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66c5de9420ac769e5f5435ea | 10.26434/chemrxiv-2024-mt4nk | Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions | Quantum-chemical fragmentation methods offer an attractive approach for the accurate calculation of protein--ligand interaction energies. While the Molecular Fractionation with Conjugate Caps (MFCC) scheme offers a rather straightforward approach for this purpose, its accuracy is often not sufficient. Here, we upgrade the MFCC scheme for the calculation of protein--ligand interactions by including many-body contributions. The resulting fragmentation scheme is an extension of our previously developed MFCC-MBE(2) scheme [\textit{J. Comput. Chem.} \textbf{44}, 1634–1644 (2023)]. For a diverse test set of protein--ligand complexes, we demonstrate that by upgrading the MFCC scheme with many-body contributions, the error in protein--ligand interaction energies can be reduced significantly, and generally yields errors below 20 kJ/mol. Our scheme allows for systematically reducing these errors by including higher-order many-body contributions. As it combines the use of single amino acid fragments with high accuracy, our scheme provides an ideal starting point for the parametrization of accurate machine learning potentials for proteins and protein--ligand interactions. | Johannes R. Vornweg; Christoph Jacob | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c5de9420ac769e5f5435ea/original/protein-ligand-interaction-energies-from-quantum-chemical-fragmentation-methods-upgrading-the-mfcc-scheme-with-many-body-contributions.pdf |
60c747854c89194336ad2d15 | 10.26434/chemrxiv.11708136.v1 | Protic Ionic Liquid-Derived Coordination Polymer Glass for Anhydrous Proton Conductor with Moldability | Herein, we focused on
coordination polymer (CP) glass as a hybrid, soft electrolyte to meet these
criteria. We applied a protic ionic liquid of which components work also as
bridging ligand to construct CP structure with Zn<sup>2+</sup> ions. The
structural analysis of the CP glass reveals that network formation results in
enhancement of the properties of proton conductivity and viscoelasticity. The CP
glass features a high anhydrous proton conductivity (<i>σ</i> = 13.3 mS cm<sup>−1</sup>
at 120 °C) and high transport number of proton (0.94). Fabricated fuel cell
with this CP glass membrane exhibits a high open circuit voltage (0.96 V) and a
power density (0.15 W cm<sup>−2</sup>) under dry conditions at 120 °C. | Tomohiro Ogawa; Kazuki Takahashi; Sanjog S. Nagarkar; Koji Ohara; You-Lee Hong; Yusuke Nishiyama; Satoshi Horike | Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747854c89194336ad2d15/original/protic-ionic-liquid-derived-coordination-polymer-glass-for-anhydrous-proton-conductor-with-moldability.pdf |
65b8de779138d23161092e9c | 10.26434/chemrxiv-2024-55822 | A Water-Soluble Cycloparaphenylene: Synthesis and Application as a Supramolecular Receptor with Visible Fluorescence | We report the first synthesis of water-soluble [9]cycloparaphenylene derivative containing three hydrindacene (1,2,3,5,6,7-hexahydro-s-indacene) units with four carboxylates at the 2,6-positions via a macrocyclic gold complex. This crown-shaped macrocyclic compound exhibits remarkable water solubility, with a maximum solubility of 16 mmol L-1 (2.6 g/100 mL), as well as strong visible fluorescence in water (λem = 447 nm, φF = 0.64, brightness (ε×φF) = 5.1×104). This molecule effectively encapsulates cationic guest compounds, such as methyl viologen dichloride, as indicated by a change in visible fluorescence. | Ryo Morito; Takayuki Kataoka; Kunio Saito; Kohtaro Osakada; Tomohito Ide; Yoshitaka Tsuchido; Hidetoshi Kawai | Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b8de779138d23161092e9c/original/a-water-soluble-cycloparaphenylene-synthesis-and-application-as-a-supramolecular-receptor-with-visible-fluorescence.pdf |
6696fb9801103d79c5334f4f | 10.26434/chemrxiv-2024-s3hx8 | Nitrous Oxide Production via Nitroxyl by a Multicopper Oxidase from a Nitrifying Archaeon | Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of oceanic nitrous oxide (N2O) emissions, although biochemical origins of this N2O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase (MCO), Nmar_1354, from the AOA Nitrosopumilus maritimus. We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH2OH) to dioxygen (O2) reduction. This HNO undergoes several downstream reactions, although a significant fraction rapidly dimerizes to yield N2O. These results afford a possible enzymatic origin of AOA-derived N2O and reveal a unique enzymatic reaction for producing HNO. | Robert Voland; Hongsen Wang; Hector Abruña; Kyle Lancaster | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6696fb9801103d79c5334f4f/original/nitrous-oxide-production-via-nitroxyl-by-a-multicopper-oxidase-from-a-nitrifying-archaeon.pdf |
6167e19e7d3da50870f7592a | 10.26434/chemrxiv-2021-46v82 | High performance ambipolar organic mixed ionic-electronic conductor for adaptive logic circuits and neuromorphic electronics | Organic mixed ionic-electronic conductors (OMIECs) are central to bioelectronic applications such as biosensors, health monitoring devices and neural interfaces, and have facilitated efficient next-generation brain-inspired computing and biohybrid systems. Most OMIECs are hole-conducting (p-type) materials, while complimentary logic circuits and various biosensors require electron-conducting (n-type) materials too. Here we show an ambipolar mixed ionic-electronic polymer that achieves high on/off ratios with high ambient p- and n- type stability. We highlight the versatility of the material by demonstrating its use as a neuromorphic memory element, an adaptable ambipolar complementary logic inverter, and a neurotransmitter sensor. The ambipolar operation of this material allows for straightforward monolithic fabrication and integration, and opens a route towards more sophisticated complex logic and adaptive circuits. | Yanxi Zhang; Eveline van Doremaele; Gang Ye; Tim Stevens; Jun Song; Ryan Chiechi; Yoeri van de Burgt | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6167e19e7d3da50870f7592a/original/high-performance-ambipolar-organic-mixed-ionic-electronic-conductor-for-adaptive-logic-circuits-and-neuromorphic-electronics.pdf |
67a9f6e16dde43c9084752f5 | 10.26434/chemrxiv-2025-t373h | High Triplet Energy Iridium(III) NHC Complexes as Photocatalysts | Iridium(III) photocatalysts of the type Ir(C^N)3 and [Ir(C^N)2(N^N)]+ (where C^N and N^N rep-resent cyclometalating and ancillary ligands, like 2-phenylpyridinato and 2,2’-bipyridine, re-spectively) have seen widespread use over the past two decades. One of the most popular is fac-Ir(ppy)3, a strongly photoreducing photocatalyst (E*ox = -1.75 V vs. SCE in MeCN) that pos-sesses a reasonably high triplet energy (ET = 2.54 eV in MeCN). Despite its popularity, there has been relatively little exploration of other homoleptic neutral iridium(III) complexes as photo-catalysts. Replacement of the pyridyl moiety of the C^N ligands with more strongly -donating N-heterocyclic carbene (NHC) groups affords complexes with much higher bandgaps and ET, and significantly cathodically shifted ground-state redox potentials. In this study, mer- and fac¬¬-Ir(pmi)3 (where pmi represents 1-phenyl-3-methylimidazolin-2-ylidene-C,C2¬) were investigated as photocatalysts. These isomeric complexes have exceptionally high ET = 3.28 and 3.30 eV, re-spectively, and are very strongly reducing photocatalysts (E*ox = -2.72 and -2.67 V vs. SCE re-spectively). Both complexes consistently outperformed fac¬¬-Ir(ppy)3 across a range of photore-dox, energy transfer, and metallaphotoredox transformations. Additionally, Ir(pmi)3 exhibited significantly improved photostability compared to fac-Ir(ppy)3. This study highlights Ir(pmi)3 as an easy to synthesize, powerful, and versatile photocatalyst that should be a welcome addi-tion into the toolbox of photocatalysts for the synthetic organic chemist. | Máire Griffin; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Inorganic Chemistry; Photochemistry (Org.); Organometallic Compounds; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a9f6e16dde43c9084752f5/original/high-triplet-energy-iridium-iii-nhc-complexes-as-photocatalysts.pdf |
6545240848dad2312001fbf6 | 10.26434/chemrxiv-2023-1dmdx | Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across Protein Families | Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction networks across evolutionarily-related groups of proteins. KIN is available for download under a GNU General Public License, version 2, from https://www.github.com/kamerlinlab/KIN. KIN can operate on experimentally determined structures, predicted structures, or molecular dynamics trajectories, providing insight into both conserved and missing interactions across evolutionarily related proteins. This provides useful insight both into protein evolution, as well as a tool that can be exploited for protein engineering efforts. As a showcase system, we demonstrate applications of this tool to understanding the evolutionary-relevant conserved interaction networks across the class A β-lactamases. | Dariia Yehorova; Rory Crean; Peter Kasson; Shina Caroline Lynn Kamerlin | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6545240848dad2312001fbf6/original/key-interaction-networks-identifying-evolutionarily-conserved-non-covalent-interaction-networks-across-protein-families.pdf |
629f29ebb749a087ba9ad1d9 | 10.26434/chemrxiv-2022-5mj8x-v2 | Identification of chitin allomorphs in poorly crystalline samples based on the complexation with ethylenediamine | Chitin is a key component of hard parts in many organisms, but the biosynthesis of the two distinctive chitin allomorphs, α- and β-chitin, is not well-understood. The accurate determination of chitin allomorphs in natural biomaterials is vital. Many chitin-secreting living organisms, however, produce poorly crystalline chitin which leads to spectrums with only broad lines and imprecise peak positions under conventional analytical methods such as X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FT-IR), and solid state nuclear magnetic resonance spectroscopy (NMR), resulting in inconclusive identification of chitin allomorphs. Here, we developed a novel method for discerning chitin allomorphs based on their different complexation capacity and guest selectivity, using ethylenediamine (EDA) as a complexing agent. From the peak shift observed in XRD profiles of the chitin/EDA complex, the chitin allomorphs can be clearly discerned. By testing this method on a series of samples with different chitin allomorphs and crystallinity, we show that the sensitivity is sufficiently high to detect the chitin allomorphs even in near-amorphous, very poorly crystalline samples. This is a powerful tool for determining the chitin allomorphs in phylogenetically important chitin-producing organisms and will pave the way to clarify the evolution and mechanism of chitin biosynthesis. | Noriyuki Isobe; Yuto Kaku; Satoshi Okada; Sachiko Kawada; Keiko Tanaka; Yoshihiro Fujiwara; Ryota Nakajima; Dass Bissessur; Chong Chen | Polymer Science; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629f29ebb749a087ba9ad1d9/original/identification-of-chitin-allomorphs-in-poorly-crystalline-samples-based-on-the-complexation-with-ethylenediamine.pdf |
60c75931567dfec4abec69ab | 10.26434/chemrxiv.14669532.v1 | Lithium-Conducting Self-Assembled Organic Nanotubes | <p>Supramolecular
polymers are compelling platforms for the design of stimuli-responsive materials
with emergent functions. Here, we report the assembly of an amphiphilic
nanotube for Li-ion conduction that exhibits high ionic conductivity,
mechanical integrity, electrochemical stability, and solution processability. Imine
condensation of a pyridine-containing diamine with a triethylene glycol
functionalized isophthalaldehyde yields pore-functionalized macrocycles. Atomic
force microscopy, scanning electron microscopy, and <i>in solvo</i> X-ray
diffraction reveal that macrocycle protonation under their mild synthetic
conditions drives assembly into high-aspect ratio (>10<sup>3</sup>) nanotubes
with three interior triethylene glycol groups. Electrochemical impedance
spectroscopy demonstrates that lithiated nanotubes are efficient Li<sup>+</sup>
conductors, with an activation energy of 0.42 eV and a peak room temperature
conductivity of 3.91 × 10<sup>-5</sup> S cm<sup>-1</sup>. <sup>7</sup>Li NMR
and Raman spectroscopy demonstrate that lithiation occurs exclusively within
the nanotube interior and implicates the glycol groups in facilitating efficient
Li<sup>+</sup> transduction. Linear sweep voltammetry and galvanostatic lithium
plating-stripping tests reveal that this nanotube-based electrolyte is stable
over a wide potential range and supports long-term cyclability. These findings demonstrate how coupling
synthetic design and supramolecular structural control can yield
high-performance ionic transporters that are amenable to device relevant
fabrication. More broadly, these results demonstrate the technological
potential of chemically designed self-assembled nanotubes. </p> | Michael Strauss; Insu Hwang; Austin Evans; Anusree Natraj; Xavier Aguilar-Enriquez; Ioannina Castano; Emily Roesner; Jang Wook Choi; William Dichtel | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75931567dfec4abec69ab/original/lithium-conducting-self-assembled-organic-nanotubes.pdf |
61cd2250f52bc4acf7d1ef4a | 10.26434/chemrxiv-2021-kjghp | Ni-Electrocatalytic C(sp3)–C(sp3) Doubly Decarboxylative Coupling | This work presents a modern spin on one of the oldest known Csp3–Csp3 bond forming reactions in synthetic chemistry: the Kolbe electrolysis. This reaction holds incredible promise for synthesis, yet its use has been near non-existent in mainstream organic synthesis. In contrast to the strongly oxidative electrolytic protocol employed traditionally since the 19th century, the present method utilizes in situ generated redox-active esters (RAEs) which are combined with a mildly reductive Ni-electrocatalytic cycle. It can be used to heterocouple 1o, 2o, and even certain 3o RAEs with a protocol reminiscent of amide bond formation in terms of simplicity. Due to its mild nature the reaction tolerates a range of functional groups, is scalable, and was strategically enlisted for the synthesis of 25 known compounds to reduce overall step-counts by 74%. | benxiang zhang; yang gao; yuta hioki; martins oderinde; jennifer qiao; kevin rodriguez; hai-jun zhang; yu kawamata; phil baran | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cd2250f52bc4acf7d1ef4a/original/ni-electrocatalytic-c-sp3-c-sp3-doubly-decarboxylative-coupling.pdf |
638db2cf14d92d63eba16c1f | 10.26434/chemrxiv-2022-0lbq4 | Revealing the evolution towards complex N-glycan specificities of human H1 influenza A viruses. | Influenza virus infection remains a threat to human health since viral hemagglutinins are constantly drifting, escaping infec-tion and vaccine-induced antibody responses. During antigenic drift H3 hemagglutinins have evolved to recognize a2,6 sialylated branched N-glycans with long glycan chains with at least three N-acetyllactosamine units (tri-LacNAc). In this work, we combined glycan arrays and tissue binding analyses with NMR experiments to characterize the interaction of a family of H1 variants, including the one responsible for the last pandemic outbreak. We also analyzed one H6 to understand if the preference for tri-LacNAc motifs is a general trend in recent zoonotic human-type receptor binding adapted viruses. In addition, we developed a new NMR approach to perform competition experiments between glycans with similar compositions and different lengths. Pandemic H1 viruses differ from previous seasonal H1 viruses by a strict preference for a minimum of di-LacNAc structural motif that are in turn present on the ferret upper respiratory tract. | Angeles Canales; Javier Sastre; Jose M Orduña; Javier Pérez-Castells; Gema Domínguez; Roosmarijn van der Woude; Francisco Javier Cañada; Corwin M Nycholat; James C Paulson; Geert-Jan Boons; Jesús Jiménez-Barbero; Robert Paul de Vries | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638db2cf14d92d63eba16c1f/original/revealing-the-evolution-towards-complex-n-glycan-specificities-of-human-h1-influenza-a-viruses.pdf |
666854bf409abc034527d6b4 | 10.26434/chemrxiv-2024-fs2m8 | Photorheologic silicone composites with adaptive properties by utilizing light-degradable organosilica nanoparticles as fillers | Implementing inorganic filler particles is a powerful method for improving the mechanical properties of the formed composites. Fillers made of silicon dioxides can be found in countless polymeric materials. Because the interaction of the silica with the polymer determines the physical properties, factors like the surface-to-volume ratio (controlled via the particle size) and surface modification are important. Systems in which the particles are just physically dispersed in the polymer behave significantly differently to those for covalent anchoring of the fillers. Another possible functionality of the filler particles we focus on in the current publication is that they can bring stimuli-responsive properties to the system. Our concept is that photo-degradable organosilica nanoparticles can change the mechanical properties of a polymer/filler composite after it has been prepared. Because of the of the huge applicability of polysiloxanes ranging from building materials to medicine, silicones were selected as the center of interest for the current paper. After the synthesis of organosilica nanoparticles containing a bridging nitrobenzyl ether, and the investigation of the photochemical decomposition processes, the preparation of the composites is described. It is shown that vinyl groups attached to the surfaces are crucial for securing a homogeneous distribution of the filler particles inside the polymer matrix. Finally, the light-induced decomposition of the organosilica is executed and the mechanical properties are investigated by dynamic mechanical analysis. Other than expected, the material becomes stiffer. This effect is explained by a coupled increase of the surface-to-volume ratio of the silica particles accompanied by the emergence of hydroxy groups which interact with the polysiloxane backbone. | Florian Klodwig; Laura Finck; Nina Ehlert; Henning Menzel; Sebastian Polarz | Polymer Science; Polymer blends; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666854bf409abc034527d6b4/original/photorheologic-silicone-composites-with-adaptive-properties-by-utilizing-light-degradable-organosilica-nanoparticles-as-fillers.pdf |
666706ed409abc03451476aa | 10.26434/chemrxiv-2024-mktsd | The electronic spin state of diradicals obtained from the nuclear perspective: the strange case of Chichibabin radicals | With a view towards the development of molecular spintronics, non-linear optics, and qubits, a great amount of research effort aims to establish the factors which govern the spin classification of diradicals. Electron spin resonance (ESR) is an indispensable tool for such research. However, in some cases, the mere presence of an ESR spectrum is insufficient to ascertain that the presumed diradical is indeed a triplet state. In a comparative case study of a Chichibabin diradical and a monoradical analogue, we show how the signals from different spin states present in liquid solutions of these species may be disentangled. Ultimately, the correct spin classification depends on ESR techniques which probe the spin quantum number directly. In this work, electron nuclear double resonance experiments reveal that the nuclei provide the clearest experimental probe of the electronic spin configuration. | Gabriel Moise; Saleta Fernandez; Kit Joll; Mikhail Vaganov; Fatima Garcia; Christiane R. Timmel; Diego Pena; Arzhang Ardavan | Physical Chemistry; Organic Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666706ed409abc03451476aa/original/the-electronic-spin-state-of-diradicals-obtained-from-the-nuclear-perspective-the-strange-case-of-chichibabin-radicals.pdf |
