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664f4566418a5379b0173cd4 | 10.26434/chemrxiv-2024-4nr8m | Chemiexcitation Acceleration of 1,2-Dioxetanes via a Spiro-Fused Inductive Electron-Withdrawing Motifs | The chemiluminescent light-emission pathway of phenoxy-1,2-dioxetane luminophores attracts growing interest within the scientific community. Dioxetane probes undergoing rapid flash-type chemiexcitation exhibit higher detection sensitivity than those with a slow glow-type chemiexcitation rate, predominantly due to the higher number of photons produced within a given time interval. We discovered that dioxetanes fused to non-strained six-member rings, with hetero atoms or inductive electron-withdrawing groups, present both accelerated chemiexcitation rates and elevated chemical stability compared to dioxetanes fused to four-member strained rings. DFT computational simulations supported the chemiexcitation acceleration observed by spiro-fused six-member rings with inductive electron-withdrawing groups of dioxetanes. Specifically, a spiro-dioxetane with a six-member sulfone ring exhibited a chemiexcitation rate 293-fold faster than that of spiro-adamantyl-dioxetane. A turn-ON dioxetane probe for the detection of the enzyme β-galactosidase, containing the six-member sulfone unit, exhibited a S/N value of 108 in LB cell growth media. This probe demonstrated a substantial increase in detection sensitivity towards E. coli bacterial cells expressing β-galactosidase, with an LOD value that is 44-fold more sensitive than that obtained by the adamantyl counterpart. The accelerated chemiexcitation and the elevated chemical stability presented by dioxetane containing a spiro-fused six-member ring with a sulfone inductive electron-withdrawing group, make it an ideal candidate for designing efficient turn-on chemiluminescent probes with exceptionally high detection sensitivity. | Maya David; Thomas Leirikh; Omri Shelef; Sara Gutkin; Tal Kopp; Qingyang Zhou; Pengchen Ma; Micha Fridman; Kendall Houk; Doron Shabat | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664f4566418a5379b0173cd4/original/chemiexcitation-acceleration-of-1-2-dioxetanes-via-a-spiro-fused-inductive-electron-withdrawing-motifs.pdf |
64136bc12bfb3dc251e205b2 | 10.26434/chemrxiv-2023-8r07w | Preparation of artificial gold metalloenzymes with enantioselective reductase-like activity by combining genetic engineering and protein chemistry
| The conjugation of Au complexes with proteins and enzymes, generating new types of artificial metalloenzymes, has proven to be interesting and effective to obtain materials with improved properties such as higher stability, catalytic activity and selectivity. In this work, a novel method has been developed for the synthesis and design of artificial gold metalloenzymes at 50ºC in aqueous media, using two genetically modified variants of the alkalophilic lipase Geobacillus thermocatenulatus (GTL). The only difference between these two enzymatic variants is the possible coordination of the Au via active site (GTL-114) or Lid site (GTL-193). TEM analysis of the metalloenzymes revealed the formation of Au (0) nanoparticles with different structures (nanowires, nanorods, nanoshells, nanoclusters) and sizes depending on the mutant and the pH used during the synthesis. Characterisation by fluorescence spectroscopy demonstrated that conjugation of the enzyme to Au altered the tertiary structure of the protein. On the other hand, all metalloenzymes showed excellent reductase like activity. Finally, the selectivity of the enzyme-Au bioconjugates was tested in the asymmetric reduction of acetophenone to 1-phenylethanol in aqueous medium at room temperature. The protein environment played a key role in the reactivity and selectivity of the metalloenzymes, obtaining chiral nanoparticles with an enantiomeric excess of up to 39% towards (R)-1-phenylethanol after two hours of reaction using GTL-114 pH 10 as catalyst. | Carla Garcia-Sanz; Blanca de las Rivas; Jose M. Palomo | Biological and Medicinal Chemistry; Catalysis; Nanoscience; Biochemistry; Bioengineering and Biotechnology; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64136bc12bfb3dc251e205b2/original/preparation-of-artificial-gold-metalloenzymes-with-enantioselective-reductase-like-activity-by-combining-genetic-engineering-and-protein-chemistry.pdf |
60c752994c891907f8ad4159 | 10.26434/chemrxiv.13315235.v1 | Structures of LnmK a Bifunctional Acyltransferase/Decarboxylase with Substrate Analogs Reveals Basis for Selectivity and Stereospecificity | We solved crystal structures of LnmK, which that carries out both acyltransfer and decarboxylation in polyketide synthase pathways. Our structures have substrate analogs bound that reveal interactions that likely occur with the substrate and allow modelling of conformational changes and intermediate states.<br /> | Lee M Stunkard; Benjamin J. Kick; Jeremy Lohman | Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752994c891907f8ad4159/original/structures-of-lnm-k-a-bifunctional-acyltransferase-decarboxylase-with-substrate-analogs-reveals-basis-for-selectivity-and-stereospecificity.pdf |
60c748a1469df4b695f43a78 | 10.26434/chemrxiv.11888838.v2 | On the Performances of Density Functionals for Open Shell First-Row Transition Metal Compounds | <p>The
selection of density functional is the key to obtain useful results in a computational
work. Due to their complexity in terms of electronic structures, open-shell
first-row transition metal complexes are difficult to be correctly described by
most functionals. In this work, totally 19 reactions involving V, Cr, Mn, Fe,
Co, Ni complexes, either monometallic or bimetallic, were used as testing set
for 18 functionals ranging from generalized gradient approximation (GGA) to
doubly-hybrid functionals, with experimental electron affinities and ligand
association energies as standard. It is shown that for monometallic complexes
PBE0-D3BJ and B3LYP-D3BJ perform the best, whereas MN15 and MN15L are the
optimal functionals for bimetallic compounds. On the other hand, the accuracy
of DLPNO-CCSD(T) is not significantly better than the best-performing
functionals, and the use of doubly-hybrid functionals is risky.</p> | Yumiao Ma | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748a1469df4b695f43a78/original/on-the-performances-of-density-functionals-for-open-shell-first-row-transition-metal-compounds.pdf |
60c74021bb8c1ae96b3d9d37 | 10.26434/chemrxiv.7454252.v2 | Towards Understanding the Phenytoin-like Antiepileptic Effect of Cannabidiol and Related Phytocannabinoid Metabolites: Insights from Molecular Modeling | <div> Cannabidiol
(CBD), a nonpsychotropic constituent of <i>Cannabis
sativa</i>, has recently been approved by the US FDA for the treatment
of certain forms of pediatric epilepsy. The
mechanism by which CBD exerts its antiepileptic effects, however, is not
known. Herein we describe the results of molecular modeling studies
comparing the
stereoelectronic properties of phenytoin (PHT) with those of CBD and its
carboxylic acid
metabolite, as well as of 7-hydroxycannabidivarin. Also, the
cyclohexenecarboxylic acid core of
7-COOH-CBD perfectly mimics the unsaturated bioactive metabolite
of the commonly used antiepileptic valproic acid was also noted. We propose that C–7
oxidized phytocannabinoid metabolites are involved in the phenytoin-like
anticonvulsant effects of the parent phytocannabinoid drugs.</div> | Istvan Ujvary; Antal Lopata | Bioorganic Chemistry; Natural Products; Stereochemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74021bb8c1ae96b3d9d37/original/towards-understanding-the-phenytoin-like-antiepileptic-effect-of-cannabidiol-and-related-phytocannabinoid-metabolites-insights-from-molecular-modeling.pdf |
60c74f91702a9b73d118bbea | 10.26434/chemrxiv.12885476.v2 | Biosynthesis of Chlorinated Lactylates in Sphaerospermopsis sp. LEGE 00249 | Lactylates are an important group of molecules in the food and cosmetic industries. A series of natural halogenated 1-lactylates – chlorosphaerolactyaltes (<b>1</b>-<b>4</b>) – were recently reported from <i>Sphaerospermopsis</i> sp. LEGE 00249. Here, we identify the <i>cly</i> biosynthetic gene cluster, containing all the necessary functionalities to generate and release the natural lactylates. Using a combination of stable isotope-labeled precursor feeding and bioinformatic analysis, we propose that dodecanoic acid and pyruvate are the key building blocks in the biosynthesis of <b>1</b>-<b>4</b>. We additionally report minor analogues of these molecules<b> </b>with varying alkyl chains. The discovery of the <i>cly</i> gene cluster paves the way to accessing industrially-relevant lactylates through pathway engineering. | Kathleen Abt; Raquel Castelo-Branco; Pedro Leao | Biochemistry; Bioengineering and Biotechnology; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f91702a9b73d118bbea/original/biosynthesis-of-chlorinated-lactylates-in-sphaerospermopsis-sp-lege-00249.pdf |
6605a5d09138d23161913c3c | 10.26434/chemrxiv-2024-rn2rz | Unveiling solvent effects on β-scissions through Metadynamics and Mean Force Integration | This study introduces a methodology that combines accelerated molecular dynamics and Mean Force Integration (MFI) to investigate solvent effects on chemical reaction kinetics. The newly developed methodology is applied to the $\beta$-scission of Butyl Acrylate (BA) dimer in polar (water) and non-polar (xylene, BA monomer) solvents. The results show that solvation in both polar and non-polar environments reduces the free energy barrier of activation by $\sim$ 4 [kcal/mol] and decreases the pre-exponential factor twofold. Employing a hybrid QM/MM approach with explicit solvent modelling, we compute kinetic rate constants that better match experimental measurements compared to gas-phase calculations. This methodology presents promising potential for accurately predicting kinetic rate constants in liquid-phase polymerization and depolymerization processes. | Francesco Serse; Antoniu Bjola; Matteo Salvalaglio; Matteo Pelucchi | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Chemical Kinetics; Statistical Mechanics | CC BY NC 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6605a5d09138d23161913c3c/original/unveiling-solvent-effects-on-scissions-through-metadynamics-and-mean-force-integration.pdf |
65b82400e9ebbb4db93ca794 | 10.26434/chemrxiv-2023-2fl3h-v2 | Understanding and Fine Tuning the Propensity of ATP-Driven Liquid-Liquid Phase Separation with Oligolysine | Liquid-Liquid Phase Separation (LLPS) plays pivotal roles in the organization and functionality of living cells. It is imperative to understand the underlying driving forces behind LLPS and to control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool to investigate systems comprising oligolysine and adenosine triphosphate (ATP) under conditions of various ionic concentrations and oligolysine lengths. Consistent with experimental observations, our CG simulations captured the formation of LLPS upon the addition of ATP and tendency of dissociating under high ionic concentration. The primary driving force behind this phenomenon is the electrostatic interaction between oligolysine and ATP. An in-depth analysis on the structural properties of LLPS was conducted, where the oligolysine structure remained unchanged with increased ionic concentration and the addition of ATP led to a more pronounced curvature, aligning with the observed enhancement of $\alpha$-helical secondary structure in experiments. In terms of the dynamic properties, the introduction of ATP led to a significant reduction in translational and vibrational degrees of freedom but not rotational degrees of freedom. Through keeping the total number of charged residues constant and varying their entropic effects, we constructed two systems of similar biochemical significance and further validated the entropy effects on the LLPS formation. These findings provide a deeper understanding of LLPS formation and shed lights on the development of novel bioreactor and primitive artificial cells for synthesizing key chemicals for certain diseases. | Qiang Zhu; Yongxian Wu; Ray Luo | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b82400e9ebbb4db93ca794/original/understanding-and-fine-tuning-the-propensity-of-atp-driven-liquid-liquid-phase-separation-with-oligolysine.pdf |
60c74eefee301cb855c7a5d7 | 10.26434/chemrxiv.12821387.v1 | High Resolution Infrared Spectroscopy of Naphthalene and Cenaphthene Dimers | Non-covalent interactions are rapidly gaining interest as they are often crucial in determining the properties of materials, and key to supramolecular chemistry and to biochemistry. Non-covalent Polycyclic Aromatic Hydrocarbon (PAH) complexes are in particular relevant to astrochemistry and combustion chemistry where they are involved in the initial steps of condensation and soot formation, respectively. Here, we investigated non-covalent π-π stacking and CH-π interactions in naphthalene and acenaphthene clusters using high resolution IR-UV spectroscopy in combination with quantum chemical calculations. We identified spectral shifts that occur upon complexation and thereby evaluated predicted potential energy surfaces. The results provide strong indications for a prevalent parallel naphthalene dimer, showing that π-π stacking interactions become significant for bicyclic and larger PAHs. | A.K. Lemmens; Pragya Chopra; Diksha Garg; Amanda Steber; Melanie Schnell; W.J. Buma; Anouk Rijs | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eefee301cb855c7a5d7/original/high-resolution-infrared-spectroscopy-of-naphthalene-and-cenaphthene-dimers.pdf |
