hartwig cross-coupling of (hetero)aryl halides with unprotected aminoglutarimide to afford diverse Cereblon Binding Motifs is disclosed. This C-N cross-coupling method development was enabled by high throughput combinatory screening of key reaction parameters namely solvents, temperatures and ligands. Scope studies revealed generality across various heteroaryl and aryl halides, with the reaction proceeding under mild conditions. In comparison, this method demonstrated strategic superiority over previously reported approaches, as evidenced by a significant step count reduction from known syntheses in the patent literature. | Jacqueline Gu; Martins Oderinde; Hui Li; Frederick Roberts; Jacob Ganley; Maximilian Palkowitz | Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c8b048a4e53c48765f6dfa/original/expedited-aminoglutarimide-c-n-cross-coupling-enabled-by-high-throughput-experimentation.pdf |
657031b1cf8b3c3cd7e56da0 | 10.26434/chemrxiv-2023-rs2xc-v2 | Zero-field splitting tensor of the triplet excited states of aromatic molecules: A valence full-π complete active space self-consistent field study | A method to predict D tensor in the molecular frame with multiconfigurational wavefunctions in large active space was proposed, and spin properties of the lowest triplets of aromatic molecules were examined with full-π active space; such calculations were challenging because the size of active space grows exponentially with the number of π electrons. In the method, the exponential growth of the complexity is resolved by the density matrix renormalization group (DMRG) algorithm. From the D tensor, we can directly determine the direction of the magnetic axes and the ZFS parameters, D- and E-values, of the phenomenological spin Hamiltonian with their signs, which are not usually obtained in ESR experiments. The method using the DMRG-CASSCF wavefunction can give correct results even when the sign of D- and E-values are sensitive to the accuracy of the prediction of the D tensor and existing methods fail to predict the correct magnetic axes. | Katsuki Miyokawa; Yuki Kurashige | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657031b1cf8b3c3cd7e56da0/original/zero-field-splitting-tensor-of-the-triplet-excited-states-of-aromatic-molecules-a-valence-full-complete-active-space-self-consistent-field-study.pdf |
660ad1b866c138172969f730 | 10.26434/chemrxiv-2024-nkfv0 | Mixed stereochemistry macrocycle acts as a helix-stabilizing peptide N-cap | Interactions between proteins and α-helical peptides are abundant in the human cell. Many of these interactions are linked to disease and have been the focus of drug discovery campaigns. However, the large interfaces formed between multiple turns of α-helix and a binding protein represent a significant challenge to inhibitor discovery. Modified peptides featuring helix-stabilizing macrocycles have shown promise as inhibitors of these interactions. Here, we tested the ability of N-terminal to side-chain thioether-cyclized peptides to inhibit the α-helix binding protein Mcl-1, by screening a trillion-scale peptide library using RaPID technology. The top enriched peptides were lariats, featuring a small, four amino acid N-terminal macrocycle followed by a short linear sequence that resembled the natural α-helical Mcl-1 ligands. These ‘Heliats’ (Helical lariats) bound Mcl-1 with mid-nM affinity, and inhibited the interaction between Mcl-1 and a natural peptide ligand. Macrocyclization was found to stabilize α-helical structures, and significantly contribute to affinity and potency. Yet, the 2nd and 3rd positions within the macrocycle were permissible to sequence variation, so that a minimal macrocyclic motif, of an N-acetylated D-phenylalanine at the 1st position thioether connected a cysteine at the 4th, could be grafted into a natural peptide and stabilize helical conformations. We found that D-stereochemistry is more helix-stabilizing than L- at the 1st position in the motif, as the D-amino acid can utilize polyproline II torsional angles that allow for more optimal intrachain hydrogen bonding. This mixed stereochemistry macrocyclic N-cap is synthetically accessible, requiring only minor modifications to standard solid-phase peptide synthesis, and its compatibility with RaPID peptide screening can provide ready access to helix-focused peptide libraries for de novo inhibitor discovery. | Fabian Hink; Julen Aduriz-Arrizabalaga; Xabier Lopez; Hiroaki Suga; David De Sancho; Joseph Matthew Rogers | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660ad1b866c138172969f730/original/mixed-stereochemistry-macrocycle-acts-as-a-helix-stabilizing-peptide-n-cap.pdf |
66c6cec0f3f4b05290b38ceb | 10.26434/chemrxiv-2024-ls64n | Molecular mechanism of the triplet states formation in bodipy-phenoxazine photosensitizer dyads confirmed by ab initio prediction of the spin polarization | Efficient formations of excited triplet states on the metal-free photosensitizer dyads, bodipy-phenoxazine (BDP-PXZ) and tetramethylbodipy-phenoxazine (TMBDP-PXZ), were investigated by ab initio calculations. We revealed the reason why two different triplet transient species, 3CT and 3BDP, can co-exist only for BDP-PXZ as observed in the previous study with the TR-EPR measurements. It was found that the state mixing of 3CT enables the transition from 1CT to 3CT and 3BDP states only for BDP-PXZ . This mixing effect is commonly seen in the singlet states of twisted intermolecular charge transfer molecules, though the key factor that determines the mixing of the excited states of the dyes was found to be the electron-donating ability of the substituents rather than their steric hindrance. The mechanism was corroborated by comparing the spin polarization ratio of the triplet spin-sublevels measured by the TR-EPR with the theoretical predictions. The spin polarization ratio of the triplets should contain information about the transition via intersystem crossing, e.g. the twisted angle of two chromophores of the dyad, and thus it can be a powerful tool to analyze the molecular mechanism of photochemical processes at the electronic structure level. These insights on molecular structures’ effect provided by this theoretical study would be a compass to molecular design for metal-free triplet photosensitizers. | Maria Kosaka; Katsuki Miyokawa; Yuki Kurashige | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c6cec0f3f4b05290b38ceb/original/molecular-mechanism-of-the-triplet-states-formation-in-bodipy-phenoxazine-photosensitizer-dyads-confirmed-by-ab-initio-prediction-of-the-spin-polarization.pdf |
