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60c748cdee301ca1d5c79961 | 10.26434/chemrxiv.11822676.v2 | Synthesis, Structure and Reactivities of Pentacoordinated Phosphorus–Boron Bonded Compounds | The isolation and reactivities of two pentacoordinated<br />phosphorus–tetracoordinated boron bonded compounds were explored. A strong Lewis acidic boron reagent and electronwithdrawing ligand system were required to form the pentacoordinated phosphorus state of the P–B bond. The first compound, a phosphoranyl-trihydroborate, gave a THF stabilised phosphoranyl-borane intermediate upon a single hydride abstraction in THF. This compound could undergo a unique rearrangement reaction, which involved a two-fold ring expansion, to give a fused bicyclic compound or it could act as a mono-hydroboration reagent. The hydroboration reactivity of the intermediate was found to be more reactive towards alkynes over alkenes with good to moderate regioselectivity towards the terminal carbon. The second compound, a phosphoranyl-triarylborate, was found to have different reactivity as it was highly stable towards acids and bases. This is thought to be due to the large bulk around the P–B bond as shown in the crystal structure.<br /> | Nathan O'Brien; Naokazu Kano; Nizam Havare; Ryohei Uematsu; Romain Ramozzi; Keiji Morokuma | Main Group Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748cdee301ca1d5c79961/original/synthesis-structure-and-reactivities-of-pentacoordinated-phosphorus-boron-bonded-compounds.pdf |
62a9e1e9eb1f0cce0389be1f | 10.26434/chemrxiv-2022-lw81f | Gelatin modified with alkoxysilanes (GelmSi) forms hybrid hydrogels for bioengineering applications | Biopolymers are ideal candidates for the development of hydrogels for tissue engineering applications. However, chemical modifications are required to further improve their mechanical properties, in particular to cross-link them for long-lasting applications or biofabrication. Herein, we developed a novel gelatin-based hydrogel precursor, “GelmSi”. Gelatin was chosen as starting material because of its biocompatibility and bioactivity, favouring cell adhesion and migration. Alkoxysilane moieties were introduced in a controlled manner on the lysine side chains of gelatin to obtain a hybrid precursor which reacts in physiological conditions, forming covalent siloxane bonds and allowing the formation of a three-dimensional chemical network. On the contrary to unmodified gelatin, siloxane covalent network dramatically increases the stiffness and the thermal stability of the resulting gelatin-based hydrogel, making it suitable for cell encapsulation and cell culture. The biorthogonality and versatility of the GelmSi hybrid hydrogel unlock a broad range of gelatin-based bioengineering applications. | Matthieu Simon; Marie Maumus; Baptiste Legrand; Lilian Sole; Marjorie Dufaud; Ahmad Medhi; Christian Jorgensen; Danièle Noël; Gilles Subra | Biological and Medicinal Chemistry; Materials Science; Biocompatible Materials; Bioengineering and Biotechnology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a9e1e9eb1f0cce0389be1f/original/gelatin-modified-with-alkoxysilanes-gelm-si-forms-hybrid-hydrogels-for-bioengineering-applications.pdf |
65ba2de1e9ebbb4db958dcfb | 10.26434/chemrxiv-2024-tk50j-v2 | Raney Nickel-Catalyzed Deuterium Labeling of Nitrogen-Containing Heterocycles and Pharmaceuticals under Continuous Flow Conditions | Deuterium-labeled compounds play a pivotal role in physical organic chemistry, life sciences, and materials science. This has resulted in a surge of interest in deuterium-labeled active pharmaceutical ingredients in recent years. In this study, we present a continuous flow Raney nickel-catalyzed hydrogen isotope exchange process that boasts compatibility with a wide spectrum of nitrogen-containing heterocycles and pharmaceutical compounds. The broad applicability of the developed method was demonstrated through successful labeling of various purine bases, imidazoles, pyridines, and active pharmaceutical ingredients, including complex structures like abacavir and remdesivir. Control experiments revealed Raney nickel's crucial role in the exchange process, showcasing the superiority of the continuous flow approach over batch reactions. Furthermore, a scaled-up experiment demonstrated the robustness of the catalyst. | Ferenc Minya; Ádám Mészáros; Eszter Csizmadia; Dávid Suskó; Mounir Raji; Gellért Sipos | Organic Chemistry; Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba2de1e9ebbb4db958dcfb/original/raney-nickel-catalyzed-deuterium-labeling-of-nitrogen-containing-heterocycles-and-pharmaceuticals-under-continuous-flow-conditions.pdf |
66c65f20f3f4b05290aa1790 | 10.26434/chemrxiv-2024-qd0wm | Single-Molecule Conductance of Staffanes | We report the first conductance measurements of [n]staffane (bicyclopentane) oligomers in single-molecule junctions. Our studies reveal two quantum transport characteristics unique to staffanes that emerge from their strained bicyclic structure. First, though staffanes are composed of weakly conjugated C-C σ-bonds, staffanes carry a shallower conductance decay value (β = 0.84 ± 0.02 n-1) than alkane chain analogs (β = 0.96 ± 0.03 n-1) when measured with the scanning tunneling microscopy break junction (STM-BJ) technique. Staffanes are thus more conductive than any other σ-bonded organic backbone reported in the literature on a per atom basis. Density functional theory (DFT) calculations suggest staffane backbones are more effective conduits for charge transport because their significant bicyclic ring strain destabilizes the HOMO-2 energy, aligning it more closely with the Fermi energy of gold electrodes as oligomer order increases. Second, the monostaffane is significantly lower conducting than expected. DFT calculations suggest that short monostaffanes sterically enforce insulating gauche interelectrode orientations over syn orientations; these steric effects are alleviated in longer staffanes. Moreover, we find that [2-5]staffane wires may accommodate axial mechanical strain by “rod-bending”. These findings show for the first time how bicyclic ring strain can enhance charge transmission in saturated molecular wires. These studies showcase the STM-BJ technique as a valuable tool for uncovering the stereoelectronic proclivities of molecules at material interfaces. | Ashley Pimentel; Lan Pham; Veronica Carta; Timothy Su | Physical Chemistry; Organic Chemistry; Nanoscience; Physical Organic Chemistry; Nanodevices; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c65f20f3f4b05290aa1790/original/single-molecule-conductance-of-staffanes.pdf |
60c759124c8919beb3ad4cd8 | 10.26434/chemrxiv.14637756.v1 | Environmentally Sensitive Luminescence Reveals Spatial Confinement, Dynamics and Their Molecular Weight Dependence in a Polymer Glass | Polymer glasses have an irregular structure. Among
the causes for such complexity are the chemically distinct chain end-groups that
are the most abundant irregularities in any linear polymer. In this work we
demonstrate that chain end induced defects allow polymer glasses to create
confined environments capable of hosting small emissive molecules. Using
environmentally sensitive luminescent complexes we show that the size of these
confinements depends on molecular weight and can dramatically affect the photoluminescence
of free or covalently bound emissive complexes. We confirm the impact of chain
end confinement on the bulk glass transition in poly(methyl acrylate) and show
that commonly observed T<sub>g</sub> changes induced by the chain ends should
have a structural origin. Finally, we demonstrate that size and placement of luminescent
molecular probes in pMA can dramatically affect the probe luminescence and its
temperature dependence suggesting that polymer glass is a highly irregular and
complex environment marking its difference with conventional small molecule
solvents. Considering the ubiquity of luminescent glassy materials, our work
lays down a blueprint for designing them with structural considerations in
mind, ones where packing density and chain end size are key factors. | Stephen Picken; Georgy Filonenko | Dyes and Chromophores; Polymer morphology; Sensors; Coordination Chemistry (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759124c8919beb3ad4cd8/original/environmentally-sensitive-luminescence-reveals-spatial-confinement-dynamics-and-their-molecular-weight-dependence-in-a-polymer-glass.pdf |
6620ba42418a5379b01663ff | 10.26434/chemrxiv-2024-h06cg | Time-Dependent Kohn-Sham Electron Dynamics Coupled with Nonequilibrium Plasmonic Response via Atomistic Electromagnetic Model | Computational modeling of plasmon-mediated molecular photophysical and photochemical behaviours can help us better understand and tune the bound molecular properties and reactivity, and make better decisions to design and control nanostructures. However, computational investigations of coupled plasmon-molecule systems are challenging due to the lack of accurate and efficient protocols to evaluate these systems. Here we present a hybrid scheme by combining real time time-dependent density functional theory (RT-TDDFT) method with time-domain frequency dependent fluctuating charge (TD-ωFQ) model. At first, we transform ωFQ, which was formulated in the frequency domain, to time-domain and derive its equation-of-motion formulation. The TD-ωFQ introduces the nonequilibrium plasmonic response of metal nanoparticle (MNP) and atomistic interactions to the electronic excitation of QM region. Then we combine TD-ωFQ with RT-TDDFT. The derived RT-TDDFT/TD-ωFQ scheme allows us to effectively simulate the plasmon-mediated “real-time” electronic dynamics and even the coupled electron-nuclear dynamics by combining with the nuclear dynamics approaches. As a first application of the RT-TDDFT/TD-ωFQ method, we study the nonradiative decay rate and plasmon-enhanced absorption spectra of two small molecules in the proximity of sodium MNPs. Thanks to the atomistic nature of ωFQ model, the edge effect of MNP to absorption enhancement has also been investigated.
and unveiled. | Xunkun Huang; Wenshu Zhang; WanZhen Liang | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6620ba42418a5379b01663ff/original/time-dependent-kohn-sham-electron-dynamics-coupled-with-nonequilibrium-plasmonic-response-via-atomistic-electromagnetic-model.pdf |
66a13a895101a2ffa8e1239e | 10.26434/chemrxiv-2024-64knm | A Lead(II) Substituted Triplet Carbene | Reaction of the pincer-type ligand L3 supported complex [L3PbBr][BArF24] (1) with Li[(C(=N2)TMS)] furnishes [L3Pb(C(=N2)TMS)][BArF24] (2). Diazo-compound 2 eliminates dinitrogen upon irradiation affording formal plumba-alkyne 3, which persists in cold fluoroarene solutions. Variable temperature UV/Vis and NMR spectroscopies in combination with quantum-chemical calculations identify 3 as a metal-substituted triplet carbene. In-crystallo irradiation of [L3Pb(C(=N2)TMS)(tol)][BArF24] (2∙tol) provides a snapshot of intermolecular C–H bond insertion with toluene (4). | Fabian Dankert; Julian Messelberger; Abinash Swain; Ugo Authesserre; David Scheschkewitz; Bernd Morgenstern; Dominik Munz | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Bond Activation; Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a13a895101a2ffa8e1239e/original/a-lead-ii-substituted-triplet-carbene.pdf |
655bccc66e0ec7777f59747e | 10.26434/chemrxiv-2023-68jzh | Shape-Aware Synthon Search (SASS) for virtual screening of synthon-based chemical spaces | Virtual screening of large-scale chemical libraries has become increasingly useful for identifying high-quality candidates for drug discovery. While it is possible to exhaustively screen chemical spaces that number on the order of billions, indirect combinatorial approaches are needed to efficiently navigate larger, synthon-based virtual spaces. We describe Shape-Aware Synthon Search (SASS), a synthon-based virtual screening method that carries out shape similarity searches in the synthon space instead of the enumerated product space. SASS can replicate results from exhaustive searches in ultra-large, combinatorial spaces with high recall on a variety of query molecules while only scoring a small subspace of possible enumerated products, thereby significantly accelerating large-scale, shape-based virtual screening. | Chen Cheng; Paul Beroza | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655bccc66e0ec7777f59747e/original/shape-aware-synthon-search-sass-for-virtual-screening-of-synthon-based-chemical-spaces.pdf |
63fff6ad937392db3d49b06b | 10.26434/chemrxiv-2023-1p6sn | H2S Scavenger as A Universal Strategy to Deplete Bacteria-derived H2S for Antibacterial Sensitization | Bacteria-derived H2S plays multifunctional protective roles against antibiotics insult, and H2S biogenesis pathway is emerging as a viable target for the antibacterial adjuvant design. However, the development of a pan-inhibitor against H2S-synthesizing enzymes is exceedingly challenging and severely underdeveloped. Herein, we propose an alternative strategy to downregulate the H2S levels in H2S-producing bacteria, which depletes the bacteria-derived H2S chemically by H2S scavengers without acting on the synthesizing enzymes. After the screening of chemically diversified scaffolds and a structural optimization campaign, a potent and specific H2S scavenger was successfully identified, which displayed efficient H2S depletion in several H2S-producing bacteria, potentiated both bactericidal agents and photodynamic therapy, enhanced the bacterial clearance of macrophages, disrupted the formation of bacterial biofilm and increased the sensitivity of bacterial persister cells to antibiotics. Most importantly, such an H2S scavenger exhibited very pronounced synergistic effects with gentamicin in a methicillin-resistant Staphylococcus aureus (MRSA) infected peritonitis mouse model. In aggregate, our results not only provided an effective strategy to deplete bacteria-derived H2S and firmly established the H2S biogenesis pathway as a viable target for persisters and drug-resistant bacteria, but also delivered a promising antibacterial adjuvant for potential clinical translation. | Ye Gao; Xu Wang; Xia Wang; Ziwei Hu; Miao Liu; Chunhua Qiao; Yipeng Wang; Xingyue Ji | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fff6ad937392db3d49b06b/original/h2s-scavenger-as-a-universal-strategy-to-deplete-bacteria-derived-h2s-for-antibacterial-sensitization.pdf |
64fc2f9799918fe537a1aea9 | 10.26434/chemrxiv-2023-jm387 | A machine learning approach to designing tough and degradable polyamides based on multiblock structures | The development of environmentally friendly plastics is receiving renewed attention for a sustainable society. The trade-off between toughness and degradability is one of the issues associated with biodegradable polymers, which prevents these materials from being broadly utilised. However, designing biodegradable polymers that overcome these issues is often difficult. In this study, we demonstrate that machine-learning techniques can contribute to the development of multiblock polyamides composed of Nylon6 and alpha-amino acid segments that are satisfactorily mechanically tough and degradable. Multi-objective optimisation based on Gaussian process regression suggested appropriate alpha-amino acid sequences for polyamides endowed with both properties. Physical factors associated with the sequence as well as higher-order multiblock-derived structures were revealed to be essential for endowing these polymers with satisfactory properties. Furthermore, these materials are degradable in natural muddy water. Our method provides a useful approach for designing and understanding environmentally friendly plastics and other materials with multiple properties. | Yoshifumi Amamoto; Chie Koganemaru; Ken Kojio; Atsushi Takahara; Sayoko Yamamoto; Kazuki Okazawa; Yuta Tsuji; Toshimitsu Aritake; Kei Terayama | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Biodegradable Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fc2f9799918fe537a1aea9/original/a-machine-learning-approach-to-designing-tough-and-degradable-polyamides-based-on-multiblock-structures.pdf |
611f5b10e65e2d35481c4e5c | 10.26434/chemrxiv-2021-4xtg9 | Size-induced amorphous structure in tungsten oxide
nanoparticles | The properties of functional materials are intrinsically linked to their atomic structure. When going to the nanoscale, size-induced structural changes in atomic structure often occur, however these are rarely well-understood. Here, we systematically investigate the atomic structure of tungsten oxide nanoparticles as a function of the nanoparticle size and observe drastic changes when the particles are smaller than 5 nm, where the particles are amorphous. The tungsten oxide nanoparticles are synthesized by thermal decomposition of ammonium metatungstate hydrate in oleylamine and by varying the ammonium metatungstate hydrate concentration, the nanoparticle size, shape and structure can be controlled. At low concentrations, nanoparticles with a diameter of 2-4 nm form and adopt an amorphous structure that locally resembles the structure of polyoxometalate clusters. When the concentration is increased the nanoparticles become elongated and form nanocrystalline rods up to 50 nm in length. The study thus reveals a size-dependent amorphous structure when going to the nanoscale and provides further knowledge on how metal oxide crystal structures changes at extreme length scales. | Mikkel Juelsholt; Andy Sode Anker; Troels Lindahl Christiansen; Mads Ry Jørgensen; Innokenty Kantor; Daniel Risskov Sørensen; Kirsten Marie Ørnsbjerg Jensen | Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611f5b10e65e2d35481c4e5c/original/size-induced-amorphous-structure-in-tungsten-oxide-nanoparticles.pdf |
648488534f8b1884b71ae449 | 10.26434/chemrxiv-2023-97zdb | Antibody-PROTAC Conjugate Enables Selective Degradation of Receptor-Interacting Serine/Threonine-Protein Kinase 2 (RIPK2) in HER+ Cell Lines | Proteolysis targeting chimeras (PROTACs) are a family of heterobifunctional molecules that are now realising their promise as a therapeutic strategy for targeted protein degradation. However, one limitation of existing designs is the lack of cell-selective targeting of the protein degrading payload. This manuscript reports a cell-targeted approach to degrade receptor-interacting serine/threonine-protein kinase 2 (RIPK2) in HER2+ cell lines. An antibody-PROTAC conjugate is prepared containing a protease cleavable linkage between the antibody and the corresponding degrader. Potent RIPK2 degradation is observed in HER2+ cell lines, whereas an equivalent anti-IL4 antibody-PROTAC conjugate shows no degradation at therapeutically relevant concentrations. No RIPK2 degradation was observed in HER2- cell lines for both bioconjugates. This work demonstrates the potential for cell-selective delivery of PROTAC scaffolds by engaging with signature extracellular proteins expressed on the surface of particular cell types. | Karina Chan; Preethi Soundarya Sathyamurthi; Markus Queisser; Michael Mullin; Harry Shrives; Diane Coe; Glenn Burley | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648488534f8b1884b71ae449/original/antibody-protac-conjugate-enables-selective-degradation-of-receptor-interacting-serine-threonine-protein-kinase-2-ripk2-in-her-cell-lines.pdf |