60c74522842e658556db25ab | 10.26434/chemrxiv.9974354.v1 | Functional Polyselenoureas for Selective Gold Recovery Prepared from Catalyst-Free Multicomponent Polymerizations of Elemental Selenium | Selenium-containing polymers with fascinating functionalities are highly desired but are rarely developed due to their underexplored synthetic methods. Herein, through careful design of monomer structures and polymerization conditions, a series of catalyst-free multicomponent polymerizations (MCPs) of elemental selenium with aliphatic/aromatic diamines and diisocyanides were reported to directly convert elemental selenium to polyselenoureas with long-term stability, good solubility, well-characterized structures, and unique functionalities. The MCPs enjoy wide monomer scope and fast conversion in 1 min, delivering 18 polyselenoureas with high molecular weights (Mws up to 94 600 g/mol) in high yields (up to 99%). Furthermore, the polyselenoureas can be used for the extraction of Au3+ from mixed metal ion solutions in practical conditions with high selectivity, sensitivity (< 1 μg/L), efficiency (> 99.99%), and capacity (up to 665.60 mg·Au3+/g) within 1 min, and elemental gold can be further recovered after pyrolysis of the polymer complexes. | Xiuying Wu; Hua Lin; Fengying Dai; Rongrong Hu; Ben Zhong Tang | Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74522842e658556db25ab/original/functional-polyselenoureas-for-selective-gold-recovery-prepared-from-catalyst-free-multicomponent-polymerizations-of-elemental-selenium.pdf |
64a838cf9ea64cc16799a7ce | 10.26434/chemrxiv-2023-d1tsj | Tailored Broad-Spectrum Emission in Hybrid Aggregation Induced Emission (AIE)-MOFs: Boosting White Light Efficiency in Electrospun Janus Microfibers | Advances in energy-efficient lighting and display technologies demand innovative materials with tailored broad-spectrum emission properties. Hybrid aggregation-induced emission metal-organic frameworks (AIE-MOFs) offer a promising avenue, combining unique characteristics of organic and inorganic components to yield enhanced lumi-nescence efficiency and robust material stability. Our study introduces a spectrum of D (donor)-A (acceptor) type AIE-active ligands into MOFs, enabling tunable emission across the visible spectrum, thus underscoring the versatility of these hybridized MOF materials. We further harness the emission properties of AIE-MOFs by integrating them into polymer matrices, resulting in high-performance electrospun fibers with tunable emission. A significant achievement involves the fabrication of Janus-type white light-emitting AIE-MOF fiber composites via side-by-side electrospinning, accomplishing a high quantum yield of 58%, which doubled the performance of homogeneous fibers. Complement-ing our experimental findings, we employ micro-Raman and nano-FTIR as local spectroscopic probes, affording a deeper understanding of the material properties and the mechanisms contributing to enhanced light emission. In our understanding, this study presents an unconventional implementation of hybrid AIE-MOFs in Janus-type structures for white light emission. It significantly improves the efficiency of white light sources in optoelectronics, charting a promising direction for future research in the emergent AIE-MOF field. | Vishal Kachwal; Samraj Mollick; Jin-Chong Tan | Materials Science; Polymer Science; Composites; Dyes and Chromophores; Hybrid Organic-Inorganic Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a838cf9ea64cc16799a7ce/original/tailored-broad-spectrum-emission-in-hybrid-aggregation-induced-emission-aie-mo-fs-boosting-white-light-efficiency-in-electrospun-janus-microfibers.pdf |
62bbabcb13b85bbc5237bf46 | 10.26434/chemrxiv-2022-xg8zw | The Impact of the Different Geometrical Restrictions on the Nonadiabatic Photoisomerization of Biliverdin Chromophore | The photoisomerization mechanism of the chromophore of bacterial biliverdin (BV) phytochromes is explored with the nonadiabatic dynamics simulation by using the on-the-fly trajectory surface-hopping method at the semi-empirical OM2/MRCI level. Particularly, the current study focuses on the influence of the geometrical constrains on the nonadiabatic photoisomerization dynamics of the BV chromophore. Here a rather simplified approach is employed in the nonadiabatic dynamics to capture the features of geometrical constrains, which adds the mechanical restriction on the specific moieties of the BV chromophore. This simplified method provides a rather quick approach to examine the influence of the geometrical restrictions on the photoisomerization. As expected, different constrains bring the distinctive influences on the photoisomerization mechanism of the BV chromophore, giving either strong or minor modification of both involved reaction channels and excited-state lifetimes after the constrains are added in different ring moieties. These observations not only contribute to the primary understanding of the role of the spatial restriction caused by biological environments in photoinduced dynamics of the BV chromophore, but also provide useful ideas for the artificial regulation of the photoisomerization reaction channels of phytochrome proteins. | Yuan Fang; Haiyi Huang; Kunni Lin; Chao Xu; FengLong Gu; Zhenggang Lan | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bbabcb13b85bbc5237bf46/original/the-impact-of-the-different-geometrical-restrictions-on-the-nonadiabatic-photoisomerization-of-biliverdin-chromophore.pdf |
67d40b2b6dde43c908c48365 | 10.26434/chemrxiv-2025-170hh | Structural Changes Induced by the Promoter Ga in Nanocrystalline ZnO Support Used in Methanol Catalysis | Ga has an ionic radius fitting the radius of Zn much better than Al, which makes it an interesting candidate for doping of ZnO, which is relevant in context with Cu/ZnO-catalysts and with transparent conductive oxides. Here, the structural changes of Ga-doping of nano-scale ZnO, which is obtained via thermal decomposition of hydrozincite, are studied by a combination of X-ray diffraction, 71Ga/1H MAS NMR, quantum-chemical calculations and electron microscopy techniques. By quantum chemical calculations the NMR fingerprint of different Ga point defects is predicted, the calculations are validated against experimental data for different crystalline compounds. The relevant point defect in ZnO could be identified by the point symmetry of the isolated defect and comparison to the calculated values. The kinetic solubility limit for Ga in ZnO is determined by X-ray diffraction and NMR. It is shifted to higher values as compared to the Al variant. Finally, the distribution of Ga and H atoms within the nano-scale material is studied by “paramagnetically assisted surface peak assignment” (PASPA) NMR, REDOR and electron microscopy which shows that for Ga substitution ratios above the solubility limit the excess of Ga is incorporated into a heavily disordered or amorphous, hydrogen-rich surface-layer. | Jan Konrad Wied; Benjamin Mockenhaupt; Sebastian Mangelsen; Ulrich Schürmann; Lorenz Kienle; Malte Behrens; Jörn Schmedt auf der Günne | Inorganic Chemistry; Solid State Chemistry; Spectroscopy (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d40b2b6dde43c908c48365/original/structural-changes-induced-by-the-promoter-ga-in-nanocrystalline-zn-o-support-used-in-methanol-catalysis.pdf |
6505b1ffb338ec988a948566 | 10.26434/chemrxiv-2023-555vg | Ligand Steric Profile Tunes the Reactivity of Indium Phosphide Clusters | Indium phosphide quantum dots have become an industrially relevant material for solid-state lighting and wide color gamut displays. The synthesis of indium phosphide quantum dots from indium carboxylates and tris(trimethylsilyl)phosphine (P(SiMe3)3) is understood to proceed through the formation of magic-sized clusters, with In37P20(O2CR)51 being the key isolable intermediate. The reactivity of the In37P20(O2CR)51 cluster is a vital parameter in controlling conversion to quantum dots. Here, we report structural perturbations to In37P20(O2CR)51 clusters induced by tuning the steric properties of a series of substituted phenylacetate ligands. This approach allows for control over reactivity with P(SiMe3)3, where meta-substituents enhance the susceptibility to ligand displacement and para-substituents hinder phosphine diffusion to the core. Thermolysis studies show that with complete cluster dissolution, steric profile can modulate the nucleation period, whereas partial dissolution from indium carboxylate loss results in conversion to uniform InP cores with a narrow, 419 nm absorbance. The enhanced stability from ligand engineering also allows for the isolation and structural characterization by single-crystal X-ray diffraction of a new III-V magic-sized cluster with formula In26P13(O2CR)39. This intermediate is thought to precede the In37P20(O2CR)51 cluster on the InP reaction coordinate. The physical and electronic structure of this cluster are analyzed, providing new insight into previously unrecognized relationships between II-VI and III-V materials and the discrete growth of III-V cluster intermediates. | Soren Sandeno; Kyle Schnitzenbaumer; Sebastian Krajewski; Ryan Beck; Dylan Ladd; Kelsey Levine; Damara Dayton; Michael Toney; Xiaosong Li; Werner Kaminsky; Brandi Cossairt | Inorganic Chemistry; Nanoscience; Kinetics and Mechanism - Inorganic Reactions; Ligands (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2023-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6505b1ffb338ec988a948566/original/ligand-steric-profile-tunes-the-reactivity-of-indium-phosphide-clusters.pdf |
60c73e0b842e65471adb184a | 10.26434/chemrxiv.6267383.v1 | The Metalloid Reductase of Pseudomonas Moravenis Stanleyae Conveys Nanoparticle Mediated Metalloid Tolerance | In the present work we have identified a glutathione reductase like metalloid reductase (GRLMR) responsible for mediating selenite tolerance in <i>Pseudomonas moravenis</i> stanleyae through the enzymatic generation of Se(0) nanoparticles. This enzyme has an unprecedented substrate specificity for selenodiglutathione (K<sub>m</sub>= 336 μM) over oxidized glutathione (K<sub>m</sub>=8.22 mM). This enzyme was able to induce selenite tolerance in foreign bacterial cell lines by increasing the IC<sub>90</sub> for selenite from 1.9 mM in cell lacking the GRLMR gene to 21.3 mM for cells containing the GRLMR gene. It was later confirmed by STEM and EDS that Se nanoparticles were absent in control cells and present in cells expressing GRLMR. Structural analysis suggests the lack of a sulfur residue in the substrate/product binding pocket may be responsible for this unique substrate specificity. | Richard Nemeth; Mackenzie Neubert; Thomas Ni; Christopher J. Ackerson | Biochemistry; Cell and Molecular Biology; Chemical Biology; Microbiology; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e0b842e65471adb184a/original/the-metalloid-reductase-of-pseudomonas-moravenis-stanleyae-conveys-nanoparticle-mediated-metalloid-tolerance.pdf |
656d8137cf8b3c3cd7bd3752 | 10.26434/chemrxiv-2023-3cvfd | A nanomedicine approach to targeting cuproplasia in cancer: Labile copper sequestration using polydopamine nanoparticles blocks tumor growth in vivo through altering metabolism and redox homeostasis. | Copper plays critical roles as a metal active site cofactor and metalloallosteric signal for enzymes involved in cell proliferation and metabolism, making it an attractive target for cancer therapy. In this study, we investigated the efficacy of polydopamine nanoparticles (PDA NPs), classically applied for metal removal from water, as a therapeutic strategy for depleting intracellular labile copper pools in triple negative breast cancer models through the metal-chelating groups present on PDA surface. By using the activity-based sensing probe FCP-1, we could track the PDA-induced labile copper depletion while leaving total copper levels unchanged, and link it to the selective MDA-MB-231 cell death. Further mechanistic investigations revealed that PDA NPs increased reactive oxygen species (ROS) levels, potentially through the inactivation of superoxide dismutase 1 (SOD1), a copper-dependent antioxidant enzyme. Additionally, PDA NPs were found to interact with the mitochondrial membrane, resulting in an increase in mitochondrial membrane potential, which may contribute to enhanced ROS production. We employed an in vivo tumor model to validate the therapeutic efficacy of PDA NPs. Remarkably, in the absence of any additional treatment, the presence of PDA NPs alone led to a significant reduction in tumor volume by a factor of 1.66 after 22 days of tumor growth. Our findings highlight the potential of PDA NPs as a promising therapeutic approach for selectively targeting cancer by modulating copper levels and inducing oxidative stress, leading to tumor growth inhibition as shown in these triple negative breast cancer models. | Javier Bonet Aletá; Miguel Encinas-Giménez; Miku Oi; Aidan T. Pezacki; Victor Sebastián; Alba de Martino; Ana Martín-Pardillos; Pilar Martin-Duque; José L. Hueso; Christopher J. Chang; Jesús Santamaría | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656d8137cf8b3c3cd7bd3752/original/a-nanomedicine-approach-to-targeting-cuproplasia-in-cancer-labile-copper-sequestration-using-polydopamine-nanoparticles-blocks-tumor-growth-in-vivo-through-altering-metabolism-and-redox-homeostasis.pdf |