671e0f9c1fb27ce124bcbea2 | 10.26434/chemrxiv-2024-5f7jc | Bio-based graphene-encapsulated Co@CS catalyzed selective hydrogenation of nitrile to amines via flow synthesis | Amines are basic components of bioactive compounds, natural products, drugs, and functional materials. Catalytic hydrogenation of nitrile compounds to corresponding amines is a green and efficient production method. Compared with heterogenous metal catalyzed batch reactions in high pressure of hydrogen, the flow synthesis method using heterogeneous metal catalysts can achieve higher catalyst efficiency and productivity, as well as much safer practical application. Moreover, the development of multiple utilizations of sustainable biomass materials especially in developing biobased materials for catalysts is highly demanding. So in this work, advanced flow synthesis methodology was used to prepare primary amines via bio-based chitosan Co@CS heterogeneous catalyst through the catalytic hydrogenation of nitrile. The effects of temperature, pressure, ammonia concentration, and liquid flow rate on the flow reaction were investigated. Under the optimal reaction conditions, the benzonitrile (BN) conversion rate was greater than 99%, and the selectivity of benzylamine exceeded 99%. The synthesized graphene-encapsulated Co-based catalyst with chitosan as the carrier material was tested for a long time to verify the stability of the Co@CS catalyst. The substrate expansion experiments of various aromatic nitriles gave satisfactory primary amine yields. Due to its exceptional mass and heat transport properties, the H-Flow system offers an efficient route for the large-scale synthesis of primary amines from biomass platform compounds in industrial production. This study provides new ideas and references for preparing highly selective primary amines by industrial-scale hydrogenation of nitrile compounds. | Siyi Mi; Jianguo liu | Catalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671e0f9c1fb27ce124bcbea2/original/bio-based-graphene-encapsulated-co-cs-catalyzed-selective-hydrogenation-of-nitrile-to-amines-via-flow-synthesis.pdf |
67385bf77be152b1d03b4e07 | 10.26434/chemrxiv-2024-pwkq5 | Accelerating Enzyme Engineering with Quantum Power: Quest for Quantum Advantage in Biocatalysis | Imagine a computer capable of solving currently unsolvable problems. Quantum computing leverages the principles of quantum mechanics to tackle complex challenges that would take classical computers centuries to complete. In this Commentary, we explore the current state of quantum computing development and how it will revolutionise the way we discover and design biocatalysts for practical use. | Jiri Damborsky; Petr Kouba; Josef Sivic; David Bednar; Stanislav Mazurenko | Theoretical and Computational Chemistry; Catalysis; Artificial Intelligence; Quantum Computing; Biocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67385bf77be152b1d03b4e07/original/accelerating-enzyme-engineering-with-quantum-power-quest-for-quantum-advantage-in-biocatalysis.pdf |
60c746c1f96a00f617286ded | 10.26434/chemrxiv.9730031.v3 | Hierarchical Porous Carbon Arising from MOF Encapsulated Bacteria and its Energy Storage Potential | Hierarchical porous carbons (HPCs) hold great promise in energy-related applications owing to their excellent chemical stability and well-developed porous structures. Attention has been drawn toward developing new synthetic strategies and precursor materials that permit greater control over composition, size, morphology, and pore structure. There is a growing trend of employing metal-organic frameworks (MOFs) as HPC precursors as their highly customizable characteristics favor new HPC syntheses. In this article, we report a biomimetically grown bacteria-templated MOF synthesis where the bacteria not only facilitate the formation of MOF nanocrystals, but also provides morphology and porosity control. The resultant HPCs show improved electrochemical capacity behavior compared to pristine MOF derived HPCs. Considering the broad availability of bacteria and ease of its production, in addition to significantly improved MOF growth efficiency on bacterial templates, we believe that bacteria-templated MOF is a promising strategy to produce a new generation of HPCs. <br /> | Shaobo Li; Xiaoshuang Zhou; Zhuo Chen; Fabian C. Herbert; Rangana Jayawickramage; Samitha
D. Panangala; Michael A. Luzuriaga; Sampath B. Alahakoon; Shashini Mohottalalage; Xin Meng; Ling Fei; John P. Ferraris; Ron Smaldone; Jeremiah J. Gassensmith | Carbon-based Materials; Core-Shell Materials; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Energy Storage; Power | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c1f96a00f617286ded/original/hierarchical-porous-carbon-arising-from-mof-encapsulated-bacteria-and-its-energy-storage-potential.pdf |
66f3725f12ff75c3a15fb9cb | 10.26434/chemrxiv-2024-8f3jf-v3 | Controlled quantum well formation on DNA-wrapped carbon nanotubes via peroxide-mediated aryl diazonium reduction | Quantum well defect-modified single walled carbon nanotubes are environmentally sensitive nanomaterials with wide-ranging applications in biosensing, imaging, light harvesting, quantum computing, energy storage and catalysis. The most common method for covalent functionalization of nanotubes for biosensing applications involves reactions with aryl diazonium salts to generate sp3 aryl defect sites, commonly followed by wrapping with single stranded DNA. We describe herein a rapid aryl diazonium functionalization reaction directly compatible with DNA-wrapped nanotubes. The reaction uses mild aqueous conditions at physiological pH and can be easily monitored in real-time via fluorescence analysis to control the degree of functionalization. Overall, this reaction greatly simplifies the production of covalently functionalized DNA-wrapped carbon nanotubes, expanding their potential for industrial and biomedical applications. | Stanislav Piletsky; Erin Keblish; Daniel Heller | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f3725f12ff75c3a15fb9cb/original/controlled-quantum-well-formation-on-dna-wrapped-carbon-nanotubes-via-peroxide-mediated-aryl-diazonium-reduction.pdf |
60da341b2616116d148cb7ba | 10.26434/chemrxiv-2021-3rpsq | Peculiar anharmonicity of Ruddlesden Popper metal halides: Temperature-dependent phonon dephasing | The anharmonicity of the Ruddlesden Popper metal-halide lattice, and its consequences on their electronic and optical properties, is paramount in their basic semiconductor physics. It is thus critical to identify specific anharmonic optical phonons that govern their photophysics . Here, we address the nature of phonon-phono scattering probabilities of the resonantly excited optical phonons that dress the electronic transitions in these materials by means of variable-temperature resonant impulsive stimulated Raman measurements. Based on the temperature dependence of the coherent phonon lifetimes, we isolate the dominant anharmonic phonon and quantify its phonon-phonon interaction strength. Intriguingly, we also observe that the anharmonicity is distinct for different phonons, with a few select modes exhibiting temperature-independent coherence lifetimes, indicating their predominantly harmonic nature. However, the population and dephasing dynamics of excitons are dominated by the anharmonic phonon. | Esteban Rojas Gatjens; Carlos Silva Acuña; Ajay Ram Srimath Kandada | Physical Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60da341b2616116d148cb7ba/original/peculiar-anharmonicity-of-ruddlesden-popper-metal-halides-temperature-dependent-phonon-dephasing.pdf |
64c1011b9ed5166e937e93c5 | 10.26434/chemrxiv-2023-fgxxm-v2 | Selective Synthesis of 1,3-Substituted Cuneanes: En Route to Potent Bioisosteres of m-Substituted Benzenes | We herein disclose a method to obtain 1,3-substituted cuneane by selective isomerization of 1,4-substituted cubanes. The electronic property of the substituent strongly affects the isomerization ratio of 1,3-substituted cuneane and 2,6-substituted cuneane. Based on structural similarity, we considered that 1,3-substituted cuneane would be a bioisostere of m-substituted benzene. The synthesis of a cuneane analogs of pharmaceuticals having m-substituted benzene moiety and its biological and in silico evaluation are also described. | Shota Nagasawa; Kan Fujiwara; Ryusei Maeyama ; Ryosuke Segawa; Noriyasu Hirasawa; Takatsugu Hirokawa; Yoshiharu Iwabuchi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c1011b9ed5166e937e93c5/original/selective-synthesis-of-1-3-substituted-cuneanes-en-route-to-potent-bioisosteres-of-m-substituted-benzenes.pdf |
60c7470c469df49258f4377d | 10.26434/chemrxiv.11521827.v1 | Imine as a Linchpin Approach for Distal C(sp2)–H Functionalization | <p>Despite
the widespread applications of C–H functionalization, controlling site
selectivity remains a significant challenge. Covalently attached directing
group (DG) served as an ancillary ligand to ensure proximal <i>ortho</i>-,
distal <i>meta</i>- and <i>para</i>-C-H functionalization over the
last two decades. These covalently linked DGs necessitate two extra steps for a
single C–H functionalization: introduction of DG prior to C–H activation and
removal of DG post-functionalization. We introduce here a transient directing
group for distal C(<i>sp<sup>2</sup></i>)-H
functionalization <i>via</i> reversible
imine formation. By overruling facile proximal C-H bond
activation by imine-<i>N</i> atom, a
suitably designed pyrimidine-based transient directing group (TDG) successfully
delivered selective distal C-C
bond formation. Application of this transient directing group strategy for
streamlining the synthesis of complex organic molecules without any necessary
pre-functionalization at the distal position has been explored.</p> | Sukdev Bag; Sadhan Jana; Sukumar Pradhan; Suman Bhowmick; Nupur Goswami; Soumya Kumar Sinha; Debabrata Maiti | Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7470c469df49258f4377d/original/imine-as-a-linchpin-approach-for-distal-c-sp2-h-functionalization.pdf |
6396bd5e836ceb609c7e3aa5 | 10.26434/chemrxiv-2022-r1txp | Supramolecular chemistry of two new bis(1,2,3-triazolyl)pyridine macrocycles: metal complexation, self–assembly and anion binding | Two new macrocycles containing the bis(1,2,3-triazolyl)pyridine (btp) motif were prepared in high yields from a btp diazide precursor (1). Solution 1H NMR studies show that this diazide undergoes self–assembly with divalent transition metal ions to form ML2 complexes with pendant azide groups, apparently suitable for conversion into metal-templated catenanes; however attempts to form these catenanes were unsuccessful. Instead a new macrocycle containing two btp motifs was prepared, which forms a nanotube structure in the solid state. Reduction of the azide groups to amines followed by amide bond formation was used to convert 1 into macrocycle 8 containing btp and isophthalamide functionalities. This macrocycle binds halide and oxalate anions in acetonitrile solely through the isophthalamide motif, and binds aromatic dicarboxylates very strongly through both the isophthalamide amide donors and the btp triazole donors. The macrocycle was complexed with Pd(II) and the resulting complexes were shown to bind strongly to halide anions. The solid state structures of these [Pd·8·X]BF4 (X = Cl–, Br–, I–) were investigated by X-ray crystallography, which showed that [Pd·8·Br] forms an unusual “chain of dimers” structure assembled by metal complexation, N–H···Br– hydrogen bonding and short Pd···Pd contacts. | Arthur David; Rosemary Goodwin; Nicholas White | Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6396bd5e836ceb609c7e3aa5/original/supramolecular-chemistry-of-two-new-bis-1-2-3-triazolyl-pyridine-macrocycles-metal-complexation-self-assembly-and-anion-binding.pdf |
669e424bc9c6a5c07a704989 | 10.26434/chemrxiv-2024-lb5z3 | Proposal of an Approach to Explore Photocatalysts by Two-stage Machine Learning Model | In the field of data-driven material development, bias in a dataset often causes difficulties in building a regression model when machine learning methods are applied. One of inorganic functional materials facing such a difficulty is photocatalysts. In this study, we propose a two-stage machine learning model to predict the activity for hydrogen evolution (H2/µmol h-1) from an aqueous solution containing sacrificial reagents over metal-sulfide photocatalysts under visible light irradiation. This two-stage machine learning model consists of the following two parts: a first regression model that predicts the activity for sacrificial hydrogen evolution and a second classification model that determines the reliability of the values predicted by the first regression model. We also propose a search scheme for variables related to the experimental conditions based on the proposed two-stage machine learning model. The proposed two-stage machine learning model improves the prediction accuracy of the activity compared with the first regression model. | Wataru Takahara; Ryuto Baba; Yosuke Harashima; Tomoaki Takayama; Shogo Takasuka; Yuichi Yamaguchi; Akihiko Kudo; Mikiya Fujii | Theoretical and Computational Chemistry; Catalysis; Machine Learning; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e424bc9c6a5c07a704989/original/proposal-of-an-approach-to-explore-photocatalysts-by-two-stage-machine-learning-model.pdf |
60c75987842e654df9db4a3c | 10.26434/chemrxiv.14709072.v1 | Coarse-Grained Molecular Dynamics Simulations of Nanoplastics Interacting with a Hydrophobic Environment in Aqueous Solution | <div><div><div><p>Nanoplastics (NPs) are emerging threats for marine and terrestrial ecosystems, but little is known about their fate in the environment at the molecular scale. In this work, coarse-grained molecular dynamics simulations were performed to investigate nature and strength of the interaction between NPs and hydrophobic environments. Specifically, NPs were simulated with different hydrophobic and hydrophilic polymers while carbon nanotubes (CNTs) were used to mimic surface and confinement effects of hydrophobic building blocks occurring in a soil environment. The hydrophobicity of CNTs was modified by introducing different hydrophobic and hydrophilic functional groups at their inner surfaces. The results show that hydrophobic polymers have a strong affinity to adsorb at the outer surface and to be captured inside the CNT. The accumulation within the CNT is even increased in presence of hydrophobic functional groups. This contribution is a first step towards a mechanistic understanding of a variety of processes connected to interaction of nanoscale material with environmental systems. Regarding the fate of NPs in soil, the results point to the critical role of the hydrophobicity of NPs and soil organic matter (SOM) as well as of the chemical nature of functionalized SOM cavities/voids in controlling the accumulation of NPs in soil. Moreover, the results can be related to water treatment technologies as it is shown that the hydrophobicity of CNTs and functionalization of their surfaces may play a crucial role in enhancing the adsorption capacity of CNTs with respect to organic compounds and thus their removal efficiency from wastewater.</p><p><br /></p></div></div></div> | Lorenz Dettmann; Oliver Kühn; Ashour A. Ahmed; Oliver Kuehn | Environmental Science; Soil Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75987842e654df9db4a3c/original/coarse-grained-molecular-dynamics-simulations-of-nanoplastics-interacting-with-a-hydrophobic-environment-in-aqueous-solution.pdf |
60c749c64c89192addad3113 | 10.26434/chemrxiv.12053535.v2 | Discovery of Aptamers Targeting Receptor-Binding Domain of the SARS-CoV-2 Spike Glycoprotein | The
World Health Organization has declared the outbreak of a novel coronavirus (SARS-CoV-2
or 2019-nCoV) as a global pandemic. However, the mechanisms behind the
coronavirus infection are not yet fully understood, nor are there any targeted
treatments or vaccines. In this study, we identified high-binding-affinity aptamers targeting SARS-CoV-2
RBD, using an ACE2 competition-based aptamer selection strategy and a machine
learning screening algorithm. The K<sub>d</sub> values of the optimized CoV2-RBD-1C
and <a>CoV2-RBD-</a>4C aptamers against RBD were 5.8 nM and
19.9 nM, respectively. Simulated interaction modeling, along with competitive
with experiments, suggests that two aptamers may have partially identical
binding sites at ACE2 on SARS-CoV-2 RBD. These aptamers present an opportunity
for generating new probes for
recognition of SARS-CoV-2, and could provide assistance in the diagnosis and
treatment of SARS-CoV-2 while providing a new tool for in-depth study of the
mechanisms behind the coronavirus infection. | Yanling Song; Jia Song; Xinyu Wei; Mengjiao Huang; Miao Sun; Lin Zhu; Bingqian Lin; Haicong Shen; Zhi Zhu; Chaoyong Yang | Analytical Chemistry - General; Biochemical Analysis; Bioinformatics and Computational Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749c64c89192addad3113/original/discovery-of-aptamers-targeting-receptor-binding-domain-of-the-sars-co-v-2-spike-glycoprotein.pdf |
671a590b1fb27ce1246dd727 | 10.26434/chemrxiv-2024-53gtc | Putting the “P” back in Delayed Fluorescence – Silylethynyl Substitution Generates Efficient Pyrene Annihilators for Red-to-Blue Photon Upconversion | Triplet-triplet annihilation photon upconversion (TTA-UC) converts low-energy photons to higher-energy ones under low-intensity incoherent excitation, thus enabling applications in fields ranging from medicine to solar energy conversion. Silylethynyl mono- and di-substitution of acenes, offers an attractive route to creating new annihilators that operate with minimal energy loss. Here, we demonstrate this approach can be extended to pyrene, yielding annihilators that display efficient red-to-blue upconversion. While pyrene is the namesake of P-type delayed fluorescence, the original name for triplet-triplet annihilation, it is known to be a poor annihilator due to its propensity for forming excimers. By tetra-substituting pyrene with silylethynyl groups, we substantially hinder excimer formation while simultaneously minimizing the energy gap between the singlet and triplet pair states that participate in TTA-UC, yielding outstanding annihilators for red-to-blue upconversion that operate with quantum yields of upwards of 19% (30% when corrected for inner filter effects). Further, we find reducing the bulkiness of the silyl substituents is key to achieving high TTA-UC quantum yields, which highlights the importance of annihilator side group selection when optimizing photon upconversion. | Jussi Isokuortti; Connor J. O'Dea; Seth R. Allen; Serhii Vasylevskyi; Zachariah A. Page; Sean T. Roberts | Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a590b1fb27ce1246dd727/original/putting-the-p-back-in-delayed-fluorescence-silylethynyl-substitution-generates-efficient-pyrene-annihilators-for-red-to-blue-photon-upconversion.pdf |
62cc76d4fb638124d9d75fe0 | 10.26434/chemrxiv-2022-93kwv-v2 | PdCu Electrocatalysts for Selective Nitrate and Nitrite Reduction to Nitrogen | Electrocatalytic conversion of nitrate in waste can enable efficient waste remediation (NO3- to N3) or waste valorization (NO3- to NH4+) depending on the selectivity of the catalyst. Palladium and copper electrocatalysts typically exhibit exceptional nitrate and nitrite binding properties, allowing for effective destruction of nitrate. However, rational steering of selectivity through material design remains a critical challenge for PdCu electrocatalyst. Here, we use the electrochemical underpotential deposition method to synthesize palladium nanocube electrocataysts with controlled copper surface coverage (e.g. partial and full copper coatings). We then examine the potential for NO3- destruction (conversion) and catalyst selectivity. We identify that partial copper-coated Pd nanocubes effectively facilitate the reduction of 95% of NO3-. Partial surface coverage of copper also allows exposure of Pd(100) surface facets, allowing selective reduction of NO3- to N3 with 89% selectivity over 20 consecutive cycles (80 hours). Complete copper-covered Pd nanocubes effectively facilitate the reduction of 98.8% of NO3-. Complete coverage of copper also prevented exposure of Pd surfaces (100), promoting selective reduction of NO2- to NH4+ with a 70% selectivity over 20 consecutive cycles (80 hours). Density functional theory (DFT) calculations show that NO3- and NO2- can easily be reduced to NO* on the Cu surface (100). The adsorbed NO* then migrates favorably from the Cu(100) surface to the Pd(100) surface, where NO* is hydrogenated to form an NOH* intermediate that readily dissociates to generate N*. N* can then be coupled with NO* on the surface of Pd (100) with high NO* coverage to form N2O*, which is the precursor intermediate for N2 formation. | Jeonghoon Lim; Yu Chen; David Cullen; Seung Woo Lee; Thomas Senftle; Marta Hatzell | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cc76d4fb638124d9d75fe0/original/pd-cu-electrocatalysts-for-selective-nitrate-and-nitrite-reduction-to-nitrogen.pdf |