6662569191aefa6ce1f5495f | 10.26434/chemrxiv-2024-v3q40 | Quantitative Reactivity Models for Oxidative Addition to L2Pd(0): Additional Substrate Classes, Solvents, and Mechanistic Insights | Quantitative molecular structure-reactivity models are useful for generating predictions to guide synthesis design, and in formulating and testing mechanistic hypotheses. We report an expanded multivariate linear regression (MLR) model for the rate of (hetero)aryl (pseudo)halide oxidative addition to L2Pd(0), here exemplified by Pd(PCy3)2. This builds on a prior model from our group, with additional substrate classes (aryl chlorides and iodides) and reaction solvents (THF, toluene, THF/DMF mixture). Overall solvent effects across the entire substrate set are minimal under these conditions, enabling a unified MLR model without introduction of new molecular descriptors beyond the original five. Examining the mechanistic origin of the two molecular electrostatic potential (ESP) descriptors led to generation of a simpler, four descriptor model that is suitable for aryl halides, but not for 2-halopyridines. Using this model we identified a mechanistic outlier, 2-pyridyl triflate, which undergoes a nucleophilic displacement oxidative addition that does not involve the adjacent nitrogen atom. Finally, we discuss the relationship between C–X bond strength and oxidative addition rates, and compare the intrinsic bond strength index (IBSI) to bond dissociation enthalpy (BDE) as a bond strength descriptor. | Jingru Lu; Holly Celuszak; Irina Paci; David Leitch | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Chemoinformatics - Computational Chemistry; Bond Activation; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6662569191aefa6ce1f5495f/original/quantitative-reactivity-models-for-oxidative-addition-to-l2pd-0-additional-substrate-classes-solvents-and-mechanistic-insights.pdf |
60c747a8567dfe101aec488d | 10.26434/chemrxiv.11760552.v1 | Wavelength-Gated Photoreversible Polymerization and Topology Control | We exploit the wavelength dependence of [2+2] photocycloadditions and -reversions of styrylpyrene to exert unprecedented control over the photoreversible polymerization and topology of telechelic building blocks. Blue light affords high molar mass polymers that are stable at wavelengths exceeding 430 nm yet highly responsive to shorter wavelengths. UVB irradiation induces a rapid depolymerization yielding linear oligomers, whereas violet light generates cyclic entities. Different colors of light thus allow switching between a depolymerization that either proceeds through cyclic or linear topologies. The light-controlled topology formation was evidenced by correlation of mass spectrometry (MS) with size exclusion chromatography (SEC) and ion mobility data.<br /> | Hendrik Frisch; Kai Mundsinger; Berwyck Poad; Stephen Blanksby; Christopher Barner-Kowollik | Organic Polymers; Polymerization (Polymers); Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747a8567dfe101aec488d/original/wavelength-gated-photoreversible-polymerization-and-topology-control.pdf |
60c75757702a9b22a618ca80 | 10.26434/chemrxiv.13634981.v3 | BAR-based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region | <div><p>The indirect
construction of the free energy landscape at Quantum mechanics (QM)/ molecular
mechanics (MM) levels provides a feasible alternative to the direct QM/MM free
energy simulations. The main idea under the indirect method is constructing a
thermodynamic cycle, exploring the configurational space at a computationally
efficient but less accurate low-level Hamiltonian, and performing an alchemical
correction to obtain the thermodynamics at an accurate but computationally
demanding high-level Hamiltonian. In our previous works, we developed a
multi-dimensional nonequilibrium free energy simulation framework to obtain
QM/MM free energy landscapes indirectly. Specifically, we considered obtaining semi-empirical
QM (SQM) results by combining the MM results and the MM-to-SQM correction and
obtaining the QM results by combining the SQM results and the SQM-to-QM
correction. In this work, we explore the possibility of changing the region for
electronic structure calculations in the multi-scale QM/MM treatment, which
could also be considered as a change of the level of theory. More generally,
the multi-dimensional nonequilibrium Hamiltonian-variation/perturbation
framework could be used to obtain transformations between different
Hamiltonians of interest, such as changing the QM theory, the size of the QM
region, and the basis set simultaneously. </p>
<p> </p></div> | Zhaoxi Sun; Zhirong Liu | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry; Quantum Mechanics; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75757702a9b22a618ca80/original/bar-based-multi-dimensional-nonequilibrium-pulling-for-indirect-construction-of-qm-mm-free-energy-landscapes-varying-the-qm-region.pdf |
62367954a4ed957a7e266b9d | 10.26434/chemrxiv-2022-1rqhk | Supramolecular Modification of a Metal-Organic Framework Increases Flexibility and Switchability: Experimental Insights into Structural Deformation of ZIF-8 | Use of chemical modulators during the synthesis of a coordination framework is an important strategy to affect and tune properties of porous materials. Herein, we introduce an approach to understanding structural modulation and deformation of soft, porous crystals in the context of gas adsorption by using atomic force microscopy (AFM) nanoindentation and physisorption analysis. Modified nanocrystals of the prototypical zeolitic-imidazolate framework-8 (ZIF-8) were generated in triethylamine (Et3N) via an in-situ supramolecular modulation method. We demonstrate that using triethylamine as a modulator results in a conspicuous decrease in elastic modulus (0.7 ± 0.2 GPa) compared to the unmodified nanocrystals of ZIF-8 (2.1 ± 0.8 GPa). Argon gas adsorption analysis also reveals that the more flexible, amine-modified framework exhibited gradual and cooperative gate-opening structural transitions (P/P0 = 0.33 ± 0.02) compared to the steep and stepwise characteristics of unmodified samples of ZIF-8 (P/P0 = 0.45 ± 0.02). The differences in Argon gas pressure-induced structural deformations correspond to the decrease in elastic modulus of base-modified nanocrystals of ZIF-8, likely a consequence of the impact of Et3N on the relative number of point defects and hydrogen bonds in the framework. Our study demonstrates how a combination of AFM nanoindentation, gas uptake, and spectroscopic characterization can be applied to understand structural and energetic changes upon adsorption in flexible framework materials. | Al Tiba; Jason Perman; Leonard MacGillivray; Alexei Tivanski | Materials Science; Nanoscience; Energy; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Nanoscience; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62367954a4ed957a7e266b9d/original/supramolecular-modification-of-a-metal-organic-framework-increases-flexibility-and-switchability-experimental-insights-into-structural-deformation-of-zif-8.pdf |
60c74c41469df477d9f4404e | 10.26434/chemrxiv.12451922.v1 | Theoretical Study of the Optical Spectra of SARS-CoV-2 Proteins | Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined easily or quickly. Herein, we provide calculated circular dichroism (CD) spectra in the far- and near-UV, and infra-red (IR) spectra in the amide I region for experimental structures and computational models of SARS-CoV-2 proteins. The near-UV CD spectra offer greatest sensitivity in assessing the accuracy of models. | Zhuo Li; Jonathan Hirst | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c41469df477d9f4404e/original/theoretical-study-of-the-optical-spectra-of-sars-co-v-2-proteins.pdf |
63c916d82f7a7a2068cb8e89 | 10.26434/chemrxiv-2023-527dl | COOPERATIVE H2 ACTIVATION AT A NICKEL(0)-OLEFIN CENTER | Catalytic olefin hydrogenation reactions are ubiquitous in organic synthesis. Most proposed catalytic cycles for the homogeneous hydrogenation of olefins using molecular H2 start with the oxidative addition of H2 by metal complexes to form two reactive M–H bonds, often via a non-classical metal dihydrogen (M–H2) intermediate. Previous reports had provided indirect evidence for an alternative mechanism involving direct hydrogen transfer from a metal-bound H2 molecule to a metal-bound olefin without the oxidative addition step. However, the key metal(olefin)(H2) and the corresponding ligand-to-ligand hydrogen transfer (LLHT) step had not been directly observed. Herein, we show that incorporating a precoordinated olefin in a P(C=C)P pincer ligand framework allows for the observation of both a non-classical Ni-(H2) complex and the Ni(alkyl)(hydrido) product of LLHT in rapid equilibrium with dissolved H2. The utility of this cooperative H2-activation mechanism for catalysis is demonstrated in the semihydrogenation of diphenylacetylene under mild conditions. Mechanistic investigations supported by DFT calculations back the central role of LLHT for both cooperative H2 activation and catalytic semihydrogenation. These results provide an experimental basis for the role of LLHT steps in olefin hydrogenation mechanisms and demonstrate the utility of olefin-based pincer ligands for cooperative catalysis with non-noble metals. | María L. G. Sansores-Paredes; Martin Lutz; Marc-Etienne Moret | Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Ligand Design; Small Molecule Activation (Organomet.) | CC BY 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c916d82f7a7a2068cb8e89/original/cooperative-h2-activation-at-a-nickel-0-olefin-center.pdf |
63444d22f764e69a3a166679 | 10.26434/chemrxiv-2022-3nspm | In-situ analysis of corrosion products in molten salt: concurrent X-ray absorption and electrochemistry reveal both ionic and metallic species | Understanding and controlling the physical and chemical processes at molten salt‐alloy interfaces is vital for molten‐salt nuclear reactors. Corrosion processes in molten salts are highly dependent on the redox potential of the solution that changes with the addition of fission and corrosion products. Therefore, reactor designers develop online electrochemical methods of salt monitoring. But electrochemical spectroscopy relies on the deconvolution of broad peaks, a process that may be imprecise in the presence of multiple species in the solution. Here, we describe our developments towards monitoring the concentration and the chemical state of corrosion products in the melt by a combination of electrochemistry and X-ray absorption spectroscopy. We placed NiCr foil in molten FLiNaK and found the presence of both Ni2+ ions and metallic Ni in the melt, which we attribute to the disintegration of the corroding foil due to Cr dealloying. Although extremely challenging, spectroelectrochemical measurements add a promising rich new data stream for online salt monitoring. | Sean Fayfar; Guiqiu Zheng; Dave Sprouster; Matthew Marshall; Eli Stavitski; Denis Leshchev; Boris Khaykovich | Physical Chemistry; Energy; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63444d22f764e69a3a166679/original/in-situ-analysis-of-corrosion-products-in-molten-salt-concurrent-x-ray-absorption-and-electrochemistry-reveal-both-ionic-and-metallic-species.pdf |
628ba8d0809e325fd299cc1f | 10.26434/chemrxiv-2022-jh1lx | Direct Structure Determination from Spherulites using 3D Electron Diffraction | The spherulitic morphology is considered to be the most common morphology of crystalline materials and is particularly apparent in melt-crystallized products. Yet, historically, the polycrystalline nature of spherulites has hindered successful crystal structure determination. Here, we report for the first time the direct structure determination of a small molecule organic compound in spherulite form using 3D electron diffraction (3D ED). We employed vemurafenib (VMN), a clinical drug used for the treatment of BRAF-mutant melanoma, as a model compound. VMN has four known polymorphs (α-, β-, γ-, and δ-VMN), three of which were discovered by melt crystallization. We first solved the crystal structures of α-, β-, and γ-VMN from both open and compact spherulite samples using 3D ED, and the resulting structures were highly consistent with those solved by single-crystal X-ray diffraction. We then determined the previously unknown crystal structure of δ-VMN—the least stable polymorph which cannot be cultivated as a single crystal—directly from the spherulite sample resulting from spontaneous nucleation. We unexpectedly discovered a new polymorph during our studies, denoted as Form ε. Single crystals of ε-VMN are extremely thin and are not suitable for study by X-ray diffraction. Again, we determined the structure of ε-VMN from both open and compact spherulite forms. This successful structure elucidation of all five VMN polymorphs demonstrates the possibility of removing the time-consuming step of single crystal growth and directly determining structures from spherulite samples. Thereby, this discovery will improve the efficiency and broaden the scope of polymorphism research, especially within the field of melt-crystallization. | Shuting Li; Molly Lightowler; Xiao Ou; Siyong Huang; Yifan Jiang; Xizhen Li; Xiaodong Zou; Hongyi Xu; Ming Lu | Physical Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628ba8d0809e325fd299cc1f/original/direct-structure-determination-from-spherulites-using-3d-electron-diffraction.pdf |
620c4ecfe0f5295bccb40973 | 10.26434/chemrxiv-2022-262lh | Fluoromethylketone-fragment conjugates designed as covalent modifiers of EcDsbA are atypical substrates | Disulfide bond protein A (DsbA) is an oxidoreductase enzyme that catalyzes the formation of disulfide bonds in Gram-negative bacteria. In Escherichia coli, DsbA (EcDsbA) is essential for bacterial virulence, thus inhibitors have the potential to act as antivirulence agents. A fragment-based screen was conducted against EcDsbA and herein we describe the development of a series of compounds based on a phenylthiophene hit identified from the screen. A novel thiol reactive and “clickable” ethynylfluoromethylketone was designed for reaction with azide-functionalized fragments to enable rapid and versatile attachment to a range of fragments. The resulting fluoromethylketone conjugates showed selectivity for reaction with the active site thiol of EcDsbA, however unexpectedly, turnover of the covalent adduct was observed. A mechanism for this turnover was investigated and proposed which may have wider ramifications for covalent reactions with dithiol-disulfide oxidoreducatases. | Bradley Doak; Rebecca Whitehouse; Kieran Rimmer; Martin Williams; Begona Heras; Sofia Caria; Olga Ilyichova; Mansha Vazirani; Biswaranjan Mohanty; Jason Harper; Martin Scanlon; Jamie Simpson | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620c4ecfe0f5295bccb40973/original/fluoromethylketone-fragment-conjugates-designed-as-covalent-modifiers-of-ec-dsb-a-are-atypical-substrates.pdf |
61b0dcdbdcbea2f0f19abb15 | 10.26434/chemrxiv-2021-3pq2v | Nanoscale electrochemical 3D deposition of cobalt with nanosecond voltage pulses in an STM | To explore a minimal feature size of <100 nm with electrochemical additive manufacturing, we use a strategy originally applied to microscale electrochemical machining for the nanoscale deposition of Co on Au. The concept’s essence is the localization of electrochemical reactions below a probe during polarization with ns-long voltage pulses. As shown, a confinement that exceeds that predicted by a simple model based on the time constant for one-dimensional double layer charging enables a feature size of <50 nm for 2D patterning. We further indirectly verify the potential for out-of-plane deposition by tracking growth curves of high-aspect-ratio deposits. Importantly, we report a lack of anodic stability of Au tips used for patterning. As an inert probe is the prerequisite for controlled structuring, we experimentally verify an increased resistance of Pt probes against degradation. Consequently, the developed setup and processes show a path towards reproducible direct 2D and 3D patterning of metals at the nanoscale. | Alain Reiser; Rolf Schuster; Ralph Spolenak | Materials Science; Nanoscience; Materials Processing; Nanostructured Materials - Materials; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b0dcdbdcbea2f0f19abb15/original/nanoscale-electrochemical-3d-deposition-of-cobalt-with-nanosecond-voltage-pulses-in-an-stm.pdf |
60c73f20337d6c5e99e264df | 10.26434/chemrxiv.7261559.v1 | Ibogaine Modifies GDNF, BDNF and NGF Expression in Brain Regions Involved in Mesocorticolimbic and Nigral Dopaminergic Circuits | <p>Ibogaine is a psychedelic alkaloid which has
been subject of intense scientific research due to its reported ability to
attenuate drug-seeking behavior. Recent work suggested that ibogaine effects on
alcohol self-administration in rats was related to the release of Glial Cell
Derived Neurotrophic Factor (GDNF) in the Ventral Tegmental Area (VTA), a
mesencephalic region which hosts soma of dopamine neurons. It is well known
that neurotrophic factors (NFs) mediate the neuroadaptations induced in the
mesocorticolimbic dopaminergic system by repeated exposure to drugs. Although
previous reports have shown ibogaine´s ability to induce GDNF expression in rat
midbrain, there are no studies addressing its effect on the expression of GDNF,
Brain Derived Neurotrophic Factor (BDNF) or Nerve Growth Factor (NGF) in
distinct regions containing dopaminergic neurons. In this work, we examined the
effect of ibogaine acute administration on the expression of these NFs in the VTA,
Prefrontal Cortex (PFC), Nucleus Accumbens (NAcc) and the Substantia Nigra
(SN). Thus, rats were i.p. treated with ibogaine 20 mg/kg (I<sub>20</sub>), 40
mg/kg (I<sub>40</sub>) or vehicle, and NFs expression was analyzed after 3 and
24 hours. Only at 24 h an increase of the expression for the three NFs were
observed in a site and dose dependent manner. Results for GDNF showed that only
I<sub>40</sub> selectively upregulated its expression in the VTA and SN. Both
doses of ibogaine elicited a large increase in the expression of BDNF in the
NAcc, SN and PFC, while a significant effect was found in the VTA only for I<sub>40</sub>.