60c747a3f96a001028286f75 | 10.26434/chemrxiv.11750544.v1 | An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models | <div><div><div><p>Protein-ligand binding affinity is a key pharmacodynamic endpoint in drug discovery. Sole reliance on experimental design, make, and test cycles is costly and time consuming, providing an opportunity for computational methods to assist. Herein, we present results comparing random forest and feed-forward neural network proteochemometric models for their ability to predict pIC50 measurements for held out generic Bemis-Murcko scaffolds. In addition, we assess the ability of conformal prediction to provide calibrated prediction intervals in both a retrospective and semi-prospective test using the recently released Grand Challenge 4 data set as an external test set. In total, random forest and deep neural network proteochemometric models show quality retrospective performance but suffer in the semi-prospective setting. However, the conformal predictor prediction intervals prove to be well calibrated both retrospectively and semi-prospectively showing that they can be used to guide hit discovery and lead optimization campaigns.</p></div></div></div> | conor parks; Zied Gaieb; Rommie Amaro | Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747a3f96a001028286f75/original/an-analysis-of-proteochemometric-and-conformal-prediction-machine-learning-protein-ligand-binding-affinity-models.pdf |
66eb53db12ff75c3a1bea48d | 10.26434/chemrxiv-2024-31fl1-v2 | Automated Membrane Characterization: In-situ Monitoring of the Permeate and Retentate Solutions using a 3D Printed Permeate Probe Device | Self-driving laboratories and automated experiments can accelerate the design workflow and decrease errors associated with experiments that characterize membrane transport properties. Within this study, we use 3D printing to design a custom stirred cell that incorporates inline conductivity probes in the retentate and permeate streams. The probes provide a complete trajectory of the salt concentrations as they evolve over the course of an experiment. Here, automated diafiltration experiments are used to characterize the performance of commercial NF90 and NF270 polyamide membranes over a predetermined range of KCl concentrations from 1-100 mM. The measurements obtained by the inline conductivity probes are validated using offline post-experiment analyses. Compared to traditional filtration experiments, the probes decrease the amount of time required for an experimentalist to characterize membrane materials by more than 50× and increase the amount of information generated by 100×. Device design principles to address the physical constraints associated with making conductivity measurements in confined volumes are proposed. Overall, the device developed within this study provides a foundation to establish high-throughput, automated membrane characterization techniques. | Jonathan Ouimet; Faraj Al-Badani; Xinhong Liu; Laurianne Lair; Zachary Muetzel; Alexander Dowling; William Phillip | Chemical Engineering and Industrial Chemistry; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66eb53db12ff75c3a1bea48d/original/automated-membrane-characterization-in-situ-monitoring-of-the-permeate-and-retentate-solutions-using-a-3d-printed-permeate-probe-device.pdf |
63da867133b6976c48031bbe | 10.26434/chemrxiv-2023-qrf85 | Gargoyles: An Open Source Graph-based molecular optimization method based on Deep Reinforcement Learning | Automatic optimization methods for compounds in the vast compound space are important for drug discovery and material design. Several machine learning-based molecular generative models for drug discovery have been proposed, but most of these methods generate compounds from scratch and are not suitable for exploring and optimizing around arbitrary compounds. In this study, we developed a compound optimization method based on molecular graphs using deep reinforcement learning. This method searches for compounds on a fragment-by-fragment basis and at high density by generating fragments to be added atom by atom. Experimental results confirmed that the QED, the optimization target set in this study, was enhanced by searching around the starting compound. This means that the generated compounds are structurally similar to the starting compounds, indicating that the method is suitable for starting generation from a given compound. The source code is available at https://github.com/sekijima-lab/GARGOYLES. | Daiki Erikawa; Nobuaki Yasuo; Masakazu Sekijima | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da867133b6976c48031bbe/original/gargoyles-an-open-source-graph-based-molecular-optimization-method-based-on-deep-reinforcement-learning.pdf |
60c74438702a9beae718a79b | 10.26434/chemrxiv.8181704.v2 | Role of Structural Defects in the Adsorption and Separation of C3 Hydrocarbons in Zr-Fumarate-MOF (MOF-801) | An effective separation of propylene/propane mixtures is one of the most important processes in the petrochemical industry. Incidentally this separation is challenging due to the extensive similarities between both gases in terms of physicochemical properties such as, but not only limited to, boiling point, kinetic diameter and molecular weight. A drive to switch to less energy consuming processes, like adsorption or membrane separation, has highlighted several microporous metal organic frameworks as promising materials. In this work, we present a combined numerical and experimental investigation on propane and propylene adsorption in Zr-fumarate-MOF (also known as MOF-801), a small pore isoreticular analogue of UiO-66. Here, we demonstrate how the presence of structural defects can completely change the sorptive properties and separation performance of the Zr-fumarate-MOF, with enhanced capacity and gas diffusion rates for C3-sized hydrocarbons at the cost of kinetic selectivity. Extensive GCMC simulations performed on mixed defective supercells show that a percentage of missing cluster defects of around 1/8<sup>th</sup> can best account for the experimental results. Furthermore, analysis of low-frequency phonon spectra is used to explain gaseous diffusion in the original pristine material. A slight preference for propane over propylene is highlighted in the defective sample, and confirmed through column breakthrough experiments, suggesting the potential applicability of the Zr-fumarate-MOF in this challenging separation.<br /> | Paul Iacomi; Filip Formalik; Joao Marreiros; Jin Shang; Justyna Rogacka; Alexander Mohmeyer; Peter Behrens; Rob Ameloot; Bogdan Kuchta; Philip L. Llewellyn | Hybrid Organic-Inorganic Materials; Separation Science; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Coordination Chemistry (Organomet.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74438702a9beae718a79b/original/role-of-structural-defects-in-the-adsorption-and-separation-of-c3-hydrocarbons-in-zr-fumarate-mof-mof-801.pdf |
66426e8a91aefa6ce1e2e637 | 10.26434/chemrxiv-2024-fl2mb | Unraveling the structure and composition of Li4Mn2O4.5 (Li2O•Li0.667Mn1.333O2) electrodes for lithium batteries
| This communication addresses the debate about the composition and structure of a lithium-rich manganese oxide electrode with a fully disordered Li-Mn-O rock salt component that was first reported as Li4Mn2O5 (Li2O•2LiMnO2), by Freire et al. in 2015. When prepared at 800 C, it has been determined that the formula of this compound can be designated more accurately as Li4Mn2O4.5, alternatively Li2O•Li0.667Mn1.333O2, or close thereto. The cubic, disordered Li0.667Mn1.333O2 (or Li0.333Mn0.667O) rock salt component, in which the manganese ions adopt an average oxidation state of 2.5+, transforms to a clearly-defined spinel configuration during electrochemical cycling. The electrochemical activation process during the initial charge reaction appears to include the oxidation of the manganese ions by oxygen released by the Li2O component between 4.5 and 4.6 V. In complete contrast, nickel-substituted electrodes, such as Li2O•2LiMn0.5Ni0.5O2 and Li2O•2LiMn0.475Ni0.475Co0.050O2, in which the manganese ions adopt a tetravalent state, have disordered rock salt components that are electrochemically inactive. | Adam Tornheim; Anh Vu; Indrani Roy; Christopher Johnson; Jason Croy; Michael Thackeray | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66426e8a91aefa6ce1e2e637/original/unraveling-the-structure-and-composition-of-li4mn2o4-5-li2o-li0-667mn1-333o2-electrodes-for-lithium-batteries.pdf |
64b47402ae3d1a7b0dd40899 | 10.26434/chemrxiv-2023-m9tzh | The chemical metamorphosis of taxane diterpenes by synthetic design | The construction of molecular carbon frameworks stands as the fundamental objective of organic chemistry. The carbon skeleton of each organic molecule serves as the foundation for its three-dimensional structure, playing a pivotal role in determining its physical and biological properties. Within the realm of synthesis, the ability to access complex molecules while prioritizing skeletal diversification serves as a crucial factor in advancing the frontiers of efficient synthetic design. In line with this pursuit, our team has developed a versatile synthetic strategy. This strategy not only enables structural diversification but also facilitates the metamorphosis of complex molecular frameworks, such as the taxane diterpenes, into one another. Through our innovative approach, we have unlocked the transformative power to interconvert and manipulate these intricate structures. The implications of our findings extend beyond conventional synthetic chemistry, presenting exciting opportunities for creating a diverse array of molecules with unparalleled flexibility. This achievement opens new avenues for exploration and holds promise for future advancements and applications in this dynamic scientific field. | Lu Pan; Fabian Schneider; Moritz Ottenbruch; Rainer Wiechert; Tatjana List; Philipp Schoch; Bastian Mertes; Tanja Gaich | Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b47402ae3d1a7b0dd40899/original/the-chemical-metamorphosis-of-taxane-diterpenes-by-synthetic-design.pdf |
66ab373101103d79c56a331c | 10.26434/chemrxiv-2024-tddfc-v3 | Regio-MPNN: Predicting Regioselectivity for General Metal-Catalyzed Cross-Coupling Reactions using Chemical Knowledge Informed Message Passing Neural Network | As a fundamental problem in organic chemistry, synthesis planning aims at designing energy and cost-efficient reaction pathways for target compounds. In synthesis planning, it is crucial to understand regioselectivity, or the preference of a reaction over competing reaction sites. Precisely predicting regioselectivity enables early exclusion of unproductive reactions and paves the way to designing high-yielding synthetic routes with minimal separation and material costs. However, it is still at emerging state to combine chemical knowledge and data-driven methods to make practical predictions for regioselectivity. At the same time, metal-catalyzed cross-coupling reactions have profoundly transformed medicinal chemistry, and thus become one of the most frequently encountered types of reactions in synthesis planning. In this work, we for the first time introduce a chemical knowledge informed message passing neural network(MPNN) framework that directly identifies the intrinsic major products for metal-catalyzed cross-coupling reactions with regioselective ambiguity. Integrating both first principle methods and data-driven methods, our model achieves an overall accuracy of 96.51% on the test set of eight typical metal-catalyzed cross-coupling reaction types, including Suzuki-Miyaura, Stille, Sonogashira, Buchwald-Hartwig, Hiyama, Kumada, Negishi, and Heck reactions, outperforming other commonly used model types. To integrate electronic effects with steric effects in regioselectivity prediction, we propose a quantitative method to measure the steric hindrance effect. Our steric hindrance checker can successfully identify regioselectivity induced solely by steric hindrance. Notably under practical scenarios, our model outperforms 6 experimental organic chemists with an average working experience of over 10 years in the organic synthesis industry in terms of predicting major products in regioselective cases. We have also exemplified the practical usage of our model by fixing routes designed by open-access synthesis planning software and improving reactions by identifying low-cost starting materials. To assist general chemists in making prompt decisions about regioselectivity, we have developed a free web-based AI-empowered tool. Our code and web tool have been made available at https://github.com/Chemlex-AI/regioselectivity and https://ai.tools.chemlex.com/region-choose, respectively. | Baochen Li; Yuru Liu; Haibin Sun; Rentao Zhang; Yongli Xie; Klement Foo; Frankie Mak; Ruimao Zhang; Tianshu Yu; Sen Lin; Peng Wang; Xiaoxue Wang | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ab373101103d79c56a331c/original/regio-mpnn-predicting-regioselectivity-for-general-metal-catalyzed-cross-coupling-reactions-using-chemical-knowledge-informed-message-passing-neural-network.pdf |
60c746e94c891990cead2be8 | 10.26434/chemrxiv.11341850.v1 | Photocatalytic Proton Reduction by a Computationally Identified, Molecular Hydrogen-Bonded Framework | For the first time, a hydrogen-bonded organic
framework is shown to be an effective photocatalyst for the production of
hydrogen from water. The crystal structure of this molecular material is found
to be key to good activity with a chemically identical but amorphous version
showing orders of magnitude lower proton reduction rates. | Catherine Aitchison; Christopher M. Kane; David P. McMahon; Peter Spackman; Angeles Pulido; Xiaoyan Wang; Liam Wilbraham; Linjiang Chen; Rob Clowes; Martijn Zwijnenburg; Seb Sprick; Marc Little; Graeme Day; Andrew
I. Cooper | Photocatalysis | CC BY 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746e94c891990cead2be8/original/photocatalytic-proton-reduction-by-a-computationally-identified-molecular-hydrogen-bonded-framework.pdf |
