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67b1e78a81d2151a02b673b7 | 10.26434/chemrxiv-2025-g32fr | Synthesis of CsPbBr₃ Decorated ZIF-8 Nanocomposite for Enhanced Photocatalytic Performance | CsPbBr₃ (CPB) perovskite nanocrystals (NCs) have attracted considerable interest due to their outstanding charge carrier mobility, long diffusion lengths, and efficient visible light absorption, making them ideal candidates for photocatalysis, light-emitting diodes (LEDs), solar cells, and photodetectors. However, their practical applications are limited by poor environmental stability. We employed a metal-organic framework (MOF) to address this challenge as a stabilizing matrix, selecting ZIF-8 for its exceptional thermal and chemical stability, high surface area, and versatile synthesis routes. The CPB/ZIF-8 nanocomposite was synthesized by integrating hot-injection-produced CPB nanocrystals with ZIF-8 using an optimized mixing approach, ensuring a uniform NCs distribution. Electron microscopy (EM) analysis confirmed the well-controlled and uniform distribution of the NCs on the surface of the ZIF-8. Moreover, the Fourier-transform infrared spectroscopy (FTIR) revealed ligand exchange, where the imidazole linkers of the ZIF-8 structure replace the NCs ligands. The process promotes almost epitaxial attachment of the latter, thus promoting effective charge interactions in the integration process. The unshifted absorbance spectra verified the preservation of optical activity, whereas a 92% quenching in photoluminescence (PL) indicated efficient charge separation and reduced electron-hole recombination. To investigate charge transfer mechanisms, photocatalytic dye degradation under visible light irradiation was employed using methyl orange (MO) and bromocresol green (BCG) as model dyes. The CPB/ZIF-8 nanocomposite exhibited significantly enhanced photocatalytic performance, achieving 1.48 and 1.75 times higher degradation rates for MO and BCG, respectively, compared to pristine CPB NCs. Electron paramagnetic resonance (EPR) studies demonstrated superior radical generation capabilities, particularly hydroxyl radicals (•OH), further confirming enhanced charge transfer and photocatalytic efficiency. These findings underscore the synergistic interaction between CPB NCs and ZIF-8, positioning the CPB/ZIF-8 nanocomposite as a promising material for photocatalysis and optoelectronic applications. | Alen Sam Thomas; Philip Nathaniel Immanuel; Neena Prasad; Achiad Goldreich; Jonathan Prilusky; Lena Yadgarov | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b1e78a81d2151a02b673b7/original/synthesis-of-cs-pb-br3-decorated-zif-8-nanocomposite-for-enhanced-photocatalytic-performance.pdf |
65cc12cd66c1381729975d02 | 10.26434/chemrxiv-2024-xd474 | Molecular Field Analysis in Half-Titanocene Complexes: Computational Study towards Data-Driven in silico Optimization of Single-Site Olefin Polymerization Catalysts | We performed molecular field analysis using computed data of half-titanocene-catalyzed olefin polymerization. The activation energies of ethylene insertion, propylene insertion, and the energy differences between ethylene insertion and β-hydrogen transfer calculated with DFT methods were employed as target variables for regression analysis. Molecular fields (voxel data) calculated from corresponding transition-state structures were used as descriptors. The structural information visualized based on the molecular field-based regression analysis provided a catalyst design guideline. A phosphinimide catalyst designed following the guideline showed enhanced computed free energy values. According to a previous report, the designed catalyst exhibited higher activity and polymer molecular weight in ethylene polymerization compared to a high performance phosphinimide catalyst in the training samples. | Shigeru Yamaguchi; Takahiro Kikuchi; Kenichi Tanaka; Ikuko Takamiya | Theoretical and Computational Chemistry; Catalysis; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cc12cd66c1381729975d02/original/molecular-field-analysis-in-half-titanocene-complexes-computational-study-towards-data-driven-in-silico-optimization-of-single-site-olefin-polymerization-catalysts.pdf |
649b219f9ea64cc1670f8c2f | 10.26434/chemrxiv-2023-2vj1l-v2 | Ru(II) Complexes with Protic- and Anionic-Naked-NHC Ligands for Cooperative Activation of Small Molecules | A set of ruthenium(II)-protic-N-heterocyclic carbene complexes, [Ru(NNCH)(PPh3)2(X)]Cl (1, X=Cl and 2, X=H) and their deprotonated forms [Ru(NNC)(PPh3)2(X)] (1ʹ, X=Cl and 2ʹ, X=H) are reported where NNC is a new unsymmetrical pincer ligand. The four complexes are interconvertible by simple acid-base chemistry. The combined theoretical and spectroscopic investigations indicate charge segregation in anionic-NHC complexes (1ʹ and 2ʹ) and can be described from a Lewis pair perspective. The chemical reactivity of deprotonated complex 1ʹ shows cooperative small molecule activation. Complex 1ʹ activates H-H bond of hydrogen, C(sp3)-I bond of iodomethane, and C(sp)-H bond of phenylacetylene. The activation of CO2 using anionic NHC complex 1ʹ at moderate temperature and ambient pressure and subsequent conversion to formate is also described. All the new compounds have been characterized using ESI-MS, 1H, 13C, and 31P NMR spectroscopy. Molecular structures of 1, 2, and 2ʹ have also been determined with single-crystal X-ray diffraction. The cooperative small molecule activation perspective broadens the scope of potential applications of anionic-NHC complexes in small molecule activation, including the conversion of carbon dioxide to formate, a much sought after reaction in the renewable energy and sustainable development domains. | Shambhu Nath; Ekta Yadav; Abhinav Raghuvanshi; Amrendra K. Singh | Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649b219f9ea64cc1670f8c2f/original/ru-ii-complexes-with-protic-and-anionic-naked-nhc-ligands-for-cooperative-activation-of-small-molecules.pdf |
64d9e72bdfabaf06ff400f98 | 10.26434/chemrxiv-2023-kp9mz | Shining light on inverted singlet-triplet emitters | The inversion of the lowest singlet and triplet excited states, observed in several triangle-shaped organic molecules containing conjugated carbon and nitrogen atoms, is an astonishing result that implies the breakdown of Hund's rule. The phenomenon attracted interest for its potential towards triplet harvesting in organic LEDs. On a more fundamental vein, the singlet-triplet (ST) inversion sheds new light on the role of electron correlations in the excited state landscape of pi-conjugated molecules. Relying on the celebrated Pariser-Parr-Pople model, the simplest model for correlated electrons in pi-conjugated systems, we demonstrate that the ST inversion does not require triangle-shaped molecules nor any specific molecular symmetry. Indeed, the ST inversion does not require strictly non-overlapping HOMO and LUMO orbitals, but rather a small gap and a small exchange integral between the frontier orbitals. | Matteo Bedogni; Davide Giavazzi; Francesco Di Maiolo; Anna Painelli | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d9e72bdfabaf06ff400f98/original/shining-light-on-inverted-singlet-triplet-emitters.pdf |
60c7518af96a00329c28802a | 10.26434/chemrxiv.12756461.v2 | Mitigating Damage to Hybrid Perovskites Using Pulsed-Beam TEM | Mitigation of electron-beam damage of methylammonium lead iodide (MAPbI<sub>3</sub>) using a modified laser-driven pulsed-beam TEM is demonstrated. For the same dose rates and total doses, it is shown that using a pulsed electron beam causes less damage to MAPbI<sub>3</sub> than a conventional thermionic (random) beam. Varying electron-pulse size (<i>i.e.</i>, number of electrons per pulse) and the time between pulses is also studied. It is found that damage increases with increasing pulse size and with decreasing time between pulses. Above a certain pulse size, more damage is caused by the pulsed beam than by conventional approaches.<br /> | Elisah VandenBussche; Catherine Clark; Russell Holmes; David Flannigan | Hybrid Organic-Inorganic Materials; Physical and Chemical Processes; Physical and Chemical Properties; Radiation | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7518af96a00329c28802a/original/mitigating-damage-to-hybrid-perovskites-using-pulsed-beam-tem.pdf |
60c748f2337d6c1604e27625 | 10.26434/chemrxiv.11923593.v2 | Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations | <p>We investigate the UV absorption spectra of a series of cationic GxG (where
x denotes a guest residue) peptides in aqueous solution and find that the
spectra of a subset of peptides with x = A, L, I, K, N, and R (and, to a lesser
extent, peptides with x = D and V) vary as a function of temperature. To
explore whether or not this observation reflects conformational dependencies,
we carry out time-dependent density functional calculations for the polyproline
II (pPII) and β-strand conformations of a limited set of tripeptides (x = A, V,
I, L, and R) in implicit and explicit water. We find that the calculated CD
spectra for pPII can qualitatively account for the experimental spectra irrespective
of the water model. The reproduction of the <i>β</i>-strand
UV-CD spectra, however, requires the explicit consideration of water. Based on
the calculated absorption spectra, we explain the observed temperature
dependence of the experimental spectra as being caused by a reduced dispersion
(larger spectral density) of the overlapping NV<sub>2</sub> band and the
influence of water on electronic transitions in the β-strand conformation.
Contrary to conventional wisdom, we find that both the NV<sub>1</sub> and NV<sub>2</sub>
band are the envelopes of contributions from multiple transitions that involve
more than just the HOMOs and LUMOs of the peptide groups. A natural transition
orbital analysis reveals that some of the transitions with significant
oscillator strength have a charge-transfer character. The overall manifold of
transitions, in conjunction with their strengths and characters, depends on the
peptide’s backbone conformation, peptide hydration, and also on the side chain
of the guest residue. It is particularly noteworthy that molecular orbitals of
water contribute significantly to transitions in <i>β</i>-strand conformations. Our results reveal that peptide groups,
side chains, and hydration shells must be considered as an entity for a physically
valid characterization of UV absorbance and circular dichroism. </p> | Anshuman Kumar; Siobhan E. Toal; David DiGuiseppi; Reinhard Schweitzer-Stenner; Bryan Wong | Biochemistry; Biophysics; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748f2337d6c1604e27625/original/water-mediated-electronic-structure-of-oligopeptides-probed-by-their-uv-circular-dichroism-absorption-spectra-and-time-dependent-dft-calculations.pdf |
675315def9980725cf406364 | 10.26434/chemrxiv-2024-gz0vj | Catalyst-Free Depolymerization of Aromatic and Aliphatic
Polyesters Using Me3SiI | Iodotrimethylsilane (Me3SiI) promotes the depolymerization of a variety of alkyl and aromatic polyesters, such as poly(ethylene succinate) (PES), polylactic acid (PLA) as well as polyethylene and polybutylene terephthalates (PET, PBT), in the absence of catalyst. The monomer products, e.g. the silylester monomers and/or their value-added derivatives, involving reactive iodo groups (alkyl iodides and acyl iodides), are obtained in high yields. The reaction outcomes are influenced by the solvent choice (e.g. CH2Cl2, CH3CN), temperature (25 °C to 200 °C) and the amount of Me3SiI. The depolymerization of PES gives the corresponding silylester which then cyclizes into succinic anhydride. With PLA the ester CH3CH2CO2SiMe3 and propionyl iodide (CH3CH2COI) are formed. They can be selectively obtained by adjusting the reaction conditions. As expected, the decomposition of aromatic polymers PET and PBT affords the bis(trimethylsilyl) terephthalate compound (1,4-{CO2SiMe3}2C6H4). In the case of PET, the formation of the latter species is hampered by the I2, released by the decomposition of the generated diiodoethane. The initial addition of an iodine trap (1 pentyne) avoids these side reactions. This work demonstrates that the length of the carbon chain linking the carboxylic acid units is a crucial factor influencing the ease of the reaction and the nature of the products. | Jean-Claude BERTHET; Thibault CANTAT; Marie KOBLYLARSKI; Xin LIU | Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675315def9980725cf406364/original/catalyst-free-depolymerization-of-aromatic-and-aliphatic-polyesters-using-me3si-i.pdf |
63e083def1da89c6837a9f79 | 10.26434/chemrxiv-2023-tnht6 | Blue Organic Light-Emitting Diode with a Turn-on Voltage at 1.47 V | Among the three primary colors, blue emission in organic light-emitting diodes (OLEDs) are highly important but very difficult to develop. OLEDs have already been commercialized; however, blue OLEDs have the problem of requiring a high applied voltage due to the high-energy of blue emission. Herein, an ultralow voltage turn-on at 1.47 V for blue emission with a peak wavelength at 462 nm (2.68 eV) is demonstrated in an OLED device. This OLED reaches 100 cd/m2, which is equivalent to the luminance of a typical commercial display, at 1.97 V. Blue emission from the OLED is achieved by the selective excitation of the low-energy triplet states at a low applied voltage by using the charge transfer (CT) state as a precursor and the triplet-triplet annihilation, which forms one emissive singlet from two triplet excitons. We found that the essential component for efficient blue emission is a smaller energy difference between the CT state and triplet exciton, accelerating the energy transfer between the two states and achieving the optimal performance by avoiding direct decay from the CT state to the ground state. Our study demonstrates that the developed OLED allows for a much longer operation lifetime than that from a typical blue phosphorescent OLED because the blue emission originates from a stable low-energy triplet exciton that avoids degrading the constituent materials. | Seiichiro Izawa; Masahiro Morimoto; Keisuke Fujimoto; Koki Banno; Yutaka Majima; Masaki Takahashi; Shigeki Naka; Masahiro Hiramoto | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e083def1da89c6837a9f79/original/blue-organic-light-emitting-diode-with-a-turn-on-voltage-at-1-47-v.pdf |
60c75594337d6c34bee28c94 | 10.26434/chemrxiv.14130317.v1 | Assessment of the Effect of Process Conditions and Material Characteristics of Alkali Metal Salt-Promoted MgO-Based Sorbents on Their CO2 Capture Performance | CO<sub>2</sub> capture using alkali metal salt
(AMS)-promoted MgO-based sorbents at intermediate temperatures (300 – 500 °C)
has gained increased interest recently. The prospects of such materials for CO<sub>2</sub>
capture were assessed in this work. We investigated the most reactive MgO-based
sorbents that have been reported in the literature, i.e., MgO promoted with a
combination of various AMS (incl. NaNO<sub>3</sub>, LiNO<sub>3</sub>, K<sub>2</sub>CO<sub>3</sub>
and Na<sub>2</sub>CO<sub>3</sub>), and examined how particle size (from powder
to pelletized 500 μm particles) and reaction conditions (calcination/carbonation
temperature, and partial pressure of CO<sub>2</sub>) affect the cyclic CO<sub>2</sub>
uptake using a thermogravimetric analyzer (TGA) at ambient pressure. The TGA results
showed that the CO<sub>2</sub> uptake of the sorbents decreased significantly
after pelletization, losing 74 % of its initial capacity. However, the CO<sub>2</sub>
uptake capacity of the pelletized sorbents continued to increase over 100 cycles
and reached a value (~ 0.46 g<sub>CO2</sub>/g<sub>sorbent</sub>) close to that of the
powdery sample (~ 0.53 g<sub>CO2</sub>/g<sub>sorbent</sub>). Analysis via X-ray
diffraction (XRD), inductively coupled plasma optical emission spectroscopy
(ICP-OES), scanning electron microscope (SEM) and N<sub>2</sub> physisorption
suggests that the increase in CO<sub>2</sub> uptake was related to a change of
the nature of the alkali species within the molten phase that is reflected by
their re-crystallization behavior when cooling them down to room temperature,
and appeared to be affected by the CO<sub>2</sub> partial pressure present
during carbonation. Finally, the CO<sub>2</sub> capture performance of the
best-performing sorbents was evaluated in a packed bed reactor, in order to assess
whether the most reactive sorbents are capable of removing a significant amount
of CO<sub>2</sub> from a gas stream at ambient pressure. The CO<sub>2</sub>
uptake of the sorbents in the packed bed experiments was very close to that in
the TGA experiments; however, the CO<sub>2</sub> capture efficiency was less
than 10 %, which currently appears too low for an industrial post-combustion
CO<sub>2</sub> capture process to be viable. New material developments should
not only focus on improving the rate of formation of MgCO<sub>3</sub> from MgO,
but also assess whether CO<sub>2</sub> removal with such sorbents is
actually feasible. | Jian Chen; Lunbo Duan; Felix Donat; Christoph Müller | Environmental Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75594337d6c34bee28c94/original/assessment-of-the-effect-of-process-conditions-and-material-characteristics-of-alkali-metal-salt-promoted-mg-o-based-sorbents-on-their-co2-capture-performance.pdf |
65e544b3e9ebbb4db9d83515 | 10.26434/chemrxiv-2024-xxzs9 | Introducing Type Ⅲ Metal Complex-Stabilized Olefin Radical Cation Induced Addition: A New Mechanism for Palladium-Catalyzed Wacker-Type Oxidation of Terminal Alkenes | To expand the substrate scope of the recently named “Radical Cation Induced Addition (RCIA)”, allowing functionalization of inactivated alkenes, the concept of “metal complex-stabilized olefin RCIA” as a type III RCIA is introduced here, with a rational design on the delocalization of radical spin the via metal-olefin interaction and through space interaction with other ligands. The feasibility of Pd-olefin radical cation complex via one-electron oxidation enabled by an oxidant is demonstrated in the Pd-catalyzed Wacker-type oxidation of terminal alkenes. The new mechanisms involved with “Pd(II) to Pd(I) catalytic cycle” matches the reported kinetic data of both the Wacker process and the Tsuji-Wacker oxidation of olefins to ketones and/or aldehydes, and it could explain the long-time unexplained phenomenon of a water nucleophilic attack onto a negatively charged π-olefin coordinated with Pd atom. Furthermore, with the new mechanisms, the stereochemistry of the debated syn/anti attack and the regioselective control in Tsuji-Wacker oxidation for either ketones or aldehydes would also be well explainable. A new concept of “on Pd through space interactions” is too proposed to explain the root of the anti-Markovnikov selectivity by the resulted “through space conjugation”. Implications in the rational design of recyclable Pd precatalysts with a water-soluble ligand for aldehyde selective Tsuji-Wacker oxidation of olefins with the concept of “in-situ surfactant”, and implications for the rational design of domino/one-pot reactions toward sustainable complex molecules with functionalities starting from olefins, by merging with organocatalysis, are also included. | Liuqun Gu | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Organocatalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e544b3e9ebbb4db9d83515/original/introducing-type-iii-metal-complex-stabilized-olefin-radical-cation-induced-addition-a-new-mechanism-for-palladium-catalyzed-wacker-type-oxidation-of-terminal-alkenes.pdf |
60c73eda0f50dba1f8395701 | 10.26434/chemrxiv.7150094.v1 | Enzymatic Modification of N-Terminal Proline Residues Using Phenol Derivatives | A convenient enzymatic strategyis reported for the modification of proline residues in the N-terminal positions of proteins. Using a tyrosinase enzyme isolated from Agaricus bisporus(abTYR), phenols and catechols are oxidized to highly reactive o-quinone intermediates that then couple to N-terminal proline residues in high yield. Key advantages of this bioconjugation method include (1) the use of air-stable precursors that can be prepared on large scale if needed, (2) mild reaction conditions, including low temperatures, (3) the targeting of native functional groups that can be introduced readily on most proteins, and (4) the use of molecular oxygen as the sole oxidant. This coupling strategy was successfully demonstrated for the attachment of a variety of phenol-derivatized cargo molecules to a series of protein substrates, including self-assembled viral capsids, enzymes, and a chitin binding domain (CBD). The ability of the CBD to bind to the surfaces of yeast cells was found to be unperturbed by this modification reaction.<br /> | Johnathan Maza; Daniel Bader; Lifeng Xiao; Alan Marmelstein; Daniel D. Brauer; Adel M. ElSohly; Matthew
J. Smith; Matthew Francis | Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eda0f50dba1f8395701/original/enzymatic-modification-of-n-terminal-proline-residues-using-phenol-derivatives.pdf |