60c7491fbb8c1aaaa93dadc3 | 10.26434/chemrxiv.12032670.v1 | Borinic Acids as New Fast-Responsive Triggers for Hydrogen Peroxide Detection. | Detection of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), which is responsible for numerous damages when overproduced, is crucial for a better understanding of H<sub>2</sub>O<sub>2</sub>-mediated signalling in physiological and pathological processes. For this purpose, various“<i>off-on</i>” small fluorescent probes relying on a boronate trigger have been developed. However, they suffer from low kinetics and do not allow forH<sub>2</sub>O<sub>2</sub>-detection<sub></sub>with a short response time. Therefore, more reactive sensors are still awaited. To address this issue, we have successfully developed the first generation of borinic-based fluorescent probes containing a coumarin-scaffold. We determined the <i>in vitro</i>kinetic constants of the probe toward H<sub>2</sub>O<sub>2</sub>-promotedoxidation. We measured 1.9x10<sup>4</sup>m<sup>-1</sup>.s<sup>-1</sup>as a second order rate constant, which is 10 000 faster than its boronic counterpart (1.8 m<sup>-1</sup>.s<sup>-1</sup>). This remarkable reactivity was also effective in a cellular context, rendering the borinic trigger an advantageous new tool for H<sub>2</sub>O<sub>2</sub>detection. | Blaise Gatin-Fraudet; Roxane Ottenwelter; Thomas Le Saux; Thomas Lombès; Aurélie Baron; Philippe Durand; Stephanie Norsikian; Gilles Doisneau; Yann Bourdreux; Dominique Guianvarc’h; Marie Erard; Ludovic Jullien; Dominique Urban; Boris Vauzeilles | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7491fbb8c1aaaa93dadc3/original/borinic-acids-as-new-fast-responsive-triggers-for-hydrogen-peroxide-detection.pdf |
6467bdabf2112b41e9d3a241 | 10.26434/chemrxiv-2021-fdd6d-v2 | Role of adatom defects in the adsorption of polyaromatic hydrocarbons on metallic substrates | The adsorption of polyaromatic hydrocarbons (PAHs) on metallic substrates is of interest in the field of optoelectronics, due to the possibility of designing complex materials with tunable properties through surface functionalization with organic molecules. Much of the modelling research in this field has focused on perfectly symmetrical (pristine) substrates. There is limited information on the effect of substrate irregularities, such as adatoms, on the binding of PAHs onto substrates. Here, we examine how the presence of substrate-bound adatoms affects the binding of coronene and hexahelicene monomers and dimers on Au(111) and Cu(111) substrates, using a density functional theory approach. We found that helicene monomers were more effectively able to adapt to the presence of the adatoms than coronene, by coiling around the adatoms. Whereas upon adsorption on a pristine (111) surface, coronene can establish significantly stronger dispersive interactions than helicenes, adatom defects reverse the trend. For helicenes, the extent of flattening near the surface and molecular coiling are strongly influenced by the size of the defect, as a result of the interplay between the molecule’s drive to maximize overlap with the underlying surface and the enhanced reactivity of the low-coordinated adatoms. | Dushanthi Dissanayake; Yarra Hassan; Emilian Tuca; Irina Paci | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6467bdabf2112b41e9d3a241/original/role-of-adatom-defects-in-the-adsorption-of-polyaromatic-hydrocarbons-on-metallic-substrates.pdf |
62696897368ab65c018f372e | 10.26434/chemrxiv-2022-x5wgq | A Versatile DIY Route for Incorporation of a Wide Range of Electrode Materials into Rotating Ring Disk Electrodes | Rotating ring disk electrodes (RRDEs) are a powerful and versatile tool for mechanistically investigating electrochemical reactions at electrode surfaces, particularly in the area of electroanalysis and catalysis. Despite their importance only limited electrode materials (typically glassy carbon, platinum and gold) and combinations thereof are available commercially. In this work we present a method employing 3D printing in conjunction with machined brass components to produce housing which can accommodate any electrode material in e.g. pressed powdered pellet, wafer, rod, foil or vapor deposited onto a conductive substrate, form. In this way the range and usability of RRDEs is extended. This custom DIY approach to producing RRDEs, also enables RRDEs to be produced at a significant fraction of the cost of commercial RRDEs. To illustrate the versatility of our approach, co-planar boron doped diamond (BDD) RRDEs are fabricated for the first time, using the approach described. Experimental collection efficiencies for the redox couple FcTMA+/FcTMA2+ are found to be very close to those predicted theoretically. BDD electrodes serve as an ideal electrocatalyst support due to their low background currents, wide solvent window in aqueous solution and chemical and electrochemical stability in acid and alkali solutions. The BDD RRDE configuration is employed to investigate the importance of surface incorporated non-diamond carbon in BDD on hydrogen peroxide generation via the oxygen reduction reaction in acid solutions. | Joshua Tully; Zhaoyan Zhang; Irina Terrero Rodríguez; Lee Butcher; Julie Macpherson | Analytical Chemistry; Energy; Analytical Apparatus; Electrochemical Analysis; Fuel Cells | CC BY NC 4.0 | CHEMRXIV | 2022-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62696897368ab65c018f372e/original/a-versatile-diy-route-for-incorporation-of-a-wide-range-of-electrode-materials-into-rotating-ring-disk-electrodes.pdf |