625716685b9009b6f20ce3cc | 10.26434/chemrxiv-2022-b3n3j | Directed Evolution of Flavin-Dependent Halogenases for Atroposelective Halogenation of 3-Aryl-4(3H)-quinazolinones via Kinetic or Dynamic Kinetic Resolution | In this study, we engineer a variant of the flavin-dependent halogenase RebH that catalyzes site- and atroposelective halogenation of 3-aryl-4(3H)-quinazolinones via kinetic or dynamic kinetic resolution. The required directed evolution uses a combination of random and site-saturation mutagenesis, substrate walking using two probe substrates, and a two-tiered screening approach involving analysis of variant conversion and then enantioselectivity of improved variants. The resulting variant, 3-T, provides >99:1 e.r. for the (M)-atropisomer of the major brominated product, 25-fold improved conversion, and 91-fold improved site-selectivity relative to the parent enzyme on the probe substrate used in the final rounds of evolution. This high activity and selectivity translates well to several additional substrates with varied steric and electronic properties. Computational modeling and docking simulations are used to rationalize the effects of key mutations on substrate scope and site- and atroposelectivity. Given the range of substrates that have been used for atroposelective synthesis via electrophilic halogenation, these results suggest that FDHs could find many additional applications for atroposelective catalysis. More broadly, this study highlights how RebH can be engineered to accept structurally diverse substrates that enable its use for enantioselective catalysis. | Harrison M. Snodgrass; Dibyendu Mondal; Jared Lewis | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Stereochemistry; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625716685b9009b6f20ce3cc/original/directed-evolution-of-flavin-dependent-halogenases-for-atroposelective-halogenation-of-3-aryl-4-3h-quinazolinones-via-kinetic-or-dynamic-kinetic-resolution.pdf |
652f845987198ede0785a4fc | 10.26434/chemrxiv-2023-nzcw8 | Computationally-Assisted Discovery and computational
NMR Assignment of a Highly-binding PXR Natural
Diterpenoids | We report here the orchestration of molecular ion networking (MoIN) and a set of computationally assisted structural elucidation approaches in the discovery of a new class of 4,5-seco-abietane diterpenoids that possess anti-inflammatory bioactivity targeting the pregnane X receptor (PXR). Rubescens A represents the first in a new class of 4,5-seco-abietane diterpenoids, discovered from Isodon. rubescens (I. rubescens). The molecule was discovered with the guidance of molecular ion networking (MoIN) analysis and untargeted pull down experiment. The structure was elucidated and determined using extensive spectroscopic analysis in conjunction with computationally assisted quantifiable structure elucidation tools. In the docking study, Rubescens A binds well to PXR, COX-2 and ATP binding domain of some protein kinases involved in inflammatory pathways. | Zhiwei Bian; Hongyi Li; Jiabao Liu; Xiaoying Liu; Shian Hu; Daneel Ferreira; Mark T. Hamann; Shengpeng Wang; Yeun-Mun Choo; Xiaojuan Wang | Organic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652f845987198ede0785a4fc/original/computationally-assisted-discovery-and-computational-nmr-assignment-of-a-highly-binding-pxr-natural-diterpenoids.pdf |
60c74e70ee301c1165c7a4d0 | 10.26434/chemrxiv.12756395.v1 | Total Synthesis of Putative Structure of Asperipin-2a and Stereochemical Reassignment | The total synthesis of the putative structure of asperipin-2a is described. The synthesis features ether cross-links between the
phenolic oxygen of Tyr6 and β position of Tyr3 and the phenolic oxygen of Tyr3 and the β position of Hpp1 in the unique 17- and 14-membered
bicyclic structure of asperipin-2a, respectively. The synthesized putative structure does not match the natural product and a stereochemical
reassignment is postulated. | SADEGH SHABANIBALAJADEH; JONATHAN WHITE; Craig Hutton | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e70ee301c1165c7a4d0/original/total-synthesis-of-putative-structure-of-asperipin-2a-and-stereochemical-reassignment.pdf |
60c759b9337d6c8fa5e2945f | 10.26434/chemrxiv.13714195.v3 | X-Ray Transient Absorption Reveals the 1Au (Nπ*) State of Pyrazine in Electronic Relaxation | Electronic relaxation in organic chromophores often proceeds via states not directly accessible by photoexcitation. We report on the photoinduced dynamics of pyrazine that involves such states, excited by a 267 nm laser and probed with X-ray transient absorption spectroscopy in a table-top setup. In addition to the previously characterized <sup>1</sup>B<sub>2u</sub> (ππ*) (S<sub>2</sub>) and <sup>1</sup>B<sub>3u</sub> (nπ*) (S<sub>1</sub>) states, the participation of the optically dark <sup>1</sup>A<sub>u</sub> (nπ*) state is assigned by a combination of experimental X-ray core-to-valence spectroscopy, electronic structure calculations, nonadiabatic dynamics simulations, and X-ray spectral computation. Despite <sup>1</sup>A<sub>u</sub> (nπ*) and <sup>1</sup>B<sub>3u</sub> (nπ*) states having similar energies at relaxed geometry, their X-ray absorption spectra differ largely in transition energy and oscillator strength. The <sup>1</sup>A<sub>u</sub> (nπ*) state is populated about 200 femtoseconds after electronic excitation and plays a key role in the relaxation of pyrazine to the ground state. | Valeriu Scutelnic; Shota Tsuru; Mátyás Imre Pápai; Zheyue Yang; Michael Epshtein; Tian Xue; Eric Haugen; Yuki Kobayashi; Anna Krylov; Klaus Braagaard Møller; Sonia Coriani; Stephen Leone | Physical Organic Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759b9337d6c8fa5e2945f/original/x-ray-transient-absorption-reveals-the-1au-n-state-of-pyrazine-in-electronic-relaxation.pdf |
60c745a3337d6c275de27002 | 10.26434/chemrxiv.10079186.v1 | Spontaneous and Template-Directed Emergence of Low-Symmetry Foldamers from Dynamic Homomeric Sequences | Creating large objects from simple subunits rarely results in structures that are of low symmetry as well as of low polydispersity. We now report the spontaneous and uniquely selective oligomerization of simple monomer units into oligomers that are of uniform length, have complex low symmetry structures and are conformationally well-defined. The occurrence of such structures is both frequent and diverse. It is driven by the spontaneous folding into three-dimensional shapes akin to those exhibited by biopolymers. We also show that templates can direct the formation of new functional foldamers. The resulting structures carry imprints of the templates and are therefore capable of binding these. This behavior resembles that of molecularly imprinted polymers (MIPs), with the important distinction that the selected oligomers are uniform and conformationally well-defined, whereas MIPs suffer from heterogeneity in structure, shape and size. | Charalampos Pappas; Pradeep Mandal; Bin Liu; Brice Kauffmann; Xiaoming Miao; David Komaromy; Waldemar Hoffmann; Christian Manz; Rayoon Chang; Kai Liu; Kevin Pagel; Ivan Huc; Sijbren Otto | Bioorganic Chemistry; Combinatorial Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Nanostructured Materials - Materials; Oligomers; Biopolymers; Organic Polymers; Polymer chains; Polymerization (Polymers); Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745a3337d6c275de27002/original/spontaneous-and-template-directed-emergence-of-low-symmetry-foldamers-from-dynamic-homomeric-sequences.pdf |
6697bce401103d79c5416dd9 | 10.26434/chemrxiv-2024-tl9lx | Deciphering the Formation Process of 2D to 3D Halide Perovskite Thin Films | The challenge of obtaining high-performing organo-metal halide perovskite (MHP) thin films of various dimensions for different applications persists. For this purpose, a comprehensive understanding of the growth mechanism and crystallization process of 2D to 3D MHP films during thermal annealing, as the crucial step of most MHP film preparations, is required. Here, we investigate the formation mechanism of MHP which composition varies from 2D to 3D. For this systemic description, eight different initial precursor solution systems and two organic cation spacers have been investigated. They have allowed us to unveil the complex relationship between the growth direction of various phases and the direction of solvent removal. Then, we have comprehensively analyzed the internal structure changes of the MHP low-dimension phases and found a phase splitting phenomenon and revealed a partial spacer elimination during thermal annealing. Our original findings reveal various 2D phase transitions from the film surface to the bottom by a sequential process involving the partial elimination of spacer, phase decomposition, and recrystallization. These generalizable results provide valuable insights for future synthesis optimizations and to produce high-performance MHP film-based devices for a wide range of applications. | Daming Zheng; Karol Vegso; Nada Mrkyvkova; Yuriy Halahovets; Antoine Seyeux; Marie Cresp; Boxue ZHANG; Min Liu; Philippe Marcus; Peter Siffalovic; Thierry Pauporte | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6697bce401103d79c5416dd9/original/deciphering-the-formation-process-of-2d-to-3d-halide-perovskite-thin-films.pdf |
626fb782368ab62766957279 | 10.26434/chemrxiv-2022-bqwk3 | An [FeIII8] molecular oxyhydroxide | An [FeIII8] hexagonal bipyramid, which represents an all ferric piece of molecular magnetite, displays antiferromagnetic exchange between the two capping tetrahedral ions and the six ring octahedral ions resulting in a spin ground state, S = 10. | Euan Brechin; Daniel Cutler; Marco Coletta; Mukesh Singh; Angelos Canaj; Laura McCormick; Simon Coles; Jürgen Schnack | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Transition Metal Complexes (Inorg.) | CC BY 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626fb782368ab62766957279/original/an-fe-iii8-molecular-oxyhydroxide.pdf |
60c752c2469df4a5a4f44c1f | 10.26434/chemrxiv.13341902.v1 | Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of IMP Type Metallo-β-Lactamases | In an attempt to exploit the hydrolytic mechanism by which β-lactamase enzymes degrade cephalosporins, we designed and synthesized a series of novel cephalosporin prodrugs aimed at delivering thiol-based inhibitors of metallo-β-lactamases (MBLs) in spatiotemporally controlled fashion. Notably, while enzyme-mediated hydrolysis of the β-lactam ring was found to occur, it was not accompanied by release of the thiol-based inhibitors. Nonetheless, the cephalosporin prodrugs, especially thiomandelic acid conjugate (<b>8</b>), demonstrated potent inhibition of IMP-type MBLs, with IC<sub>50</sub> values in the nanomolar range. In addition, conjugate <b>8</b> was also found to greatly reduce the MIC of meropenem against an IMP-28 producing clinical isolate of <i>K. pneumoniae</i>. The results of kinetic experiments indicate that these prodrugs inhibit IMP-type MBLs by acting as slowly turned-over substrates. Structure-activity relationship studies revealed that both phenyl and carboxyl moieties of <b>8</b> are crucial for its potency. Furthermore, modeling studies indicate that productive interactions of the thiomandelic acid moiety of <b>8</b> with residues Trp28 and Lys161 within the IMP active site may contribute to the observed inhibitory potency and selectivity. | Kamaleddin Tehrani; Nicola Wade; Vida Mashayekhi; Nora Brüchle; Willem Jespers; Koen Voskuil; Diego Pesce; Matthijs J. van Haren; Gerard van Westen; Nathaniel Martin | Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752c2469df4a5a4f44c1f/original/novel-cephalosporin-conjugates-display-potent-and-selective-inhibition-of-imp-type-metallo-lactamases.pdf |
64949aab24989702c2cbe498 | 10.26434/chemrxiv-2023-nnrc0-v2 | All-Organic Battery Based on Deep Eutectic Solvent and Redox-Active Polymers | Sustainable battery concepts are of great importance for the energy storage demands of the future. Organic batteries based on redox-active polymers are one class of promising storage systems to meet these demands, in particular when combined with environmentally friendly and safe electrolytes. Deep Eutectic Solvents (DESs) represent a class of electrolytes that can be produced from sustainable sources and exhibit in most cases no or only a small environmental impact. Because of their non-flammability, DESs are safe, while providing an electrochemical stability window almost comparable to established battery electrolytes and much broader than typical aqueous electrolytes. Here, we report the first all-organic battery cell based on a DES electrolyte composed of sodium bis(trifluoromethanesulfonyl)imide (NaTFSI) and N-methylacetamide (NMA) alongside the electrode active materials poly(2,2,6,6-tetramethylpiperidin-1-yl-oxyl methacrylate) (PTMA) and crosslinked poly(vinylbenzylviologen) (X-PVBV2+). The resulting cell shows two voltage plateaus at 1.07 V and 1.58 V and achieves Coulombic efficiencies of 98 %. Surprisingly, the X-PVBV/X-PVBV+ redox couple turned out to be much more stable in NaTFSI:NMA 1:6 than the X-PVBV+/X-PVBV2+ couple, leading to asymmetric capacity fading during cycling tests. | Matthias Uhl; . Sadeeda; Philipp Penert; Philipp A. Schuster; Benjamin W. Schick; Simon Muench; Attila Farkas; Ulrich S. Schubert; Birgit Esser; Alexander J. C. Kuehne; Timo Jacob | Physical Chemistry; Polymer Science; Energy; Organic Polymers; Energy Storage; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64949aab24989702c2cbe498/original/all-organic-battery-based-on-deep-eutectic-solvent-and-redox-active-polymers.pdf |