62ab171be00d4e4be22c954b | 10.26434/chemrxiv-2022-dwfsr-v2 | Stressing the differences in alizarin and purpurin dyes through UV-visible light absorption and 1 H-NMR spectroscopies | Three anthraquinone-based chromophores (9,10-anthraquinone, alizarin, purpurin) are compared from the point of view of their experimental and computed NMR and UV-visible light absorption spectra. Using an hybrid (explicit/implicit) solvent model, each proton chemical shift can be reproduced with an error less than 7\%, even when such protons are engaged in inter-molecular hydrogen bonds with the solvent or when the analyzed sample contains a significant amount of impurities, for instance 9,10-anthraquinone in purpurin. All the steady-state UV-visible absorption spectra feature a significant vibrational progression in the first absorption band. The shape of the corresponding computed spectra, including vibronic couplings obtained with the Adiabatic Hessian approach and the Franck-Condon and Hertzberg-Teller approximation of the transition dipole, are in excellent agreement with the experimental one. The importance and the nature of the vibronic couplings are different for the three molecules, even if they only differ by the number of hydroxyl groups. | Roger-Charles Tissier; Baptiste Rigaud; Pierre Thureau; Miquel Huix-Rotllant; Maguy Jaber; Nicolas FERRE | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ab171be00d4e4be22c954b/original/stressing-the-differences-in-alizarin-and-purpurin-dyes-through-uv-visible-light-absorption-and-1-h-nmr-spectroscopies.pdf |
60c743c19abda26ff5f8c248 | 10.26434/chemrxiv.9642830.v1 | A Phage-Assisted Continuous Selection Approach for Deep Mutational Scanning of Protein-Protein Interactions | Protein-protein interactions (PPIs) are critical for organizing molecules in a cell and mediating signaling pathways. Dysregulation of PPIs are often key drivers of disease. To better understand the biophysical basis of such disease processes – and to potentially target them - it is critical to understand the molecular determinants of PPIs. Deep mutational scanning (DMS) facilitates the acquisition of large amounts of biochemical data by coupling selection with high throughput sequencing (HTS). The challenging and labor-intensive design and optimization of a relevant selection platform for DMS, however, limits the use of powerful directed evolution and selection approaches. To address this limitation, we designed a versatile new phage assisted continuous selection (PACS) system using our proximity-dependent split RNA polymerase (RNAP) biosensors with the aim of greatly simplifying and streamlining the design of a new selection platform for PPIs. After characterization and validation using the model KRAS/RAF PPI, we generated a library of RAF variants and subjected them to PACS and DMS. Our HTS data revealed that amino acid (aa) positions 66, 84, and 89 on RAF, key residues in the KRAS/RAF PPI, are intolerant to mutations. We also identified a subset of residues with broad aa substitution tolerance, aa positions 52, 55, 76, and 79. Due to the plug and play nature of RNAP biosensors, this method can easily be extended to other PPIs. More broadly, this, and other methods under development, supports the application of evolutionary and high-throughput approaches to bear on biochemical problems, moving towards a more comprehensive understanding of sequence-function relationships in proteins. | Julia Zinkus-Boltz; Craig Devalk; Bryan Dickinson | Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743c19abda26ff5f8c248/original/a-phage-assisted-continuous-selection-approach-for-deep-mutational-scanning-of-protein-protein-interactions.pdf |
60c7532df96a0052452883bb | 10.26434/chemrxiv.11336852.v5 | Synthesis and styrene copolymerization of halogen novel ring-substituted isobutyl phenylcyanoacrylates | <p></p><p>Novel oxy ring-trisubstituted isobutyl
phenylcyanoacrylates, RPhCH=C(CN)CO<sub>2</sub>CH<sub>2</sub>CH(CH<sub>3</sub>)<sub>2</sub><sub> </sub>, where R is 5-bromo-2,4-dimethoxy, 2-bromo-3-hydroxy-4-methoxy, 3-chloro-2,6-difluoro,
4-chloro-2,6-difluoro, 2,3,5-trichloro, 2,3,6-trichloro, 2,3,4-trifluoro,
2,3,5-trifluoro, 2,4,5-trifluoro, 2,4,6-trifluoro, 3,4,5-trifluoro, 2,3,5,6-tetrafluoro,
2,3,4,5,6-pentafluoro were synthesized by the piperidine catalyzed Knoevenagel condensation of
ring-substituted benzaldehydes and isobutyl cyanoacetate and characterized by
CHN analysis, IR, <sup>1</sup>H and <sup>13</sup>C NMR. The acrylates were
copolymerized with styrene in solution with radical initiation (ABCN) at 70°C. The compositions of the copolymers were calculated
from nitrogen analysis. </p><br /><p></p> | Escalante, Gabrielle; Escalante, Victoria; Amanda A. Hartoun; Cynhia B. Hsu; Yousef A. Ibrahim; Will R. Jones; Charles Y. Jun; Madeleine M. Karpiuk; Eghe S. Obaseki; Phillip A. Osak; Jessica R. Schwartzwald; Ryan W. Sloan; Sara M. Rocus; William S. Schjerven; Gregory Kharas | Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7532df96a0052452883bb/original/synthesis-and-styrene-copolymerization-of-halogen-novel-ring-substituted-isobutyl-phenylcyanoacrylates.pdf |
60c7505b567dfe3d93ec5842 | 10.26434/chemrxiv.13022840.v1 | The Ocean’s Elevator: Evolution of the Air-Seawater Interface During a Small-Scale Algal Bloom | We explore in situ the surface properties of
marine algal blooms of diatom monocultures by utilizing surface techniques of Brewster angle
microscopy (BAM) imaging, vibrational sum frequency generation spectroscopy (SFG), and
infrared reflection absorption spectroscopy (IRRAS). Over the course of the bloom, the marine
algae produce surface-active biogenic molecules that temporally partition to the topmost interfacial
layers and are selectively probed through surface imaging and spectroscopic measurements. BAM
images show morphological structural changes and heterogeneity in the interfacial films with
increasing density of surface-active biogenic molecules. Film thickness calculations quantified
the average surface thickness over time. The image results reveal an ~5 nm thick surface region in
the late stages of the bloom which correlates to typical sea surface nanolayer thicknesses. Our surface-specific SFG spectroscopy results show significant
diminishing in the intensity of the dangling OH bond of surface water molecules consistent with
organic molecules partitioning and replacing water at the air-seawater interface as the algal bloom
progresses. Interestingly, we observe a new broad peak appear between 3500 cm<sup>-1</sup> to 3600 cm<sup>-1</sup> in
the late stages of the bloom that is attributed to weak hydrogen bonding interactions of water to
the surface-active biogenic matter. IRRAS confirms the presence of organic molecules at the
surface as we observe increasing intensity of vibrational alkyl modes and the appearance of a
proteinaceous amide band. Our work shows the often overlooked but vast potential of tracking
changes in the interfacial regime of small-scale laboratory marine algal blooms. By coupling
surface imaging and vibrational spectroscopies to complex, time-evolving, marine-relevant
systems, we provide additional insight into unraveling the temporal complexity of sea spray
aerosol compositions. | Mickey Rogers; Jennifer Neal; Ankur Saha; Abdullah Algarni; Thomas Hill; Heather Allen | Atmospheric Chemistry; Microscopy; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7505b567dfe3d93ec5842/original/the-ocean-s-elevator-evolution-of-the-air-seawater-interface-during-a-small-scale-algal-bloom.pdf |
60c74ed9702a9b633d18ba7c | 10.26434/chemrxiv.12813377.v1 | CO2 Hydrogenation to Methanol with Ga- and Zn-Doped Mesoporous Cu/SiO2 Catalysts Prepared by the Aerosol-Assisted Sol-Gel Process | The preparation of copper-based heterogeneous catalysts dedicated to the hydrogenation of CO2 to methanol typically relies on multi-step procedures carried out in batch. These steps are precisely tailored to introduce the active phase (Cu) and the promoters (e.g. zinc, gallium) onto a preformed support, to maximize catalyst performance. However, each process step – often carried out in batch – can be associated with the formation of waste and with the consumption of energy, thereby negatively impacting the environmental performance of the overall catalyst preparation procedure. Here, we propose a direct and continuous production process for the synthesis of efficient catalysts for the CO2 to methanol reaction. Gallium- and zinc-promoted mesoporous Cu-SiO2 catalysts are prepared in one step by the aerosol-assisted sol-gel process. The catalysts consist of spherical microparticles and feature high specific surface area and pore volume, with interconnected pores of about 6 nm. A strong promoting effect of Ga and Zn is highlighted, boosting the selectivity for methanol at the expense of CO. Upon calcination, we show that Cu species – initially trapped in the silica matrix – undergo a migration towards the catalyst surface and a progressive sintering. After optimization, the catalysts obtained via such direct route compete with the best catalysts reported in the literature and obtained via multi-step approaches. <br /> | Charlie Paris; Alejandro Karelovic; Raydel Manrique; Solène Le Bras; François Devred; Damien Debecker | Catalysts; Nanostructured Materials - Materials; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ed9702a9b633d18ba7c/original/co2-hydrogenation-to-methanol-with-ga-and-zn-doped-mesoporous-cu-si-o2-catalysts-prepared-by-the-aerosol-assisted-sol-gel-process.pdf |
64f8849379853bbd78390e7d | 10.26434/chemrxiv-2023-w3kpt | Optimizing Silver Nanowire Synthesis for Direct Ink Writing Applications: A Parametric Study | This work presents a parametric study for optimizing the synthesis of silver nanowires (AgNWs) using a polyol method for conductive ink applications. The effects of various parameters, including reaction time, reaction temperature, and the type of metal halide employed during synthesis, on the properties of the AgNWs are systematically investigated. The kinetics of AgNW formation are analyzed by temporal UV-Vis spectroscopy and TEM. To elaborate on the complexity of the metal halide employed during the production of silver nanowires, we have conducted various sets of experiments revealing the role of the metal in classical polyol synthesis. We have demonstrated that even though the stoichiometric ratio of Ag+/Cl- is kept constant, the type of halide source is directly related to the formation of high-yield silver nanowires. The optimized synthesis conditions are found to result in AgNWs with high aspect ratios to prepare a conductive ink with desired viscoelastic properties for direct writing applications. The AgNW ink prepared with a 4 wt.% PEO mixture can automatically level itself at the specified frequency, while the 5 wt.% solution requires an external force to spread out. The frequency sweep experiments revealed that both mixtures have a crossover point where their behavior changes. The crossover point for the 4 wt.% mixture is approximately 12 rad/s, whereas for the 5 wt.% mixture, it is 2.5 rad/s. As a result, the 5 wt.% mixture takes longer to spread out than the 4 wt.% mixture. | Elif Sümeyye Cirit; Seda Aygul Akyuz; Volkan Can; Zeliha Cansu Canbek Ozdil | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f8849379853bbd78390e7d/original/optimizing-silver-nanowire-synthesis-for-direct-ink-writing-applications-a-parametric-study.pdf |
63513b2caca198a4f6ddad83 | 10.26434/chemrxiv-2022-kxsm6-v2 | Exploiting retro oxa-Michael chemistry in polymers | One way to obtain recyclable polymeric materials is to include reversible bonds in polymers. Herein, we study the reversibility of the oxa-Michael reaction, explore its scope and limitations in simple model systems and further in linear polymers and polymer networks. Results show that for the retro oxa-Michael reactions of sulfone, acrylate or acrylonitrile based adducts elevated temperatures (> 100 °C) and Brønsted bases (e.g. KOH) are needed. Alcohols in oxa-Michael adducts can easily be exchanged within minutes. Further, oxa-Michael polymers can be depolymerized into small fragments in presence of alcohols and show self-healing characteristics in networks. | Karin Ratzenboeck; Johanna Uher; Ema Zagar; David Pahovnik; Christian Slugovc | Organic Chemistry; Polymer Science | CC BY NC 4.0 | CHEMRXIV | 2022-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63513b2caca198a4f6ddad83/original/exploiting-retro-oxa-michael-chemistry-in-polymers.pdf |
610c914a424ea388fd84122c | 10.26434/chemrxiv-2021-bwcv6-v2 | Machine Learning Dynamic Correlation in Chemical Kinetics | The kinetics of surface reactions are often described using a lattice model. Since it is expensive to propagate the configuration probabilities of the entire lattice, it is practical to consider the occupation probabilities of a typical site or a cluster of sites instead. This amounts to a moment closure approximation of the chemical master equation (CME). Unfortunately, simple closures, such as the mean-field (MF) and the pair approximation (PA), exhibit weaknesses in systems with significant long-range correlation. In this paper, we show that machine learning (ML) can be used to construct accurate moment closures in chemical kinetics, using the lattice Lotka-Volterra model (LLVM) as a model system. We trained feed-forward neural networks (FFNNs) on kinetic Monte Carlo (KMC) results at select values of rate constants and initial conditions. Given the same level of input as PA, the machine learning moment closure (MLMC) gave accurate predictions of the instantaneous three-site occupation probabilities. Solving the kinetic equations in conjunction with MLMC gave drastic improvements in the simulated dynamics and descriptions of the dynamical regimes throughout the parameter space. In this way, MLMC is a promising tool to interpolate KMC simulations or construct pre-trained closures that would enable researchers to extract useful insight at a fraction of the computational cost. | Changhae Andrew Kim; Nathan D. Ricke; Troy Van Voorhis | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610c914a424ea388fd84122c/original/machine-learning-dynamic-correlation-in-chemical-kinetics.pdf |
66e84cb951558a15ef27eb53 | 10.26434/chemrxiv-2024-43xbn | Cross-coupling reactions with nickel, visible light, and tert-butylamine as a bifunctional additive | Transition metal catalysis is crucial for the synthesis of complex molecules, with ligands and bases playing a pivotal role in optimizing cross-coupling reactions. Despite advancements in ligand design and base selection, achieving effective synergy between these components remains challenging. We present here a general approach to nickel-catalyzed photoredox reactions employing tert-butylamine as a cost-effective bifunctional additive, acting as the base and ligand. This method proves effective for C–O and C–N bond-forming reactions with a diverse array of nucleophiles, including phenols, aliphatic alcohols, anilines, sulfonamides, sulfoximines, and imines. Notably, the protocol demonstrates significant applicability in biomolecule derivatization and facilitates sequential one-pot functionalizations. Spectroscopic investigations revealed the robustness of the dynamic catalytic system, while elucidation of structure-reactivity relationships demonstrated how computed molecular properties of both the nucleophile and electrophile correlated to reaction performance, providing a foundation for effective reaction outcome prediction. | Jonas Düker; Maximilian Philipp; Thomas Lentner; Jamie Cadge; João Lavarda; Ruth Gschwind; Matthew Sigman; Indrajit Ghosh; Burkhard Koenig | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e84cb951558a15ef27eb53/original/cross-coupling-reactions-with-nickel-visible-light-and-tert-butylamine-as-a-bifunctional-additive.pdf |
67883cf9fa469535b932e2aa | 10.26434/chemrxiv-2025-7n07q | HTA - An open-source software for assigning heads and tails to SMILES in polymerization reactions | Artificial Intelligence (AI) techniques are transforming the computational discovery and design of polymers. The key enablers for polymer informatics are machine-readable molecular string representations of the building blocks of a polymer, i.e., the monomers. In monomer strings, such as SMILES, symbols at the head and tail atoms indicate the locations of bond formation during polymerization. Since the linking of monomers determines a polymer’s properties, the performance of AI prediction models will, ultimately, be limited by the accuracy of the head and tail assignments in the monomer SMILES. Considering the large number of polymer precursors available in chemical data bases, reliable methods for the automated assignment of head and tail atoms are needed. Here, we report a method for assigning head and tail atoms in monomer SMILES by analyzing the reactivity of their functional groups. In a reference data set containing 206 polymer precursors, the HeadTailAssign (HTA) algorithm has correctly predicted the polymer class of 204 monomer SMILES, representing an accuracy of 99%. The head and tail atoms were correctly assigned to 187 monomer SMILES, representing an accuracy of 91%. The HTA code is available for validation and reuse at https://github.com/IBM/HeadTailAssign | Brenda de Souza Ferrari; Ronaldo Giro; Mathias Steiner | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Inorganic Polymers; Organic Polymers; Polymer chains | CC BY 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67883cf9fa469535b932e2aa/original/hta-an-open-source-software-for-assigning-heads-and-tails-to-smiles-in-polymerization-reactions.pdf |
673796765a82cea2fa3d7a59 | 10.26434/chemrxiv-2024-c9np0 | Cooperative CO2 activation involving a mononuclear aluminum(II) intermediate | An important aspect of sustainable chemistry research is the discovery of novel chemical mechanisms by which otherwise inert molecules become activated toward useful transformations by earth’s most abundant elements. Compounds involving the most abundant metal on earth, aluminum, most commonly involve AlIII ions due to their noble gas electronic configurations. Although compounds with AlI ions have also been studied, the chemistry of AlII ions is nearly unknown and may contain undiscovered reaction manifolds. Here, we report the CO2 activation chemistry of an AlII complex supported by a chelating, dianionic ligand and investigate the electronic structure details and reaction mechanisms required to access this reactivity. We found that a heterobinuclear complex, (NON)Al- FeCp(CO)2 (1), undergoes reversible Al-Fe bond homolysis at ambient conditions to reveal the [(NON)Al]·/[CpFe(CO)2]· radical pair in situ. The presence of predominantly Al-centered spin density (i.e., an AlII ion) within this radical pair was established using experiments with radical scavengers as well as electronic structure calculations. Exposure of 1 to CO2 atmosphere resulted in insertion of CO2 into the Al-Fe bond. This net 2-electron CO2 reduction process was computationally modeled using quantum chemical calculations and direct dynamics simulations, revealing that reduction involves two 1-electron steps and, thus, depends on stabilization of high-energy [CO2]· - by coordination to aluminum. This mechanism for CO2 activation is unexpected given the canonical predisposition of CO2 for multi-electron reduction processes and demonstrates the possibility of discovering new reaction profiles of earth- abundant elements in unusual oxidation states. | Roushan Singh; Kevin Quirion; Joshua Telser; Daniel Ess; Neal Mankad | Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.); Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673796765a82cea2fa3d7a59/original/cooperative-co2-activation-involving-a-mononuclear-aluminum-ii-intermediate.pdf |
64dcbf59dfabaf06ff5dbe69 | 10.26434/chemrxiv-2023-57wf2 | Construction of Si-Stereogenic Silanols via Enantioselective Pd-Catalyzed C–H Alkenylation | The construction of silicon-stereogenic silanols via the Pd-catalyzed intermolecular C–H alkenylation with the assistance of a commercially available L-pyroglutamic acid has been realized for the first time. Employing the oxime ether as the directing group, the silicon-stereogenic silanol derivatives could be readily prepared with excellent enantioselectivities, featuring a broad substrate scope and good functional group tolerance. Mechanistic studies indicate that L-pyroglutamic acid could stabilize the Pd catalyst and provide excellent chiral induction. Preliminary computational studies unveil the origin of the enantioselectivity in the C–H bond activation step. | Jia-Hui Zhao; Jian-Ye Zou; Sheng-Ye Zhang; Yichen Wu; Peng Wang | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dcbf59dfabaf06ff5dbe69/original/construction-of-si-stereogenic-silanols-via-enantioselective-pd-catalyzed-c-h-alkenylation.pdf |
61b4cc02535d6394779931aa | 10.26434/chemrxiv-2021-9nhm1-v2 | Sanitize It Yourself: Web-based molecular sanitization for machine-generated chemical structures | Many computer-aided drug design (CADD) methods using deep learning have recently been proposed to explore the chemical space toward novel scaffolds efficiently.
However, there is a tradeoff between the ease of generating novel structures and the chemical feasibility of structural formulas.
