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66b097c801103d79c5c8a64a | 10.26434/chemrxiv-2024-hnc81 | Synthesis of Thienoacenes by Electrochemical Double C–S Cyclization Using a Halogen Mediator: Utility of an S-MOM Group for Halogen-Mediated Electrolysis | Electrochemical synthesis of [1]benzothieno[3,2-b][1]benzothiophene (BTBT) derivatives from S-methoxymethyl (MOM)-protected bis(o-sulfanylphenyl)acetylene derivatives is described. In the presence of Bu4NBr as a halogen mediator, electrochemical double C–S cyclization proceeded smoothly. MOM protection of thiols was essential for the reaction. While S-Me or S-p-methoxybenzyl (PMB)-protected bis(o-sulfanylphenyl)acetylenes did not afford BTBT and bromocyclized products were predominantly obtained, BTBT was selectively obtained when a similar compound protected with an S-MOM group was used in the reaction. Addition of H2O was significant for the reaction as both a sacrificial agent and a trapping agent for the eliminated MOM group. A variety of symmetrical and asymmetrical BTBT derivatives were obtained under the optimal conditions. Control experiments and DFT calculations suggest that the double-cyclization did not proceed concertedly, but rather in a stepwise fashion. The S-MOM protection strategy is also effective for the electrochemical synthesis of a more π-expanded thienoacene such as dibenzo[d,d’]thieno[3,2-b;4,5-b’]dithiophene (DBTDT). | Koichi Mitsudo; Takuya Nagahara; Nozomi Kataura; Toki Yonezawa; Yuri Tachibana; Nolan Soulié; Keisuke Shigemori; Eisuke Sato; Hiroki Mandai; Seiji Suga | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b097c801103d79c5c8a64a/original/synthesis-of-thienoacenes-by-electrochemical-double-c-s-cyclization-using-a-halogen-mediator-utility-of-an-s-mom-group-for-halogen-mediated-electrolysis.pdf |
60c752c4702a9b244f18c226 | 10.26434/chemrxiv.13347368.v1 | MM-PBSA and the Importance of the Dielectric Constant for Kinase Drug Design | Predicting the interactions between a set of small molecules and its target plays a critical role in drug discovery and development. Especially in later stages of the drug design process, when a reduced set of molecules is in focus, reliable and accurate binding affinity estimations are important for targeted modifications of given lead molecules.<div><div>Current limitations in affinity prediction originate from the lack of accurate estimates for solvation energy and entropy. MM-PBSA and the related MM-GBSA aim at providing better estimates.</div><div>From our studies we infer that the common approach using one dielectric constant for the binding pocket may be misleading (here in the case of a kinase), especially when designed ligands/drugs contain charges. Thus, a range of selected values for the solute dielectric constant is preferred for better and more reliable comparisons.</div></div> | Melanie Schneider; Gilles Labesse | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2020-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752c4702a9b244f18c226/original/mm-pbsa-and-the-importance-of-the-dielectric-constant-for-kinase-drug-design.pdf |
65e36a5a66c13817290e9c78 | 10.26434/chemrxiv-2023-mjtsp-v2 | Defluorination of HFCs by a Magnesium Reagent | Reaction of a series of HFCs with a nucleophilic main group reagent containing a Mg–Mg bond results in defluorination to form the corresponding magnesium fluoride complex. In the case of 1,1,1,2-tetrafluoroethane (HFC-134a) generation of the fluoride occurs alongside selective formation of 1,1-difluoroethene. This is a highly unusual reactivity pattern for HFC-134a, which more commonly reacts by deprotonation and HF elimination. DFT calculations have been carried out to better understand the selectivity and compare the barriers for sp3 C–F bond activation with sp3 C–H bond activation in this system. | Daniel Sheldon; Joseph Parr; Mark Crimmin | Organic Chemistry; Inorganic Chemistry; Main Group Chemistry (Inorg.); Reaction (Inorg.); Small Molecule Activation (Inorg.) | CC BY 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e36a5a66c13817290e9c78/original/defluorination-of-hf-cs-by-a-magnesium-reagent.pdf |
64d9e4584a3f7d0c0d24aecf | 10.26434/chemrxiv-2023-lz4k6 | A Hydrogen-Bonded Organic Framework Equipped
with a Molecular Nano-Valve | The concept of a molecular nano-valve is applied to a newly synthesized biocompatible hydrogen-bonded organic framework (HOF), termed RSS-140, in order to load, trap, and subsequently release an antioxidant on command. Specifically, we exploit the pore windows of RSS-140 (i.e., β-CD cavities) to first load and trap the antioxidant, Trolox, within the internal pores of the HOF (Trolox⊂RSS-140) and, to prevent it from leaching, utilize supramolecular chemistry to complex azobenzene (Azo) with β-CD (Trolox⊂Azo@RSS-140). The molecular nano-valve is fully realized upon exposing Trolox⊂Azo@RSS-140 to UV light with a specific wavelength, which induces Azo isomerization, Azo decomplexation from β-CD, and subsequent release of Trolox from the pores of RSS-140. The biocompatibility and non-toxicity of Trolox⊂Azo@RSS-140, together with the absolute control over the nano-valve opening, was established to yield a system that safely and slowly releases Trolox for longer-lasting antioxidant efficacy. As the field of supramolecular chemistry is rich with similar systems and many such systems can be used as building blocks to construct HOFs or other extended framework materials, we envision the molecular nano-valve concept to be applied widely for controllably delivering molecular cargo for diverse applications. | Sara Ghazal; Sarah Tabbalat; Felipe Gandara; Ala'a Al-Ghourani; Samah Abusulieh; Mahmoud Abdellatief; Suhair Sunoqrot; Kyle Cordova | Organic Chemistry; Materials Science; Supramolecular Chemistry (Org.); Biocompatible Materials; Controlled-Release Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d9e4584a3f7d0c0d24aecf/original/a-hydrogen-bonded-organic-framework-equipped-with-a-molecular-nano-valve.pdf |
61b8b1357f367e24dd529549 | 10.26434/chemrxiv-2021-2kfrp | Thorough investigation on the high-temperature polymorphism of dipentyl-perylenediimide: thermal expansion vs polymorphic transition. | N,N’-dipentyl-3,4,9,10-perylendiimide (PDI-C5) is an organic semiconducting material which has been extensively investigated as model compound for its optoelectronic properties. It is known to be highly thermally stable, that it exhibits solid-state transitions with temperature and that thermal treatments lead to an improvement in its performance in devices. Here we report a full thermal characterization of PDI-C5 by combination of differential scanning calorimetry, variable temperature X-ray diffraction, hot stage microscopy, and variable temperature Raman spectroscopy. We identified two high temperature polymorphs, form II and form III, which form respectively at 112 °C and at 221 °C and we determined their crystal structure from powder data. Form II is completely reversible upon cooling with low hysteresis, while form III revealed a different thermal behaviour upon cooling depending on the technique and crystal size. The crystal structure’s features of the different polymorphs are discussed and compared, and we looked into the role of the perylene core and alkyl chains during solid-state transitions. The thermal expansion principal axis of PDI-C5 crystal forms is reported showing that all the reported forms possess negative thermal expansion (X1) and large positive thermal expansion (X3) which are correlated to thermal behaviour observed. | Francesco Marin; Serena Tombolesi; Tommaso Salzillo; Omer Yaffe; Lucia Maini | Organic Chemistry; Materials Science; Dyes and Chromophores; Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b8b1357f367e24dd529549/original/thorough-investigation-on-the-high-temperature-polymorphism-of-dipentyl-perylenediimide-thermal-expansion-vs-polymorphic-transition.pdf |
656765c0cf8b3c3cd768999b | 10.26434/chemrxiv-2023-m3fhg-v2 | Preliminary Results showing Poor Potential of Thermo-catalytic Treatment towards Resource Recovery from Waste Biopolymers | Menace caused by littered plastics has become a common knowledge. Bio-derived or biocompostible or biodegradable polymers are advocated as a solution. Many reports have raised doubt about their environment-friendliness. Here we attempted several biopolymers to catalytically crack in presence of hydrogen over zeolite-based catalysts to explore if valuable products can be recovered. Very few polymers afforded appreciable liquid product yield. Gases generated neither condense at about 4 ºC nor dissolve in solvent like toluene, hexane, etc. Next, to bring the polymers in contact with the catalyst, we tried to dissolve them in various solvents. However, only some polymers dissolved in only γ-valerolactone (GVL). Due to the solvent, relatively more polymer converted into liquid product. Considerable aromatic yield was obtained from GVL- Cellulose acetate butyrate system. Though valuable liquid compounds were obtained, poor liquid yields and product concentrations raise a question mark on catalytic conversion method. Separation of products necessitates energy-intensive methods. | parimal parikh; rutvik savani | Catalysis; Chemical Engineering and Industrial Chemistry; Acid Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656765c0cf8b3c3cd768999b/original/preliminary-results-showing-poor-potential-of-thermo-catalytic-treatment-towards-resource-recovery-from-waste-biopolymers.pdf |
60c750dd567dfee77cec5930 | 10.26434/chemrxiv.13087730.v1 | A New Method for Transcarbamation and Amidation from Benzyl Carbamate | <div>Abstracts: A convenient, and efficient method for Transcarbamation and conversion of</div><div>benzyl carbamates to amide using potassium carbonate in alcohols under heating condition</div><div>is described.</div> | Sudershan Reddy Gondi | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2020-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750dd567dfee77cec5930/original/a-new-method-for-transcarbamation-and-amidation-from-benzyl-carbamate.pdf |
647ad63cbe16ad5c57635baa | 10.26434/chemrxiv-2023-38t1v | Zirconium Coordination Chemistry and its Role in Optimizing Hydroxymate Chelation: Insights from Molecular Dynamics | In the last decade, there has been a growth in using Zirconium-89 (89 Zr) as a radionuclide in nuclear medicine for cancer diagnostic imaging and drug discovery processes. One of the most popular chelators for 89 Zr, is desferrioxamine (DFO) which acts as a hexadentate ligand. The coordination structure of the Zr4+-DFO complex has primarily been informed by DFT-based calculations which typically ignore temperature and therefore entropic and dynamic solvent effects. In this work, free energy calculations using molecular dynamics simulations, where the conformational fluctuations of both the ligand and the solvent are explicitly included, are used to compare the binding of Zr4+ cation with two different chelators, DFO and 4HMS, the latter of which has been recently proposed as a better chelator. We find that thermal induced disorder leads an open hexadentate chelate structure of Zr4+-DFO complex, leaving the Zr4+ metal exposed to the solvent. A stable coordination of Zr4+ with 4HMS, however, is formed involving both hydroxamate groups and water molecules in a more closely packed structure. | Giulia Sormani; Aruna Korde; Alex Rodriguez; Melissa Denecke; Ali Hassanali | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647ad63cbe16ad5c57635baa/original/zirconium-coordination-chemistry-and-its-role-in-optimizing-hydroxymate-chelation-insights-from-molecular-dynamics.pdf |
60c74bf4f96a00d0972876d2 | 10.26434/chemrxiv.12389777.v1 | MetalWalls: A Classical Molecular Dynamics Software Dedicated to the Simulation of Electrochemical Systems | Applied electrochemistry plays a key role in many technologies, such as Li-ion batteries, fuel cells, supercapacitors, solar cells, etc. It is therefore at the core of many research programs all over the world. However, fundamental electrochemical investigations remain scarce. In particular, electrochemistry is among the fields for which the gap between theory and experiment is the largest. From the computational point of view, there is no classical molecular dynamics (MD) software devoted to the simulation of electrochemical systems while other fields such as biochemistry or material science have dedicated tools. "MetalWalls" (MW), a MD code dedicated to electrochemistry, fills this gap. Its main originality is the inclusion of a series of methods which allow a constant electrical potential to be applied to the electrode materials. It also allows the simulation of bulk liquids or solids using the polarizable ion model and the aspherical ion model. MW is designed to be used on high-performance computers and it has already been employed in a number of scientific publications. It was for example used to study the charging mechanism of supercapacitors, nanoelectrowetting and water desalination devices. | Abel Marin-Laflèche; Matthieu Haefele; Laura Scalfi; Alessandro Coretti; Thomas Dufils; Guillaume Jeanmairet; Stewart Reed; Alessandra Serva; Roxanne Berthin; Camille Bacon; Sara Bonella; Benjamin Rotenberg; Paul Anthony Madden; Mathieu Salanne | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf4f96a00d0972876d2/original/metal-walls-a-classical-molecular-dynamics-software-dedicated-to-the-simulation-of-electrochemical-systems.pdf |
60c73d0ef96a002e9e285cfd | 10.26434/chemrxiv.5384293.v1 | Mapping the “Extra Solvent Power, ESP” of Ionic Liquids for Monomers, Polymers and Globular Nanoparticles | Understanding the miscibility behavior of ionic
liquid (IL) / monomer, IL / polymer and IL / nanoparticle mixtures is critical
for the use of ILs as green solvents in polymerization processes, and to
rationalize recent observations concerning the superior solubility of some
proteins in ILs when compared to standard solvents. In this work, the most
relevant results obtained in terms of a three-component Flory-Huggins theory
concerning the “Extra Solvent Power, ESP” of ILs when compared to traditional
non-ionic solvents for monomeric solutes (case I), linear polymers (case II)
and globular nanoparticles (case III) are presented. Moreover, useful ESP maps
are drawn for the first time for IL mixtures corresponding to case I, II and
III. Finally, a potential pathway to improve the miscibility of non-ionic
polymers in ILs is also proposed. | Jose A. Pomposo | Organic Polymers; Polyelectrolytes - Polymers; Polymer blends | CC BY NC ND 4.0 | CHEMRXIV | 2017-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0ef96a002e9e285cfd/original/mapping-the-extra-solvent-power-esp-of-ionic-liquids-for-monomers-polymers-and-globular-nanoparticles.pdf |
60c7502c702a9be36a18bcfb | 10.26434/chemrxiv.12999812.v1 | Post-Synthetic Modification of Covalent Organic Frameworks via in Situ Polymerization of Aniline for Enhanced Capacitive Energy Storage | <div>
<p>Covalent organic frameworks (COFs) with layered architecture with
open nanochannels and high specific surface areas are promising candidates for
energy storage. However, the low
electrical conductivity of two-dimensional COFs often limits their scope in
energy storage applications. The conductivity of COFs can be enhanced
through post-synthetic modification with conducting polymers. Herein, we
developed polyaniline (PANI) modified triazine-based COFs via <i>in situ</i>
polymerization of aniline with the porous frameworks. The composite materials
showed high conductivity of 1.4-1.9 x 10<sup>-2</sup> S cm<sup>-1</sup> at room
temperature with 10-fold enhancement in specific capacitance than the pristine
frameworks. The fabricated supercapacitor exhibited a high energy density of
24.4 W h kg<sup>-1</sup> and a power density of 200 W kg<sup>-1</sup> at 0.5 A g<sup>-1 </sup>current density. Moreover,
the device fabricated using the conducting polymer-triazine COF composite can
light up a green light-emitting diode for 1 min after being charged for 10 s.</p></div> | Tapas Dutta; Abhijit Patra | Composites; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7502c702a9be36a18bcfb/original/post-synthetic-modification-of-covalent-organic-frameworks-via-in-situ-polymerization-of-aniline-for-enhanced-capacitive-energy-storage.pdf |
6160af8a2aca5315955d5855 | 10.26434/chemrxiv-2021-zcv78 | Nanoplastic transport in aqueous environments: The role of chemo-electric properties and hydrodynamic forces for nanoplastic-mineral interaction. | The fate and transport characteristics of nanoplastic (NP) through different environmental systems is largely governed by physio-chemical processes and their specific interaction with environmental constituents (i.e., minerals, dissolved species, suspended particles). A hydrodynamic component present in almost all terrestrial and marine aqueous environments impact the physio-chemical processes micron-scale is largely overlooked in NP transport studies.
Therefore, we tested the interaction behavior of nanosized plastic polystyrene particles of various coatings in the presence of minerals abundant in the Earth crust within a hydrodynamic continuum representing flow rates from groundwater to surface water systems.
Our batch experiments show that particle-mineral adsorption is largely driven by the magnitude of opposite charge configurations, which is either produced by mineral type or specific nanoplastic surface coating. Zetapotential serves as a good predictor of adsorption between uncoated and carboxyl-coated polystyrene with minerals. It fails, however, to predict adsorption behavior between NH2 coated polystyrene and apatite or feldspars, due to the more complex and varying compositions of these minerals. Incorporating the hydrodynamic force component into the particle- mineral interaction scheme reproduces those adsorption trends at slow flowrates of 1e-04 m/d.
However, increasing flow rates by a factor of 100 modifies charge-driven adsorption between minerals and plastics.