Finally, NGF was found to be upregulated in all regions after I<sub>40</sub>,
while a selective upregulation was found in PFC and VTA for the I<sub>20</sub>
treatment. An increase in the content of mature GDNF was observed in the VTA
but no significant increase in the mature BDNF protein content was found in all
the studied areas. Interestingly, an increase in the content of proBDNF was
detected in the NAcc for both treatments. Further research is needed to
understand the neurochemical bases of these changes, and to confirm their
contribution to the anti-addictive properties of ibogaine. </p> | Soledad Marton; Bruno González; Sebastián Rodríguez; Ernesto Miquel; Laura Martínez Palma; Mariana Pazos; José Pedro Prieto; Paola Rodríguez; Dalibor Sames; Gustavo Seoane; Cecilia Scorza; Patricia Cassina; Ignacio Carrera | Natural Products; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f20337d6c5e99e264df/original/ibogaine-modifies-gdnf-bdnf-and-ngf-expression-in-brain-regions-involved-in-mesocorticolimbic-and-nigral-dopaminergic-circuits.pdf |
6617dbcb418a5379b0a16578 | 10.26434/chemrxiv-2024-0hd8r | Using Interaction Fingerprints as a Strategy of Protein-Ligand Interaction Patterns Recognition and Post-Docking Analysis | Analysis of ligand-protein structures can elucidate many biological mechanisms and guide molecular docking studies. Intermolecular interactions can be encoded in different ways. Binary vectors that represent that information can be called “interaction fingerprints,” and working with them is a good strategy to work with a large set of structures. We developed NEQUIM Contact System (NCS) software that generates and analyzes interaction fingerprints of protein-ligand complexes. We employed different encoding vectors available using NCS and we implemented a new strategy that includes sequence alignment and generation of models based on data sets of known structures. Post-docking analysis of virtual screening (VS) of targets PDE5, CDK2, HIVRT, and P38 showed a large increase of area under the curve (AUC) for an optimized protocol for each target. The best increase in AUC results for each target are P38 (116%), PDE5 (64%), HIVRT (40%), and CDK2 (4%). | Andrelly Martins-José; Julio CD LOPES | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6617dbcb418a5379b0a16578/original/using-interaction-fingerprints-as-a-strategy-of-protein-ligand-interaction-patterns-recognition-and-post-docking-analysis.pdf |
60c75a7e842e657aebdb4af5 | 10.26434/chemrxiv.13551182.v5 | Steric effects vs. electron delocalization: a new look into stability of diastereomers, conformers and constitutional Isomers | <div>
<p>A quantum chemical investigation of
the stability of compounds with identical formulas was carried out on 23
classes of compounds made of C, N, P, O, S atoms as core structures and
halogens H, F, Cl, Br, I as substituents. All possible structures were
generated and investigated by quantum mechanical methods. The prevalence of a
formula in which its <i>Z</i> configuration, <i>gauche</i> conformation or <i>meta</i>
isomer is the most stable form is calculated and discussed. Quantitative and
qualitative models to explain the stability of 23 classes of halogenated
compounds were also proposed.</p></div> | Sopanant Datta; Taweetham Limpanuparb | Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75a7e842e657aebdb4af5/original/steric-effects-vs-electron-delocalization-a-new-look-into-stability-of-diastereomers-conformers-and-constitutional-isomers.pdf |
62d0f6fd724581bfc496e857 | 10.26434/chemrxiv-2022-636c2 | Improved Prediction of Maximum EQE in TADF-based OLEDs Through Ensemble Learning | In recent times, we have seen colossal growth in the field of Thermally Activated Delayed Fluorescence (TADF)-based OLEDs in terms of synthesis and applications in sensing and imaging. However, the device-level application is still limited to the unpredictability of external quantum efficiency (EQE). Although theoretical research involving internal quantum efficiency (IQE) and mechanistic pathways for reverse intersystem crossing (rISC) in TADF systems have been explored quite rigorously, investigation on EQE is lacking. With the emergence of data-driven analysis being the fourth paradigm of science (empirical, theoretical, and computational being the previous three), we have employed ML models on 30 features of 123 samples, availed from literature to predict the EQEmax. On the one hand, the employed models capture device selectivity but are prevalent in the emissive range of chromophores. We have shown that Gradient Boosting (GB), an ensemble learning model, has been able to predict EQEmax with r2 score of 0.71±0.04/0.84 and a low RMSE of 4.22±0.55/2.53 for the train/test set. Considering the current state-of-the-art (SOTA), this is the best model which can predict for TADF chromophores of any emissive range and delineate the effect of device architecture. We also have carried out feature importance analysis to make this so-called black-box model interpretable. This analysis has helped to figure out essential parameters responsible for better EQE efficiency. Even the learning curve is still ascending, proving that the model can improve its prediction if more training examples are provided in the future. All the computations can be done using easily accessible cloud computations. | BIDHAN CHANDRA GARAIN; Swapan K. Pati | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2022-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d0f6fd724581bfc496e857/original/improved-prediction-of-maximum-eqe-in-tadf-based-ole-ds-through-ensemble-learning.pdf |
652fc89b2431cc1daccf3ab2 | 10.26434/chemrxiv-2023-pwt6p | Effect of Increasing Ligand Conjugation in Cu(I) Photosensitizers on NiO Semiconductor Surfaces | Dye-sensitized photoelectrochemical cells may be used as heterogeneous catalysts for fuel-forming and redox reactions. We describe here the synthesis, characterization, and study of ground and excited state properties of three Cu(I) complexes involving three different ligands with varying electron accepting capacities. Femtosecond and nanosecond transient absorption studies confirm the formation of a singly reduced acceptor ligand after photoexcitation of the Cu(I) centre. These complexes are surface anchored onto nanostructured NiO on conductive fluorine-doped tin oxide on glass to fabricate photocathodes. It was found that even though the ligands with increasing conjugation have effects on the formation of the final excited state in solution, they exhibit similar photocurrents upon white light illumination suggesting hole transfer to NiO happening in advance of the formation of the final excited state. | Zujhar Singh; Joseph Chiong; Saeid Kamal; Marek Majewski | Inorganic Chemistry; Coordination Chemistry (Inorg.); Electrochemistry; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652fc89b2431cc1daccf3ab2/original/effect-of-increasing-ligand-conjugation-in-cu-i-photosensitizers-on-ni-o-semiconductor-surfaces.pdf |
6722265a5a82cea2fa84092a | 10.26434/chemrxiv-2024-3c8dz | Size-exclusion chromatography–electrospray-ionization mass spectrometry to characterize end group and chemical distribution of poly(lactide-co-glycolide) co-polymers | The characterization of the microstructure of in vivo degradable polyesters is gaining increased interest thanks to their high-performance applications, such as drug delivery systems. The design of such material requires a high level of understanding of the critical material attributes of the polyesters, such as molecular-weight distribution (MWD), chemical-composition distribution (CCD), and end-groups (functionality-type distribution, FTD). Size-exclusion chromatography (SEC) hyphenated with mass spectrometry (MS) yields SEC-MS, which is an effective method for analyzing the microstructure of polymers. While the MWD can be determined by size-exclusion chromatography hyphenated with ultraviolet spectrometry and refractive index (SEC-UV/RI), the CCD and FTD can be determined by SEC-MS. However, previous applications of SEC-MS have failed to address the risk of polymer fragmentation during the analysis process. It is crucial to establish whether SEC-MS methods can be applied to biodegradable polymers and to recognize if fragmentation processes occurred during the SEC separation or during the ESI-MS process.
In this study, we investigate whether SEC-MS methods can be applied to PLGA biodegradable polyesters. The research demonstrates that the choice of alkali metal salt used during ionization strongly influences the stability of PLGA during SEC-MS analysis. CsI was found to minimize fragmentations during ESI-MS, simplifying the MS spectra and allowing isomeric PLGA structures to be distinguished. The resulting method facilitates end-group and CCD determination. Additionally, when combined with selective degradation, the described method can provide insights in the “blockiness” of the polymer and support the development of sequence-controlled PLGA synthesis.
| Masashi Serizawa; Pieter van Delft; Peter J. Schoenmakers; Ron A. H. Peters; Andrea F.G. Gargano | Analytical Chemistry; Polymer Science; Drug delivery systems; Organic Polymers; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6722265a5a82cea2fa84092a/original/size-exclusion-chromatography-electrospray-ionization-mass-spectrometry-to-characterize-end-group-and-chemical-distribution-of-poly-lactide-co-glycolide-co-polymers.pdf |
60c7443d337d6c1605e26d79 | 10.26434/chemrxiv.9768095.v1 | Diverting Radical-Anionic C-H Amidation to a C-N/C-O Cascade for the Construction of Hydroxyisoindolines from Unprotected Amides | <p>An intramolecular C(sp<sup>3</sup>)-H amidation proceeds in the presence of <i>t</i>-BuOK, molecular oxygen, and DMF. The success of this reaction hinges on the deprotonation of a mildly acidic N-H bond and selective radical activation of a benzylic C(sp<sup>3</sup>)-H bond towards hydrogen atom transfer (HAT)<i>. </i>DFT calculations suggest a thermodynamically favorable sequence of steps mediated by the generation of a radical-anion intermediate. As this intermediate starts to form a two-centered/three-electron (<i>2c,3e)</i>C-N bond, the extra electron is “ejected” into the π*-orbital of the aromatic core. The resulting cyclic radical-anion is readily oxidized by molecular oxygen to forge the C-N bond of the product. The transformation of a relatively weak reductant into a stronger reductant (i.e., “reductant upconversion”) allows one to use mild oxidants such as molecular oxygen. In contrast, the second stage of NH/CH activation forms a highly stabilized radical-anion intermediate incapable of electron transfer to molecular oxygen. Hence, the oxidation is impossible and an alternative reaction path opens via coupling between the radical anion intermediate and either superoxide or hydroperoxide radical. The hydroperoxide intermediate transforms into the final hydroxyisoindoline products under basic conditions. The use of TEMPO as an additive was found to activate less reactive amides. The combination of experimental and computational data outlines a conceptually new mechanism for the conversion of unprotected amides into hydroxyisoindolines proceeding as a sequence of C-H amidation and C-H oxidation.</p> | Quintin Elliott; Gabriel dos Passos Gomes; Christopher Evoniuk; Igor Alabugin | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7443d337d6c1605e26d79/original/diverting-radical-anionic-c-h-amidation-to-a-c-n-c-o-cascade-for-the-construction-of-hydroxyisoindolines-from-unprotected-amides.pdf |
60c7517f9abda21490f8dc0d | 10.26434/chemrxiv.13175063.v1 | The Impact of Hydrogen Valence on Its Bonding and Transport in Molten Fluoride Salts | <p>Interest in molten salts has increased significantly over the last decade due to their potential application in various clean-energy technologies including hydrogen generation, solar heat storage, and advanced nuclear power plants. In the development of new molten salt-based fission and fusion systems, controlling hydrogen poses a critical challenge due to its ability to corrode structural materials as <sup>3</sup>H<sup>+</sup>, and its potential to cause significant radioactive release as diffusive <sup>3</sup>H<sup>0</sup>. Yet, the chemistry and transport behavior of the hydrogen species remain poorly understood despite several decades of research. Using ab initio molecular dynamics, we present a coupled examination of hydrogen valence, speciation and transport in the prototypical salts 66.6%LiF-33.3¾F<sub>2</sub> (Flibe) and 46.5%LiF-11.5%NaF-42%KF (Flinak). We discovered significant differences between <sup>3</sup>H<sup>0</sup> and <sup>3</sup>H<sup>+</sup>transport behaviors. <sup>3</sup>H<sup>+</sup> diffuses 2-4 times slower than <sup>3</sup>H<sup>0</sup>, which can be ascribed to hydrogen bonding and complexation in solution. This work helps explain varying experimental results and provides useful species transport data for designing hydrogen control systems for molten salts. </p> | Stephen T. Lam; Qing-Jie Li; Jonathan P. Mailoa; Charles Forsberg; Ronald Ballinger; Ju Li | Computational Chemistry and Modeling; Transport Phenomena (Chem. Eng.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7517f9abda21490f8dc0d/original/the-impact-of-hydrogen-valence-on-its-bonding-and-transport-in-molten-fluoride-salts.pdf |
62c721c95163112dc71543e3 | 10.26434/chemrxiv-2022-jfvdk-v2 | High Humidity Shaker Aging to Access Chitin and Cellulose Nanocrystals | Nature’s potential in affording functional biomaterials is often hindered by extraction conditions. To isolate nanocrystalline domains in polysaccharides high solvent usage is warranted while low reactivity and yields are also limiting factors. In this report, the first solvent-free pathway to access carboxylated chitin and cellulose nanocrystals with excellent mass balance is described, relying on a new method coined high-humidity shaker aging (HHSA). The method involves a brief and mild grinding of the polysaccharide with ammonium persulfate followed by an aging phase under high-humidity and on a shaker plate. Insights into the mechanism were uncovered, which highlighted the unique role of high humidity to afford a gradual uptake of water by the material up to deliquescence when the reaction is complete. This process was then validated for direct synthesis of nanocrystals from biomass sources including crab and soft wood pulp. | Tony Jin; Tracy Liu; Faezeh Hajiali; Madison Santos; Yali Liu; Davis Kurdyla; Sophie Regnier ; Sabahudin Hrapovich; Edmond Lam ; Audrey Moores | Organic Chemistry; Polymer Science; Nanoscience; Biopolymers; Cellulosic materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c721c95163112dc71543e3/original/high-humidity-shaker-aging-to-access-chitin-and-cellulose-nanocrystals.pdf |
672ccb1e5a82cea2fa62e83c | 10.26434/chemrxiv-2024-vxxlr | Efficient Piancatelli rearrangements of HMF derivatives under microwave activation or subcritical water conditions to produce functionalized hydroxylated cyclopentenones | HMF (5-hydroxymethylfurfural), a renewable raw material from biomass, was used as starting material to provide 5-aryl-4-hydroxymethyl-4-hydroxycyclopentenones with functionalized aryl groups. In a first time, arylic substituents were added to the aldehyde moiety of HMF under rhodium- or palladium-catalyzed 1,2-addition of arylboronic acids, in mild conditions to respect the very sensitive HMF reactivity. In a second time, these non-symmetrical furan-2,5-dicarbinols, through Piancantelli rearrangement, provided the desired cyclopentenones under microwave activation or subcritical water conditions (100 °C and 100 bars) using the Zippertex technology, in regio- and diastereoselective manner. These synthetized bis-hydroxylated cyclopentenone derivatives exhibited significant antimicrobial activities against gram-positive bacteria Micrococcus luteus, Bacillus subtilis and gram-negative bacteria Echerichia coli. | Sparta YOUSSEF-SALIBA; Clémentine MAYET; Elsa VAN ELSLANDE; Géraldine LE GOFF; Jean-Francois BETZER | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672ccb1e5a82cea2fa62e83c/original/efficient-piancatelli-rearrangements-of-hmf-derivatives-under-microwave-activation-or-subcritical-water-conditions-to-produce-functionalized-hydroxylated-cyclopentenones.pdf |
60c73cc9f96a004011285ca5 | 10.26434/chemrxiv.14751534.v1 | Breaking Scaling Relationships in CO2 Reduction on Copper Alloys with Organic Additives | <p>Boundary conditions for catalyst
performance in the conversion of common precursors such as N<sub>2</sub>, O<sub>2</sub>,
H<sub>2</sub>O, and CO<sub>2</sub> are governed by linear free energy and
scaling relationships. Knowledge of these limits offers an impetus for
designing strategies to alter reaction mechanisms to improve performance.
Towards a more sustainable carbon economy, understanding the basis of catalytic
selectivity for CO<sub>2</sub> conversion to chemical feedstocks/fuels is key.
Herein, high-throughput experimentation on 14 bulk copper bimetallic alloys
allowed for data-driven identification of a fundamental linear scaling
relationship between methane and C<sub>2+</sub> products that constrains the
Faradaic efficiency for C–C coupling. We have furthermore demonstrated that
coating the electrodes with a molecular film breaks the scaling relationship to
promote C<sub>2+</sub> product formation.</p> | Yunchieh Lai; Nicholas Watkins; Alonso Rosas-Hernández; Arnaud Thevenon; Gavin P. Heim; Lan Zhou; Jonas Peters; John Gregoire; Theodor Agapie | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9f96a004011285ca5/original/breaking-scaling-relationships-in-co2-reduction-on-copper-alloys-with-organic-additives.pdf |
60c75830f96a001a9a288da1 | 10.26434/chemrxiv.14519448.v1 | DFT-Based Approach Enables Deliberate Tuning of Alloy Nanostructures Plasmonic Properties | <div>Using DFT we calculated band structures and dielectric functions of multiple binary alloy systems. The obtained data enabled us to elucidate the interconnection between alloy composition, fundamental properties such as band structure and their optical properties. The analysis provides the explanation for the smooth change of optical properties in the UV/VIS range and reveals the appearance of strong optical losses in the IR range due to interband transitions. Since they are present in all alloys but not in pure metals we identify such transitions as an emergent property of alloying. To predict plasmonic properties of different alloy nanostructures we performed electrodynamics simulations based on calculated and experimental dielectric functions. The results showed that that calculations based on the standardly used PBE functional in some cases drastically deviate from experiment-based results, and the calculations with an equally efficient GLLB-SC functional are superior. <br /></div> | Matej Bubaš; J. Sancho Parramon | Alloys; Optical Materials; Plasmonic and Photonic Structures and Devices; Computational Chemistry and Modeling; Optics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75830f96a001a9a288da1/original/dft-based-approach-enables-deliberate-tuning-of-alloy-nanostructures-plasmonic-properties.pdf |
6267fa5aed4d88847e193a6a | 10.26434/chemrxiv-2022-cjqqb-v2 | A consistent picture of phosphate–divalent cation binding from models with implicit and explicit electronic polarization | The binding of divalent cations to the ubiquitous phosphate group is essential for a number of key biological processes, such as DNA compaction, RNA folding or interaction of some proteins with membranes. Yet, probing their binding sites, modes and associated binding free energy is a challenge for both experiments and simulations. In simulations, standard force fields strongly overestimate the interaction between phosphate groups and divalent cations. Here, we examine how different strategies to include electronic polarization effects in force fields—implicitly through the use of scaled charges or pair-specific Lennard-Jones parameters, or explicitly with the polarizable force fields Drude and AMOEBA—capture the interaction of a model phosphate compound, dimethylphosphate, with calcium and magnesium divalent cations. We show that both implicit and explicit approaches, when carefully parametrized, are successful in capturing the overall binding free energy, and that common trends emerge from the comparison of different simulation approaches. Overall, the binding is very moderate, slightly weaker for Ca2+ than Mg2+, and the solvent-shared ion pair is the most stable. Our results thus suggest practical ways to capture the divalent cations with biomolecular phosphate groups in complex biochemical systems. In particular, the computational efficiency of implicit models makes them ideally suited for large-scale simulations of biological assemblies, with improved accuracy compared to state-of-the-art fixed-charge force fields. | Julie Puyo; Marie Juillé; Jérôme Hénin; Carine Clavaguéra; Elise Duboué-Dijon | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6267fa5aed4d88847e193a6a/original/a-consistent-picture-of-phosphate-divalent-cation-binding-from-models-with-implicit-and-explicit-electronic-polarization.pdf |