To overcome the limitations of computational filtering, we have implemented a web-based software in which users can share and evaluate computer-generated compounds. The web service is available at https://sanitizer.chemical.space/. | Naruki Yoshikawa; Kentaro Rikimaru; Kazuki Yamamoto | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b4cc02535d6394779931aa/original/sanitize-it-yourself-web-based-molecular-sanitization-for-machine-generated-chemical-structures.pdf |
64cb817769bfb8925a48a5b2 | 10.26434/chemrxiv-2023-6whwl-v2 | Visible-Light-Driven Alkene Dicarboxylation with Formate and CO2 Under Mild Conditions | The low-cost formate salt was used as the reductant and part of the carboxyl source in a visible-light-driven dicarboxylation of diverse alkenes, including simple styrenes. The highly competing hydrocarboxylation side reaction was successfully overridden. Good yields of products were obtained under mild reactions at ambient temperature and pressure of CO2. The dual role of formate salt may stimu-late the discovery of a range of new transformations under mild and friendly conditions. | Fulin Zhang; Xiao-Yang Wu; Pan-Pan Gao; Hao Zhang; Zhu Li; Shangde Ai; Gang Li | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cb817769bfb8925a48a5b2/original/visible-light-driven-alkene-dicarboxylation-with-formate-and-co2-under-mild-conditions.pdf |
625c0ea711b146242525ad37 | 10.26434/chemrxiv-2022-nh350 | Protobiotic network reproducers are compositional attractors: enhanced probability for life’s origin | The origin of life must have involved an unlikely transition from chaotic chemistry to reproducing supramolecular structures. Previous quantitative analyses of reproducing mutually catalytic networks made of simple molecules have led to increasing popularity of this pre-RNA scenario for life’s origin. Here, we investigate in detail the reproduction characteristic of the GARD computer-simulated physicochemically rigorous lipid-based model. This model displays compatibility with heterogeneous environments, addresses the network’s spatial demarcation, and portrays trans-generational compositional information transfer. However, we find that compositionally reproducing states are extremely rare, suggesting that random roaming would be a vastly inefficient path towards reproduction. Rewardingly, further scrutiny shows that all self-reproducing states are also dynamic attractors of the catalytic network. This suggests a greatly enhanced propensity for the spontaneous emergence of reproduction and primal evolution, vastly augmenting the likelihood of protolife appearance. | Amit Kahana; Lior Segev; Doron Lancet | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2022-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625c0ea711b146242525ad37/original/protobiotic-network-reproducers-are-compositional-attractors-enhanced-probability-for-life-s-origin.pdf |
60c749164c891972efad3037 | 10.26434/chemrxiv.12024756.v1 | LOBSTER: Local Orbital Projections, Atomic Charges, and Chemical Bonding Analysis from Projector-Augmented-Wave-Based DFT | We present an update on recently developed methodology and functionality in the computer program LOBSTER (Local Orbital Basis Suite Towards Electronic-Structure Reconstruction) for chemical-bonding analysis in periodic systems. LOBSTER is based on an analytic projection from projector-augmented wave (PAW) densityfunctional theory (DFT) computations [J. Comput. Chem. 2013, 34, 2557], reconstructing chemical information in terms of local, auxiliary atomic orbitals and thereby opening the output of PAW-based DFT codes to chemical interpretation. We demonstrate how LOBSTER has been improved by taking into account time reversal symmetry, thereby speeding up the DFT and LOBSTER calculations by a factor of 2. Over the recent years, the functionalities have also been continually expanded, including accurate projected densities of states (DOS), crystal orbital Hamilton population (COHP) analysis, atomic and orbital charges, gross populations, and the recently introduced 𝒌-dependent COHP. The software is offered free-of-charge for non-commercial research. | Ryky Nelson; Christina Ertural; Janine George; Volker Deringer; Geoffroy Hautier; Richard Dronskowski | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749164c891972efad3037/original/lobster-local-orbital-projections-atomic-charges-and-chemical-bonding-analysis-from-projector-augmented-wave-based-dft.pdf |
60c73e59337d6c096ae26320 | 10.26434/chemrxiv.6958334.v1 | A Closed Loop Discovery Robot Driven by a Curiosity Algorithm Discovers Proto-Cells That Show Complex and Emergent Behaviours | <p><b>We
describe a chemical robotic discovery assistant equipped with a curiosity
algorithm (CA) that can efficiently explore a complex chemical system in search
of complex emergent phenomena exhibited by proto-cell droplets. The CA-robot is
designed to explore proto-cell formulations in an open-ended way with no
explicit discovery or optimization target. By applying the CA-robot to the
study of multicomponent oil-in-water proto-cell droplets, we discovered an
order of magnitude more instances of interesting behaviours than possible with a
random parameter search. Among them, a formulation displaying a sudden and
highly specific response to temperature was discovered. Six modes of proto-cell
droplet motion were identified and classified using a time-temperature phase diagram
and probed using a variety of techniques including NMR, which allowed the
design of a payload release system triggered by temperature. This work shows
how objective free search can lead to the discovery of useful and unexpected
properties, with real-world applications in
formulation chemistry.</b></p> | Jonathan Grizou; Laurie J. Points; Abhishek Sharma; Leroy Cronin | Interfaces; Self-Assembly; Solution Chemistry; Transport phenomena (Physical Chem.); Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e59337d6c096ae26320/original/a-closed-loop-discovery-robot-driven-by-a-curiosity-algorithm-discovers-proto-cells-that-show-complex-and-emergent-behaviours.pdf |
6661df6391aefa6ce1ed07d6 | 10.26434/chemrxiv-2024-45wll-v2 | Metal- versus Ligand-Centered Reactivity of a Cobalt-Phenylenediamide Complex with Electrophiles | A new series of [CoIII–CF3]n+ complexes supported by a bidentate redox-active ligand with is presented. The cationic [Co–CF3]+ complex was first obtained by reacting [CpCo(tBuUreaopda)] (Cp = cyclopentadienyl, opda = o-phenylenediamide) with an electrophilic trifluoromethyl source, for which the redox-active phenylenediamide ligand serves as a 2e– reservoir to generate [CpCp(tBuUreabqdi)(CF3)]+ (bqdi = benzoquinonediimine). Electrochemical studies of [Co–CF3]+ revealed two reversible 1e– reductions. Chemical reduction with 1 or 2 equiv. reducing agent enabled isolation of the neutral and anionic complexes, respectively, where the [CoIII–CF3] bond remains intact in all three oxidation states (n = +1, 0, −1). Structural analysis shows systematic changes to the redox-active ligand backbone upon reduction, consistent with sequential ligand-centered electron transfer in the series [bqdi]0 to [s-bqdi]•– to [opda]2–. In contrast, the reaction of [CpCo(tBuUreaopda)] with alkyl triflates resulted in ligand-centered alkylation at the ureayl groups instead of the targeted Co–alkyl bond formation, suggesting less favorable bond formation at cobalt and greater nucleophilic accessibility of the ligand compared to the metal center. | Minzhu Zou; Sewwandi Kuruppu; Thomas Emge; Kate Waldie | Organometallic Chemistry; Ligands (Organomet.); Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6661df6391aefa6ce1ed07d6/original/metal-versus-ligand-centered-reactivity-of-a-cobalt-phenylenediamide-complex-with-electrophiles.pdf |
66d73f93cec5d6c14204fa58 | 10.26434/chemrxiv-2024-8cfcc-v2 | Mechanism of Plasmon-Driven Molecular Jackhammers in Mechanical Opening and Disassembly of Membranes | Plasmon-driven molecular jackhammers (MJH) are a type of molecular machine that converts photon energy into mechanical energy. Upon insertion into lipid bilayers followed by near infrared light activation, plasmon-driven MJH mechanically open cellular membranes through a process that is not inhibited by reactive oxygen species (ROS) inhibitors and does not induce thermal heating. The molecular mechanism by which the plasmon-driven MJH open and disassembles cellular membranes has not hitherto been established. Here we differentiate the mechanical mechanism in MJH from the ROS-mediated chemical effects in photodynamic therapy or thermal effects in photothermal therapy. We further present a detailed molecular mechanism for the plasmon-driven MJH disassembly of lipid bilayers. The mechanical studies on plasmon-driven MJH disassembly processes on artificial lipid bilayers are done using ROS-unreactive saturated phytanoyl phospholipids. We were able to capture in real-time the lipid bilayer disassembly by MJH using fluorescence confocal microscopy on saturated phospholipids in giant unilamellar vesicles. | Ciceron Ayala-Orozco; Vardan Vardanyan; Katherine Lopez-Jaime; Zicheng Wang; Jorge Seminario; Anatoly Kolomeisky; James Tour | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d73f93cec5d6c14204fa58/original/mechanism-of-plasmon-driven-molecular-jackhammers-in-mechanical-opening-and-disassembly-of-membranes.pdf |
662f5d8e418a5379b002a2eb | 10.26434/chemrxiv-2024-5k9kg | Co(III)-Catalyzed Coupling of Enaminones with Oxadiazolones for Imidazole Synthesis | Skeleton speciation-oriented synthesis as the conventional wisdom of synthetic methodology development prioritizes skeleton as the center of attention for organic speciation, the creation of organic species with differentiated structure-defining feature. The passive as-is assembly of appendages as a secondary accessory inevitably leads to the convergence of appendage pattern on skeleton. We report herein a synthetic practice of appendage speciation-oriented synthesis, emphasizing appendages as the focal point for organic speciation. This synthetic modality seeks, proactively, the maximization of type-, position-, and configuration-variance of appendages through both in situ and ex situ appendage speciation. A Co(III) catalytic protocol in accord with this synthetic modality has been established for coupling of enaminones and oxadiazolones to imidazoles, allowing the achievement of full position-variance of appendages. This translates to expanded reaction and structural development scope and can provide a fertile ground for productive organic synthesis. | Shuaixin Fan; Weiping Wu; Yachun Su; Xuanzhen Han; Zhixin Wang; Jin Zhu | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662f5d8e418a5379b002a2eb/original/co-iii-catalyzed-coupling-of-enaminones-with-oxadiazolones-for-imidazole-synthesis.pdf |
62904a6f24011e90ef0c05e4 | 10.26434/chemrxiv-2022-4218f | Excellent room temperature catalytic activity for formaldehyde oxidation on a single-atom iron catalyst in a moist atmosphere | For human safety, efficient removal of formaldehyde in indoor environments is essential. However, removing formaldehyde from indoor environment given the temperature and moisture remains a challenge. In this study, a metal-organic framework-based single-atom iron catalyst (FeSA) is proposed as a candidate catalyst for oxidation of formaldehyde. The optimal structure between different coordination environments of FeSA was screened by density functional theory (DFT) calculation. Guided by the theoretical results, FeSA with 5 nitrogen coordination (FeSA-N5-C) was selected and prepared experimentally for evaluation. The activity tests revealed that the removal efficiency of formaldehyde reached 85.5% at 25°C and 75% relative humidity, which is not possible for traditional catalysts. More importantly, moisture boosts catalytic oxidation of formaldehyde to some extent, illustrating that FeSA-N5-C is robust for practical applications. To our knowledge, this is the first report of single-atom catalyst for catalytic oxidation of formaldehyde, opening up a new avenue for design of high activity and strongly water-resistant catalysts. | zhijian Liu; jihao Wei; guikai zhang; dewang zhang; jing zhang; weijie yang; chonghchong Wu; Gates Ian D. | Catalysis | CC BY 4.0 | CHEMRXIV | 2022-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62904a6f24011e90ef0c05e4/original/excellent-room-temperature-catalytic-activity-for-formaldehyde-oxidation-on-a-single-atom-iron-catalyst-in-a-moist-atmosphere.pdf |
6659448521291e5d1db5d909 | 10.26434/chemrxiv-2024-4wkrq | Synthesis and Reactivity of Di(9-anthly)methyl Radical | The di(9-anthryl)methyl (DAntM) radical was synthesized and investigated to elucidate its optical, electrical properties, and reactivity. The generation of the DAntM radical was confirmed by its ESR spectrum, which showed two broad signals. The unpaired electron is primarily localized on the central sp2 carbon and slightly delocalized over the two anthryl moieties. Although the DAntM radical undergoes dimerization in solution, the radical still remains even at 190 K due to the bulky nature of the two anthryl group. Interestingly, upon exposure to air, the purple color of the radical solution quickly fades to orange, resulting in decomposition to give 9-anthryl aldehyde and anthroxyl radical derivatives. | Tomohiko Nishiuchi; Kazuma Takahashi; Yuta Makihara; Takashi Kubo | Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6659448521291e5d1db5d909/original/synthesis-and-reactivity-of-di-9-anthly-methyl-radical.pdf |
60c756f70f50db4996398198 | 10.26434/chemrxiv.14347754.v1 | Magnetoelectric Coupling on the Fused Azulene Oligomers | <div><div><div><p>The global magnetic phase diagram for fused azulene oligomers is obtained by using a fermionic Hubbard Hamiltonian, a intermediate model between the molecular (Pariser-Parr-Pople empiric Hamiltonian) and spin-1/2 antiferromagnetic Heisenberg approaches. As a function of the on-site coulomb repulsion and the oligomer size we show that fused azulene transitions from a singlet (S = 0) to a higher-spin (S = 1, 2, 3) ground state. Near the quantum magnetic phase transition the electric dipole moment, present on fused azulene molecules, couples with the magnetic moment leading to a divergent magnetoelectric susceptibility at the boundary lines of the magnetic phase diagram. These spontaneous electric and magnetic polarizations, together with the magnetoelectric coupling between them, indicate that fuzed azulene molecules are potentially strong candidates for purely organic multiferroic materials.</p></div></div></div> | Alexandra Valentim; Daniel
J. Garcia; João A. Plascak | Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756f70f50db4996398198/original/magnetoelectric-coupling-on-the-fused-azulene-oligomers.pdf |
6389a7507b7c916dbfdf92ea | 10.26434/chemrxiv-2022-7sx1d-v3 | Basic principle of soft ionization mass spectrometry and development of ion source | Since the discovery of soft ionization technology represented by electrospray, the basic principle of soft ionization technology - how analyte is charged remains an unsolved mystery. In this paper, the basic principle of soft ionization technology is discussed, some summarized basic physical and chemical principles are briefly described, and its application in the development of ion source is discussed. | jiehong luo | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6389a7507b7c916dbfdf92ea/original/basic-principle-of-soft-ionization-mass-spectrometry-and-development-of-ion-source.pdf |
6504cda599918fe53703ec2c | 10.26434/chemrxiv-2023-z15zd | Introducing N-X Anomeric Amides: Powerful Electrophilic Halogenation Reagents | Electrophilic halogenation is a widely-used tool employed by medicinal chemists to either pre-functionalize molecules for further diversity or incorporate a halogen atom in drugs or drug-like compounds to solve metabolic problems or modulate off-target effects. Current methods to increase the power of halogenation rely either on the invention of new reagents or activating commercially available reagents with various additives such as Lewis/Brønsted acids, Lewis bases and hydrogen bonding activators. There is a high demand for new reagents that can halogenate otherwise unreactive compounds under mild conditions. Herein we report the invention a new class of powerful halogenating reagents based on anomeric amides, taking advantage of the energy stored in the pyramidalized nitrogen of N-X anomeric amides as a driving force. These robust halogenating methods are compatible with a variety of functional groups and heterocycles, as exemplified on over 50 compounds (including 13 gram-scale examples and 1 flow chemistry scale-up). Their high halogenating prowess is also demonstrated in other reactivity contexts. A DFT computational study supports the defining role of the anomeric amide motif. | Yu Wang; Cheng Bi; Yu Kawamata; Lauren Grant; Lacey Samp; Paul Richardson; Shasha Zhang; Kaid Harper; Maximilian Palkowitz; Aris Vasilopolous; Michael Collins; Martins Oderinde; Chet Tyrol; Doris Chen; Erik LaChapelle; Jennifer Qiao; Phil Baran | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6504cda599918fe53703ec2c/original/introducing-n-x-anomeric-amides-powerful-electrophilic-halogenation-reagents.pdf |
634a9b6186473aac91140255 | 10.26434/chemrxiv-2022-dhcdh | Copolymerization Reactivity Ratio Inference: Determining Confidence Contours in Parameter Space via a Bayesian Hierarchical Approach | Confidence contours in parameter space are a helpful tool to compare and classify determined estimators. For more intricate parameter estimations of non-linear nature or complex error structures, the procedure of determining confidence contours is a statistically complex task. For polymer chemists, such particular cases are encountered in determination of reactivity ratios in copolymerization. Hereby, determination of reactivity ratios in copolymerization requires non-linear parameter estimation.
Additionally, data may possess (possibly correlated) errors in both dependent and independent variables.
A common approach for such non-linear estimations is the error-in-variables model yielding statistically unbiased estimators. Regarding reactivity ratios, to date published procedures neglect the non-Gaussian structure of the error estimates which is a consequence of the non-linearity of the model. In this publication, this issue is addressed by employing a Bayesian hierarchical model, which correctly propagates the errors of all variables.
We detail the statistical procedure in chemist friendly language to encourage confident usage of our tool.
Our approach is based on a \texttt{Python} program requiring minimal installation effort. A detailed manual of the code is included in the appendix of this work, in an effort to make this procedure available to all interested polymer chemists. | Robert Reischke | Theoretical and Computational Chemistry; Polymer Science; Chemical Engineering and Industrial Chemistry; Polymerization kinetics; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634a9b6186473aac91140255/original/copolymerization-reactivity-ratio-inference-determining-confidence-contours-in-parameter-space-via-a-bayesian-hierarchical-approach.pdf |
6273ed5cd55550cf438e9c0a | 10.26434/chemrxiv-2022-3zrrl | Identification of Potential SARS-CoV-2 Inhibitors Using Flexible Docking Based Drug Repurposing of Antivirals | A selection of antiviral compounds from the Drug Repurposing Hub were screened as potential inhibitors against SARS-CoV-2 protein targets using CIFDock, a flexible docking method. CIFDock allows for a fully flexible active site of the protein-ligand complex and retaining of explicit water molecules throughout docking simulations. This method provides a more thorough conformational space search than is attainable by rigid docking methods, and thus a more accurate representation of the binding interactions between these antiviral compounds and the SARS-CoV-2 protein targets. Four proteins critical to viral function were selected as targets of the study: the main protease (Mpro), the papain-like protease (PLpro), the transmembrane protease (TMPRSS2), and the RNA-dependent RNA-polymerase (RdRp). The results reveal potential SARS-CoV-2 viral inhibitors from this library of antivirals, based on favorable Glide scores of the docked protein-ligand poses. The antiviral compounds brecanavir, mozenavir, palinavir, sovaprevir, and telinavir yielded excellent binding scores across all protease targets. Additionally, these particular antivirals have not yet been investigated in clinical trials nor in vitro studies regarding COVID-19. Therefore, these compounds can be recommended for further research against SARS-CoV-2, based on extensive docking analysis with relevant protein targets.