653b74f4c573f893f135084d | 10.26434/chemrxiv-2023-5nhdj-v3 | Automated statistical analysis of Raman spectra of nanomaterials | Both at the academic and the industrial level, material scientists are exploring routes for mass production and functionalization of graphene, carbon nanotubes (CNT), carbon dots, 2D materials, and heterostructures of these. Proper application of the novel materials requires fast and thorough characterization of the samples. Raman spectroscopy stands out as a standard non-invasive technique capable of giving key information on the structure and electronic properties of nanomaterials, including the presence of defects, degree of functionalization, diameter (in the case of CNT), different polytypes, doping, etc. Here, we present a computational tool to automatically analyze the Raman spectral features of nanomaterials, which we illustrate with the example of CNT and graphene. The algorithm manages hundreds of spectra simultaneously and provides statistical information (distribution of Raman shifts, average values of shifts and relative intensities, standard deviations, correlation between different peaks, etc.) of the main spectral features defining the structure and electronic properties of the samples, as well as publication-ready graphical material. | Natalia Martín; Matthew Eaton; Sara Moreno-Da Silva; Alicia Naranjo; Emilio Perez | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653b74f4c573f893f135084d/original/automated-statistical-analysis-of-raman-spectra-of-nanomaterials.pdf |
64f9d32db6ab98a41c03994e | 10.26434/chemrxiv-2023-d1wgj-v3 | Simplifying the Temporal Analysis of Products Reactor | The Temporal Analysis of Products (TAP) experiment provides an unparalleled level of kinetic insight into heterogenous catalytic materials, but due to the complex and expensive instrumentation required, its application has been limited to a small group of dedicated researchers. Herein we demonstrate through a series of designs that precisely defined TAP experiments can be performed on systems far smaller and simpler than previously imagined. The pulse reactors described in this work utilise readily available components and so can be assembled, operated, and maintained with minimal training. Using the case study of CO oxidation over a Pt/SiO2 catalyst we show that precise kinetic, mechanistic, and surface composition information is feasible using our single-valve design. With the developments outlined in this work we aim to decrease the activation barrier to TAP and open up the technique to a new generation of researchers. | Lilliana Brandão; Eric High; Taek-Seung Kim; Christian Reece | Catalysis; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f9d32db6ab98a41c03994e/original/simplifying-the-temporal-analysis-of-products-reactor.pdf |
60c74e0f9abda21f38f8d589 | 10.26434/chemrxiv.12696143.v1 | Luminescent Molecular Switches Based on Dicationic P-Doped Polycyclic Aromatic Hydrocarbons | We report the efficient
synthesis of electron-acceptors based on cationic P-doped PAHs (Polycyclic
Aromatic Hydrocarbons). Both
endo- and exo-skeletal modifications of the p-core
allow fine-tuning their optical and
redox properties. Combined experimental (spectrolectrochemical and Electron Paramagnetic Resonance) and theoretical studies provide an in-depth
characterization of the reduced species and specifically of the stable radical
cations formed. Finally, electrochemical modulation of
fluorescence highlights the potential of these intrinsically switchable electroactive
fluorophores. | Thomas Delouche; Antoine Vacher; Thierry Roisnel; Marie Cordier; Jean-Frederic Audibert; Boris Le Guennic; Fabien Miomandre; Denis Jacquemin; Muriel Hissler; Pierre-Antoine Bouit | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e0f9abda21f38f8d589/original/luminescent-molecular-switches-based-on-dicationic-p-doped-polycyclic-aromatic-hydrocarbons.pdf |
670e1554cec5d6c1422fe5ad | 10.26434/chemrxiv-2024-9xjl6 | Ring-in-Ring Assembly Facilitates the Synthesis of a Cyclopara-phenylene Hetero[3]Catenane | Cycloparaphenylenes (CPPs) represent a significant challenge for the synthesis of mechanically interlocked architectures, because they lack heteroatoms, which precludes traditional active and passive template methods. To circumvent this problem and explore the fundamental and functional properties of CPP rotaxanes and catenanes, researches have resorted to unusual non-covalent and even to labor-intensive covalent template approaches. Herein, we report a ring-in-ring non-covalent template strategy that makes use of the surprisingly strong non-covalent inclusion of crown ethers into suitably sized CPPs. By threading a secondary ammonium salt through the crown ether and closing the third ring via Cu-AAC click reaction, we obtained a hetero-[3]catenane comprising [12]CPP, 24-crown-8 and a dibenzylammonium macrocycle. X-ray crystallography shed light on the ring-in-ring pre-organization and the [3]catenane topology was confirmed by NMR and MS-MS studies. Molecular simulations provided insights into the intriguing ring-vs.-ring-vs.-ring dynamics of the [3]catenane, which are highly dependent on the protonation state of the dibenzylammonium site. This ring-in-ring assembly strategy opens new avenues for the synthesis of complex CPP architectures and their use in functional supramolecular systems. | Wudi Shi; Yaning Hu; Luigi Leanza; Yevhenii Shchukin; Patrick A. Hoffmann; Menghua Li; Chengbing Ning; Zhong-Yan Cao; Yuanqing Xu; Pingwu Du; Max von Delius; Giovanni M. Pavan; Youzhi Xu | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670e1554cec5d6c1422fe5ad/original/ring-in-ring-assembly-facilitates-the-synthesis-of-a-cyclopara-phenylene-hetero-3-catenane.pdf |
60c75075469df49036f44889 | 10.26434/chemrxiv.12651908.v2 | Organophotoredox-Catalyzed Direct C-H Functionalization of “Drug Prejudice” at Room Temperature | <p>Organophotocatalytic C─H bond
functionalization has attracted lot of attention in the past several years due
to the possibility of catalysing reactions in a metal-free environment. Continuing on these lines, we repot herein an
organophotoredox catalyzed C─H functionalization of imidazo[1,2-a]pyridines
and related heterocycles with malonates under mild conditions providing
excellent yields of the products at room temperature. Although, C─3 functionalization of imidazo[1,2-a]pyridines
are known, this is the first report involving malonates as coupling partners
leading to the synthesis of a range of functionalized products including
Zolpidem, a sedative-hypnotic medicine. </p> | Narendra Chaubey; Anant Kapdi; Biswanath Maity | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75075469df49036f44889/original/organophotoredox-catalyzed-direct-c-h-functionalization-of-drug-prejudice-at-room-temperature.pdf |
621dc6cadaa4fb33a27b733b | 10.26434/chemrxiv-2022-3cmtq | Visible-Light-Induced Phosgenation Reaction of Amines by Oxygenation of Chloroform Using Chlorine Dioxide | Carbamoyl chloride supports modern society as a building block for pharmaceuticals, agrochemicals, and polymers. Although carbamoyl chlorides are generally synthesized via the reaction of amines with phosgene (COCl2), these applications of COCl2 have recently been avoided because of its high toxicity. Herein, we report the visible-light-induced in-situ preparation of COCl2 through the oxygenation of chloroform in the presence of chlorine dioxide, which leads to the safe constructions of carbamoyl chlorides with good-to-high yields and wide substrate scopes. In addition, this method can also be applied to the synthesis of various carbonates that are the starting materials for resins such as polycarbonates and polyurethanes. | Haruyasu Asahara; Nozomi Takao; Maiko Moriguchi; Tsuyoshi Inoue; Kei Ohkubo | Organic Chemistry; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2022-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621dc6cadaa4fb33a27b733b/original/visible-light-induced-phosgenation-reaction-of-amines-by-oxygenation-of-chloroform-using-chlorine-dioxide.pdf |
67262111f9980725cfdd571c | 10.26434/chemrxiv-2024-l1k70 | Molecular characteristics of saturated halogenated disinfection byproducts in chlorinated urban eutrophic lake water elucidated by ultrahigh-resolution mass spectrometry | Lake eutrophication affects the molecular composition of aquatic dissolved organic matter (DOM) and halogenated disinfection byproducts (Xn-DBPs). However, the effects of autochthonous DOM on the Xn-DBPs formation during disinfection of natural eutrophic water from the perspective of biological metabolism are still poorly revealed. Herein, the natural urban eutrophic lake (UEL) water with slight eutrophication was employed to elucidate the discrepancies in Xn-DBPs formation between autochthonous and allochthonous DOM based on the ultrahigh-resolution mass spectrometry. The increased operational taxonomic units, microbial cell density and relative abundance of genus Microcystis in the collected samples indicated the slight algal bloom of the lake. The prefiltration decreased the total number of Xn-DBPs in the chlorinated UEL water. The number and its proportion of nitrogenous Xn-DBPs in chlorinated UEL water samples were significantly larger (p < 0.05) than those for chlorinated SRNOM. Microbes dominated by Microcystis contributed largely to releasing autochthonous DOM due to the microbial cell lysis and microbe-derived Xn-DBPs species upon disinfection. The Xn-DBPs species mainly derived from microorganisms were highly saturated, reduced, bioavailable, nitrogenous, and toxic but lowly oxidized and aromatic than terrestrially derived Xn-DBPs species. Moreover, the connection between microbial lipid metabolism and Xn-DBPs species exclusively identified in chlorinated UEL water indicated the considerable contribution of lipid metabolites to saturated Xn-DBPs species. Our findings not only shed light on the effects of algae on the molecular composition of DOM and Xn-DBPs species but also deepen the understanding towards the formation mechanisms of microbe-derived Xn-DBPs species from the view of microbial metabolic pathways. | Shixi Wu; Qing-Long Fu; Manabu Fujii; Jibao Liu; Ahmed Elreedy; Xin Yang; Pingqing Fu; Yanxin Wang | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67262111f9980725cfdd571c/original/molecular-characteristics-of-saturated-halogenated-disinfection-byproducts-in-chlorinated-urban-eutrophic-lake-water-elucidated-by-ultrahigh-resolution-mass-spectrometry.pdf |
6666ede9409abc034513336f | 10.26434/chemrxiv-2024-pwqjt-v2 | Advancing Catalysis Research through FAIR Data Principles Implemented in a Local Data Infrastructure - A Case Study of an Automated Test Reactor | Findable, Accessible, Interoperable, and Reusable (FAIR) data is currently emerging as an indispensable element in the advancement of science and requires the development of new methods for data acquisition, storage and sharing. This is becoming even more critical as the increasing application of artificial intelligence demands significantly higher data quality in terms of reliability, reproducibility and consistency of datasets. This paper presents methods for the digital and automatic acquisition and storage of data and metadata in catalysis experiments based on open-source software solutions. The successful implementation of a digitalization concept, which includes working according to machine-readable standardized operating procedures (SOPs) is outlined using a reactor for catalytic tests that has been automated with the open-source software tool EPICS (Experimental Physics and Industrial Control System). The process of data acquisition, standardized analysis, upload to a database and generation of relationships between database entries is fully automated. Application programming interfaces (APIs) have been developed to enable data exchange within the local data infrastructure and beyond to overarching repositories, paving the way for autonomous catalyst discovery and machine learning applications. | Abdulrhman Moshantaf; Michael Wesemann; Simeon Beinlich; Heinz Junkes; Julia Schumann; Baris Alkan; Pierre Kube; Clara Patricia Marshall; Nils Pfister; Annette Trunschke | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666ede9409abc034513336f/original/advancing-catalysis-research-through-fair-data-principles-implemented-in-a-local-data-infrastructure-a-case-study-of-an-automated-test-reactor.pdf |
66caf874f3f4b0529011b198 | 10.26434/chemrxiv-2023-h76kd-v2 | Rational Screening of Mn(II) Metal-Ligand Complexes for Using as MRI Contrast Agents Using Machine Learning | Recent decades have shown a good progress in all the fields of the advanced diagnostic capabilities and personalized medicine. The smart contrast agents (SCAs) that may appear the important element of the proper diagnosis specification should become the standard in a normal clinical practice. Most widely used contrast agents are the kinetically inert and thermodynamically stable complexes of organic ligands with Gd(III) metal ion. However, known safety concerns associated with high toxicity and severe side effects due to demetallization reactions leading to the formation of free Gd(III) ion necessitate the demand in the contrast agents of new generation. It is expected that one of the alternatives will be ML complexes with essential paramagnetic metals such as the Mn(II), Mn(III) and Fe(III). In this study, the experimental data on Mn(II)-based contrast agents (CAs) including the key functional characteristics such as the relaxation enhancement characteristics, kinetic inertness and thermodynamic stability were analyzed. The machine learning methods were used in a combination with the physicochemical and substructure(topology)-based features to estimate the missed experimental data concerned the thermodynamic stability and relaxivity characteristics evaluated at certain conditions. The analysis of the experimental data has shown that the bispidine scaffold can be considered as the reference point for the ligand search as providing with a sufficient compromise for all the investigated functional characteristics of CAs. The analysis of the literature suggests using iodine and fluorine substituents for the electronic and steric hindrance thus preventing the cleavage of the bonds while the histidine residue can be recommended for the pH sensitivity of MRI CAs while targeting the OATPs (organic anion transporting polypeptides) to achieve the hepatobiliary clearance as well as for the enhanced contrast for hepatobiliary system thus personalizing the MRI investigation. We assume that the "proton sponge" effects may contribute to the enhanced kinetic inertness characteristics of the ligands. | Natalia Kireeva; Aslan Yu. Tsivadze | Inorganic Chemistry; Transition Metal Complexes (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66caf874f3f4b0529011b198/original/rational-screening-of-mn-ii-metal-ligand-complexes-for-using-as-mri-contrast-agents-using-machine-learning.pdf |
60c742704c8919e55dad2490 | 10.26434/chemrxiv.8296193.v1 | Nano-Folded Gold Electrocatalysts Enhance the Selectivity of Carbon Dioxide Reduction | <p>The local structure and geometry of catalytic interfaces can influence the selectivity of chemical reactions. Here, using a pre-strained polymer, we uniaxially compress a thin gold film to form a nano-folded catalyst. We observe two kinds of folds and can tune the ratio of loose to tight folds by varying the extent of pre-strain in the polymer. We characterize the nano-folded catalysts using x-ray diffraction, scanning, and transmission electron microscopy. We observe grain reorientation and coarsening in the nano-folded gold catalysts. Electroreduction of carbon dioxide with these nano-folded catalysts reveals an enhancement of Faradaic efficiency for carbon monoxide formation by a factor of about four. This result suggests that electrolyte mass transport limitations and an increase of the local pH in the tight folds of the catalyst outweigh the effects of alterations in grain characteristics. Together, our studies demonstrate that nano-folded geometries can significantly alter grain characteristics, mass transport, and catalytic selectivity. </p> | Kam Sang Kwok; Yuxuan Wang; Michael Cao; Hao Shen; Weinan Xu; David Muller; Chao Wang; David Gracias | Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Electrochemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742704c8919e55dad2490/original/nano-folded-gold-electrocatalysts-enhance-the-selectivity-of-carbon-dioxide-reduction.pdf |
631b41e0faf4a469380c0243 | 10.26434/chemrxiv-2022-27jmk | Amination of Nitro-Substituted Heteroarenes by Nucleophilic Substitution of Hydrogen | An open-air method for the transition metal-free direct amination of nitro(hetero)arenes by anilines is disclosed. In this methodology, an aromatic C-H bond is substituted via oxidative nucleophilic aromatic substitution of hydrogen (ONSH). DFT calculations and mechanistic studies support a dianion pathway with oxidation by molecular oxygen as the rate-limiting step. | Michael D. Mandler; Nina Suss; Antonio Ramirez; Christopher A. Farley; Darpandeep Aulakh; Yeheng Zhu; Sarah C. Traeger; Amy Sarjeant; Merrill L. Davies; Bruce A. Ellsworth; Alicia Regueiro-Ren | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631b41e0faf4a469380c0243/original/amination-of-nitro-substituted-heteroarenes-by-nucleophilic-substitution-of-hydrogen.pdf |
66f583d2cec5d6c1424c8b23 | 10.26434/chemrxiv-2024-0kztt | Composition Variation Reveals the Non-Ideal Mixing of Components in (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O and the Benefits of this Variation in Sodium Ion-Battery | The reversible transformation between a multiphase and single-phase state has been used as a hallmark for entropy stabilization in the system (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O. it was shown that cations are fully random and homogeneous in this single-phase material, providing a way to estimate its configurational entropy. The deliberate variation of this entropy led to the conclusion that (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O is primarily stabilized by this configurational entropy. Here, we show that this phase transformation observed in (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O could originate from a Jahn-Teller distortion rather than entropy stabilization. We further demonstrate through composition variation that the consolute temperature depends on the nature of the components rather than the number of components. In addition, we show that there is significant cation ordering in these systems, further casting doubts on the role of configurational entropy as the main stabilizing term. Finally, we demonstrate that this compositional variation can be used to tune the voltage of these complex metal oxides to improve their reactivity in a sodium-ion cell. | Modeste Tegomoh; Kug-Seung Lee; Anne Co | Physical Chemistry; Materials Science; Energy; Ceramics; Energy Storage; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f583d2cec5d6c1424c8b23/original/composition-variation-reveals-the-non-ideal-mixing-of-components-in-mg0-2co0-2ni0-2cu0-2zn0-2-o-and-the-benefits-of-this-variation-in-sodium-ion-battery.pdf |
619639919960f300bab0f4a8 | 10.26434/chemrxiv-2021-z8rk6 | Transformer Neural Network-Based Molecular Optimization Using General Transformations | Molecular optimization aims to improve the drug profile of a starting molecule. It is a fundamental problem in drug discovery but challenging due to (i) the requirement of simultaneous optimization of multiple properties and (ii) the large chemical space to explore. Recently, deep learning methods have been proposed to solve this task by mimicking the chemist's intuition in terms of matched molecular pairs (MMPs). Although MMPs is a typical and widely used strategy by medicinal chemists, it offers limited capability in terms of exploring the space of solutions. There are more options to modify a starting molecule to achieve desirable properties, e.g. one can simultaneously modify the molecule at different places including changing the scaffold. This study trains the same Transformer architecture on different datasets. These datasets consist of a set of molecular pairs which reflect different types of transformations. Beyond MMP transformation, datasets reflecting general transformations are constructed from ChEMBL based on two approaches: Tanimoto similarity (allows for multiple modifications) and scaffold matching (allows for multiple modifications but keep the scaffold constant) respectively. We investigate how the model behavior can be altered by tailoring the dataset while keeping the same model architecture. Our results show that the models trained on differently prepared datasets transform a given starting molecule in a way that it reflects the nature of the dataset used for training the model. These models could complement each other and unlock the capability for the chemists to pursue different options for improving a starting molecule. | Jiazhen He; Eva Nittinger; Christian Tyrchan; Werngard Czechtizky; Atanas Patronov; Esben Jannik Bjerrum; Ola Engkvist | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619639919960f300bab0f4a8/original/transformer-neural-network-based-molecular-optimization-using-general-transformations.pdf |