66da1fb612ff75c3a185b081 | 10.26434/chemrxiv-2024-qzb1v | Computational Investigation of the Chemical Bond Between An(III) Ions and Soft Donor Ligands | The chemical bonding of actinide metal ions with both arene and borohydride ligands is explored via quantum chemical methods to understand how the transuranic elements differ from uranium with respect to their interaction with soft donor ligands. Specifically, the [An(arene)(BH4)3] complexes (AnMe6 , An = Np, Pu, U, arene C6Me6) are studied. Density functional theory (DFT) shows that, when the complexes are neutral, the interaction between the metal ions and the soft-donor ligands is governed by electrostatic interactions. Molecular orbital analysis, with both the DFT and the complete active space (CASSCF) method, shows that as one moves from U to Pu, the energy gap between the 5f orbitals of the metal ion and the ligand π∗ orbitals gradually increases, leading to a weaker metal-ligand interaction. Upon reduction to AnMe6−, the An–arene distances contract by 0.1-0.2 ̊A compared to the neutral complex, leading stronger metal-ligand interactions with varying degrees of δ-bonding depending on the actinide. Specifically, orbital mixing decreases from UMe6− to PuMe6−. In the high-spin state, UMe6− has two electrons in the two δ-bonding orbitals, while NpMe6− and PuMe6− have only one electron in a single δ-bonding orbital. In the lower-spin states, these bonding orbitals become even more delocalized and the population of the δ∗ orbital increases from U to Pu. This is consistent with the increased An–arene distances, weaker interactions, and decreasing covalency across the series. | SABYASACHI ROY CHOWDHURY; Naomi Rehberg; Bess Vlaisavljevich | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bonding; Lanthanides and Actinides; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66da1fb612ff75c3a185b081/original/computational-investigation-of-the-chemical-bond-between-an-iii-ions-and-soft-donor-ligands.pdf |
60c75123337d6cf367e284b5 | 10.26434/chemrxiv.13123178.v1 | Controlling the Shape and Chirality of an Eight-crossing Molecular Knot | <p>The knotting of biomolecules impacts their function, and enables them to carry out new tasks. Likewise, complex topologies underpin the operation of many synthetic molecular machines. The ability to generate and control more complex knotted architectures is essential to endow these machines with more advanced functions. Here we report the synthesis of a molecular knot with eight crossing points, consisting of a single organic loop woven about six templating metal centres, <i>via</i> one-pot self-assembly from a simple pair of dialdehyde and diamine subcomponents and a single metal salt. The structure and topology of the knot were established by NMR spectroscopy, mass spectrometry and X-ray crystallography. Upon demetallation, the purely organic strand relaxes into a symmetric conformation, whilst retaining the topology of the original knot. This knot is topologically chiral, and may be synthesised diastereoselectively through the use of an enantiopure diamine building block.<b></b></p> | John P. Carpenter; Charlie McTernan; Jake L. Greenfield; Roy Lavendomme; Tanya
K. Ronson; Jonathan Nitschke | Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75123337d6cf367e284b5/original/controlling-the-shape-and-chirality-of-an-eight-crossing-molecular-knot.pdf |
60c774dc4c89190187ad4f3a | 10.26434/chemrxiv.10000232.v5 | Mechanical and structural consequences of associative dynamic cross-linking in acrylic diblock copolymers | <p>The composition of low-T<sub>g</sub> <i>n</i>-butylacrylate-<i>block</i>-(acetoxyaceto)ethyl acrylate block polymers is investigated as a strategy to tune the properties of dynamically cross-linked vinylogous urethane vitrimers. As the proportion of the cross-linkable block is increased, the thermorheological properties, structure, and stress relaxation evolve in ways that cannot be explained by increasing cross-link density alone. Evidence is presented that network connectivity defects such as loops and dangling ends are increased by microphase separation. The thermomechanical and viscoelastic properties of block copolymer-derived vitrimers arise from the subtle interplay of microphase separation and network defects.</p><div><br /></div><p></p> | Jacob Ishibashi; Ian Pierce; Alice Chang; Aristotelis Zografos; Bassil El-Zaatari; Yan Fang; Steven Weigand; Frank S. Bates; Julia Kalow | Organic Polymers; Polymer morphology; Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c774dc4c89190187ad4f3a/original/mechanical-and-structural-consequences-of-associative-dynamic-cross-linking-in-acrylic-diblock-copolymers.pdf |
60c7494abdbb89e9b3a39140 | 10.26434/chemrxiv.12046905.v1 | Binary and Ternary 3D nanobundles Transition Metal Oxides Functionalized Carbon Xerogels as Electrocatalysts toward Oxygen Reduction Reaction | This work describes preparation of novel binary and ternary transition metal oxides functionalized carbon xerogel. The characterization data reveals that the functionalized metal oxides are in the form of nanobundles with different lengths and widths. these prepared electrocatalysts show excellent performance as electrocatalysts for oxygen reduction reaction. | Abdalla Abdelwahab; Francisco Carrasco-Marín; Agustín F. Pérez-Cadenas | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7494abdbb89e9b3a39140/original/binary-and-ternary-3d-nanobundles-transition-metal-oxides-functionalized-carbon-xerogels-as-electrocatalysts-toward-oxygen-reduction-reaction.pdf |
66b147ad01103d79c5d3cc92 | 10.26434/chemrxiv-2024-dm50n | LiCOMPGNN - Lightweight Contextual Message Passing for Crystalline Materials Property Prediction | Graph neural networks have recently met huge success in various inference tasks including materials property prediction amongst many others. Nevertheless, having an inherently locally-based representation capacity as they do, global representation of materials' structures can only only be achieved by expanding the model complexity which in turn scales up training times and memory consumption. In this work we focus on efficiently capturing global interactions ``in-model'', through long-range edge attentions with minimal memory footprints. We introduce a novel ``contextual'' message passing scheme that better captures global interactions by attending on edges from both the local and global environment of each node in an edge-update fashion. The performance of the proposed model (LiCOMPGNN) is tested on a diverse set of materials property prediction benchmarks and demonstrates competitiveness against state-of-the-art models in several prediction tasks whilst being an order of magnitude smaller in terms of trainable parameters. We further augment the framework to a multiplex graph setting for solid-state data with reciprocal space features taken into account in a multimodal message passing regime. We demonstrate the representation capacity of the proposed variant along with others in maintaining supercell invariance in crystalline property prediction tasks. | Zachary Humphreys; Xenophon Evangelopoulos; Stavros Gerolymatos; Edward O. Pyzer-Knapp; Andrew I. Cooper | Theoretical and Computational Chemistry; Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b147ad01103d79c5d3cc92/original/li-compgnn-lightweight-contextual-message-passing-for-crystalline-materials-property-prediction.pdf |