| Luke Warrensford; Amanda Pittman; Fiona Kearns; Jordan Hale; Kira Astronskas; Steven Austin; Ryan Young; Louise Allcock; Sarah Dietrick; Bill Baker; Henry Lee Woodcock | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6273ed5cd55550cf438e9c0a/original/identification-of-potential-sars-co-v-2-inhibitors-using-flexible-docking-based-drug-repurposing-of-antivirals.pdf |
60c74196842e6509c1db1ee7 | 10.26434/chemrxiv.8067554.v1 | Local Structure Order Parameters and Site Fingerprints for Quantification of Coordination Environment and Crystal Structure Similarity | Structure characterization and classification is frequently based on local environment information of all or selected atomic sites in the crystal structure. Therefore, reliable and robust procedures to find coordinated neighbors and to evaluate the resulting coordination pattern (e.g., tetrahedral, square planar) are critically important for both traditional and machine learning approaches that aim to exploit site or structure information for predicting materials properties. Here, we introduce new local structure order parameters (LoStOPs) that are specifically designed to rapidly detect rotationally symmetric (e.g., tetrahedron) as well as asymmetric local coordination environments (e.g., square pyramid). Furthermore, we introduce a Monte Carlo optimization approach to ensure that the different LoStOPs are comparable with each other. We then apply the new local environment descriptors to define site and structure fingerprints and to measure similarity between 61 known coordination environments and 40 commonly studied crystal structures, respectively. After extensive testing and optimization, we determine the most accurate structure similarity assessment procedure to compute all 2.45 billion structure similarities between each pair of the ≈ 70,000 materials that are currently present in the Materials Project database.<br /> | Nils Zimmermann; Anubhav Jain | Aggregates and Assemblies; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74196842e6509c1db1ee7/original/local-structure-order-parameters-and-site-fingerprints-for-quantification-of-coordination-environment-and-crystal-structure-similarity.pdf |
62e376ed7f3aa6012ffc2e12 | 10.26434/chemrxiv-2022-bsmdl | Predicting Highly Enantioselective Catalysts Using Tunable Fragment Descriptors | Catalyst optimization process is typically relying on an inductive and qualitative assumption of chemists based on screening data. While machine learning models using molecular properties or calculated 3D structures enable quantitative data evaluation, costly quantum chemical calculations are often required. In contrast, readily available binary fingerprint descriptors are time- and cost-efficient, but their predictive performance remains insufficient. Here, we describe a machine learning model based on fragment descriptors, which are fine-tuned for asymmetric catalysis and represent cyclic or polyaromatic hydrocarbons, enabling robust and efficient virtual screening. Using training data with only moderate selectivities, we designed theoretically and validated experimentally new catalysts showing higher selectivities in a previously unaddressed transformation. | Nobuya Tsuji; Pavel Sidorov; Chendan Zhu; Yuuya Nagata; Timur Gimadiev; Alexandre Varnek; Benjamin List | Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e376ed7f3aa6012ffc2e12/original/predicting-highly-enantioselective-catalysts-using-tunable-fragment-descriptors.pdf |
66844cd95101a2ffa830f155 | 10.26434/chemrxiv-2024-63zr5-v2 | Synergistic Photoprotection: Enhanced Stability of Vulpinic Acid through Interaction with Exocellular Polysaccharides | Lichens have been of great interest in exobiological studies due to their remarkable tolerance to ultraviolet (UV) radiation. These organisms employ extracellular pigments for screening high-energy solar radiation, allowing the photosynthetically active radiation to pass through and be utilized by the photosymbiont. These pigments are found co-occurring within polysaccharide scaffolds in the lichen cortex. Despite extensive studies on isolated lichen pigments, the potential role of exopolysaccharides (EPS) in the photoprotective system of lichens has remained unclear. We report detailed photophysical studies on the wolf lichen pigment vulpinic acid in pullulan, a polysaccharide that mimics lichen EPS. Solid phase studies demonstrate that the pigment’s photostability is greatly enhanced in the pullulan polysaccharide matrix. Analysis of ultrafast transient absorption infrared spectroscopy indicates potential interactions of the polysaccharide inhibiting the relaxation pathway of vulpinic acid upon UV photoexcitation. These polysaccharides interrupt an intramolecular proton transfer that traditionally leads to photodecomposition of the isolated vulpinic acid compound. These results suggest a crucial role of EPS in the photoprotective systems of lichens. The interaction between vulpinic acid and pullulan exemplifies a non-spectator role of polysaccharides in photoprotection, potentially contributing to the extraordinary resilience of lichens and cyanobacteria. This polysaccharide-pigment interaction may represent a general strategy among extremophiles to mitigate UV-induced damage, highlighting the importance of interdisciplinary approaches in unraveling complex biological systems. | Tanzil Mahmud; Derek Moore; Ilya Dergachev; Henry Sun; Sergey Varganov; Matthew Tucker; Christopher Jeffrey | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Biophysical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66844cd95101a2ffa830f155/original/synergistic-photoprotection-enhanced-stability-of-vulpinic-acid-through-interaction-with-exocellular-polysaccharides.pdf |
6753174ef9980725cf407b68 | 10.26434/chemrxiv-2024-0z9l6 | A new class of ligand derived from the reactions of bis(dialkylphosphino)amines and 9-diazofluorene: preparation, structure and reactivity | The reaction of tetra(isopropyl)diphosphazane (iPr-PNP) or tetraphenyldiphosphazane (Ph-PNP) with 9-diazofluorene (9-DAF) affords new chelating phosphazene ligands [F(NN)P(R)2NP(R)2(NHN)F] where F = fluorenylidene and R = iPr (1a) or Ph (1b). 1b has been shown to react with ZnEt2 and AlMe3 giving mononuclear organometallic complexes 4 and 5, respectively, while the reaction with NaH generates the chelated sodium complex 6. The complexes have been fully characterized and their solid-state structures have been authenticated using single-crystal X-ray diffraction. Complexes 4 and 5 have been used as catalysts for the ring-opening copolymerization (ROCOP) of cyclohexene oxide (CHO) and phthalic anhydride (PA). These complexes selectively gave polyesters through the ROCOP of PA and CHO in the presence of bis(triphenylphosphine)iminium chloride (PPNCl) as a nucleophilic co-catalyst, yielding moderate molar mass polyesters with narrow dispersity (e.g. Mn = 10.1 kg mol−1 and Đ = Mw/Mn = 1.25). | Matthew Laprade; Katherine Robertson; Jason Clyburne; Christopher Kozak | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.); Polymerization (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6753174ef9980725cf407b68/original/a-new-class-of-ligand-derived-from-the-reactions-of-bis-dialkylphosphino-amines-and-9-diazofluorene-preparation-structure-and-reactivity.pdf |
61ba60c77f367e357055016f | 10.26434/chemrxiv-2021-4wp0x | Mechanistic Insight into the Precursor Chemistry of ZrO2 and HfO2 Nanocrystals; towards Size-Tunable Syntheses | One can nowadays readily generate monodisperse colloidal nanocrystals, but a retrosynthetic analysis is still not possible since the underlying chemistry is often poorly understood. Here, we provide insight into the reaction mechanism of colloidal zirconia and hafnia nanocrystals synthesized from metal chloride and metal isopropoxide. We identify the active precursor species in the reaction mixture through a combination of nuclear magnetic resonance spectroscopy (NMR), density functional theory (DFT) calculations, and pair distribution function (PDF) analysis. We gain insight into the interaction of the surfactant, tri-n-octylphosphine oxide (TOPO), and the different precursors. Interestingly, we identify a peculiar X-type ligand redistribution mechanism that can be steered by the relative amount of Lewis base (L-type). We further monitor how the reaction mixture decomposes using solution NMR and gas chromatography, and we find that ZrCl4 is formed as a by-product of the reaction, limiting the reaction yield. The reaction proceeds via two competing mechanisms: E1 elimination (dominating) and SN1 substitution (minor). Using this new mechanistic insight, we adapted the synthesis to optimize the yield and gain control over nanocrystal size. These insights will allow the rational design and synthesis of complex oxide nanocrystals. | Rohan Pokratath; Dietger Van den Eynden; Susan Rudd Cooper; Jette Katja Mathiesen; Valérie Waser; Mike Devereux; Simon Billinge; Markus Meuwly; Kirsten M. Ø. Jensen; Jonathan De Roo | Physical Chemistry; Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Kinetics and Mechanism - Inorganic Reactions; Ligands (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ba60c77f367e357055016f/original/mechanistic-insight-into-the-precursor-chemistry-of-zr-o2-and-hf-o2-nanocrystals-towards-size-tunable-syntheses.pdf |
63f7c0af32cd591f126166a1 | 10.26434/chemrxiv-2023-2ng8k | Irreversible Inactivation of SARS-CoV-2 by Lectin Engagement with Two Glycan Clusters on the Spike Protein | Host cell infection by SARS-CoV-2, similar to that by HIV-1, is driven by a conformationally metastable and highly glycosylated surface entry protein complex, and infection by these viruses has been shown to be inhibited by the mannose-specific lectins Cyanovirin-N (CV-N) and Griffithsin (GRFT). We discovered in this study that CV-N and His6-tagged GRFT not only inhibit SARS-CoV-2 infection but also lead to irreversibly inactivated pseudovirus particles. The irreversibility effect was revealed by the observation that pseudoviruses first treated with either CV-N or GRFT and then washed to remove all soluble lectin did not recover infectivity. Infection inhibition of SARS-CoV-2 pseudovirus mutants with single-site glycan mutations in Spike suggested that two glycan clusters in S1 are important for both CV-N and GRFT inhibition, one cluster associated with the RBD (receptor binding domain) and the second with the S1/S2 cleavage site. We observed lectin antiviral effects with several SARS-CoV-2 pseudovirus variants, including the recently emerged omicron, as well as a fully infectious coronavirus, therein reflecting the breadth of lectin antiviral function and the potential for pan-coronavirus inactivation. Mechanistically, observations made in this work indicate that multivalent lectin interaction with S1 glycans is likely a driver of the lectin infection inhibition and irreversible inactivation effect and suggest the possibility that lectin inactivation is caused by an irreversible conformational effect on Spike. Overall, lectins' irreversible inactivation of SARS-CoV-2, taken with their breadth of function, reflects the therapeutic potential of multivalent lectins targeting the vulnerable metastable Spike before host cell encounter. | Aakansha Nangarlia; Farah Fazloon Hassen; Gabriela Canziani; Praneeta Bandi; Choya Talukder; Fengwen Zhang; Douglas Krauth; Ebony Gary; David Weiner; Paul Bieniasz; Sonia Navas-Martin; Barry O'Keefe; Charles Ang; Irwin Chaiken | Biological and Medicinal Chemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f7c0af32cd591f126166a1/original/irreversible-inactivation-of-sars-co-v-2-by-lectin-engagement-with-two-glycan-clusters-on-the-spike-protein.pdf |
60c740624c8919dde4ad210d | 10.26434/chemrxiv.7718633.v1 | Ab Initio Molecular Dynamics Simulations of the Ferroelectric-Paraelectric Phase Transition in Sodium Nitrite | This paper reports on the first <i>ab initio</i> molecular dynamics study of the ferroelectric Sodium Nitrite, shedding light on its order-disorder phase transition. The remnant polarization P<sub>r</sub> was calculated using a Mulliken population analysis and maximally localized Wannier functions. Especially the Wannier based model is in excellent agreement with experimental findings and previous Berry phase calculations. The simulations predict a ferroelectric Curie temperature T<sub>c</sub> between 400 K and 450 K in good agreement with the experimental value of 437 K. In addition, the anomalous lattice behavior (shrinking of the c-axis) during the phase transition is reproduced. The crystal field effect in the material could be quantified by investigating the molecular dipoles based on the maximally localized Wannier functions and the intermolecular charge transfer by analysing the Mulliken charges. In agreement with earlier experimental and theoretical findings, the polarization reversal mechanism was found to be dominated by a c-axis rotation of the Nitrite ions. The molecular insight into such a simple and prototypical material serves as a basis for a further development of more complex crystalline order-disorder ferroelectrics. | Johannes P. Dürholt; Rochus Schmid | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740624c8919dde4ad210d/original/ab-initio-molecular-dynamics-simulations-of-the-ferroelectric-paraelectric-phase-transition-in-sodium-nitrite.pdf |
653932a7a8b423585a2f608e | 10.26434/chemrxiv-2023-1v49c | Oligomerization of lithium ions in water-in-salt electrolytes | Water-in-salts (WiS) have recently emerged as promising electrolytes for energy storage applications, ranging from aqueous batteries to supercapacitors. Here, ab initio molecular dynamics is used to study the structure of a 21 m LiTFSI WiS. The simulation reveals a new feature, in which the lithium ions form oligomer-like nanochains that involve up to 10 ions. Despite the strong Coulombic interaction between them, the ions in the chains are found at a distance of 2.5 Angstroms. They display a drastically different solvation shell compared to the isolated ions, in which they share on average two water molecules. The nanochains have a highly transient character due to the low free energy barrier for forming/breaking them. Providing new insights into the nanostructure of WiS electrolytes, our work calls for re-evaluating our current knowledge of highly concentrated electrolytes and the impact of the modification of solvation of active species on their electrochemical performances. | Kateryna Goloviznina; Alessandra Serva; Mathieu Salanne | Physical Chemistry; Energy; Energy Storage; Physical and Chemical Properties; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653932a7a8b423585a2f608e/original/oligomerization-of-lithium-ions-in-water-in-salt-electrolytes.pdf |
65e75a0b66c13817294293d2 | 10.26434/chemrxiv-2024-knzkq-v2 | Assessing the Catalytic Role of Native Glucagon Amyloid Fibrils | Glucagon stands out as a pivotal peptide hormone, instrumental in controlling blood glucose levels and lipid metabolism. While the formation of glucagon amyloid fibrils has been documented, their biological functions remain enigmatic. Recently, we demonstrated experimentally that glucagon amyloid fibrils can act as catalysts in several biological reactions, including esterolysis, lipid hydrolysis, and dephosphorylation. Herein we present a multiscale quantum mechanics/molecular mechanics (QM/MM) simulation of the acylation step in the esterolysis of para-nitrophenyl acetate (p-NPA), catalyzed by native glucagon amyloid fibrils, serving as a model system to elucidate their catalytic function. This step entails a concerted mechanism, involving proton transfer from serine to histidine, followed by the nucleophilic attack of serine oxy anion on the carbonyl carbon of p-NPA. We computed the binding energy and free-energy profiles of this reaction using the PDLD/S-LRA-2000 and the empirical valence bond (EVB) methods. This included simulations if the reaction in an aqueous environment and in the fibril, enabling us to estimate the catalytic effect of the fibril. Our calculations obtained a barrier of 23.4 kcal∙mol–1 for the enzyme-catalyzed reaction, compared to the experimental value of 21.9 kcal∙mol–1 (and a calculated catalytic effect of 3.2 kcal∙mol–1 compared to the observed effect of 4.7 kcal∙mol–1) This close agreement together with the barrier reduction when transitioning from the reference solution reaction to the amyloid fibrils provides supporting evidence to the catalytic role of glucagon amyloid fibrils. Moreover, by employing the PDLD/S-LRA-2000 approach further reinforced exclusively the enzyme's catalytic role. The results presented in this study contribute significantly to our understanding of the catalytic role of glucagon amyloid fibrils, marking, to the best of our knowledge, the first mechanistic investigation of fibrils using QM/MM methods. Therefore, our findings offer fruitful insights for future research on the mechanisms of related amyloid catalysis. | Ashim Nandi; Aoxuan Zhang; Elad Arad; Raz Jelinek; Arieh Warshel | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Biophysics; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e75a0b66c13817294293d2/original/assessing-the-catalytic-role-of-native-glucagon-amyloid-fibrils.pdf |
65d4207566c138172905efcc | 10.26434/chemrxiv-2024-m8m60-v2 | Rational design of metal-organic cages to increase the number of components via dihedral angle control | The general principles of discrete, large self-assemblies composed of numerous components are not unveiled and the artificial formation of such entities is a challenging topic. In metal-organic cages, design strategies for tuning the coordination directions in multitopic ligands by the bend and twist angles were previously developed to solve this problem. In this study, the importance of remote geometric communications between components is emphasized, realizing several types of metal-organic assemblies based on dihedral angle control in multitopic ligands although they have the same coordination directions. Self-assembly of a tritopic ligand with dihedral angles θ = 36° and a cis-protected Pd(II) ion afforded M9L6 and M12L8 cages as kinetic and thermodynamic products, respectively, whereas an M12L8 sheet was formed when θ = 90°. Geometric analyses of strains in the subcomponent rings revealed that remote geometric communications among neighboring multitopic ligands through coordination bonds are key for large assemblies. | Tsukasa Abe; Keisuke Takeuchi; Shuichi Hiraoka | Inorganic Chemistry; Supramolecular Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d4207566c138172905efcc/original/rational-design-of-metal-organic-cages-to-increase-the-number-of-components-via-dihedral-angle-control.pdf |
6421264e647e3dca999010ac | 10.26434/chemrxiv-2023-17v42 | Energetic and Kinetic Origin of CALB Interfacial Activation Revealed by PaCS-MD/MSM | Conformational dynamics of Candida antarctica Lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), the Markov state model (MSM), and mainly focused on the lid-opening motion closely related to substrate binding. All-atom MD simulation of CALB was conducted in water and that around the interface constructed by water and tricaprylin. CALB initially situated in water and separated by layers of water from the interface is spontaneously adsorbed onto the tricaprylin surface during MD simulation. The opening and closing motions of the lid are simulated by PaCS-MD and subsequent MSM analysis provided the free energy landscape and time scale of the conformational transitions among the closed, semi-open, and open states. The closed state is the most stable in the water system but the stable conformation in the interface system shifts to the semi-open state. In the interface system, the transition probability to the open state is higher than in the water system. These effects could explain the energetics and kinetics origin of previously reported interfacial activation of CALB. We also suggest two types of mechanisms for substrate binding in which small and hydrophilic substrates bind without interfacial activation while large and bulky substrates bind via interfacial activation. These findings could help expand the application of CALB towards a wide variety of substrates. | Tegar Wijaya; Akio Kitao | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6421264e647e3dca999010ac/original/energetic-and-kinetic-origin-of-calb-interfacial-activation-revealed-by-pa-cs-md-msm.pdf |
616d452bf718df10cce2815e | 10.26434/chemrxiv-2021-208vk | An eight-state molecular sequential switch
featuring a dual single-bond rotation photoreaction
| Typical photowitches interconvert between two different states by simple isomerization reactions, which represents a fundamental limit for applications. To expand the switching capacity usually different photoswitches have to be linked together leading to strong increase in molecular weight, diminished switching function, and less precision and selectivity of switching events. Herein we present an approach for solving this essential problem with a different photoswitching concept. A basic molecular switch architecture provides precision photoswitching between eight different states via controlled rotations around three adjacent covalent bonds. All eight states can be populated one after another in an eight-step cycle by alternating between photochemical Hula-Twist isomerizations and thermal single bond rotations. By simply changing solvent and temperature the same switch can also undergo a different cycle instead interconverting just five isomers in a selective sequence. This behavior is enabled through the discovery of an unprecedented photoreaction, a one photon dual single bond rotation. | Aaron Gerwien; Benjamin Jehle; Marvin Irmler; Peter Mayer; Henry Dube | Physical Chemistry; Organic Chemistry; Nanoscience; Photochemistry (Org.); Physical Organic Chemistry; Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616d452bf718df10cce2815e/original/an-eight-state-molecular-sequential-switch-featuring-a-dual-single-bond-rotation-photoreaction.pdf |
60c753204c89190c84ad426f | 10.26434/chemrxiv.13388042.v1 | Extended Nucleation and Superfocusing in Colloidal Semiconductor Nanocrystal Synthesis | The hot injection synthesis of colloidal semiconductor nanocrystals is renowned for producing nanocolloids with superb size dispersions. Burst nucleation and diffusion-controlled size focusing during growth have been invoked to rationalize this characteristic, yet experimental evidence supporting the pertinence of these concepts is scant. Using a well-established CdSe synthesis followed with in situ X-ray scattering, we show that nucleation is an extended event that overlaps with growth and can last for 15-20% of the reaction time. Moreover, we find that size focusing outpaces predictions of diffusion-limited growth. This observation supports the conclusion that nanocrystal growth is dictated by the surface reactivity, which drops sharply for larger nanocrystals. Kinetic reaction simulations demonstrate this so-called superfocusing can lengthen the nucleation period and promote size-focusing. The finding that narrow size dispersions can emerge from the counteracting effects of extended nucleation and reaction-limited size focusing ushers in an evidence-based perspective that turns hot injection into a rational scheme to produce monodisperse nanocolloids. | P. Tim Prins; Federico Montanarella; Kim Dümbgen; Yolanda Justo; Johanna C. van der Bok; Stijn Hinterding; Jaco Geuchies; Jorick Maes; Kim De Nolf; Sander Deelen; Hans Meijer; Thomas Zinn; Andrei Petukhov; Freddy Rabouw; Celso de Mello Donega; Daniel Vanmaekelbergh; Zeger Hens | Nanostructured Materials - Materials; Optical Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Chemical Kinetics; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753204c89190c84ad426f/original/extended-nucleation-and-superfocusing-in-colloidal-semiconductor-nanocrystal-synthesis.pdf |