626425d8bdc9c2630be00e8f | 10.26434/chemrxiv-2022-kxkt3 | In-Liquid Plasma Modified Nickel Foam: NiOOH/NiFeOOH Active Site Multiplication for Electrocatalytic Alcohol, Aldehyde, and Water Oxidation | The oxygen evolution reaction (OER) and the value-added selective oxidation of renewable organic substrates are the most promising reactions to supply electrons and protons for the synthesis of sustainable fuels. To meet industrial requirements, new methods for a simple, fast, environmentally friendly, and cheap synthesis of robust, self-supported, high surface area electrodes are required. Herein, we report on a novel in liquid plasma electrolysis approach for the growth of hierarchical nanostructures on nickel foam. Under retention of the morphology, iron could be incorporated into this high surface area electrode. For the oxidation of 5-hydroxymethylfurfural and benzyl alcohol, the iron free plasma treated electrode is more suitable reaching current densities up to 800 mA/cm² with Faradaic efficiencies above 95%. For the OER, the iron incorporated nickel foam electrode reached the industrially relevant current density of 500 mA/cm² at 1.473±0.013 VRHE (60 °C) and showed no activity decrease over 140 h. The different effects of the iron doping is rationalised using MeOH doping and in situ Raman spectroscopy. Furthermore, we could separate changes in intrinsic activity per active site and number of active sites for the OER as well as reveal diffusion limitations of the organic oxidation reactions which we explain with respect to the surface morphology. We anticipate that the plasma modified high surface area nickel foam could potentially be applied for various electrocatalytic processes. | J. Niklas Hausmann; Pramod V. Menezes; Gonela Vijaykumar; Konstantin Laun; Thomas Diemant; Ingo Zebger; Timo Jacob; Matthias Driess; Prashanth W. Menezes | Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Redox Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626425d8bdc9c2630be00e8f/original/in-liquid-plasma-modified-nickel-foam-ni-ooh-ni-fe-ooh-active-site-multiplication-for-electrocatalytic-alcohol-aldehyde-and-water-oxidation.pdf |
60c75445ee301c0c3ac7af27 | 10.26434/chemrxiv.13635374.v1 | Are There Only Fold Catastrophes in the Diels–Alder Reaction Between Ethylene and 1,3–Butadiene? | This work revisits the topological characterization of the Diels–Alder reaction between 1,3–butadiene and ethylene. In contrast to the currently accepted rationalization, we here provide strong evidence in support of a representation in terms of seven structural stability domains separated by a sequence of 10 elementary catastrophes, but all only of the fold type, i.e., C<sub>4</sub>H<sub>6</sub> + C<sub>2</sub>H<sub>4 </sub>: 1–7– [FF]F[F<sup>†</sup>F<sup>†</sup>][F<sup>†</sup>F<sup>†</sup>][FF]F<sup>†</sup>–0 : C<sub>6</sub>H<sub>10</sub>. Such an unexpected finding provides fundamental new insights opening simplifying perspectives concerning the rationalization of the CC bond formation in pericyclic reactions in terms of the simplest Thom’s elementary catastrophe, namely the one–(state) variable, one–(control) parameter function. | Leandro Ayarde-Henriquez; Cristian Guerra; Mario Duque-Noreña; Elizabeth Rincón; Patricia Pérez; Eduardo Chamorro | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75445ee301c0c3ac7af27/original/are-there-only-fold-catastrophes-in-the-diels-alder-reaction-between-ethylene-and-1-3-butadiene.pdf |
669e8de5c9c6a5c07a8a8dde | 10.26434/chemrxiv-2024-047bl | Strength of London dispersion forces in organic structure directing agent – zeolite assemblies | Herein, we study the London dispersion forces between organic structure directing agents (OSDAs) and silica zeolite frameworks (FWs) among the ensemble of possible intermolecular interactions. We consider tetraalkyl-ammonium or -phosphonium OSDAs that are fully templating different silica FWs. Starting with calculations using density functional theory with dispersion correction (DFT-D3), we demonstrate that the interaction energy for dispersion forces between the OSDA and the silica FW is strictly correlated to the number of H atoms in the OSDA, irrespective of the specific structures of OSDAs or FWs. We also show that this correlation is independent of variations in formal charges and thermal motions. All calculations considered – DFT-D3 and ab-initio molecular dynamics with Born-Oppenheimer molecular dynamics (BOMD) scheme undertaken by us, and molecular mechanics (MM) from an accessible database (OSDB) – lead to the same trend. We estimate the energy of these dispersion forces to be ca. -2 kcal.mol-1 per H for efficient H-O contacts. This value is twice the energy of dispersion forces between n-alkane molecules, obtained using the same level of calculations. Such a deviation that might be explained by differences in electron polarizabilities highlights the great attraction existing between alkyl groups and siloxane bonds forming OSDA-zeolite host-guest assemblies. | Karima Ata; Tzonka Mineva; Bruno Alonso | Theoretical and Computational Chemistry; Physical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e8de5c9c6a5c07a8a8dde/original/strength-of-london-dispersion-forces-in-organic-structure-directing-agent-zeolite-assemblies.pdf |
60c74026337d6cfe08e2666c | 10.26434/chemrxiv.7229054.v2 | Light-driven charge accumulation of a molecular Cu(I) complex for storage of photoredox equivalents | The diurnal day/night cycle is presently of great interest for harvesting solar energy aimed at rendering suitable energy storage schemes. To this end we present a noble-metal free system based on a Cu(I) 4H-imidazolate complex, that is efficiently photoreduced in the presence of a sacrificial donor. The two-electron reduced species obtained can be stored in the dark for more than 14 hours. In a dark reaction, the photoredox equivalents can subsequently be transferred to the electron acceptors methyl viologen or oxygen, while the starting Cu(I) complex is almost completely regained. Repetition of this process revealed a charging capacity of 72% after four cycles. The implications of light-driven charge accumulation and prolonged storage times for solar battery and photoredox catalysis are discussed | Martin Schulz; Nina Hagmeyer; Frerk Wehmeyer; Johannes
G. Vos; Benjamin Dietzek | Photochemistry (Org.); Transition Metal Complexes (Inorg.); Energy Storage; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74026337d6cfe08e2666c/original/light-driven-charge-accumulation-of-a-molecular-cu-i-complex-for-storage-of-photoredox-equivalents.pdf |
67dcdf1c81d2151a0246d930 | 10.26434/chemrxiv-2025-5n9m1 | CH-pi Interactions Confer Orientational Flexibility in
Protein-Carbohydrate Binding Sites | Protein-carbohydrate binding is essential for biological function and is driven by non-covalent interactions, including hydrogen bonds and CH-pi stacking interactions. CH-pi stacking interactions are favorable and have high orientational flexibility; however, we lack a comprehensive understanding of the roles that they play in protein binding affinity and selectivity. To evaluate the role of CH-pi stacking interactions and their interplay with hydrogen bonds, we curated a set of proteins bound to B-D-galactoside-containing carbohydrates with varied numbers and orientations of CH-pi stacking interactions, numbers of hydrogen bonds, and lengths of carbohydrate ligands. We employ well-tempered metadynamics simulations to obtain binding free energy landscapes. We show that the free energy landscapes of each protein are broad and that the favored CH-pi stacking interaction orientation varies depending on the conformation of the protein binding site. Complexes with extended carbohydrate ligands that form additional hydrogen bonds resulted in more specific orientational dependence. Conversely, complexes with mutations that decreased the number of hydrogen bonds had the opposite effect, broadening the free energy landscape significantly and resulting in the occupation of multiple distinct CH-pi stacking interaction orientations. Thus, hydrogen bonds play a key role in defining the binding orientation. We next show that forming multiple CH-pi stacking interactions facilitates the dynamics necessary for the translocation of polysaccharide ligands within a protein binding site. Our work shows the cooperative nature of hydrogen bonds and CH-pi stacking interactions, demonstrating that tuning the number and positions of these interactions through protein engineering should alter ligand recognition or support ligand movement in protein binding sites. | Allison M. Keys; David W. Kastner; Laura L. Kiessling; Heather J. Kulik | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dcdf1c81d2151a0246d930/original/ch-pi-interactions-confer-orientational-flexibility-in-protein-carbohydrate-binding-sites.pdf |
6647c97491aefa6ce14a4a92 | 10.26434/chemrxiv-2024-j58fh | The effect of local chain stiffness on oligomer crystallization from a melt | While the process by which a polymer crystal nucleates from the melt has been extensively studied via molecular simulation, differences in polymer models and simulated crystallization conditions have led to seemingly contradictory results. We make steps to resolve this controversy by computing low-temperature phase diagrams of oligomer melts using Wang-Landau Monte Carlo simulations. Two qualitatively different crystallization mechanisms are possible depending on the local bending stiffness potential. Polymers with a discrete bending potential crystallize via a single-step mechanism, whereas polymers with a continuous bending potential can crystallize via a two-step mechanism that includes an intermediate nematic phase. Other model differences can be quantitatively accounted for using an effective volume fraction and a temperature scaled by the bending stiffness. These results suggest that at least two universality classes of nucleation exist for melts and that local chain stiffness is a key determining factor in the mechanism of nucleation. | Pierre Kawak; Christopher Akiki; Douglas Tree | Theoretical and Computational Chemistry; Polymer Science; Polymer morphology; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6647c97491aefa6ce14a4a92/original/the-effect-of-local-chain-stiffness-on-oligomer-crystallization-from-a-melt.pdf |
60c73cc9bdbb895546a37b7e | 10.26434/chemrxiv.14754216.v1 | First, Do Not Degrade - an Alternative View on Polymer Laser Sintering | <p>In the work, for the
first time, the method of Dual Beam Laser Sintering of polymers (DBLS) was
presented, in which, instead of heating the entire volume of the polymer
throughout the entire process, a second, additional laser was used for
selective in terms of volume and time heating of the material. The principle of
operation and the design of the prototype are presented. Using the developed
station, an experiment was carried out for sintering samples from technical
polylactide powder as a function of selected process parameters. It confirmed
the functionality of the method and proved that the sintering process can be
controlled in a fairly wide range for the proposed method. A preliminary
comparison of changes in the physicochemical properties of the obtained samples
in relation to the samples sintered by standard laser sintering was carried out
using Gel Permeation Chromatography, Fourier Transform Infrared Reflectance and
Differential Scanning Calorimetry. The experiment showed that the presented
method has the potential to limit the thermal degradation of sensitive polymer
materials.</p> | Arkadiusz Antończak; Mateusz Wieczorek; Paulina Dzienny; Bartłomiej Kryszak; Anna Krokos; Piotr Gruber; Michał Olejarczyk; Małgorzata Gazińska | Biocompatible Materials; Biodegradable Materials; Materials Processing; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9bdbb895546a37b7e/original/first-do-not-degrade-an-alternative-view-on-polymer-laser-sintering.pdf |
60c742ed9abda28131f8c0d8 | 10.26434/chemrxiv.8850518.v1 | Eppur Si Riscalda - and yet, It (Just) Heats Up: Further Comments on “Quantifying Hot Carrier and Thermal Contributions in Plasmonic Photocatalysis” | <div>Our Comment [1] on recent attempts to distinguish thermal and non-thermal (``hot carrier'') contributions to plasmon-assisted photocatalysis [2] initiated a re-evaluation process of previous literature on the topic within the nano-plasmonics and chemistry communities. The Response of Zhou et al [3] attempts to defend the claims of the original paper [2].</div><div><br /></div><div>In this manuscript, we show that the Response [3] presents additional data that further validates our central criticism: inaccurately measured temperatures (that are lower than the actual temperature of the catalyst) led Zhou \etal to incorrectly claim conclusive evidence of non-thermal effects. We identify flaws in the experimental setup (e.g. the use of the default settings for the thermal camera and incorrect positioning of the thermometer) that may have led Zhou et al to make such claims. We further show that the Response contains several factual errors and does not address the technical problems we identified with the data acquisition in [2]. We demonstrate that both the Response [3] and the original paper [2] contain additional faults, for example, in the power determination and in the normalization of the rate to the catalyst volume, and exhibit misconceptions regarding the thermo-optic response of metal nanostructures. The burden of proof required by the proposal of a novel physical mechanism has simply not been met, especially when the existing data can be modeled exquisitely by conventional theory.</div><div>[1] Y. Sivan, J. Baraban, I. W. Un & Y. Dubi, Science Vol. 364, Issue 6439, eaaw9367. <a href="https://science.sciencemag.org/content/364/6439/eaaw9367.abstract">https://science.sciencemag.org/content/364/6439/eaaw9367.abstract</a> </div><div><br /></div><div>[2] <a href="https://science.sciencemag.org/content/362/6410/69">https://science.sciencemag.org/content/362/6410/69</a></div><div><br /></div><div>[3] <a href="https://science.sciencemag.org/content/364/6439/eaaw9545">https://science.sciencemag.org/content/364/6439/eaaw9545</a></div> | Yonatan Sivan; Joshua H. Baraban; Yonatan Dubi | Catalysts; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Photocatalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ed9abda28131f8c0d8/original/eppur-si-riscalda-and-yet-it-just-heats-up-further-comments-on-quantifying-hot-carrier-and-thermal-contributions-in-plasmonic-photocatalysis.pdf |
67c76692fa469535b9f4d015 | 10.26434/chemrxiv-2025-4n5rj | Comparative Analysis of the Chemical Composition and Cytotoxic Activity of Broccoli By-products as a Source of Bioactive Compounds | Broccoli is one of the most widely consumed cruciferous vegetables worldwide; however, only about 30%—primarily the florets—are consumed, while the remaining parts are considered waste. In this study, we analyzed broccoli by-products from Mexican crops, specifically evaluating the ethanolic extracts of bagasse (BB) and residual leaves (BL) for their growth-inhibitory effects on PC-3, HeLa, and Hep3B cancer cell lines. Both BB and BL selectively inhibited cervical cancer cell proliferation by approximately 50%.
A principal component analysis (PCA) of volatile compounds identified three main groups: fatty acids, methyl esters, sterols, and diterpenoids. Notably, sterols were the predominant components in the hexane fraction of broccoli bagasse (BB-H) (>90%), whereas fatty acids were the most abundant in the hexane fraction of broccoli leaves (BL-H) (>50%). Furthermore, two phytoalexins, caulilexin C (1) and 3-indoleacetonitrile (2), were isolated and characterized by NMR, exhibiting IC50 values of 23.43 and 33.65 μg/mL, respectively, against the HeLa cell line. Also, they showed desirable drug-like properties.
These findings provide valuable insights into the chemical composition of broccoli by-products from Mexican crops, emphasizing their potential as a source of bioactive compounds with pharmaceutical and food applications.
| Araceli Guerrero-Alonso; Leticia González-Maya; Jessica Nayelli Sánchez-Carranza; Alberto Marbán-González; Silvia Marquina Bahena; Laura Alvarez; Mayra Antunez-Mojica | Agriculture and Food Chemistry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c76692fa469535b9f4d015/original/comparative-analysis-of-the-chemical-composition-and-cytotoxic-activity-of-broccoli-by-products-as-a-source-of-bioactive-compounds.pdf |
6285499fa42e9c880b456f6f | 10.26434/chemrxiv-2022-wpn9c-v2 | Folding Coarse-Grained Oligomer Models with PyRosetta | Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses and generate folding principles at the CG scale to inform the design process of new foldamer chemistries. We demonstrate CG PyRosetta’s ability to identify minimum energy structures with a diverse structural search over a range of simple models and two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structure. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side-chains, while specific backbone bond-angles influence the specific helix type found in folded structures. | Theodore L. Fobe; Christopher C. Walker; Garrett A. Meek; Michael R. Shirts | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6285499fa42e9c880b456f6f/original/folding-coarse-grained-oligomer-models-with-py-rosetta.pdf |
6102ee6f1f990cbbcaa57b8b | 10.26434/chemrxiv-2021-0dwfq | Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations | The lack of conformational sampling in virtual screening projects can lead to inefficient results because many of the potential drugs may not be able to bind to the target protein during the static docking simulations. Here, we performed ensemble docking for around 2000 FDA approved drugs with the RNA-dependent RNA polymerase (RdRp) protein of SARS-CoV-2 as target. The representative protein structures were generated by clustering classical molecular dynamics trajectories, which were evolved using three solvent scenarios, namely, pure water and benzene/water and phenol/water mixtures. The introduction of dynamic effects in the theoretical model showed to improve the docking results in terms of the number of strong binders and binding sites in the protein. Some of the discovered pockets were found only for the cosolvent simulations, where the nonpolar probes induced local conformational changes in the protein that lead to the opening of transient pockets. In addition, the selection of the ligands based on a combination of the binding free energy and binding free energy gap between the best two poses for each ligand provided more suitable binders than the selection of ligands based solely on one of the criteria. The application of cosolvent molecular dynamics to enhance the sampling of the configurational space is expected to improve the efficacy of virtual screening campaigns of future drug discovery projects. | P. Bernát Szabó; Francesc Sabanés Zariquiey ; Juan José Nogueira | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6102ee6f1f990cbbcaa57b8b/original/cosolvent-and-dynamic-effects-in-binding-pocket-search-by-docking-simulations.pdf |
675c59bd7be152b1d0dec02b | 10.26434/chemrxiv-2024-flr1l | How Reliable is Coin Cell-Based Ranking of Li Anode Coulombic Efficiency? | Lithium (Li) metal Coulombic efficiency (CE) benchmarking has historically been conducted in coin cells. Recently, journals have required detailed reporting of factors like cycling conditions and electrolyte composition, which influence CE. However, variability in cell assembly is often overlooked. This study investigates how representative parameters (crimping load, spacer count, spring type) impact internal cell mechanics, CE accuracy, and comparisons across electrolytes. Internal pressure, both during and after crimping, varied (~100–170 kPa steady-state) depending on construction, producing a range in measured CE especially when CE is low. When comparing different but self-consistent cell construction methods applied to a set of electrolytes with diverse CE, absolute CE values exhibited notable variation, but CE rankings were generally robust. Literature CE benchmarks are best reproduced when allowing cell construction methods to vary between electrolytes, highlighting a major potential source of variance in reported data. Implications for best reporting practices are discussed. | Kyle Jiang; Kyeong-Ho Kim; Betar Gallant | Energy; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c59bd7be152b1d0dec02b/original/how-reliable-is-coin-cell-based-ranking-of-li-anode-coulombic-efficiency.pdf |