This study highlights the unabating importance of hydrodynamic conditions when predicting nanoplastic transport in different subsurface environments, and has implications for nanoplastic behavior in both terrestrial and marine aqueous environments.
| Sascha Müller; Jacek Fiutowski; Horst-Günter Rubahn ; Nicole Rita Posth | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6160af8a2aca5315955d5855/original/nanoplastic-transport-in-aqueous-environments-the-role-of-chemo-electric-properties-and-hydrodynamic-forces-for-nanoplastic-mineral-interaction.pdf |
60c74cb0bdbb89727ca39845 | 10.26434/chemrxiv.12471671.v1 | Total Correlation Spectroscopy Across All NMR-Active Nuclei by Mixing at Zero Field | Multidimensional
Nuclear Magnetic Resonance (NMR) is based on the combination of
well-established building blocks for polarization transfer. These blocks are
used to design correlation experiments through one or a few chemical bonds or
through space. Here, we introduce a building block that enables polarization
transfer across all NMR-active nuclei in a coupled network of spins: isotropic
mixing at Zero and Ultra-Low Field (ZULF). Exploiting mixing under ZULF-NMR
conditions, heteronuclear TOtal Correlation SpectroscopY (TOCSY) experiments were
developed to highlight coupled spin networks. We demonstrate <sup>1</sup>H-<sup>13</sup>C
and <sup>1</sup>H-<sup>15</sup>N correlations in ZULF-TOCSY spectra of labelled
amino acids, which allow one to obtain cross-peaks among all hetero-nuclei
belonging to the same coupled network, even when the direct interaction between
them is negligible. We also demonstrate the interest of ZULF-TOCSY to analyze
complex mixtures on the supernatant of ISOGRO, a growth medium of isotope-labelled
biomolecules. ZULF-TOCSY enables the quick identification of individual compounds
in the mixture by their coupled spin networks. The ZULF-TOCSY method will lead
to the development of a new toolbox of experiments to analyze complex mixtures by
NMR. | Ivan V. Zhukov; Alexey S Kiryutin; Fabien Ferrage; Gerd Buntkowsky; Alexandra V. Yurkovskaya; Konstantin Ivanov | Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cb0bdbb89727ca39845/original/total-correlation-spectroscopy-across-all-nmr-active-nuclei-by-mixing-at-zero-field.pdf |
675017535a82cea2faefc420 | 10.26434/chemrxiv-2024-gtxv4 | Recycling of Polyolefins Using Recycled PVC under Sunlight | The recycling of polyolefin plastics is often hindered by high energy consumption and low economic efficiency. In particular, the recycling of poly(vinyl chloride) (PVC) is especially challenging. Here, we present an innovative protocol to recycle discarded PVC into a photothermal catalyst for the depolymerization of polyolefins under sunlight. By dechlorinating the PVC, we harness its unique ability to converts sunlight into the energy required to break C-C bonds in polyolefins. This protocol allows for the transformation of low-density polyethylene (LDPE), high-density polyethylene (HDPE), and polypropylene (PP) into waxes enriched with terminal olefins, which can be further utilized for the synthesis of surfactant. Furthermore, this protocol enables the conversion of polystyrene, poly(methyl methacrylate), poly(α-methyl styrene), styrene-acrylonitrile copolymer, and acrylonitrile-butadiene-styrene (ABS) into their respective monomers. This broad applicability makes our protocol suitable for the recycling of a wide range of real-life plastic products and their mixtures under ambient environment. Notably, with the aid of just 0.1 wt% catalyst, a successful depolymerization of kilogram-scale PS waste, such as plastic cups, using solar energy has been achieved. Additionally, the catalysts derived from PVC can be reused, thereby enhancing the sustainability and cost-effectiveness of the depolymerization of polyolefins. Our study presents a promising solution to the recycling of PVC and polyolefin plastics, leveraging solar energy to create a sustainable and efficient recycling process. | Heng Liu; Ding-Wei Ji; Su-Yang Xu; Zhi-Hui Wang; Shi-Yu Guo; Qing-An Chen | Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675017535a82cea2faefc420/original/recycling-of-polyolefins-using-recycled-pvc-under-sunlight.pdf |
64e75d733fdae147fabb61f0 | 10.26434/chemrxiv-2023-6z1xd | Insights into Conformational Ensembles of Compositionally Identical Disordered Peptidomimetics | While the conformational ensembles of disordered peptides and peptidomimetics are complex and challenging to characterize, they are a critical component in the paradigm connecting macromolecule sequence, structure, and function. In molecules that do not adopt a single predominant conformation, the conformational ensemble contains rich structural information that, if accessible, can provide fundamental understanding related to desirable functions such as cell penetration of a therapeutic or the generation of tunable enzyme-mimetic architecture. To address the fundamental challenge of describing broad conformational ensembles, we developed a model system of peptidomimetics comprised of polar glycine and hydrophobic N-butylglycine to characterize using a suite of analytical techniques, including replica exchange molecular dynamics atomistic simulations and liquid chromatography coupled to ion mobility spectrometry, which allowed us to distinguish the conformations of compositionally identical model sequences. However, differences between these model sequences were more challenging to resolve with characterization tools developed for intrinsically disordered proteins and polymers. These tools include double electron-electron resonance (DEER) spectroscopy and diffusion ordered spectroscopy (DOSY) NMR. Finally, we introduce a facile colorimetric assay that employs immobilized sequences leveraging a solvatochromic probe, Reichardt’s dye, to visually reveal conformational trends consistent with the experimental and computational analysis, thus providing a rapid and complementary method to characterize macromolecular disorder and unravel the complexity of conformational ensembles, either as an isolated or multiplexed technique. | Erin C. Day; Keila C. Cunha; Jianhan Zhao; Audra J. DeStefano; James N. Dodds; Melissa A. Yu; Songi Han; Erin S. Baker; Joan-Emma Shea; Rebecca B. Berlow; Abigail S. Knight | Theoretical and Computational Chemistry; Analytical Chemistry; Polymer Science; Polymer chains | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e75d733fdae147fabb61f0/original/insights-into-conformational-ensembles-of-compositionally-identical-disordered-peptidomimetics.pdf |
6482a4904f8b1884b70a5dba | 10.26434/chemrxiv-2023-7p62f | Ab-Initio Anharmonic Analysis of Complex Vibrational Spectra of Phenylacetylene and Fluorophenylacetylenes in the Acetylenic and Aromatic C–H Stretching Region | Vibrational spectra in the acetylenic and aromatic C–H stretching region of phenylacetylene and fluorophenylacetylenes viz., 2-fluorophenylacetylene, 3-fluorophenylacetylene and 4-fluorophenylacetylene, were measured using IR-UV double resonance spectroscopic method. The spectra, in both acetylenic and aromatic C–H stretching regions, were complex exhibiting multiple bands. Ab-initio anharmonic calculations with quartic potential (QP) using B97D3/6-311++G(d,p) and vibrational configuration interaction (VCI) were able to capture all important spectral features, in both the regions of the experimentally observed spectra for all four molecules considered in the present work. Interestingly, for phenylacetylene, the spectrum in the acetylenic C–H stretching region emerges due to anharmonic coupling of mode localized on the acetylenic moiety along with the other ring modes which also involve displacements on the acetylenic group, which is in contrast to what has been proposed and propagated in the literature. In general, this coupling scheme is invariant to the fluorine atom substitution. For the aromatic C–H stretching region the observed spectrum emerges due to the coupling of the C–H stretching with C–C stretching and C–H in-plane bending modes. | Sumitra Singh; Qian-Rui Huang; Jake A Tan; Jer-Lai Kuo; G Naresh Patwari | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6482a4904f8b1884b70a5dba/original/ab-initio-anharmonic-analysis-of-complex-vibrational-spectra-of-phenylacetylene-and-fluorophenylacetylenes-in-the-acetylenic-and-aromatic-c-h-stretching-region.pdf |
6550f01adbd7c8b54b2058e3 | 10.26434/chemrxiv-2023-rk6sp | Modeling Gas Adsorption and Mechanistic Insights into Flexibility in Isoreticular Metal–Organic Frameworks using High-Dimensional Neural Network Potentials | Metal–organic frameworks (MOFs), known for their remarkable porous and well-organized structures, have found extensive use in various applications including gas storage. Predicting the bulk properties from atomistic simulations as well as gas uptakes and adsorption mechanism requires the most accurate definition of MOF systems. The application of ab initio molecular dynamics to these extensive periodic systems exceeds current computational capabilities. Consequently, alternative strategies need to be devised to lower computational costs without compromising accuracy. In this work, we construct high dimensional neural network potentials (HDNNP) to describe rotationally and translationally invariant energies and forces of isoreticular metal organic framework (IRMOF) series at the DFT level of accuracy using the fragmentation technique so as to study H2 and CH4 adsorption isotherms considering the flexibility of MOFs during gas adsorption by means of “adsorption relaxation” model in which MD and GCMC simulations were performed simultaneously. Our results showed that classical simulations may diverge from experiments due to the failure of the force field when accounting for flexibility in MOFs whereas our HDNNP follows a much better trend to experimental values. Moreover, we show that the real number of CH4 uptake values of IRMOF-10 can be much more than what classical force field predicts. In addition, adsorption relaxation simulations enable us to characterize behavior of MOF atoms and distribution of gas molecules during the adsorption process, giving the most detailed mechanistic picture. | Omer Tayfuroglu; Yunus Zorlu; Abdulkadir Kocak | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Machine Learning; Quantum Mechanics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6550f01adbd7c8b54b2058e3/original/modeling-gas-adsorption-and-mechanistic-insights-into-flexibility-in-isoreticular-metal-organic-frameworks-using-high-dimensional-neural-network-potentials.pdf |
659bc01be9ebbb4db9adee01 | 10.26434/chemrxiv-2023-sm1x3-v2 | Developing an Asthma Attack Alert System by Signal Processing of Breathing Sounds | Objective: Asthma is a widespread cause of hospitalizations and even deaths across all age groups worldwide, making it a significant health concern. Its prevalence and burden have been reported in Turkey, with allergic rhinitis frequencies ranging from 11.8% to 36.4% in five different centers. Asthma prevalence in Turkey varies between 6% and 15% in children and between 2% and 17% in adults. In this context, the aim is to design and develop a device capable of detecting asthma attacks by analyzing respiratory sounds and alerting the patient. The project's objectives include providing rapid pre-attack warnings without disturbing the patient, employing an air pollution sensor, and incorporating two distinct warning mechanisms.
Methods: This research employs a series of methods to analyze the respiratory sounds of asthma patients and detect asthma attacks. Initially, a literature review was conducted to identify critical factors for detecting asthma attacks, focusing on developing new technologies and non-invasive methods to obtain respiratory sounds. Arduino and MATLAB tools were employed to develop sound analysis and data processing. Subsequently, filtering and statistical calculations were performed.
In the final stage, various visualizations such as sound signal, filtered sound signal, FFT, and power spectrum were created to present the obtained results through a user-friendly interface. The two-stage alert system incorporates the ability to detect asthma attacks based on wheezing sounds and air pollution.
Results: In consideration of the prevalence and severity of asthma, this study addresses a device designed for early diagnosis of the attack. The device is equipped to analyze respiratory sounds within the frequency range of 100-1000 Hz, enabling differentiation between wheezes and rhonchi. The utilization of this device has the potential to enhance the quality of life for asthma patients and provide the opportunity for early intervention by anticipating attack situations.
Conclusion: By focusing on the analysis of respiratory sounds, this research demonstrates the feasibility of monitoring asthma attacks through non-invasive methods. The developed programs and equipment have the potential to offer asthma patients a more effective way of life. | Darin Sawah; MAHA SAHLOUL; BAYAN TURKIEH; Bahattin karagözoğlu | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Bioengineering and Biotechnology | CC BY NC 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659bc01be9ebbb4db9adee01/original/developing-an-asthma-attack-alert-system-by-signal-processing-of-breathing-sounds.pdf |
60c73f1cbdbb8913fda37f3a | 10.26434/chemrxiv.7246946.v1 | Phonon Abundance-Stiffness-Lifetime Transition from the Mode of Heavy Water to Its Confinement and Hydration | <div>A combination of the temporally- and spatially-resolved phonon spectroscopy has enabled calibration of hydrogen bond transition from the vibration mode of heavy water to the core-shelled nanodroplet and the sub-nanosized ionic hydration shell in terms of phonon abundance-lifetime-stiffness. It is uncovered that charge injection by salt solvation and skin formation by molecular undercoordination (often called confinement) share the same supersolidity of H–O (D–O as a probe) bond contraction, O:H elongation, and electron polarization. The bond transition stems the solution viscosity, surface stress, and slows down the molecular dynamics. The skin reflection further hinders phonon energy dissipation and thus lengthens the phonon lifetime of the nanodroplet.</div> | Chang Sun | Nanostructured Materials - Nanoscience; Clusters; Interfaces; Physical and Chemical Processes; Solution Chemistry; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1cbdbb8913fda37f3a/original/phonon-abundance-stiffness-lifetime-transition-from-the-mode-of-heavy-water-to-its-confinement-and-hydration.pdf |
6723ca677be152b1d099aecc | 10.26434/chemrxiv-2024-m5v9g | Electrifying P(V): Access to Polar and Radical Reactivity | Electrochemical, fully stereoselective P(V)-radical hydrophosphorylation of olefins and carbonyl compounds using a P(V) reagent is disclosed. By strategically selecting the anode material, radical reactivity is accessible for alkene hy-drophosphorylation whereas a polar pathway operates for ketone hydrophosphorylation. The mechanistic intricacies of these chemoselective transformations was explored in-depth | Mahdi Jafarzadeh ; Molhm Nassir; Luca Gherardi; Nicholas Raheja; Yu Kawamata; Phil S. Baran | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6723ca677be152b1d099aecc/original/electrifying-p-v-access-to-polar-and-radical-reactivity.pdf |
60c748450f50db42ea39673a | 10.26434/chemrxiv.11874072.v1 | Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study | <div>
<div>
<div>
<p>Phosphate and sulfate esters have important roles as biological building blocks and in regulating
cellular processes. However, while there has been substantial experimental and computational
investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis,
there is far less (in particular computational) work on sulfate ester hydrolysis. Here, we report a
detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different
DFT functionals and both pure implicit solvation as well as mixed implicit/explicit solvation with
varying numbers of explicit water molecules. We consider both the impact of how the system is
modeled on computed linear free energy relationships (LFER) and the nature of the transition
states. Although our calculations consistently underestimate the absolute activation free energies,
we obtain good agreement with experimental LFER data when using pure implicit solvent, and
excellent agreement with experimental kinetic isotope effects for all models used. Our calculations
suggest that the hydrolysis of sulfate diesters proceeds through loose transition states, with
minimal bond formation to the nucleophile and with bond cleavage to the leaving group already
initiated. Comparison to prior work indicates that these transition states are similar in nature to
those of analogous reactions such as the alkaline hydrolysis of neutral arylsulfonate monoesters or
charged phosphate diesters and fluorophosphates. Obtaining more detailed insight into the
transition states involved assists in understanding the selectivity of enzymes that hydrolyze these
reactions; however, this work also highlights the methodological challenges involved in reliably
modeling sulfate ester hydrolysis.
</p>
</div>
</div>
</div> | Klaudia Szeler; Nicholas Williams; Alvan C. Hengge; Shina Caroline Lynn Kamerlin | Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748450f50db42ea39673a/original/modeling-the-alkaline-hydrolysis-of-diaryl-sulfate-diesters-a-mechanistic-study.pdf |
60c75122842e650023db3b37 | 10.26434/chemrxiv.13120301.v1 | Interfacial Reactivity and Speciation Emerging from Namontmorillonite Interactions with Water and Formic Acid at 200°C: Insights from Reactive Molecular Dynamics Simulations, Infrared Spectroscopy, and X-ray Scattering Measurements | Reactive organic fluid - mineral interactions at elevated temperatures contribute to the evolution
of planetary matter. One of the less studied but important transformations in this regard involves
the reactions of formic acid with naturally occurring clays such as sodium montmorillonite. To
advance a mechanistic understanding of these interactions, we use ReaxFF reactive molecular
dynamics simulations in conjunction with infrared (IR) spectroscopy and X-ray scattering
experiments to investigate the speciation behavior of water-formic acid mixtures on sodium
montmorillonite interfaces at 473 K and 1 atm. Using a newly developed reactive forcefield, we
show that the experimental IR spectra of unreacted and reacted mixture can be accurately
reproduced by ReaxFF/MD. We further benchmark the simulation predictions of sodium carbonate
and bicarbonate formation in the clay interlayers using Small and Wide-Angle X-ray Scattering
measurements. Subsequently, leveraging the benchmarked forcefield, we interrogate the pathway
of speciation reactions with emphasis on carbonate, formate, and hydroxide groups elucidating the
energetics, transition states, intermediates, and preferred products. We also delineate the
differences in reactivities and catalytic effects of clay edges, facets, and interlayers owing to their
local chemical environments, which have far reaching consequences in their speciation behavior.
The experimental and simulation approaches described in this study and the transferable
forcefields can be applied translationally to advance the science of clay-fluid interactions for
several applications including subsurface fluid storage and recovery and clay-pollutant dynamics | Murali Gopal Muraleedharan; Hassnain Asgar; Seung Ho Hahn; Nabankur Dasgupta; Greeshma Gadikota; Adri C.T. van Duin | Environmental Science; Geochemistry; Soil Science; Space Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75122842e650023db3b37/original/interfacial-reactivity-and-speciation-emerging-from-namontmorillonite-interactions-with-water-and-formic-acid-at-200-c-insights-from-reactive-molecular-dynamics-simulations-infrared-spectroscopy-and-x-ray-scattering-measurements.pdf |
642112fa91074bccd056190e | 10.26434/chemrxiv-2022-gk3n6-v2 | CarbonAI, A Non-Docking Deep learning based small molecule virtual screening platform | Structure-based virtual screening is a promising in silico technique that integrates computational methods into drug discovery. The most extensively used method in structure-based virtual screening is molecular docking. However, the docking process is not computationally efficient and simultaneously accurate due to classic mechanics-based scoring functions. These can only approximate, but not reach, quantum mechanics precision. In order to reduce the computational cost of the protein-ligand scoring process and use data-driven approaches to boost the scoring function accuracy, deep learning non-docking methods can be used by utilizing 3D structure or 1D sequence information of the protein target. This method can minimize the error inherited from molecular docking methods and avoid the extensive computational cost of docking. Furthermore, these two methods are integrated into an easy-to-use framework, CarbonAI, that provides both choices for researchers. Graph neural network (GNN) is employed in the 3D version and BiLSTM has been adopted in the sequence version of CarbonAI, respectively. To verify our approaches, different experiments were performed on two datasets, an open dataset Directory of Useful Decoys: Enhanced (DUD.E) and an in-house proprietary dataset without computer generated artificial decoys (NoDecoy). On DUD.E we achieved a state-of-the-art AUC of 0.981 and on NoDecoy we achieved an AUC of 0.974 whereas on the conventional docking program, the respective AUC performance is less than 0.8. The CarbonAI engine also reaches a state-of-the-art enrichment factor at top 2 percent for 36.2 folds. We have also retrospectively validated the CarbonAI models with various wet lab experimental data, and the results demonstrated a consistently accurate performance. Furthermore, the inference speed of the engine was benchmarked using the openly available 2021 Enamine REAL Database (RDB), that comprises over 1.36 billion molecules in 4050 core-hours using our CarbonAI non-docking method (CarbonAI-ND). The inference speed of CarbonAI-ND is about 36000 molecule per core-hour, compared to typical docking methods' speed of 20, which is about 16000 times faster than conventional docking method. Overall, the experiments indicate that CarbonAI is accurate and computationally efficient with good generalization to different molecular targets for virtual screening. | Junfeng Wu; Kevin Jin; Yang Jiao; Xiaojie Wang; Siwei Li; Lurong Pan | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642112fa91074bccd056190e/original/carbon-ai-a-non-docking-deep-learning-based-small-molecule-virtual-screening-platform.pdf |
60c75052702a9b61a218bd53 | 10.26434/chemrxiv.13019960.v1 | Distributed Multi-Objective Bayesian Optimization for the Intelligent Navigation of Energy Structure Function Maps For Efficient Property Discovery | Energy-structure-function (ESF) maps have emerged as a powerful tool for in silico materials design, coupling crystal structure prediction techniques with property simulations to assess the potential for new candidate materials to display desirable
properties. Despite continuing increases to accessible computational power, however, the computational cost of acquiring an ESF
map often remains too high to allow integration into true high-throughput virtual screening techniques. In this paper, we propose
the next evolution of the ESF map, which uses parallel Bayesian optimization to selectively acquire energy and property data, generating the same levels of insight at a fraction of the computational cost by limiting the expensive property calculations to a small
fraction of the predicted crystal structures associated with a molecule. We utilize this approach to obtain a two orders of magnitude
speedup on a previous ESF study that focused on methane capture materials, saving over 500,000 CPUh from the original protocol.