60c7527f469df47de5f44ba3 | 10.26434/chemrxiv.13298048.v1 | Cyclam-Based Chelators Bearing Phosphonated Pyridine Pendants for 64Cu-PET Imaging : Synthesis, Physico-Chemical Studies, Radiolabeling and Bioimaging. | Herein we present the preparation of two novel cyclam-based macrocycles (te1pyp and cb-te1pyp), bearing phosphonate-appended pyridine side-arms for the coordination of copper(II) ions in the context of 64Cu PET imaging. The two ligands have been prepared through conventional protection-alkylation sequences on cyclam, and their coordination properties have been thoroughly investigated. The corresponding copper complexes have been fully characterized in the solid-state (X-Ray diffraction analysis) and in solution (EPR and UV-Vis spectroscopies). Potentiometric studies, combined with spectrometry, have also allowed us to determine their thermodynamic stability constants, confirming their high affinity for copper(II) cations. The kinetic inertness of the complexes has also been verified by acid-assisted dissociation experiments, enabling their use in 64Cu-PET imaging in mice for the first time. Indeed, the two ligands could be quantitatively radiolabeled under mild conditions, and the resulting 64Cu complexes have demonstrated excellent stability in serum. PET imaging demon-strated a set of features emerging from the combination of picolinates and phosphonate units: high stability in vivo, fast clear-ance from the body via renal elimination, and most interestingly, very low fixation in the liver. The latter is in contrast with what was observed for monopicolinate cyclam (te1pa), that had a non-negligible accumulation in the liver, owing probably to its different charge and lipophillicity. These results thus pave the way for the use of such phosphonated pyridine chelators for in vivo 64Cu-PET imaging. | Richard Knighton; Thibault Troadec; Valerie Mazan; Patricia Le Saëc; Séverine Marionneau-Lambot; Thomas Le Bihan; Nathalie Saffon-Merceron; Nathalie Le Bris; Michel Chérel; Alain Faivre-Chauvet; Mourad Elhabiri; Loïc J. Charbonnière; Raphael Tripier | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry; Ligands (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7527f469df47de5f44ba3/original/cyclam-based-chelators-bearing-phosphonated-pyridine-pendants-for-64cu-pet-imaging-synthesis-physico-chemical-studies-radiolabeling-and-bioimaging.pdf |
67652b07fa469535b9382bd3 | 10.26434/chemrxiv-2024-trm90 | Biological Evaluation of Cleavable Linkers in Exatecan-Based Antibody-Drug Conjugates: A Comparative Study of DXd and Exo-Linker Platforms | Antibody-drug conjugates (ADCs) represent a transformative class of cancer therapies that combine the specificity of monoclonal antibodies with the cytotoxicity of potent drug payloads. This study presents the development and evaluation of a novel exolinker designed to enhance ADC stability and pharmacokinetics by addressing the limitations associated with traditional cleavable linkers. Using trastuzumab conjugated with a payload linker consisting of an exo-linker and exo-EVC-Exatecan (APL-1082), we examined key parameters, including in vivo efficacy and pharmacokinetic profiles in rat models, to directly compare it with the clinically validated trastuzumab-deruxtecan (T-DXd, Enhertu). Our Exo-linker ADC demonstrated superior stability and maintained drug-to-antibody ratios (DAR) with reduced aggregation and hydrophobicity compared to T-DXd, suggesting an improved pharmacokinetic profile. Additionally, combining the Exo-linker with AJICAP site-specific conjugation technology enabled the production of high-DAR ADCs, achieving a DAR of 10 with promising homogeneity and physicochemical properties. Collectively, these findings underscore the potential of the exo-linker as a versatile platform for next-generation ADCs, offering enhanced stability, efficacy, and expanded therapeutic possibilities. | Tomohiro Watanabe; Yusuke Iwai; Natsuki Shikida; Jason T. Stofleth; Takuya Seki; Kazutaka Shimbo; Yutaka Matsuda | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67652b07fa469535b9382bd3/original/biological-evaluation-of-cleavable-linkers-in-exatecan-based-antibody-drug-conjugates-a-comparative-study-of-d-xd-and-exo-linker-platforms.pdf |
66b0c7da01103d79c5cbf1e3 | 10.26434/chemrxiv-2024-xkjhd | Development of tailless homologue receptor (TLX) agonist chemical tools | The tailless homologue receptor (TLX) is a ligand-activated transcription factor acting as master regulator of neural stem cell homeostasis. Despite its promising potential in neurodegenerative disease treatment, TLX ligands are rare but required to explore phenotypic effects of TLX modulation and for target validation. We have systematically studied and optimized a TLX agonist scaffold obtained by fragment fusion. Structural modification enabled the development of two TLX agonists endowed with nanomolar potency and binding affinity. Both exhibited favorable chemical tool characteristics including high selectivity and low toxicity. Most notably, the TLX agonists comprise different scaffolds and display high chemical diversity enabling a use as set for target identification and validation studies. | Emily C. Hank; Minh Sai; Till Kasch; Isabelle Meijer; Julian Marschner; Daniel Merk | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b0c7da01103d79c5cbf1e3/original/development-of-tailless-homologue-receptor-tlx-agonist-chemical-tools.pdf |
60c7401dbdbb89bf7ba380f6 | 10.26434/chemrxiv.7597631.v1 | Investigating the Effect of Alumina Shaping on the Sorption Properties of Promising Metal-Organic Frameworks | Three promising MOF candidates, UiO-66(Zr), MIL-100(Fe) and MIL-127(Fe) are shaped through granulation with a rho-alumina binder. Subsequently, changes in the surface characteristics and adsorption performance are evaluated through adsorption microcalorimetry at 303 K with several common probes (N<sub>2</sub>, CO<sub>2</sub>, CO, CH<sub>4</sub>, C<sub>2</sub>H<sub>6</sub>, C<sub>3</sub>H<sub>8</sub>, C<sub>3</sub>H<sub>6</sub> and C<sub>4</sub>H<sub>10</sub>), generating a detailed picture of adsorbate-adsorbent interactions. Vapour adsorption experiments with water and methanol were further used to gauge changes in hydrophobicity caused by the addition of the alumina binder. Upon shaping, a decrease in gravimetric capacity and specific surface area is observed, accompanied by an increased capacity on a volumetric basis, attributed to densification induced by the shaping process, as well as a surprising lack of pore environment changes. However, the magnitude of these effects depends on the MOF, suggesting a high dependence on material structure. Out of the three materials, MIL-127(Fe) shows the least changes in adsorption performance and is highlighted as a promising candidate for further study. | Paul Iacomi; U-Hwang Lee; Anil H. Valenkar; Jong-San Chang; Philip L. Llewellyn | Hybrid Organic-Inorganic Materials; High-throughput Screening; Coordination Chemistry (Inorg.); Interfaces; Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7401dbdbb89bf7ba380f6/original/investigating-the-effect-of-alumina-shaping-on-the-sorption-properties-of-promising-metal-organic-frameworks.pdf |
651b1745a69febde9e1c3364 | 10.26434/chemrxiv-2023-49gtb | A Serine Ligation Method Based on Mitsunobu Reaction and O-to-N Acyl Transfer | A ligation protocol has been developed in which a peptide containing an N-terminal serine is linked via its side-chain alcohol to the C-terminal carboxylate of a second peptide by Mitsunobu esterification. N-Deprotection of the serine and subsequent exposure to a weak amine base triggers O-to-N acyl transfer, delivering the desired ligation product. A unique aspect of this strategy is the use of the C-terminal carboxylate as a nucleophile rather than as an electrophile. As a result, the ligation occurs without evidence of epimerization. A broad scope of C-terminal nucleophiles is tolerated, including proline and hindered beta-branched residues. | Regina So; Braxton Felix; Ankur Jalan; Michael Kopach; Steven Castle | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651b1745a69febde9e1c3364/original/a-serine-ligation-method-based-on-mitsunobu-reaction-and-o-to-n-acyl-transfer.pdf |
60c746679abda2980af8c738 | 10.26434/chemrxiv.11317808.v1 | Variational Forward-Backward Charge Transfer Analysis Based on Absolutely Localized Molecular Orbitals: Energetics and Molecular Properties | <div>
<div>
<div>
<p>To facilitate the understanding of charge transfer (CT) effects in dative complexes,
we propose a variational forward-backward (VFB) approach to decompose the overall
CT stabilization energy into contributions from forward and backward donation in the framework of energy decomposition analysis based on absolutely localized molecular orbitals (ALMO-EDA). Such a decomposition is achieved by introducing two additional
constrained intermediate states in which only one direction of CT is permitted. These
two “one-way” CT states are variationally relaxed such that the associated nuclear
forces can be readily obtained. This allows for a facile integration into the previously
developed adiabatic EDA scheme so that the molecular property changes arising from forward and back donation can be separately assigned. Using ALMO-EDA augmented
by this VFB model, we investigate the energetic, geometric, and vibrational features of
complexes composed of CO and main group Lewis acids (BH3, BeO/BeCO3), and complexes of the N2, CO, and BF isoelectronic series with [Ru(II)(NH3)5]2+. We identify
that the shift in the stretching frequency of a diatomic π-acidic ligand (XY), such as
CO, results from a superposition of the shifts induced by permanent electrostatics and
backward CT: permanent electrostatics can cause an either red or blue shift depend-
ing on the alignment of the XY dipole in the dative complex, and this effect becomes
more pronounced with a more polar XY ligand; the back-donation to the antibonding
π orbital of XY always lowers the X−Y bond order and thus red-shifts its stretching
frequency, and the strength of this interaction decays rapidly with the intermolecular
distance. We also reveal that while σ forward donation contributes significantly to energetic stabilization, it affects the vibrational feature of XY mainly by shortening the
intermolecular distance, which enhances both the electrostatic interaction and back-
ward CT but in different rates. The synergistic effect of the forward and backward
donations appears to be more significant in the transition metal complexes, where the
forward CT plays an essential role in overcoming the strong Pauli repulsion. These
findings highlight that the shift in the XY stretching frequency is not a reliable metric
for the strength of π back-donation. Overall, the VFB-augmented EDA scheme that
we propose and apply in this work provides a useful tool to characterize the role played
by each physical component that all together lead to the frequency shift observed. </p>
</div>
</div>
</div> | Matthias Loipersberger; Yuezhi Mao; Martin Head-Gordon | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746679abda2980af8c738/original/variational-forward-backward-charge-transfer-analysis-based-on-absolutely-localized-molecular-orbitals-energetics-and-molecular-properties.pdf |
60c73eabbb8c1a994a3d9970 | 10.26434/chemrxiv.7077872.v1 | Peak Force Visible Microscopy for Determination of Exciton Diffusion Length in Organic Photovoltaic Blends | In this article, we developed a new nano spectroscopic technique, peak force visible (PF-vis) microscopy, which is based on the peak force tapping mode in an atomic force microscope to both visualize nanoscale morphology and estimate exciton diffusion lengths of donor domains in organic photovoltaic blends. Nano phase-separations in P3HT:PCBM and TFB:PCBM blend films were clearly revealed by PF-vis microscopy with a high spatial resolution less than 10 nm. A model that correlates PF-vis signal and the exciton diffusion length was also developed to estimate the diffusion lengths of P3HT and TFB to be 2.9±0.3 and 9.0±1.5 nm, respectively. PF-vis microscopy is expected to assist the evaluation of OPV materials, therefore accelerating the pace of innovation of OPVs. | Haomin Wang; Le Wang; Yuequn Shang; Zhijun Ning; Xiaoji Xu | Microscopy; Spectroscopy (Anal. Chem.); Photovoltaics; Optics | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eabbb8c1a994a3d9970/original/peak-force-visible-microscopy-for-determination-of-exciton-diffusion-length-in-organic-photovoltaic-blends.pdf |
632f1bfd2984c92bf56b778d | 10.26434/chemrxiv-2022-cqgkx | Energy loss for droplets bouncing off
superhydrophobic surfaces | A water droplet can bounce off superhydrophobic
surfaces multiple times before coming to a
stop. The energy loss for such droplet rebounds
can be quantified by the ratio of the rebound
speed UR and the initial impact speed UI , i.e.,
its restitution coefficient e = UR/UI . Despite
much work in this area, there is still incomplete
mechanistic explanation for the energy loss for
rebounding droplets. Here, we measured e for
sub-millimetric and millimetric sized droplets
impacting two different superhydrophobic surfaces
over a wide range of UI = 4–400 cm s−1.
We proposed simple scaling laws to explain the
observed non-monotonic dependence of e on UI .
In the limit of low UI , energy loss is dominated
by contact-line pinning and e is sensitive to the
surface wetting properties, in particular to contact
angle hysteresis Δcos θ of the surface. In
contrast, in the limit of high UI , e is dominated
by inertial-capillary effects and does not depend
on Δcos θ. | Calvin Thenarianto; Xue Qi Koh; Dan Daniel | Materials Science; Nanoscience | CC BY 4.0 | CHEMRXIV | 2022-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632f1bfd2984c92bf56b778d/original/energy-loss-for-droplets-bouncing-off-superhydrophobic-surfaces.pdf |
60c74433702a9bd4d818a773 | 10.26434/chemrxiv.9703013.v1 | DNA-Based Synthetic Growth Factor Surrogates with Fine-Tuned Agonism | Designing synthetic surrogates of functional
proteins is an important, albeit challenging, task in the field of chemistry. A
strategy toward the design of synthetic agonists for growth factors or cytokine
receptors that elicit a desired signal activity has been in high demand, as
such ligands hold
great promise as safer and more effective therapeutics. In the present study, we used a DNA aptamer as a building block and described the strategy-guided design of a synthetic receptor agonist with fine-tuned
agonism. | Ryosuke Ueki; Momoko Akiyama; Shinsuke Sando | Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74433702a9bd4d818a773/original/dna-based-synthetic-growth-factor-surrogates-with-fine-tuned-agonism.pdf |
6272a44d44bdd561a9567534 | 10.26434/chemrxiv-2022-b7vj8-v2 | 3D and 2D aromaticies: Like oil and water? The case of benzocarborane derivatives and 3D/3D fusions | 2D/2D fusion of aromatic halves leading to a global aromatic is found in many polycyclic aromatic hydrocarbons. 3D/3D aromaticity is also found in fused boranes that follow the Jemmis’ mno rule, but 2D/3D aromaticity is difficult or impossible to achieve. | Miquel Solà; Jordi Poater; Francesc Teixidor; Clara Viñas | Theoretical and Computational Chemistry; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6272a44d44bdd561a9567534/original/3d-and-2d-aromaticies-like-oil-and-water-the-case-of-benzocarborane-derivatives-and-3d-3d-fusions.pdf |
62277f5b97f210991b01cace | 10.26434/chemrxiv-2022-zdq74 | A photo-responsive transmembrane anion transport relay | Ion transport across lipid membranes in biology is controlled by stimuli-responsive membrane channels and molecular machine ion pumps such as ATPases. Here, we report a synthetic molecular machine-like ion transport relay, in which transporters in opposite sides of a lipid bilayer membrane facilitate transport by passing ions between them. By incorporating a photo-responsive telescopic arm into the relay design, this process is reversibly controlled in response to irradiation with blue and green light. Transport occurs only in the extended state when the length of the arm is sufficient to pass the anion between transporters located on opposite sides of the membrane. In contrast, the contracted state of the telescopic arm is too short to mediate effective transport. The system acts as a stimuli-responsive ensemble of machine-like components, reminiscent of ro-botic arms in a factory assembly line, working cooperatively to mediate ion transport. This work points to new prospects for us-ing lipid bilayer membranes as scaffolds for confining, orientating and controlling the relative positions of molecular machines, thus enabling multiple components to work in concert, and opening up new applications in biological contexts. | Toby Johnson; Amir Sadeghi-Kelishadi; Matthew Langton | Biological and Medicinal Chemistry; Organic Chemistry; Nanoscience; Organic Synthesis and Reactions; Photochemistry (Org.); Supramolecular Chemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62277f5b97f210991b01cace/original/a-photo-responsive-transmembrane-anion-transport-relay.pdf |
64f1d9a779853bbd78ddeef6 | 10.26434/chemrxiv-2023-1d4ld | Peri-Anthracenethioindigo: a Scaffold for Efficient All-Red-Light and NIR Molecular Photoswitching | Photoswitching with red light is a greatly desired capability to evade photodamage and achieve specific photoresponses. In virtually all cases however, only one switching direction uses red light while for the reverse switching UV or visible light is needed. All-red-light photoswitching brings with it the obvious advantage of pushing photoswitching to the limit of the low-energy spectrum but no viable system is available currently. In this work we report on peri-anthracenethioindigo (PAT) as molecular scaffold for highly efficient all-red-light photoswitching with outstanding performance and property profile. The PAT photoswitch provides NIR absorption up to 850 nm, large negative photochromism with more than 140 nm maxima shifts and changes color from green to blue upon irradiation with two shades of red light. Thermal stability of the metastable Z isomer is high with a corresponding half-life of several days at 20 °C. Application for red-light responsive polymers undergoing pronounced and reversible green to blue color changes is demonstrated evidencing spatially resolved photoswitching. The PAT photoswitch thus offers unique responsiveness to very low energy light together with predictable and large geometrical changes within a rigid molecular scaffold. We expect a plethora of applications for PAT in the near future in all chemistry-related areas. | Laura Köttner; Elias Ciekalski; Henry Dube | Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f1d9a779853bbd78ddeef6/original/peri-anthracenethioindigo-a-scaffold-for-efficient-all-red-light-and-nir-molecular-photoswitching.pdf |
6712253212ff75c3a1c5ec38 | 10.26434/chemrxiv-2024-32h0p | ULaMDyn: Enhancing Excited-State Dynamics Analysis Through Streamlined Unsupervised Learning | The analysis of nonadiabatic molecular dynamics (NAMD) data presents significant challenges due to its high dimensionality and complexity. To address these issues, we introduce ULaMDyn, a Python-based, open-source package designed to automate the unsupervised analysis of large datasets generated by NAMD simulations. ULaMDyn integrates seamlessly with the Newton-X platform and employs advanced dimensionality reduction and clustering techniques to uncover hidden patterns in molecular trajectories, enabling a more intuitive understanding of excited-state processes. Using the photochemical dynamics of fulvene as a test case, we demonstrate how ULaMDyn efficiently identifies critical molecular geometries and critical nonadiabatic transitions. The package offers a streamlined, scalable solution for interpreting large NAMD datasets. It is poised to facilitate advances in the study of excited-state dynamics across a wide range of molecular systems. | Max Pinheiro Jr. ; Matheus O. Bispo; Rafael S. Mattos; Mariana Telles do Casal; Bidhan Chandra Garain; Josene M. Toldo; Saikat Mukherjee; Mario Barbatti | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6712253212ff75c3a1c5ec38/original/u-la-m-dyn-enhancing-excited-state-dynamics-analysis-through-streamlined-unsupervised-learning.pdf |
60c74aa3567dfed594ec4de1 | 10.26434/chemrxiv.12235400.v1 | Super-Heavy Elements (Z = 100-109) Treated as Calcium Clusters: First Ionization Energies | <p>In
the present work, it is shown that the first ionization energies for
super-heavy elements (Z= 100-109) can be calculated by a semi-empirical method,
if the super-heavy elements are treated (modelled) as calcium clusters. The
values calculated in the present work are in good agreement compared with those
from literature (modelling the super-heavy elements themselves, based on
relativistic quantum mechanics). </p> | Robson de Farias | Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aa3567dfed594ec4de1/original/super-heavy-elements-z-100-109-treated-as-calcium-clusters-first-ionization-energies.pdf |
62a47f2cfe677dbf414c0076 | 10.26434/chemrxiv-2022-p891w | Understanding the processability of graphite blend electrodes with silicon nanoparticles | The manufacturing process aims to optimize the parameters leading to enhanced Lithium-Ion Battery (LiB) electrode properties. Particularly, developing silicon/graphite blends could be an alternative for boosting LiB energy density while using the longstanding properties of graphite. Here, we report the manufacturing parameters impact of the mixing, coating, and calendering steps on the properties of silicon/graphite blend electrodes. The mixing process was assessed by the solid and silicon content dependency, where the viscosity increases when increasing the solid and decreasing the silicon content. Moreover, the slurry rheology directly impacts the mechanical stability of the electrode when coating using thicker comma gaps. The calendering step evidences a porosity threshold necessary for adequate ionic resistance and cycling life. We found that porosities between 45% to 56% for these silicon/graphite blends yield higher performance. Lower than 30% porosity highly impacts the electrochemical performance in a detrimental way. | Diana Zapata Dominguez; Alejandro A. Franco | Physical Chemistry; Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a47f2cfe677dbf414c0076/original/understanding-the-processability-of-graphite-blend-electrodes-with-silicon-nanoparticles.pdf |