63ee40541d2d184063995388 | 10.26434/chemrxiv-2023-wsx83 | Robust local thickness estimation of sub-micrometer specimen by 4D-STEM | We present a quantitative four-dimensional scanning transmission electron microscopy (4D-STEM)imaging technique (q4STEM) for local thickness estimation across amorphous specimen such asobtained by focused ion beam (FIB)-milling of lamellae for (cryo-)TEM analysis. Our method isbased on measuring spatially resolved diffraction patterns to obtain the angular distribution of electronscattering, or the ratio of integrated virtual dark and bright field STEM signals, and their quantitativeevaluation using Monte Carlo simulations. The method is independent of signal intensity calibrationsand only requires knowledge of the detector geometry, which is invariant for a given instrument.We demonstrate that the method yields robust thickness estimates for sub-micrometer amorphousspecimen using both direct detection and light conversion 2D-STEM detectors in a coincident FIBSEMand a conventional SEM. Due to its facile implementation and minimal dose requirements,we anticipate that this method will find applications for in-situ thickness monitoring during lamellafabrication of beam-sensitive materials. | Radim Skoupy; Daan B. Boltje; Miroslav Slouf; Katerina Mrazova; Tomas Laznicka; Clémence M. Taisne; Vladislav Krzyzanek; Jacob P. Hoogenboom; Arjen J. Jakobi | Analytical Chemistry; Nanoscience; Imaging; Microscopy; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ee40541d2d184063995388/original/robust-local-thickness-estimation-of-sub-micrometer-specimen-by-4d-stem.pdf |
678f6a0ffa469535b9f59b92 | 10.26434/chemrxiv-2025-wl8h1 | Rational Enzyme Evolution by Facilitating Correlated Motion along the Reaction | Enzymes are highly efficient and specific protein catalysts that play an essential role in regulating metabolic processes in living organisms. By modulating the rates of chemical reactions, enzymes tune fundamental essential biological functions. Directed evolution is a widely used strategy to enhance protein functionality by selecting variants with desirable traits through random mutation and recombination. However, this approach often relies heavily on chemical intuition and demands substantial experimental resources, including labor-intensive mutagenesis. In contrast, rational enzyme engineering leverages mechanistic insights to enhance efficiency and reduce costs. This study presents a mutation strategy guided by the correlated motion of protein during enzymatic reactions, validated through four mutations across two proteins. The results underscore the potential of this approach to streamline and advance enzyme evolution. | Lianxin Wang; Yuanfei Xue; Jia-Ning Wang; Yan Mo; Ye Mei | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678f6a0ffa469535b9f59b92/original/rational-enzyme-evolution-by-facilitating-correlated-motion-along-the-reaction.pdf |
66170fe091aefa6ce14b6aba | 10.26434/chemrxiv-2024-qzzm4 | Moldable plastics (polycaprolactone) can be acutely toxic to developing zebrafish and activate nuclear receptors in mammalian cells | Popularized on social media, hand-moldable plastics are formed by consumers into tools, trinkets, and dental prosthetics. Despite the anticipated dermal and oral contact, manufacturers share little information with consumers about these materials. Inherent to their function, moldable plastics pose a risk of dermal and oral exposure to unknown leachable substances. We analyzed 12 moldable plastics advertised for modeling and dental applications and determined them to be polycaprolactone (PCL) or thermoplastic polyurethane (TPU). The bioactivities of the most popular brands advertised for modeling applications of each type of polymer were evaluated using a zebrafish embryo bioassay. Both products were sold as microplastic-sized resin pellets. While water-borne exposure to the TPU pellets did not affect the targeted developmental endpoints at any concentration tested, the PCL pellets were acutely toxic above 1 pellet/mL. Aqueous leachates of the PCL pellets demonstrated similar toxicity. Methanolic extracts from the PCL pellets were assayed for their bioactivity using the Attagene FACTORIAL platform. Of the 69 measured endpoints, the extracts activated nuclear receptors and transcription factors for xenobiotic metabolism (pregnane X receptor, PXR), lipid metabolism (peroxisome proliferator-activated receptor gamma, PPARg), and oxidative stress (nuclear factor erythroid 2-related factor 2, NRF2). By non-targeted high-resolution comprehensive two-dimensional gas chromatography (GC×GC-HRT), we tentatively identified several compounds in the methanolic extracts, including PCL oligomers, a phenolic antioxidant, and residues of suspected anti-hydrolysis and crosslinking additives. In a follow-up zebrafish embryo bioassay, because of its stated high purity, biomedical grade PCL was tested to mitigate any confounding effects due to chemical additives in the PCL pellets; it elicited comparable acute toxicity. From these orthogonal and complementary experiments, we suggest that the toxicity was due to oligomers and nanoplastics released from the PCL rather than chemical additives. These results challenge the perceived and assumed inertness of plastics and highlight their multiple sources of toxicity. | Bryan James; Alexander Medvedev; Sergei Makarov; Robert Nelson; Christopher Reddy; Mark Hahn | Biological and Medicinal Chemistry; Polymer Science; Earth, Space, and Environmental Chemistry; Organic Polymers; Environmental Science; Bioengineering and Biotechnology | CC BY 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66170fe091aefa6ce14b6aba/original/moldable-plastics-polycaprolactone-can-be-acutely-toxic-to-developing-zebrafish-and-activate-nuclear-receptors-in-mammalian-cells.pdf |
635a3f0318a8cc47f85370f1 | 10.26434/chemrxiv-2022-xtrqr-v3 | Elucidating Electrocatalytic Oxygen Reduction Kinetics via Intermediates by Time-Dependent Electrochemiluminescence | Facile evaluation of oxygen reduction reaction (ORR) kinetics for massive electrocatalysts is critical for sustainable fuel cells development and industrial H2O2 production. Despite great success in ORR studies by mainstream strategies, such as membrane electrode assembly, rotation electrode technique and advanced surface-sensitive spectroscopy, the time/spatial distribution of reactive oxygen species (ROS) intermediates in the diffusion layer is still unknown. By time-dependent electrochemiluminescence (Td-ECL), here we report an intermediate-oriented methodology for ORR kinetics analysis. Thanks to multiple ultra-sensitive stoichiometric reactions between ROS and the ECL emitter, except for electron transfer numbers and rate constants, the potential-dependent time/spatial distribution of ROS was successfully obtained for the first time. Such uncovered exclusive information would guide fuel cells and H2O2 production with maximized activity and durability, for instance, a larger overpotential would be beneficial to electrocatalysts of 2e reduction for H2O2 production, because of the high yield of H2O2 and low concentration of attackable O2•. This work would pave the exploration of not only the fundamentals of unambiguous ORR mechanism but also the durability of electrocatalysts for practical applications. | Kaiqing Wu; Ran Chen; Zhixin Zhou; Xinghua Chen; Yanqin Lv; Jin Ma; Yanfei Shen; Songqin Liu; Yuanjian Zhang | Catalysis; Analytical Chemistry; Energy; Electrochemical Analysis; Electrocatalysis; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635a3f0318a8cc47f85370f1/original/elucidating-electrocatalytic-oxygen-reduction-kinetics-via-intermediates-by-time-dependent-electrochemiluminescence.pdf |
60c74e33469df439d4f443fc | 10.26434/chemrxiv.12670901.v2 | Direct Access to Mono-Protected Homoallylic 1,2-Diols via Dual Chromium/ Photoredox Catalysis | <p>A dual
catalytic strategy enables the efficient synthesis of mono-protected
homoallylic 1,2-diols by coupling abundant aldehydes with simple (silyl) enol
ethers, thus providing direct access to this important motif without the
(super)stoichiometric use of prefunctionalized metal-allyl species. A variety
of silyl- and alkyl-based protecting groups is shown and functional group tolerance,
chemoselectivity and scalability are highlighted. </p> | Felix Schäfers; Linda Quach; J. Luca Schwarz; Mar Saladrigas; Constantin G. Daniliuc; Frank Glorius | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Stereochemistry; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e33469df439d4f443fc/original/direct-access-to-mono-protected-homoallylic-1-2-diols-via-dual-chromium-photoredox-catalysis.pdf |
65c4d015e9ebbb4db9ebc595 | 10.26434/chemrxiv-2024-3r7sf | Photochemical Formation and Electronic Structure of an Alkane 𝜎-Complex from Time-Resolved Optical and X-ray Absorption Spectroscopy | C-H bond activation reactions with transition metals typically proceed via the formation of alkane 𝜎-complexes, where an alkane C-H 𝜎-bond binds to the metal. Due to the weak nature of metal-alkane bonds, 𝜎-complexes are challenging to characterize experimentally. Here, we photochemically prepare the model 𝜎-complex Cr(CO)5-alkane from Cr(CO)6 in octane solution and characterize the nature of its metal-ligand bonding interactions. Using femtosecond optical absorption spectroscopy, we find photo-induced CO dissociation from Cr(CO)6 to occur within the 100 fs time-resolution of the experiment. Rapid geminate recombination by a fraction of molecules is found to occur with a time constant of 150 fs. The formation of bare Cr(CO)5 in its singlet ground state is followed by complexation of an octane molecule from solution with a time constant of 8.2 ps. Picosecond X-ray absorption spectroscopy at the Cr L-edge and O K-edge provides unique information on the electronic structure of the Cr(CO)5-alkane 𝜎-complex both from the metal and ligand perspectives. We find substantial destabilization of the lowest unoccupied molecular orbital upon coordination of the C-H bond to the undercoordinated Cr center in the Cr(CO)5-alkane 𝜎-complex, accompanied with rehybridization between metal and ligand orbitals. Our study demonstrates the value of combining optical and X-ray spectroscopic methods as complementary tools to study the properties of alkane 𝜎-complexes as the decisive intermediates in C-H bond activation reactions. | Raphael Jay; Michael R. Coates; Huan Zhao; Marc-Oliver Winghart; Peng Han; Ru-Pan Wang; Jessica Harich; Ambar Banerjee; Hampus Wikmark; Mattis Fondell; Erik T. J. Nibbering; Michael Odelius; Nils Huse; Philippe Wernet | Physical Chemistry; Organometallic Chemistry; Bond Activation; Spectroscopy (Organomet.); Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c4d015e9ebbb4db9ebc595/original/photochemical-formation-and-electronic-structure-of-an-alkane-complex-from-time-resolved-optical-and-x-ray-absorption-spectroscopy.pdf |
60c74cc5469df42772f44141 | 10.26434/chemrxiv.12532301.v1 | Accelerating Biocatalytic Hydrogenations using the H-Cube Flow Reactor | Translation of redox biocatalysis into a commercial H-Cube hydrogenation flow reactor was achieved using immobilized enzyme systems for biocatalytic hydrogenations. Carbon-supported enzymes for H2-driven NADH recycling and NADH-dependent C=O reductions were handled comparably to supported metal catalysts. High activity at room temperature with 2 bar H2 was attained, highlighting that biocatalytic strategies enable implementation of hydrogenation reactions under mild conditions. High conversions were achieved in short residence times (< 2 s), with high biocatalyst turnover frequencies (1,420 min-1) and space-time yields (7.9 kg L-1 h-1). These results represent the first example of direct biocatalytic hydrogenation in a commercial flow reactor. | Barnabas Poznansky; Lisa Thompson; Holly Reeve; Kylie Vincent | Process Chemistry; Biocatalysis; Heterogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cc5469df42772f44141/original/accelerating-biocatalytic-hydrogenations-using-the-h-cube-flow-reactor.pdf |
60c7555af96a000bb6288857 | 10.26434/chemrxiv.14095931.v1 | Temperature Dependent Anomalous Mn2+ Emission and Excited State Dynamics in Mn2+-Doped MAPbCl3-xBrx Nanocrystals | In hybrid perovskites, MAPbI<sub>3</sub> and MAPbBr<sub>3</sub> have been extensively studied for their optical and photovoltaic properties, but MAPbCl<sub>3</sub> is significantly less investigated for its optical and photovoltaic properties due to its low photoluminescence quantum yield (PL QY) and a large<br />band gap. However, the large band gap makes it a suitable host for doping transition metal ions to explore new optical properties. We synthesized nanocrystals (NCs) of MAPbCl<sub>3</sub> doped with Mn<sup>2+</sup> by simple ligand assisted reprecipitation method. The reaction temperature and Pb to Mn feed ratio were optimized by preparing a series of Mn<sup>2+</sup>-doped MAPbCl<sub>3</sub> NCs. The prepared NCs show bright Mn<sup>2+</sup> emission with ~13% PL QY suggesting an efficient energy transfer from host NCs to Mn<sup>2+</sup>. Since the large bandgap of MAPbCl3 precludes the possibility of investigating temperature dependent PL and lifetime measurements to understand the excited state dynamics, we carried out these experiments on Mn<sup>2+</sup> doped MAPbCl<sub>2.7</sub>Br<sub>0.3</sub> with the Br concentration adjusted to bring the bandgap of the alloyed system within the limits of the experimental technique. Our studies establish an anomalous behavior of Mn<sup>2+</sup> PL emission in this host. These results reveal the origin of a temperature mediated energy transfer from exciton to Mn<sup>2+</sup> and provides an understanding of the underlying mechanisms of PL properties of this new class of NCs.