642b1318db1a20696e7755c8 | 10.26434/chemrxiv-2023-8lvbl | A “Common-Precursor” Protein Mimetic Approach to Rescue Aβ Aggregation-mediated Alzheimer’s Phenotypes | Abberent protein-protein interactions (aPPIs) are associated with an array of pathological conditions, which make them important therapeutic targets. The aPPIs are mediated via specific chemical interactions that spread over a large and hydrophobic surface. Therefore, ligands that can complement the surface topography and chemical fingerprints could manipulate aPPIs. Oligopyridylamides (OPs) are synthetic protein mimetics that have been shown to manipulate aPPIs. However, the previous OP library used to disrupt these aPPIs was moderate in number (~30 OPs) with very limited chemical diversity. The onus is on the laborious and time-consuming synthetic pathways with multiple chromatography steps. We have developed a novel chromatography-free technique to synthesize a highly diverse chemical library of OPs using a “common-precursor” approach. We significantly expanded the chemical diversity of OPs using a chromatography-free high-yielding method. To validate our novel approach, we have synthesized an OP with identical chemical diversity to a pre-existing OP-base potent inhibitor of Aβ aggregation, a process central to Alzheimer’s disease (AD). The newly synthesized OP ligand (RD242) was very potent in inhibiting Aβ aggregation and rescuing AD phenotypes in an in vivo model. Moreover, RD242 was very effective in rescuing AD phenotypes in a post-disease onset AD model. We envision that our “common-precursor” synthetic approach will have tremendous potential as it is expandable for other oligoamide scaffolds to enhance affinity for disease-relevant targets. | Ryan Dohoney; Johnson Joseph; Charles Baysah; Alexandra Thomas; Apshara Siwakoti; Tyler Ball; Sunil Kumar | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642b1318db1a20696e7755c8/original/a-common-precursor-protein-mimetic-approach-to-rescue-a-aggregation-mediated-alzheimer-s-phenotypes.pdf |
60c745624c89199610ad29a5 | 10.26434/chemrxiv.10007783.v1 | Plasmonic Oligomers With Tunable Conductive Nanojunctions | <p>Plasmonic
particles can be welded together, but controlling the metallurgy of the
hotspots is a challenge in colloidal chemistry. In this paper, we demonstrate
an original method that connects gold particles to their neighbors by another
metal of choice. To achieve this goal, we first assemble gold bipyramids in a
tip-to-tip configuration, yielding short chains of variable length. The good
colloidal stability and surface accessibility make the nanochains suitable
seeds to grow metallic junctions in a second step. We follow the oligomer
formation and the deposition of the second metal (i.e. silver or palladium) <i>via</i> UV/Vis spectroscopy and we map the
plasmonic properties of the nanostructures at nanometer scale using electron
energy loss spectroscopy. The formation of silver bridges leads to a huge
redshift of the longitudinal plasmon modes into the mid-infrared region, while
the addition of palladium results in a redshift accompanied by significant
plasmon damping. </p> | Xiaoyan Li; Jieli Lyu; Claire Goldmann; Mathieu Kociak; Doru Constantin; Cyrille Hamon | Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745624c89199610ad29a5/original/plasmonic-oligomers-with-tunable-conductive-nanojunctions.pdf |
65be07d49138d2316156f18a | 10.26434/chemrxiv-2024-3qhsj | Comment on room temperature colossal superparamagnetic order in aminoferrocene–graphene molecular magnets | A re-examination of recent claims of room temperature colossal superparamagnetic behaviour of a material based on graphene oxide (GO) modified by well-known aminoferrocene has been undertaken. The synthetic claims of the well-known and commercially available aminoferrocene do not bear scrutiny, neither from new data obtained nor from the data presented in the original paper. The density functional theory-derived model developed to describe the apparent magnetic properties of the material is based on an artefact that occurs through poor choice of the starting model for the GO. | Gayathri Athavan; François-Xavier Coudert; Robin Bedford | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65be07d49138d2316156f18a/original/comment-on-room-temperature-colossal-superparamagnetic-order-in-aminoferrocene-graphene-molecular-magnets.pdf |
65f1cd75e9ebbb4db9a1891e | 10.26434/chemrxiv-2024-rtv95-v2 | Exploring Reversible Redox behavior in the 6H-BaFeO3-d (0 < d < 0.4) System. Impact of Fe3+/Fe4+ Ratio on Catalytic Properties. | This work is devoted to evaluating the relationship between oxygen content and catalytic activity on the CO oxidation process of the 6H-type BaFeO3-δ system, showing that a higher Fe oxidation state improved the catalytic performance of the oxides, confirming the involvement of the lattice oxygen in the catalytic process. The redox behavior of the catalyst, followed mainly by neutron thermodiffraction under different atmospheres, allows us to determine the structure of the anionic and cationic sublattices showing a structural transition from the hexagonal symmetry (P63/mmc) of the ideal 6H type to orthorhombic (Cmcm) caused for the octahedra distortion when the Fe3+ concentration increases up to 40% (δ values higher than 0.2) The redox process is topotactic and the 6H basic structure is maintained in the δ range (0<δ<0.4). | Daniel Gutiérrez-Martín; Áurea Varela; María Hernando; Almudena Torres-Pardo; Emilio Matesanz; Isabel Gómez-Recio; José María González-Calbet; María Teresa Fernández-Díaz; José Juan Calvino; Miguel Ángel Cauqui; María Pilar Yeste; Marina Parras | Inorganic Chemistry; Catalysis; Solid State Chemistry; Heterogeneous Catalysis; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f1cd75e9ebbb4db9a1891e/original/exploring-reversible-redox-behavior-in-the-6h-ba-fe-o3-d-0-d-0-4-system-impact-of-fe3-fe4-ratio-on-catalytic-properties.pdf |
67d3b76e81d2151a0251fbcf | 10.26434/chemrxiv-2025-76p6j | Permutationally Invariant Fourier Series for Accurate and Robust Data-Driven Many-Body Potentials | We present a robust solution to the long-standing challenge of eliminating unphysical energy predictions, or "holes," in machine-learned many-body potentials, which can destabilize simulations when encountering configurations beyond the training set. By leveraging permutationally invariant Fourier series (PIFSs) within the MB-nrg data-driven many-body formalism, we introduce a new approach that significantly enhances the numerical stability of MB-nrg potential energy functions (PEFs) while preserving accuracy and transferability. Unlike conventional strategies that attempt to "plug holes" by expanding training datasets, PIFSs provide a more fundamental and efficient means of ensuring physically meaningful extrapolation across diverse molecular configurations. Using water as a benchmark system, we demonstrate that the MB-pol(PIFS) PEF retains the high accuracy of MB-pol across gas and condensed phases while extending the PEF’s stability to a much broader range of thermodynamic conditions. Our results suggest that the PIFS-based MB-nrg many-body formalism provides a general framework for constructing accurate and robust physics-based/machine-learned potentials applicable to a broad range of molecular systems. | Xuanyu Zhu; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d3b76e81d2151a0251fbcf/original/permutationally-invariant-fourier-series-for-accurate-and-robust-data-driven-many-body-potentials.pdf |
67a61a186dde43c908efe239 | 10.26434/chemrxiv-2025-55sz5 | Direct, asymmetric, and stereodivergent reactions of N-azidoacetyl thioimides with aromatic acetals catalyzed by chiral nickel(II) complexes. A new approach to the synthesis of syn- and anti-β-alkoxy-α-amino acids | A new approach to the synthesis of any of the potential stereoisomers of β-alkoxy-α-amino acids derived from phenylalanine, tyrosine, tryptophan, and other β-aryl counterparts is reported. Such a method hinges on direct and asymmetric Lewis acid–mediated aldol-like reactions of N-azidoacetyl thioimides with dialkyl acetals from aromatic aldehydes catalyzed by chiral nickel(II) complexes. This produces at will both the corresponding syn and anti adducts, which can be smoothly converted into enantiomerically pure intermediates, such as dipeptide fragments. In turn, computational calculations have unveiled the clues for a better understanding of such a stereocontrolled carbon–carbon bond–forming transformation. | Miguel Mellado-Hidalgo; Joan Conejos-Jalencas; Saúl F. Teloxa; Andrea Suárez-Herrera; Luke McCall; Anna Maria Costa; Pedro Romea Garcia; Fèlix Urpí; Gabriel Aullón; Cristina Puigjaner | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a61a186dde43c908efe239/original/direct-asymmetric-and-stereodivergent-reactions-of-n-azidoacetyl-thioimides-with-aromatic-acetals-catalyzed-by-chiral-nickel-ii-complexes-a-new-approach-to-the-synthesis-of-syn-and-anti-alkoxy-amino-acids.pdf |
60c757284c8919a4bead4961 | 10.26434/chemrxiv.14374562.v1 | First-Principles Investigation of Ti2CSO and Ti2CSSe Janus MXene Structures for Li and Mg Electrodes | <div>
<div>
<div>
<p>While lithium battery electrodes are constantly being improved in terms of their properties, discovering new materials with alternative energy carriers like Mg are important to lower the cost of
production and to enhance the energy density. MXenes are a type of highly investigated materials
with promising energy applications due to their excellent electronic conductivity and good mechanical and dynamical stability. Experimentally realized Janus MoSSe nanosheets provided promising
results for battery electrodes. It is known that the surface terminations of MXenes highly affect
on the electrochemical properties and the diffusion barriers of ions. Inspired by this, we studied
Ti2CSO and Ti2CSSe Janus MXenes for Li and Mg electrodes. Our density functional theory-based,
first-principles calculations indicate that both monolayers are thermodynamically, mechanically, and
dynamically stable. We calculated that the average voltages for Li and Mg adsorbed Ti2CST (T = O,
Se) MXenes are approximately 0.95 and 0.2 V, respectively. The maximum voltage for Ti2CSTLix is
about 2 V, and that for Ti2CSTMgx is around 0.45 V. The Mg adsorbed Ti2CSO monolayer exhibits
the highest gravimetric capacity (524.54 mAh/g) compared to that of other Janus MXenes considered
in this paper. For Ti2CSSeLix, we obtained a higher capacity (230.45 mAh/g) and a lower diffusion
barrier (0.191 eV) than that of most of the Li adsorbed S-functionalized MXenes.
</p>
</div>
</div>
</div> | Edirisuriya Siriwardane; Jianjun Hu | Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2021-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757284c8919a4bead4961/original/first-principles-investigation-of-ti2cso-and-ti2cs-se-janus-m-xene-structures-for-li-and-mg-electrodes.pdf |
677c1e3bfa469535b9fcb844 | 10.26434/chemrxiv-2025-p97c2 | Beyond Numerical Hessians: Higher-Order Derivatives for Machine Learning Interatomic Potentials via Automatic Differentiation | The development of machine learning interatomic potentials (MLIPs) has revolutionized computational chemistry by enhancing the accuracy of empirical force fields while retaining a large computational speed-up compared to first-principles calculations. Despite these advancements, the calculation of Hessian matrices for large systems remains challenging, in particular, because analytical second-order derivatives are often not implemented. This necessitates the use of computationally expensive finite-difference methods, which can furthermore display low precision in some cases. Automatic differentiation (AD) offers a promising alternative to reduce this computational effort and make the calculation of Hessian matrices more efficient and accurate. Here, we present the implementation of AD-based second-order derivatives for the popular MACE equivariant graph neural network architecture. The benefits of this method are showcased via a high-throughput prediction of heat capacities of porous materials with the MACE-MP-0 foundation model. This is essential for precisely describing gas adsorption in these systems and was previously only possible with bespoke ML models or expensive first-principles calculations. We find that the availability of foundation models and accurate analytical Hessian matrices offers comparable accuracy to bespoke ML models in a zero-shot manner, and additionally allows investigating finite size and rounding errors in the first-principles data. | Nils Gönnheimer; Karsten Reuter; Johannes T. Margraf | Theoretical and Computational Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677c1e3bfa469535b9fcb844/original/beyond-numerical-hessians-higher-order-derivatives-for-machine-learning-interatomic-potentials-via-automatic-differentiation.pdf |
6218ff1157a9d25b206a2c86 | 10.26434/chemrxiv-2022-npd5r-v2 | Programmed Polyene Cyclization Enabled by Chromophore Disruption
| A versatile polyene cyclization strategy was developed that exploits conjugated -ionyl derivatives. Photomediated disruption of the extended -system within these chromophores unveils a contra-thermodynamic polyene that engages in a Heck-type cyclization to afford [4.4.1]-propellanes. The connectivity of overbred polycycles generated from this process is controlled by the position of the requisite C–Br bond. Thus, compared to conventional biomimetic polyene cyclization, this approach allows for complete control of regiochemistry and facilitates incorporation of both electron-rich and electron-deficient (hetero)aryl groups. This strategy was successfully applied to the total synthesis of taxodione and salviasperanol, two isomeric abietane-type diterpenes that previously could not be prepared along the same synthetic pathway. | James Frederich; Megan Solans; Vitalii Basistyi; James Law; Noah Bartfield | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6218ff1157a9d25b206a2c86/original/programmed-polyene-cyclization-enabled-by-chromophore-disruption.pdf |
651dc675bda59ceb9ae073a6 | 10.26434/chemrxiv-2023-rgdbm-v2 | Mechanistic Insights into Copper(I) and Copper (II) Cation Exchange Reactions in CdSe Nanoplatelets | In this study, we investigated the synthesis of copper selenide nanoplatelets (NPLs) through a cation exchange reaction (CER) in 5 monolayers thick CdSe NPLs using Cu(I) and Cu(II) precursors. We discovered that the exposure of CdSe NPLs to Cu(I) precursor led to the transformation of NPLs into Cu2−xSe while maintaining their nanoplatelet morphology. The replacement of Cd(II) with Cu(I) prevailed over the formation of doped structures. In the case of Cu(II) precursor, we observed that Cu(II) was first reduced to Cu(I) before being intercalated into the host lattice, resulting in synthesis of Cu2−xSe, similar to CER with Cu(I) precursors but without preservation of the initial morphology of NPLs. Interestingly, the presence of oxygen was found to facilitate the cation exchange processes in CdSe NPLs, whereas a nitrogen atmosphere suppressed the CER. Despite the similar ionic sizes of Cu(I) and Cu(II), the substitution of Cd(II) with Cu(II) was found to be challenging, possibly due to the involvement of redox processes resulting in the significant deterioration of initial CdSe NPLs. We demonstrate that CER can achieve near-complete substitution of cadmium atoms with monovalent copper under room temperature. Understanding the processes involved in CERs is crucial for engineering more complex structures, such as high entropy nanoparticles involving cation exchange with different oxidation states and development of material synthesis using machine learning and artificial intelligence approaches. | Progna Banerjee; Alexander Filatov; Xiaobing Zuo; Benjamin Diroll; Elena Shevchenko | Materials Science; Nanoscience; Coating Materials; Optical Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651dc675bda59ceb9ae073a6/original/mechanistic-insights-into-copper-i-and-copper-ii-cation-exchange-reactions-in-cd-se-nanoplatelets.pdf |
6793fa6e81d2151a02d5f581 | 10.26434/chemrxiv-2025-4610b | Chromatographic Dynamic Chemisorption: An Alternative to Conventional Estimation of Metallic Dispersion | Rigorous standards for reporting the rate of catalytic turnovers over metallic nanoparticles entail normalizing the observed macroscopic observable rate with the active site density. Techniques like transmission electron micrographs and estimating carbon monoxide/ hydrogen uptake have been employed to characterize the active site density of Group 8 dispersed nanoparticles. Based on the principle of dynamic carbon monoxide (CO) chemisorption, the work delineates a novel technique using a gas chromatograph (GC) to estimate the active site density. The dispersion of a Micromeritics™ standard, which provides a benchmark, was measured using the proposed method and compared with conventional techniques. Furthermore, the dispersion of supported platinum group catalysts, varying in supported identity and metal loading, was measured. The amount of dispersed metal as low as 0.02 mg could be estimated by this technique. | Atharva S. Burte; Abeer O. Abouthman; Shreya Thakkar; Nicholas Capra; Joshua Gopeesingh; Omar A. Abdelrahman | Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6793fa6e81d2151a02d5f581/original/chromatographic-dynamic-chemisorption-an-alternative-to-conventional-estimation-of-metallic-dispersion.pdf |
62a640f08f92d976e04e9c95 | 10.26434/chemrxiv-2022-nsgck | Tandem rigidification and π-extension as a key tool for the development of a narrow linewidth yellow hyperfluorescent OLED system. | Hyperfluorescence (HF), a relatively new phenomenon utilizing excitons transfer between two luminophores, requires careful pairwise tuning of molecular energy levels and is proposed to be the crucial step toward the development of new, highly effective OLED systems. To date, barely a few HF yellow emitters with desired narrowband emission but moderate external quantum efficiency (EQE <20%) have been reported. This is because a systematic strategy embracing both Förster Resonance Energy Transfer (FRET) and triplet to singlet (TTS) transition as complementary mechanisms for effective excitons transfer has not yet been proposed. Herein, we present a rational approach, which allows to through subtle structural modification, a pair of compounds built from the same donor and acceptor subunits, but with varied communication between these ambipolar fragments, to be obtained. The TADF-active dopant is based on a naphthalimide scaffold linked to the nitrogen of a carbazole moiety, which through the introduction of an additional bond leads not only to π-cloud enlargement but also rigidifies and inhibits rotation of the donor. This structural change prevents TADF, and allows to guide bandgaps and excited states energies to simultaneously pursue FRET and TTS process. New OLED devices utilizing the presented emitters show excellent external quantum efficiency (up to 27%) and narrow full width at half maximum (40nm), which is a consequence of very good alignment of energy levels. The presented design principles prove that only a minor structural modification is needed to obtain commercially applicable dyes for HF OLED devices. | Krzysztof Bartkowski; Paola Zimmermann Crocomo; Michał Kochman; Dharmendra Kumar; Adam Kubas; Przemysław Data; Marcin Lindner | Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a640f08f92d976e04e9c95/original/tandem-rigidification-and-extension-as-a-key-tool-for-the-development-of-a-narrow-linewidth-yellow-hyperfluorescent-oled-system.pdf |
6752a2577be152b1d01e5261 | 10.26434/chemrxiv-2024-9vm9l | Assembling Branched and Macrocyclic Peptides on Proteins | A two-step, biocompatible strategy enables site-specific generation of branched and macrocyclic peptide–protein conjugates. Surface-exposed cysteines on proteins are modified by a small bifunctional reagent at near-physiological pH, followed by cyanopyridine–aminothiol click reactions to create branched or macrocyclic peptide architectures. This method offers design strategies for next-generation protein therapeutics. | Sven Ullrich; Santhanalaxmi Kumaresan; Marina Rahman; Bishvanwesha Panda; Richard Morewood; Christoph Nitsche | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6752a2577be152b1d01e5261/original/assembling-branched-and-macrocyclic-peptides-on-proteins.pdf |