678b2a71fa469535b9774f41 | 10.26434/chemrxiv-2025-jhhxw | Elucidating the Boundary of Intercalation vs. Sequestration in Supramolecular Polymers by Retrosynthetic Design Towards the Construction of Complex Supramolecular Systems | Controlled social self-sorting by intercalation can offer distinct properties at the supramolecular level that go beyond the sum of its parts. Likewise, controlling narcissistic self-sorting by sequestration can induce unique system properties such as dilution-induced self-assembly. In contrast, the interface between the two extreme cases has hitherto remained underexplored and clear design rules remain elusive. Herein we demonstrate that by fine-tuning the molecular similarity of supramolecular synthons in a complex system, intricate control over concerted supramolecular equilibria can be achieved. By reducing the molecular similarity, a former intercalator can be tuned to become a strong or weak sequestrators. As a consequence, either uncommon dual supramolecular sequestration or an unprecedented competitive hybrid mechanism between sequestration and intercalation in tertiary mixtures could be demonstrated. We are hopeful that the results presented herein will contribute to the development and understanding of concerted processes in complex supramolecular systems. | Nils Bäumer; Soichiro Ogi; Shigehiro Yamaguchi | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678b2a71fa469535b9774f41/original/elucidating-the-boundary-of-intercalation-vs-sequestration-in-supramolecular-polymers-by-retrosynthetic-design-towards-the-construction-of-complex-supramolecular-systems.pdf |
62dfeef6a8e4dcd86b1d773d | 10.26434/chemrxiv-2022-nrmf0-v2 | Efficiency and suitability when exploring the conformational space of phase transfer catalysts | In this study, a complete exploration of the conformational space of phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most significant and relevant conformational analysis approaches have been chosen to characterise the main Cinchona alkaloid-based phase transfer catalysts. This particular guiding study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and providing recommendations regarding suitable and efficient choices of methods for analysis. | Iñigo Iribarren; Cristina Trujillo | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62dfeef6a8e4dcd86b1d773d/original/efficiency-and-suitability-when-exploring-the-conformational-space-of-phase-transfer-catalysts.pdf |
60c7555e842e65ea13db4311 | 10.26434/chemrxiv.14095891.v1 | Microscopic Insights into Charge Formation and Energetics in N-Doped Organic Semiconductors | <p>In the molecular doping of organic semiconductors</p><p>(OSC), achieving efficient charge generation</p><p>and managing the energetic cost for charge</p><p>release from local molecular charge transfer</p><p>complexes (CTCs) to the host matrix is of</p><p>central importance. Experimentally tremendous</p><p>progress has been made in this direction.</p><p>However, the relation between OSC film</p><p>structure on a nanoscopic level including different</p><p>inter-molecular geometrical arrangements</p><p>and the macroscopic properties of doped OSC</p><p>films is usually only established quite indirectly.</p><p>Explicit microscopic insights into the underlying</p><p>doping mechanisms and resulting electronic</p><p>structure are still scarce and mostly limited</p><p>to the study of the individual molecular constituents</p><p>or isolated bi-molecular dopant:host</p><p>complexes. In the present study we investigate</p><p>n-type doping of the frequently investigated</p><p>OSC materials ZnPC and F8ZnPc and</p><p>their mixtures which are n-doped with 2-Cyc-</p><p>DMBI. We report significant electronic differences</p><p>for complexes with nominally the same</p><p>material composition but different geometrical</p><p>structures. One specific important finding in</p><p>this context is that complexes containing two</p><p>adjacent dopant molecules show much reduced</p><p>ionization energy values, leading to substantially</p><p>reduced energy cost for charge release. Furthermore our results demonstrate that important</p><p>trends towards macroscopic system behavior</p><p>can already be obtained with increasing</p><p>size and varying composition of the relatively</p><p>small molecular dopant-host complexes considered,</p><p>including systematic shifts in the Fermi</p><p>level energies in the doped OSC.</p> | Chuanding Dong; Stefan Schumacher | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7555e842e65ea13db4311/original/microscopic-insights-into-charge-formation-and-energetics-in-n-doped-organic-semiconductors.pdf |
639bfabf81e4baeff64f38a4 | 10.26434/chemrxiv-2022-8pn7l | A convergent fragment coupling strategy to access quaternary stereogenic centers | The formation of quaternary stereogenic centers via convergent fragment coupling is a longstanding challenge in organic synthesis. Here, we report a strategy for the formation of quaternary stereogenic centers in polycyclic systems based upon the semi-pinacol reaction. In the key transformation, two fragments of a similar size and complexity are joined by a 1,2-addition of an alkenyl lithium to an epoxy ketone, and the resulting epoxy silyl ether undergoes a semi-pinacol rearrangement catalyzed by N-(trimethylsilyl)bis(trifluoromethanesulfonyl)imide (TMSNTf2) or trimethylsilyl trifluoromethanesulfonate (TMSOTf). Polycyclic scaffolds were generated in high yields and the reaction conditions tolerated a variety of functional groups including esters, silyl ethers, enol ethers, and aryl triflates. This method provides a useful strategy for the synthesis of complex polycyclic natural product-like scaffolds with quaternary stereogenic centers from simplified fragments. | Jeff Kerkovius; Alice Wong; Victor Mak; Sarah Reisman | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639bfabf81e4baeff64f38a4/original/a-convergent-fragment-coupling-strategy-to-access-quaternary-stereogenic-centers.pdf |
60c7480f702a9b10a118aef8 | 10.26434/chemrxiv.11853399.v1 | A Multi-Layer Approach to the Equation of Motion Coupled-Cluster Method for the Electron Affinity | We have presented a multi-layer implementation of the equation of motion coupled-cluster method for the electron affinity, based on local and pair natural orbitals. The method gives consistent accuracy for both localized and delocalized anionic states. It results in many fold speedup in computational timing as compared to the canonical and DLPNO based implementation of the EA-EOM-CCSD method. We have also developed an explicit fragment-based approach which can lead to even higher speed-up with little loss in accuracy. The multi-layer method can be used to treat the environmental effect of both bonded and non-bonded nature on the electron attachment process in large molecules.<br /> | Soumi Haldar; Achintya Kumar Dutta | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7480f702a9b10a118aef8/original/a-multi-layer-approach-to-the-equation-of-motion-coupled-cluster-method-for-the-electron-affinity.pdf |
6218dbb0c3e9da78fb772726 | 10.26434/chemrxiv-2022-24zf4-v2 | Merging Rh-catalyzed C-H Functionalization and Cascade Cyclization to Enable Propargylic Alcohols as Three-Carbon Synthons: Experimental and Computational Investigations | Reported herein is an unprecedented reactivity of propargyl alcohols as “Three-Carbon Synthons” in a Rh(III)-catalyzed C-H functionalization of acetanilides, leading to the synthesis of core structures of isocryptolepine, gamma-carbolines, dihydrochromeno[2,3-b]indoles, and diindolylmethanes derivatives. The transformation involves a Rh(III)-catalyzed C-H functionalization and heteroannulation to yield indoles followed by a cascade cyclization with both external and internal nucleophiles to afford diverse products. The role of the hydroxy group, the key function of the silver additive, the origin of the unique reverse regioselectivity and the rate-determining step, are rationalized in conformity with the combination of experimental, noncovalent interaction analysis and DFT studies. This protocol is endowed with several salient features, including one-pot multistep cascade approach, exclusive regioselectivity, high bond-forming efficiency, and synthesis of a variety of molecular frameworks. | Prajyot Nagtilak; Manoj Mane; Supreeth Prasad; Luigi Cavallo; Dean Tantillo; Manmohan Kapur | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6218dbb0c3e9da78fb772726/original/merging-rh-catalyzed-c-h-functionalization-and-cascade-cyclization-to-enable-propargylic-alcohols-as-three-carbon-synthons-experimental-and-computational-investigations.pdf |
60c740e3ee301c5c81c78b25 | 10.26434/chemrxiv.7854974.v1 | Preparation and Crystal Structure of 1,2-Bis(2,5-Dimethylthiophen-3-Yl)ethane-1,2-Dione | Preparation, crystal structure and <sup>1</sup>H NMR spectrum of 1,2-bis(2,5-dimethylthiophen-3-yl)ethane-1,2-dione is reported. The title compound is a convenient starting material for the preparation of photochromic diarylethenes with various backbones.<br /> | Paweł Pakulski; Dawid Pinkowicz | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e3ee301c5c81c78b25/original/preparation-and-crystal-structure-of-1-2-bis-2-5-dimethylthiophen-3-yl-ethane-1-2-dione.pdf |
662a48d021291e5d1daef493 | 10.26434/chemrxiv-2024-749j2-v2 | Unlocking Metal-Ligand Cooperative Catalytic Photochemical Benzene Carbonylation: A Mechanistic Approach | A key challenge in green synthesis is the catalytic transformation of renewable substrates at high atom and energy efficiency, with minimal exergonicity (ΔG≈0). Non-thermal pathways, i.e., electrochemical and photochemical, can be used to leverage renewable energy resources to drive chemical processes at well-defined energy input and efficiency. Within this context, photochemical benzene carbonylation to produce benzaldehyde is a particularly interesting, albeit challenging, process that combines unfavorable thermodynamics (DG° = 1.7 kcal/mol) and the breaking of strong C-H bonds (113.5 kcal/mol) with full atom efficiency and renewable starting materials. Nevertheless, little progress has been made since this transformation was first reported, in 1980s and ’90s. By following a mechanistic approach, applying spectrophotochemical and computational tools, we sought to gain a detailed understanding of the non-thermal C-H activation of benzene using metal-ligand cooperative (MLC) PNP rhodium complexes. This allowed us to unlock catalytic MLC benzene carbonylation promoted by irradiation in the near-visible UV region (390 nm) for the first time. | Francesco Crisanti; Michael Montag; David Milstein; Julien Bonin; Niklas von Wolff | Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a48d021291e5d1daef493/original/unlocking-metal-ligand-cooperative-catalytic-photochemical-benzene-carbonylation-a-mechanistic-approach.pdf |
65b3b22de9ebbb4db90836a2 | 10.26434/chemrxiv-2024-qm047 | Application of cis-MoO2(OV)2 in Protection of Radiation-Induced DNA Damage | This study investigates the synthesis of a molybdenum complex with a notable capacity to safeguard DNA against radiation-induced damage. Comprehensive analyses reveal that not only the complex [cis-MoO2(OV)2] exhibits a significant radioprotective efficacy which can shield 89% of damaged CT DNA but also the ligand (OV) show a good amount of protection. At a concentration of 2 mM and a radiation dosage of 20 Gy, cis-MoO2(OV)2 demonstrates the ability to protect approximately 85% of radiation-induced damage to plasmid (pUC19) DNA also from gamma rays. These findings underscore the considerable potential of cis-MoO2(OV)2 as an effective radioprotector for normal tissues in radiotherapy. Notably, the complex's capacity to mitigate DNA damage caused by radiation holds significant promise, presenting implications for the advancement of novel therapeutic strategies across various medical conditions. | Priyangana Deb | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b3b22de9ebbb4db90836a2/original/application-of-cis-mo-o2-ov-2-in-protection-of-radiation-induced-dna-damage.pdf |
63a83816b9c5f64908df574c | 10.26434/chemrxiv-2022-7fh2v-v3 | Construction of Cascade Nanozymatic Networks for Cell Mimic with Highly Selective Recognition and Linear Perception to H2O2 | A single stimulus leading to multiple responses is an essential function of many biological enzymatic reaction networks, which enable complex life activities. Owing to the lack of allosteric regulation of natural enzymes, it is challenging to duplicate a similar network using non-living chemicals. Herein, we report a nanozymatic cascade reaction network that demonstrates multiple responses of different modes and intensities upon a single H2O2 stimulus based on a single-atom nanozyme (Co-N-CNTs). Taking the two-electron cascade oxidation of 3,3’,5,5’-tetramethylbenzidine (TMB) as an example, the endogenous product H2O2 competitively inhibited substrates in the first one-electron oxidation at the Co-N4 active site on Co-N-CNTs, while accelerated the second one-electron oxidation under a micellar nanozyme. Using such a nanozymatic network, the feedback and feedforward regulation of product transformation were further applied to microfluidic flow reactors as a cell mimic. Owing to the unique varieties of response in intensities and modes, the proposed cell mimic demonstrated highly selective recognition and linear perception of H2O2 against over 20 interferences in a wide range of concentrations (0.01-100 mM), reminiscent of a primordial life-like process in mutable and harsh conditions. | Caixia Zhu; Zhixin Zhou; Xuejiao J. Gao; Yanhong Tao; Xuwen Cao; Yuan Xu; Yanfei Shen; Songqin Liu; Yuanjian Zhang | Biological and Medicinal Chemistry; Catalysis; Analytical Chemistry; Biochemical Analysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a83816b9c5f64908df574c/original/construction-of-cascade-nanozymatic-networks-for-cell-mimic-with-highly-selective-recognition-and-linear-perception-to-h2o2.pdf |
67929b3afa469535b98d316b | 10.26434/chemrxiv-2025-hgplj | Tuning Quantum Yield to Maximize Nitric Oxide Release Under Red and NIR Light in Photoresponsive Ruthenium Salen Materials | Photoresponsive Ruthenium salen complexes can release NO under blue, red, and NIR light irradiation. The well-known RuNO(Salen) complex was synthesized initially, which exhibited significant NO release when irradiated with red (627 nm) and NIR (810 nm) light, achieving quantum yields of 0.107 ± 0.01 and 0.00100 ± 0.00007, respectively. Due to the stability and tunability of Salen ligands, further modifications to the Salen structure noticeably influenced the photoreactivity and NO release, where introduction of an -OH group to the 4-position, meta to the imine, emerged as the ideal configuration across to maximize NO release, especially with red and NIR light. Remarkably, incorporating a longer alkyl chain to form the ruthenium-based polymer also significantly enhanced NO release, suggesting improved interactions between the ruthenium center and nitrosated species in polymeric systems that incorporate RuNO(salen) moieties. Additionally, experiments utilizing biological tissue barriers demonstrated that red and NIR light effectively penetrated tissues, stimulating NO release from the RuNO(salen-polymer) in solution, thereby underscoring the potential of these complexes in targeted therapeutic applications. This work elucidates the structure-activity relationship in photoresponsive RuNO(salen) complexes and paves the way for innovative application of materials that can release NO with specific timing and duration of light irradiation, such technology has promising implications in catheter-related infection prevention, where NO release could act as an antimicrobial agent, minimizing infection risk through local, controlled release within catheter systems. | Fatima Naser Aldine; Dayana A. Muizzi; Irene F. Baraza; Joseph C. Furgal; Alexis D. Ostrowski | Inorganic Chemistry; Polymer Science; Inorganic Polymers; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67929b3afa469535b98d316b/original/tuning-quantum-yield-to-maximize-nitric-oxide-release-under-red-and-nir-light-in-photoresponsive-ruthenium-salen-materials.pdf |
67ad2d576dde43c908a37bc8 | 10.26434/chemrxiv-2025-352vm | Machine learning-guided materials and system co-design for high-pressure hydrogen compression | Cost effective and reliable hydrogen compression remains a challenging barrier in the wide-spread adoption of hydrogen as an energy carrier. The prevailing technology of mechanical compression suffers from several drawbacks, some of which can be addressed by non-mechanical compression strategies (e.g., electrochemical or metal hydride-based thermal compression). Thermally driven metal hydride compression strategies typically rely on multi-stage metal hydride-based compressors; however, discovering or optimizing low-stability metal hydrides that can pressurize hydrogen upwards of 1000 bar is difficult, both with respect to computational predictions and experimental validation. Here we (1) demonstrate that simple machine learning-derived design rules can inform rational design of alloying strategies yielding low-stability hydrides, (2) validate their experimental pressure-composition-temperature (PCT) isotherms up to 875 bar, and (3) utilize a dynamic systems-level model of a metal hydride compressor design to evaluate their performance under realistic operating conditions. Importantly, this analysis yields predicted operational efficiencies of both 2-stage (90-875 bar) and 3-stage (20-875 bar) metal hydride compressors to enable further evaluation of this technology and its techno-economic outlook. | Matthew Witman; Brendan Davis; Vitalie Stavila; Terry Johnson | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Alloys; Fuels - Materials; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ad2d576dde43c908a37bc8/original/machine-learning-guided-materials-and-system-co-design-for-high-pressure-hydrogen-compression.pdf |
671a6efe1fb27ce1246f94dc | 10.26434/chemrxiv-2024-3w9kv | Multiple Emission Peaks Hinder Polariton Condensation in 2D Perovskite Microcavities | Two-dimensional metal halide phases, commonly known as 2D perovskites, have emerged as promising materials for exciton polaritons, particularly for polariton condensation. This process entails the spontaneous accumulation of population in the polariton ground state and relies on efficient energy relaxation. In this class of materials, this relaxation is mediated by exciton reservoir emission, which pumps polariton states through radiative pumping. To achieve strong light-matter coupling and sustain a high polariton density, the material must possess excitations with large oscillator strength and high exciton binding energy. While 2D perovskites exhibit these desirable characteristics, there are no reports of room-temperature polariton condensation and only one successful demonstration at cryogenic temperatures. In this work, we systematically explore the role of energy alignment between the exciton reservoir emission and the lower polariton branch in populating the polariton ground state via radiative pumping. Through cavity detuning, we shift the lower polariton energy minimum to overlap with the emission of the exciton reservoir at different energies. We identify that the multiple radiative pathways of 2D perovskites lead to inefficient radiative pumping of the lower polariton branch at the lowest energy state, ultimately posing challenges for polariton condensation in this class of materials.
| Martin Gomez-Dominguez; Victoria Quirós-Cordero; Esteban Rojas-Gatjens; Katherine A Koch; Evan J Kumar; Carlo A.R Perini; Natalie Stingelin; Carlos Silva; Ajay Ram Srimath Kandada; Vinod Menon; Juan-Pablo Correa-Baena | Energy | CC BY 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a6efe1fb27ce1246f94dc/original/multiple-emission-peaks-hinder-polariton-condensation-in-2d-perovskite-microcavities.pdf |
6349782b4b0af3795bc55465 | 10.26434/chemrxiv-2022-18bff | Assessing the role of the Kohn-Sham density in the calculation of the low-lying Bethe-Salpeter excitation energies | We adopt the GW many-body perturbation theory
in conjunction with the Bethe-Salpeter equation (BSE) to compute 57 excitation energies of a set of 37 molecules in order to shed light on the dependence on the initial Kohn-Sham (KS) density functional. By using the PBEh global hybrid and a self-consistent scheme on the eigenvalue, our calculations show a weak correlation between the change in the BSE energies upon variation of the exact exchange fraction (α) and the change in the GW quasiparticle energy of the corresponding electronic levels, pointing to the critical role of the KS electronic density.