<br /> | Bhushan Kore; Shyamashis Das; D. D. Sarma | Hybrid Organic-Inorganic Materials; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7555af96a000bb6288857/original/temperature-dependent-anomalous-mn2-emission-and-excited-state-dynamics-in-mn2-doped-ma-pb-cl3-x-brx-nanocrystals.pdf |
660184919138d23161408522 | 10.26434/chemrxiv-2024-kk8l6 | A Triazolium-Based Fluorophore Intercalated in Layered Double Hydroxides: from Simple Syntheses to Bright Solid-State Luminescence | This study presents the intercalation into Layered Double Hydroxides (LDHs) of two sulfonated organic molecules featuring the mesoionic triazolium scaffold. These sulfonated fluorophores exhibited excellent solubility in aqueous basic solutions, facilitating their compatibility with the synthesis of LDHs through coprecipitation methods. We applied the size-matching interlayer space (SMIS) approach by substituting a portion of a mono- or dianionic surfactant used in LDHs preparation by the sulfonated fluorophore, we aimed to match the size of the luminescent interleaved guest effectively. Our investigation focused on two anion spacers: the classic monoanionic dodecyl sulfate (DS) and the dianionic phenylene dipropionate (PPA). Our results indicated that the latter spacer allowed a more efficient insertion of the fluorescent guest. Thermal resistance analysis underscored the robustness of the final hybrid materials, suggesting a promising design strategy for luminescent materials when applied in diverse applications. | Guillaume Zerbib; Amélie Roux; Laurène Salat; Federico Cisnetti; Damien Boyer; Geneviève Chadeyron; Fabrice Leroux | Organic Chemistry; Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660184919138d23161408522/original/a-triazolium-based-fluorophore-intercalated-in-layered-double-hydroxides-from-simple-syntheses-to-bright-solid-state-luminescence.pdf |
6532693987198ede07e0f7e8 | 10.26434/chemrxiv-2023-94j3x | PET Functional Upcycling through Surface-Assisted Growth of Ni-BDC MOFs and Laser-Induced Carbonization towards Bend Resistive Sensor | The growing accumulation of waste polyethylene terephthalate (PET) presents a significant environmental challenge requiring the development of sustainable recycling methods. In this study, we propose a novel approach for upcycling PET waste into bend resistive sensors through laser-assisted carbonization of surface-grown Ni-BDC (BDC = 1,4-benzenedicarboxylate). The fabrication process involves the solvothermal formation of a homogeneous Ni-BDC layer, followed by treatment with a 405 nm laser system to create a graphene-like layer with enhanced conductivity (sheet resistance 6.2 ± 3.4 Ω per square). The developed sensor demonstrates remarkable robustness, a linear response in a wide bending angle range (6 to 44º), as well as excellent mechanical stability and stiffness. This contribution paves the way for the development of cost-effective and eco-friendly devices based on low-cost polymer waste as a resource for applications in the Internet of Things. | Dmitry Kogolev; Ekaterina Kurtsevich; Maxim Fatkullin; Alexey Zinovyev; Alina Gorbunova; Raul Rodriguez; Olga Guselnikova; Rabah Boukherroub; Pavel Postnikov | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Wastes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6532693987198ede07e0f7e8/original/pet-functional-upcycling-through-surface-assisted-growth-of-ni-bdc-mo-fs-and-laser-induced-carbonization-towards-bend-resistive-sensor.pdf |
612934fdac3219aac06a6d9d | 10.26434/chemrxiv-2021-f4dh4 | Metal-organic frameworks induce hypergolic ignition of bulk metals | We demonstrate the unprecedented ability to induce hypergolic behavior, i.e. rapid and spontaneous ignition upon contact with an oxidizer, in non-hypergolic metal fuels by blending them with hypergolic metal-organic frameworks (HMOFs). Using magnesium, aluminum or zinc metal as the fuel, we demonstrate materials with ignition delays (IDs) below 50 ms, and calculated specific impulse (Isp) in the 220-250 s range. These parameters are comparable to those of toxic and carcinogenic hydrazine-based hypergols conventionally used in aerospace technologies, suggesting a route to develop cleaner, safer propulsion systems. | Hatem Titi; Joseph Marrett; Olivier Jobin; Cristina Mottillo; Blaine Fiss; Audrey Moores; Étienne Robert; Robin Rogers; Tomislav Friscic | Energy; Earth, Space, and Environmental Chemistry; Space Chemistry; Fuels - Energy Science; Power; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612934fdac3219aac06a6d9d/original/metal-organic-frameworks-induce-hypergolic-ignition-of-bulk-metals.pdf |
6781474d81d2151a029a82d6 | 10.26434/chemrxiv-2025-n24f8 | Permeation Enhancer-Induced Membrane Defects Assist the Oral Absorption of Peptide Drugs | The passive membrane permeation of small-molecule drugs and relatively small hydrophobic peptides is relatively well understood. In contrast, how long polar peptides can directly pass through a membrane has remained a mystery. This process can be achieved with transcellular permeation enhancers, contributing significantly to the oral transcellular absorption of important peptide drugs like semaglutide — the active component in Ozempic, which is used as Rybelsus in a successful oral formulation. Here we now provide, for the first time, a detailed, plausible molecular mechanism of how such a polar peptide can realistically pass through a membrane paired with the permeation enhancer salcaprozate sodium (SNAC). We provide not only simulation results, obtained with scalable continuous constant pH molecular dynamics (CpHMD) simulations, but also experimental evidence (NMR, DOSY, and DLS) to support this unique passive permeation mechanism. Our computational and experimental evidence points toward the formation of permeation-enhancer-filled, fluid membrane defects, in which the polar peptide can be submerged in a process analogous to sinking in quicksand. | Severin T. Schneebeli; Kyle J. Colston; Kyle T. Faivre | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Theory - Computational; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2025-01-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6781474d81d2151a029a82d6/original/permeation-enhancer-induced-membrane-defects-assist-the-oral-absorption-of-peptide-drugs.pdf |
60c744e8ee301c513dc791ea | 10.26434/chemrxiv.9923642.v1 | Sulfur- and Nitrogen-Containing Porous Donor-Acceptor Polymers as Real-Time Optical and Chemical Sensors | Fully aromatic, organic polymers have the advantage
of being composed from light, abundant elements, and are hailed as candidates
in electronic and optical devices “beyond silicon”, yet, applications that make
use of their π-conjugated backbone and optical bandgap are lacking outside of
heterogeneous catalysis. Herein, we use a series of sulfur- and
nitrogen-containing porous polymers (SNPs) as real-time optical and electronic
sensors reversibly triggered and re-set by acid and ammonia vapors. Our SNPs
incorporate donor-acceptor and donor-donor motifs in extended networks and
enable us to study the changes in bulk conductivity, optical bandgap, and
fluorescence life-times as a function of π-electron de-/localization in the pristine
and protonated states. Interestingly, we find that protonated donor-acceptor
polymers show a decrease of the optical bandgap by 0.42 eV to 0.76 eV and
longer fluorescence life-times. In contrast, protonation of a donor-donor polymer
does not affect its bandgap; however, it leads to an increase of electrical conductivity
by up to 25-fold and shorter fluorescence life-times. The design strategies
highlighted in this study open new avenues towards useful chemical switches and
sensors based on modular purely organic materials. | Yaroslav S. Kochergin; Yu Noda; Ranjit Kulkarni; Klára Škodáková; Ján Tarábek; Johannes Schmidt; Michael J. Bojdys | Optical Materials; Conducting polymers; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2019-10-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744e8ee301c513dc791ea/original/sulfur-and-nitrogen-containing-porous-donor-acceptor-polymers-as-real-time-optical-and-chemical-sensors.pdf |
649bfa29ba3e99daef2d9aae | 10.26434/chemrxiv-2023-gkl0q-v2 | Symmetric 4,6-Dialkyl/arylamino-5-nitropyrimidines: Theoretical Explanation of Why Aminolysis of Alkoxy Groups Is Favoured over Chlorine Aminolysis in Nitro-Activated Pyrimidines. | A new synthetic route to obtain symmetric disubstituted alkyl/arylaminopyrimidines under mild conditions is presented, which can be used to generate new purine libraries for drug discovery. We investigated the unexpected reaction of 6-alkoxy-4-chloro-5-nitropyrimidines with primary amines, which produced disubstituted dialkyl/arylamine pyrimidines instead of the expected 6-alkoxy-4-alkylamine-5-nitropyrimidines. To clarify this reaction, a computational study of the reaction mechanism was carried out. Our results suggest that the presence of pre-reactive molecular complexes, a phenomenon rarely reported in SNAr reactions, precedes the transition state and can facilitate the reaction. In addition, Meisenheimer complexes and transition states in the intrinsic reaction coordinate (IRC) configuration, which may influence the understanding of the reaction mechanism, were identified.