6369135780c9bf652c8ac599 | 10.26434/chemrxiv-2022-jd00z-v2 | Derivation and Implementation of the Optical Rotation Tensor for Chiral Crystals | This work reports the derivation and implementation of the electric dipole-magnetic dipole and electric dipole- electric quadrupole polarizability tensors at density functional theory level with periodic boundary conditions (DFT-PBC). These tensors are combined to evaluate the Buckingham/Dunn tensor that describes the optical rotation (OR) in oriented chiral systems. We detail several aspects of the derivation of the equations, and present test calculations that verify the correctness of the tensors formulation and of their implementation. The results show that the full OR tensor is completely origin invariant as for molecules and that PBC calculations match molecular cluster calculations on 1D chains. A preliminary investigation on the choice of density functional, basis set, and gauge indicates a similar dependence as for molecules: the functional is the primary factor that determines the OR magnitude, followed by the basis set and to a much smaller extent the choice of gauge. However, diffuse functions may be problematic for PBC calculations even if they are necessary for the molecular case. A comparison with experimental data of OR for the tartaric acid crystal shows reasonable agreement given the level of theory employed. The development presented in this work offers the opportunity to simulate the OR of chiral crystalline materials with general purpose DFT-PBC methods, which in turn may help to understand the role of intermolecular interactions on this sensitive electronic property. | Ty Balduf; Marco Caricato | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6369135780c9bf652c8ac599/original/derivation-and-implementation-of-the-optical-rotation-tensor-for-chiral-crystals.pdf |
67c010ef6dde43c908ad70c7 | 10.26434/chemrxiv-2025-18cp7 | Innovative synergistic solvent-catalyst paradigm for sustainable allylic C–H functionalization | Achieving sustainable catalytic transformations requires synergistic optimization of solvent systems, catalytic motifs and energy inputs. Herein, we report a synergistic Pd/hydroquinone catalytic system that enables aerobic allylic C–H functions under ambient conditions (rt–50 °C, air) with high turnover frequency (TOF), using ethanol/water as a green medium. This strategy achieves unparalleled synthetic efficiency and demonstrates remarkable versatility across two pivotal transformations (alkylation and amination) involving over 90 substrates (up to 99% yield), directly aligning with China’s strategic goals for decarbonizing chemical manufacturing. It also delivers exceptional stereocontrol (up to 93% ee for quaternary stereocenters) and enables advanced allylic transformations within a green framework through additional synergistic catalysis. By integrating solvent engineering with cooperative catalysis, we have developed a scalable platform for the synthesis of FDA-certified allylic pharmaceuticals and high-value chemicals. demonstrating how molecular-level innovation can drive sustainable industrial transformation. | Rui Wang; Long Zhang; Sanzhong Luo | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c010ef6dde43c908ad70c7/original/innovative-synergistic-solvent-catalyst-paradigm-for-sustainable-allylic-c-h-functionalization.pdf |
656e10c829a13c4d47a58cac | 10.26434/chemrxiv-2023-tf6b4 | Parent Porphyrin (Porphine) and its Complexes with 3d Metals | We report an improved synthesis of porphine from d-tartaric acid, its conversion to complexes with Mg(II), V(IV), Mn(III), Fe(III), Co(II), Ni(II), Cu(II) and Zn(II), their IR, UV-vis, NMR, XPS, and mass spectra, and single crystal X-ray diffraction structures of meso-tetrakis(n-hexyloxycarbonyl)porphyrin and (porphyrinato)manganese(III) bromide. | Jan Plutnar; Lucie Bednárová; Ivana Císařová; Martin Dračínský; Lenka Krepsová; Ján Tarábek; JOSEF MICHL | Physical Chemistry; Organic Chemistry; Inorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656e10c829a13c4d47a58cac/original/parent-porphyrin-porphine-and-its-complexes-with-3d-metals.pdf |
64bbe342b053dad33ab2aee3 | 10.26434/chemrxiv-2023-4w2wn | X-ray dose effects and strategies to mitigate beam damage in metal halide perovskites under high brilliance X-ray photon source | Metal halide perovskites are versatile photovoltaic and optoelectronic materials. However, they suffer from photo-structural-chemical instabilities whose intricacy requires state-of-the-art tools to investigate their properties and behavior under various conditions. In most cases, those tools strongly interact with the materials leading to undesirable transformations. This study addresses the damage caused by highly intense focused X-ray beams on hybrid organic-inorganic metal halide perovskites through a correlative multi-technique approach. Our results reveal that the damage after irradiation in the ((Cs, FAMA)Pb(Br, I)3) compound is prominent on iodine and organic components at the film surface, reducing their relative quantity. The sample morphology modifies with the formation of an excavated area, whose altered local optical properties indicate the formation of an optically inactive metal layer covering the surface. Interestingly, the bulk remains unaltered with the initial ion proportion demonstrated by the stable photoluminescence emission energy. Controlling the X-ray beam dose and environment - air, nitrogen, and cryogenic conditions - serves as a strategy to mitigate the dose harm. Hence, we combined a controlled X-ray dose with an inert N2 atmosphere to certify the conditions to probe metal halide perovskite properties while mitigating damage efficiently. Finally, we applied optimized conditions to investigate a perovskite compound using X-ray ptychography, reaching a 14-nm spatial resolution, an outcome that has never been attained so far. | Francisco M. C. da Silva; Rodrigo Szostak; Maria G. D. Guaita; Verônica C. Teixeira; Ana Flavia Nogueira; Hélio C. N. Tolentino | Physical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bbe342b053dad33ab2aee3/original/x-ray-dose-effects-and-strategies-to-mitigate-beam-damage-in-metal-halide-perovskites-under-high-brilliance-x-ray-photon-source.pdf |
633063b7cf38294943b1b613 | 10.26434/chemrxiv-2022-m4qm1 | Challenges in the modelling of elementary steps in electrocatalysis | The full understanding of electrocatalytic reactions requires a complete knowledge of the elementary steps occurring in these reactions together with the corresponding rate constants as a function of the parameters controlling the electrochemical environment. Given the complexity of electrochemical electrode/electrolyte interfaces, the modelling of elementary steps in electrocatalysis represents a substantial challenge, and there is still a need for reliable benchmark studies. Nevertheless, tremendous progress has been made in this field in recent years. Here the current status of this field will be briefly sketched, possible routes to meet the challenges will be suggested and open questions will be discussed. | Axel Gross | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Fuels - Energy Science; Electrochemistry - Mechanisms, Theory & Study | CC BY NC 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633063b7cf38294943b1b613/original/challenges-in-the-modelling-of-elementary-steps-in-electrocatalysis.pdf |
6747d8ed7be152b1d02714ba | 10.26434/chemrxiv-2024-sbwxm | Revealing the Impact of Aggregations in the Graph-based Molecular Machine Learning: Electrostatic Interaction versus Pooling Methods | Molecular structures that can be readily represented by graphs comprising constituent atoms (nodes) and their chemical bonds (edges) can also be used as input data for well-known machine learning (ML) models that process this data, such as graph neural networks (GNNs). GNNs showed a reasonable performance in the predicting properties of chemical systems. In typical applications of GNNs to chemistry-related fields, the main objective is to create an optimal molecular representation by aggregating atomic features and pooling features in the graph. In this study, we investigated two different approaches that can possibly generate better molecular representations. First, we created intermolecular edges to predict the photochemical properties of chromophore molecules in the solution. These intermolecular edges were constructed using atomic partial charges, inspired from the fact that electrostatic interaction is the main component of solute-solvent interaction. In the second approach, we investigated the effect of the aggregation and pooling functions. The results showed that intermolecular electrostatic interactions based on ground state charges prevent the GNN model from generating more effective molecular representations. On the contrary, the model demonstrated better performance when the averaging and adding operations were employed in a hybrid manner for aggregation and pooling functions. | Sanghoon Lee; Hyun Woo Kim | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6747d8ed7be152b1d02714ba/original/revealing-the-impact-of-aggregations-in-the-graph-based-molecular-machine-learning-electrostatic-interaction-versus-pooling-methods.pdf |
60c7514e9abda2ca4cf8dbd0 | 10.26434/chemrxiv.13147796.v1 | PySurf - A Framework for Database Accelerated Direct Dynamics | <div><div><div><p>Here, PySurf is introduced as an innovative code framework, which is specifically designed for rapid prototyping and development tasks for data-science applications in computational chemistry. To illustrate the potential of the framework, a code for nonadiabatic surface-hopping simulations based on the Landau-Zener algorithm is presented here. The results reveal the degree of sophistication, which can be achieved by the database accelerated energy-only surface-hopping simulations being competitive to commonly used semi-classical approaches.</p></div></div></div> | Shirin Faraji; Johannes Ehrmaier; Maximilian Menger | Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2020-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7514e9abda2ca4cf8dbd0/original/py-surf-a-framework-for-database-accelerated-direct-dynamics.pdf |
60c74395337d6c079ae26c1c | 10.26434/chemrxiv.9255611.v1 | Design of Cost-Efficient and Photocatalytically Active Zn-Based MOFs Decorated with Cu2O Nanoparticles for CO2 Methanation | <div>Here we show for the first time a MOF that is photocatalytically</div><div>active for the light-assisted CO<sub>2</sub> methanation at mild conditions</div><div>(215 °C) without the inclusion of metallic nanoparticles or any</div><div>sacrificial agent. The presence of Cu<sub>2</sub>O nanoparticles causes a 50 % increase in the photocatalytic activity. These results pave the way to developping efficient and cost-effective materials for CO<sub>2</sub> elimination.</div> | María Cabrero-Antonino; Sonia Remiro-Buenamañana; Manuel Souto; Antonio A. García- Valdivia; Duane Choquesillo-Lazarte; Sergio Navalón; Antonio Rodriguez-Diéguez; Guillermo Minguez Espallargas; Hemenegildo García | Coordination polymers; Heterogeneous Catalysis; Catalysis; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74395337d6c079ae26c1c/original/design-of-cost-efficient-and-photocatalytically-active-zn-based-mo-fs-decorated-with-cu2o-nanoparticles-for-co2-methanation.pdf |
60c743efee301c735bc79092 | 10.26434/chemrxiv.9696146.v1 | Generation and Reactivity of 2-Amido-1,3-diaminoallyl Cations: Cyclic Guanidine Annulations via Net (3+2) and (4+3) Cycloadditions | Toward a method for direct conversion of alkenes to cyclic guanidines, we report that 1,3-dipolar cycloadditions of 2-amido-1,3-diamino allylic cations with electron rich alkenes provides a new method for direct cyclic guanidine annulation. Generated under oxidative conditions, the 2-amido-1,3-diaminoallyl cations, react as 1,3-dipoles providing rapid access to 2-amino imidazolines through net (3+2) cycloadditions. The utility is demonstrated through a concise synthesis of the oroidin alkaloid, phakellin. The described 1,3-dipole also participates in net (4+3) cycloadditions with dienes. Several observations suggest a stepwise, ionic, net cycloaddition leading to initial carbocation formation as evidenced by initial formation of constitutional isomers and intervening eliminations. Complex aziridines are formed with dienes suggestive of nitrene intermediates and results in net tetra-functionalization of dienes.<br /> | Venkata Kovvuri; Haoran Xue; Daniel Romo | Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743efee301c735bc79092/original/generation-and-reactivity-of-2-amido-1-3-diaminoallyl-cations-cyclic-guanidine-annulations-via-net-3-2-and-4-3-cycloadditions.pdf |
6458b1a827fccdb3eab0898a | 10.26434/chemrxiv-2023-sgjbr-v2 | Scanning transmission X-ray spectromicroscopy: a nanotool to probe hematite nanorods for solar water splitting | We report a scanning transmission X-ray microscopy (STXM) study of hematite nanorods, prototypical photoanode used in solar water splitting. Hematite nanorods were obtained by hydrothermal growth from aqueous solutions using FeCl3 as precursor. Potentials for onset of water splitting are smaller using this synthesis method, compared to values reported for hematite photoanodes obtained by epitaxial growth. STXM revealed the presence of a hexahydrate iron chloride phase at the surface of the nanorods, which is linked to the low onset potential values. We detail the quantification approach that revealed the specific microstructure of individual hematite nanorods. | Stefan Stanescu; Dana Stanescu; Adam Hitchcock | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials | CC BY 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6458b1a827fccdb3eab0898a/original/scanning-transmission-x-ray-spectromicroscopy-a-nanotool-to-probe-hematite-nanorods-for-solar-water-splitting.pdf |
60c73f1bbdbb893205a37f24 | 10.26434/chemrxiv.7234901.v1 | Resonant Inelastic X-Ray Scattering and Non Resonant X-ray Emission Spectra from Coupled-Cluster (Damped) Response Theory | A coupled cluster protocol rooted in damped response theory is presented for computing Resonant Inelastic X-Ray Scattering spectra of molecules in gas-phase. Working equations are reported for both linear (i.e., equation-of-motion) and non-linear<br />parametrizations of the coupled-cluster wavefunction response. A simple scheme to<br />compute non-resonant X-ray emission spectra is also proposed. Illustrative results are<br />presented for water. | Rasmus Faber; Sonia Coriani | Theory - Computational; Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1bbdbb893205a37f24/original/resonant-inelastic-x-ray-scattering-and-non-resonant-x-ray-emission-spectra-from-coupled-cluster-damped-response-theory.pdf |
62de5e4913e365db98e52f8f | 10.26434/chemrxiv-2022-hs7ln | Non-Kasha fluorescence of pyrene emerges from a dynamic equilibrium between excited states | Pyrene fluorescence after a high-energy electronic excitation exhibits a prominent band shoulder not present after excitation at low energies. The standard assignment of this shoulder as a non-Kasha emission from the second-excited state (S2) has been recently questioned. To elucidate this issue, we simulated the fluorescence of pyrene using two different theoretical approaches based on the vertical convolution and nonadiabatic dynamics with nuclear ensemble approaches. To conduct the necessary nonadiabatic dynamics simulations with high-lying electronic states and deal with fluorescence timescales of about 100 ns of this large molecule, we developed new computational protocols. The results from both approaches confirm that the band shoulder is, in fact, due to S2 emission. We show that the non-Kasha behavior is a dynamic-equilibrium effect, not caused by a metastable S2 minimum. However, it requires considerable vibrational energy, which can only be achieved in collisionless regimes after transitions into highly excited states. This strict condition explains why the S2 emission was not observed in some experiments. | Gabriel Braun; Itamar Borges Jr.; Adelia A. J. Aquino; Hans Lischka; Felix Plasser; Silmar A. do Monte; Elizete Ventura; Saikat Mukherjee; Mario Barbatti | Theoretical and Computational Chemistry; Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62de5e4913e365db98e52f8f/original/non-kasha-fluorescence-of-pyrene-emerges-from-a-dynamic-equilibrium-between-excited-states.pdf |
6716678383f22e4214b0dbac | 10.26434/chemrxiv-2024-qvhhd | PepMNet: A Hybrid Deep Learning Model for Predicting Peptide Properties Using Hierarchical Graph Representations | Peptides are a powerful class of molecules that can be applied to a range of problems including biomaterials development and drug design. Currently, machine learning-based property prediction models for peptides primarily rely on amino acid sequence, resulting in two key limitations: first, they are not compatible with non-natural peptide features like modified sidechains or staples, and second, they use human-crafted features to describe the relationships between different amino acids, which reduces the model’s flexibility and generalizability. To address these challenges, we have developed PepMNet, a deep learning model that integrates atom-level and amino acid-level information through a hierarchical graph approach. The model first learns from an atom-level graph and then generates amino acid representations based on the atomic information captured in the first stage. These amino acid representations are then combined using graph convolutions on an amino acid-level graph to produce a molecular-level representation, which is then passed to a fully connected neural network for property prediction. We evaluated this architecture by predicting two peptide properties: chromatographic retention time (RT) as a regression task and antimicrobial peptide (AMP) as a classification task. For the regression task, PepMNet achieved an average R² of 0.980 across eight datasets, which spanned different dataset sizes and three liquid chromatography (LC) methods. For the classification task, we developed an ensemble of five models to reduce overfitting and ensure robust classification performance, achieving an area under the receiver operating curve (AUC-ROC) of 0.978 and an average precision of 0.981. Overall, our model illustrates the potential for hierarchical deep learning models to learn peptide properties without relying on human engineering amino acid features. | Daniel Garzon; Omid Akbari; Camille Bilodeau | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6716678383f22e4214b0dbac/original/pep-m-net-a-hybrid-deep-learning-model-for-predicting-peptide-properties-using-hierarchical-graph-representations.pdf |
67964db86dde43c90877b5a8 | 10.26434/chemrxiv-2025-cs0r1 | Assessing Structure and Dynamics of Iron Complexes Supported by Tris(amidate)amine Ligands | Chelating ligand platforms derived from tris(2-aminoethyl)amine (TREN) can facilitate low coordination numbers and provide opportunities to tune the steric and electronic profile of the secondary coordination sphere. Herein, we examine the ability of two related tris(amidate)amine ligands to stabilize low-coordinate complexes of trivalent iron, and further use molecular dynamics (MD) simulations to gain insight into the dynamics of both the primary and secondary coordination spheres. Our cavitand-inspired ligand allows for the isolation of four-coordinate FeLOCH2O via oxidation of the anionic ferrous precursor, yielding the first crystallographically characterized example of an iron(III) species in a trigonal monopyramidal geometry. While this discovery is enabled by the rigid macrocycle in the secondary coordination sphere, MD simulations suggest that this macrocycle negligibly alters dynamics in the primary coordination sphere, and suggests a route by which exogenous ligands may bypass the rigid cavity opening yet still access the intracavity coordination site in [MLOCH2O]n complexes. | Lucy Huffman; Anjana Seshadri; Christopher Hastings; William Brennessel; Ignacio Franco; Brandon Barnett | Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67964db86dde43c90877b5a8/original/assessing-structure-and-dynamics-of-iron-complexes-supported-by-tris-amidate-amine-ligands.pdf |
661358d321291e5d1d578d1a | 10.26434/chemrxiv-2024-ws426 | BOTTS: Rapid viscoelastic master curves through broadband optimized time-temperature superposition of windowed chirps from widely available DMA equipment | Modern materials design strategies take advantage of the increasing amount of materials property data available and increasingly complex algorithms to take advantage of that data. However, viscoelastic materials resist this trend towards increased data rates due to the very material time-dependence that should be measured. Therefore, viscoelasticity measurements present a roadblock for data collection in an important aspect of material design.
For thermorheologically simple materials, time-temperature superposition (TTS) has for many years provided a method to accelerate relaxation spectrum measurements relative to, for example, very long creep experiments. However, TTS itself currently faces a speed limit originating in the common logarithmic discrete frequency sweep (DFS) mode of operation. In DFS, measurement time is proportional (by a factor much greater than one) to the lowest frequency of measurement. This state of affairs has not improved for TTS for half a century or more.