Through acceleration of the acquisition of ESF-type insight, we pave the way for the use of ESF maps in automated ultra-high
throughput screening pipelines. This greatly reduce the opportunity risk associated with the choice of system to calculate. For example, it will allow researchers to use ESF maps in the search for physical properties where the computational costs are currently
just intractable, or to investigate orders of magnitude more systems for a given computational cost.<br /> | Edward Pyzer-Knapp; Graeme Day; Linjiang Chen; Andrew
I. Cooper | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75052702a9b61a218bd53/original/distributed-multi-objective-bayesian-optimization-for-the-intelligent-navigation-of-energy-structure-function-maps-for-efficient-property-discovery.pdf |
649de0209ea64cc1672f90a9 | 10.26434/chemrxiv-2023-4vptd-v2 | Heavy versus Light Lanthanide Selectivity for Graphene Oxide Films is Concentration Dependent | Rare earths are important materials in various technologies such as catalysis and optoelectronics. Graphene oxide (GO) is a promising material for separation applications, including the isolation of lanthanides from complex mixtures. Previous works using fatty acid monolayers have demonstrated preferential heavy versus light lanthanide adsorption, which has been attributed to differences in lanthanide ion size. In this work, we used interfacial X-ray fluorescence measurements to reveal that GO thin films at the air/water interface have no lanthanide selectivity for dilute subphases. However, at high subphase concentrations ~8x more Lu adsorb than La. By comparing GO results with an ideal monolayer with a carboxylic acid headgroup, arachidic acid (AA), we demonstrate that the number of Lu ions adsorbed to GO is significantly higher than the number expected to compensate the surface charge. Vibrational sum frequency generation (SFG) spectroscopy results on both GO thin films and AA monolayers reveal a red-shifted SFG signal in the OH region, which we attribute to partial dehydration of the adsorbed ions and carboxylic acid headgroups. Liquid surface X-ray reflectivity data show that the GO thin film structure does not significantly change between the very dilute and concentrated subphases. We speculate that the functional groups of both GO and AA facilitate cation dehydration, which is essential for ion adsorption. Heavy lanthanide Lu has stronger ion-ion correlations that can overcome electrostatic repulsion between cations at higher concentrations compared to light lanthanide La, meaning GO and AA can exhibit apparent overcharge with Lu. Lastly, the layered structure of the GO films and reactive chemical nature of GO itself can accommodate ion adsorption. | Amanda J. Carr; Seung Eun Lee; Ahmet Uysal | Physical Chemistry; Nanoscience; Interfaces; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649de0209ea64cc1672f90a9/original/heavy-versus-light-lanthanide-selectivity-for-graphene-oxide-films-is-concentration-dependent.pdf |
669e242ac9c6a5c07a665861 | 10.26434/chemrxiv-2024-1vp1n-v3 | A versatile entry to unnatural, disulfide-linked amino acids and peptides through the disulfuration of azlactones | Despite the evident demand and promising potential of disulfide-functionalized amino acids and peptides in linker chemistry and peptide drug discovery, those disulfurated specifically at the α-position constitute a unique yet rather highly underexplored chemical space. In this study, we have developed a method for preparing SS-linked amino acid/peptide derivatives through a base-catalyzed disulfuration reaction of azlactones, followed by the ring-opening functionalization. The disulfuration reaction proceeds under mild conditions, yielding disulfurated azlactones in excellent yields across a variety of N-dithiophthalimides and diverse azlactones derived from various amino acids and peptides. Leveraging the ready availability of N-dithiophthalimides from several bilateral disulfurating reagents, this method allows for the modular integration of functional molecules and azlactones into SS-linkage in two-step operations. Furthermore, due to the transformability of the azlactone moiety through ring-opening with various nucleophiles, our method provides a wide variety of functional molecule-tagged amino acids and oligopeptides bearing SS-linkages in a modular and time-efficient manner, serving as a valuable tool for linker chemistry and peptide chemistry. | Masaki Iwata; Yuzuki Takami; Hayato Asanuma; Kenya Hosono; Hibiki Ohno; Naohiko Yoshikai; Kazuya Kanemoto | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e242ac9c6a5c07a665861/original/a-versatile-entry-to-unnatural-disulfide-linked-amino-acids-and-peptides-through-the-disulfuration-of-azlactones.pdf |
67dd80296dde43c908bdf11c | 10.26434/chemrxiv-2025-9l3r1 | Two-dimensional hetero-structures: on the reaction between MoS2 and graphene | Little is understood of the chemical interactions between nanomaterials in 2D hetero-structures of transition metal dichalcogenides and graphene. We prepared hetero-structures of MoS2 and graphene. X-ray photoelectron spectroscopy of the hetero-structures revealed an increase in an sp3-hybridized C component in the graphene component, while infra-red spectroscopy showed O–H, C=C, C–O and C–H moieties, which were not found in pristine graphene or MoS2. Thermogravimetric analysis of the hetero-structures showed thermal instability and carbonaceous decay at lower temperatures than in pristine precursors. We thus demonstrate a chemical change to graphene in such hetero-structures and offer evidence for a chemically non-innocent interaction between graphene and MoS2. Our discovery demonstrates the potential chemical non-innocence behaviour of 2D nanomaterials in hetero-structured devices. | Ciaran McGlynn; Aleksandra Krajewska; Xin Chen; Aidan McDonald | Inorganic Chemistry; Reaction (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd80296dde43c908bdf11c/original/two-dimensional-hetero-structures-on-the-reaction-between-mo-s2-and-graphene.pdf |
660464bd66c1381729fdd4ae | 10.26434/chemrxiv-2024-sxxg3 | Modelling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches | The amount of innovative applications for DNA nowadays is growing quickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deep understanding of the charge transfer process along the strand, as well as its redox properties. These features are computationally simulated and analyzed in detail throughout this work by combining molecular dynamics, multilayer schemes and the Marcus theory. The one-electron oxidation potential and the hole delocalization have been analyzed for six DNA double strands that cover all possible binary combinations of nucleotides. The results have revealed that the one-electron oxidation potential decreases with respect to the single-stranded DNA, giving evidence that the greater rigidity of a double helix induces an increase in the capacity of storing the positive charge generated upon oxidation. In addition, the hole is mainly stored in nucleobases with large reducer character, i.e., purines, especially when those are arranged in a stacked configuration in the same strand. From the computational point of view, the sampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number of representative conformations generated by a clustering analysis provides accurate results when compared with those obtained from the sampling, reducing considerably the computational cost. | Jesús Lucia-Tamudo; Sergio Díaz-Tendero; Juan Jose Nogueira | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660464bd66c1381729fdd4ae/original/modelling-one-electron-oxidation-potentials-and-hole-delocalization-in-double-stranded-dna-by-multilayer-and-dynamic-approaches.pdf |
65bb790066c1381729ba6a9a | 10.26434/chemrxiv-2023-47d99-v3 | Boundary Conditions for Promotion versus Poisoning in Copper-Gallium-based CO2–to–Methanol Hydrogenation Catalysts | Cu-Ga-based CO2-to-methanol hydrogenation catalysts are known to display a range of catalytic performance depending on their preparation. Here, using surface organometallic chemistry, we have prepared a series of silica-supported 3-6 nm Cu1-xGaxOy nanoparticles with a range of xGa to establish how the concentration of Ga and alloy formation affect the activity. Cu is always fully metallic in this series, while Ga is partially alloyed with Cu in the core and partially oxidized on the surface. These materials display a volcano-type activity behavior, where methanol formation is promoted when xGa < 0.13-0.18 and is suppressed at higher values, indicating a poisoning of the catalysts. In situ X-ray absorption spectroscopy shows that GaOx species over promoted Cu0.93Ga0.07-SiO2 catalyst are much more redox active than those over the poisoned Cu0.77Ga0.23-SiO2. In situ infrared spectroscopy detected methoxy intermediates over the promoted Cu0.93Ga0.07-SiO2 catalyst, while no formate or methoxy species could be observed over the poisoned Cu0.77Ga0.23-SiO2. The absence of reactive intermediates and irreversible oxidation of GaOx over poisoned catalyst suggests encapsulation of Cu by GaOx shell resulting in low activity. | Jan L. Alfke; Maria Tejeda-Serrano; Sumant Phadke; Andrei Tereshchenko; Terry Z. H. Gani; Lukas Rochlitz; Seraphine B. X. Y. Zhang; Lin Lin; Christophe Copéret; Olga V. Safonova | Physical Chemistry; Inorganic Chemistry; Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bb790066c1381729ba6a9a/original/boundary-conditions-for-promotion-versus-poisoning-in-copper-gallium-based-co2-to-methanol-hydrogenation-catalysts.pdf |
60c75888702a9b6c7018cd41 | 10.26434/chemrxiv.14191865.v1 | Cu-Based Turn-on Fluorescent Sensors for Cu-rich Amyloid β Aggregates | <div>Protein misfolding and metal dishomeostasis are two key</div><div>pathological factors of Alzheimer’s disease. Previous studies have showed that Cu‐mediated Aβ aggregation pathways lead to formation of neurotoxic Aβ oligomers. Herein, we reported a series of picolinic acid‐based Cu‐activatable sensors, which can be used for the fluorescence imaging of Cu‐rich Aβ aggregates.</div> | Yiran Huang; Liang Sun; Liviu M. Mirica | Bioinorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75888702a9b6c7018cd41/original/cu-based-turn-on-fluorescent-sensors-for-cu-rich-amyloid-aggregates.pdf |
62b97a0fe84dd141030557ae | 10.26434/chemrxiv-2022-4hq5r | Photoinduced Concerted Dual Single-bond Rotation of a Nitrogen-containing System Realized by Chalcogen Substitution | Conformational change caused by photochemical concerted multiple bond rotation is a very rare event. Thus, it is a critical challenge to expand this chemistry because it has higher potential to more precisely modulate the molecular function of molecules. Here, we describe a novel nitrogen-containing molecular system exhibiting photoinduced concerted rotation, which is the first example of successfully incorporating heteroatoms into a system exhibiting photoinduced concerted rotation. Sufficient kinetic stability and photosensitivity to realize photoinduced concerted rotation can be brought to a sterically hindered benzamide system by chalcogen substitution. The photoinduced C-N/C-C concerted rotation of the thioamide derivative can be directly observed, and it was found that the thioamide system exhibits the ability to generate different conformers depending on external stimuli. A theoretical study also supported the selective occurrence of photoinduced C-N/C-C concerted rotation. It is expected that the system can be utilized to modulate the functions of organic compounds. | Shotaro Nagami; Akira Katsuyama; Rintaro Kaguchi; Tohru Taniguchi; Kenji Monde; Satoshi Ichikawa | Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.); Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b97a0fe84dd141030557ae/original/photoinduced-concerted-dual-single-bond-rotation-of-a-nitrogen-containing-system-realized-by-chalcogen-substitution.pdf |
632d7cc6ea6a2216b1fb0d03 | 10.26434/chemrxiv-2022-7dsqd | Rhodium-catalyzed Anti-Markovnikov Transfer Hydroiodination of Terminal Alkynes | A rhodium-catalyzed anti-Markovnikov hydroiodination of aromatic and aliphatic terminal alkynes is reported. Depending on the choice of ligand and substrate, either (E)- or (Z)-configured alkenyl iodides are obtained in high to exclusive isomeric purity. The reaction exhibits a broad substrate scope and high functional group tolerance, employing easily accessible or commercially available aliphatic iodides as HI surrogates through a shuttle process. The synthesized vinyl iodides were applied in several C–C and C–heteroatom bond-forming reactions with full retention of the stereoselectivity. The developed method could be used to significantly shorten the total synthesis of a marine cis-fatty acid. Additionally, initial deuterium-labeling experiments and stoichiometric reactions shed some light on the potential reaction mechanism. | Philip Boehm; Niklas Kehl; Bill Morandi | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632d7cc6ea6a2216b1fb0d03/original/rhodium-catalyzed-anti-markovnikov-transfer-hydroiodination-of-terminal-alkynes.pdf |
60c75005ee301c8da1c7a7cc | 10.26434/chemrxiv.12974246.v1 | Visible-Light Triggered Templated Ligation on Surface Using Furan-Modified PNAs | Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. Translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. White light irradiation in combination with recognition of a short 22mer oligo sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format. | Alex Manicardi; Enrico Cadoni; Annemieke Madder | Photochemistry (Org.); Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75005ee301c8da1c7a7cc/original/visible-light-triggered-templated-ligation-on-surface-using-furan-modified-pn-as.pdf |
65804ae3e9ebbb4db9316869 | 10.26434/chemrxiv-2023-kxpj1-v2 | Spectroscopy of yttrium scandate doped with ytterbium ion | The spectral-kinetic properties of Yb3+ optical centers in YScO3 crystal fiber were studied using selective laser spectroscopy. Various spectral characteristics of the Yb3+ optical centers were determined, including homogeneous and inhomogeneous broadening values, Stark level splitting, and the lifetime of Yb3+ ion optical centers. Three distinct types of Yb3+ optical centers were identified. The first optical center, with a lifetime of III77K = 4.05 ms, was formed due to the substitution of Y3+ for Yb3+ ions in the local site of С3i. The other two Yb3+ optical centers, with lifetimes of I77K = 1.0 ms (СII2(Y3+) center) and II77K = 0.620 ms (СII2(Sc3+)), respectively, were formed as a result of the substitution of Y3+ and Sc3+ for Yb3+ in the local site of C2. | Olimkhon Alimov; Maksim Doroshenko; Elena Dobretsova; Ksenia Pierpoint; Sergey Rusanov; Vitaly Kashin; Vladimir Tsvetkov | Materials Science | CC BY 4.0 | CHEMRXIV | 2023-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65804ae3e9ebbb4db9316869/original/spectroscopy-of-yttrium-scandate-doped-with-ytterbium-ion.pdf |
60c7484ebb8c1a48913dac4f | 10.26434/chemrxiv.11860941.v1 | The Chemical Bond Across the Periodic Table: Part 1 – First Row and Simple Metals | <p>Chemical bond plays a central role in
the description of the physicochemical properties of molecules and solids and it
is essential to several fields in science and engineering, governing the
material’s mechanical, electrical, catalytic and optoelectronic properties,
among others. Due to this indisputable importance,
a proper description of chemical bond is needed, commonly obtained through
solving the Schrödinger equation of the system with either molecular orbital
theory (molecules) or band theory (solids). However, connecting these seemingly
different concepts is not a straightforward task for students and there is a gap
in the available textbooks concerning this subject. This work presents a
chemical content to be added in the physical chemistry undergraduate courses, in
which the framework of molecular orbitals was used to qualitatively explain the
standard state of the chemical elements and some properties of the resulting
material, such as gas or crystalline solids. Here in Part 1, we were able to
show the transition from Van der Waals clusters to metal in alkali and alkaline
earth systems. In Part 2 and 3 of this three-part work, the present framework
is applied to main group elements and transition metals. The original content
discussed here can be adapted and incorporated in undergraduate and graduate
physical chemistry and/or materials science textbooks and also serves as a
conceptual guide to subsequent disciplines such as quantum chemistry, quantum
mechanics and solid-state physics.</p> | Gabriel Freire Sanzovo Fernandes; Leonardo dos Anjos Cunha; Francisco Bolivar Correto Machado; Luiz Ferrão | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7484ebb8c1a48913dac4f/original/the-chemical-bond-across-the-periodic-table-part-1-first-row-and-simple-metals.pdf |
67134563cec5d6c142938180 | 10.26434/chemrxiv-2024-1z6t2 | Modulation of the Magnetic Anisotropy via Ligand Field in Sandwiched Erbium Complexes | Among lanthanide based single molecule magnets (SMMs), erbium(III) is the Kramers ion, apart from dysprosium(III), which provides the magnetic bistability in presence of a suitable coordination environment. However, Er-based SMMs exhibit significantly less magnetic anisotropy than Dy because their prolate electronic density necessitates equatorially correlated ligands to minimize the charge contact with the Er atom. Here, in this work, we have computationally investigated the heteroleptic organometallic complexes with an Er(III) atom sandwiched between two distinct cyclic rings (five and eight membered) with the aim to tune the magnetic anisotropy via exploiting the ligand field. The ligand field is manipulated by substituting one of the C atoms from the five-membered ring with the heteroatoms (groups 14 and 15), while the other (eight-membered) ring remains intact. The electronic and magnetic properties have been investigated using first-principle based ab initio approaches. The distortion in the planarity of five-membered ring generated by the larger heteroatom affects the bonding with magnetic Er and consequently the electronic structure. This is observed to modify the ligand field and the magnetic axis, thereby improving the magnetic relaxation barrier. | Sakshi Nain; Md. Ehesan Ali | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Lanthanides and Actinides; Magnetism; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67134563cec5d6c142938180/original/modulation-of-the-magnetic-anisotropy-via-ligand-field-in-sandwiched-erbium-complexes.pdf |
678edcb0fa469535b9e18efc | 10.26434/chemrxiv-2025-zlkz5 | Improvement of Fourteen Coupled Global Potential Energy Surfaces of 3A′ States of O + O2 | We improved the potential energy surfaces for fourteen coupled 3A′ states of O3 by using parametrically managed diabatization by deep neural network (PM-DDNN) with three improvements: (1) We use a new functional form for the parametrically managed activation function, which ensures the continuity of the coordinates used in the parametric management. (2) We used higher weighting for low-lying states to achieve smoother potential energy surfaces. (3) The asymptotic behavior of the coupled potential energy surfaces was further refined by utilizing a better low-dimensional potential. As a result of these improvements, we obtained significantly smoother potentials that are better suited for dynamics calculations. For the new version of 14 coupled 3A′ surfaces, the entire set of 532,560 adiabatic energies are fit with a mean unsigned error (MUE) of 45 meV, which is only 0.7% of the mean energy in the data set, which is 6.24 eV. | Xiaorui Zhao; Yinan Shu; Qinghui Meng; Jie J. Bao; Xuefei Xu; Donald Truhlar | Physical Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678edcb0fa469535b9e18efc/original/improvement-of-fourteen-coupled-global-potential-energy-surfaces-of-3a-states-of-o-o2.pdf |