6612d62e91aefa6ce10b9ae2 | 10.26434/chemrxiv-2024-fvzpq | Guidance on how to use the IUPAC Gold Book as a canonical source for textual definitions in chemical ontologies | This whitepaper aims to provide guidance to improve standardization and quality of ontologies development and curation concerning term definitions. We outline an approach on how definitions of The IUPAC Compendium of Chemical Terminology (colloquially known as the "Gold Book") could be applied as a definition source for scientific ontologies. It addresses domain experts and ontology developers equally. We summarize good practices on the writing of ontology in general and how these can be utilized by incorporating Gold Book definitions for writing Gold Book-based ontology definitions. Several examples are provided for such term definitions including recommendations on how to reference Gold Book definitions. | Philip Strömert; Johannes Hunold; Stuart Chalk; Leah McEwen; Oliver Koepler | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6612d62e91aefa6ce10b9ae2/original/guidance-on-how-to-use-the-iupac-gold-book-as-a-canonical-source-for-textual-definitions-in-chemical-ontologies.pdf |
66f9f8f912ff75c3a1e46cef | 10.26434/chemrxiv-2024-rwz5n | Switchable and stereospecfic C-glycosylation strategy via formal functional group deletion | Carbohydrates constitute an important class of biologically relevant natural products. Among the synthetic glycomimetics, C-glycosides are particularly interesting due to their chemical and metabolic stability towards acidic and enzymatic hydrolysis at the anomeric position. The stereochemical outcomes of traditional methodologies to access C-glycosides rely heavily on substrate control. Herein, we report the first synthetic strategy to access diverse C-glycosides with precise stereochemical control at the anomeric position via formal functional group deletion, where both α- and β-anomers of furanoses and pyranoses can be obtained as single stereoisomers. Additionally, the broad scope of heterocyclic C-glycosides obtained via this strategy further illustrates its potential for empowering future application in both chemical biology research and drug discovery. | Xiaoshen Ma; Stephen Sujansky | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f9f8f912ff75c3a1e46cef/original/switchable-and-stereospecfic-c-glycosylation-strategy-via-formal-functional-group-deletion.pdf |
60c7453cbdbb8917daa389b5 | 10.26434/chemrxiv.9989711.v1 | Cancer Cells Possess Different Isotopic Enrichment | Although the dynamics of telomeres during the life expectancy of normal cells have been extensively studied, there are still some unresolved issues regarding this research field. For example, the conditions required for telomere shortening leading to malignant transformation are not fully understood. In this work, we mass analyzed DNA of normal and cancer cells for comparing telomere isotopic compositions of white blood cells and cancer cells. We have found that the 1327 Da and 1672 Da characteristic telomere mass to charge cause differential mass distributions of about 1 Da for determining isotopic variations among normal cells relative to cancer cells. These isotopic differences are consistent with a prior theory that replacing primordial isotopes of 1H, 12C, 14N, 16O, 24Mg, 31P and/or 32S by nonprimordial, uncommon isotopes of 2D, 13C, 15N, 17O, 25Mg and/or 33S leads to altered enzymatic dynamics for modulating DNA and telomere codons towards transforming normal cells to cancer cells. The prior theory and current data are consistent also with a recently observed non-uniform methylation in DNA of cancer cells relative to more uniform methylation in DNA of normal cells.<br /><br /> | Reginald Little; Orit Uziel | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453cbdbb8917daa389b5/original/cancer-cells-possess-different-isotopic-enrichment.pdf |
64bd86d7ae3d1a7b0d38d40f | 10.26434/chemrxiv-2023-qxtdc | Clarifying the local structure of dopants in garnet solid-state electrolytes for lithium-ion batteries | The high Li-ion conductivity and wide electrochemical stability of Li-rich garnets (Li7La3Zr2O12) make them one of the leading solid electrolyte candidates for solid-state batteries. Dopants such as Al and Ga are typically used to enable stabilisation of the high Li+ ion-conductive cubic phase at room temperature. Although numerous studies exist that have characterized the electrochemical properties, structure, and lithium diffusion in Al- and Ga-LLZO, the local structure and site occupancy of dopants in these compounds are not well understood. Two broad 27Al or 69,71Ga resonances are often observed with chemical shifts consistent with tetrahedrally coordinated Al/Ga in the magic angle spinning nuclear magnetic resonance (MAS-NMR) spectra of both Al- and Ga-LLZO, which have been assigned to either Al and/or Ga occupying 24d and 96h/48g sites in the LLZO lattice or to the different Al/Ga configurations that arise from different arrangements of Li around these dopants. In this work, we unambiguously show that the side products γ-LiAlO2 and LiGaO2 lead to the high frequency resonance observed by NMR spectroscopy and that both Al and Ga only occupy the 24d site in the LLZO lattice. Furthermore, it was observed that the excess Li often used during synthesis leads to the formation of these side-products by consuming the Al/Ga dopants. In addition, the consumption of Al/Ga dopants lead to the tetragonal phase formation commonly observed in the literature even after careful mixing of precursors. The side-products can exist even after sintering, thus controlling the Al/Ga content in the LLZO lattice, substantially influencing the lithium-ion conductivity in LLZO as measured here by electrochemical impedance spectroscopy. | Sundeep Vema; Astrid Berge; Supreeth Nagendran; Clare Grey | Materials Science; Inorganic Chemistry; Energy; Ceramics; Solid State Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bd86d7ae3d1a7b0d38d40f/original/clarifying-the-local-structure-of-dopants-in-garnet-solid-state-electrolytes-for-lithium-ion-batteries.pdf |