| Laura Cordoba Gomez; Alvaro Lorente-Macias; Maria Jose Pineda de las Infantas y Villatoro ; Andres Garzon-Ruiz; Juan J. Diaz-Mochon | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649bfa29ba3e99daef2d9aae/original/symmetric-4-6-dialkyl-arylamino-5-nitropyrimidines-theoretical-explanation-of-why-aminolysis-of-alkoxy-groups-is-favoured-over-chlorine-aminolysis-in-nitro-activated-pyrimidines.pdf |
67d861cffa469535b98c491a | 10.26434/chemrxiv-2025-z2bkd | Design of new thorium nuclear clock materials based on polyatomic ions | Compounds of polyatomic anions are investigated theoretically as hosts for thorium in nuclear clock devices. The 229Th nucleus has an excited state at 8.355 eV which can be reached using a VUV laser as demonstrated in recent experiments. Incorporating 229Th into a host crystal is an essential step towards developing an ultra-stable nuclear clock. To be a suitable host, a material must have a band gap larger than the nuclear transition frequency. Thus, most research to date has focused on fluorides like LiSrAlF6 and CaF2, for they feature ionic bonding and large band gaps. However, ionicity of chemical bonding can be pushed to its limits by use of superhalogens - polyatomic anions whose electron affinity can be greater than that of the halogens. An additional concern for fluorides is the presence of 19F nuclear spins in the material that can couple to the spin of the 229Th, detrimental to clock performance. In this work we investigate salts containing superhalogen anions, with the goal of identifying promising new hosts for 229Th clocks. Specifically, we investigate compounds of Ca, Sr, and Ba with three anions - [BF4]- , [ClO4]- , and [SO4]2- . By computing the electronic properties of the pure and thorium-doped materials, we predict that M(BF4)2 have the widest band gaps, making them a promising materials class. On the other hand, MSO4 could produce the most accurate clocks by eliminating inhomogeneous broadening due to nuclear spin interactions. These results may guide experimental searches for new 229Th clock materials and offer new opportunities to study this unique nuclear transition in the solid state. | Harry Morgan; Hoang Bao Tran Tan; Andrei Derevianko; Ricky Elwell; James Terhune; Eric Hudson; Anastassia Alexandrova | Theoretical and Computational Chemistry; Inorganic Chemistry; Nuclear Chemistry; Solid State Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d861cffa469535b98c491a/original/design-of-new-thorium-nuclear-clock-materials-based-on-polyatomic-ions.pdf |
668e5baf01103d79c597e0b2 | 10.26434/chemrxiv-2024-r9ljm-v2 | Evaluation of Reinforcement Learning in
Transformer-based Molecular Design | Designing compounds with a range of desirable properties is a fundamental challenge in drug discovery. In
pre-clinical early drug discovery, novel compounds are often designed based on an already existing promising
starting compound through structural modifications for further property optimization. Recently,
transformer-based deep learning models have been explored for the task of molecular optimization by training
on pairs of similar molecules. This provides a starting point for generating similar molecules to a given input
molecule, but has limited flexibility regarding user-defined property profiles. Here, we evaluate the effect of
reinforcement learning on transformer-based molecular generative models. The generative model can be
considered as a pre-trained model with knowledge of the chemical space close to an input compound, while
reinforcement learning can be viewed as a tuning phase, steering the model towards chemical space with
user-specific desirable properties. The evaluation of two distinct tasks - molecular optimization and scaffold
discovery - suggest that reinforcement learning could guide the transformer-based generative model towards
the generation of more compounds of interest. Additionally, the impact of pre-trained models, learning steps
and learning rates are investigated.
Scientific Contribution:
Our study investigates the effect of reinforcement learning on a transformer-based generative model initially
trained for generating molecules similar to starting molecules. The reinforcement learning framework is applied
to facilitate multiparameter optimisation of starting molecules. This approach allows for more flexibility for
optimizing user-specific property profiles and helps finding more ideas of interest. | Jiazhen He; Alessandro Tibo; Jon Paul Janet; Eva Nittinger; Christian Tyrchan; Werngard Czechtizky; Ola Engkvist | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668e5baf01103d79c597e0b2/original/evaluation-of-reinforcement-learning-in-transformer-based-molecular-design.pdf |
6515ca3f00659409120f31a5 | 10.26434/chemrxiv-2023-qq029 | Thermally Activated Delayed Fluorescence Emitters Showing Wide-Range Near-infrared Piezochromism and their use in Deep-Red OLEDs | Organic small molecules exhibiting both thermally activated delayed fluorescence (TADF) and wide-ranging piezochromism (∆λ > 150 nm) in the near-infrared region have rarely been reported in the literature. We present three emitters MeTPA-BQ, tBuTPA-BQ and TPPA-BQ based on a hybrid acceptor, benzo[g]quinoxaline-5,10-dione, that emit via TADF, having photoluminescence quantum yields, ΦPL, of 39-42% at photoluminescence (PL) maxima, λPL, of 625-670 nm in 2 wt% doped films in 4,4′-bis(N-carbazolyl)-1,1′-biphenyl (CBP). Despite their similar chemical structures, the PL properties in the crystalline states of MeTPA-BQ (λem = 735 nm, ΦPL = 2%) and tBuTPA-BQ (λem = 657 nm, ΦPL = 11%) are significantly different. Further, compounds tBuTPA-BQ and TPPA-BQ showed a significant PL shift of ~98 and ~165 nm upon grinding of the crystalline samples, respectively. Deep-red organic light-emitting diodes with MeTPA-BQ and tBuTPA-BQ were also fabricated, which showed maximum external quantum efficiencies, EQEmax, of 10.1% (λEL = 650 nm) and 8.5% (λEL= 670 nm), respectively. | Sudhakar Pagidi; Abhishek Kumar Gupta; David Cordes; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6515ca3f00659409120f31a5/original/thermally-activated-delayed-fluorescence-emitters-showing-wide-range-near-infrared-piezochromism-and-their-use-in-deep-red-ole-ds.pdf |
60c75139567dfe61c0ec59f3 | 10.26434/chemrxiv.13135769.v1 | A Bi-Functional Polymeric Coating for the Co-Imobilization of Proteins and Peptides on Microarray Substrates | The analytical performance of the microarray technique in screening the affinity and reactivity of several probes towards a specific target, is highly affected by the coupling chemistry adopted to bind probes to the surface. However, the surface functionality limits the biomolecules that can be attached to the surface to a single type of molecule (DNA, protein, or peptide), thus forcing the execution of separate analyses to compare the performance of different species in recognizing their targets. Here we introduce a new N, N-dimethylacrylamide-based polymeric coating, bearing simultaneously different functionalities (N-acryloyloxysuccinimide and azide groups) to allow an easy and straightforward method to co-immobilize proteins and oriented peptides on the same substrate. The bi-functional copolymer has been obtained by partial post polymerization modification of the functional groups (NAS) of a common precursor. A deep characterization of the copolymer was carried out by means of NMR to quantify the percentage of NAS that has been transformed into azido groups. The polymer was then used to coat surfaces onto which both native antibodies and alkyne modified peptides were immobilized, to perform the phenotype characterization of extracellular vesicles (EVs). Ultimately, this strategy represents a convenient method to reduce the number of analysis, thus possible systematic or random errors, besides offering a drastic shortage in time, reagents and costs. | Laura Sola; Dario Brambilla; Alessandro Mussida; Roberto Consonni; Francesco Damin; Marina Cretich; Alessandro Gori; Marcella Chiari | Coating Materials; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75139567dfe61c0ec59f3/original/a-bi-functional-polymeric-coating-for-the-co-imobilization-of-proteins-and-peptides-on-microarray-substrates.pdf |
67aa0e7afa469535b9beda77 | 10.26434/chemrxiv-2025-ddpk3 | Ferrocene-containing tetrahydropyridazines via domino chemistry | Since its discovery over 70 years ago, ferrocene has played a pivotal role in nearly every facet of synthetic chemistry, spanning materials science to medicinal chemistry. The unique properties of ferrocene and its derivatives have unsurprisingly made them privileged structures in asymmetric catalysis, the synthesis of biologically active compounds, and components for organoelectronics. In this work, we present a straightforward method for synthesizing ferrocene-based tetrahydropyridazines via a one-pot, base-catalyzed domino condensation of 4-chloro-1-ferrocenylbutan-1-one with monosubstituted hydrazines. Methanol was identified as the optimal solvent for reactions with arylhydrazines, while benzene yielded the best results for reactions involving alkylhydrazines. | Kyrylo Tymoshenko; Svitlana Shishkina; Vitalii Palchykov | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Base Catalysis; Crystallography – Organic | CC BY NC 4.0 | CHEMRXIV | 2025-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aa0e7afa469535b9beda77/original/ferrocene-containing-tetrahydropyridazines-via-domino-chemistry.pdf |
63e155a1805bad91da1ebfe7 | 10.26434/chemrxiv-2022-5xr00-v3 | Temperature Dependence of the Relative Rates of Chlorination and Hydrolysis of N2O5 in NaCl-Water Solutions. | We have measured the temperature dependence of the ClNO<sub>2</sub> product yield in competition with hydrolysis following N<sub>2</sub>O<sub>5</sub> uptake to aqueous NaCl solutions. For NaCl-D<sub>2</sub>O solutions spanning 0.0054 M to 0.21 M, the ClNO<sub>2</sub> product yield decreases on average by only 43 % from 5 to 25 C. Less reproducible measurements at 0.54 M and 2.4 M NaCl also fall within this range. The ratio of the rate constants for chlorination and hydrolysis of N<sub>2</sub>O<sub>5</sub> in D<sub>2</sub>O is determined on average to be 1150±90 at 25 C up to 0.21 M NaCl, favoring chlorination. This ratio is observed to decrease significantly at the two highest concentrations. An Arrhenius analysis reveals that the activation energy for hydrolysis is just 3.0±1.5 kJ/mol larger than for chlorination up to 0.21 M, indicating that Cl<sup>-</sup> and D<sub>2</sub>O attack on N<sub>2</sub>O<sub>5</sub> have similar energetic barriers despite the differences in charge and complexity of these reactants. In combination with the measured pre-exponential ratio favoring chlorination of {300\ }_{-200}^{+400}, we conclude that the strong preference of N<sub>2</sub>O<sub>5</sub> to undergo chlorination over hydrolysis is driven by dynamic and entropic, rather than enthalpic, factors. Molecular dynamics simulations elucidate the distinct solvation between strongly hydrated Cl<sup>-</sup> and the hydrophobically solvated N<sub>2</sub>O<sub>5</sub>. Combining this molecular picture with the Arrhenius analysis implicates the role of water in mediating interactions between such distinctly solvated species and suggests a role for diffusion limitations on the chlorination reaction. | Steven J. Kregel; Thomas F. Derrah; SeokJin Moon; David T. Limmer; Gilbert M. Nathanson; Timothy H. Bertram | Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Chemical Kinetics; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e155a1805bad91da1ebfe7/original/temperature-dependence-of-the-relative-rates-of-chlorination-and-hydrolysis-of-n2o5-in-na-cl-water-solutions.pdf |
65cf4b5266c1381729c8d11f | 10.26434/chemrxiv-2024-df1wk | A straightforward method to prevent the under-estimated problem of aspartimide formation during chemical ligation-mediated protein synthesis | Formation of a five-membered ring aspartimide through the attack of a backbone amide to the side chain of aspartate and asparagine residues is a long-known side-reaction in solid phase peptide synthesis, and is also associated with in vivo protein ageing and instability of purified proteins. Conversely, its possible occurrence during chemical ligation-based protein synthesis, in particular when using the gold-standard reaction NCL (native chemical ligation), is dubious. We herein report a systematic study which demonstrates that the prevalence of this side-reaction may have been overlooked, due to the difficulty to identify it through standard HPLC analytical methods, but also the in situ conversion of aspar-timide into other byproducts, having the same molecular mass as the parent aspartate residue. We show that the for-mation of aspartimide and related byproducts can be limited by adopting "good NCL practices", which involve restricting the ligation temperature and reaction times, as well as replacing the commonly used phosphate buffer with HEPES. How-ever, the efficiency of such precautions is expected to vary considerably depending on the sequence of the target protein, and the amount of byproducts is expected to grow with the length of the target protein, as a result of the number of NCL reactions and potential aspartimide hotspots. To overcome such limitations, we developed a novel straightforward and potentially generally applicable methodology based on the temporary protection of the backbone nitrogen by a 2-(4-aminobutanoyloxy)-4-methoxybenzyl (GABA-Hmb) group. This strategy was validated by the byproduct-free synthesis of SUMO-2 and a SUMOylated peptide mimic. | El hadji Cisse; Vincent Aucagne | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cf4b5266c1381729c8d11f/original/a-straightforward-method-to-prevent-the-under-estimated-problem-of-aspartimide-formation-during-chemical-ligation-mediated-protein-synthesis.pdf |