66ead39251558a15ef5949eb | 10.26434/chemrxiv-2024-qwnb2 | Activation of small molecules by ambiphilic NHC-stabilized phosphinoborenium cation: formation of boreniums with B-O-C, B-O-B, and B-O-P structural motifs | The reactivity of the phosphinoborenium cation supported by a 1,3,4,5-tetramethylimidazolin-2-ylidene ligand toward small molecules was explored. The phosphinoborenium cation exhibited dual Lewis acid–base properties due to the presence of the Lewis acidic boron center and the Lewis basic phosphido ligand connected by a covalent bond. The reaction of the title cation with CO2 led to the insertion of a CO2 molecule into the P-B bond. The obtained borenium CO2-adduct underwent hydrolysis, forming an N-heterocyclic carbene stabilized diborenium dication bearing a B-O-B functionality. The activation of N2O proceeded via the insertion of an oxygen atom into the B-P bond of the parent cation, yielding a borenium cation with a phosphinite moiety. An alternative synthetic pathway to borenium cations with a B-O-P skeleton was achieved via the activation of secondary phosphine oxides by the phosphinoborenium cation. Furthermore, borenium cations and diborenium dications with B-O-C structural motifs were obtained from the reaction of the title compound with perfluorinated tert-butyl alcohol and hydroquinone, respectively. The structure of the obtained borenium cations is discussed based on multinuclear NMR spectroscopy, X-ray diffraction, and density functional theory calculations. | Tomasz Wojnowski; Anna Ordyszewska; Hanna Halenka; Iwona Anusiewicz; Jarosław Chojnacki; Kinga Kaniewska-Laskowska; Rafał Grubba | Inorganic Chemistry; Frustrated Lewis Pairs; Main Group Chemistry (Inorg.); Small Molecule Activation (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ead39251558a15ef5949eb/original/activation-of-small-molecules-by-ambiphilic-nhc-stabilized-phosphinoborenium-cation-formation-of-boreniums-with-b-o-c-b-o-b-and-b-o-p-structural-motifs.pdf |
60c74589702a9b15dd18aa28 | 10.26434/chemrxiv.10055429.v1 | Kinobead/LC-MS Phosphokinome Profiling Enables Rapid Analyses of Kinase-Dependent Cell Signaling Networks | <p>Kinase-catalyzed
protein phosphorylation is fundamental to eukaryotic signal transduction,
regulating most cellular processes. Kinases are frequently dysregulated in
cancer, inflammation and degenerative diseases, and because they can be
inhibited with small molecules, they became important drug targets. Accordingly,
analytical approaches that determine kinase activation states are critically
important to understand kinase-dependent signal transduction, and to identify novel
drug targets and predictive biomarkers. Multiplexed inhibitor beads (MIBs or
kinobeads) efficiently enrich kinases from cell lysates for LC-MS analysis. When
combined with phosphopeptide enrichment, kinobead/LC-MS can also quantify the
phosphorylation state of kinases, which determines their activation state. However,
an efficient kinobead/LC-MS kinase phospho-profiling protocol that allows
routine analyses of cell lines and tissues has not yet been developed. Here, we
present a facile workflow that quantifies the global phosphorylation state of kinases
with unprecedented sensitivity. We also found that our kinobead/LC-MS protocol can
measure changes in kinase complex composition and show how these changes can indicate
kinase activity. We demonstrate the utility of our approach in specifying
kinase signaling pathways that control the acute steroidogenic response in
Leydig cells; this analysis establishes the first comprehensive framework for
the post-translational control of steroid biosynthesis. <b></b></p> | Martin Golkowski; Venkata Narayana Vidadala; Ho-Tak Lau; Anna Shoemaker; Masami Shimizu-Albergine; Joseph A. Beavo; Dustin J. Maly; Shao-En Ong | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74589702a9b15dd18aa28/original/kinobead-lc-ms-phosphokinome-profiling-enables-rapid-analyses-of-kinase-dependent-cell-signaling-networks.pdf |
64140a67dab08ad68f40ecdb | 10.26434/chemrxiv-2023-j168d | Understanding Molecular Aggregation of Ligand-protected Atomically-Precise Metal Nanoclusters | Atomically precise ligand-protected nanoclusters (MPC) have emerged as an important class of molecules due to their unique structural features and diverse potential applications, including nano-electronics, bio-imaging, as sensors and drug carriers. Understanding the atomistic details of their intermolecular interaction is of paramount interest for designing, synthesizing, and system-specific applications. Crystal structures of various MPCs provide details related to molecular packing and intermolecular interactions. While these experiments reveal macroscopic, mostly static properties, they are often limited by the spatial and temporal resolutions in delineating the microscopic dynamical details. Here we apply molecular dynamics and enhanced sampling simulations to study the aggregation of Au25(pMBA)18 MPCs in the solution phase. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and periodic crystals. The free energy profiles obtained from enhanced sampling simulations of dimerization reveal a pivotal role of the protonated states of the ligands as well as the solvation shell in mediating the molecular aggregation process in solution. In the solid phase, the MPCs’ ligands have suppressed conformational flexibility owing to many facile intermolecular hydrogen bonds and π- stacks. Our work provides unprecedented molecular-level details of the aggregation process and conformational dynamics of MPCs ligands in the solution and crystalline phases, which will help rational design of new MPCs with specific properties. | Vikas Tiwari; Dr. Tarak Karmakar | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64140a67dab08ad68f40ecdb/original/understanding-molecular-aggregation-of-ligand-protected-atomically-precise-metal-nanoclusters.pdf |
60c73d8dbb8c1aeec13d977e | 10.26434/chemrxiv.5851701.v1 | Effect of Hydrated Metal Salts on the Coordination Product of Cobalt(II) halide and PNP Type Ligand, 2,6-bis(di-tertbutylphosphinomethyl) pyridine | Chemical treatment of CoX<sub>2</sub><b><sup>. </sup></b>6H<sub>2</sub>O (X = Cl,
Br, I) with the potentially tridentate PNP pincer ligand 2,6-bis(di-<i>tert</i>-butylphosphinomethyl)pyridine in
1:1 molar ratio results in cobalt(II) halide-PNP pincer complexes. The effect
of the hydrated metal source on molecular structure and geometry of the
complexes was studied by single crystal X-ray diffraction analysis. The
complexes are neutral and the cobalt center adopts a penta-coordinate system
with potential atropisomerization. Within
the unit cell there are two distinct molecules per asymmetric unit. One of the
two phosphorus atoms in the PNP ligand was observed to be partially oxidized to
phosphinoxide. Disorder in the structure reflects a mixture of square pyramidal
and distorted tetrahedral geometry. | Tasneem Siddiquee; Abdul Goni | Coordination Chemistry (Organomet.); Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d8dbb8c1aeec13d977e/original/effect-of-hydrated-metal-salts-on-the-coordination-product-of-cobalt-ii-halide-and-pnp-type-ligand-2-6-bis-di-tertbutylphosphinomethyl-pyridine.pdf |
60c746c5469df44732f43705 | 10.26434/chemrxiv.11388339.v1 | Combinatorial Screening Yields Discovery of 29 Metal Oxide Photoanodes for Solar Fuel Generation | Combinatorial synthesis combined with high throughput electrochemistry enabled discovery of 29 ternary oxide photoanodes, 14 with visible light response for oxygen evolution. Y3Fe5O12 and trigonal V2CoO6 emerge as particularly promising candidates due to their photorepsonse at sub-2.4 eV illumination. | Lan Zhou; Aniketa Shinde; Dn Guevarra; Matthias Richter; Helge Stein; Yu Wang; Paul Newhouse; John Gregoire | Catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c5469df44732f43705/original/combinatorial-screening-yields-discovery-of-29-metal-oxide-photoanodes-for-solar-fuel-generation.pdf |
64d98072dfabaf06ff3bb719 | 10.26434/chemrxiv-2023-s9w9p | DFT-guided Development of New Hemilabile (P^N) Ligands for Gold-(I/III) RedOx Catalysis : Application to the Thiotosylation of Aryl Iodides | Ligand-enabled oxidative addition of Csp2-X bonds to Au(I) centers has recently appeared as a valuable strategy for the development of catalytic RedOx processes. Several cross-coupling reactions that were previously considered difficult to achieve were reported lately, thus expanding the synthetic potential of gold(I) complexes beyond the traditional nucleophilic functionalization of pi-systems. MeDalPhos has played an important role in this development and, despite several studies on alternative structures, remains so far, the only general ligand for such process. We report herein the discovery and the DFT-guided structural optimization of a new family of hemilabile (P^N) ligands that can promote oxidative addition of aryl iodides to gold(I). These flexible ligands, which possess a common 2-methylamino heteroaromatic N-donor motif, are structurally and electronically tunable, beyond being easily accessible and affordable. The corresponding Au(I) complexes were shown to outperform the reactivity of (MeDalPhos)Au(I) in a series of alkoxy- and amidoarylation of alkenes. Their synthetic potential and comparatively higher reactivity were further highlighted in the thiotosylation of aryl iodides, a challenging unreported C-S cross-coupling reaction that could not be achieved under classical Pd(0/II) catalysis and that allows a general and divergent access to aryl sulfur derivatives. | Karim Muratov; Emil Zaripov; Maxim V. Berezovski; Fabien Gagosz | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d98072dfabaf06ff3bb719/original/dft-guided-development-of-new-hemilabile-p-n-ligands-for-gold-i-iii-red-ox-catalysis-application-to-the-thiotosylation-of-aryl-iodides.pdf |
60c73e98ee301c1988c78755 | 10.26434/chemrxiv.5406907.v5 | Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo | <div>Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation timescales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes.</div><div><br /></div><div>In this technique the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over two orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step towards applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding Modes of Ligands using Enhanced Sampling (BLUES) package which is freely available on GitHub.</div> | Samuel Gill; Nathan M. Lim; Patrick Grinaway; Ariën S. Rustenburg; Josh Fass; Gregory Ross; John D. Chodera; David Mobley | Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e98ee301c1988c78755/original/binding-modes-of-ligands-using-enhanced-sampling-blues-rapid-decorrelation-of-ligand-binding-modes-using-nonequilibrium-candidate-monte-carlo.pdf |
64cc94ec4a3f7d0c0d907b3c | 10.26434/chemrxiv-2023-80dsg | Amphiphilic Acetylacetone-Based Carbon Dots | On-going development of carbon dots (CDs) for different applications calls for search of novel methods for their synthesis and surface functionalization. For fabrication of light-emitting devices (LEDs), CDs should be soluble in non-polar solvents that are used for ink-printing of their functional layers, apart from the obvious requirement of bright luminescence. Herein, we introduce amphiphilic CDs synthesized from a mixture of benzoic acid and ethylenediamine in acetylacetone, which satisfy both above mentioned requirements. These CDs are quasi-spherical nanoparticles 20-50 nm in size, holding aliphatic, carbonyl, amide, imine, and carbamate groups at the surface which renders them amphiphilic and soluble in a variety of substances with relative polarity ranging from 0.002 to 1, such as toluene, chloroform, alcohols, and water. By variation of the molar ratio of benzoic acid and ethylenediamine, an optimal value for photoluminescence quantum yield of 36 % in non-polar solvents is achieved. Importantly, these CDs are easily mixable with a charge transport polymer – polyvinylcarbazole, a common component of organic LEDs. As a demonstration of use of developed amphiphilic CDs in LEDs, green emitting charge-injection devices are fabricated with a broad emission band centered at 515 nm, maximal luminance of 1716 cd/m2, and ССT of 5627 K. | Sergei Cherevkov; Evgeniia Stepanidenko; Mikhail Miruschenko; Andrei Zverkov; Igor Margaryan; Igor Spiridonov; Denis Danilov; Aleksandra Koroleva; Evgeniy Zhizhin; Marina Baidakova; Roman Sokolov; Maria Sandzhieva; Elena Ushakova; Andrey Rogach | Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cc94ec4a3f7d0c0d907b3c/original/amphiphilic-acetylacetone-based-carbon-dots.pdf |
647c86c54f8b1884b7d41aea | 10.26434/chemrxiv-2023-j7l2r | Single Phase Transition Leads to the Coffee Ring Deposition of Nanoparticles in an Evaporating Sessile Droplet | The coffee-ring formation upon evaporation of a sessile droplet laden with dispersed particles occurs via capillary flow of the fluid towards the three-phase pinned contact line. In the process, the particles are carried towards the contact line followed by gradual deposition that accelerates towards the end of drying. However, we have observed using surface enhanced Raman spectroscopy (SERS) with gold nanoparticles that the deposition process at the contact line occurred in a short window of time that was akin to a phase transition and that was complete well before the drying of the droplet. Further, the concentration of nanoparticles at the time of deposition was the same irrespective of the initial concentrations studied, the value of which was calculated to have been on the order of 13 M. | SUJAY PAUL; ARUN CHATTOPADHYAY | Physical Chemistry; Nanoscience; Interfaces; Physical and Chemical Processes; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647c86c54f8b1884b7d41aea/original/single-phase-transition-leads-to-the-coffee-ring-deposition-of-nanoparticles-in-an-evaporating-sessile-droplet.pdf |
60c74102469df46b17f42d5e | 10.26434/chemrxiv.7824707.v2 | Pathway Complexity in the Stacking of Imine-linked Macrocycles Related to Two-Dimensional Covalent Organic Frameworks | This work reports on the assembly of imine-linked macrocycles that serve as models of two-dimensional covalent organic frameworks (2D COFs). Interlayer interactions play an important role in the formation of 2D COFs, yet the effect of monomer structure on COF formation, crystallinity, and susceptibility to exfoliation are not well understood. For example, monomers with both electron-rich and electron-poor π-electron systems have been proposed to strengthen interlayer inter-actions and improve crystallinity. Here we probe these effects by studying the stacking behavior of imine-linked macrocycles that represent discrete models of 2D COFs. <div><br /></div><div>Specifically, macrocycles based on terephthaldehyde (PDA) or 2,5-dimethoxyterephthaldehyde (DMPDA) stack upon cooling molecularly dissolved solutions. Both macrocycles assemble cooperatively with similar ΔHe values of -97 kJ/mol and -101 kJ/mol, respectively, although the DMPDA macrocycle assembly process showed a more straightforward temperature dependence. Circular dichroism spectroscopy performed on macrocycles bearing chiral side chains revealed a helix reversion process for the PDA macrocycles that was not observed for the DMPDA macrocycles. <br /></div><div><br /></div><div>Given the structural similarity of these monomers, these findings demonstrate that the stacking processes associated with nanotubes derived from these macrocycles, as well as for the corresponding COFs, are complex and susceptible to kinetic traps, casting doubt on the relevance of thermodynamic arguments for improving materials quality. <br /></div> | Shiwei Wang; Anton Chavez; Simil Thomas; Hong Li; Nathan C. Flanders; Chao Sun; Michael J. Strauss; Lin Chen; Albert J. Markvoort; Jean-Luc Bredas; William Dichtel | Physical Organic Chemistry; Stereochemistry; Supramolecular Chemistry (Org.); Aggregates and Assemblies; Polymerization kinetics; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74102469df46b17f42d5e/original/pathway-complexity-in-the-stacking-of-imine-linked-macrocycles-related-to-two-dimensional-covalent-organic-frameworks.pdf |
60c74b02f96a009e43287545 | 10.26434/chemrxiv.12279551.v1 | Infrared Scattering-Type Scanning Near-Field Optical Microscopy in Water | <div><div><div><p>Infrared (IR) absorption spectroscopy detects state and chemical composition of biomolecules solely by their inherent vibrational fingerprints. Major disadvantages like the lack of spatial resolution and sensitivity were compensated lately by the use of pointed probes as local sensors enabling the detection of quantities as few as hundreds of proteins with nanometer precision. This makes infrared scattering-type scanning near-field optical microscopy a very powerful tool in life science. The strong absorption of infrared radiation of liquid water, however, still prevents to simply access the measured quantity – light scattered at the probing atomic force microscope tip. Here we report on the local IR response of biological membranes immersed in aqueous bulk solution. We make use of a silicon solid immersion lens as substrate and focusing optics to achieve detection efficiencies sufficient to yield IR near-field maps of purple membranes. We scrutinized our experimental findings by applying theoretical models. Finally, we suggest a means to improve the imaging quality by laser scanning assisted scattering-type scanning near-field optical microscopy. We believe that IR scattering-type scanning near-field optical microscopy will resolve biological structures in their native environments at nm resolution without the need for labeling.</p></div></div></div> | Emanuel Pfitzner; Joachim Heberle | Biophysics; Optics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b02f96a009e43287545/original/infrared-scattering-type-scanning-near-field-optical-microscopy-in-water.pdf |
6584885c9138d23161357040 | 10.26434/chemrxiv-2023-dkr1h | Convenient one-pot synthesis and biological evaluation of novel 3,5-dimethyl-1H-pyrazole-1-carbothiohydrazide derivatives as new anti-tumor agents against both liver carcinoma (HepG2) and lung carcinoma (A549) cell lines | Pyrazle constituents have garnered consideration mainly because of their presumed biological and curative properties. Therefore, the goal of the presented research is to create some novel pyrazole-1-carbothiohydrazide derivatives with predicted biological functions using an accessible one-pot synthesis employing 3,5-dimethyl-1H-pyrazole-1-carbothiohydrazide (1) as a facile antecedent. The component 1 and 1,3-diphenylpropane-1,3-dione (2) interacted resulting in pyrazole derivative 3 when ethanol or acetic acid were supplied. However, when the substance 1 interacted in ethanol with either 2 or acetyl acetone 5, using the catalytic proportion of triethylamine offered, it yielded compounds 4 and 6 respectively. Ingredient 1 was subjected to additional reactions with ethyl cyanoacetate (7), stearic acid 10, or equivalent carboxylic acids 12a-c, resulted in the formation of 9, 11, and 13a-c consequently. Additionally, when 1 was combined with α-haloketones 14 or 16, it yielded the corresponding 1,3,4-thiadiazine derivatives, 15 and 17. Every designed product's chemical structure was established according to spectroscopic and analytical results. The cytotoxic activities of the synthesized chemicals were assessed against two carcinoma cell lines, and compared to the standard drug Cisplatin using the colorimetric MTT assay. Furthermore, the results revealed that chemical 17 was the most active against the liver and lung carcinoma cell lines giving potent IC50 value of 5.35 and 8.74 μM, respectively, compared with reference drug cisplatin (3.78 and 6.39 μM). Interestingly, ingredient 17 when evaluated for their toxicity against normal lung fibroblast (MRC-5) cells exhibited low toxic effects indicating the safe use. Generally, our results exerted promising bioactive compounds. | Marwa Fouad; Mahmoud Elaasser | Organic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6584885c9138d23161357040/original/convenient-one-pot-synthesis-and-biological-evaluation-of-novel-3-5-dimethyl-1h-pyrazole-1-carbothiohydrazide-derivatives-as-new-anti-tumor-agents-against-both-liver-carcinoma-hep-g2-and-lung-carcinoma-a549-cell-lines.pdf |