661f153b21291e5d1dfc9d40 | 10.26434/chemrxiv-2024-zvtvr-v2 | Illuminating Anions in Biology with Genetically Encoded Fluorescent Biosensors | Anions are critical to all life forms. Anions can be absorbed as nutrients or biosynthesized. Anions shape a spectrum of fundamental biological processes at the organismal, cellular, and subcellular scales. Genetically encoded fluorescent biosensors can capture anions in action across time and space dimensions with microscopy. The firsts of such technologies were reported more than 20 years ago for monoatomic chloride and polyatomic cAMP anions. However, the recent boom of anion biosensors illuminates the unknowns and opportunities that remain for toolmakers and end users to meet across the aisle to spur innovations in biosensor designs and applications for discovery anion biology. In a first-of-its-kind review, we will canvas progress made over the last three years for biologically relevant anions that can be classified as halides, oxyanions, carboxylates, and nucleotides. | Mariah Cook; Shelby Phelps; Jasmine Tutol; Derik Adams; Sheel Dodani | Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f153b21291e5d1dfc9d40/original/illuminating-anions-in-biology-with-genetically-encoded-fluorescent-biosensors.pdf |
61d47d0602c2147c1f3c5399 | 10.26434/chemrxiv-2022-99kr5 | Novel copolymers of vinyl acetate. 4. Halogen ring-substituted ethyl 2-cyano-3-phenyl-2-propenoates | Novel copolymers of vinyl acetate and halogen ring-substituted ethyl 2-cyano-3-phenyl-2-propenoates, RPhCH=C(CN)CO2C2H5 (where R is 2-Br, 3-Br, 4-Br, 2-Cl, 3-Cl, 4-Cl, 2-F, 3-F, 4-F, 2,3-dichloro, 2,4-dichloro, 2,6-dichloro, 3,4-dichloro, 2,4-difluoro, 2-bromo-3,4-dimethoxy) were prepared in solution with radical initiation at 70C. The propenoates were synthesized by the piperidine catalyzed Knoevenagel condensation of halogen ring-substituted benzaldehydes and ethyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C-NMR. The compositions of the copolymers were calculated from nitrogen analysis and the structures were analyzed by IR, 1H and 13C-NMR. Thermal behavior of the copolymers was studied by DSC (Tg) and TGA. Decomposition of the copolymers in nitrogen occurred in two steps, first in the 159-500ºC range with residue (8.8-15.2 wt%), which then decomposed in the 500-650ºC range. | Benjamin Y. Killam; Rebecca J. Amend; Margaret A. Budz; Ashley B. Collins; Shannon M. Hinz; Amanda C. Johnson; Lesli N. Kibler; Sirena Z. Salem; British A. Scott; Irene Skukan; Erin K. Staunton; Katherine J. Sweeney; Andrew Strang; Rhiannon E. Tennant; Daniel Weber; Ayesha Z. Worsham; Gregory B Kharas | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d47d0602c2147c1f3c5399/original/novel-copolymers-of-vinyl-acetate-4-halogen-ring-substituted-ethyl-2-cyano-3-phenyl-2-propenoates.pdf |
60c745e1bdbb896d79a38afa | 10.26434/chemrxiv.10280507.v1 | Increasing the Cytotoxicity of Ru(II) Polypyridyl Complexes by Tuning the Electronic Structure of Dioxo Ligands | <div>Due to the great potential expressed by an anticancer drug candidate previously reported by our group, namely Ru-sq ([Ru(DIP)2(sq)](PF6) (DIP: 4,7-diphenyl-1,10-phenanthroline, sq: semiquinonate ligand), we describe in this work a structure-activity relationship (SAR) that involves a broader range of derivatives resulting from the coordination of different catecholate-like dioxoligands to the same Ru(DIP)2 core. More in detail, we chose catechols carrying either electron-donating or electronwithdrawing groups EDG or EWG and investigated the physico-chemical and biological properties of their complexes. Several pieces of experimental evidences demonstrated that the coordination of catechols bearing EDGs led to deep red positively charged complexes 1–4 in which the preferred oxidation state of the dioxoligand is the uninegatively charged semiquinonate. Complexes 5 and 6, on the other hand, are blue/violet neutral complexes which carry an EWG substituted dinegatively charged catecholate ligand. The biological investigation of complexes 1–6 led to the conclusion that the difference in their physico-chemical properties has a strong impact on their biological activity. Thus, complexes 1–4 expressed much higher cytotoxicities than complexes 5 and 6. Complex 1 constitutes the most promising compound of the series and was selected for a more in-depth biological investigation. Apart from its remarkably high cytotoxicity (IC50 = 0.07–0.7 μM in different cancerous cell lines) complex 1 was taken up by HeLa cells very efficiently by a passive transportation mechanism. Moreover, its moderate accumulation in several cellular compartments (i.e. nucleus, lysosomes, mitochondria and cytoplasm) is extremely advantageous in the search of a potential drug with multiple modes of action. Further DNA metalation and metabolic studies pointed to the direct interaction of complex 1 with DNA and to the severe impairment of the mitochondrial function. Multiple targets, together with its outstanding cytotoxicity, make complex 1 a valuable candidate in the field of chemotherapy research.</div> | Anna Notaro; Marta Jakubaszek; Nils Rotthowe; Federica Maschietto; Patrick Felder; Bruno Goud; Mickaël Tharaud; Ilaria Ciofini; Fethi Bedioui; Rainer
F. Winter; Gilles Gasser | Bioinorganic Chemistry; Electrochemistry; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745e1bdbb896d79a38afa/original/increasing-the-cytotoxicity-of-ru-ii-polypyridyl-complexes-by-tuning-the-electronic-structure-of-dioxo-ligands.pdf |
60c741a79abda26c6ff8beb9 | 10.26434/chemrxiv.8075204.v1 | QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface | The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results confirm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces. | Prasanth Babu Ganta; Oliver Kühn; Ashour A. Ahmed | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a79abda26c6ff8beb9/original/qm-mm-simulations-of-organic-phosphorus-adsorption-at-the-diaspore-water-interface.pdf |