We utilize recent work in experimental rheometry on windowed chirps to collect three decades of complex modulus data simultaneously. Furthermore, the three-decade chirp response is recorded in the time it would take to collect only the lowest frequency data point of a traditional DFS experiment, resulting in a 500% speedup in data collection. In BOTTS, we superpose several isothermal chirp responses to produce a master curve in a fraction of the time of the traditional DFS-TTS technique. The chirp responses have good, albeit nontrivial, signal-to-noise properties. We use linear error propagation and a noise-weighted least squares approach to automatically incorporate all the data in a reliable shifting method. Using model thermoset polymers, we show DFS-TTS and BOTTS results are comparable, and therefore BOTTS data represent a first step towards a fast, reproducible method for master curve generation from existing rheological measurement instruments. | Richard Sheridan; Stefan Zauscher; Catherine Brinson | Materials Science; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661358d321291e5d1d578d1a/original/botts-rapid-viscoelastic-master-curves-through-broadband-optimized-time-temperature-superposition-of-windowed-chirps-from-widely-available-dma-equipment.pdf |
67ae694ffa469535b938275c | 10.26434/chemrxiv-2025-qfdlq | Metal-Free Catalytic Cross-Coupling of Esters and Boranes | Over the last 50 years, palladium-catalyzed cross-coupling has become ubiquitous in chemical synthesis from laboratory to commercial scale. Due to the great importance of these reactions, extensive research efforts have been devoted to improving the sustainability, cost, and diversity of the catalysts and coupling partners. Herein, we report the rational design and experimental validation of a metal-free catalyst for cross-coupling of formate esters with organoboranes, forming aldehydes under mild, additive-free conditions. The novel mechanism establishes a model for direct C(acyl)–C(sp2) bond formation, a motif previously inaccessible via metal-free or radical-free cross-coupling pathways. Overall, this boron/nitrogen-based system is found to even outperform the efficacy of state-of-the-art nickel catalysts for ester cross-coupling, demonstrating the utility of main-group catalysts in efficiently activating challenging bonds. | Gabriella Morin; Christina McCabe; Douglas Turnbull; Victoria Pham-Tran; Marc-André Légaré | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Frustrated Lewis Pairs; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae694ffa469535b938275c/original/metal-free-catalytic-cross-coupling-of-esters-and-boranes.pdf |
60c74c2b469df423adf4401f | 10.26434/chemrxiv.12441920.v1 | Electrochemical Characteristics of BIS 2062 Carbon Steel Under Simulated Ocean Acidification Scenario | Dear Professor,<div><p>I am herewith enclosing a research paper entitled “<b>Electrochemical characteristics of BIS 2062 carbon
steel under simulated ocean acidification scenario.</b>” authored by Devika
KR, and me. </p>
<p>The research
paper highlights the behavior of carbon steel in acidified natural seawater. Ocean acidification is a burning issue under
climate change. Several studies have undertaken to understand the behavior
marine organisms and marine environment. No studies have initiated regarding
the deterioration of materials due to ocean acidification. Large number of materials
were deployed in the ocean with different objectives. These materials are under
risk as the ocean acidification continues. We believe this is the first attempt
to study the impact of ocean acidification on carbon steel. </p>
<p>The study
conducted to evaluate the impact of ocean acidification on BIS 2062 boat
building steel. The results showed that the carbon steel will deteriorate 2 to
3 times higher when pH was changed from 8.05 to 7.90. The data highlights the
immediate need to redesign the marine materials within 1-2 decade. The paper
also highlights the possible mechanism of deterioration under different pH
scenario.</p><p>Thanking you</p><p>Sincerely</p><p>ashrafp</p><br /></div> | K R DEVIKA; P MUHAMED ASHRAF | Electrochemical Analysis; Electrochemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c2b469df423adf4401f/original/electrochemical-characteristics-of-bis-2062-carbon-steel-under-simulated-ocean-acidification-scenario.pdf |
661d160521291e5d1de07b9d | 10.26434/chemrxiv-2024-3bbg8-v2 | Synthesis of alkyne- and azide-functionalised aziridine and epoxide carbocycles for development of selective glucuronidase mechanism-based inhibitors | Heparanase (HPSE) is an endo-acting beta-glucuronidase and the only known enzyme responsible for the regulation of extracellular heparan sulfate (HS) structures, a glycosaminoglycan (GAG) occurring in conjugation with a protein class called heparan sulfate proteoglycans (HSPGs) in the extracellular matrix (ECM). The enzyme is found to be significantly upregulated in aggressive cancer types aiding cell proliferation by increased degradation of HS. Inhibition of HPSE reduces cancer growth making it an interesting druggable target for cancer treatment and diagnostics. Only few of the known efficient HPSE inhibitors have progressed through clinical studies and none of them has been approved yet. We here present the synthesis of three cyclophellitol scaffolds, based on known mechanism-based inhibitors of HPSE. These novel scaffolds are amenable to facile elaboration via copper-catalysed azide-alkyne cycloadditions to aid in exploring the structure-activity relationship for selective inhibitors of HPSE. | Helena Ehren; Seino Jongkees; Tom Wennekes | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d160521291e5d1de07b9d/original/synthesis-of-alkyne-and-azide-functionalised-aziridine-and-epoxide-carbocycles-for-development-of-selective-glucuronidase-mechanism-based-inhibitors.pdf |
675c85b2085116a13353ce8b | 10.26434/chemrxiv-2024-3gt4f | A Self Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations | There are currently over 160,000 protein crystal structures obtained by X-ray diffraction with resolutions of 1.5Å or greater in the Protein Data Bank. At these resolutions hydrogen atoms do not resolve and heavy atoms such as oxygen, carbon, and nitrogen are indistinguishable. This leads to ambiguity in the rotamer and protonation states of multiple amino acids, notably asparagine, glutamine, histidine, serine, tyrosine, and threonine. When the rotamer and protonation states of these residues changes, so too does the electrochemical surface of a binding site. A variety of computational tools have been developed to assign these states for these residues based on a crystal protein structure by evaluating the possible states and typically deciding on one single state for each residue. We posit that multiple rotamer and protonation states of residues are consistent with the resolved structure of the proteins and introduce a protonation and rotamer assignment tool that identifies an ensemble of rotamer and protonation states that are consistent with the X-ray scattering data of the protein. Here, we present a Rotamer and Protonation state Assignment (RAPA) tool that analyzes local hydrogen bonding environments in the resolved structures of proteins and identifies a set of unique rotamer and protonation states that are energetically consistent with the crystal structure. We evaluate all RAPA predicted states in unrestrained molecular dynamics simulations and find that there are multiple configurations for each protein which match the X-ray results with RMSDs of less than 1.0Å for the atoms with the lowest 90% B-factors. We find that for most protein systems (62 of 77) there are 8 or fewer possible states suggesting that there is no combinatorial explosion of accessible configurations for a majority of proteins. This suggests that investigating all energetically accessible rotamer and protonation states for most proteins is computationally feasible and that the selection of single states is arbitrary. | Mossa Ghattas; Prerna Gera; Steven Ramsey; Anthony Cruz Balberdy; Nathaniel Abraham; Daniel McKay; Tom Kurtzman | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c85b2085116a13353ce8b/original/a-self-consistent-approach-to-rotamer-and-protonation-state-assignments-rapa-moving-beyond-single-protein-configurations.pdf |
67c17b24fa469535b94a7c4e | 10.26434/chemrxiv-2025-sfckm | Elastoviscoplastic Model of Shellac-Butanol Solutions and its Application in Coated Paper Barrier Property Analysis | We used quasi-steady shear-rheometry and oscillatory-rheometry measurements to characterise rheological behavior of 5\%-15\% (w/v)} shellac in butanol solutions. A subtle shear-thickening followed by shear-thinning behavior was observed at all shear rates. The shear-dependent moduli $G'$ and $G''$ showed the presence of linear and non-linear viscoelastic regions and were modeled using an elasto-viscoplastic Saramito model, with viscoplastic viscosity modeled using the Herschel-Bulkley model. We applied the Landau-Levich theory to predict shellac coating thickness on paper substrates, with capillary number, viscosity, velocity, strain rate and surface tension as input. The water vapor transmission rate across the coated paper was characterised by Fick's diffusion model, giving an inverse dependence on coating thickness in broad agreement with experimental data. | Ashish Garg; Deepak Poddar; Faiz Ahmad; Sudip K. Pattanayek; Gaurav Goel | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Industrial Manufacturing; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c17b24fa469535b94a7c4e/original/elastoviscoplastic-model-of-shellac-butanol-solutions-and-its-application-in-coated-paper-barrier-property-analysis.pdf |
6462c9a6f2112b41e9a0302a | 10.26434/chemrxiv-2023-lkdf3 | A Non-Rate-Determining Redox Process Dictates the Oxygen Evolution Tafel Slope of MnO2 | Electrocatalytic activity is markedly influenced by the Tafel slope, which dictates the sensitivity of the catalytic current with respect to the potential. Differences in the Tafel slope between electrocatalysts have been rationalized based on redox pre-equilibria preceding the rate-determining step. However, no study has experimentally observed a non-rate-determining redox event that directly correlates with the Tafel slope. Here, we show that the Tafel slope of the oxygen evolution reaction (OER) on alpha-MnO2 is markedly influenced by a Mn(III)/Mn(II) redox process located 500 mV more negative than the OER onset potential. Upon repeated cyclic voltammetry sweeps, a correlation was observed between the Tafel slope and the peak position of a redox event, which was assigned to a Mn(III)/Mn(II) redox couple based on the potential dependence of the UV-vis spectra. Notably, the UV-vis absorption of Mn(III) did not diminish even after the OER was initiated, and another redox process was observed at the OER onset, indicating that Mn(III)/Mn(II) is not the rate-determining step for OER on alpha-MnO2 in alkaline pH. Numerical simulations using physicochemical parameters of Mn(III)/Mn(II) obtained from trumpet plot analyses reproduce the experimental Tafel plots, indicating that even non-rate-determining steps should be considered during catalyst design. | Koichi Yatsuzuka; Kiyohiro Adachi; Daisuke Hashizume; Ryuhei Nakamura; Hideshi Ooka | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6462c9a6f2112b41e9a0302a/original/a-non-rate-determining-redox-process-dictates-the-oxygen-evolution-tafel-slope-of-mn-o2.pdf |
6759f30f7be152b1d0a9a0fb | 10.26434/chemrxiv-2024-mfpcn-v2 | Enhanced Sampling with Sub-optimal Collective Variables: Reconciling Accuracy and Convergence Speed | We introduce an enhanced sampling algorithm to obtain converged free energy landscapes of molecular rare events, even when the collective variable (CV) used for biasing is not optimal. Our approach samples a time-dependent target distribution by combining the On-the-fly probability enhanced sampling (OPES) and its exploratory variant, OPES Explore (OPESe). This promotes more transitions between the relevant metastable states and accelerates the convergence speed of the free energy estimate. This is accomplished We demonstrate the successful application of this combined algorithm on the two-dimensional Wolfe-Quapp potential, millisecond timescale ligand-receptor binding in trypsin-benzamidine complex, and folding-unfolding transitions in chignolin mini-protein. Our proposed algorithm can compute accurate free energies at an affordable computational cost and is robust in terms of the choice of collective variables, making it particularly promising for the simulation of complex biomolecular systems. | Dhiman Ray; Valerio Rizzi | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Biophysical Chemistry; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6759f30f7be152b1d0a9a0fb/original/enhanced-sampling-with-sub-optimal-collective-variables-reconciling-accuracy-and-convergence-speed.pdf |
60c74062842e65b18edb1c9e | 10.26434/chemrxiv.7719125.v1 | Synthesis, Characterization, and Post-Synthetic Modification of a Micro/Mesoporous Zirconium-Tricarboxylate Metal-Organic Framework: Towards the Addition of Acid Active Sites | <div>
<p>Zr-MOFs are characterized by their high thermal and
chemical stability which may facilitate their application in heterogeneous
catalysis. However, these well-known microporous materials could see restricted
their applications in heterogeneous catalysis if large reactants exceed their
pore sizes leading to unavailable surface areas. In this work, we studied the
effect of acetic acid concentration, used as the modulator, on the formation of
micro/mesoporous materials. This inclusion of a modulator during synthesis and
its removal by activation process generate materials with missing linker
defects. We showed that an increase in the concentration of modulator leads to
an improvement of calculated apparent surface area and a modification of
MOF-808 pore structure by producing mesopores at the expense of micropores.
Furthermore, we performed a post-synthetic modification of the MOF-808. We
observed the expected sulfation of the zirconium oxo-cluster but also the
sulfonation of the organic ligand. Also,
we found that only the families of mesopores and the larger micropores are
interconnected within the material, and the ultramicropores seems to be
isolated from the porous structure. The PSM process led to the addition of Lewis and Brønsted acid sites to the MOF-808.
Experimental results were complemented by theoretical calculations using
Density Functional Theory (DFT) and Ab Initio Molecular Dynamics (AIMD)
simulations. The rationalization of the synthesis conditions effect and the post-synthetic
sulfation process on final properties presented in this paper can serve as a
basis for engineering of defects towards the synthesis of solid acid catalysts
from MOF 808.</p>
</div>
<br /> | Carolina Ardila-Suárez; Ana María Díaz-Lasprilla; Laura Alejandra Díaz Vaca; Perla B Balbuena; Víctor Gabriel Baldovino Medrano; Gustavo E Ramírez-Caballero | Organometallic Compounds; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74062842e65b18edb1c9e/original/synthesis-characterization-and-post-synthetic-modification-of-a-micro-mesoporous-zirconium-tricarboxylate-metal-organic-framework-towards-the-addition-of-acid-active-sites.pdf |
617b879c3c169d7bf086757a | 10.26434/chemrxiv-2021-6dhhs | Controlled sequential assembly of metal-organic polyhedra into colloidal gels with high chemical complexity | Assembling many chemical components into a material in a controlled manner is one of the biggest challenges in chemistry. Particularly porous materials with multivariate character within their scaffolds are expected to demonstrate synergistic properties. In this study, we show a synthetic strategy to construct porous networks with multiple chemical components. By taking advantage of the hierarchical nature of a colloidal system based on metal-organic polyhedra (MOPs), we developed a two-step assembly process to form colloidal networks; assembling of MOPs with the organic linker to the formation of MOP network as a colloidal particle, followed by further connecting colloids by additional crosslinkers, leading to colloidal networks. This synthetic process allows not only for the use of different organic linkers for connecting MOPs and colloidal particles, respectively, but for assembling different colloidal particles formed by various MOPs. The proof-of-concept of this tuneable multivariate colloidal gel system offers an alternative to developing functional porous soft materials with multifunction. | Min Ying Tsang; Shun Tokuda; Po-Chun Han; Zaoming Wang; Alexandre Legrand; Marina Kawano; Masahiko Tsujimoto; Yuki Ikeno; Kenji Urayama; Kevin C.-W. Wu; Shuhei Furukawa | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617b879c3c169d7bf086757a/original/controlled-sequential-assembly-of-metal-organic-polyhedra-into-colloidal-gels-with-high-chemical-complexity.pdf |
6436f0441d262d40ea547402 | 10.26434/chemrxiv-2023-p200m | Rapid Prototyping of Lab-scale Electrolysis Cells Using Stereolithography and Electroless Plating | Electrolysis research is typically conducted using commercially available cells with standard designs that are difficult to modify or custom-machined parts that are time-consuming to produce. Herein, we describe a method to rapidly produce lab-scale electrolysis cells that uses high-resolution, high-fidelity stereolithography 3D printing combined with electroless metal plating. Cells prepared by the printing/electroless plating method were compared to the same cells machined in Ti for CO electrolysis experiments. The printed cells showed very similar performance to the machined cells across a wide current density range (up to 250 mA cm-2) and demonstrated 24 h of stable operation in a zero-gap configuration. This work demonstrates the ability to prototype electrochemical cell designs in a fraction of the time required using conventional machining. | Gage Wright; Benjamin Charnay; Joshua Rabinowitz; Ruperto Mariano; Matthew Kanan | Catalysis; Energy; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6436f0441d262d40ea547402/original/rapid-prototyping-of-lab-scale-electrolysis-cells-using-stereolithography-and-electroless-plating.pdf |
647f47c74f8b1884b7ee26aa | 10.26434/chemrxiv-2023-6d7r9-v2 | Exploring the Progress and Mechanisms of Hydrogen Evolution Catalyzed by Cobaloximes: A Comprehensive Review | In recent years, significant progress has been made in the development of cobalt diamine-dioxime complexes, which have emerged as promising molecular catalysts. These catalysts offer several advantages, including enhanced stability against hydrolysis and versatility in various reaction conditions. Through derivatization of the ligand at the hydrocarbon chain connecting the two imine functions, the cobalt diamine-dioxime catalyst can be conveniently coupled with surfaces or photosensitizers. This modification provides a more efficient approach compared to the original cobaloximes. Notably, the cobalt diamine-dioxime catalyst has demonstrated activity in H2 evolution under fully aqueous conditions, both when immobilized onto electrode materials and in light-driven homogeneous conditions. These remarkable properties create opportunities for the construction of molecular-based photocathodes, serving as a critical component in dye-sensitized photoelectrochemical cells. | Humaira Yeasmin; Salma Begum; Md Akteruzzaman; MD MOTIUR MAZUMDER | Inorganic Chemistry; Catalysis; Energy | CC BY NC 4.0 | CHEMRXIV | 2023-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647f47c74f8b1884b7ee26aa/original/exploring-the-progress-and-mechanisms-of-hydrogen-evolution-catalyzed-by-cobaloximes-a-comprehensive-review.pdf |
62bf3b972530212302865f5b | 10.26434/chemrxiv-2022-mt165-v2 | AlInP(001) surface structure and electronic properties | Total-energy and electronic structure calculations based on density-functional theory are performed in order to determine the atomic structure and electronic properties of Al0.5In0.5P(001) surfaces. It is found that most of the stable surfaces obey the electron counting rule and are characterized by surface atom dimerization. The dimer related surface states are predicted to occur in the vicinity of the bulk band edges. For a very narrow range of preparation conditions, ab initio thermodynamics predicts metal atomic wires formed by surface cations. In case of typical metalorganic vapor-phase epitaxy growth conditions, a surface covered with a monolayer of buckled phosphorus dimers, where half of the phosphorus atoms are hydrogen-saturated, is found to be stable. The occurrence of this structure is confirmed by low energy electron diffraction and X-ray photoelectron spectroscopy data measured on epitaxially grown Al0.52In0.48P(001) epilayers lattice matched to GaAs. | Luis Joel Glahn; Isaac Azahel Ruiz Alvarado; Sergej Neufeld; Mohammad Amin Zare Pour; Agnieszka Paszuk; David Ostheimer; Sahar Shekarabi; Oleksandr Romanyuk; Dominik Christian Moritz; Jan Philipp Hofmann; Wolfram Jaegermann; Thomas Hannappel; Wolf Gero Schmidt | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Physical and Chemical Properties; Surface | CC BY 4.0 | CHEMRXIV | 2022-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bf3b972530212302865f5b/original/al-in-p-001-surface-structure-and-electronic-properties.pdf |
624d836a3affe49a21411d96 | 10.26434/chemrxiv-2022-h22dk | Population and Coherence Dynamics in Large Conjugated Porphyrin Nanorings | In photosynthesis nature exploits the distinctive electronic properties of chromophores arranged in supramolecular rings for efficient light harvesting. Among synthetic supramolecular cyclic structures, porphyrin nanorings have attracted considerable attention as they have a resemblance to naturally occurring light-harvesting structures but offer the ability to control ring size and the level of disorder. Here, broadband femtosecond transient absorption spectroscopy, with pump pulses in resonance with either the high or the low energy sides of the inhomogeneously broadened absorption spectrum, is used to study the population dynamics and ground and excited state vibrational coherence in large porphyrin nanorings. A series of fully conjugated, alkyne bridged, nanorings constituted of between ten and forty porphyrin units is studied. Pump-wavelength dependent fast spectral evolution is observed. A fast rise or decay of the stimulated emission are observed when large porphyrin nanorings are excited on, respectively, the high or low energy side of the absorption spectrum. Such dynamics are consistent with the hypothesis of a variation in transition dipole moment across the inhomogeneously broadened ground state ensemble. Oscillatory dynamics on the sub-ps time domain are observed in both pumping conditions. A combined analysis of the excitation wavelength-dependent transient spectra along with the amplitude and phase evolution of the oscillations allows assignment to vibrational wavepackets evolving on either ground or excited states electronic potential energy surfaces. Even though porphyrin nanorings support highly delocalized electronic wavefunctions, with coherence length spanning tens of chromophores, the measured vibrational coherences remain localised on the monomers. The main contributions to the beatings are assigned to two vibrational modes localised on the porphyrin cores: a Zn-N stretching mode and a skeletal methinic/pyrrolic C-C stretching and in-plane bending mode. | Giovanni Bressan; Michael Jirasek; Harry L. Anderson; Stephen R. Meech; Ismael A. Heisler | Physical Chemistry; Optics; Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624d836a3affe49a21411d96/original/population-and-coherence-dynamics-in-large-conjugated-porphyrin-nanorings.pdf |
64329797736114c96333c9e5 | 10.26434/chemrxiv-2023-j0rj6-v2 | N-heteroacenes as an organic gain medium for room temperature masers | The development of future quantum devices such as the maser, i.e., the microwave analog the laser, could be well-served by exploration of chemically tuneable organic materials. Current iterations of room temperature organic solid-state masers are composed of an inert host material that is doped with a spin-active molecule. In this work, we have systematically modulated the structure of three nitrogen-substituted tetracene derivatives to augment their photoexcited spin dynamics and then evaluated their potential as novel maser gain media. To facilitate these investigations, we adopted an organic glass former, 1,3,5-tri(1-naphthyl)benzene (1-TNB) to act a universal host. These chemical modifications impacted the rates of intersystem crossing, triplet spin polarisation, triplet decay and spin-lattice relaxation, leading to significant consequences on the conditions required to surpass the maser threshold. | Max Attwood; Xiaotian Xu; Michael Newns; Zhu Meng; Rebecca Ingle; Hao Wu; Xi Chen; Weidong Xu; Wern Ng; Temitope Abiola; Vasilos Stavros; Mark Oxborrow | Physical Chemistry; Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64329797736114c96333c9e5/original/n-heteroacenes-as-an-organic-gain-medium-for-room-temperature-masers.pdf |
645a6218a32ceeff2d5bb866 | 10.26434/chemrxiv-2023-j0qh7 | Enantioselective Nickel-Catalyzed Reductive Decarboxylative C(sp3)-C(sp2) Cross-Coupling of Malonic Acid Derivatives | The first enantioselective reductive decarboxylative C(sp3)-C(sp2) cross-coupling of malonic acid derivatives are reported via the intermediacy of redox-active esters (RAEs). A newly modified chiral bis-imidazoline ligand was identified as the optimal ligand to enable this reaction, providing direct access to valuable chiral aryl esters with high efficiency and excellent enantioselectivity. Our protocol is featured by its broad scope and exceptional compatibility with a variety of functional groups, even in the context of late-stage functionalization. In addition, C(sp2)−I could be selectively functionalized with bromo(iodo)arene. The detailed mechanistic studies supported a radical based cross-coupling mechanism. | Jia-Bao Wang; Shuai-Shuai Fang; Yu Shen; Xiao-Ting Liu; Ming-Hong Li; Ming Shang | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645a6218a32ceeff2d5bb866/original/enantioselective-nickel-catalyzed-reductive-decarboxylative-c-sp3-c-sp2-cross-coupling-of-malonic-acid-derivatives.pdf |
60c74128f96a00c4422863c9 | 10.26434/chemrxiv.7985657.v1 | Analytical Derivatives of the Individual State Energies in Ensemble Density Functional Theory Method: II. Implementation on Graphical Processing Units (GPUs) | Conical intersections control excited state reactivity and thus elucidation and prediction of their shapes and locations is crucial for photochemistry. To locate these intersections one needs accurate and efficient electronic structure methods. Unfortunately, the most accurate methods (e.g. XMS-CASPT2) are computationally difficult for large molecules. The state-interaction state-averaged restricted ensemble referenced Kohn-Sham (SI-SA-REKS) method is a computationally efficient alternative. The application of SI-SA-REKS to photochemistry was previously hampered by a lack of analytical nuclear gradients and nonadiabatic coupling matrix elements. We have recently derived analytical energy derivatives for the SI-SA-REKS method and implemented the method effectively on graphical processing units (GPUs). We demonstrate that our implementation gives the correct topography and energetics of conical intersections for several examples. Furthermore, our implementation of SI-SA-REKS is computationally efficient – the observed scaling with molecular size is sub-quadratic, i.e. O(N<sup>1.77</sup>). This demonstrates the promise of SI-SA-REKS for excited state dynamics of large molecular systems. | Fang Liu; Michael Filatov; Todd J. Martínez | Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74128f96a00c4422863c9/original/analytical-derivatives-of-the-individual-state-energies-in-ensemble-density-functional-theory-method-ii-implementation-on-graphical-processing-units-gp-us.pdf |
630845a5f07ee15d1cf206a6 | 10.26434/chemrxiv-2022-xfx89 | Foregrounding the code: Computational chemistry instructional activities using a highly readable fluid simulation code | Most computational chemistry instructional activities are based around students running chemical simulations via a graphical user interface (GUI). GUI-based activities offer many advantages, as they enable students to run chemical simulations with a few mouse clicks. Although these activities are excellent for introducing students to the capabilities of chemical simulations, the disadvantage is that the students’ experience is not representative of how professional computational chemists work. Just as it is important that students in an organic chemistry instructional lab gain hands-on experience with equipment commonly used by professional organic chemists, students of computational chemistry must gain hands-on experience with coding, as professional computational chemists do not rely on GUIs; we write code. Motivated by the need for instructional activities that provide hands-on experience with computer code, a pair of activities were created around a free lightweight (runs on standard laptops) open-source Lennard-Jones (LJ) fluid simulation code written in Python, a programming language that prioritizes readability. The first activity, aimed at undergraduate physical chemistry lab courses, involves students writing Python code in a Jupyter Notebook that is used to run LJ simulations and fit a Van der Waals gas model to data produced by the LJ fluid simulations. The second is a jigsaw activity, aimed at advanced undergraduate or graduate students, where students are assigned different sections of the LJ fluid simulation code, and must demonstrate the functionality of their section to the class by both giving an oral presentation and sharing a Jupyter Notebook demonstration of their own design.