6791885bfa469535b95afe2e | 10.26434/chemrxiv-2025-qv284 | Hydration of a Polyaromatic Hydrocarbon in Anionic Perylene-Water Clusters | We present infrared photodissociation spectra of hydrated perylene anion clusters with up to four water molecules, as well as electronic structure calculations based on density functional theory. Water molecules form weak hydrogen bonds to the system of the perylene anion. For clusters with more than one water molecule, water-water hydrogen bonds are formed, which are generally stronger than water- hydrogen bonds. The resulting water networks exist as water subclusters on the surface of the carbon frame of perylene. We observe temperature dependent dynamic effects, which highlight large amplitude motions of the water network and the shallowness of the potential energy surfaces governing the structures of these clusters. | Heinrich Salzmann; J. Mathias WEBER | Physical Chemistry; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6791885bfa469535b95afe2e/original/hydration-of-a-polyaromatic-hydrocarbon-in-anionic-perylene-water-clusters.pdf |
64cc0c87dfabaf06ffa751ae | 10.26434/chemrxiv-2023-zvj61 | 4,4-Difluoroproline as a Unique 19F NMR Probe of Proline Conformation | Despite the importance of proline conformational equilibria (trans versus cis amide, exo versus endo ring pucker) on protein structure and function, there is a lack of convenient ways to probe proline conformation. 4,4-Difluoroproline (Dfp) was identified to be a sensitive 19F NMR-based probe of proline conformational biases and of cis-trans isomerism. Within model compounds and disordered peptides, the diastereotopic fluorines of Dfp exhibit similar chemical shifts (ΔδFF = 0–3 ppm) when a trans X–Dfp amide bond is present. In contrast, the diastereotopic fluorines exhibit a large (ΔδFF = 5–12 ppm) difference in chemical shift in a cis X–Dfp prolyl amide bond. DFT calculations, X-ray crystallography, and solid-state NMR spectroscopy indicated that the ΔδFF directly reports on the relative preference of one proline ring pucker over the other: a fluorine which is pseudo-axial (i.e. the pro-4R-F in an exo ring pucker, or the pro-4S-F in an endo ring pucker) is downfield, while a fluorine which is pseudo-equatorial (i.e. pro-4S-F when exo, or pro-4R-F when endo) is upfield. Thus, when a proline is disordered (a mixture of exo and endo ring puckers, as at trans-Pro in peptides in water), it exhibits a small Δδ. In contrast, when the Pro is ordered (i.e. when one ring pucker is strongly preferred, as in cis-Pro amide bonds, where the endo ring pucker is strongly favored), a large Δδ is observed. Dfp can be used to identify inherent induced order in peptides and to quantify proline cis-trans isomerism. Using Dfp, we discovered that the stable polyproline II helix (PPII) formed in the denatured state (8 M urea) exhibits essentially equal populations of the exo and endo proline ring puckers. In addition, the data with Dfp suggested the specific stabilization of PPII by water over other polar solvents. These data strongly support the importance of carbonyl solvation and n→π* interactions for the stabilization of PPII. Dfp was also employed to quantify proline cis-trans isomerism as a function of phosphorylation and the R406W mutation in peptides derived from the intrinsically disordered protein tau. Dfp is minimally sterically disruptive and can be incorporated in expressed proteins, suggesting its broad application in understanding proline cis-trans isomerization, protein folding, and local order in intrinsically disordered proteins. | Himal K. Ganguly; Brice A. Ludwig; Megh R. Bhatt; Caitlin M. Tressler; Anil K. Pandey; Caitlin M. Quinn; Shi Bai; Glenn P. A. Yap; Neal J. Zondlo | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Biochemistry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cc0c87dfabaf06ffa751ae/original/4-4-difluoroproline-as-a-unique-19f-nmr-probe-of-proline-conformation.pdf |
663e324221291e5d1deea542 | 10.26434/chemrxiv-2023-rn6c8-v2 | An Exceedingly Low-Coordinate Platinum(0)-Germylene for E–H Bond Activation and Catalytic Hydrodehalogenation | Pairing transition metals and heavier tetrylenes (Si, Ge, Sn, Pb) holds great potential for cooperative bond activation and catalysis. In this work, we investigate the reactivity of an exceptionally low-coordinate Pt(0)/Ge(II) system that emerges from the reaction between the monoligated platinum(0) precursor [(PMe2ArDipp2)Pt(olefin)] with germylene dimer [ArDipp2GeCl]2 (where ArDipp2 = C6H3-2,6-(C6H3-2,6-iPr2)2)). The resulting complex revealed remarkable ability for cooperative bond activation. Stoichiometric reactions with dihydrogen, water, methanol, ammonia and alkynes unveil the formation of Pt(II)-germyl compounds, characterized by distinct isomeric forms, whose flexibility derives from the particularly low-coordination. Its catalytic potential is explored in the hydrodehalogenation of aliphatic, aromatic and main-group halides under dihydrogen atmosphere using both thermal and photochemical conditions, demonstrating promising conversions even for more challenging alkyl chlorides. | Sonia Bajo; Enrique Soto; Marta Fernandez-Buenestado; Joaquin López-Serrano; Jesus Campos | Organometallic Chemistry; Bond Activation; Catalysis; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663e324221291e5d1deea542/original/an-exceedingly-low-coordinate-platinum-0-germylene-for-e-h-bond-activation-and-catalytic-hydrodehalogenation.pdf |
60c7541bbb8c1aeb073dc195 | 10.26434/chemrxiv.13160750.v3 | Self-Guiding Polymeric Prodrug Micelles with Two Aggregation-Induced Emission Photosensitizers for Enhanced Chemo-Photodynamic Therapy | <p>Nowadays,
aggregation-induced emission luminogens (AIEgens) with reactive oxygen species
(ROS) generating ability have been used as photosensitizers for imaging guided
photodynamic therapy (PDT). To achieve enhanced antitumor outcomes, combining
AIEgens-based PDT with chemotherapy is an efficient strategy. However, the
therapeutic efficiency is hampered by the limited cellular uptake efficiency
and the appropriate light irradiation occasion. In this paper, a self-guiding
polymeric micelle (TB@PMPT) composed of two AIE photosensitizers and a
reduction-sensitive paclitaxel prodrug (PTX-SS-N<sub>3</sub>) was established
for enhanced chemo-photodynamic therapy by a dual-stage light irradiation
strategy. When the micelles were accumulated in tumor tissues, the first light
irradiation (L<sub>1</sub>, 6 min) was utilized to facilitate cellular uptake
by “photochemical internalization” (PCI). Then the intracellular glutathione
(GSH) would induce the PTX release, micelles disassembly and the aggregation
state change of AIEgens. The fluorescence signal change of two AIEgens-based
ratiometric fluorescent probe could not only precisely guide the second light
irradiation (L<sub>2</sub>, 18 min) for sufficient ROS production, but also
monitor the non-fluorescent drug PTX release in turn. Both <i>in vivo</i> and <i>in
vitro</i> studies demonstrated that the dual-stage light irradiation strategy
employed for TB@PMPT micelles exhibited superior therapeutic effect than only
24-min continuous light irradiation.<br /></p> | Xiaoqing Yi; Jingjing Hu; Jun Dai; Xiaoding Lou; Zujin Zhao; Fan Xia; Ben Zhong Tang | Biochemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7541bbb8c1aeb073dc195/original/self-guiding-polymeric-prodrug-micelles-with-two-aggregation-induced-emission-photosensitizers-for-enhanced-chemo-photodynamic-therapy.pdf |
66cca130f3f4b052902aa0b1 | 10.26434/chemrxiv-2024-hrt51 | MMAEVe: a Versatile Program for Constructing Systems for Molecular Dynamics Simulations and Visualization | Molecular dynamics simulations are commonly used for the study of membrane-protein systems. Current tools for building membrane-proteins systems are limited in their ability to incorporate multiple protein components in a set-up and their ability to operate using a variety of different forcefields for the lipid component. Here, we present a simple but effective membrane builder, MMAEVe, that can be used to construct massive protein-membrane systems of mixed composition. MMAEVe is open-sourced and available at https://github.com/AppleIntusion/MMAEVe, it is maintained and tested for Linux systems. A comprehensive tutorial and a benchmarking script are included with the source-code. | Samuel Lindsay; Wesley Sanchez; Yumin Li | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cca130f3f4b052902aa0b1/original/mmae-ve-a-versatile-program-for-constructing-systems-for-molecular-dynamics-simulations-and-visualization.pdf |
670f77dd51558a15ef3892bd | 10.26434/chemrxiv-2024-dz0pz | Frameworks Construction with Rhodium-Organic Cuboctahedra via Rigid Linker Incorporation | The architectural characteristics of metal-organic frameworks (MOFs) can be examined through their net topology, which consists of nodes and linkers. A node's connectivity and site symmetry are likely the key elements influencing the net topology of MOFs. Metal-organic polyhedra (MOPs) function effectively as nodes when used as supermolecular building blocks (SBBs). The SBB approach offers a powerful strategy for the deliberate design of macroscale materials, ranging from soft materials such as gels, polymers, and membranes to crystalline frameworks. However, achieving highly ordered structures with robust and air-stable rhodium-based MOPs (RhMOPs) presents a significant challenge. To investigate how to control the precise spatial distribution of RhMOPs as SBBs for constructing crystalline extended networks, here, we present a strategy for synthesizing MOFs by coordinating RhMOPs with rigid bridging linkers 1,4-diazabicyclo[2.2.2]octane (dabco). The resulting crystalline framework exhibited high microporosity and four times higher adsorption capacity than the parent MOP solids. | Yu-Shan Lin; Javier Lopez-Cabrelles; Chia-Her Lin; Shuhei Furukawa | Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670f77dd51558a15ef3892bd/original/frameworks-construction-with-rhodium-organic-cuboctahedra-via-rigid-linker-incorporation.pdf |
63bef4391f1258c73a9a22b5 | 10.26434/chemrxiv-2023-79q07 | Breaking bud: the effect of direct chemical modifications of phytocannabinoids on their bioavailability, physiological effects, and therapeutic potential. | Tetrahydrocannabinol (THC) and cannabidiol (CBD) are the two ”major cannabinoids”. However, their incorporation into clinical and nutraceutical preparations is challenging, owing to their limited bioavailability, low water solubility, and variable pharmacokinetic profiles. Understanding the organic chemistry of the major cannabinoids provides us with potential avenues to overcome these issues through derivatization. The resulting labile pro-drugs offer ready cannabinoid release in vivo, have augmented bioavailability, or demonstrate interesting pharmacological properties in their own right. This review identifies, tabulates, and discusses a subset of these advanced derivatization strategies for the major cannabinoids, where the starting material is the pure phytocannabinoid itself, and the final product either a cannabinoid pro-drug, or a novel
pharmacoactive material. | Abhinandan Banerjee; John Hayward; John Trant | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bef4391f1258c73a9a22b5/original/breaking-bud-the-effect-of-direct-chemical-modifications-of-phytocannabinoids-on-their-bioavailability-physiological-effects-and-therapeutic-potential.pdf |
64d2ae694a3f7d0c0dd611e2 | 10.26434/chemrxiv-2023-67hfc-v2 | Tutorial: Determining Best Practices for Using Genetic Algorithms in Molecular Discovery | Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this work, we examine the general effects of a number of hyperparameters, such as population size, elitism rate, selection method, mutation rate, and convergence criteria, on key GA performance metrics. We show that using a self-termination method with a minimum Spearman's rank correlation coefficient of 0.8 between generations maintained for 50 consecutive generations along with a population size of 32, 50% elitism rate, 3- way tournament selection, and a 40% mutation rate provides the best balance of finding the overall champion, maintaining good coverage of elite targets, and improving relative speedup for general use in molecular design GAs. | Brianna Greenstein; Danielle Elsey; Geoffrey Hutchison | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d2ae694a3f7d0c0dd611e2/original/tutorial-determining-best-practices-for-using-genetic-algorithms-in-molecular-discovery.pdf |
60c73fa49abda2bd9ff8bb43 | 10.26434/chemrxiv.7370048.v2 | Infrared Spectroscopic Characterization of Phosphate Binding at the Goethite-Water Interface | <div><div><div><p>The interaction between phosphates and soil mineral surfaces, such as Fe- and Al-(oxyhydr)oxides, plays a crucial role in the P immobilization and thus its availability for plants. The reactions of phosphates with Fe-hydroxides and especially goethite have been studied extensively. But a molecular-level picture about the phosphate binding mechanism at the goethite-water interface is still lacking. Therefore, in the current contribution we have explored the molecular binding mechanism for the adsorbed phosphate at the goethite–water interface by performing sorption kinetics experiments for orthophosphate and characterizing the adsorbed species by FT-IR spectroscopy. In parallel, periodic DFT calculations have been performed to explore the interaction mechanism as well as to calculate the IR spectra for monodentate (M) and bidentate (B) orthophosphate complexes at two different goethite surface planes (010 and 100) in the presence of water. In general, our interaction energy results give evidence that the mono-protonated B phosphate complex is more favored to be formed at the goethite–water interface although the M motif could exist as a minor fraction. Moreover, it was found that water plays an important role in controlling the phosphate adsorption process at the goethite surfaces. The interfacial water molecules form H-bonds (HBs) with the phosphate as well as with the goethite surface atoms. Further, some water molecules form covalent bonds with goethite Fe atoms while others dissociate at the surface to protons and hydroxyl groups. The present theoretical assignment of IR spectra introduces a benchmark for characterizing experimental IR data for the adsorbed KH2PO4 species at the goethite–water interface. In particular, IR spectra of the mono-protonated (2O+1Fe) B complex at the 010 goethite surface plane and the M complex at the 100 goethite surface plane were found to be consistent with the experimental data. In order to explore the role of different abundancies of surface planes and binding motifs, IR spectra obtained from weighted averages have been analyzed. Results confirmed the above conclusions drawn from interaction energy calculations.</p></div></div></div> | Ashour A. Ahmed; Stella Gypser; Peter Leinweber; Dirk Freese; Oliver Kühn | Computational Chemistry and Modeling; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fa49abda2bd9ff8bb43/original/infrared-spectroscopic-characterization-of-phosphate-binding-at-the-goethite-water-interface.pdf |
6219fb0ace899b9070a4488b | 10.26434/chemrxiv-2022-7rzxw | Intermolecular amination of allenes via twofold photocatalytic nitrene transfer reactions | The amination with monovalent, nitrogen-based intermediates constitutes an important reaction for the construction of valuable amines. The high basicity of reagents, reaction intermediates or products however poses significant challenges to metal-catalyzed amination through coordination and blocking of catalytically active sites and hampering their efficiency. In this context, high-yielding intermolecular amination reaction of allenes remain an unsolved challenge in organic synthesis and general methods are not available. Herein, we describe a photochemical approach towards the intermolecular amination of allenes via free nitrene radical anions as the key reactive intermediate. This reaction proceeds without the participation of catalyst-bound nitrogen species and can thus overcome current limitations. We report on the application in the amination of allenes to give azetidine and cyclopropyl amines with a broad and general substrate scope. Experimental and theoretical studies were performed to provide an understanding of the reaction mechanism and rationalize the high efficiency of this photocatalytic approach. | Yujing Guo; Claire Empel; Chao Pei; Hao Fang; Sripati Jana; Rene M. Koenigs | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6219fb0ace899b9070a4488b/original/intermolecular-amination-of-allenes-via-twofold-photocatalytic-nitrene-transfer-reactions.pdf |
667c2b6701103d79c52ffe1f | 10.26434/chemrxiv-2024-hpk8g | Zweifel Olefination for C-Glycosylation | Starting from glycal derivatives, the Zweifel olefination presents an elegant opportunity to access C-glycosides in a selective manner. a-Lithiation of D-glucal, L-rhamnal, D-xylal and L-arabinal scaffolds was employed as a starting point in the synthesis of corresponding unsaturated aryl-, heteroaryl- and alkenyl-C-glycosides. This provides a straightforward strategy towards pharmacorelevant gliflozins and other unreported rhamnal- and xylal-analogs. | Florian Trauner; Bilel Boutet; Fabian Pilz; Verena Weber; dorian didier | Organic Chemistry; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c2b6701103d79c52ffe1f/original/zweifel-olefination-for-c-glycosylation.pdf |
674b97847be152b1d0859698 | 10.26434/chemrxiv-2024-cmbzb-v2 | Enhanced Chemical Method for Bispecific Antibody Production: Leveraging Site-Specific Conjugation and Stable Crosslinker Technology | Bispecific antibodies (BisAbs) represent a major breakthrough in biotherapeutics by combining the functionalities of two different antibodies to unlock their potential for a wide range of applications. Conventional BisAb production has relied on labor-intensive and complex genetic-engineering methods. This chapter introduces a cutting-edge protocol that circumvents the need for genetic modifications by using chemical conjugation strategies. We present a streamlined, fully chemical methodology for generating BisAbs that leverages the precision of the AJICAP second-generation technology for accurate site-specific conjugation. In addition, this chapter explores the application of haloketone chemistry as an improved and more effective replacement for traditional maleimide-based crosslinking techniques for the fusion of two antibody-related proteins. The analytical performance and results of the newly developed BisAb were thoroughly investigated, highlighting its high efficiency and effectiveness. This innovative approach represents a significant step forward in the production of BisAbs and offers a simpler, more accessible, and potentially scalable alternative to traditional genetic-engineering techniques. | Tomohiro Fujii; Yutaka Matsuda | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674b97847be152b1d0859698/original/enhanced-chemical-method-for-bispecific-antibody-production-leveraging-site-specific-conjugation-and-stable-crosslinker-technology.pdf |
62c8920a6383266dc946ad00 | 10.26434/chemrxiv-2022-s3d4b | A Systematic Review on the Kappa Opioid Receptor and Its Ligands: New Directions for the Treatment of Pain, Anxiety, Depression, and Drug Abuse | Kappa opioid receptor (KOR) is a member of the opioid receptor system, the G protein-coupled receptors that are expressed throughout the peripheral and central nervous systems and play crucial roles in the modulation of antinociception and a variety of behavioral states like anxiety, depression, and drug abuse. KOR agonists are known to produce potent analgesic effects and have been employed clinically for the treatment of pain, while KOR antagonists have displayed efficacy in the treatment of anxiety and depression. This review summarizes the history, design strategy, discovery, and development of KOR ligands. KOR agonists are categorized into G protein-biased KOR agonists and β-arrestin recruitment-biased KOR agonists, based on their degrees of bias. Mechanisms and associated effects of the G protein signaling pathway and β-arrestin recruitment signaling pathway are also discussed. Meanwhile, KOR antagonists are categorized into three groups, long-acting, intermediate-acting, and short-acting, based on their durations of action. In addition, we have special sections for mixed KOR agonists and selective peripheral KOR agonists. Mechanisms of action and pharmacokinetic, pharmacodynamic, and behavioral studies for each of these categories are also discussed in this review. | Md Imdadul Khan; Benjamin Sawyer; Nicholas Akins; Hoang Le | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c8920a6383266dc946ad00/original/a-systematic-review-on-the-kappa-opioid-receptor-and-its-ligands-new-directions-for-the-treatment-of-pain-anxiety-depression-and-drug-abuse.pdf |