In order to address the arbitrariness in the mean field choice, we adopt an orbital-tuning scheme where the amount of exact exchange is tuned to fulfill the ionization potential theorem in DFT. The performance of the proposed scheme is found to be similar to M06-2X and PBEh with α=75%, consistent with tuned-values of α ranging between 60% and 80%. Interestingly, the best performers yield systematically smaller errors for n → π∗ excitations than for π → π∗. | Aseem Rajan Kshirsagar; Roberta Poloni | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6349782b4b0af3795bc55465/original/assessing-the-role-of-the-kohn-sham-density-in-the-calculation-of-the-low-lying-bethe-salpeter-excitation-energies.pdf |
62fcfe00f8cdca24e7fc78d5 | 10.26434/chemrxiv-2022-4h8lf-v2 | The discovery of high affinity and metabolically stable allosteric cyclin-dependent kinase 2 (CDK2) inhibitors from screening through lead optimization | Despite the status of cyclin-dependent kinase 2 (CDK2) as a validated target for both anticancer and contraceptive indications, a CDK2 inhibitor with exquisite selectivity has been historically challenging, largely due to the structural similarity of the ATP-binding site where most kinase inhibitors bind. We previously discovered an allosteric pocket in CDK2 with potential to bind a compound with desirable selectivity. Using high-throughput and virtual screening methods, we discovered and structurally confirmed an anthranilic acid scaffold that binds this pocket with high affinity. We previously reported that these allosteric CDK2 inhibitors demonstrate a negative cooperative relationship with cyclin binding, are selective for CDK2 over the structurally similar kinase CDK1 and show potential as a non-hormonal contraceptive agent. In this work, we describe our screening and lead optimization efforts that led to the discovery of compounds in this series like EF-4-177 with nanomolar affinity for CDK2. EF-4-177 is metabolically stable with a desirably long ½ life and adequate tissue distribution in mice, demonstrating the potential of this series as a therapeutic. This work details the discovery of the highest affinity allosteric CDK inhibitors reported and shows promise for further development of this series to yield an efficacious and selective allosteric CDK2 inhibitor. | Erik B. Faber; Nan Wang; Kristen John; Luxin Sun; David Burban; Henry L. Wong; Rawle Francis; Defeng Tian; Kwon H. Hong; An Yang; Liming Wang; Mazen Elsaid; Hira Khalid; Nicholas Levinson; Ernst Schönbrunn; Jon E. Hawkinson; Gunda Georg | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fcfe00f8cdca24e7fc78d5/original/the-discovery-of-high-affinity-and-metabolically-stable-allosteric-cyclin-dependent-kinase-2-cdk2-inhibitors-from-screening-through-lead-optimization.pdf |
64f5b840dd1a73847f29f818 | 10.26434/chemrxiv-2023-f7bvw | Water-assisted generation of catalytic interface:
The case of interfacial Pt-FeOx(OH)y sites active in
preferential carbon monoxide oxidation
| The surface of supported heterogeneous catalysts often contains adsorbed water and hydroxyl groups even when water is not directly added to the reaction stream. Nonetheless, the reactivity of adsorbed water and hydroxyl groups is rarely considered. We demonstrate that water and hydroxyl groups can not only directly participate in the catalytic oxidation processes but are also able to generate and stabilize the catalytically active metal-oxide interface. We show that the reduction of Pt-Fe-supported catalysts with hydrogen in the presence of adsorbed water or steam allows for achieving one of the highest preferential carbon monoxide oxidation activities at ambient temperature. These conditions create active iron-associated hydroxyl groups next to platinum nanoparticles with enhanced reactivity towards carbon mon-oxide oxidation. Density functional theory calculations suggest that hydroxylation of oxidic iron species stabilizes the FeOx(OH)y/Pt interface, via strong metal-support interaction, which is confirmed by chemisorption measurements. Kinetic experiments, including those with 18O-labeled water, in combination with operando infrared spectroscopy, show that water and hydroxyl groups directly participate in preferential carbon monoxide oxidation. A quantitative correlation between the catalytic activity of Pt-FeOx(OH)y/γ-Al2O3 catalysts and the Fe2+ concentration, obtained using operando X-ray absorption spectroscopy, shows that the number of active Fe2+ sites and the carbon monoxide oxidation rate per active site can be significantly increased by water-assisted pretreatment with hydrogen. This work provides a new example of positive role of strong metal-support interaction for the design of more active catalysts. | Ilia I. Sadykov; Dennis Palagin; Frank Krumeich; Igor V. Plokhikh; Jeroen A. van Bokhoven; Maarten Nachtegaal; Olga V. Safonova | Physical Chemistry; Catalysis; Heterogeneous Catalysis; Redox Catalysis; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f5b840dd1a73847f29f818/original/water-assisted-generation-of-catalytic-interface-the-case-of-interfacial-pt-fe-ox-oh-y-sites-active-in-preferential-carbon-monoxide-oxidation.pdf |
6422ea9891074bccd06e3712 | 10.26434/chemrxiv-2023-s7zp9-v2 | Ultrabright two-photon excitable red-emissive fluorogenic probes for fast and wash-free bioorthogonal labeling in live cells | Fluorogenic bioorthogonal reactions are promising tools for tracking small molecules or biomolecules in living organisms. Two-photon excitation, by shifting absorption towards the red, significantly increases the signal-to-noise ratio and decreases photodamages, while allowing to image about 10 times deeper than with a confocal. However, efficient two-photon excitable fluorogenic probes are currently lacking. We report here the design and synthesis of fluorogenic probes based on a two-photon excitable fluorophore and a tetrazine quenching moiety. These probes react with bicyclo[6.1.0]no-4-yn-9yl)methanol (BCN) with good to impressive kinetic rate constant (up to 1.1x103 M-1.s-1) and emit in the red window with moderate to high turn-on. TDDFT allowed to rationalize both the kinetic and fluorogenic performance of the different probes. The best candidate displays a turn-on of 13.8-fold measured by fluorescence intensities quantification in living cells under one-photon excitation, whereas a value of 3 is enough for live-cell imaging with high contrast. Moreover, live-cell imaging under two-photon excitation confirmed that there was no need for washing to monitor the reaction between BCN and this probe as a turn-on of 8.0-fold was measured under two-photon excitation. Finally, the high two-photon brightness of the clicked adduct (>300 GM) allows the use of a weak laser power compatible with in vivo imaging. | Marie Auvray; Delphine Naud-Martin; Gaëlle Fontaine; Frédéric Bolze; Gilles Clavier; Florence Mahuteau-Betzer | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422ea9891074bccd06e3712/original/ultrabright-two-photon-excitable-red-emissive-fluorogenic-probes-for-fast-and-wash-free-bioorthogonal-labeling-in-live-cells.pdf |
65a2a8bae9ebbb4db912951b | 10.26434/chemrxiv-2024-zf116 | Markovnikov Selective Hydroboration of Aryl Alkenes Catalyzed by Quaternary Ammonium Salts | Despite recent advancements in the development of catalytic Markovnikov-selective hydroboration of alkenes, the metal-free procedure has long remained an unsolved challenge. Here, we report an organocatalytic Markovnikov-selective hy-droboration of aryl alkenes using a commercially available quaternary ammonium catalyst. The method is operationally simple, scalable, and compatible with a wide variety of substrates and it can be successfully applied in the synthesis of active pharmaceutical ingredients (API) such as Chlorphenoxamine. Through in-depth experimental and DFT studies, we elucidate a nuanced understanding of the mechanism and regioselectivity of this reaction. | Paweł Huninik; Hoyoung Im; Jakub Szyling; Mu-Hyun Baik; Jędrzej Walkowiak | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a2a8bae9ebbb4db912951b/original/markovnikov-selective-hydroboration-of-aryl-alkenes-catalyzed-by-quaternary-ammonium-salts.pdf |
662a7ae891aefa6ce16b6418 | 10.26434/chemrxiv-2024-xs262 | Star-shaped conformers generated by co-evolutionary docking predict cross-fitting glycoprotein trimer pre-fusion interfaces on VHSV fish rhabdovirus | Despite the abundant diseases caused by rhabdoviruses on plants, animals and men, there are no approved therapeutic drugs. This work targeted viral hemorrhagic septicemia viruses (VHSV), a group of representative rhabdoviruses causing devastating world-wide diseases on fish farmed-species. In particular, their glycoprotein (gpGVHSV) trimers were computationally targeted at its earliest pre-fusion inner interface. Co-evolution initiated from an optimized 2D-molecular parent and the corresponding gpGVHSV -conformer 3D cavity, generated tens of thousands of raw-children, and selected hundreds of cross-fitting conformer variations in a few scaffolds. Their predicted drug-like high affinities in nanoMolar ranges, low toxicities and targeting the pre-fusion inner interface were confirmed by independent algorithms | julio coll | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a7ae891aefa6ce16b6418/original/star-shaped-conformers-generated-by-co-evolutionary-docking-predict-cross-fitting-glycoprotein-trimer-pre-fusion-interfaces-on-vhsv-fish-rhabdovirus.pdf |
60c7447f4c89197b52ad2807 | 10.26434/chemrxiv.9849806.v1 | Atmospheric Pressure Microplasma for Antibacterial Silver Nanoparticle/Chitosan Nanocomposites With Tailored Properties | <p>Room temperature atmospheric pressure
microplasma (APM) was deployed for the first time for the in situ synthesis of
anti-bacterial silver nanoparticle / chitosan (AgNP/CS) nanocomposites. The
plasma induced liquid chemistry plays a role in the in situ formation of AgNP,
the size distribution of which depends on the silver salt precursor
concentration. The microplasma process has also simultaneously tailored the
physical properties of the composites, rendering more crosslinked chitosan polymer
network with shorter molecular chains. The formation of AgNP within the <i>in situ</i> modified chitosan has led to
nanocomposites with overall improved mechanical properties and better stability
in simulated body fluid. Our plasma synthesized AgNP/CS nanocomposites also
demonstrate effective antibacterial properties against <i>E. Coli</i> and <i>S. Aureus</i>
bacterial strains, showing their promise in potential antimicrobial
applications.</p> | Daye Sun; Jonathan Turner; Nan Jiang; Songsong Zhu; Li Zhang; Brian Falzon; Colin McCoy; PAUL MAGUIRE; Davide Mariotti; dan Sun | Composites | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7447f4c89197b52ad2807/original/atmospheric-pressure-microplasma-for-antibacterial-silver-nanoparticle-chitosan-nanocomposites-with-tailored-properties.pdf |
672bc0775a82cea2fa4665e3 | 10.26434/chemrxiv-2024-q7rc7 | Direct photochemical control of imine exchange reactions | External light stimulus is used to reach out-of-equilibrium states in systems of three imines. By adjusting the wavelength, speci c components of the system are addressed. The photostationary states change the composition, exceeding what is possible under thermal excitation. Intermolecular energy transfer in complex systems is described and underlaying mechanisms propose | Harry Robson; Petr Kovaricek | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672bc0775a82cea2fa4665e3/original/direct-photochemical-control-of-imine-exchange-reactions.pdf |
6333edeb084700950b8c2885 | 10.26434/chemrxiv-2022-6s89g | Discovery of 2,6-Dihalopurines as Stomata Opening Inhibitors: Implication of an LRX-mediated H+-ATPase Phosphorylation Pathway | Stomata are pores in the leaf epidermis of plants and their opening and closing regulate gas exchange and water transpiration. Stomatal movements play key roles in both plant growth and stress responses. In recent years, small molecules regulating stomatal movements have been used as a powerful tool in mechanistic studies, as well as key players for agricultural applications. Therefore, the development of new molecules regulating stomatal movement and the elucidation of their mechanisms have attracted much attention. We herein describe the discovery of 2,6-dihalopurines, AUs, as a new stomatal opening inhibitor, and their mechanistic study. Based on biological assays, AUs may involve in the pathway related with plasma membrane H+-ATPase phosphorylation. In addition, we identified leucine-rich repeat extensin proteins (LRXs), LRX3, LRX4 and LRX5 as well as RALF, as target protein candidates of AUs by affinity based pull down assay and molecular dynamics simulation. The mechanism of stomatal movement related with the LRXs–RALF is an unexplored pathway, and therefore further studies may lead to the discovery of new signaling pathways and regulatory factors in the stomatal movement. | Kenichiro Itami; Ayaka Ueda; Yusuke Aihara; Shinya Sato; Keiko Kano; Emi Mishiro-Sato; Hiroyuki Kitano; Ayato Sato; Kazuhiro Fujimoto; Takeshi Yanai; Kazuma Amaike; Toshinori Kinoshita | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6333edeb084700950b8c2885/original/discovery-of-2-6-dihalopurines-as-stomata-opening-inhibitors-implication-of-an-lrx-mediated-h-at-pase-phosphorylation-pathway.pdf |
60c743f69abda21734f8c2b2 | 10.26434/chemrxiv.9725450.v1 | Design and Development of a Video Game to Assess Problem-Solving Competence in Chemistry Education | <p>The aim of this study is to present how to implement the constructive
learning theory and self-determination theory into a video game. This
video game is designed as a new
kind of teaching
tool for chemistry
concepts and as an assessment tool for domain-specific problem-solving competence, by applying a problem-solving model and the
factors of self-determination theory through game elements. These types of
video games are designed not only to have fun
and motivate students, but also to help the teachers and educators to assess
their students according to their weaknesses and strengths in each particular
phase of the competence. Thus, educators could improve their teaching
strategy or use the tools to improve weak areas. Based on this idea, we developed ALCHEMIST. ALCHEMIST targeted
the 9th-grade students in the German chemistry curriculum. The scientific
content is about acids, bases, and indicators, and is designed and based on the
problem-solving model to access this competence of the students. The 3D game
framework was chosen for this game
since it makes the game efficient, interactive and drives it into more virtual reality. The designing process was complicated, as it includes
multidisciplinary work across psychology, design,
scientific content, development and programming, which makes it challenging. To cover these points, we followed
a game design model, adding some steps to cover the educational needs and the aim of the game.</p><p>In order to make the game more effective and
interactive, and to drive it into a more
virtual world, the 3D game framework was chosen for this game since for this
age group a 3D educational game is
expected to be more effective (Gunter
et al, 2008; Terzidou et al, 2012) .