60c7596f9abda2d940f8eae5 | 10.26434/chemrxiv.14696595.v1 | Inside the Black Box: A Physical Basis for the Effectiveness of Deep Generative Models of Amorphous Materials | <p>We have recently demonstrated an effective protocol for the simulation of amorphous molecular configurations using the PixelCNN generative model (J. Phys. Chem. Lett. 2020, 11, 20, 8532). The morphological sampling of amorphous materials via such an autoregressive generation protocol sidesteps the high computational costs associated with simulating amorphous materials at scale, enabling practically unlimited structural sampling based on only small-scale experimental or computational training samples. An important question raised but not rigorously addressed in that report was whether this machine learning approach could be considered a physical simulation in the conventional sense. Here we answer this question by detailing the inner workings of the underlying algorithm that we refer to as the Morphological Autoregression Protocol or MAP. <br /></p> | Michael Kilgour; Lena Simine | Aggregates and Assemblies; Dyes and Chromophores; Thin Films; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7596f9abda2d940f8eae5/original/inside-the-black-box-a-physical-basis-for-the-effectiveness-of-deep-generative-models-of-amorphous-materials.pdf |
60c74861f96a00a39628706b | 10.26434/chemrxiv.11901513.v1 | Biocompatible Direct Deposition of Functionalized Nanoparticles using Shrinking Surface Plasmonic Bubble | <p>Functionalized nanoparticles (NPs) are the
foundation of diverse applications, such as photonics, composites, energy
conversion, and especially biosensors. In many biosensing applications, concentrating
the higher density of NPs in the smaller spot without deteriorating
biofunctions is usually an inevitable step to improve the detection limit,
which remains to be a challenge. In this work, we demonstrate biocompatible
deposition of functionalized NPs to an optically transparent surface using
shrinking surface plasmonic bubbles. Leveraging the shrinking bubble can enable
to mitigate any potential biomolecules degradation by strong photothermal
effect, which has been a big obstacle of bridging plasmonic bubbles with
biomolecules. The deposited NPs are closely packed in a micro-sized spot (as
small as 3 μm), and the functional molecules are able to survive the process as
verified by their strong fluorescence signals. We elucidate that the contracting
contact line of the shrinking bubble forces the NPs captured by the contact
line to a highly concentrated island. Such a shrinking surface bubble
deposition (SSBD) is low temperature in nature as no heat is added during the
process. Using a hairpin DNA-functionalized gold NP suspension as a model
system, SSBD is shown to enable much stronger fluorescence signal compared to
the optical pressure deposition and the conventional steady thermal bubble
contact line deposition. The demonstrated SSBD technique capable of directly depositing
functionalized NPs may benefit a wide range of applications, such as the
manufacturing of multiplex biosensors.</p> | Seunghyun Moon; Qiushi Zhang; Dezhao Huang; Satyajyoti Senapati; Hsueh-Chia Chang; Eungkyu Lee; Tengfei Luo | Biocompatible Materials; Plasmonic and Photonic Structures and Devices; Sensors; Bioengineering and Biotechnology; Fluid Mechanics; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74861f96a00a39628706b/original/biocompatible-direct-deposition-of-functionalized-nanoparticles-using-shrinking-surface-plasmonic-bubble.pdf |
60c757bdbdbb89f799a3ac6e | 10.26434/chemrxiv.14455983.v1 | Actinide Arene-Metalates: Ion Pairing Effects on the Electronic Structure of Unsupported Uranium-Arene Sandwich Complexes | Chatt reaction methods were employed to synthesize the first well characterized actinide-arene sandwich complexes. Namely, addition of [UI<sub>2</sub>(THF)<sub>3</sub>(μ-OMe)]<sub>2</sub>⸱THF (<b>2⸱THF</b>) to THF solutions containing 6 equiv. of K[C<sub>14</sub>H<sub>10</sub>] generates the dimeric complexes [K(18-crown-6)(THF)<sub>2</sub>]<sub>2</sub>[U(η<sup>6</sup>-C<sub>14</sub>H<sub>10</sub>)(η<sup>4</sup>-C<sub>14</sub>H<sub>10</sub>)(μ-OMe)]<sub>2</sub>⸱4THF (<b>118C6</b>⸱4THF) and {[K(THF)<sub>3</sub>][U(η<sup>6</sup>-C<sub>14</sub>H<sub>10</sub>)(η<sup>4</sup>-C<sub>14</sub>H<sub>10</sub>)(μ-OMe)]}<sub>2</sub> (<b>1THF</b>) upon crystallization of the products in THF in the presence or absence of 18-crown-6, respectively. Both <b>118C6</b>⸱4THF and <b>1THF</b> are thermally stable in the solid-state at room temperature; however, after crystallization, they become insoluble in THF or DME solutions and instead gradually decompose upon standing. X-ray diffraction analysis reveals <b>118C6</b>⸱4THF and <b>1THF</b> to be structurally similar, possessing uranium centers sandwiched between anthracene ligands of mixed tetrahapto and hexahapto ligation modes. Yet, the two complexes are distinguished by the close contact potassium-arene ion pairing that is seen in <b>1THF</b> but absent in <b>118C6</b>⸱4THF, which is observed to have a significant effect on the electronic characteristics of the two complexes. Structural analysis, SQUID magnetometry data, XANES spectral characterization, and computational analyses are generally consistent with U(IV) formal assignments for the metal centers in both <b>118C6</b>⸱4THF and 1THF, though noticeable differences are detected between the two species. For instance, the effective magnetic moment of <b>1THF</b> (3.74 µB) is significantly lower than that of <b>118C6</b>⸱4THF (4.40 µB) at 300 K. Furthermore, the XANES data shows the U LIII-edge absorption energy for 1THF to be 0.9 eV higher than that of <b>118C6</b>⸱4THF, suggestive of more oxidized metal centers in the former. Of note, CASSCF calculations on the model complex {[U(η<sup>6</sup>-C<sub>14</sub>H<sub>10</sub>)(η<sup>4</sup>-C<sub>14</sub>H<sub>10</sub>)(μ-OMe)]<sub>2</sub>}<sup>2-</sup> (<b>1*</b>) shows highly polarized uranium-arene interactions defined by π-type bonds where the metal contributions are primarily comprised by the 6d-orbitals (7.3± 0.6%) with minor participation from the 5f-orbitals (1.5 ± 0.5%). These unique complexes provide new insights into actinide-arene bonding interactions and show the sensitivity of the electronic structures of the uranium atoms to coordination sphere effects.<br /> | Jesse Murillo; Rina Bhowmick; Katie
L. M. Harriman; Alejandra Gomez-Torres; Joshua Wright; Robert W. Meulenberg; Pere Miro Ramirez; Alejandro
J. Metta-Magaña; Muralee Murugesu; Bess Vlaisavljevich; Skye Fortier | Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757bdbdbb89f799a3ac6e/original/actinide-arene-metalates-ion-pairing-effects-on-the-electronic-structure-of-unsupported-uranium-arene-sandwich-complexes.pdf |
67c9a47681d2151a02527f9d | 10.26434/chemrxiv-2025-8bj28 | Development of a Transferable Density FunctionalTight Binding Model for Organic Molecules at the Water/Platinum Interface | A computationally efficient and transferable approach for modeling reactions at metal/water interfaces could significantly accelerate our understanding and ultimately development of new catalytic transformations, particularly in the context of the emerging field of biomass conversion. Here, we present a parametrization of Pt-X (X = H, O, C) density functional tight-binding (DFTB) for addressing this need. We firstly constructed Pt-H, Pt-O, and Pt-C repulsive potential splines. These pair-wise parameters were then augmented to include many-body interactions using the Chebyshev Interaction Model for Efficient Simulation (ChIMES). We compare the geometrical and energetic performances of both DFTB and DFTB/ChIMES methods to DFT reference data across a variety of organic molecules at platinum surface from nanoparticles to single-crystal surfaces. DFTB shows limited transferability between extended crystal surfaces to small nanoparticles. This transferability is significantly improved through the introduction of three-body interactions with Pt in DFTB/ChIMES, which provides consistent results across the various systems, with reductions in the RMSD from around 30 kcal/mol in DFTB to around 10 kcal/mol. We demonstrate the stability and reliability of the obtained parameters by performing metadynamics simulations for the adsorption of phenol on Pt(111). We observe that DFTB itself is undersolvating the surface, leading to only one or two chemisorbed water molecule in a c(4x6) unit cell. In contrast, DFTB/ChIMES leads to a coverage of about 0.5 ML and successfully captures the chemisorbed mode of phenol both at the solid/liquid and the solid/gas interface. Furthermore, in agreement with experimental measurements, the adsorption energy at the solid/liquid interface is significantly smaller compared to the solid/gas interface. Furthermore, we highlight that even with DFTB, where we can accumulate dynamics for more than 1 ns for a given system, the simulations are not fully converged. | Qing Wang; Mingjun Gu; Carine Michel; Nir Goldman; Thomas Niehaus; Stephan N. Steinmann | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c9a47681d2151a02527f9d/original/development-of-a-transferable-density-functional-tight-binding-model-for-organic-molecules-at-the-water-platinum-interface.pdf |
65a7e07a9138d2316121d6a7 | 10.26434/chemrxiv-2023-f38b5-v2 | Graphormer-IR: Graph Transformers Predict Experimental IR Spectra Using Highly Specialized Attention | Given that Infrared (IR) spectroscopy is a crucial tool in various chemical and forensic domains, improved in silico methods for predicting experimental spectra are needed due to the time and accuracy limitations of ab initio methods. We employ Graphormer, a graph neural network (GNN) transformer, to predict IR spectra using only Simplified Molecular-Input Line-Entry System (SMILES) strings. Our dataset includes 53,528 high-quality spectra with elements H, C, N, O, F, Si, S, P, Cl, Br, and I in five phases. When using only atomic numbers for node encodings, Graphormer-IR achieved mean test Spectral Information Similarity (SIS_μ) of 0.8449±0.0012 (n=5), surpassing the state-of-the-art Chemprop-IR (SIS_μ = 0.8409 ± 0.0014, n=5), with only 36% of the encoded information. Augmenting node embeddings with additional node-level descriptors in learned embeddings generated through a multi-layer perceptron improves scores to SIS_μ = 0.8523±0.0006, a total improvement of 19.7σ. These improved scores show how Graphormer-IR excels in capturing long-range interactions like hydrogen bonding, anharmonic peak positions in experimental spectra, and stretching frequencies of uncommon functional groups. Scaling our architecture to 210 attention heads demonstrates specialist-like behavior for distinct IR frequencies that improves model performance. Our model utilizes novel architectures, including a global node for phase encoding, learned node feature embeddings, and a 1D smoothing CNN. Graphormer-IR’s innovations underscore its value over traditional message-passing neural networks (MPNNs) due to its expressive embeddings and ability to capture long-range intra-molecular relationships. | Cailum Stienstra; Liam Hebert; Patrick Thomas; Alexander Haack; Jason Guo; Scott Hopkins | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a7e07a9138d2316121d6a7/original/graphormer-ir-graph-transformers-predict-experimental-ir-spectra-using-highly-specialized-attention.pdf |
64ed9d6079853bbd78a73fb0 | 10.26434/chemrxiv-2023-27t53 | Machine Learning for Analysis of Experimental Scattering and Spectroscopy Data in Materials Chemistry | The rapid growth of materials chemistry data, driven by advancements in large-scale radiation facilities as well as laboratory instruments, has outpaced conventional data analysis and modelling methods, which can require enormous manual effort. To address this bottleneck, we investigate the application of supervised and unsupervised machine learning (ML) techniques for scattering and spectroscopy data analysis in materials chemistry research. Our perspective focuses on ML applications in powder diffraction (PD), pair distribution function (PDF), small-angle scattering (SAS), inelastic neutron scattering (INS), and X-ray absorption spectroscopy (XAS) data, but the lessons that we learn are generally applicable across materials chemistry. We review the ability of ML to efficiently and accurately identify physical and structural models and extract information from experimental data. Furthermore, we discuss the challenges associated with supervised ML and highlight how unsupervised ML can mitigate these limitations, thus enhancing experimental materials chemistry data analysis. Our perspective emphasises the transformative potential of ML in materials chemistry characterisation and identifies promising directions for future applications. The perspective aims to guide newcomers to ML-based experimental data analysis, alerting them to the potential pitfalls and offering guidance for success. | Andy S. Anker; Keith T. Butler; Raghavendra Selvan; Kirsten Marie Ørnsbjerg Jensen | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ed9d6079853bbd78a73fb0/original/machine-learning-for-analysis-of-experimental-scattering-and-spectroscopy-data-in-materials-chemistry.pdf |
64a2de7c9ea64cc16760297e | 10.26434/chemrxiv-2023-nshlt | Stepwise Tuning the Mechanical Flexibility of 1D Coordination Polymer Single Crystals | Mechanically flexible coordination polymers (CPs) represent new directions for advanced materials design. We herein report unprecedented complexity in the design of isostructural mechanically flexible CPs, with elastic, plastic, and delaminating properties. Ab initio simulations show how these properties can be rationalised by analysis of the simulated elastic tensor. | Biswajit Bhattacharya; Adam Michalchuk; Dorothee Silbernagel; Heinz Sturm; Franziska Emmerling | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a2de7c9ea64cc16760297e/original/stepwise-tuning-the-mechanical-flexibility-of-1d-coordination-polymer-single-crystals.pdf |
65aa944166c1381729d1b501 | 10.26434/chemrxiv-2024-lmx75 | Electronic structure orientation as a map of in-plane antiferroelectricity in beta'- Indium(III) Selenide | Antiferroelectric (AFE) materials are excellent candidates for sensors, capacitors, and data storage due to their electrical switchability and high-energy storage capacity. However, imaging the nanoscale landscape of AFE domains is notoriously inaccessible, which has hindered development and intentional tuning of AFE materials. Here, we demonstrate that polarization-dependent photoemission electron microscopy (PD-PEEM) can resolve the arrangement and orientation of in-plane AFE domains on the nanoscale, despite the absence of a net lattice polarization. Through direct determination of electronic transition orientations and analysis of domain boundary constraints, we establish that antiferroelectricity in beta'-In2Se3 is a robust property from the nanometer to the 10s µm scale, confirming beta'-In2Se3 is an excellent candidate for applications requiring control of AFE polarization. Ultimately, the understanding of nanoscale AFE domain organization presented here opens the door to new investigations in the influence of domain formation and orientation on charge transport and dynamics. | Joseph L. Spellberg; Lina Kodaimati; Prakriti P. Joshi; Nasim Mirzajani; Liangbo Liang; Sarah B. King | Physical Chemistry; Materials Science; Nanostructured Materials - Materials; Spectroscopy (Physical Chem.); Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aa944166c1381729d1b501/original/electronic-structure-orientation-as-a-map-of-in-plane-antiferroelectricity-in-beta-indium-iii-selenide.pdf |
66228b5b91aefa6ce1e8c7af | 10.26434/chemrxiv-2024-q01kl | Room Temperature Formate Ester Transfer Hydrogenation Enables an Electrochemical-Thermal Organometallic Cascade for Methanol Syn-thesis from CO2 | The reduction of CO2 to synthetic fuels is at the core of energy storage efforts. However, the formation of energy-dense liquid fuels such as methanol remains a major challenge, particularly under low temperature and pressure conditions that can be coupled to renewable electricity sources via electrochemistry. A multicatalyst system pairing an electrocatalyst with a thermal organometallic catalyst is introduced here, enabling the room temperature reduction of 1 atmosphere of CO2 to methanol. The reaction sequence involves: (i) the reduction of CO2 to formate by the electrocatalyst [Cp*Ir(bpy)Cl]+ (bpy = 2,2’-bipyridine), (ii) Fischer esterification of formate to isopropyl formate catalyzed by trifluoromethanesulfonic acid (HOTf), and (iii) thermal transfer hydrogenation of isopropyl formate to methanol facilitated by the organometallic catalyst (H-PNP)Ir(H)3 (H-PNP = bis[(2-diisopropyl-phosphino]ethyl)amine). Reaction development led to mutually compatible conditions for a one-pot CO2 reduction in isopropanol electrolyte at ambient temperature and 1 atmosphere CO2. The isopropanol solvent plays sever-al crucial roles: activating formate ion as isopropyl formate, donating hydrogen for the reduction of formate ester to methanol via transfer hydrogenation, and lowering the barrier for transfer hydrogenation through hydrogen bonding interactions. In addition to reporting a method for room temperature reduction of challenging ester substrates, this work provides a proto-type for pairing electrochemical and thermal organometallic reactions that can guide the design and development of multi-catalyst cascades. | Sergio Fernández; Eric Assaf; Shahbaz Ahmad; Benjamin Travis; Julia Curley; Nilay Hazari; Mehmed Ertem; Alexander Miller | Catalysis; Organometallic Chemistry; Energy; Electrocatalysis; Homogeneous Catalysis; Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66228b5b91aefa6ce1e8c7af/original/room-temperature-formate-ester-transfer-hydrogenation-enables-an-electrochemical-thermal-organometallic-cascade-for-methanol-syn-thesis-from-co2.pdf |
60c741850f50db13f8395b0d | 10.26434/chemrxiv.8059625.v1 | Neither Solid Nor Liquid Nor Vapor: Hydrogen Bonding Structure of Water Confined in Metal-Organic Frameworks with Open Metal Sites | <div>
<div>
<div>
<p>Water in confinement exhibits properties significantly different from bulk water due to
frustration in the hydrogen-bond network induced by interactions with the substrate. Here, we
combine infrared spectroscopy and advanced molecular dynamics simulations to probe the
structure of confined water as a function of relative humidity within a metal-organic framework
containing cylindrical pores lined with an ordered array of cobalt open coordination sites.
Building upon the quantitative agreement between experimental and theoretical spectra, we
demonstrate that water at low relative humidity initially binds to the open metal sites and
subsequently forms disconnected one-dimensional chains of hydrogen-bonded water molecules
bridging between the cobalt sites. Upon further increase in relative humidity, these water chains
nucleate pore filling, with water molecules occupying the entire pore interior before the relative
humidity reaches 30%. Systematic analysis of the rotational and translational dynamics indicates
heterogeneity in this pore-confined water, with water molecules displaying distinct levels of
mobility as a function of the distance from the pore surface.
</p>
</div>
</div>
</div> | Adam Rieth; Kelly M. Hunter; Mircea Dinca; Paesani Lab | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Interfaces; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Statistical Mechanics; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741850f50db13f8395b0d/original/neither-solid-nor-liquid-nor-vapor-hydrogen-bonding-structure-of-water-confined-in-metal-organic-frameworks-with-open-metal-sites.pdf |
60c754c1842e6578c3db41fb | 10.26434/chemrxiv.12846836.v3 | Ensemble Generalized Kohn-Sham Theory: The Good, the Bad, and the Ugly | Two important extensions of Kohn-Sham (KS) theory are generalized KS theory and ensemble KS theory. The former allows for non-multiplicative potential operators and greatly facilitates practical calculations with advanced, orbital-dependent functionals. The latter allows for quantum ensembles and enables the treatment of, e.g., open systems and excited states. Here, we combine the two extensions, both formally and practically, first via an exact yet complicated formalism, then via a computationally tractable variant that involves a controlled approximation of ensemble "ghost interactions" by means of an iterative algorithm. The resulting formalism is illustrated using selected examples. This opens the door to the application of generalized KS theory in more challenging quantum scenarios and to the improvement of ensemble theories for the purpose of practical and accurate calculations.<br /><br /> | Tim Gould; Leeor Kronik | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754c1842e6578c3db41fb/original/ensemble-generalized-kohn-sham-theory-the-good-the-bad-and-the-ugly.pdf |
6451f0d527fccdb3ea68780a | 10.26434/chemrxiv-2022-4ppf0-v2 | Nucleation of Co and Ru Precursors on Silicon with Different Surface Terminations: Impact on Nucleation Delay | The early transition metals Ruthenium (Ru) and Cobalt (Co) are of high interest as replacements for Cu in next generation interconnects. Plasma-enhanced atomic layer deposition (PE-ALD) is used to deposit metal thin films in high-aspect ratio structures of vias and trenches in nanoelectronic devices. At the initial stage of deposition, the surface reactions between the precursors and the starting substrate are vital to understand nucleation of the film and optimize the deposition process through minimising so-called nucleation delay in which film growth is only observed after tens to hundreds of ALD cycles. The reported incubation period (or nucleation delay) of Ru ranges from 10 ALD cycles to 500 ALD cycles and the growth-per-cycle (GPC) varies from report to report. No systematic studies on nucleation day of Co PE-ALD were found in the literature. In this study, we use first principles density functional theory (DFT) simulations to investigate the reactions between the precursors RuCp2 and CoCp2 with Si substrates that have different surface terminations to reveal the atomic scale reaction mechanism at the initial stages of metal nucleation. The substrates include (1) H:Si(100), (2) NHx-terminated Si(100), (3) H:SiNx/Si(100). Ligand exchange reaction via H transfer to form CpH on H:Si(100), NHx-terminated Si(100) and H:SiNx/Si(100) surfaces is simulated and shows that pre-treatment with N2/H2 plasma to yield an NHx-terminated Si surface from H:Si(100) can promote the ligand exchange reaction to eliminate Cp ligand for CoCp2. Our DFT results show that the surface reactivity of CoCp2 is highly dependent on substrate surface terminations, which explains why the reported incubation period and GPC vary from report to report. This difference in reactivity at different surface terminations may be useful for selective deposition. For Ru deposition, RuCp2 is not a useful precursor, showing highly endothermic ligand elimination reactions on all studied terminations. | Ji Liu; Rita Mullins; Hongliang Lu; David Wei Zhang; Michael Nolan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6451f0d527fccdb3ea68780a/original/nucleation-of-co-and-ru-precursors-on-silicon-with-different-surface-terminations-impact-on-nucleation-delay.pdf |
60c74b104c891910f5ad3388 | 10.26434/chemrxiv.12276464.v1 | Reversible Electrochemical Ion Intercalation at an Electrified Liquid|liquid Interface Functionalised with Porphyrin Nanostructures | <p><a>Ion
intercalation into solid matrices influences the performance of key components
in most energy storage devices (Li-ion batteries, supercapacitors, fuel cells, <i>etc.</i>).