60c73dd60f50db62e2395564 | 10.26434/chemrxiv.5573287.v2 | Surface confinement induces the formation of solid - like insulating ionic liquid nanostructures | We report on the modification of the electric properties of the imidazolium-based [BMIM][NTf2] ionic liquid upon surface confinement in the sub-monolayer regime. Solid-like insulating nanostructures of [BMIM][NTf2] spontaneously form on a variety of insulating substrates, at odd with the liquid and conductive nature of the same substances in the bulk phase. A systematic spatially-resolved investigation by atomic force microscopy of the morphological, mechanical and electrical properties of [BMIM][NTf2] nanostructures showed that this liquid substance rearranges into lamellar nanostructures with a high degree of vertical order and enhanced resistance to mechanical compressive stresses and very intense electric fields, denoting a solid-like character. The morphological and structural reorganization has a profound impact on the electric properties of supported [BMIM][NTf2] islands, which behave like insulator layers with a relative dielectric constant between 3 and 5, comparable to those of conventional ionic solids, and significantly smaller than those measured in the bulk ionic liquid. These results suggest that in the solid-like ordered domains confined either at surfaces or inside the pores of the nanoporous electrodes of photo-electrochemical devices, the ionic mobility and the overall electrical properties can be significantly perturbed with respect to the bulk liquid phase, which would likely influence the performance of the devices.<br /> | Massimiliano Galluzzi; Simone Bovio; Paolo Milani; Alessandro Podestà | Interfaces; Physical and Chemical Properties; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd60f50db62e2395564/original/surface-confinement-induces-the-formation-of-solid-like-insulating-ionic-liquid-nanostructures.pdf |
65fdb61fe9ebbb4db9485e02 | 10.26434/chemrxiv-2024-wb8xd | Nonadiabatic photodynamics of amantadine and cyanoadamantane cations: Departure from the energy gap law? | Cations of diamondoids and derivatives thereof have recently become the subject of experimental, spectroscopic studies due to their potential role in astrochemistry. In particular, their electronic spectra and photoinduced dynamics trigger great interest. Here, we report on computational investigations of two nitrogen-containing derivatives of the adamantane cation (Ada+, C10H16+), the amantadine cation (Ama+, C10H15NH2+) and the cyanoadamantane cation (Ada-CN+, C10H15CN+). Specifically, we study electronic (vibrationally resolved) spectra and nonadiabatic molecular dynamics (modeled using the surface hopping approach based on semiempirical electronic structure theory) of these radical cations. The internal conversion time constants as well as reactive relaxation outcomes (cage-opening and hydrogen loss) are compared for the two derivatives and also with the case of Ada+ [Roy et al., Theor. Chem. Acc. 2023, 142, 71]. Remarkably, we find a longer ground-state recovery time for Ada-CN+ than for Ama+ (for the same excitation energy window), despite a smaller excitation energy for the former. Thus, a static energy gap law cannot be used to rationalize nonadiabatic dynamics and excited-state lifetimes in this case: Dynamics and details of the couplings between several states play a decisive role. | Bonasree Roy; Evgenii Titov; Peter Saalfrank | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fdb61fe9ebbb4db9485e02/original/nonadiabatic-photodynamics-of-amantadine-and-cyanoadamantane-cations-departure-from-the-energy-gap-law.pdf |
657b4c3e9138d23161a61b9d | 10.26434/chemrxiv-2023-bcxh8 | Gauging Iron-Sulfur Cubane Reactivity from Covalency: Trends with Oxidation State | We investigated the room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge position provides a qualitative, but convenient alternative to the traditional spectro¬scopic descriptors used to identify oxidation states in these systems, which we demonstrate by providing a calibration curve. Furthermore, high energy resolution fluorescence detected XAS (HERFD-XAS) at the S K-edge was used to measure Fe-S bond covalencies and record their variation with the average valence of the Fe atoms. While the Fe-S(thiolate) covalency evolves linearly, gaining 11% per bond and hole, the Fe-S(3) covalency evolves asystematically, reflecting changes in the magnetic exchange mechanism. A strong discontinuity manifested for superoxidation to the all-ferric state, distinguishing its electronic structure and its potential (bio)chemical role from its redox congeners. We highlight the functional implications of these trends on the reactivity of iron-sulfur cubanes. | Liam Grunwald; Daniel Abbott; Victor Mougel | Inorganic Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657b4c3e9138d23161a61b9d/original/gauging-iron-sulfur-cubane-reactivity-from-covalency-trends-with-oxidation-state.pdf |
66faa2dbcec5d6c142ad527e | 10.26434/chemrxiv-2024-9chdb | Dynamic covalent DNA networks to translate multiple inputs into programmable outputs | Inspired by naturally occurring protein dimerization networks, in which a set of proteins interact with each other to achieve highly complex input-output behaviours, we demonstrate here a fully synthetic DNA-based dimerization network that enables highly programmable input-output computations. Our DNA-based dimerization network consists of DNA oligonucleotide monomers modified with reactive moieties that can covalently bond with each other to form dimer outputs in an all-to-all or many-to-many fashion. By designing DNA-based input strands that can specifically sequester DNA monomers, we can control the size of the reaction network and thus fine-tune the yield of each DNA dimer output in a predictable manner. Thanks to the programmability and specificity of DNA-DNA interactions, we show that this approach can be used to control the yield of different dimer outputs using different inputs. The approach is also versatile and we demonstrate dimerization networks based on two different covalent reactions: thiol-disulfide and strain-promoted azide-alkyne click (SPAAC) reactions. Finally, we show here that the DNA-based dimerization network can be used to control the yield of a functional dimer output, ultimately controlling the assembly and disassembly of DNA nanostructures. The dynamic covalent DNA networks shown here provide a way to convert multiple inputs into programmable outputs that can control a broader range of functions, including ones that mimic those of living cells. | Brannetti Simone; Serena Gentile; Del Grosso Erica; Sijbren Otto; Francesco Ricci | Physical Chemistry; Analytical Chemistry; Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66faa2dbcec5d6c142ad527e/original/dynamic-covalent-dna-networks-to-translate-multiple-inputs-into-programmable-outputs.pdf |
64dcf7454a3f7d0c0d45ca3c | 10.26434/chemrxiv-2023-ngqd8 | ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design | Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiment is evaluating ligands that are likely to be synthesized. Here we provide a solution to this impediment with our ReaLigands library that contains >30,000 monodentate, bidentate (didentate), tridentate, and larger ligands cultivated by dismantling experimentally reported crystal structures. Individual ligands from mononuclear crystal structures were identified using a modified depth-first search algorithm and charge was assigned using a machine learning model based on quantum-chemical calculated features. In the library ligands are sorted based on direct ligand-to-metal atomic connections and on denticity. Representative principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) analyses were used to analyze several tridentate ligand categories, which revealed both the diversity of ligands and connections between ligand categories. We also demonstrated the utility of this library by implementing it with our building and optimization tools, which resulted in the very rapid generation of barriers for 750 bidentate ligands for Rh-hydride ethylene migratory insertion | Daniel Ess; Shusen Chen; Zack Meyer; Brendan Jensen; Alex Kraus; Allison Lambert | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dcf7454a3f7d0c0d45ca3c/original/rea-ligands-a-ligand-library-cultivated-from-experiment-and-intended-for-molecular-computational-catalyst-design.pdf |
648b681fbe16ad5c57fa3d4a | 10.26434/chemrxiv-2023-t60dq | Analyzing Fluoride Binding by Group 15 Lewis Acids: Pnictogen Bonding in the Pentavalent State | We report the results of a computational investigation into fluoride binding by a series of pentavalent pnictogen Lewis acids: pnictogen pentahalides (PnX5), tetraphenyl pnictogeniums (PnPh4+), and triphenyl pnictogen tetrachlorocatecholates (PnPh3Cat). Activation strain and energy decomposition analyses of the Lewis adducts clearly delineate the electrostatic and orbital contributions to these acid-base interactions, but they also highlight the importance of Pauli repulsion and molecular flexibility in determining relative Lewis acidity among the pnictogens. | Logan Maltz; Francois Gabbai | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.); Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648b681fbe16ad5c57fa3d4a/original/analyzing-fluoride-binding-by-group-15-lewis-acids-pnictogen-bonding-in-the-pentavalent-state.pdf |
60c752c1ee301ce69ac7ac7f | 10.26434/chemrxiv.13340804.v1 | Super-Resolution Mapping of a Chemical Reaction Driven by Plasmonic Near-Fields | Plasmonic nanoparticles have recently emerged as promising photocatalysts for light-driven chemical conversions. The illumination of these particles results in the generation of highly energetic charge carriers, elevated surface temperatures, and enhanced electromagnetic fields around them. Distinguishing between these often-overlapping processes is of paramount importance for the rational design of future plasmonic photocatalysts. However, the study of chemical reactions mediated by plasmonic effects is typically performed at the ensemble level and, therefore, limited by the intrinsic heterogeneity of the catalyst particles. Here, we report an in-situ single particle study of a chemical reaction driven solely by plasmonic near-fields. Using super-resolution fluorescence microscopy, we achieve single turnover temporal resolution and ~30 nm spatial resolution. This sub-particle accuracy permits the construction of a clear correlation between the simulated electric field distribution around individual metal nanoparticles and their super-resolved catalytic activity maps. Our results can easily be extended to systems with more complex electric field distributions, thereby guiding the design of future advanced photoactive materials. | Ruben Hamans; Matteo Parente; Andrea Baldi | Catalysts; Core-Shell Materials; Nanostructured Materials - Materials; Optical Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Spectroscopy (Inorg.); Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Optics; Photochemistry (Physical Chem.); Physical and Chemical Processes; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752c1ee301ce69ac7ac7f/original/super-resolution-mapping-of-a-chemical-reaction-driven-by-plasmonic-near-fields.pdf |
60c745b9bdbb89800da38aad | 10.26434/chemrxiv.10128653.v1 | Fluorine Mass Balance and Suspect Screening in Marine Mammals from the Northern Hemisphere | There is increasing evidence that the ~20
routinely monitored per- and polyfluoroalkyl substances (PFASs) account for only
a fraction of extractable organofluorine (EOF) occurring in the environment. To
assess whether PFAS exposure is being underestimated in marine mammals from the
Northern Hemisphere, we performed a fluorine mass balance on liver tissues from
11 different species using a combination of targeted PFAS analysis, EOF and
total fluorine determination, and suspect screening. Samples were obtained from
the east coast United States (US), west and east coast of Greenland, Iceland,
and Sweden from 2000-2017. Of the 36 target PFASs, perfluorooctane sulfonate (PFOS)
dominated in all but one Icelandic and three US samples, where the 7:3
fluorotelomer carboxylic acid (7:3 FTCA) was prevalent. This is the first
report of 7:3 FTCA in polar bears (~1000 ng/g, ww) and cetaceans (<6-190
ng/g, ww). In 18 out of 25 samples, EOF was not
significantly greater than fluorine concentrations derived from sum target
PFASs. For the remaining 7 samples (mostly from the US east coast), 30-75%
of the EOF was unidentified. Suspect screening revealed an additional 33 PFASs
(not included in the targeted analysis) bringing the total to 59 detected PFASs
from 12 different classes. Overall, these results highlight the importance of a
multi-platform approach for accurately characterizing PFAS exposure in marine
mammals. | Kyra Spaan; Carmen van Noordenburg; Merle Plassmann; Lara Schultes; Susan D. Shaw; Michelle Berger; Mads Peter Heide-Jørgensen; Aqqalu Rosing-Asvid; Sandra Granquist; Rune Dietz; Christian Sonne; Frank Rigét; Anna Roos; Jonathan Benskin | Environmental Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745b9bdbb89800da38aad/original/fluorine-mass-balance-and-suspect-screening-in-marine-mammals-from-the-northern-hemisphere.pdf |
668e4322c9c6a5c07ada54e8 | 10.26434/chemrxiv-2024-vsrjz-v2 | Facet {100} Fosters Resonance Energy Transfer in Ni/Co-doped CsPbBr3 Nanocrystals | The design of an effective light harvester with metal-doped perovskite nanocrystals (M:PNCs) aims at achieving directional energy flow. The potential of crystal facets needs to be assessed for dictating energy transfer dynamics of M:PNCs. Herein we have engineered facets of amine-capped CsPbBr3 perovskite nanocrystals by doping with a trace amount of Ni and Co ions. Ni-doped CsPbBr3 (Ni:PNC) showcases structural heterogeneity with regular cubic and rod shapes whereas bimetallic-doped CsPbBr3 (Ni:Co:PNC) evolves to an elongated dodecahedron structure. Structural analysis using Rietveld Refinement strongly corroborates the construction of dodecahedron structure for Ni:Co:PNC through systematic displacement of Cs ions. Energy transfer from doped nanocrystals to Rhodamine B (RhB) occurs through dipole-dipole interaction, known as Fluorescence Resonance Energy Transfer (FRET). The emergence of isoemissive point, and rise-time of RhB conclusively establish Resonance Energy Transfer mechanism. Energy transfer in thin films occurs at much faster rate than in toluene medium. {100} facet-dominated Ni:PNC registers a FRET efficiency of 94% whereas {111}, {002} facet-dominated Ni:Co:PNC restricts at 21% FRET efficiency. The distance between donor and acceptor, RDA dictates the dynamics of energy transfer, rather than spectral overlap, and photoluminescence quantum yield of these doped-nanocrystals. Surface composition of facets, typically Cs ions perhaps plays a decisive role in regulating the binding constant of donor and acceptor. Our study demonstrates the importance of facets of nanocrystals in tuning the desired energy transfer processes for photocatalytic applications. | Suvadeep Panda; Gourab Roy; Tathamay Basu; Debashis Panda | Physical Chemistry; Nanoscience; Energy; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668e4322c9c6a5c07ada54e8/original/facet-100-fosters-resonance-energy-transfer-in-ni-co-doped-cs-pb-br3-nanocrystals.pdf |
65608c60cf8b3c3cd7044f13 | 10.26434/chemrxiv-2023-n24kf | Guiding Transient Peptide Assemblies with Structural Elements Around Abiotic Phosphate Fuels | Biochemical energy carriers, such as triphosphates (ATP, GTP) drive selective processes, by incorporating chemical information (Adenine vs. Guanine) in their structure. These recognition elements match with complex machineries through a variety of non-covalent interactions, enabling specific targeting of functions. In contrast, most approaches in non-equilibrium systems do not consider the structure of the fuel as a critical element to control the processes. Herein, we show that the amino acid side chains (A, F, Nap) in the structure of activated aminoacyl phosphate esters can direct assembly and reactivity in the context of non-equilibrium structure formation. We focus on the ways in which the activated amino acids guide structure formation and how structures and reactivity cross regulate when constructing different assemblies. Through the chemical functionalization of energy-rich aminoacyl phosphate esters, we are able to control the coupling yield to esters and thioesters upon adding dipeptides containing tyrosine or cysteine amino acid residues. The structural elements around the phosphate esters guide the lifetime of the structures formed and their supramolecular assemblies, which can further be influenced by the structure and reactivity of dipeptide substrates. Moreover, we demonstrate that an aminoacyl phosphate ester incorporating a tyrosine residue (Y) can autonomously generate a pool of high energy molecules, where dynamic oligomerization and de-oligomerization of esters occurs in a single step process. These findings suggest that activated amino acids with varying reactivity and energy contents can pave the way for designing and fabricating structured fuels | Charalampos Pappas; Mahesh Pol; Kun Dai; Ralf Thomann; Sandra Moser | Organic Chemistry; Materials Science; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65608c60cf8b3c3cd7044f13/original/guiding-transient-peptide-assemblies-with-structural-elements-around-abiotic-phosphate-fuels.pdf |
62cd112f14201f029731cfeb | 10.26434/chemrxiv-2022-97hl0-v2 | Activity Enhancement of Defective Carbon Nitride for Photocatalytic Ammonia Generation by Modification with Pyrite | Photocatalytic nitrogen fixation under ambient conditions is currently widely explored in an attempt to develop a sustainable alternative for the Haber-Bosch process. In this work we combine defect-rich C3N4, one of the most investigated photocatalysts reported in literature for ammonia generation, with earth-abundant and bioinspired FeS2 to improve the activity for ammonia production. By this combination, an activity enhancement of approx. 400 % compared to unmodified C3N4 was achieved. The optimal FeS2 loading was established to be 1 wt.%, with ammonia yields of up to 800 µg L-1 after irradiation for 7 hours. By detailed material characterization of the electronic and material properties of the composites before and after the photocatalytic reaction, we reveal that NH3 generation occurs not photocatalytically from N2, but via a light-induced reduction of =N-CN groups adjacent to nitrogen vacancies in the structure of defect-rich C3N4. FeS2 acts similar to a co-catalyst, enhancing the ammonia yield by π-back-donation from Fe-centers to the imine nitrogen of the defect-rich C3N4, thereby activating the structure and boosting the ammonia generation from cyano groups. | Judith Zander; Jana Timm; Morten Weiss; Roland Marschall | Catalysis; Energy; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cd112f14201f029731cfeb/original/activity-enhancement-of-defective-carbon-nitride-for-photocatalytic-ammonia-generation-by-modification-with-pyrite.pdf |
652d69e8bda59ceb9ab597c3 | 10.26434/chemrxiv-2023-x9vb8 | Citric acid as electrolyte additive in aqueous Magnesium-Air battery used in Antarctic climate | The Magnesium-Air battery is a very attractive energy source due to its high specific energy, low cost and the possibility of rapid mechanical recharge. The use of citric acid as an additive to the electrolyte (sea water) prevents the precipitation of Mg(OH)2 and enhances the behaviour of the magnesium electrode. Due to the better access of electrolyte to the electrode surface, ohmic and polarization resistances are reduced, and the rate of electrochemical reaction is increased. The equilibrium potential is displaced towards lower values for both pure magnesium and magnesium alloy AZ63.Citric acid favours also the performance of the GDE by removing the Mg(OH)2 precipice.