Moreover, the use of avatars in the
3D virtual environment establishes non-verbal communication (NVC) features,
which can foster collaboration interactions, and enhance the student’s ability
to apply abstract knowledge later in reality (Dede, 1992; Tsiatsos and Terzidou, 2010). The log file provided shows the player points and gameplay path which indicates the performance levels for each
problem set. Also, it can help teachers to evaluate
each particular phase of problem-solving competence. After the success
of the development of our game-based theoretical background, it will be tested and validated by experts in chemistry education. This validation process should examine if the
problem-solving model is correctly applied and test the significance of the
game design, scientific content and
the game’s objective.</p><p>It may also be of
interest to develop such video games with scientific content and educational
background in other fields. It also would be a
success for the scientist to apply the
scientific content through a fantasy 3D video game to the students at different
ages to have fun, to learn, and to
assess their competencies.</p> | Amany Annaggar; Rüdiger Tiemann | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f69abda21734f8c2b2/original/design-and-development-of-a-video-game-to-assess-problem-solving-competence-in-chemistry-education.pdf |
62c9f2963be5f14c5415029a | 10.26434/chemrxiv-2022-pkqs1-v2 | An Approach to High Throughput Measurement of Accurate Retention Data in Liquid Chromatography | Efforts to model and simulate various aspects of liquid chromatography (LC) separations (e.g., retention, selectivity, peak capacity, injection breakthrough) depend on experimental retention measurements to use as the basis for the models and simulations. Often these modeling and simulation efforts are limited by datasets that are too small because of the cost (time and money) associated with making the measurements. Other groups have demonstrated improvements in throughput of LC separations by focusing on “overhead” associated with the instrument itself – for example, between-analysis software processing time, and autosampler motions. In this paper we explore the possibility of using columns with small volumes (i.e., 5 mm x 2.1 mm i.d.) compared to conventional columns (e.g., 100 mm x 2.1 mm i.d.) that are typically used for retention measurements. We find that isocratic retention factors calculated for columns with these dimensions are different by about 20%; we attribute this difference – which we interpret as an error in measurements based on data from the 5 mm column – to extra-column volume associated with inlet and outlet frits. Since retention factor is a thermodynamic property of the mobile/stationary phase system under study, it should be independent of the dimensions of the column that is used for the measurement. We propose using ratios of retention factors (i.e., selectivities) to translate retention measurements between columns of different dimensions, so that measurements made using small columns can be used to make predictions for separations that involve conventional columns. We find that this approach reduces the difference in retention factors (5 mm compared to 100 mm columns) from an average of 18% to an average absolute difference of 1.7% (all errors less than 8%). This approach will significantly increase the rate at which high quality retention data can be collected to thousands of measurements per instrument per day, which in turn will likely have a profound impact on the quality of models and simulations that can be developed for many aspects of LC separations. | Dwight Stoll; Gudrun Kainz; Tina Dahlseid; Trevor Kempen; Tyler Brau; Bob Pirok | Analytical Chemistry; Analytical Apparatus; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c9f2963be5f14c5415029a/original/an-approach-to-high-throughput-measurement-of-accurate-retention-data-in-liquid-chromatography.pdf |
64aeed2eba3e99daeffb3bc7 | 10.26434/chemrxiv-2023-fphj8-v2 | Photovoltaic Wafering Silicon Kerf Loss as Raw Material: Example of Negative Electrode for Lithium-Ion Battery | Silicon powder kerf loss from diamond wire sawing in the photovoltaic wafering industry is a highly appealing source material for use in lithium-ion battery negative electrodes. Here, it is demonstrated for the first time that the kerf particles from three independent sources contain ~50 % amorphous silicon. The crystalline phase is in the shape of nano-scale crystalline inclusions in an amorphous matrix. From literature on wafering technology looking at wafer quality, the origin and mechanisms responsible for the amorphous content in the kerf loss powder are explained. In order to better understand for which applications the material could be a valuable raw material, the amorphicity and other relevant features are thoroughly investigated by a large amount of experimental methods. Furthermore, the kerf powder was crystallized and compared to the partly amorphous sample by operando X-ray powder diffraction experiments during battery cycling, demonstrating that the powders are relevant for further investigation and development for battery applications. | Mads C. Heintz; Jekabs Grins; Aleksander Jaworski; Gunnar Svensson; Thomas Thersleff; William R. Brant; Rebecka Lindblad; Andrew J. Naylor; Kristina Edström; Guiomar Hernández | Materials Science; Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64aeed2eba3e99daeffb3bc7/original/photovoltaic-wafering-silicon-kerf-loss-as-raw-material-example-of-negative-electrode-for-lithium-ion-battery.pdf |
67ca1a796dde43c908d1386a | 10.26434/chemrxiv-2025-jcfn4 | A Vibration-Induced Emission-Based Ratiometric Sensor For Detection Of Anions In Aqueous Solution | Sensors that respond to anions via vibration-induced emission (VIE) have recently emerged as effective tools for discrimination between closely-related carboxylate species in non-competitive, organic solvents. However, the utility of this sensing mechanism has not yet been demonstrated for anions in aqueous media. Here, we prepared two sensors, monoZnDPA-DPAC and ZnDPA-DPAC, with either one or two anion-binding motifs. These systems are capable of binding to anions in water. Dual emission via VIE is maintained in solvent mixtures of up to 70% water. ZnDPA-DPAC provides a unique, ratiometric response to citrate and phosphate, which was used for the accurate quantification of aqueous solutions of these anions. | Stephen M. Butler; Nikki A Tzioumis; Katrina A Jolliffe | Organic Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca1a796dde43c908d1386a/original/a-vibration-induced-emission-based-ratiometric-sensor-for-detection-of-anions-in-aqueous-solution.pdf |
60c74957bdbb89503aa39169 | 10.26434/chemrxiv.12052803.v1 | Influence of VC and FEC Additives on Interphase Properties of Carbon in Li-Ion Cells Investigated by Combined EIS & EQCM-D | <div>The electrolyte additives vinylene carbonate (VC) and fluoroethylene carbonate (FEC) are well known for increasing the lifetime of a Li-ion battery cell by supporting the formation of an effective solid electrolyte interphase (SEI) at the anode. In this study combined simultaneous electrochemical impedance spectroscopy (EIS) and <i>operando</i> electrochemical quartz crystal microbalance with dissipation monitoring (EQCM-D) are employed together with <i>in situ</i> gas analysis (OEMS) to study the influence of VC and FEC on the passivation process and the interphase properties at carbon-based anodes. In small quantities both additives reduce the initial interphase mass loading by 30 to 50 %, but only VC also effectively prevents continuous side reactions and improves anode passivation significantly. VC and FEC are both reduced at potentials above 1 V vs. Li<sup>+</sup>/Li in the first cycle and change the SEI composition which causes an increase of the SEI shear storage modulus by over one order of magnitude in both cases. As a consequence, the ion diffusion coefficient and conductivity in the interphase is also significantly affected. While small quantities of VC in the initial electrolyte increase the SEI conductivity, FEC decomposition products hinder charge transport through the SEI and thus increase overall anode impedance significantly. </div> | Paul Kitz; Matthew Lacey; Petr Novák; Erik Berg | Electrochemical Analysis; Electrochemistry; Energy Storage; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74957bdbb89503aa39169/original/influence-of-vc-and-fec-additives-on-interphase-properties-of-carbon-in-li-ion-cells-investigated-by-combined-eis-eqcm-d.pdf |
60c74c2c9abda28ad1f8d225 | 10.26434/chemrxiv.12410213.v1 | Photoactivatable dihydroalkaloids for cancer theranostics with AIE characteristics | Chemotherapeutics with systemic administration usually suffer from low treatment efficacy and off-target toxicity. In contrary, the photoactivatable cancer theranostics can achieve image-guided precise control of therapeutic dose and location. However, the conventional photoactivatable chemotherapeutics usually require decoration of chemotherapeutics with additional photo-responsive groups through tedious synthetic procedures, which can lead to undesirable toxic byproducts and seriously restrict their applications. Herein, we propose a new strategy for photoactivatable caner theranostics based on photooxidative dehydrogenation reaction, which is only associating with water as the byproduct. To demonstrate the power of this strategy, we utilized the natural dihydrobenzo[c]phenanthridine alkaloids of DHCHE and DHSAN as photoactivatable theranostics to achieve selective imaging and killing of cancer cells by in situ transformation into nucleus-targeted CHE and SAN under light irradiation. Notably, CHE is featured with aggregation-induced emission (AIE) characteristics, which can be used for precise control of the photoactivatable therapeutic dose. This photoactivatable strategy based on dihydroalkaloids is thus promising for precise cancer treatment in clinic.<br /> | Xia Ling; Letao Huang; Youzhen Li; Qing Wan; Zhiming Wang; Anjun Qin; Meng Gao; Ben Zhong Tang | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c2c9abda28ad1f8d225/original/photoactivatable-dihydroalkaloids-for-cancer-theranostics-with-aie-characteristics.pdf |
60dcbbcbe0330e1f5812b927 | 10.26434/chemrxiv-2021-41kh8 | New inhibitors of p38 mitogen-activated protein kinase: Repurposing of existing drugs with deep learning | P38-alpha (MAPK14) is a protein kinase that is implicated in the pathological mechanisms of BAG3 P209L myofibrillar myopathy, cancers, Alzheimer’s disease and other diseases like rheumatoid arthritis. Inhibition of p38 has shown promise as treatment for these diseases. Traditional drug discovery methods were unable to create both effective and safe small molecule inhibitors, so we used machine learning to elucidate potential p38 blockers from existing FDA-approved drugs. Using available bioactivity data, we determined the best existing p38 inhibitors and applied fingerprint clustering to isolate the compounds with similar structures. Descriptors were calculated for these clustered compounds and the most important of these descriptors were determined through a machine-learning based feature selection algorithm. This data served as the training set for a deep neural network that was fine-tuned to a 92% validation accuracy. The neural network model was applied to a database of FDA-approved drugs, revealing 149 potential p38 inhibitors, whose efficacy were confirmed by docking simulations to be statistically significantly higher than random FDA drugs and slightly higher than known inhibitors. Our study not only reveals potential treatments for p38-mediated diseases but also demonstrates the capability of integrating various machine-learning techniques and computational algorithms to predict novel functions of existing pharmaceuticals. | Aakarsh Vermani; Valentina Kouznetsova; Igor Tsigelny | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2021-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dcbbcbe0330e1f5812b927/original/new-inhibitors-of-p38-mitogen-activated-protein-kinase-repurposing-of-existing-drugs-with-deep-learning.pdf |
6172f3d84c04e8fd058c80bc | 10.26434/chemrxiv-2021-r4dlq | Guest-induced misfolding of a crown-ether-functionalized ortho-phenylene | A crown-ether-functionalized o-phenylene tetramer has been synthesized and co-assembled with monotopic and ditopic, achiral and chiral secondary ammonium ion guests. NMR spectroscopy shows that the o-phenylene forms both 1:1 and 1:2 complexes with monotopic guests while remaining well-folded. Binding of an elongated ditopic guest, however, forces the o-phenylene to misfold by pulling the terminal rings apart. A chiral ditopic guest biases the o-phenylene twist sense. | Sumalatha Peddi; Molly C. Bookout; Gopi Nath Vemuri; C. Scott Hartley | Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6172f3d84c04e8fd058c80bc/original/guest-induced-misfolding-of-a-crown-ether-functionalized-ortho-phenylene.pdf |
672b1509f9980725cf466be1 | 10.26434/chemrxiv-2024-bjcbm | Investigating the Mechanism of Kainate Receptor and Identifying its Inhibitors Using In-Silico Techniques | The GluK1 receptor, an ionotropic glutamate receptor, operates as a ligand-gated ion channel. Opioids stand as the most potent pain-relieving medications currently prescribed in the medical field. Inhibiting this receptor is anticipated to result in a reduction of dopamine release in the Nucleus Accumbens, effectively preventing the primary factor contributing to addiction. In addition, in the absence of the glutamate, the GluK1 receptor cavity should shrink and expand in the presence of it. We hypothesized that the glutamate binding and unbinding in the receptor cavity should result in major conformational changes (cavity opening and closing activity) in the glutamate binding site. In the current research, we utilized computational techniques, specifically molecular dynamics simulations, to initiate an examination of the GluK1 receptor and its mechanism for binding with glutamate. Additionally, we employed molecular docking methods to predict compounds capable of binding to the glutamate binding site, potentially inhibiting this receptor. Our simulations have highlighted that the primary fluctuations within the receptor predominantly occur during glutamate binding. Lastly, we have also proposed a mechanism for how glutamate binds to the receptor. | Amrutha Kara; Gaurav Sharma | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672b1509f9980725cf466be1/original/investigating-the-mechanism-of-kainate-receptor-and-identifying-its-inhibitors-using-in-silico-techniques.pdf |
625355f0ed4d88348b06c1de | 10.26434/chemrxiv-2022-k76gn | Phosphine-Mediated Three-Component Bioconjugation of Amino- and Azidosaccharides in Ionic Liquids | Bioconjugation of carbohydrates has advanced the modern chemical biology and medical science research by incorporation of desired functionalities to the oxygen-rich biomolecules. However, the labeling process or selective chemical reaction of carbohydrates have been a challenging task because of their chemical, functional, and structural diversities, and no single chemical modification tool can be universally applicable to all the target substrates in different environments. In this report, we have developed a bioconjugation strategy for labeling of carbohydrate derivatives through a phosphine-mediated three-component coupling reaction in an ionic liquid medium. The multiple characterization methods identified a urea group as the reaction product of the phosphine-mediated coupling through the installation of carbonyl group from carbon dioxide in air and loss of nitrogen gas from the azide group. We have developed purification protocols to facilitate the cleanup and analysis of ionic liquid-based bioconjugation processes, which can be used for a diverse set of carbohydrate derivatives. The phosphine-mediated urea-forming reaction was applied to a variety of amine- and azide-containing carbohydrates such as antibiotics, anti-tumor agent, and polysaccharide with corresponding azide- and amine-based reagent, respectively. The ionic liquid-based bioconjugation was amenable for the chemical modification of the mammalian cell lysate in an azide-dependent manner. Thus, the present report represents not only the advancement of the nonaqueous bioconjugation method for carbohydrate derivatives from the reaction development perspectives, but also their practical utility for creation of carbohydrate conjugates as well as a study tool of the biomolecule through the bioorthogonal chemistry-like reactivity. | Jun Ohata; Yvonne Hall; Chiamaka Uzoewulu; Zeinab Nizam; Seiya Ishizawa; Hisham El-Shaffey | Biological and Medicinal Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625355f0ed4d88348b06c1de/original/phosphine-mediated-three-component-bioconjugation-of-amino-and-azidosaccharides-in-ionic-liquids.pdf |
60c757f9702a9bdb7018cbd4 | 10.26434/chemrxiv.12996665.v1 | A Comprehensive Discovery Platform for Organophosphorus Ligands for Catalysis | The design of molecular catalysts typically involves reconciling multiple conflicting property requirements, largely relying on human intuition and local structural searches. However, the vast number of potential catalysts requires pruning of the candidate space by efficient property prediction with quantitative structure-property relationships. Data-driven workflows embedded in a library of potential catalysts can be used to build predictive models for catalyst performance and serve as a blueprint for novel catalyst designs. Herein we introduce <i>kraken</i>, a discovery platform covering monodentate organophosphorus(III) ligands providing comprehensive physicochemical descriptors based on representative conformer ensembles. Using quantum-mechanical methods, we calculated descriptors for 1,558 ligands, including commercially available examples, and trained machine learning models to predict properties of over 300,000 new ligands. We demonstrate the application of <i>kraken</i> to systematically explore the property space of organophosphorus ligands and how existing datasets in catalysis can be used to accelerate ligand selection during reaction optimization. | Tobias Gensch; Gabriel dos Passos Gomes; Pascal Friederich; Ellyn Peters; Theophile Gaudin; Robert Pollice; Kjell Jorner; AkshatKumar Nigam; Michael Lindner D'Addario; Matthew S. Sigman; Alan Aspuru-Guzik | Physical Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Homogeneous Catalysis; Organocatalysis; Catalysis; Ligand Design; Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757f9702a9bdb7018cbd4/original/a-comprehensive-discovery-platform-for-organophosphorus-ligands-for-catalysis.pdf |
63d3d70c1a1eadde46b9d860 | 10.26434/chemrxiv-2023-05pvx | Chemoenzymatic oxidation of diols catalyzed by co-immobilized flavins and dehydrogenases | Enzyme driven oxidations catalyzed by alcohol dehydrogenases rely on the in situ NAD(P)+ regeneration. A wide variety of chemoenzymatic and fully enzymatic methods have been reported over the last 30 years to integrate the cofactor regeneration in biocatalytic oxidations. However, the most examples are limited to homogeneous systems where the reuse of both enzymes and chemical catalysts are challenging. In this work, we co-immobilized an alcohol dehydrogenase from Bacillus stearothermophilus with a flavin derivative (FMN), which performs as an organocatalyst that oxidizes NADH back to NAD+. This latter oxidized cofactor is sequentially utilized by the dehydrogenase to oxidize 1,-diols. Remarkably, the immobilization chemistry of the FMN determines its efficiency to recycle the nicotinamide cofactor and, unlike in its free state, the immobilized FMN can oxidizes NADH in dark. This was possible because the support where both enzyme and FMN are immobilized also captures NADH, and makes the electron transfer from the substrates to the cofactors more efficient. This work illustrates how the co-immobilization and confinement of bio and chemical catalysts on solid materials (heterogeneous system) enable chemoenzymatic cascades that are precluded in solution (homogeneous system). | Sergio Fernando Castillo Pacheco; Maria Jesus Moran Plata; José Ignacio Santos; Luca Salassa; Fernando López-Gallego | Materials Science; Catalysis; Chemical Engineering and Industrial Chemistry; Biocatalysis; Heterogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d3d70c1a1eadde46b9d860/original/chemoenzymatic-oxidation-of-diols-catalyzed-by-co-immobilized-flavins-and-dehydrogenases.pdf |
60c73f1c702a9b6796189ea0 | 10.26434/chemrxiv.7243454.v1 | Deswelling Induced Morphological Changes in Dual pH and Temperature Responsive Ultra-Low Crosslinked Poly (N-Isopropyl Acrylamide)-Co-Acrylic Acid Microgels | <div>We demonstrated the deswelling
induced morphological change in dual pH and Temperature responsive ultra-low crosslinked Poly (N-isopropyl acrylamide)-co-acrylic
acid microgels. The responsivity with pH and temperature were studied by light scattering and atomic force microscopy. Light scattering
data suggest that at pH 4.5 the microgels undergo multiple transitions
associated with collapse of pNIPAm-rich segments and repulsion between the
AAc-rich segments. The evolution of punctate structures around the periphery or
throughout the whole microgels at pH 4.5 and 6.5 respectively was revealed by AFM,
further illustrating the heterogeneous deswelling present in the ionized
copolymer microgels.</div><div>The impact of this
study and understanding how ionization state of copolymer dictates the overall
structural properties of microgels will widen our understanding for their applications in biotechnology</div> | Molla Islam; Maddie Tumbarello; Andrew Lyon | Hydrogels; Polymer chains; Polymer morphology; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1c702a9b6796189ea0/original/deswelling-induced-morphological-changes-in-dual-p-h-and-temperature-responsive-ultra-low-crosslinked-poly-n-isopropyl-acrylamide-co-acrylic-acid-microgels.pdf |
64a542d49ea64cc1677a096d | 10.26434/chemrxiv-2023-6jvnf | Filling the blank space: Branched 4-nonylphenols isomers are responsible for robust constitutive androstane receptor (CAR) activation by nonylphenol | 4-Nonylphenol (4-NP), a para-substituted phenolic compound mixture comprising a straight or branched carbon chain, is a widespread ubiquitous environmental pollutant and food contaminant. 4-NP, particularly the branched form, has been identified as an endocrine disruptor with potent activities on estrogen nuclear receptors. Constitutive Androstane Receptor (CAR, NR1I3) is another crucial nuclear receptor that regulates hepatic lipid, glucose, and steroid metabolism and is involved in endocrine disruption mechanism. The nonylphenol mixture has been described as an extremely potent activator of both human and rodent CAR. However, detailed mechanistic aspects of CAR activation by NP are enigmatic and it is not known if 4-NP can directly interact with the CAR ligand binding domain (LBD).
Here we examined interactions of individual branched (22NP, 33NP, and 353NP) and linear 4-NPs with CAR and its variants using molecular dynamics (MD) simulations, cellular experiments with various CAR constructs or CAR ligand binding domain (LBD) mutants, or in differentiated HepaRG hepatocyte cellular model.