| Gianmarc Grazioli; Adam Ingwerson; David Santiago; Heekun Cho; Patrick Regan | Chemical Education; Chemical Education - General | CC BY NC 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630845a5f07ee15d1cf206a6/original/foregrounding-the-code-computational-chemistry-instructional-activities-using-a-highly-readable-fluid-simulation-code.pdf |
60c751f8842e65938edb3c63 | 10.26434/chemrxiv.13118378.v2 | Binding of Inhibitors to the Monomeric and Dimeric SARS-CoV-2 Mpro | <div>
<p>SARS-CoV-2
rapidly infects millions of people worldwide since December 2019. There is
still no effective treatment for the virus, resulting in the death of more than
one million of patients. Inhibiting the activity of SARS-CoV-2 main protease
(Mpro), 3C-like protease (3CLP), is able to block the viral replication and
proliferation. In this context, our study has revealed that in silico screening
for inhibitors of SARS-CoV-2 Mpro can be reliably done using the monomeric
structure of the Mpro instead of the dimeric one. Docking and fast pulling of
ligand (FPL) simulations for both monomeric and dimeric forms correlate well
with the corresponding experimental binding affinity data of 30 compounds. The
obtained results were also confirmed via binding pose and noncovalent contact analyses.
Our study results show that it is possible to speed up computer-aided drug
design for SARS-CoV-2 Mpro by focusing on the monomeric form instead of the
larger dimeric one.</p></div> | Nguyen Minh Tam; Pham Cam Nam; Duong Tuan Quang; Nguyen
Thanh Tung; Van Vu; Son Tung Ngo | Bioinformatics and Computational Biology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751f8842e65938edb3c63/original/binding-of-inhibitors-to-the-monomeric-and-dimeric-sars-co-v-2-mpro.pdf |
60d4b39e403d9919d1bc5045 | 10.26434/chemrxiv-2021-cz105 | Dipole Moment and Charge Reorganization in Photoredox Catalysts | We report evidence of excited-state ion pair reorganisation in a cationic iridium (III) photoredox catalyst in 1,4-dioxane. Microwave-frequency dielectric-loss measurements allow us to assign both ground and excited-state molecular dipoles and excited-state polarizability volumes. These measurements show significant changes in ground-state dipole moment between [Ir[dF(CF_{3})ppy]_{2}(dtbpy)]PF_{6} (10.74 Debye) and [Ir[dF(CF_{3})ppy]_{2}(dtbpy)]BAr^{F}_{4} (4.86 Debye). Photoexcitation of each complex results in population of highly mixed ligand centered and metal-to-ligand charge transfer states. Relaxation to the lowest lying excited-state leads to a negative change in the dipole for [Ir[dF(CF_{3})ppy]_{2}(dtbpy)]PF_{6}, and a positive change in dipole for [Ir[dF(CF_{3})ppy]_{2}(dtbpy)]BAr^{F}_{4}. These observations are consistent with a sub-nanosecond reorganization with the PF_{6}^{-} counter-ion. Taken together, these observations suggest contact-ion pair formation in [Ir[dF(CF_{3})ppy]_{2}(dtbpy)]PF_{6}. The ion pair reorganisation we observe with the PF_{6}^{-} may modify both the thermodynamic potential available for electron transfer and inhibit oxidative catalysis, providing a possible mechanism for recently observed trends in similar complexes. | Justin Earley; Anna Zieleniewska; Hunter Ripberger; Megan Lazorski; Zachary Mast; Hannah Sayre; Robert Knowles; James McCusker; Gregory Scholes; Obadiah Reid; Garry Rumbles | Physical Chemistry; Inorganic Chemistry; Catalysis; Photocatalysis; Redox Catalysis; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d4b39e403d9919d1bc5045/original/dipole-moment-and-charge-reorganization-in-photoredox-catalysts.pdf |
60c744f4337d6c718be26eac | 10.26434/chemrxiv.9881609.v1 | Polymer-Solvent Phase Separation and Criticality in the Formation of Porous Polymeric Solids: A Modeling Study | <p>This manuscript describes a model for simulating the properties of polymer-solvent mixtures and the nonequilibrium processes that lead to their demixing and gel formation. In this model, the description of the system is based on a coarse grained lattice model of the polymer density field whose parameters can be chosen to reflect the microscopic characteristics of specific chemical systems. By using a lattice model, we are able to perform block renormalization and thereby access study the critical behavior of these systems upon demixing. We relate this critical behavior to the hierarchical structure of the resulting extended gel-like polymer network.</p> | Adam Willard; Paul E. Teichen | Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744f4337d6c718be26eac/original/polymer-solvent-phase-separation-and-criticality-in-the-formation-of-porous-polymeric-solids-a-modeling-study.pdf |
60c754f1469df43fb9f45047 | 10.26434/chemrxiv.13870592.v1 | Genetically-Encoded Discovery of Proteolytically Stable Bicyclic Inhibitors of Morphogen NODAL | In
this manuscript, we developed a Two-fold Symmetric Linchpin (<b>TSL</b>) that converts
readily available phage display peptides libraries made of 20 common amino
acids to genetically-encoded libraries of bicyclic peptides displayed on phage.
<b>TSL</b> combines an aldehyde-reactive
group and two thiol-reactive groups; it bridges two side chains of cysteine [C]
with an N-terminal aldehyde group derived from the N-terminal serine [S],
yielding a novel bicyclic topology that lacks a free N-terminus. Phage display
libraries of SX<sub>1</sub>CX<sub>2</sub>X<sub>3</sub>X<sub>4</sub>X<sub>5</sub>X<sub>6</sub>X<sub>7</sub>C
sequences, where X<i><sub>i</sub></i> is any
amino acids but Cys, were converted to a library of bicyclic <b>TSL</b>-[<u>S</u>]X<sub>1</sub><u>[C]</u>X<sub>2</sub>X<sub>3</sub>X<sub>4</sub>X<sub>5</sub>X<sub>6</sub>X<sub>7</sub>[<u>C]</u>
peptides in 45 ± 15%
yield. Using this library and protein morphogen NODAL as a target, we
discovered bicyclic macrocycles that specifically antagonize NODAL-induced
signaling in cancer cells. At a 10 µM concentration, two discovered bicyclic
peptides completely suppressed NODAL-induced phosphorylation of SMAD2 in P19
embryonic carcinoma. The <b>TSL</b>-[<u>S</u>]Y<u>[C]</u>KRAHKN[<u>C]</u>
bicycle inhibited NODAL-induced proliferation of NODAL-Tky-nu ovarian carcinoma
cells with apparent IC50 1 µM. The same bicycle at 10 µM concentration did not
affect the growth of the control Tky-nu cells. <b>TSL</b>-bicycles remained
stable over the course of the 72 hour-long assays in a serum-rich cell-culture
medium. We further observed general stability in mouse serum and in a mixture of
proteases (Pronase<sup>TM</sup>) for 33 diverse bicyclic macrocycles of
different ring sizes, amino acid sequences, and cross-linker geometries. <b>TSL</b>-constrained peptides expand the
previously reported repertoire of phage display bicyclic architectures formed
by cross-linking Cys side chains. We anticipate that it will aid the discovery
of proteolytically stable bicyclic inhibitors for a variety of protein targets. | Jeffrey Y. K. Wong; Raja Mukherjee; Olena Bilyk; Jiayuan Miao; Vivian Triana; Mark Miskolzie; Yu-Shan Lin; Antoine Henninot; John Dwyer; Serhii Kharchenko; Anna Iampolska; Dmitriy Volochnyuk; John J. Postovit; Ratmir Derda | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754f1469df43fb9f45047/original/genetically-encoded-discovery-of-proteolytically-stable-bicyclic-inhibitors-of-morphogen-nodal.pdf |
6778e3ba81d2151a02d73370 | 10.26434/chemrxiv-2025-dhj18 | Efficient organic X-ray scintillators achieved by hybridized local and charge-transfer emitters with through-space heavy atom-π interactions | The design and fabrication of organic X-ray imaging scintillators with large Stokes shift, narrow-band, fast, and efficient radioluminescence becomes an attractive research direction in many fields, such as medical diagnostics, scientific instruments and high-energy physics. However, the trade-off between these diverse scintillation properties is an enormous challenge facing almost all scintillators. To overcome this limitation, in this work, we developed a strategy based on through-space heavy atom-π interactions to improve the performance of organic scintillators by introducing alkyl bromides into hybridized local and charge transfer (HLCT) emitters. Specifically, the HLCT state's locally excited characters result in a short radiative lifetime (3.74 ns) and a narrow radioluminescence bandwidth (56 nm). The HLCT state's charge-transfer features yield a large Stokes shift (> 100 nm). Meanwhile, through-space bromine-π interactions enhance the photoluminescence quantum yield to 100%. Notably, a high X-ray imaging resolution (> 40.0 lp mm−1) was achieved, making the highest spatial resolution for organic scintillators reported to date. This work provides a method to design scintillators with excellent comprehensive performances and paves the way towards promising applications for high-resolution X-ray imaging. | Chensen Li; Yaohui Li; Minghui Wu; Fancheng Kong; Binxia Jia; Zonghang Liu; Philip C.Y. Chow; Zheng Zhao; Ryan T. K. Kwok; Jacky W. Y. Lam; Yucheng Liu; Shengzhong (Frank) Liu; Ben Zhong Tang | Organic Chemistry; Organic Compounds and Functional Groups; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6778e3ba81d2151a02d73370/original/efficient-organic-x-ray-scintillators-achieved-by-hybridized-local-and-charge-transfer-emitters-with-through-space-heavy-atom-interactions.pdf |
60c7486f842e651549db2bbb | 10.26434/chemrxiv.11907291.v1 | A General Approach to Deboronative Radical Chain Reaction with Pinacol Alkylboronic Esters | The generation of carbon-centered radicals from air-sensitive organoboron compounds via nucleohomolytic substitution at boron is one of the most general methods to generate non-functionalized and functionalized radicals. Due to their reduced Lewis acidity, the very popular, air-stable, and readily available alkylboronic pinacol esters are not suitable substrates for this process. Herein, is reported their <i>in situ</i> conversion to alkylboronic catechol esters by boron-transesterification with a substoichiometric amount of catechol methyl borate (MeO–Bcat) telescoped onto a wide array of radical chain processes. This simple one-pot, radical-chain, deboronative protocol allows for the conversion of pinacol boronic esters into iodides, bromides, chlorides, and thioethers. The process is also suitable the formation of nitriles and allylated compounds via C–C bond formation using sulfonyl radical traps. Finally, a particularly mild protocol for the protodeboronation of pinacol boronic esters is given. The power of combining radical and classical boron chemistry, is illustrated with a highly modular 5-membered ring formation using a combination of a three-component coupling reaction and a protodeboronative cyclization. | Emy André-Joyaux; Andrey Kuzovlev; Nicholas D. C. Tappin; Philippe Renaud | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7486f842e651549db2bbb/original/a-general-approach-to-deboronative-radical-chain-reaction-with-pinacol-alkylboronic-esters.pdf |
60c74687bdbb89158aa38c1d | 10.26434/chemrxiv.11342477.v1 | Synthesis of 1,2-Dihydroquinolines via Hydrazine-Catalysed Ring-Closing Carbonyl-Olefin Metathesis | The synthesis of 1,2-dihydroquinolines by the
hydrazine-catalysed ring-closing carbonyl-olefin metathesis (RCCOM) of
N-prenylated 2-aminobenzaldehydes is reported. Substrates with a variety of
substitution patterns are shown, and the compatibility of these conditions with
a range of additives is demonstrated.
With an acid-labile protecting group on the nitrogen atom, in situ
deprotection and autoxidation furnishes quinolines. In comparison to related oxygen-containing
substrates, the cycloaddition step of the catalytic cycle is shown to be
slower, but the cycloreversion is found to be more facile. | Yunfei Zhang; Jae Hun Sim; Samantha N. Macmillan; Tristan Lambert | Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74687bdbb89158aa38c1d/original/synthesis-of-1-2-dihydroquinolines-via-hydrazine-catalysed-ring-closing-carbonyl-olefin-metathesis.pdf |
6716d58a12ff75c3a11ea646 | 10.26434/chemrxiv-2024-j57mx | S273 phosphorylation restricts PPARy structural dynamics - a multiscale modeling view on the mechanisms of obesity metabolism | The nuclear receptor PPARγ is a promising target for treating type 2 diabetes mellitus. It regulates gene expression related to insulin and lipid metabolism. The obesity-linked phosphorylation of PPARγ S273 disrupts the expression of a specific subset of PPARγ-controlled genes linked to insulin metabolism, such as adiponectin. Previous research has demonstrated that this post-translational modification alters interactions with several coregulators, thereby influencing the expression of upstream genes. However, the effects of phosphorylation on the structural dynamics of PPARγ have not yet been fully understood. In this study, we applied atomistic and coarse-grained molecular dynamics simulations to examine the structural and dynamic changes induced by S273 phosphorylation. We observed that the phosphorylation impacts the dynamics of adjacent residues and influences more distantly located structural regions. Furthermore, S273 phosphorylation alters the flexibility of H12, the region responsible for canonical interaction with coregulators, potentially accounting for the previously observed differential interactions. These findings provide new insights into the mechanisms of gene expression regulation and may expand the avenues into diabetes therapy studies through PPARγ modulation. Moreover, they highlight the potential of combined atomistic and coarse-grained simulations to elucidate modifications of structural dynamics in proteins upon post-translational modification. | Marieli Mariano Gonçalves Dias; Cristina Gil Herrero; Ana Carolina Migliorini Figueira; Sebastian Thallmair | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6716d58a12ff75c3a11ea646/original/s273-phosphorylation-restricts-ppa-ry-structural-dynamics-a-multiscale-modeling-view-on-the-mechanisms-of-obesity-metabolism.pdf |
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