A functioning battery is tested under polar conditions at the Bulgarian Antarctic station at Livingstone island. | Iliyan Popov; Boris Shirov; Temenuzhka Spasova; Yovka Milusheva; Adlin Dancheva; Reneta Boukoureshtlieva | Energy; Earth, Space, and Environmental Chemistry; Energy Storage; Power | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652d69e8bda59ceb9ab597c3/original/citric-acid-as-electrolyte-additive-in-aqueous-magnesium-air-battery-used-in-antarctic-climate.pdf |
60c74ffd567dfe0675ec57cb | 10.26434/chemrxiv.11292119.v2 | A Two-Dimensional Metallacycle Cross-Linked Switchable Polymer for Fast and Highly Efficient Phosphorylated Peptide Enrichment | <p>The selective and efficient capture of phosphopeptides is critical for comprehensive and in-depth phosphoproteome analysis. However, this remains a significant challenge due to the inherently low abundance of these species in complex bio-samples. In this paper, we report a switchable two-dimensional (2D) supramolecular polymer that can serve as an ideal platform for the enrichment of phosphopeptides. A positively charged metallacycle incorporated into the polymer endows the material with a high affinity for phosphopeptides. Importantly, the stimuli-responsive nature of the polymer facilitates switchable binding affinity of phosphopeptides, resulting in its excellent performance in phosphopeptide enrichment and separation from model proteins. The polymer has a high enrichment capacity (165 mg/g) and detection sensitivity (2 fmol), high enrichment recovery (88%), excellent specificity, and rapid enrichment and separation properties. Additionally, we have demonstrated the capture of phosphopeptides from the tryptic digest of real bio-samples illustrating the potential of this polymeric material in phosphoproteomic studies.</p> | Li-Jun Chen; jun-long zhu; Fan-Fan Zhu; Xu-Qing Wang; Jin Wen; Hai-Bo Yang; Philip Gale | Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ffd567dfe0675ec57cb/original/a-two-dimensional-metallacycle-cross-linked-switchable-polymer-for-fast-and-highly-efficient-phosphorylated-peptide-enrichment.pdf |
60c74290842e65b38fdb20b9 | 10.26434/chemrxiv.8311235.v1 | Aqueous Flow Reactor and Vapour-Assisted Synthesis of Aluminium Dicarboxylate Metal-Organic Frameworks for Use as Water Adsorbents | Energy-efficient indoors temperature control can be realised through adsorption chillers or adsorption heat pumps based on the reversible adsorption and desorption of water in porous materials. Stable microporous aluminium-based metal-organic frameworks (MOFs) present promising water sorption properties for this goal. The development of synthesis routes that make use of available and affordable building blocks and avoid the use of organic solvents is crucial to advance this field. In this work, two scalable synthesis routes under mild reaction conditions were developed for aluminium-based MOFs: (1) in aqueous solutions using a continuous flow reactor and (2) through the vapour-assisted conversion of solid precursors. Fumaric acid, its methylated analogue mesaconic acid, as well as mixtures of the two were used as linkers. The synthesis conditions determine the crystal structure (symmetry and topology), either the MIL-53 or MIL-68 type with square-grid or kagome-grid topology, respectively. Fine-tuning resulted in new MOF materials thus far inaccessible through conventional synthesis routes. Furthermore, by varying the linker ratio, the water sorption properties can be continuously adjusted while retaining the sigmoidal isotherm shape advantageous for heat transformation applications. | Timothée Stassin; Steve Waitschat; Niclas Heidenreich; Helge Reinsch; Finn Puschkell; Dmitry Kravchenko; Ivo Stassen; Jonas van Dinter; Rhea Verbeke; Marcel Dickmann; Werner Egger; Ivo Vankelecom; Dirk De Vos; Rob Ameloot; Norbert Stock | Hybrid Organic-Inorganic Materials; Structure | CC BY NC 4.0 | CHEMRXIV | 2019-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74290842e65b38fdb20b9/original/aqueous-flow-reactor-and-vapour-assisted-synthesis-of-aluminium-dicarboxylate-metal-organic-frameworks-for-use-as-water-adsorbents.pdf |
60c73d0e0f50db0792395410 | 10.26434/chemrxiv.5395012.v1 | Transition probability approach for direct calculation of coefficients of Configuration Interaction wave function | To reduce the computation cost of Configuration Interaction (CI) method, a new technique is used to calculate the coefficients of doubly excited determinants directly from orbital energies, orbital overlap matrix and electron population obtained from Hartree Fock level run. This approach to approximate the coefficients of CI wave function is termed as <b>transition probability approximated CI (TPA-CI).</b> In principle, calculated dynamical electron correlation energy of TPA-CI and Full CI (FCI) are equivalent. It is observed that computed TPA-CI correlation energies of hydrogen, water, ammonia and ozone are very close to FCI values, within 5% error. The potential energy curve of the hydrogen molecule is also studied and it is found that the energy is minimum at its equilibrium bond length.<br /><br /> | Arijit Bag | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e0f50db0792395410/original/transition-probability-approach-for-direct-calculation-of-coefficients-of-configuration-interaction-wave-function.pdf |
625ec82788636c3acf17bcee | 10.26434/chemrxiv-2022-90jc8 | Limits to scaling relations between adsorption energies? | Linear scaling relations have led to an understanding of trends in catalytic activity and selectivity of many reactions in heterogeneous and electro-catalysis. Yet, linear scaling between the chemisorption energies of any two small molecule adsorbates is not guaranteed. A prominent example is the lack of scaling between the chemisorption energies of carbon and oxygen on transition metal surfaces. In this work, we show that this lack of scaling originates from different re-normalised adsorbate valence energies of lower-lying oxygen versus higher-lying carbon. We develop a model for chemisorption of small molecule adsorbates within the d-band model by combining a modified form of the Newns-Anderson hybridisation energy with an effective orthogonalization term. We develop a general descriptor to a priori determine if two adsorbates are likely to scale with each other. | Sudarshan Vijay; Georg Kastlunger; Karen Chan; Jens Nørskov | Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625ec82788636c3acf17bcee/original/limits-to-scaling-relations-between-adsorption-energies.pdf |
636b9f018e0d358a9e143f4e | 10.26434/chemrxiv-2022-vh97c-v3 | A Enamide-based diastereoselective synthesis of isoindolo[2,1-a]quinolin-11(5H)-ones with three contiguous stereogenic centers | A stereoselective synthesis of isoindolo[2,1-a]quinolin-11(5H)-ones containing three contiguous
stereogenic centers is described. This Lewis-acid mediated reaction of enamides with N-aryl- affords
the desired fused heterocyclic isoindolinones in high yields and diastereoselectivities. Scope and
limitations of this method are discussed. The stereochemical outcome of this transformation indicates
a stepwise reaction pathway. | Miro Halaczkiewicz; Harald Kelm; Georg Manolikakes | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636b9f018e0d358a9e143f4e/original/a-enamide-based-diastereoselective-synthesis-of-isoindolo-2-1-a-quinolin-11-5h-ones-with-three-contiguous-stereogenic-centers.pdf |
60c74062702a9b573418a0a6 | 10.26434/chemrxiv.7726166.v1 | The Influence of Residence Time Distribution on Continuous Flow Polymerization | <p>Continuous-flow
chemistry is emerging as an enabling technology for the synthesis of precise
polymers. Despite recent advances in this rapidly growing field, there remains
a need for a fundamental understanding of how fluid dynamics in tubular
reactors influence polymerizations. Herein, we report a comprehensive study of
how laminar flow influences polymer structure and composition. Tracer
experiments coupled with in-line UV-vis spectroscopy demonstrate how viscosity,
tubing diameter, and reaction time affect the residence time distribution (RTD)
of fluid in reactor geometries relevant for continuous-flow polymerizations. We
found that the breadth of the RTD has strong, statistical correlations with
reaction conversion, polymer molar mass, and dispersity for polymerizations
conducted in continuous flow. These correlations were demonstrated to be
general to a variety of different reaction conditions, monomers, and
polymerization mechanisms. Additionally, these findings inspired the design of
a droplet flow reactor that minimizes the RTD in continuous-flow
polymerizations and enables the continuous production of well-defined polymer
at a rate of 1.4 kg/day. </p> | Marcus Reis; Travis Varner; Frank Leibfarth | Organic Polymers; Polymer chains; Polymerization (Polymers); Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74062702a9b573418a0a6/original/the-influence-of-residence-time-distribution-on-continuous-flow-polymerization.pdf |
60c74dc89abda2e80ff8d512 | 10.26434/chemrxiv.12568088.v1 | MeteoMex: Open infrastructure for networked environmental monitoring and agriculture 4.0 | <div>Air, water, and soil are essential for terrestrial life, but pollution, overexploitation, and climate change jeopardize the availability of these primary resources. Thus, assuring human health and food production requires efficient strategies and technologies for environmental protection. Knowing key parameters such as soil moisture, air, and water quality is essential for smart farming and urban development. </div><div>The MeteoMex project aims to build simple hardware kits and their integration into current Internet-of-Things (IoT) platforms. This paper shows the use of low-end Wemos D1 mini boards to connect environmental sensors to the open-source platform ThingsBoard. Two printed circuit boards (PCB) were designed for mounting components. Analog, digital and I<sup>2</sup>C sensors are supported. The Wemos ESP8266 microchip provides WiFi capability and can be programmed with the Arduino IDE. Application examples for the MeteoMex aeria and terra kits demonstrate their functionality for air quality, soil, and climate monitoring.</div><div>Further, a prototype for monitoring wastewater treatment is shown, which exemplifies the capabilities of the Wemos board for signal processing. The data are stored in a PostgreSQL database, which enables data mining. The MeteoMex IoT system is highly scalable and of low cost, which makes it suitable for deployment in agriculture 4.0, industries, and public areas. </div><div>Circuit drawings, PCB layouts, and code examples are free to download from https://github.com/robert-winkler/MeteoMex.</div> | Robert Winkler | Atmospheric Chemistry; Environmental Science; Geochemistry; Hydrology and Water Chemistry; Soil Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dc89abda2e80ff8d512/original/meteo-mex-open-infrastructure-for-networked-environmental-monitoring-and-agriculture-4-0.pdf |
6723a97e7be152b1d0959abd | 10.26434/chemrxiv-2024-pz3xw | Heteroaromatic Swapping in Aromatic Ketones | The modification of aromatic rings to heteroaromatic rings is a widely employed strategy in medicinal chemistry, often used to modulate lipophilicity and improve metabolic stability1,2. However, achieving a one-step, generalizable transformation of aromatic rings into diverse heteroaromatic rings—termed "Heteroaromatic Swapping"—has been a persistent challenge. Ex-isting methods, including skeletal editing3 and transition-metal-catalyzed aromatic ring exchange4,5, face significant limita-tions in substrate scope. Here, we report an efficient approach to Heteroaromatic Swapping via a Claisen/retro-Claisen mech-anism6, utilizing heteroaryl esters and aromatic ketones. This method enables the selective exchange of aromatic rings with heteroaromatic rings across a broad substrate range. Notably, it overcomes the substrate restrictions of current techniques, allowing high-yield conversions of bioactive aromatic ketones into their heteroaromatic analogs. This strategy expands the molecular editing toolkit, providing a practical and versatile approach for synthesizing bioactive compounds with improved pharmacokinetic properties. | Hikaru Nakahara; Junichiro Yamaguchi | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6723a97e7be152b1d0959abd/original/heteroaromatic-swapping-in-aromatic-ketones.pdf |
651ee5fe45aaa5fdbb5d6086 | 10.26434/chemrxiv-2023-5f1vb | Improving Absorbent-Enhanced Ammonia Separation For Efficient Small Scale Ammonia Synthesis | Synthesized ammonia exiting a reactor with hydrogen and nitrogen can be selectively absorbed by MgCl2 for renewable absorbent-based Haber Bosch for dispersed ammonia manufacturing. Such separation can be more efficient even at elevated temperatures compared to the condensation method used in conventional Haber Bosch process. To determine the optimal conditions to capture and release the most ammonia per thermal cycle of sorbent salt, the sorbent capacity was measured with varying regeneration temperature, regeneration time, and sweep rate under steady-state cycling conditions. In all cases, uptake was limited to bed breakthrough, and cyclic steady state was achieved. By using lower temperature for MgCl2 regeneration (200 °C), the working capacities were maintained comparable to those at higher desorption temperatures (~ 400 ⁰C), even without the use of inert sweep gas. Using a sufficiently high regeneration temperature (~200 ⁰C) allowed for sufficiently low sweep gas that the product ammonia can exceed 72 mol% purity in a mixture of N2 and H2. These results were achieved with a short regeneration time of 20 minutes or less, which is an improvement from hour-long regeneration time previously reported. These measurements identified new operating parameters for more efficient absorber design to produce economical renewable ammonia at small scale. | C. Emmanuel Onuoha; Matthew Kale; Mahdi Malmali; Paul Dauenhauer; Alon McCormick | Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651ee5fe45aaa5fdbb5d6086/original/improving-absorbent-enhanced-ammonia-separation-for-efficient-small-scale-ammonia-synthesis.pdf |
60c751ce842e65f97cdb3c23 | 10.26434/chemrxiv.13211432.v1 | Rational Incorporation of Missing Linker Defects Within Metal-Organic Frameworks Generates Highly Active Electrocatalytic Sites | The allure of metal-organic frameworks (MOFs) in heterogeneous electrocatalysis is that catalytically
active sites may be designed a priori with an unparalleled degree of control. An emerging strategy to
generate coordinatively-unsaturated active sites is through the use of organic linkers that lack a functional
group that would usually bind with the metal node. To execute this strategy, we synthesize a model MOF,
Ni-MOF-74 and incorporate a fraction of 2-hydroxyterephthalic acid in place of 2,5-dihydroxyterephthalic
acid. The defective MOF, Ni74D, is evaluated vs. the nominally defect-free Ni74 MOF with a host of ex
situ and in situ spectroscopic and electroanalytical techniques, using the oxidation of hydroxymethylfurtural
(HMF) as a model reaction. The data indicates that Ni74D features a set of 4-coordinate Ni-O4 sites that
exhibit unique vibrational signatures, redox potentials, binding motifs to HMF, and consequently superior
electrocatalytic activity relative to the original Ni74 MOF, being able to convert HMF to the desired 2,5-
furandicarboxylic acid at 95% yield and 80% Faradaic efficiency. The strategy put forth to rationally design
coordinatively-unsaturated electrocatalytic sites and the methodology put forth in investigating their
behavior stand to bolster the understanding and growth of the field. | Nina Heidary; Daniel Chartrand; Nikolay Kornienko | Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751ce842e65f97cdb3c23/original/rational-incorporation-of-missing-linker-defects-within-metal-organic-frameworks-generates-highly-active-electrocatalytic-sites.pdf |
64e5fef7dd1a73847f5951b9 | 10.26434/chemrxiv-2023-91xz7 | POMFinder: Identifying polyoxometalate cluster structures from pair distribution function data using explainable machine learning | Characterisation of material structure with Pair Distribution Function (PDF) analysis typically involves refining a structure model against an experimental dataset. However, finding or constructing a suitable atomic model for PDF modelling can be an extremely labour-intensive task, requiring carefully browsing through large numbers of possible models. We present POMFinder, a machine learning (ML) classifier that rapidly screens a database of structures, here polyoxometalate (POM) clusters, to identify candidate structures for PDF data modelling. The approach is demonstrated to identify suitable POMs on experimental data, including in situ data collected with fast acquisition time. This automated approach shows significant potential for identifying suitable structure models for structure refinements to extract quantitative, structural parameters in materials chemistry research. The code is open source and user-friendly, making it accessible to those without prior ML knowledge. We also demonstrate that POMFinder offers a promising modelling framework for combined modelling of multiple scattering techniques compared to conventional refinement methods. | Andy S. Anker; Emil T. S. Kjær; Mikkel Juelsholt; Kirsten M. Ø. Jensen | Inorganic Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e5fef7dd1a73847f5951b9/original/pom-finder-identifying-polyoxometalate-cluster-structures-from-pair-distribution-function-data-using-explainable-machine-learning.pdf |
6329baf50847000d2c827cc2 | 10.26434/chemrxiv-2022-xvm2l | IZCp and PZCp: Redox Non-innocent Cyclopentadienyl Lig-ands as Electron Reservoirs for Sandwich Complexes | Numerous developments in the electronic and steric modification of cyclopentadienyl (Cp) ligands have led to a corresponding growth in their applications. Herein, we present two new redox non-innocent Cp compounds, imidazolium- and pyrrolinium-substituted zwitterionic Cps (IZCp 1a and PZCp 1b). The Cps were obtained in high yields and could be handled easily owing to their high stability in air and moisture, unlike other known Cps. The redox non-innocent behavior of the Cp ligands was demonstrated via experimental and computational analyses of their half-sandwich and sandwich complexes. During cyclic voltammetry, the molybdenum half-sandwich (3a, 3b) and ruthenium sandwich ([4a]PF6, [4b]PF6) complexes of IZCp and PZCp showed reversible one-electron reduction at a low potential (E1/2 ranging from −1.7 to −2.7 V vs. Fc/Fc+). This phenomenon has not been studied previously because of the high instability of the reduced complexes. DFT calculations for the reduced complexes ([3a]‾, [3b]‾, 4a, and 4b) confirmed that their spin density was mainly delocalized over the ligand center (70%–90%). EPR analysis of the isolated K[3b] and 4b indicated their ligand-centered radical structures. Furthermore, the CO stretching frequencies of K[3b] (νCO 1871.35, 1748.10, and 1698.80 cm−1) revealed that the redox non-innocent [PZCp]‾ ligand is the strongest electron-donating Cp ligand among previously reported CpMo(CO)3 derivatives (νCO > 1746 cm−1). | Hyeonjeong Choi; Seung Hyuk Yoo; Hayoung Song; Eunsung Lee | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6329baf50847000d2c827cc2/original/iz-cp-and-pz-cp-redox-non-innocent-cyclopentadienyl-lig-ands-as-electron-reservoirs-for-sandwich-complexes.pdf |