Our results demonstrate that branched 4-NPs display more stable poses to activate both wild-type (wt)CAR1 as well as CAR3 variant LBDs in MD simulations. Consistently, branched 4-NP activated CAR3 and wtCAR1 LBD more efficiently than linear 4-NP or tert-nonylphenol (22NP). Furthermore, in HepaRG cells, we observed that all NP significantly up-regulated CYP2B6, a relevant hallmark for CAR activation. This is the first study to provide detailed insights into the direct interaction between individual 4-NPs and the human CAR-LBD, as well as its dominant variant CAR3 The work could contribute to the safer use of individual NPs in many areas of industry.
| Azam Rashidian; Jan Dusek; Martin Drastik; Lucie Smutná; Kristin Fritsche; Albert Braeuning; Antti Poso; Thales Kronenberger; Petr Pavek | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a542d49ea64cc1677a096d/original/filling-the-blank-space-branched-4-nonylphenols-isomers-are-responsible-for-robust-constitutive-androstane-receptor-car-activation-by-nonylphenol.pdf |
634d308cde2a215b60a85099 | 10.26434/chemrxiv-2022-n5xkb | Catalytic Performance of Micro-Mesoporous Zirconosilicates Prepared by Non-Hydrolytic Sol-Gel in Ethanol-To-Butadiene Transformation and Related Reactions | Synthesis of 1,3-butadiene (BD) from ethanol has experienced a true renaissance in recent years due to ecological and economic reasons. The open porosity and number of Lewis acid sites in metal silicates (M = Zr, Ta) have been reported in numerous studies as key factors enabling reaching high BD productivity. However, some microporous zeolites recently displayed very high BD productivity. To gain a deeper insight, we have applied non-hydrolytic sol-gel (NHSG) – a method well-known to produce highly porous and homogeneous metal silicates – in the preparation of zirconosilicates with varying micropore volume. The porosity (N2 adsorption-desorption experiments), structure (IR, XPS, NMR, and DRUV-Vis spectroscopy, XRD, MAS NMR), and acidity (IR spectroscopy combined with pyridine adsorption) of these materials have been described in detail and compared to a benchmark sample prepared by dry impregnation. Above mentioned characterization methods proved that NHSG preparation provided highly homogeneous Zr dispersion in silica leading to almost doubled Lewis acid site numbers and higher activity in ethanol-to-butadiene (ETB) transformation, Meerwein-Ponndorf-Verley (MPV) redox reaction, and aldol condensation, in comparison to the catalyst prepared by dry impregnation. The fraction of micropore volume in micro-mesoporous samples (ranging from 27 % to 69 %) did not play a significant role: The activity in all three catalytic reactions followed the acid site numbers. The selectivity and long-term stability in ETB process were similar for catalysts prepared by NHSG and dry impregnation. | Dalibor Hradsky; Petr Machac; David Skoda; Lucie Leonova; Petr Sazama; Jana Pastvova; Dalibor Kaucky; Dalibor Vsiansky; Zdenek Moravec; Ales Styskalik | Catalysis; Acid Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634d308cde2a215b60a85099/original/catalytic-performance-of-micro-mesoporous-zirconosilicates-prepared-by-non-hydrolytic-sol-gel-in-ethanol-to-butadiene-transformation-and-related-reactions.pdf |
613e6219d5f080720fc2bb50 | 10.26434/chemrxiv-2021-dbwcv | Harnessing Colossal Magnetic Anisotropy in Sandwiched 3d^2-Metallocenes | Single-molecule magnet (SMM) based quantum technology is gaining attentions in recent years with growing focus on achieving higher barrier of magnetization reversal. Metallocenes owing unique sandwiched-structure, assure themselves as plausible molecular systems for development of novel SMMs. Here in this work, we have explicitly investigated metallocenes of first row transition metal elements, along with their one electron oxidized (cationic) and reduced (anionic) analogues, for their magnetic anisotropies (D) adopting multi-reference ab initio calculations. Herein, we report the unprecedented high D values for 3d^2 systems among all the 3d-metallocenes. | Sakshi Nain; Rishu Khurana; Md. Ehesan Ali | Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Magnetic Materials; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613e6219d5f080720fc2bb50/original/harnessing-colossal-magnetic-anisotropy-in-sandwiched-3d-2-metallocenes.pdf |
66470300418a5379b083d0da | 10.26434/chemrxiv-2024-vtdv1 | Fully Automated Reaction Operation Driven by Accurate Inline FTIR Analysis based on Linear-Combination Strategy | To accelerate advancements in organic chemistry research and development, we propose a fully automated system based on real-time inline analysis performed by Fourier-transform infrared spectroscopy and assisted by a neural network model. To rapidly collect data, a linear combination of spectral intensities was used as training data for a yield prediction model. Using this model, we demonstrated real-time yield prediction of Suzuki-Miyaura cross-coupling with remarkable accuracy. By combining this yield prediction model with real-time inline analysis and a flow chemistry setup, we have developed a fully automated system for the rapid and efficient optimization of reaction conditions and process analysis. | Yosuke Ashikari; Takashi Tamaki; Kyosuke Tomite; Yuya Yonekura; aiichiro nagaki | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66470300418a5379b083d0da/original/fully-automated-reaction-operation-driven-by-accurate-inline-ftir-analysis-based-on-linear-combination-strategy.pdf |
61794ec245f1ee876a3f73fd | 10.26434/chemrxiv-2021-x5qdj | Extended Mechanism and Rate-Limiting Step of the Plasminogen Activator Staphylokinase Revealed by Global Kinetic Analysis | The plasminogen activator staphylokinase is a fibrin-specific thrombolytic biomolecule and an attractive target for the development of effective myocardial infarction and stroke therapy. To engineer the protein rationally, a detailed understanding of the biochemical mechanism and limiting steps is essential. Conventional fitting to equations derived based on simplifying approximations may be inaccurate for complex mechanisms like that of staphylokinase. We employed a modern numerical approach of global kinetic data analysis whereby steady-state kinetics and binding affinity datasets were analyzed in parallel. Our approach provided an extended, revised understanding of the staphylokinase mechanism without simplifying approximations and determined the value of turnover number kcat of 117 s-1 that was 10,000-fold higher than that reported in the literature. The model further showed that the rate-limiting step of the catalytic cycle is the binding of staphylokinase to plasmin molecules, which occurs via an induced-fit mechanism. The overall staphylokinase effectivity is further influenced by the formation of an inactive staphylokinase.plasminogen complex. Here, we describe a quick and simplified guide for obtaining reliable estimates of key parameters whose determination is critical to fully understand the staphylokinase catalytic functionality and define rational strategies for its engineering. Our study provides an interesting example of how global numerical analysis of kinetic data can be used to better understand the mechanism and limiting factors of complex biochemical processes. | Martin Toul; Dmitri Nikitin; Martin Marek; Jiri Damborsky; Zbynek Prokop | Biological and Medicinal Chemistry; Catalysis; Biochemistry; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61794ec245f1ee876a3f73fd/original/extended-mechanism-and-rate-limiting-step-of-the-plasminogen-activator-staphylokinase-revealed-by-global-kinetic-analysis.pdf |
60c74b54bb8c1a75833db194 | 10.26434/chemrxiv.12318797.v1 | Asymmetric Total Synthesis of C9’-epi-Sinefungin | The natural nucleoside (+)-sinefungin, structurally similar to cofactor S-adenosyl-L-methionine (SAM), inhibits various SAM-dependent methyltransferases (MTs). Access to sinefungin analogues could serve as the basis for the rational design of small-molecule methyltransferase inhibitors. We developed a route to the unnatural C9’ epimer of sinefungin that employed a diastereoselective Overman rearrangement to install the key C6’ amino stereocenter. The ability for late stage modification is highlighted, opening an avenue for the discovery of new MTs inhibitors. | Ludovic Decultot; Rocco L. Policarpo; Brandon Wright; Danny Huang; Matthew Shair | Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b54bb8c1a75833db194/original/asymmetric-total-synthesis-of-c9-epi-sinefungin.pdf |
60c753c4469df43817f44dfe | 10.26434/chemrxiv.12144699.v3 | A Glycan FRET Assay for Detection and Characterization of Catalytic Antibodies to the Cryptococcus neoformans Capsule | <p>Classical antibody functions include opsonization, complement activation, and enhancement of cellular antimicrobial function. Antibodies can also have catalytic activity, although the contribution of catalysis to their biological functions has been more difficult to establish. With the ubiquity of catalytic antibodies against glycans virtually unknown, we sought to advance this knowledge. The use of a glycan microarray allowed epitope mapping of several monoclonal antibodies (mAbs) against the capsule of <i>Cryptococcus neoformans</i>. From this, we designed and synthesized two glycan based Förster Resonance Energy Transfer (FRET) probes, which we used to discover antibodies with innate glycosidase activity and analyse their enzyme kinetics, including mAb 2H1, a polysaccharide lyase, and the most efficient glycosidase to date. The validity of the FRET assay was confirmed by demonstrating that the mAbs mediate glycosidase activity on intact cryptococcal capsules, as observed by a reduction in capsule diameter. Further the mAb 18B7, a glycosidase hydrolase, resulted in the appearance of reducing ends in the capsule as labelled by hydroxylamine-armed fluorescent (HAAF) probe. Finally, we demonstrate that exposing <i>C. neoformans </i>cells to catalytic antibodies results in changes in complement deposition and increased phagocytosis by macrophages — suggesting the anti-phagocytic properties of the capsule have been impaired. Our results raise questions over the ubiquity of antibodies with catalytic activity against glycans and establish the utility of glycan-based FRET and HAAF probes as tools for investigating this activity.</p> | Conor Crawford; Maggie P. Wear; Daniel F. Q. Smith; Clotilde d'Errico; Scott McConnell; Arturo Casadevall; Stefan Oscarson | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753c4469df43817f44dfe/original/a-glycan-fret-assay-for-detection-and-characterization-of-catalytic-antibodies-to-the-cryptococcus-neoformans-capsule.pdf |
67d44e386dde43c908ca1750 | 10.26434/chemrxiv-2025-wb2fl | Quantum Dot or Not? The Effect of Ligands on the Nature of Excitations in CdS Nanoparticles. | We investigate using many-body perturbation theory the optical and electronic properties of neutral cadmium sulfide nanoparticles with the zincblende structure for which the surface is capped with either bisulfide or alkylthiolate ligands, or bisulfide or alkylthiolate ligands in combination with phosphine, phosphine oxide or amine ligands. We study the nature of the optical excitation for these particles and how the optical and electronic properties of these particles change with the size of their inorganic core. We demonstrate that for all families of particle studied, except those where the corners are capped with aromatic ligands, the optical gap, the onset of light absorption, blueshifts with deceasing particle-core size. For the particles where the corners are capped with alkyl phosphines, phosphine oxides or amines the optical gap is predicted to correspond to an excitation where both the hole and excited electron are delocalised over the inorganic core of the particle, a core-to-core excitation, and hence resemble the cartoon picture of a quantum dot. In contrast, we predict that for particles exclusively capped with bisulfide or alkylthiolate ligands, the optical gap corresponds to a charge-transfer excitation with the hole localised on a subset of ligands and only the excited-electron delocalised over the inorganic core of the particle. For particles where the corners are capped with aromatic ligands the optical gap is predicted to correspond to a ligand-to-ligand excitation, which because of its localised nature does not significantly shift with particle size. However, for these particles with aromatic ligands, core-to-core excitation, lie only slightly higher in energy, and these excited states will shift with particle size and will likely become the optical gap for large(r) particles. Moreover, as core-to-core excitations are predicted to be much more intense than ligand-to-ligand excitations, experimentally one is likely to observe a blueshift with particle size even for particle sizes where the optical gap technically is a ligand-to-ligand excitation. | Eimear Madden; Martijn Zwijnenburg | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d44e386dde43c908ca1750/original/quantum-dot-or-not-the-effect-of-ligands-on-the-nature-of-excitations-in-cd-s-nanoparticles.pdf |
653bc53aa8b423585a5f95dd | 10.26434/chemrxiv-2023-30399 | Functional group tolerant hydrogen borrowing C-alkylation | Hydrogen borrowing is an attractive and sustainable strategy for carbon-carbon bond formation that enables alcohols to be used as alkylating reagents in place of alkyl halides. However, despite intensive efforts, limited functional group tolerance is observed in this methodology, which we hypothesize is due to the high temperatures and harsh basic conditions often employed. Here we demonstrate that room temperature and functional group tolerant hydrogen borrowing can be achieved with a simple iridium catalyst in the presence of substoichiometric base without an excess of reagents. Achieving high yields necessitates the application of anaerobic conditions to counteract the oxygen sensitivity of the catalytic iridium hydride intermediate, which otherwise leads to catalyst degradation. Substrates containing heteroatoms capable of complexing the catalyst exhibit limited room temperature reactivity, but the application of moderately higher temperatures enables extension to a broad range of medicinally relevant nitrogen rich heterocycles. These newly developed conditions allow alcohols possessing functional groups that were previously incompatible with hydrogen borrowing reactions to be employed | Elliot Bailey; Timothy Donohoe; Martin Smith | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Redox Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653bc53aa8b423585a5f95dd/original/functional-group-tolerant-hydrogen-borrowing-c-alkylation.pdf |
67c477f081d2151a02bafb24 | 10.26434/chemrxiv-2025-5rp46 | Temperature-Dependent Mechanical and Phase Behavior of Pulmonary Surfactant Monolayers Studied by Dissipative Particle Dynamics Modeling and Experiments | Langmuir monolayers of dipalmitoyl phosphatidylcholine (DPPC) at air-water interfaces exhibit complex phase behavior important for pulmonary surfactant function. Despite extensive experimental and computational studies, accurately predicting their temperature-dependent properties remains challenging due to experimental limitations and computational constraints. Here, we present a novel coarse-grained computational approach using dissipative particle dynamics (DPD) that successfully reproduces the interfacial and mechanical properties of DPPC monolayers across physiologically relevant temperatures. We developed a DPD gas model with exponential repulsive potentials to simulate the air-water interface, coupled with a systematic temperature scaling methodology that enables parameter transferability across different temperatures. Our model accurately captures the air-water surface tension over a broad temperature range and reproduces experimental surface pressure-area isotherms of DPPC monolayers in quantitative agreement at 293K and within experimental uncertainty at higher temperatures. The simulations reveal detailed insights into the liquid condensed (LC) and liquid expanded (LE) phase coexistence, characterized by local thickness variations and lipid tail orientational order. At low temperatures, we observe distinct LC domains with highly ordered lipid tails coexisting with LE domains, which progressively diminish in size and mix with LE phases as temperature increases toward the critical point. Complementary experimental measurements using a temperature-controlled Langmuir trough and atomic force microscopy (AFM) confirm these phase transitions and domain formations, providing direct visualization of temperature-dependent morphological changes in DPPC monolayers. The model successfully predicts the temperature-dependent structural transitions in both monolayers and bilayers, including the gel-to-liquid crystalline phase transition, with equilibrium properties matching experimental measurements. This computationally efficient approach provides a robust framework for investigating complex surfactant systems and their interactions with nanoparticles, with broad implications for understanding pulmonary surfactant function and dysfunction in respiratory diseases. | Kolattukudy Santo; Monica Iepure; Jonathan Arrendondo; Younjin Min; Alexander Neimark | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Interfaces; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2025-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c477f081d2151a02bafb24/original/temperature-dependent-mechanical-and-phase-behavior-of-pulmonary-surfactant-monolayers-studied-by-dissipative-particle-dynamics-modeling-and-experiments.pdf |
60c74024702a9ba7a218a05a | 10.26434/chemrxiv.7665122.v1 | Nickel-Catalyzed Cross Coupling of Umpolung Carbonyls and Alkyl Halides | An effective nickel-catalyzed cross coupling of umpolung carbonyls and alkyl halides was developed. Contrary to classical alkylation techniques, this reaction utilizes umpolung carbonyls as the environmentally benign alkyl nucleophiles, providing an efficient and selective catalytic alternative to the traditional use of highly reactive alkyl organometallic reagents. | Dianhu Zhu; Leiyang Lv; Zihang Qiu; Chao-Jun Li | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74024702a9ba7a218a05a/original/nickel-catalyzed-cross-coupling-of-umpolung-carbonyls-and-alkyl-halides.pdf |
66b23c3f01103d79c5e84bbe | 10.26434/chemrxiv-2024-g4b60-v2 | AdsMT: A multi-modal transformer for predicting global minimum adsorption energy | The fast assessment of the global minimum adsorption energy (GMAE) between catalyst surfaces and adsorbates is crucial for large-scale catalyst screening. However, multiple adsorption sites and numerous possible adsorption configurations for each surface/adsorbate combination make it prohibitively expensive to calculate the GMAE through density functional theory (DFT). Thus, we designed a novel multi-modal transformer called AdsMT to rapidly predict the GMAE based on surface graphs and adsorbate feature vectors without any site-binding information. The AdsMT model effectively captures the intricate relationships between adsorbates and surface atoms through the cross-attention mechanism, hence avoiding the enumeration of adsorption configurations. Three diverse benchmark datasets were constructed, opening new avenues for further research on the challenging GMAE prediction task. Our AdsMT framework demonstrates excellent performance by adopting the tailored graph encoder and transfer learning, achieving mean absolute errors of 0.09, 0.14, and 0.39 eV, respectively. Beyond GMAE prediction, AdsMT's cross-attention scores showcase the interpretable potential to identify the most energetically favorable adsorption sites. Additionally, uncertainty quantification was integrated into our models to enhance the trustworthiness of the predictions. While primarily focused on heterogeneous catalyst screening, our multi-modal approach has potential applications across materials science and chemistry. | Junwu Chen; Xu Huang; Cheng Hua; Yulian He; Philippe Schwaller | Theoretical and Computational Chemistry; Catalysis; Machine Learning; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b23c3f01103d79c5e84bbe/original/ads-mt-a-multi-modal-transformer-for-predicting-global-minimum-adsorption-energy.pdf |
66200db391aefa6ce1c39791 | 10.26434/chemrxiv-2024-fj7mp | Synthetic process development of (R)-(+)-1,2-epoxy-5-hexene: an important chiral building block | Herein, we describe two practical approaches to synthesize (R)-(+)-1,2-epoxy-5-hexene from inexpensive and readily available raw materials and reagents. The first approach is a two-step sequence, involving an epoxidation with meta-chloroperoxybenzoic acid (mCPBA) and a chiral resolution with (salen)Co(II), producing (R)-(+)-1,2-epoxy-5-hexene in 24-30% of overall yield. The second approach utilizes the readily available (R)-epichlorohydrin as the starting material and features an epoxide ring opening reaction with allylMgCl and the NaOH mediated ring closure reaction. Development of this two-step process affords R-(+)-1,2-epoxy-5-hexene in overall isolated yields of 55-60% with an exceptional purity profile. Both approaches have been successfully demonstrated on 100-200g scales. | Daryl Guthrie; John Saathoff; Rajkumar Sahani; Aline Nunes De Souza; Daniel Cook; Samuel Hochstetler; Justina Burns; Roudabeh Moazeni-Pourasil; Janie Wierzbicki; Saeed Ahmad; Michael Laidlaw; B. Frank Gupton; Charles Shanahan; Douglas Klumpp; limei jin | Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry; Stereochemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66200db391aefa6ce1c39791/original/synthetic-process-development-of-r-1-2-epoxy-5-hexene-an-important-chiral-building-block.pdf |