60c74bfebdbb899749a396d0 | 10.26434/chemrxiv.12407711.v1 | Identification of promising drug candidates against Non-Structural Protein 15 (NSP15) from SARS-CoV-2: an in silico assisted drug-repurposing studies | <div>The recent COVID-19 pandemic caused by SARS-CoV-2 has recorded a high number of infected people across the globe. The notorious nature of the virus makes it necessary for us to identify promising therapeutic agents in a time-sensitive manner. The current study utilises an <i>in silico</i> based drug repurposing approach to identify potential drug candidates targeting non-structural protein 15 (NSP15), i.e. a uridylate specific endoribonuclease of SARS-CoV-2</div><div>which plays an indispensable role in RNA processing and viral immune evasion from the host immune system. NSP15 was screened against an in-house library of 123 antiviral drugs obtained from the DrugBank database from which three promising drug candidates were identified based on their estimated free energy of binding (<i>ΔG</i>), estimated inhibition constant (<i>Ki</i>), the orientation of drug molecules in the active site and the key interacting residues of</div><div>NSP15. The MD simulations were performed for the selected NSP15-drug complexes along with free protein to mimic on their physiological state. The binding free energies of the selected NSP15-drug complexes were also calculated using the trajectories of MD simulations of NSP15-drug complexes through MM/PBSA (Molecular Mechanics with Poisson-Boltzmann and surface area solvation) approach where NSP15-Simeprevir (-242.559 kJ/mol) and NSP15-Paritaprevir (-149.557 kJ/mol) exhibited the strongest binding affinities. Together with the results of molecular docking, global dynamics, essential dynamics and binding free energy analysis, we propose that Simeprevir and Paritaprevir are promising drug candidates for the inhibition of NSP15 and could act as potential therapeutic agents against SARS-CoV-2.</div> | Rameez Jabeer Khan; Rajat Kumar Jha; Ekampreet Singh; Monika Jain; Gizachew Muluneh Amera; Rashmi Prabha Singh; Jayaraman Muthukumaran; Amit Kumar Singh | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bfebdbb899749a396d0/original/identification-of-promising-drug-candidates-against-non-structural-protein-15-nsp15-from-sars-co-v-2-an-in-silico-assisted-drug-repurposing-studies.pdf |
60c753654c8919a513ad431e | 10.26434/chemrxiv.13488789.v1 | Large Peptide Permeation Through a Membrane Channel: Understanding Protamine Translocation Through CymA from Klebsiella Oxytoca | Quantifying the passage of the large peptide protamine (Ptm) across CymA, a passive channel for cyclodextrin uptake,
is in the focus of this study. Using a reporter-pair based fluorescence membrane assay we detected the entry of Ptm into liposomes
containing CymA. The kinetics of the Ptm entry was independent of its concentration suggesting that the permeation across CymA
is the rate-limiting factor. Furthermore, we reconstituted single CymA channels into planar lipid bilayers and recorded the ion
current fluctuations in the presence of Ptm. To this end, we were able to resolve the voltage-dependent entry of single Ptm peptide
molecules into the channel. Extrapolation to zero voltage revealed about 1-2 events per second and long dwell times, in agreement
with the liposome study. Applied-field and steered molecular dynamics simulations provided an atomistic view on the permeation.
It can be concluded that a concentration gradient of 1 M Ptm leads to a translocation rate of about 1 molecule per second and
per channel. | Sushil Pangeni; Jigneshkumar Dahyabhai Prajapati; Jayesh Arun Bafna; Nilam Mohamed; Werner M. Nau; Ulrich Kleinekathöfer; Mathias Winterhalter | Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753654c8919a513ad431e/original/large-peptide-permeation-through-a-membrane-channel-understanding-protamine-translocation-through-cym-a-from-klebsiella-oxytoca.pdf |
65d71d9e9138d23161b50e0c | 10.26434/chemrxiv-2024-c4z9r | Structure-Activity Relationships of Glucose-based PdII-Bis(NHC) Complexes in a model Suzuki-Miyaura Reaction | The authors of this work have optimized a novel synthetic route towards glucose-based Pd(II)-bis(NHC) complexes in only 4 steps with total yields up to 73 %. The synthesis route encompasses an Appel reaction towards 6-iodo-glucopyranosides, followed by acyl-protection, then quaternization with imidazoles and finally the conversion of these acyl-protected glucosyl imidazolium salts to their respective palladium(II)bis(NHC) complexes, via an intermediary silver(I) complex. Overall, 11 acyl-protected glucosyl imidazolium iodides as NHC-precursors and 14 complexes have been synthesized. The structure-activity relationships of different functionalizations in these complexes and their reactivity in a model Suzuki-Miyaura between bromobenzene and 4-tolueneboronic acid reaction has been investigated, and a highly reactive complex leading to >99 % yield at 0.005 mol% catalytic loading has been found. | Hannes Ziems; Mirai Komabayashi; Paul Lehmann; Alexander Villinger; Stefan Jopp | Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d71d9e9138d23161b50e0c/original/structure-activity-relationships-of-glucose-based-pd-ii-bis-nhc-complexes-in-a-model-suzuki-miyaura-reaction.pdf |
65b6a35f9138d23161ecf45a | 10.26434/chemrxiv-2024-xx699 | Colloidal Synthesis of Metallodielectric Janus Matchsticks | Metallodielectric Janus particles, due to their dual composition and anisotropic properties, have found applications in catalysis, actuation, and optical applications. Their practical applications are limited by the difficulty of controlling their structures while allowing mass production. In this work, we introduce a gram-scale synthesis of matchstick-shaped metallodielectric Janus particles, which feature a gold-coated silica sphere and a straight silica rod. SiO2 Janus matchsticks are synthesized in one batch by growing amine-functionalized SiO2 spheres at the end of SiO2 rods. The amine groups on the sphere surface provide nucleation sites for the chemical deposition of a gold nanolayer that yields the Au-SiO2 Janus matchsticks. We show that the aspect ratio of the Janus matchsticks can be controlled by the length of the SiO2 rods. As both silica growth and gold coating can be performed in large reaction volumes, gram-level metallodielectric Janus matchsticks can be produced for potential use as functional colloidal materials. | Yijiang Mu; Wendi Duan; Yuxuan Dai; Patrick Sullivan; Leila Deravi; Yufeng Wang; Daeyeon Lee | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b6a35f9138d23161ecf45a/original/colloidal-synthesis-of-metallodielectric-janus-matchsticks.pdf |