60c74506469df429eff4343d | 10.26434/chemrxiv.9847190.v2 | Coaction of Electrostatic and Hydrophobic Interactions: Dynamic Constraints on Disordered TrkA Juxtamembrane Domain | <p>The receptor tyrosine kinase family transmits signals into cell via a single transmembrane helix and a flexible juxtamembrane domain (JMD). Membrane dynamics makes it challenging to study the structural mechanism of receptor activation experimentally. In this study, we employ all-atom molecular dynamics with Highly Mobile Membrane-Mimetic to capture membrane interactions with the JMD of tropomyosin receptor kinase A (TrkA). We find that PIP<sub>2 </sub>lipids engage in lasting binding to multiple basic residues and compete with salt bridge within the peptide. We discover three residues insertion into the membrane, and perturb it through computationally designed point mutations. Single-molecule experiments indicate the contribution from hydrophobic insertion is comparable to electrostatic binding, and in-cell experiments show that enhanced TrkA-JMD insertion promotes receptor ubiquitination. Our joint work points to a scenario where basic and hydrophobic residues on disordered domains interact with lipid headgroups and tails, respectively, to restrain flexibility and potentially modulate protein function.</p> | Zichen Wang; Huaxun Fan; Xiao Hu; John Khamo; Jiajie Diao; Kai Zhang; Taras Pogorelov | Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74506469df429eff4343d/original/coaction-of-electrostatic-and-hydrophobic-interactions-dynamic-constraints-on-disordered-trk-a-juxtamembrane-domain.pdf |
661c358621291e5d1dd48ef2 | 10.26434/chemrxiv-2024-kf953 | The effects of solid acids as cocatalysts on the chelation-assisted hydroacylation of alkenes and alkynes | The use of homogeneous Bronsted acid cocatalysts (such as benzoic acid) in hydroacylation reactions via imine intermediates has been extensively studied, but the use of heterogeneous cocatalysts has been limited to montmorillonite K10. Thus, we can use other solid acids to increase the efficiency of the reaction. Here, we described the effects of sulfated zirconia, Al-MCM-41 or superacid modified montmorillonite on the hydroacylation of alkenes and alkynes with aldehydes via imine intermediates and in the presence of the Wilkinson complex. Furthermore, we addressed the dual role of montmorillonite, a redox reagent in the presence of TEMPO and an acid solid, allowing the direct use of benzyl alcohols as substrates to generate saturated or a-b unsaturated ketones. | Blanca I. Vergara-Arenas; Eréndira García-Ríos; Rubén Gaviño; Jorge Cárdenas; Alfredo Martinez-Garcia; Erick A. Juarez-Arellano; Adolfo López-Torres; Jose Antonio Morales-Serna | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661c358621291e5d1dd48ef2/original/the-effects-of-solid-acids-as-cocatalysts-on-the-chelation-assisted-hydroacylation-of-alkenes-and-alkynes.pdf |
654bf62b6e0ec7777f8d94f2 | 10.26434/chemrxiv-2023-146f9 | Driving electrochemical organic hydrogenations on metal catalysts by tailoring hydrogen surface coverages | Electrochemical hydrogenation using renewable electricity holds promise as a sustainable approach to organic synthesis and the valorization of biomass-derived chemicals. Current strategies in the field usually employ alkaline conditions to suppress the competing hydrogen evolution reaction, and sourcing of hydrogen atoms for the hydrogenation is thus a challenge that can be addressed through local water dissociation on the electrode surface. Herein we demonstrate the computationally-guided design of electrochemical hydrogenation catalysts by tailoring their hydrogen coverage density and binding strength. Theoretical studies predict Cu, Au and Ag (with moderate H coverages) to be promising catalysts for electrochemical hydrogenation in alkaline media, which experiments confirm for a model organic substrate attaining yields and Faradaic efficiencies up to 90%. Furthermore, Cu, a non-precious metal electrocatalyst, is shown to promote the selective hydrogenation of a broad scope of unsaturated compounds featuring C=O, C=C, C≡C, and C≡N bonds with moderate to excellent conversions and chemoselectivities. Overall, this work demonstrates how the hydrogen coverage on the electrode surface can be tailored to design electrocatalysts based on non-precious metals for the hydrogenation of organic substrates. This knowledge is envisioned to guide the development of more efficient catalysts for organic hydrogenations as well as other chemical transformations of industrial interest. | Tengfei Li; Anna Ciotti; Motiar Rahaman; Celine Wing See Yeung; Max García-Melchor; Erwin Reisner | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2023-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654bf62b6e0ec7777f8d94f2/original/driving-electrochemical-organic-hydrogenations-on-metal-catalysts-by-tailoring-hydrogen-surface-coverages.pdf |
63852ab70949e15065596320 | 10.26434/chemrxiv-2022-hhpf0 | Distinguishing the Mechanism of Electrochemical Carboxylation in CO2 eXpanded Electrolytes | We shed light on the mechanism and rate-determining steps of the electrochemical car- carboxylation of acetophenone as a function of CO2 concentration, by using robust finite element analysis model that incorporates each reaction step. Specifically, we show that the first electrochemical reduction of acetophenone is followed by the homogeneous chemical addition of CO2. The electrochemical reduction of the acetophenone-CO2 adduct is more facile than that of acetophenone, resulting in an Electrochemical-Chemical-Electrochemical (ECE) reaction pathway that appears as a single voltammetric wave. These modeling results pro- vide new fundamental insights on the complex microenvironment in CO2-rich media that pro- duces an optimum electrochemical carboxylation rate as a function of CO2 pressure. | Matthew Stalcup; Christian Nilles; Bala Subramaniam; James Blakemore; Kevin Leonard | Catalysis; Chemical Engineering and Industrial Chemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63852ab70949e15065596320/original/distinguishing-the-mechanism-of-electrochemical-carboxylation-in-co2-e-xpanded-electrolytes.pdf |
663e5db121291e5d1df21957 | 10.26434/chemrxiv-2024-rxtmz | Hardware and software solutions for implementing nanospray desorption electrospray ionization (nano-DESI) sources on commercial mass spectrometers | Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization mass spectrometry imaging (MSI) approach that has been used for imaging of biological and environmental samples with high spatial resolution and throughput. Because nano-DESI has not yet been commercialized, researchers develop their own sources and interface them with different commercial mass spectrometers. Previously, several protocols focusing on the fabrication of nano-DESI probes have been reported. In this tutorial, we discuss different hardware requirements for coupling the nano-DESI source to commercial mass spectrometers, such as the safety interlock, inlet extension, and contact closure. In addition, we describe the structure of our custom software for controlling the nano-DESI MSI platform and provide detailed instructions for its usage. With this tutorial, interested researchers should be able to implement nano-DESI experiments in their own labs. | Lixue Jiang; Ryan Hilger; Julia Laskin | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663e5db121291e5d1df21957/original/hardware-and-software-solutions-for-implementing-nanospray-desorption-electrospray-ionization-nano-desi-sources-on-commercial-mass-spectrometers.pdf |
65424ffbc573f893f19401fe | 10.26434/chemrxiv-2023-pr9ck | GASP: A pan-specific predictor of family 1 glycosyltransferase specificity enabled by a pipeline for substrate feature generation and large-scale experimental screening | Glycosylation represents a major chemical challenge; while it is one of the most common reactions in Nature, conventional chemistry struggles with stereochemistry, regioselectivity and solubility issues. In contrast, family 1 glycosyltransferase (GT1) enzymes can glycosylate virtually any given nucleophilic group with perfect control over stereochemistry and regioselectivity. However, the appropriate catalyst for a given reaction needs to be identified among the tens of thousands of available sequences. Here, we present the Glycosyltransferase Acceptor Specificity Predictor (GASP) model, a data-driven approach to the identification of reactive GT1:acceptor pairs. We trained a random forest-based acceptor predictor on literature data and validated it on independent in-house generated data on 1001 GT1:acceptor pairs, obtaining an AUROC of 0.79 and a balanced accuracy of 72%. GASP is capable of parsing all known GT1 sequences, as well as all chemicals, the latter through a pipeline for the generation of 153 chemical features for a given molecule taking the CID or SMILES as input (freely available at https://github.com/degnbol/GASP). GASP had an 83% hit rate in a comparative case study for the glycosylation of the anti-helminth drug niclosamide, significantly outperforming a hit rate of 53% from a random selection assay. However, it was unable to compete with a hit rate of 83% for the glycosylation of the plant defensive compound DIBOA using expert-selected enzymes, with GASP achieving a hit rate of 50%. The hierarchal importance of the generated chemical features was investigated by negative feature selection, revealing properties related to cyclization and atom hybridization status to be the most important characteristics for accurate prediction. Our study provides a ready-to-use GT1:acceptor predictor which in addition can be trained on other datasets enabled by the automated feature generation pipelines. | David Harding-Larsen; Christian Degnbol Madsen; David Teze; Tiia Kittilä; Mads Rosander Langhorn; Hani Gharabli; Mandy Hobusch; Felipe Mejia Otalvaro; Onur Kırtel; Gonzalo Nahuel Bidart; Stanislav Mazurenko; Evelyn Travnik; Ditte Hededam Welner | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65424ffbc573f893f19401fe/original/gasp-a-pan-specific-predictor-of-family-1-glycosyltransferase-specificity-enabled-by-a-pipeline-for-substrate-feature-generation-and-large-scale-experimental-screening.pdf |
60c73f014c8919b7aaad1ebd | 10.26434/chemrxiv.7199720.v1 | NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit | <p>Modeling nanoparticles is an essential first step to assess their capacity in different uses such as in energy storage or drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe Nano-Crystal, a novel web-based crystallographic tool, which creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. Nano-Crystal can be accessed and used at http://nanocrystal.vi-seem.eu/.</p> | Zoe Cournia; Dimitris Dellis; Alexios Chatzigoulas; konstantina karathanou | Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Structure | CC BY NC 4.0 | CHEMRXIV | 2018-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f014c8919b7aaad1ebd/original/nano-crystal-a-web-based-crystallographic-tool-for-the-construction-of-nanoparticles-based-on-their-crystal-habit.pdf |
62e67160cc34e5b4d36d755f | 10.26434/chemrxiv-2022-qkq2w | A homoleptic tris(diphosphacyclobutadiene) tripledecker sandwich complex | The synthesis and characterisation of [Co2(η4 P2C2tBu2)2(µ:η4:η4-P2C2tBu2)] (1) is described, featuring two cobalt atoms and three diphosphacyclobutadiene ligands. This compound is the first triple-decker sandwich complex which exclusively contains cyclobutadiene ligands. | Christian Roedl; Gabriele Hierlmeier; Robert Wolf | Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2022-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e67160cc34e5b4d36d755f/original/a-homoleptic-tris-diphosphacyclobutadiene-tripledecker-sandwich-complex.pdf |
60c74826567dfeb3cbec497b | 10.26434/chemrxiv.11860065.v1 | Supramolecular Assembly of U(IV) Clusters and Superatoms | Superatoms are nanometer-sized molecules or particles that can form ordered lattices, mimicking their atomic counterparts. Hierarchical assembly of superatoms gives rise to emergent properties in superlattices of quantum-dots, p-block clusters, and fullerenes. Here, we introduce a family of uranium-oxysulfate cluster anions whose hierarchical assembly in water is controlled by two parameters; acidity and the countercation. In acid, larger Ln<sup>III</sup> (Ln=La-Ho) link hexamer (U<sub>6</sub>) oxoclusters into body-centered cubic frameworks, while smaller Ln<sup>III</sup> (Ln=Er-Lu &Y) promote linking of fourteen U<sub>6</sub>-clusters into hollow superclusters (U<sub>84</sub> superatoms). U<sub>84</sub> assembles into superlattices including cubic-closest packed, body-centered cubic, and interpenetrating networks, bridged by interstitial countercations, and U<sub>6</sub>-clusters. Divalent transition metals (TM=Mn<sup>II </sup>and Zn<sup>II</sup>), with no added acid, charge-balance and promote the fusion of 10 U<sub>6</sub> and 10 U-monomers into a wheel–shaped cluster (U<sub>70</sub>). Dissolution of U<sub>70</sub> in organic media reveals (by small-angle Xray scattering) that differing supramolecular assemblies are accessed, controlled by TM-linking of U<sub>70</sub>-clusters. <br /> | Ian Colliard; Gregory Morrosin; Hans-Conrad zur Loye; May Nyman | Lanthanides and Actinides; Magnetism; Solid State Chemistry; Supramolecular Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74826567dfeb3cbec497b/original/supramolecular-assembly-of-u-iv-clusters-and-superatoms.pdf |
6159ab79cea2e96a7f069842 | 10.26434/chemrxiv-2021-0swk6 | Total Synthesis of Himastatin | The synthesis and study of antibiotic natural products with unique structures and mechanisms of action represents a proven strategy to combat the public health crisis posed by antibiotic-resistant bacteria. The natural product himastatin is an antibiotic with an unusual homodimeric structure that presents a significant synthetic challenge. We report the concise total synthesis of himastatin by a newly developed final-stage dimerization strategy that was inspired by a detailed consideration of its biogenesis. Combining our bio-inspired dimerization approach with a modular synthesis enabled expedient access to a number of designed derivatives of himastatin, including synthetic probes that provide insight into its antibiotic activity. | Kyan D'Angelo; Carly Schissel; Bradley Pentelute; Mohammad Movassaghi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6159ab79cea2e96a7f069842/original/total-synthesis-of-himastatin.pdf |
60c7550abb8c1a60c03dc34f | 10.26434/chemrxiv.14030342.v1 | Simple Acyclic Molecules Containing a Single Charge-Assisted O–H Group Can Recognize Anions in Acetonitrile:water Mixtures | Hydroxypyridinium and hydroxyquinolinium compounds containing acidic O–H groups attached to a cationic aromatic scaffold were synthesized, i.e. N-methyl-3-hydroxypyridinium (1+) and N-methyl-8-hydroxyquinolinium (2+). These very simple compounds are capable of binding to chloride very strongly in CD3CN and with moderate strength in 9:1 CD3CN:D2O. Comparison with known association constants reveal that 1+ and 2+ bind chloride in CD3CN or CD3CN:D2O with comparable affinities to receptors containing significantly more hydrogen bond donors and/or higher positive charges. Crystal structures of both compounds with coordinating anions were obtained, and feature short O–H∙∙∙anion hydrogen bonds. A receptor containing two hydroxyquinolinium groups was also prepared. While the low solubility of this compound caused difficulties, we were able demonstrate chloride binding in a competitive 1:1 CD3CN:CD3OD solvent mixture. Addition of sulfate to this compound results in the formation of a crystallographically-characterised solid state anion coordination polymer. | Rosemary Goodwin; Mitchell Blyth; Alfred Fung; Leesa Smith; Philip Norcott; Sara Tanovic; Michelle Coote; Nicholas White | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7550abb8c1a60c03dc34f/original/simple-acyclic-molecules-containing-a-single-charge-assisted-o-h-group-can-recognize-anions-in-acetonitrile-water-mixtures.pdf |
60c753ff469df42ff4f44e7a | 10.26434/chemrxiv.13187561.v3 | Restricted-Variance Constrained, Reaction Path, and Transition State Molecular Optimizations Using Gradient-Enhanced Kriging | Gaussian process regression has recently been explored as an alternative to standard surrogate models in molecular equilibrium geometry optimization. In particular, the gradient-enhanced Kriging approach in association with internal coordinates, restricted-variance optimization, and an efficient and fast estimate
of hyperparameters has demonstrated performance on par or better than standard methods.
In this report, we extend the approach to constrained optimizations and transition states
and benchmark it for a set of reactions. We compare the performance of the new developed
method with the standard techniques in the location of transition states and in constrained
optimizations, both isolated and in the context of reaction path computation.
The results show that the method outperforms the current standard in efficiency as well
as in robustness.<br /> | Ignacio Fernández Galván; Gerardo Raggi; Roland Lindh | Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753ff469df42ff4f44e7a/original/restricted-variance-constrained-reaction-path-and-transition-state-molecular-optimizations-using-gradient-enhanced-kriging.pdf |
60c755e7ee301c6254c7b253 | 10.26434/chemrxiv.13191617.v2 | Selective Crystallization via Vibrational Strong Coupling | The coupling of (photo)chemical
processes to optical cavity vacuum fields is an emerging method for modulating
molecular and material properties. Recent reports have shown that strong
coupling of the vibrational modes of solvents to cavity vacuum fields can
influence the chemical reaction kinetics of dissolved solutes. This suggests
that vibrational strong coupling might also effect other important solution-based
processes, such as crystallization from solution. Here we test this hither-to
unexplored notion, investigating pseudopolymorphism in the crystallization from
water of ZIF metal-organic frameworks inside optical microcavities. We find
that ZIF-8 crystals are selectively obtained from solution inside optical
microcavities, where the OH stretching vibration of water is strongly coupled
to cavity vacuum fields, whereas mixtures of ZIF-8 and ZIF-L are obtained otherwise.
This work suggests that cavity vacuum fields might become a tool for materials synthesis,
biasing molecular self-assembly and driving macroscopic material outcomes. | Kenji Hirai; Hiroto Ishikawa; Thibault Chervy; JAMES HUTCHISON; Hiroshi Uji-i | Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e7ee301c6254c7b253/original/selective-crystallization-via-vibrational-strong-coupling.pdf |
62f0de5369f3a5de09afab56 | 10.26434/chemrxiv-2022-3r8q9 | Non-aqueous bonding of leuprorelin to Ochratoxin A for solid-phase extraction | The anticancer leuprorelin was found to have excellent affinity to ochratoxin A (OTA), with an equilibrium constant of 2.2 × 10^8 M^-1 at 273 K (dissociation constant Kd = 4.5 nM) when functionalized into a mesoporous polymer for binding to OTA. Binding between the surface-bound leuprorelin and mycotoxin was corroborated using DFT-based analysis, and it was extended to extraction of OTA from heavily fatty matrices of coffee, achieving 95% recovery with improved cyclability as compared with immunoaffinity. | Naoki Yamato; Noriaki Kumagai; Momoha Okahira; Satoru Kosaka; Shuji Kodama; Ryohei Yamamoto; Atsushi Yamamoto; Koichiro Takao; Masanori Yamamoto | Analytical Chemistry; Polymer Science; Agriculture and Food Chemistry; Analytical Chemistry - General; Separation Science; Food | CC BY 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f0de5369f3a5de09afab56/original/non-aqueous-bonding-of-leuprorelin-to-ochratoxin-a-for-solid-phase-extraction.pdf |
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