Electrochemical methods provide key information on the thermodynamics and
kinetics of these ion transfer processes but are restricted to matrices supported
on electronically conductive substrates. In this article, the electrified liquid|liquid
interface is introduced as an ideal platform to probe the thermodynamics and
kinetics of reversible ion intercalation with non-electronically active
matrices. Zinc(II) meso-tetrakis(4-carboxyphenyl)porphyrins were self-assembled
into floating films of ordered nanostructures at the water|</a>a,a,a-trifluorotoluene interface.
Electrochemically polarising the aqueous phase negatively with respect to the
organic phase lead to organic ammonium cations intercalating into the zinc
porphyrin nanostructures by binding to anionic carboxyl sites and displacing
protons through ion exchange at neutral carboxyl sites. The cyclic
voltammograms suggested a positive cooperativity mechanism for ion
intercalation linked with structural rearrangements of the porphyrins within
the nanostructures, and were modelled using a Frumkin isotherm. The model also
provided a robust understanding of the dependence of the voltammetry on the pH
and organic electrolyte concentration. Kinetic analysis was performed using
potential step chronoamperometry, with the current transients composed of
“adsorption” and nucleation components. The latter
were associated with domains within the nanostructures where, due to structural rearrangments, ion binding and exchange
took place faster. This work opens opportunities to study the thermodynamics
and kinetics of <i>purely ionic</i> ion intercalation reactions (not induced by
redox reactions) in floating solid matrices using any desired electrochemical
method.</p> | Andrés F. Molina-Osorio; José A. Manzanares; Alonso Gamero-Quijano; Micheal D. Scanlon | Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Self-Assembly; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b104c891910f5ad3388/original/reversible-electrochemical-ion-intercalation-at-an-electrified-liquid-liquid-interface-functionalised-with-porphyrin-nanostructures.pdf |
661eb84e21291e5d1df885c8 | 10.26434/chemrxiv-2024-jwscm | Synthesis, characterization and photophysical properties of a new family of rare-earth cluster-based metal–organic frameworks | In this work, nine new rare-earth metal–organic frameworks (RE-MOFs, where RE = Lu(III), Yb(III), Tm(III), Er(III), Ho(III), Dy(III), Tb(III), Gd(III), and Eu(III)) isostructural to Zr-MOF-808 are synthesized, characterized, and studied regarding their photophysical properties. Materials with high crystallinity and surface area are obtained from a reproducible synthetic procedure that involves the use of two fluorinated modulators. At the same time, these new RE-MOFs display tunable photoluminescent properties due to efficient linker-to-metal energy transfer promoted by the antenna effect, resulting in a series of RE-MOFs displaying lanthanoid-based emissions spanning the visible and near-infrared regions of the electromagnetic spectrum. | Hudson A. Bicalho; Christopher Copeman; Helliomar P. Barbosa; P. Rafael Donnarumma; Zoey Davis; Victor Quezada-Novoa; Jose de J. Velazquez Garcia; Eva Hemmer; Ashlee J. Howarth | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661eb84e21291e5d1df885c8/original/synthesis-characterization-and-photophysical-properties-of-a-new-family-of-rare-earth-cluster-based-metal-organic-frameworks.pdf |
65aa1c5f9138d2316143514a | 10.26434/chemrxiv-2024-ks8ps | Organocatalytic hydration of activated alkynes | Hydration reactions consist of the introduction of a molecule of water into a chemical compound. This process is a particularly useful method to allow, for instance, the conversion of alkynes into carbonyls, which are strategic intermediates in the synthesis of a plethora of compounds. Herein we demonstrate that L-cysteine can catalyse the hydration of activated alkynes in a very effective and fully regioselective manner to access β-ketosulfones, amides and esters in aqueous conditions. The mild reaction conditions facilitated the integration with enzyme catalysis to access chiral β-hydroxy sulfones from the corresponding alkynes in a one-pot cascade process in good yields and excellent enantiomeric excess. These findings pave the way towards establishing a general method for metal-free, cost-effective, and more sustainable alkyne hydration processes | Jorge González-Rodríguez; Sergio González-Granda; Ivan Lavandera; Vicente Gotor-Fernández; Juan Mangas-Sanchez | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Biocatalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aa1c5f9138d2316143514a/original/organocatalytic-hydration-of-activated-alkynes.pdf |
67d8670d6dde43c90825798e | 10.26434/chemrxiv-2024-kkwwg-v4 | Adapted DFTB3 repulsive potentials reach DFT accuracy for hydride transfer reactions in enzymes | Enzymatic hydride transfer reactions play a crucial role in numerous metabolic pathways, yet their accurate computational modeling remains challenging due to the trade-off between accuracy and computational efficiency. Ideally, molecular dynamics simulations should sample all enzyme configurations along the reaction path using post Hartree-Fock or DFT QM/MM electrostatic embedding methods, but these are computationally expensive. Here, we introduce a simple approach to improve the third-order density functional tight binding (DFTB3) semi-empirical method to model hydride transfer reactions in enzymes. We identified deficiencies in DFTB3's description of the potential energy surface for the hydride transfer step in Crotonyl-CoA Carboxylase/Reductase (Ccr) and developed a systematic methodology to address these limitations. Our approach involves modifying DFTB3's repulsive potential functions using linear combinations of harmonic functions, guided by analysis of C-H and C-C distance distributions along the reaction path. The optimized DFTB3 Hamiltonian significantly improved the description of the hydride transfer reaction in Ccr, reproducing the reference DFT activation barrier within 0.1 kcal/mol. We also addressed the transferability of our method by applying it to another hydride transfer reaction bearing the 1,4-dihydropyridine motif but exhibiting distinct structural features of the reactant, as well as the hydride transfer reaction in Dihydrofolate Reductase (DHFR). In both cases our adapted DFTB3 Hamiltonian correctly reproduced the DFT reference and experimentally observed activation barriers. The low computational cost and transferability of our method will enable more accurate and efficient QM/MM molecular dynamics simulations of hydride transfer reactions, potentially accelerating research in enzyme engineering and drug design. | José Luís Velázquez-Libera; Rodrigo Recabarren; David Adrian Saez; Carlos Castillo; J. Javier Ruiz-Pernía; Iñaki Tuñón; Esteban Vöhringer-Martinez | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d8670d6dde43c90825798e/original/adapted-dftb3-repulsive-potentials-reach-dft-accuracy-for-hydride-transfer-reactions-in-enzymes.pdf |
624b4b96855ee53cdee21e12 | 10.26434/chemrxiv-2022-2g6m6 | Discovery of an orally bioavailable and selective PKMYT1 inhibitor RP-6306 | PKMYT1 is an important regulator of CDK1 phosphorylation and is a compelling therapeutic target for the treatment of certain types of DNA damage response cancers due to its established synthetic lethal relationship with CCNE1 amplification. To date, no selective inhibitors have been reported for this kinase that would allow for investigation of the pharmacological role of PKMYT1 in the treatment of cancer. To address this need we conducted a focused screening effort that identified compound 1 as a weak PKMYT1 inhibitor. Introduction of a dimethylphenol dramatically increased potency on PKMYT1. These dimethylphenol analogs were found to exist as Type III atropisomers that could be separated and profiled as single enantiomers. Structure-based drug design aided by co-crystal structures of several analogs enabled optimization of cell-based potency and kinase selectivity. Parallel optimization of ADME properties led to the identification of potent and selective inhibitors of PKMYT1 with favorable pharmacokinetics. RP-6306 inhibits the phosphorylation of CDK1 Thr14 in vivo in tumor tissue and inhibits CCNE1-amplified tumor cell growth in several preclinical xenograft models. The first-in-class clinical candidate RP-6306 is currently being evaluated in Phase 1 clinical trials (NCT04855656) for treatment of various solid tumors. | Janek Szychowski; Robert Papp; Evelyne Dietrich; Bingcan Liu; Frederic Valee; Marie-Eve Leclaire; Jimmy Fourtounis; Giovanni Martino; Alexander Perryman; Victor Pau; Shou Yun Yin; Pavel Mader; Anne Roulston; Jean-Francois Truchon; Gary Marshall; Mohamed Diallo; Nicole Duffy; Rino Stocco; Claude Godbout; Alexanne Bonneau-Fortin; Rosie Kryczka; Vivek Bhaskaran; Daniel Mao; Patrick Beaulieu; Pascal Turcotte; Stephen Orlicky; Igor Kurinov; Frank Sicheri; Yael Mamane; Michel Gallant; Cameron Black | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624b4b96855ee53cdee21e12/original/discovery-of-an-orally-bioavailable-and-selective-pkmyt1-inhibitor-rp-6306.pdf |
60c744babdbb896793a388ae | 10.26434/chemrxiv.9894224.v1 | Adsorption Isotherm Predictions for Multiple Molecules in MOFs Using the Same Deep Learning Model | <div>Tailoring the structure and chemistry of metal-organic frameworks (MOFs) enables the manipulation of their adsorption properties to suit specific energy and environmental applications. As there are millions of possible MOFs (with tens of thousands already synthesized), molecular simulation, such as grand canonical Monte Carlo (GCMC), has frequently been used to rapidly evaluate the adsorption performance of a large set of MOFs. This allows subsequent experiments to focus only on a small subset of the most promising MOFs. In many instances, however, even molecular simulation becomes prohibitively time consuming, underscoring the need for alternative screening methods, such as machine learning, to precede molecular simulation efforts. In this study, as a proof of concept, we trained a neural network as the first example of a machine learning model capable of predicting full adsorption isotherms of different molecules not included in the training of the model. To achieve this, we trained our neural network only on alchemical species, represented only by their geometry and force field parameters, and used this neural network to predict the loadings of real adsorbates. We focused on predicting room temperature adsorption of small (one- and two-atom) molecules relevant to chemical separations. Namely, argon, krypton, xenon, methane, ethane, and nitrogen. However, we also observed surprisingly promising predictions for more complex molecules, whose properties are outside the range spanned by the alchemical adsorbates. Prediction accuracies suitable for large-scale screening were achieved using simple MOF (e.g. geometric properties and chemical moieties), and adsorbate (e.g. forcefield parameters and geometry) descriptors. Our results illustrate a new philosophy of training that opens the path towards development of machine learning models that can predict the adsorption loading of any new adsorbate at any new operating conditions in any new MOF.</div> | Ryther Anderson; Achay Biong; Diego Gómez-Gualdrón | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744babdbb896793a388ae/original/adsorption-isotherm-predictions-for-multiple-molecules-in-mo-fs-using-the-same-deep-learning-model.pdf |
67de20fa81d2151a02634b1a | 10.26434/chemrxiv-2025-k9m48-v2 | Computational Simulations to Predict the Inhibitor Against Organic Anion Transporters 1 To Modulate Drug Concentration in Blood | Organic anion transporters (OAT1) are proteins that are located in the kidney and are responsible for excretion of metabolic byproducts, toxins, and drugs from the blood. Inhibiting these transporters can help in regulating the drug concentrations in the bloodstream. Recently, two separate studies have elucidated the 3D structure of OAT1 using cryogenic electron microscopy. These structures will be helpful in understanding the OAT1 drug binding and releasing mechanism. This in turn will help in designing drugs that can control the OAT1 functioning and help in controlling the drug concentration in blood. We hypothesize that the OAT1 should have a specific drug binding site where the drug can bind and cease or slower its functioning. In the current work, we have utilized molecular docking simulations to predict the inhibitors that can bind to the OAT1 substrate binding site. Ligand binding to this site will competitively inhibit the substrate, thereby inhibiting OAT1 function. A total of 5000 chemical compounds (ligands) were downloaded from the Zinc20 database for docking simulations. Based on the docking score, top five ligands were selected for further analysis. These ligands formed strong interactions with the protein, as analyzed using the PLIP web server. In addition, the ligand showed drug likeliness properties, a measure of their potential as drugs. Further analysis is required to investigate the dynamics and organic anion transport mechanism of this protein. In summary, computational tools were used to predict the OAT1 protein, offering potential for modulating drug concentrations in blood. | Sunehri Nog; Gaurav Sharma | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67de20fa81d2151a02634b1a/original/computational-simulations-to-predict-the-inhibitor-against-organic-anion-transporters-1-to-modulate-drug-concentration-in-blood.pdf |
60c74ffebdbb89a936a39e64 | 10.26434/chemrxiv.12977597.v1 | Theoretical Insights into the Effect of Halogenated Substituent on the Electronic Structure and Spectroscopic Properties of the Favipiravir Tautomeric Forms and Its Implications on the Treatment of COVID-19 | <p>In this study, we systematically investigated the electronic
structure, spectroscopic (nuclear magnetic resonance, infrared, Raman, electron
ionization mass spectrometry, UV-Vis, circular dichroism, and emission)
properties, and tautomerism of halogenated favipiravir compounds (fluorine,
chlorine, and bromine) from a computational perspective. Additionally, the
effects of hydration on the proton transfer mechanism of the tautomeric forms
of the halogenated favipiravir compounds are discussed. Our results suggest
that spectroscopic properties allow for the elucidation of such tautomeric
forms. As is well-known, the favipiravir compound has excellent antiviral
properties and hence was recently tested for the treatment of new coronavirus
(SARS-CoV-2). Through in silico modeling, in the current study, we evaluate the
role of such tautomeric forms in order to consider the effect of
drug-metabolism into the inhibition process of the main protease (M<sup>pro</sup>)
and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 virus. These findings
clearly indicated that all title compounds are better as RNA-inhibiting.</p> | Letícia Assis; Alexandre A. de Castro; João Paulo A. de Jesus; Teodorico Ramalho; Felipe La Porta | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ffebdbb89a936a39e64/original/theoretical-insights-into-the-effect-of-halogenated-substituent-on-the-electronic-structure-and-spectroscopic-properties-of-the-favipiravir-tautomeric-forms-and-its-implications-on-the-treatment-of-covid-19.pdf |
60c748e09abda21755f8cb24 | 10.26434/chemrxiv.11993460.v1 | Investigating the Melting Behaviour of Polymorphic Zeolitic Imidazolate Frameworks | <p>Recently, there has been growing interest in the amorphous states of metal–organic frameworks (MOFs). Particular focus has been given to melt-quenched MOF glasses. In this work, to improve our understanding of the factors influencing melting, the thermal response of four closely related zeolitic imidazolate frameworks (ZIFs) was studied. Electron withdrawing ligands were found to lower both the melting and glass transition temperatures, providing a promising strategy for improving the processability of MOFs in the liquid state. Crucially, dense frameworks appear to be essential for melting, with their presence also initiating the melting of open pore frameworks. This opens up the rich polymorphic landscape of ZIFs to the preparation of novel MOF liquids and glasses.</p> | Alice Bumstead; Maria Laura Rios Gomez; Michael Thorne; Adam Sapnik; Louis Longley; Joshua M. Tuffnell; Dean Keeble; David
A. Keen; Thomas Bennett | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748e09abda21755f8cb24/original/investigating-the-melting-behaviour-of-polymorphic-zeolitic-imidazolate-frameworks.pdf |
60c757c00f50db576839830b | 10.26434/chemrxiv.14458653.v1 | Synthesis of a Highly Aromatic and Planar [10]Annulene | As the next neutral structure following Hückels rule, a planar and aromatic [10]annulene is ideal to study the link between ring size and aromaticity. However, the puckered geometry of the parent [10]annulene suggests that the aromatic stabilization energy is not sufficient to overcome the ring strain that exists when the system is forced into planarity. It has been shown computationally that this ring strain can be alleviated through the addition of two or more cyclopropane rings to the periphery, thereby creating theoretically aromatic structures. An alternative strategy to eliminating the issue of ring strain was demonstrated experimentally with the successful preparation of the highly aromatic 1,6-didehydro[10]annulene. However, the system rapidly cyclizes at -40°C to a naphthalene diradical due to the close proximity of the in-plane p-orbitals present in the system. Here we show that cyclopropanating one side of the unstable annulene successfully prevents the destabilizing cross-ring interaction while maintaining a highly aromatic structure. Remarkably, the formed [10]annulene is bench stable and can be stored for extended periods of time.<br /> | Karnjit Parmar; Christa S. Blaquiere; Brianna Lukan; Sydnie Gengler; Michel Gravel | Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757c00f50db576839830b/original/synthesis-of-a-highly-aromatic-and-planar-10-annulene.pdf |
6628cbe5418a5379b0932908 | 10.26434/chemrxiv-2024-zstrb | Analogies and differences in the photoactivation mechanism of bathy and canonical bacteriophytochromes revealed by multiscale modeling | Bacteriophytochromes are light-sensing biological machines that interconvert between two spectroscopically distinct states, Pr and Pfr. The relative stability of the two states is opposite in canonical and bathy bacteriophytochromes but in both cases the switch between them is triggered by a photoisomerization of an embedded bilin chromophore, the effects of which propagate throughout the protein with different timescales. Here, we applied an integrated multiscale strategy of (QM/)MM molecular dynamics simulations and excited-state QM/MM nonadiabatic dynamics with enhanced sampling techniques to the Agrobacterium fabrum bathy phytochrome and compared the results with those obtained for the canonical phytochrome Deinococcus radiodurans. Contrary to what recently suggested, we found that the photoactivation of both phytochromes is directly triggered by the same photoisomerization process involving an hula-twist motion. However, only in the bathy phytochrome the photoproduct evolves into a heterogeneous and dynamic intermediate, Lumi-F, in which the bilin has reached the final (Pr) configurational state. Moreover, the protein pocket of the bathy phytochrome responds in a microsecond timescale, by reorienting several aminoacidic residues and causing the spine to tilt. | Giacomo Salvadori; Benedetta Mennucci | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6628cbe5418a5379b0932908/original/analogies-and-differences-in-the-photoactivation-mechanism-of-bathy-and-canonical-bacteriophytochromes-revealed-by-multiscale-modeling.pdf |
61457781a7b2492f812ef10b | 10.26434/chemrxiv-2021-mkfdj | Photophysical property and optical nonlinearity of cyclo[18]carbon (C18) precursors, C18-(CO)n (n = 2, 4, and 6): Focusing on the effect of carbonyl (-CO) groups | Considering their remarkable chemical stability, the precursors of cyclo[18]carbon (C18), C18-(CO)n (n = 2, 4, and 6), have more practical significance than the elusive C18 ring. In the present paper, the electronic spectrum and (hyper)polarizability of the C18-(CO)n (n = 2, 4, and 6) are studied by theoretical calculations and analyses for revealing the utility of introduction of carbonyl (-CO) groups on molecular optical properties. The analysis results show that the successive introduction of -CO groups leads to red-shift of the absorption spectrum, but maximum absorption of all molecules is mainly due to the charge redistribution caused by electron transition within C18 ring. Except for the vanishing first hyperpolarizability of C18-(CO)6 results from its octupolar character, the (hyper)polarizabilities of the precursors present an ascending trend with the increase of -CO groups in the molecule, and the higher-order response properties are more sensitive to the number of -CO groups. By means of (hyper)polarizability density analysis and (hyper)polarizability contribution decomposition, the fundamental reasons for the difference of (hyper)polarizability of different molecules were systematically discussed from the perspectives of physical and structural origins, respectively. As to the frequency dispersions under the incident light, the significant optical resonances were found on the hyperpolarizability of molecules C18-(CO)n (n = 2, 4, and 6), which contrast with the fact that it has inconspicuous influences on molecular polarizability. | Xia Wang; Zeyu Liu; Xiufen Yan; Tian Lu; Haowei Wang; Weiwei Xiong | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61457781a7b2492f812ef10b/original/photophysical-property-and-optical-nonlinearity-of-cyclo-18-carbon-c18-precursors-c18-co-n-n-2-4-and-6-focusing-on-the-effect-of-carbonyl-co-groups.pdf |
60c74a27337d6c8544e27816 | 10.26434/chemrxiv.12154812.v1 | Enhancing Photovoltages at p-Type Semiconductors Through a Redox-active Metal-Organic Framework Surface Coating | <p>Metal-organic frameworks (MOFs) interfaced with
visible-light-absorbing semiconductors offer a novel approach to improve
photoelectrochemical performances. When tested under 1-sun illumination, a
naphthalene diimide (NDI)-based monolayer immobilized at p-type Si(111)
undergoes two sequential one-electron reductions close to their thermodynamic potentials.