647ef139e64f843f4167e60e | 10.26434/chemrxiv-2022-xnlqz-v2 | A flexible, scalable generative network for self-supervised tomographic image reconstruction | We present a lightweight and scalable artificial neural network architecture which is used to reconstruct a tomographic image from a given sinogram. A self-supervised learning approach is used where the network iteratively generates an image that is then converted into a sinogram using the Radon transform; this new sinogram is then compared with the sinogram from the experimental dataset using a combined mean absolute error and structural similarity index measure loss function to update the weights of the network accordingly. We demonstrate that the network is able to reconstruct images that are larger than 1024 × 1024. Furthermore, it is shown that the new network is able to reconstruct images of higher quality than conventional reconstruction algorithms, such as the filtered back projection and iterative algorithms (SART, SIRT, CGLS), when sinograms with angular undersampling are used. The network is tested with simulated data as well as experimental synchrotron X-ray micro-tomography and X-ray diffraction computed tomography data. | Hongyang Dong; Simon D.M. Jacques; Winfried Kockelmann; Stephen W. T. Price; Robert Emberson; Dorota Matras; Yaroslav Odarchenko; Vesna Middelkoop; Athanasios Giokaris; Olof Gutowski; Ann-Christin Dippel; Martin v. Zimmermann; Andrew M. Beale; Keith T. Butler; Antonis Vamvakeros | Materials Science | CC BY 4.0 | CHEMRXIV | 2023-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647ef139e64f843f4167e60e/original/a-flexible-scalable-generative-network-for-self-supervised-tomographic-image-reconstruction.pdf |
60c74378f96a00fccf286807 | 10.26434/chemrxiv.9224483.v1 | Reciprocal Polarizable Embedding with a Transferable H2O Potential Function II: Application to (H2O)n Clusters & Liquid Water | The manuscript analyzes the accuracy of our recently developed reciprocal polarizable embedding scheme, where a density functional theory model of the QM region is coupled to a dipole- and quadrupole polarizable water potential of the MM region. We present calculations of water clusters and liquid water where we analyze the energy, atomic forces and total polarization to demonstrate that artifacts in energy and polarization introduced by the QM/MM coupling are small and well-behaved. Furthermore, our methodology improves the consistency of the structure of optimized water hexamer geometries when compared to results obtained with models that neglect polarization. Additionally, the manuscript provides evidence that our coupling scheme eliminates artifacts in the structure of liquid water obtained with simpler electrostatic embedding models. | Asmus Ougaard Dohn; Elvar Jónsson; Hannes Jonsson | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74378f96a00fccf286807/original/reciprocal-polarizable-embedding-with-a-transferable-h2o-potential-function-ii-application-to-h2o-n-clusters-liquid-water.pdf |
64f8481b3fdae147fa9a2421 | 10.26434/chemrxiv-2023-bm0gl | Overcoming the Strong Metal-support Interaction in Ni Clusters/TiO2 Catalyst for Selective CO2 Hydrogenation | The reverse water gas shift (RWGS) reaction is an essential step for CO2 hydrogenation, in which developing efficient and low-cost catalysts is highly desirable. Because of the excellent catalytic property in hydrogenation reaction, Ni nanoparticles are used as catalysts for CO2 methanation. However, Ni nanoparticles are very susceptible to strong metal-support interaction (SMSI) with reducible oxides at high temperatures, preventing its applications in the RWGS reaction. Hence, we develop a strategy to prepare SMSI-resistant Ni-clusters onto the surface of hydroxylated TiO2. The nickel atoms were deposited on the hydroxylated TiO2 in single-atom form and subsequently transformed to clusters with an average particle size of 1 nm after hydrogen treatment. The coating phenomenon of Ni by TiO2 due to the SMSI effect is avoided, so as to achieve the enhanced catalytic performance and excellent stability at as high as 600 C for the RWGS reaction. The strategy developed in this work pave a way for fabricating SMSI-resistant metal catalysts that can widely utilized in sustainable catalysis reactions. | Jin-Ying Li; Xiao-Meng Lai; Hao Gu; Cong-Xiao Wang; Xin-Pu Fu; Wei-Wei Wang; Qiang Fu; Feng Ryan Wang; Chao Ma; Chunjiang Jia | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f8481b3fdae147fa9a2421/original/overcoming-the-strong-metal-support-interaction-in-ni-clusters-ti-o2-catalyst-for-selective-co2-hydrogenation.pdf |
67a3513e6dde43c908ad24b2 | 10.26434/chemrxiv-2025-fqj23 | Modular, Three-Component and Concurrent One-Pot Libraries of γ-Keto Sulfones and γ-Keto Phosphine Oxides. Brønsted Acidic Eutectic Mixtures Are the Answer | A modular, three-component, and sustainable one-pot/one-step protocol has been developed for the efficient and regioselective synthesis of libraries of γ-keto sulfones and γ-keto phosphine oxides through concurrent C-C and C-X bond formation (X = S or P). The acidic eutectic mixture ChCl/p-TSA·H2O (1:2) (ChCl = choline chloride; p-TSA = p-toluenesulfonic acid) serves as both promoter and reaction medium. This transformation involves a cascade process comprising three consecutive steps: i) hydration of terminal alkynes to methyl ketones; ii) Claisen-Schmidt condensation with aldehydes, and iii) Sulfa-Michael or Phospha-Michael additions using sodium sulfinates or secondary phosphine oxides, respectively. The methodology provides high yields (up to 99%), excellent atom economy, and operational simplicity, as the products are isolated without the use of any toxic volatile organic solvents (VOCs) or tedious chromatographic purification. Its modular nature accommodates a broad range of substrates, including electron-rich and electron-deficient components, demonstrating robustness and versatility (112 examples). Furthermore, the protocol enables scalable (ten-fold) and recyclable (3 cycles) synthesis of biologically relevant γ-keto derivatives under green conditions (E-factor ≤ 10), offering a general strategy for sustainable and modular C-C and C-X bond-forming reactions. | Marina Ramos-Martín; Joaquín García-Álvarez; Alejandro Presa Soto | Organic Chemistry; Inorganic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a3513e6dde43c908ad24b2/original/modular-three-component-and-concurrent-one-pot-libraries-of-keto-sulfones-and-keto-phosphine-oxides-br-nsted-acidic-eutectic-mixtures-are-the-answer.pdf |