60c73ef8567dfe6b50ec38f1 | 10.26434/chemrxiv.7195460.v1 | Melt Electrowriting of Electroactive Poly(vinylidene difluoride) Fibers | <p>Poly(vinylidene difluoride) (PVDF) has piezoelectric properties suitable for numerous applications such as flexible electronics, sensing and biomedical materials. In this study, individual fibers with diameters ranging from 17-55 μm were processed using melt electrowriting (MEW). Electroactive PVDF fibers can be fabricated via MEW, while the polymer could remain molten for up to ten hours without noticeable changes in the resulting fiber diameter. MEW processing parameters for PVDF were investigated, including applied voltage, pressure and temperature. A rapid fiber characterization methodology for MEW that automatically determines the fiber diameters from camera images taken of microscope slides was developed and validated. The outputs from this approach followed previous MEW processing trends already identified with different polymers, although overestimation of the < 25 micron fiber diameters was observed. The transformation of the PVDF crystalline phase to the electroactive beta-phase – without poling – was confirmed using piezo-force microscopy and revealed that the PVDF fibers possess piezoelectric responses showing d33~19 pm/V.</p> | Sammy Florczak; Thomas Lorson; Tian Zheng; Miroslav Mrlik; Dietmar Hutmacher; Michael Higgins; Robert Luxenhofer; Paul Dalton | Fibers; Fluoropolymers; Organic Polymers; Polymer scaffolds; Piezoelectricity and Thermoelectricity | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ef8567dfe6b50ec38f1/original/melt-electrowriting-of-electroactive-poly-vinylidene-difluoride-fibers.pdf |
60c74f88842e656fb7db3859 | 10.26434/chemrxiv.12919022.v1 | The Role of Solubility in Thermal Field Flow Frac-tionation – A Revisited Theoretical Approach for Tuning the Separation of Chain-Walking Polymerized Polyethylene | The influence of the polymer solubility on the separation efficiency in thermal field-flow fractionation (ThFFF) was investigated for a polymer model system of differently branched chain walking polyethylenes in five different solvents, which were selected depending on their physical parameters. The understanding of polymer thermal diffusion has been elucidated using a revisited approach based on the latest thermal diffusion prediction model by Mes,<br />Kok and Tijssen combined with the Hansen solubility theory. Thereby, a significant improvement in the precision of the thermal diffusion prediction and the separation efficiency has been achieved by implementation of the temperature dependency on Hansen solubility parameters. In addition, we demonstrate a method for validation of the segmental size of polymer chains with varying topology by using the revisited thermal diffusion prediction approach in inverse mode and experimental thermal diffusion data. | Martin Geisler; Laura Plüschke; Jan Merna; Albena Lederer | Polymer chains; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f88842e656fb7db3859/original/the-role-of-solubility-in-thermal-field-flow-frac-tionation-a-revisited-theoretical-approach-for-tuning-the-separation-of-chain-walking-polymerized-polyethylene.pdf |
675eb2c9085116a13379242f | 10.26434/chemrxiv-2024-ljfs0 | Highly Stereoselective Catalytic Synthesis of Polysubstituted Housanes: Application and Mechanistic Insights | Ring-strain-enabled transformations have made significant progress, pushed the boundaries of unexplored chemical space, and emerged as a powerful tool for constructing complex molecules selectively and efficiently. Among the strained ring systems, [1.1.1]propellane, bicyclobutane (BCB), and azabicyclobutane (ABB) have garnered substantial attention and found numerous synthetic applications. In contrast, the chemistry of bicyclo[2.1.0]pentane, commonly known as housane, is scantly explored due to the lack of modular synthetic approaches. Herein, we describe a highly stereoselective, catalytic strategy for synthesizing polysubstituted housanes with up to three contiguous all-carbon-quaternary centers. The reaction is very efficient, works under mild conditions, requires visible light and organic dye as a photocatalyst, and exhibits a broad substrate scope. The post-synthetic diversification of the products via an unprecedented strain-release driven diastereospecific 1,2-ester migration that allows the rapid synthesis of functionalized bicyclic imides further highlighted the synthetic utility of the current protocol. Combined experimental studies and computational investigations revealed the origin of the reactivity and stereoselectivity. | Abdur Rouf Samim Mondal; Nakul Abhay Bapat; Durga Prasad Hari | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675eb2c9085116a13379242f/original/highly-stereoselective-catalytic-synthesis-of-polysubstituted-housanes-application-and-mechanistic-insights.pdf |
60c74979f96a00afbf287274 | 10.26434/chemrxiv.9978743.v2 | Inductive Transfer Learning for Molecular Activity Prediction: Next-Gen QSAR Models with MolPMoFiT | <p>Deep neural networks can directly learn from chemical structures without extensive, user-driven selection of descriptors in order to predict molecular properties/activities with high reliability. But these approaches typically require large training sets to learn the endpoint-specific structural features and ensure reasonable prediction accuracy. Even though large datasets are becoming the new normal in drug discovery, especially when it comes to high-throughput screening or metabolomics datasets, one should also consider smaller datasets with challenging endpoints to model and forecast. Thus, it would be highly relevant to better utilize the tremendous compendium of unlabeled compounds from publicly-available datasets for improving the model performances for the user’s particular series of compounds. In this study, we propose the <b>Mol</b>ecular <b>P</b>rediction <b>Mo</b>del <b>Fi</b>ne-<b>T</b>uning (<b>MolPMoFiT</b>) approach, an effective transfer learning method based on self-supervised pre-training + task-specific fine-tuning for QSPR/QSAR modeling. A large-scale molecular structure prediction model is pre-trained using one million unlabeled molecules from ChEMBL in a self-supervised learning manner, and can then be fine-tuned on various QSPR/QSAR tasks for smaller chemical datasets with specific endpoints. Herein, the method is evaluated on four benchmark datasets (lipophilicity, FreeSolv, HIV, and blood-brain barrier penetration). The results showed the method can achieve strong performances for all four datasets compared to other state-of-the-art machine learning modeling techniques reported in the literature so far. <br /></p> | Xinhao Li; Denis Fourches | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74979f96a00afbf287274/original/inductive-transfer-learning-for-molecular-activity-prediction-next-gen-qsar-models-with-mol-p-mo-fi-t.pdf |
60d97aaa261611396a8c9bde | 10.26434/chemrxiv-2021-749mc-v3 | From “inverted” to “superdirect“ bonds: a general concept connecting substituent angles with sigma bond strengths. The case of the CC bonds in hydrocarbons. | <div>The C-C dissociation energy with respect to geometry frozen fragments (BE) has been calculated for C2H6 as a function of = H-C-C angles. BE decreases rapidly when decreases from its equilibrium value to yield the so-called “inverted bonds” for < 90°; on the contrary BE increases</div><div>when increases to yield somehow “superdirect” bonds, following a sigmoidal variation. The central bond in Si2H6, Ge2H6 and N 2H4 as well as the C-H bond in CH3-H behaves similarly. The concept of “invertedness”/”directedness” is generalized to any CC sigma bond in hydrocarbons and characterized by the mean angle value <> of substituents. Using dynamic orbital forces (DOF) as indices, the intrinsic bond energies are studied as a function of <> for formally single bonds in a</div><div>panel of 22 molecules. This energy decreases from the strongest “superdirect” bonds in butadiyne, (<> = 180°) or tetrahedrylacetylene to the weakest “inverted bond” in cyclobutene, tetrahedrane, bicyclobutane and [1.1.1]propellane (<> = 60°), according to a sigmoidal variation. The <> parameter appears as a crude, but straightforward and robust, index of strain in cyclic molecules. Sigma bonds in multiple bonds of a panel of 11 molecules have most of time <> values less than 90°</div><div>and are significantly weaker than standard single bonds. Thus they can be considered as formally inverted or near inverted.</div><div><br /></div> | Rubén Laplaza; Julia Contreras-García; Franck Fuster; François Volatron; Patrick Chaquin | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d97aaa261611396a8c9bde/original/from-inverted-to-superdirect-bonds-a-general-concept-connecting-substituent-angles-with-sigma-bond-strengths-the-case-of-the-cc-bonds-in-hydrocarbons.pdf |
60c7419a9abda27ad3f8bea6 | 10.26434/chemrxiv.8067446.v1 | H2O as the Sole Hydrogen Source for Ni-Catalyzed Reduction of Alkenes | Herein,
we reported a nickel catalyzed hydrogenation of alkenes with water as the sole
hydrogen source. Employing Zn as reductant and water as solvent in the presence
of a catalytic amount of
nickel catalyst led to direct hydrogenation of a series of electron-rich and
electron-deficient alkenes in high yields. This protocol features unprecedented
heterocycle and functional group tolerance under facile and mild conditions. Selective
hydrogenation of the substrates containing additional reducible functionalities,
such as alkenyl, alkynyl, chloride, ketone, and benzyl group etc, was also realized. | Yichen Wu; Tao liu; Dongping Chen; Daoming Wang; Peng Wang | Organic Synthesis and Reactions; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7419a9abda27ad3f8bea6/original/h2o-as-the-sole-hydrogen-source-for-ni-catalyzed-reduction-of-alkenes.pdf |
66bc817aa4e53c4876567f41 | 10.26434/chemrxiv-2024-9dzv5-v2 | Coupled-Trajectory Surface Hopping with Sign Consistency | The framework of exact factorization (XF) has inspired a series of trajectory-based nonadiabatic dynamics methods through introducing different approximations. Recently, the coupled-trajectory surface hopping (CTSH) method has been proposed to combine the key advantages of the coupled-trajectory mixed quantum-classical method based on XF and the fewest switches surface hopping. We here present a novel variant of CTSH, namely sign-consistent CTSH (SC-CTSH), which considers proper trajectory clustering to reconstruct the nuclear density distribution and the consistency between wave function and active states to introduce decoherence. Using the exact quantum solutions as references, the high performance of SC-CTSH is benchmarked in the widely studied scattering models and compared with other related XF-based methods. Due to the incorporation of new trajectory clustering and sign consistency algorithms, SC-CTSH obtains more accurate quantum momentum and decoherence during the nonadiabatic dynamics, which makes the combination of XF and surface hopping more consistent and reliable. This study further highlights the significance of internal consistency between wave function and active states, which is important in the further development of mixed quantum-classical dynamics methods. | Rixin Xie; Zhecun Shi; Linjun Wang | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bc817aa4e53c4876567f41/original/coupled-trajectory-surface-hopping-with-sign-consistency.pdf |
626be5bb6c989c0af8c9e256 | 10.26434/chemrxiv-2022-2gcgx | Heavy-Atom Quantum Tunnelling in Spin Crossovers of Nitrenes | We simulate two recent matrix-isolation experiments at cryogenic temperatures, in which a nitrene undergoes spin crossover from its triplet state to a singlet state via quantum tunnelling. We detail the failure of the commonly applied weak-coupling method (based on a linear approximation of the potentials) in describing these deep-tunnelling reactions. The more rigorous approach of semiclassical golden-rule instanton theory in conjunction with double-hybrid density-functional theory and multireference perturbation theory does, however, provide rates and kinetic isotope effects in good agreement with experiment. In addition, these calculations locate the optimal tunnelling pathways, which provide a molecular picture of the reaction mechanism. The reactions involve substantial heavy-atom quantum tunnelling of carbon, nitrogen and oxygen atoms, which unexpectedly even continues to play a role at room
temperature. | Eric R. Heller; Jeremy O. Richardson | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemical Kinetics; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626be5bb6c989c0af8c9e256/original/heavy-atom-quantum-tunnelling-in-spin-crossovers-of-nitrenes.pdf |
6687e378c9c6a5c07a5e31ee | 10.26434/chemrxiv-2024-qkcv4 | On the Formation of a Cathode Electrolyte Interphase on High Voltage Li-ion Cathodes | The spinel oxide LiNi0.5Mn1.5O4 (LNMO) currently competes to replace the conventional layered transition metal oxide active material in Li-ion batteries. The high average operating potential (4.70 V vs. Li+/Li) challenges the stability of the electrolyte, which in turn compromises the lifetime of the Li-ion cell. Online electrochemical mass spectrometry (OEMS) is herein implemented to study the degradation processes occurring at the cathode surface. Gases continuously evolve across subsequent cycles as a result of electrolyte oxidation, a process that is found to be only potential-activated and independent of electrode surface composition. The subsequent formation of protic species autocatalyzes electrolyte salt degradation, which in turn triggers the corrosion of active material, current collector, and conductive carbons. The effectiveness of several well-known electrolyte additives, previously claimed to act as cathode electrolyte interphase (CEI) formers, were explored revealing the efficacy of phosphorus-based additives. Our study provides a rapid and quantifiable approach to tackle the major challenge of high voltage cathode materials, namely its stabilisation towards the electrolyte, and how to identify and develop an efficient CEI. | Casimir Misiewicz; Kristina Edström; Erik J. Berg | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687e378c9c6a5c07a5e31ee/original/on-the-formation-of-a-cathode-electrolyte-interphase-on-high-voltage-li-ion-cathodes.pdf |
63eca9d31d2d18406387a13b | 10.26434/chemrxiv-2023-p8qvx | Ni-catalyzed asymmetric C-P cross-coupling reaction via Ni(I)/Ni(III) two-electron pathway | Nickel demonstrates excellent performance in C-C or C-X cross-coupling reactions involving a SET process. However, the Ni(I)/Ni(III) two-electron pathway, which does not require light irradiation, is still rare, particularly in the asym-metric version. Here, we disclose a Ni(II)-catalyzed asymmetric C-P cross-coupling reaction via the Ni(I)/Ni(III) two-electron redox pathway. Combined experimental and computational research reveals that Ni(II) can be readily reduced to Ni(0) by secondary phosphine oxides, resulting in the formation of a Ni(I) active catalyst through comproportiona-tion. The discovery of the Ni(I)/Ni(III) two-electron mechanism may serve as a new paradigm of Ni catalysis, offering exciting opportunities in asymmetric reactions complementary to the traditional SET process. | Qing-Wei Zhang; Ranran Cui; Lingfei Hu; Yinqi Wang; Liyan Yuwen; Li Gao; Zhuo Huang; Weihan Wang; Gang Lu | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eca9d31d2d18406387a13b/original/ni-catalyzed-asymmetric-c-p-cross-coupling-reaction-via-ni-i-ni-iii-two-electron-pathway.pdf |
6564b61b29a13c4d471c594a | 10.26434/chemrxiv-2023-htpsm | Peripheral halogen atoms in multi-resonant thermally activated delayed fluorescence emitters: The role of heavy atom on intermolecular interactions and spin orbit coupling | Multi-resonant thermally activated delayed fluorescence materials (MR-TADF) can show narrow-band emission with high photoluminescence quantum efficiency, desirable for applications in organic light emitting diodes (OLEDS). However, they frequently suffer from slow reverse intersystem crossing (RISC) compared to established donor-acceptor TADF emitters, leading to severe device efficiency roll-off at high exciton densities. Introducing heavy atom effects (HAE) by core-substitution has been previously shown to enhance spin orbit coupling and thus RISC in MR-TADF emitters, frequently with oxygen atoms replaced by isoelectronic sulfur or selenium. Here, we explore an alternate HAE strategy using peripheral halogenation of the MR-TADF DiKTa core, comparing tBr-DiKTa and dBr-tBu-DiKTa with non-halogenated Mes3-DiKTa. The two brominated emitters demonstrate improved kRISC because of the HAE, while the rate appears to improve by an additional order of magnitude in mCP host, because of intermolecular (guest-host) interaction. Despite the beneficial hetero-intermolecular interactions, strong homo-intermolecular interactions result in enhanced non-radiative pathways and lower photoluminescence quantum yields. OLEDs of dBr-tBu-DiKTa hence showed comparable EQEmax with Mes3-DiKTa (21%) and improved efficiency roll-off until 500 cd m-2, although with accelerated roll-off beyond a critical current density. Together with comparisons in less strongly doped devices, these results show that the HAE provided by peripheral halogens improves the device performance up to 500 cd m-2, but also support detrimental intermolecular interactions that dominate at higher device currents. | Hector Miranda-Salinas; Jingxiang Wang; Andrew Danos; Tomas Matulaitis; Kleitos Stavrou; Andrew Monkman; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6564b61b29a13c4d471c594a/original/peripheral-halogen-atoms-in-multi-resonant-thermally-activated-delayed-fluorescence-emitters-the-role-of-heavy-atom-on-intermolecular-interactions-and-spin-orbit-coupling.pdf |
60c74437337d6c308de26d5b | 10.26434/chemrxiv.9759605.v1 | Photopatterned Membranes and Chemical Gradients Enable Scalable Phenotypic Organization of Primary Human Colon Epithelial Models | Biochemical
gradients across the intestinal epithelium play a major role in governing
intestinal stem cell compartmentalization, differentiation dynamics, and
organ-level self-renewal. Advances in primary cell-derived <i>in vitro</i>
models, in which a full suite of stem and differentiated cell types are
present, have vastly accelerated our understanding of intestinal homeostasis
and disease. However, scalable platforms that recapitulate the architecture and
gradients present <i>in vivo</i> are absent. We present a platform in which
individually addressable arrays of chemical gradients along the crypt long axis
can be generated, enabling scalable culture of <i>in vitro</i> colonic
epithelial replicas. The platform utilizes standardized well plate spacing,
maintains access to basal and luminal compartments, and relies on a photopatterned
porous membrane to act as diffusion windows while supporting the<i> in vitro </i>crypts.
Simultaneous fabrication of 3,875 crypts over a single membrane was developed.
Growth factor gradients were modelled and then experimentally optimized to
promote long-term health and self-renewal of the crypts which were assayed <i>in
situ</i> by confocal fluorescence microscopy. The cultured <i>in vitro</i>
crypt arrays successfully recapitulated the architecture, stem/proliferative
and differentiated cell compartmentalization, and luminal-to-basal polarity observed
<i>in vivo</i>. Furthermore, known signaling regulators produced measurable and
predictable effects on the proliferative and differentiated cell compartments.
This platform is readily adaptable to the screening of tissue from individual
patients to assay the impact of food and bacterial metabolites and/or drugs on
colonic crypt dynamics. Importantly, the cassette is compatible with a wide
range of sensing/detection modalities, and the developed fabrication methods
should find applications for other cell and tissue types. | Sam Hinman; Yuli Wang; Nancy Allbritton | Analytical Chemistry - General; Imaging; Microscopy; High-throughput Screening; Bioengineering and Biotechnology; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74437337d6c308de26d5b/original/photopatterned-membranes-and-chemical-gradients-enable-scalable-phenotypic-organization-of-primary-human-colon-epithelial-models.pdf |
60c73e98bb8c1a432c3d991a | 10.26434/chemrxiv.7038767.v1 | Two-dimensional Kagome Lattices Made of Hetero Triangulenes are Dirac Semimetals or Single-Band Semiconductors | In two dimensions, 11 lattice types are mathematically possible, the Kepler nets, but nature offers only few of them in dense crystals. Two-dimensional covalent organic frameworks (2D COFs) offer to overcome this limitation and to provide nets that are to date only possible as photonic lattices or atom-by-atom engineered surface structures. Here we discuss, based on first-principles calculations, 2D kagome lattices composed of polymerized hetero-triangulene units, planar molecules with D3h point group containing a B, C or N center atom and CH<sub>2</sub>, O or CO bridges. We explore the design principles for a functional lattice made of COFs, which involves control of π-conjugation and electronic structure of the knots. The former is achieved by the chemical potential of the bridge groups, while the latter is controlled by the heteroatom. The resulting 2D kagome COFs have a characteristic electronic structure with a Dirac band sandwiched by two flat bands and are either Dirac semimetals (C center), or single-band semiconductors - materials with either exclusively electrons (B center) or holes (N center) as charge carriers of very high mobility, reaching values of up to ~8×10<sup>3</sup> cm<sup>2</sup>V<sup>-1</sup>s<sup>-1</sup>, which is comparable to crystalline silicon. The flat bands show a delocalized electronic structure with no contribution from the center atoms, and their curvature is modulated by the bridge atoms. This suggests that the flat bands are inherent features of the kagome lattice. | Yu Jing; Thomas Heine | Organic Compounds and Functional Groups; Nanostructured Materials - Materials; Oligomers; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e98bb8c1a432c3d991a/original/two-dimensional-kagome-lattices-made-of-hetero-triangulenes-are-dirac-semimetals-or-single-band-semiconductors.pdf |
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