No photovoltage is observed until the NDI monolayer is expanded in three
dimensions in a PIZOF-type Zr(NDI) MOF (PIZOF = porous interpenetrated
zirconium organic framework). The surface-grown MOF thin film promotes photo-induced
charge separation and electron transfer across the interface and through the
film, resulting in reduction of the molecular linkers at formal potentials
>300 mV positive of their thermodynamic potentials. The apparent diffusion
coefficient is similar to that measured at a conductive electrode (10<sup>-10</sup>
cm<sup>2</sup> s<sup>-1</sup>), indicating that the observed photocurrent is
governed by charge diffusion through the Zr(NDI) MOF film. The charges
accumulated in the NDI-based MOF can be extracted by an external electron
acceptor, demonstrating sufficient conductivity throughout the MOF film to power
reductive transformations. When grown on GaP(100), the potentials of the NDI reductions
in the MOF film are shifted anodically by >700 mV compared to those of the
same MOF on conductive substrates. This photovoltage, among the highest
reported for GaP in photoelectrochemical applications, illustrates the power of
MOF thin films to improve photocathodic performance. </p> | Anna Beiler; Brian McCarthy; Ben A Johnson; Sascha Ott | Coating Materials; Hybrid Organic-Inorganic Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a27337d6c8544e27816/original/enhancing-photovoltages-at-p-type-semiconductors-through-a-redox-active-metal-organic-framework-surface-coating.pdf |
66f534aa12ff75c3a185aaf9 | 10.26434/chemrxiv-2024-z0sws | Chalcophilic Interactions: Rhenium-Sulfido and -Dithiolato Corroles | The high-temperature (~180 °C) interaction of free-base meso-triarylcorroles and Re2(CO)10 followed by exposure to PCl3 and thiols (or elemental sulfur) affords rhenium-sulfido corroles in 67-76% yields. The use of shorter reaction times, lower temperatures (~130 °C), and a dithiol (e.g., ethane-1,2-dithiol) also allows the isolation of rhenium-dithiolato corroles, presumptive intermediates on the path to ReS corroles. The ReS corroles exhibit high thermal stability and two reversible oxidations and reductions in their cyclic voltammograms, with redox potentials nearly identical to those observed for analogous ReO corroles. The electrochemical HOMO-LUMO gaps of the complexes, at 2.2 eV, are consistent with ligand-centered oxidation and reduction. The UV-vis spectra of the ReS complexes, on the other hand, differ significantly from those of their ReO counterparts. Scalar-relativistic DFT calculations suggest that this difference reflects low-energy LUMO+2 and LUMO+3 levels, consisting of Re-S π-antibonding interactions; the ReO corroles, in contrast, exhibit a larger LUMO+1/LUMO+2 gap, as expected for a relatively classical Gouterman-type metalloporphyrin analogue. The high stability of ReS corroles is consistent with geochemists’ view of rhenium as a moderately chalcophilic element (i.e., one that partitions into sulfide melts) as well as with a recent quantitative analysis of thiophilicity, which indicates that rhenium’s oxophilicity and thiophilicity are pretty much evenly balanced. | Abraham Alemayehu; Nicholas Settineri; Arianna Lanza; Abhik Ghosh | Theoretical and Computational Chemistry; Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry; Coordination Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f534aa12ff75c3a185aaf9/original/chalcophilic-interactions-rhenium-sulfido-and-dithiolato-corroles.pdf |
66d1278120ac769e5f4eb3e5 | 10.26434/chemrxiv-2024-8h389 | Determination of major chemical constituents and antimicrobial activities of essential oils extracted from Nonsaleable Grade (NSG) spices of Cymbopogon nardus, Rosmarinus officinalis, Thymus vulgaris and Coriandrum sativum seeds | Four non-saleable grade (NSG) plant spices, including Cymbopogon nardus (citronella), Rosmarinus officinalis (rosemary), Thymus vulgaris (thyme), and Coriandrum sativum (coriander) seeds were extracted using hydro-distillation. The chemical compositions of essential oils were analyzed using gas chromatography coupled with mass spectrometry (GC-MS) and the antimicrobial activities were tested to against the microbes of Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Candida albicans (C. albicans). Four essential oils are corresponding to the main functional substances of citronellal (29.562%), 1, 8- Cineole (62.267%), thymol (42.579%), and linalool (76.512%). Both the chemical constituents and antimicrobial activity of NSG essential oils were similar to both commercial products and those reported in previous studies, some of NSG essential oils even present better antimicrobial activity than commercial ones. This new approach of using NSG spices can help to reduce agricultural waste and increase the revenue of spice farmers. | Siying LIU; Lingcheng Su; Chiu-Hong Lee; Jiajun Chen; Huada Daniel Ruan | Analytical Chemistry; Agriculture and Food Chemistry; Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d1278120ac769e5f4eb3e5/original/determination-of-major-chemical-constituents-and-antimicrobial-activities-of-essential-oils-extracted-from-nonsaleable-grade-nsg-spices-of-cymbopogon-nardus-rosmarinus-officinalis-thymus-vulgaris-and-coriandrum-sativum-seeds.pdf |
60c75727bb8c1a3f1f3dc774 | 10.26434/chemrxiv.14374493.v1 | Establishing Design Principles for Emissive Organic SWIR Chromophores from Energy Gap Laws | Rational design of bright near and shortwave infrared
(NIR: 700–1000 SWIR: 1000–2000 nm) molecular and nanoscale emitters is a
fundamental scientific question with applications ranging from deep tissue
imaging to new photonic materials. However, all reported organic chromophores
with energy gaps in the SWIR have very low quantum yields. Is this the result
of a fundamental limit for the quantum yield of organic chromophores in the
SWIR? Here we combine experiment and theory to derive an energy gap quantum
yield master equation (EQME), which describes the fundamental limits in SWIR
quantum yields for organic chromophores in terms of energy gap laws for
radiative and nonradiative decay. We parametrize EQME using experimental data
from time-correlated single photon counting in the SWIR acquired using
superconducting nanowire single photon detectors operating beyond the bandgap
of silicon. Evaluating the photophysics of 21 polymethine NIR/SWIR emissive
chromophores, we explain the precipitous decline of<sub> </sub>
past 900 nm
as the result of decreased radiative rates and increased nonradiative deactivation
via high frequency vibrations as a function of singlet energy gap. From EQME we
can compare quantum yields among NIR/SWIR chromophores while accounting for
changes in energy gaps. We find that electron donating character on polymethine
heterocycles results in improvements of radiative parameters obscured by a
simultaneous redshift. We correlate this improvement to changes in transition
dipole moments across the chromenylium polymethine family. Finally, understanding
energy gap laws reveals quantitative estimates of the effect of deuteration and
molecular aggregation as strategies to increase
in the
SWIR. We experimentally demonstrate that partial deuteration of the chromophore
Flav7 results in decreased nonradiative rates and concomitant increases in
quantum yield. These insights will enable optimal chromophore designs for SWIR
fluorescence. | Hannah Friedman; Emily Cosco; Timothy Atallah; Shang Jia; Ellen Sletten; Justin Caram | Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75727bb8c1a3f1f3dc774/original/establishing-design-principles-for-emissive-organic-swir-chromophores-from-energy-gap-laws.pdf |
6405cb5acc600523a3bd0282 | 10.26434/chemrxiv-2023-2t34g | Molecular basis of the substrate specificity of the Pd-PTE phosphotriesterase: a combined QM/MM MD and electron density study | The increase of organophosphorus compounds, pesticides and flame-retardants, in wastes is an emerging ecological problem. Bacterial phosphotriesterases are capable for hydrolysis of some of them. We utilize modern molecular modeling tools to study hydrolysis mechanism of organophosphorus compounds with different leaving groups by phosphotriesterase from Pseudomonas diminuta (Pd-PTE). We compute Gibbs energy profiles for enzymes with different cations in the active site: native Zn2+ cations; Co2+ cations that increase the steady-state rate constant. A high-spin state of the cobalt-containing active site catalyzes hydrolysis. Reaction happens with two elementary steps via formation of the pentacoordinated intermediate. For substrates with good leaving groups the reaction proceeds with low energy barriers with both Zn2+ and Co2+ cations in the active site, thus the product release is likely to be a limiting step. For substrates with poor leaving groups, reaction products are destabilized relative to the ES complex that suppresses the reaction. Electron density and geometry analysis of the QM/MM MD trajectories of the intermediate states with all considered compounds allow us to discriminate substrates by their ability to be hydrolyzed by the Pd-PTE. These criteria is can be utilized to predict whether novel organophosphorus compounds can be hydrolyzed by the Pd-PTE. | Tatiana Mulashkina; Anna Kulakova; Alexander Nemukhin; Maria Khrenova | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6405cb5acc600523a3bd0282/original/molecular-basis-of-the-substrate-specificity-of-the-pd-pte-phosphotriesterase-a-combined-qm-mm-md-and-electron-density-study.pdf |
60c7401a702a9b23e418a001 | 10.26434/chemrxiv.7604642.v1 | Controlled Growth of Imine-Linked Two-Dimensional Covalent Organic Framework Nanoparticles | Covalent organic frameworks (COFs) consist of monomers arranged in predictable structures with emergent properties. However, improved crystallinity, porosity, and solution processability remain major challenges. To this end, colloidal COF nanoparticles are useful for mechanistic studies of nucleation and growth and enable advanced spectroscopy and solution processing of thin films. Here we present a general approach to synthesize imine-linked 2D COF nanoparticles and control their size by favoring imine polymerization while preventing the nucleation of new particles. The method yields uniform, crystalline, and high-surface-area particles and is applicable to several imine-linked COFs. In situ X-ray scattering experiments reveal the nucleation of amorphous polymers, which crystallize via imine exchange processes during and after particle growth, consistent with previous mechanistic studies of imine-linked COF powders. The separation of particle formation and growth processes offers control of particle size and may enable further improvements in crystallinity in the future. | Rebecca Li; Nathan C. Flanders; Austin Evans; Woojung Ji; Ioannina Castano; Lin Chen; Nathan Gianneschi; William Dichtel | Nanostructured Materials - Materials; Organic Polymers; Polymerization kinetics; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7401a702a9b23e418a001/original/controlled-growth-of-imine-linked-two-dimensional-covalent-organic-framework-nanoparticles.pdf |
674ef2045a82cea2fad43533 | 10.26434/chemrxiv-2024-z5487 | Microscopic Artificial Intelligence: An Artificial Intelligence Research Roadmap for Molecules, Materials and Proteins | The rapid progress in Artificial Intelligence (AI) has led to extraordinary achievements across various domains, significantly impacting every aspect of daily life. This advancement is also revolutionizing research in numerous scientific areas, particularly within bioinformatics, chemistry, pharmaceuticals, and materials science. In this article, we define these interdisciplinary efforts as Microscopic Artificial Intelligence (MicroAI), which focuses on understanding and generating the structures of microscopic particles such as molecules and proteins. However, the specific AI-related challenges and trends in this field remain somewhat unclear. This article briefly explains these challenges and treads from an AI perspective. | Hehe Fan; Yi Yang | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674ef2045a82cea2fad43533/original/microscopic-artificial-intelligence-an-artificial-intelligence-research-roadmap-for-molecules-materials-and-proteins.pdf |
60c74f09bdbb8977b3a39cc8 | 10.26434/chemrxiv.12436079.v2 | Chemical Robotics Enabled Exploration of Stability and Photoluminescent Behavior in Multicomponent Hybrid Perovskites via Machine Learning | <p></p><p>Hybrid organic-inorganic perovskites have
attracted immense interest as a promising material for a variety of optoelectronic
and sensing applications. However, issues regarding long-term stability have emerged
as the key bottleneck for applications and still require further study. Here, we
develop automated experimental workflow based on combinatorial synthesis and
rapid throughput characterization to explore long-term stability of these
materials in ambient conditions, and apply it to four model perovskite systems:
<a></a><a>MA<i><sub>x</sub></i>FA<i><sub>y</sub></i>Cs<sub>1-<i>x</i>-<i>y</i></sub>PbBr<sub>3</sub>,
MA<i><sub>x</sub></i>FA<i><sub>y</sub></i>Cs<sub>1-<i>x</i>-<i>y</i></sub>PbI<sub>3</sub>,
Cs<i><sub>x</sub></i>FA<i><sub>y</sub></i>MA<sub>1-<i>x</i>-<i>y</i></sub>Pb(Br<i><sub>x</sub></i><sub>+<i>y</i></sub>I<sub>1-<i>x</i>-<i>y</i></sub>)<sub>3</sub>
and Cs<i><sub>x</sub></i>MA<i><sub>y</sub></i>FA<sub>1-<i>x</i>-<i>y</i></sub>Pb(I<i><sub>x</sub></i><sub>+<i>y</i></sub>Br<sub>1-<i>x</i>-<i>y</i></sub>)<sub>3</sub></a>. We have both established a new
workflow and found out the main tendencies in the mixed cation and anion
systems, which led to the discovery of non-trivial composition regions with
high stability. The Non-negative Matrix Factorization and Gaussian
Process regression are used <i>to</i> <i>interpolate the photoluminescent
behavior of vast compositional space</i> and <i>to study the overall behavior
of the phase diagram</i>. This interpolative regression analysis helps to
distinguish mixtures that form solid solutions from those that segregate into
multiple materials, pointing out the most stable regions of the phase diagram. We find the
stability dependence on composition to be extremely non-uniform within the
composition space, suggesting the presence of potential preferential
compositional regions. <a>This proposed workflow is
universal and can be applied to other perovskite systems and
solution-processable materials. </a>Furthermore, incorporation of experimental
optimization methods, e.g., those based on Gaussian Processes, will enable the
transition from combinatorial synthesis to guide materials research and
optimization.</p><p></p> | Kate Higgins; Sai Mani Valleti; Maxim Ziatdinov; Sergei Kalinin; Mahshid Ahmadi | Hybrid Organic-Inorganic Materials; Machine Learning; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f09bdbb8977b3a39cc8/original/chemical-robotics-enabled-exploration-of-stability-and-photoluminescent-behavior-in-multicomponent-hybrid-perovskites-via-machine-learning.pdf |
60c749e3ee301cf2e8c79b56 | 10.26434/chemrxiv.12121896.v1 | Fouling Is the Beginning: Upcycling Biopolymer-Fouled Substrates for Fabricating High-Permeance Thin-Film Composite Polyamide Membranes | Commercial polymeric membranes are generally recognized to have low sustainability as membranes need to be replaced and abandoned after reaching the end of their life. At present, only techniques for downcycling end-of-life high-pressure membranes are available. For the first time, this study paves the way for upcycling fouled/end-of-life low-pressure membranes to fabricate new high-pressure membranes for water purification, forming a closed eco-loop of membrane recycling with significantly improved sustainability. | Ruobin Dai; Hongyi Han; Tianlin Wang; Jiayi Li; Chuyang Y. Tang; Zhiwei Wang | Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749e3ee301cf2e8c79b56/original/fouling-is-the-beginning-upcycling-biopolymer-fouled-substrates-for-fabricating-high-permeance-thin-film-composite-polyamide-membranes.pdf |
620d8aa2bd05a053ee09bae9 | 10.26434/chemrxiv-2022-5w90f-v3 | FTICR Mass spectrometry imaging at extreme mass resolving power using a dynamically harmonized ICR cell with 1ω or 2ω detection | MALDI mass spectrometry imaging (MALDI MSI) is a powerful analytical method providing the 2D localization of compounds from thin sections of typically but not exclusively biological samples. The dynamically harmonized ICR cell (ParaCell©) was recently introduced to achieve extreme spectral resolution capable to provide the isotopic fine structure of ions detected in complex samples. The latest improvement in ICR technology also includes 2ω detection which significantly reduces the transient time while preserving the nominal mass resolving power of the ICR cell. High-resolution MS images acquired on FT-ICR instruments equipped with 7T and 9.4T superconducting magnets and the dynamically harmonized ICR cell operating at suboptimal parameters, suffered severely from the pixel-to-pixel shifting of m/z peaks due to space-charge effects. The resulting profile average mass spectra have depreciated mass measurement accuracy and mass resolving power under the instrument specifications that affect the confidence level of the identified ions. Here we propose an analytical workflow based on the monitoring of the Total Ion Current to restrain the pixel-to-pixel m/z shift. Adjustment of the laser parameters is proposed to maintain high spectral resolution and mass accuracy measurement within the instrument specifications during MSI analyses. The optimized method has been successfully employed in replicates to perform high-quality MALDI MS images at resolving power (FWHM) above 1,000,000 in the lipid mass range across the whole image for superconducting magnets of 7T and 9.4T using 1 and 2ω detection. Our data also compare favorably with MALDI MSI experiments performed on higher magnetic field superconducting magnets, including the 21T MALDI FT-ICR prototype instrument of the NHMFL group at Tallahassee, Florida. | Mathieu Tiquet; Raphaël La Rocca; Stefan Kirnbauer; Samuele Zoratto; Daan van Kruining; Loïc Quinton; Gauthier Eppe; Pilar Martinez-Martinez; Martina Marchetti-Deschmann; Edwin De Pauw; Johann Far | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620d8aa2bd05a053ee09bae9/original/fticr-mass-spectrometry-imaging-at-extreme-mass-resolving-power-using-a-dynamically-harmonized-icr-cell-with-1-or-2-detection.pdf |
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