645285aa1ca6101a45b94f2d | 10.26434/chemrxiv-2023-7cf9d | Carbon Dioxide Radical Anion by Photoinduced Equilibration between Formate Salts and [11C, 13C, 14C]CO2 : Application to Carbon Isotope Radiolabeling | The need for carbon-labeled radiotracers is increasingly higher in drug discovery and development (carbon-14, -, t1/2 = 5730 years) as well as in PET, for in vivo molecular imaging applications (carbon-11, +, t1/2 = 20.4 min). However, the structural diversity of radiotracers is still systematically driven by the narrow available labeled sources and methodologies. In this context, the emergence of carbon dioxide radical anion chemistry might set forth potential unexplored opportunities. Based on a dynamic isotopic equilibration between formate salts and [13C, 14C, 11C]CO2, C-labeled radical anion CO2●- could be accessed under extremely mild conditions within seconds. This methodology was successfully applied to hydro-carboxylation and bis-carboxylation reactions in late-stage carbon isotope labeling of pharmaceutically relevant compounds. The relevance of the method in applied radiochemistry was showcased by the whole-body PET biodistribution profile of [11C]oxaprozin in mouse. | Augustin Malandain ; Maxime Molins; Alexandre Hauwelle; Alex Talbot; Olivier Loreau; Timothée D'Anfray; Sébastien Goutal; Nicolas Tournier; Frédéric Taran; Fabien Caillé; Davide Audisio | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645285aa1ca6101a45b94f2d/original/carbon-dioxide-radical-anion-by-photoinduced-equilibration-between-formate-salts-and-11c-13c-14c-co2-application-to-carbon-isotope-radiolabeling.pdf |
60c74f9af96a005dc4287ca6 | 10.26434/chemrxiv.12921995.v1 | Peptoid Residues Make Diverse, Hyperstable Collagen Triple Helices | The triple-helical structure of collagen, responsible for collagen’s remarkable biological and mechanical properties, has inspired both basic and applied research in synthetic peptide mimetics for decades. Since non-proline amino acids weaken the triple helix, the cyclic structure of proline has been considered necessary, and functional collagen mimetic peptides (CMPs) with diverse sidechains have been difficult to produce. Here we show that N-substituted glycines (N-glys), also known as peptoid residues, exhibit a general triple-helical propensity similar to or greater than proline, allowing synthesis of thermally stable triple-helical CMPs with unprecedented sidechain diversity. We found that the N-glys stabilize the triple helix by sterically promoting the preorganization of individual CMP chains into the polyproline-II helix conformation. Our findings were supported by the crystal structures of two atomic-resolution N-gly-containing CMPs, as well as experimental and computational studies spanning more than 30 N-gly-containing peptides. We demonstrated that N-gly sidechains with diverse exotic moieties including a ‘click’-able alkyne and a photo-sensitive sidechain can be incorporated into stable triple helices, enabling functional applications such spatio-temporal control of cell adhesion and migration on a gelatin matrix. The folding principles discovered in this study open up opportunities for a new generation of collagen mimetic therapeutics and materials with extraordinary properties. | Julian Kessler; Grace Kang; Zhao Qin; Helen Kang; Frank Whitby; Thomas Cheatham; Christopher Hill; Yang Li; S. Michael Yu | Supramolecular Chemistry (Org.); Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f9af96a005dc4287ca6/original/peptoid-residues-make-diverse-hyperstable-collagen-triple-helices.pdf |
663411dc21291e5d1d4923e0 | 10.26434/chemrxiv-2024-w7svp | Anoxic photolysis as a Route to Primary Metabolites on Early Earth | Despite many years of research, results from prebiotic chemistry experiments—where biologically relevant compounds are formed from simple monomers such as cyanate, CO2, or formaldehyde— still yield complex mixtures with only trace amounts of the molecules of interest. The prevailing idea that life originated from a sequence of chemical reactions, starting from very simple active molecules and evolving into progressively more complex systems, might be incorrect for two reasons: First, after 70 years of experiments, we still lack robust experimental demonstration of such networks; second, small reactive molecules typically do not exist in high concentrations and readily react to form tars and other complex mixtures. Here I adopt an alternative approach, demonstrating that numerous primary metabolites can be derived from tar-like mixtures through the Advanced Reduction Process (ARP). Tars are formed by polycyclic aromatic hydrocarbons (PAHs), which are widespread in the Universe and likely were the main source of organic carbon on early Earth. Under conditions thought to exist on the prebiotic Earth—characterized by sunlight, an anoxic sulfur-rich atmosphere, and iron-rich dust - PAH suspensions in water are decomposed to succinic, lactic, malonic, and glycolic acids, all known as primary metabolites in all living systems and main components of ubiquitous citric acid cycle. The sum of reaction yields for these biologically important metabolites reaches up to 40%, with individual product yields ranging from 1-15%. The simplicity of this reaction and the ubiquity of PAHs on prebiotic Earth make this process particularly appealing, suggesting it could have occurred on a vast scale on sunlit planetary surfaces. These findings may reveal an overlooked initial step in the origin of life on Earth, and potentially elsewhere in the Universe. | Olga Taran; Baris Unal | Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry; Space Chemistry; Wastes | CC BY NC 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663411dc21291e5d1d4923e0/original/anoxic-photolysis-as-a-route-to-primary-metabolites-on-early-earth.pdf |
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