664ca8ab91aefa6ce1974d55 | 10.26434/chemrxiv-2024-j230b-v2 | Direct excitation of carbonyl cyclopropanes: From divergent photo-isomerization and annulation to unified reductive C-C cleavage | We report herein our studies on the direct photoactivation of carbonyl cyclopropanes to give biradical intermediates, leading to selective cleavage of the more substituted carbon-carbon bond. Depending on the substrate structure, extended alkenes were isolated or directly reacted in a photo-Nazarov process to give bicyclic products. Based on these results, a unified reductive ring-opening reaction was developed by using diphenyl disulfide as a HAT reagent. By performing a sequential cyclopropanation/selective ring opening reaction, we achieved a CH2 insertion into the alpha,beta- bond of both acyclic and cyclic unsaturated carbonyl compounds. Our protocol therefore provides a further tool for framework-editing of carbocycles, complementing the recent progress in "skeletal editing" strategies. | Tin V. T. Nguyen; André Bossonnet; Duncan K. Brownsey; Matthew D. Wodrich; Jerome Waser | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664ca8ab91aefa6ce1974d55/original/direct-excitation-of-carbonyl-cyclopropanes-from-divergent-photo-isomerization-and-annulation-to-unified-reductive-c-c-cleavage.pdf |
651fd533bda59ceb9afbcd75 | 10.26434/chemrxiv-2023-kmhbg | Electronic Properties Modulation of NiFe-based Nanoalloy by Introducing Cu and P for Faster Oxygen Evolution Reaction Kinetics | NiFe-based structures are well known for their high Oxygen Evolution Reaction (OER) activity. But, over time, because of Fe dissolution from these structures, activity and stability decreases gradually. In this work, we have presented a one-pot facile way to introduce Cu and P centres in a NiFe-based nanoalloy to get novel transition metal-based hierarchical nanostructures that show enhanced catalytic activity as well as remarkable stability. As evident from electron micrographs (EMs) followed by Electrochemically Active Surface Area (EASA) calculations, the introduction of Cu and P increases the active surface area compared to NiFe nanoalloy. Understanding the relationship between the local geometry of catalytically active sites and the OER activity is an invincible step for more advanced material fabrication. By studying X-ray Photoelectron Spectroscopy (XPS), X-ray Absorption Near Edge Structure (XANES), and Extended X-ray Absorption Fine Structure (EXAFS) of these materials, we understood the modulation of electronic properties of NiFe-based nanoalloy by introducing Cu and P centres within it. This electronic modulation of the newly developed hierarchical structures results in faster OER kinetics with an overpotential of 213 mV at a current density of 10 mA/cm2. Moreover, electrochemical studies clearly justify that all metal centres (i.e., Ni, Fe, and Cu) are positively participating in the OER kinetics. | Arpita Nandy; Tanmay Ghosh; Ravi Kumar; Dibyendu Bhattacharyya; Dulal Senapati | Materials Science; Catalysis; Energy; Catalysts; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651fd533bda59ceb9afbcd75/original/electronic-properties-modulation-of-ni-fe-based-nanoalloy-by-introducing-cu-and-p-for-faster-oxygen-evolution-reaction-kinetics.pdf |
679832fd81d2151a02399fd4 | 10.26434/chemrxiv-2025-btg3j | Microstructure-Dependent Sodium Storage Mechanisms in Hard Carbon Anodes | Hard carbon (HC) is a leading anode material for sodium-ion batteries, but its complex microstructure complicates understanding of sodium storage mechanisms. Using X-ray total scattering and density functional theory calculations, this study clarifies how HC’s microstructural variations influence sodium storage across the slope (high potential) and plateau (low potential) regions of the potential-capacity curve. In the slope region, sodium initially adsorbs at high-binding energy defect sites and subsequently intercalates between graphene layers, adsorbing at low-binding energy defect sites, correlating with different slopes observed during initial sodiation. Initial irreversibility arises from sodium trapping at surface defects and solid electrolyte interface formation. In the plateau region, sodium simultaneously intercalates and fills pores, influenced by pore size, interlayer spacing, and defect concentration. HCs with larger pore sizes form larger sodium clusters. The proposed mechanism underscores the role of microstructure engineering in enhancing HC performance and advancing sodium-ion batteries for grid-scale energy storage. | Luis Kitsu Iglesias; Samuel Marks; Nikhil Rampal; Emma Antonio; Rafael Ferreira de Menezes; Liang Zhang; Daniel Olds; Stephen Weitzner; Kayla Sprenger; Liwen Wan; Michael Toney | Physical Chemistry; Materials Science; Energy; Carbon-based Materials; Energy Storage; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679832fd81d2151a02399fd4/original/microstructure-dependent-sodium-storage-mechanisms-in-hard-carbon-anodes.pdf |
66277b4a91aefa6ce12cc963 | 10.26434/chemrxiv-2023-0gs2b-v2 | Characterization of the bottlenecks and pathways for inhibitor dissociation from [NiFe] hydrogenase | [NiFe] hydrogenases can act as efficient catalysts for hydrogen oxidation and biofuel production. However, some [NiFe] hydrogenases are inhibited by gas molecules present in the environment, such as O2 and CO. One strategy to engineer [NiFe] hydrogenases and achieve O2 and CO-tolerant enzymes is by introducing point mutations to block the access of inhibitors to the catalytic site. In this work, we characterized the unbinding pathways of CO in complex with the wild type and 10 different mutants of [NiFe] hydrogenase from Desulfovibrio fructosovorans using τ-Random Accelerated Molecular Dynamics (τRAMD) to enhance the sampling of unbinding events. The ranking provided by the relative residence times computed with τRAMD is in agreement with experiments. Extensive data analysis of the simulations revealed that, from the two bottlenecks proposed in previous studies for the transit of gas molecules (residues 74 and 122, and residues 74 and 476), only one of them (residues 74 and 122) effectively modulates diffusion and residence times for CO. We also computed pathway probabilities for the unbinding of CO, O2 and H2 from the wild type [NiFe] hydrogenase and we observed that, while the most probable pathways are the same, the secondary pathways are different. We propose that introducing mutations to block the most probable paths, in combination with mutations to open the main secondary path used by H2, can be a feasible strategy to achieve CO and O2 resistance in the [NiFe] hydrogenase from Desulfovibrio fructosovorans. | Farzin Sohraby; Ariane Nunes Alves | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66277b4a91aefa6ce12cc963/original/characterization-of-the-bottlenecks-and-pathways-for-inhibitor-dissociation-from-ni-fe-hydrogenase.pdf |
65a87d47e9ebbb4db9689d4b | 10.26434/chemrxiv-2024-cx9rk | Photoinduced Luminescence Activation of Hydrophilic ‘Caged’ Carbons Dots | As part of our efforts to develop nanomaterials with tunable optical properties, we devised a synthetic protocol to photoactivate the luminescence of hydrophilic carbon dots by ‘caging’ the nanostructures with photocleavable 2-nitrobenzyl quenchers. Photoremovable 2-nitrobenzyl groups can be attached covalently to the surface of the carbon dots via amide-bond formation. We show that 2-nitrobenzyls efficiently quench the emission intensity of the resulting nanoconstructs and that the luminescence can be activated upon ultraviolet illumination in solution. In addition, the carbon dots can be internalized by living cells and used as bioimaging agents. | Aviya Akari; Maria Narciso; Emmanuel Fagbohun; Roberto Botelho; Stefania Impellizzeri | Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a87d47e9ebbb4db9689d4b/original/photoinduced-luminescence-activation-of-hydrophilic-caged-carbons-dots.pdf |
6662953421291e5d1d41890e | 10.26434/chemrxiv-2024-5f7nj | Bespoke All-in-one Metallaphotoredox Heterogeneous Catalysts for C-C Cross-Couplings | In synergistic catalysis, multiple catalysts or active sites work together to produce ‘the whole is greater than the sum of its parts’ effect. However, the trilemma of flexibility-stability-cost lies ahead of the multiunit heterogeneous catalyst. As complexity increases, the catalytic efficiency tends to be restricted. Here, we report a general method to tailor modular metallaphotoredox catalysts. The dyes and molecular catalysts could flexibly connect with inexpensive carbon nitride via stable covalent bonds, like LEGO® games. Tunable visible-light absorption, high electron-hole separation efficiency and steerable construction of catalytic active sites have been realized simultaneously, meanwhile the electron transfer mechanism has been clarified via operando techniques. By precisely regulating the coordination field of single-atom sites, four different metallaphotoredox-enabled C-C cross-couplings could be compatible with good cyclic stability (up to 150 hours) and anti-interference ability. | Menglong Ma; Xiaoyu Wang; Chengzhi Wang; Muhong Wang; Yingxin Huang; Yi Li; Fengying Zhang; Ying Zhou; Yu Jiang; Haoyue Sun; Jinming Wang; Xu Zhang; Kun Zheng; Weifeng Huang; Li An; Dan Qu; Xiayan Wang; Liu Yichang; Zaicheng Sun | Organic Chemistry; Catalysis; Nanoscience; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6662953421291e5d1d41890e/original/bespoke-all-in-one-metallaphotoredox-heterogeneous-catalysts-for-c-c-cross-couplings.pdf |
60c75348bb8c1a75783dbff8 | 10.26434/chemrxiv.13469985.v1 | Direct Air Capture of CO2 with Aqueous Peptides and Crystalline Guanidines | Negative emission technologies, including direct air capture (DAC) of carbon dioxide, are now considered essential for mitigating climate change, but existing DAC processes tend to have excessively high energy requirements, mostly associated with sorbent regeneration. Here we demonstrate a new approach to DAC that combines atmospheric CO<sub>2</sub> absorption by an aqueous oligopeptide (i.e., glycylglycine) with bicarbonate crystallization by a simple guanidine compound (i.e., glyoxal-bis-iminoguanidine). In this phase-changing system, the peptide and the guanidine compounds work in synergy, and the cyclic CO<sub>2</sub> capacity can be maximized by matching the p<i>K</i><sub>a</sub> values of the two components. The resulting DAC process has a significantly lower regeneration energy compared to state-of-the-art solvent-based DAC technologies. | Radu Custelcean; Kathleen A. Garrabrant; Pierrick Agullo; Neil J. Williams | Physical Organic Chemistry; Environmental Science; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75348bb8c1a75783dbff8/original/direct-air-capture-of-co2-with-aqueous-peptides-and-crystalline-guanidines.pdf |
64f6fd20dd1a73847f3b3c7e | 10.26434/chemrxiv-2023-2zv1h | New RM734-like Fluid Ferroelectrics Enabled through Protecting Group Free Synthesis | We report a novel synthetic procedure for making analogues of the widely studied ferroelectric nematogen RM734. Our new procedure focuses on building materials starting from the nitro-terminus and eschewing protecting groups, in contrast to previously reported syntheses. This new synthetic approach confers two principal advantages: firstly, the synthesis of the variants described herein is expedient, being a single step as opposed to three or more via the classical route. Secondly, by forgoing the use of benzyl groups as utilised in the original synthesis we can include functionality that is incompatible with hydrogenolysis conditions (e.g. olefins, late halogens, unsaturated heterocycles). Several of the RM734-like materials we report exhibit ferroelectric nematic phases, and we rationalise the behaviour of these materials with aid of electronic structure calculations and potential energy surface scans. | Calum Gibb; Richard Mandle | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f6fd20dd1a73847f3b3c7e/original/new-rm734-like-fluid-ferroelectrics-enabled-through-protecting-group-free-synthesis.pdf |
60c74706567dfed393ec472a | 10.26434/chemrxiv.11492844.v1 | Synthesis and Electrocatalytic HER Studies of Carbene-Ligated Cu3-xP Nanocrystals | <i>N</i>-heterocyclic
carbenes (NHCs) are an important class of ligands capable of making strong
carbon-metal bonds. Recently, there has been a growing interest in the study of
carbene-ligated nanocrystals, primarily coinage metal nanocrystals, which have
found applications as catalysts for numerous reactions. The general ability of
NHC ligands to positively affect the catalytic properties of other types of
nanocrystal catalysts remains unknown. Herein, we present the first carbene-stabilized
Cu<sub>3–<i>x</i></sub>P nanocrystals.
Inquiries into the mechanism of formation of NHC-ligated Cu<sub>3-<i>x</i></sub>P nanocrystals suggest that
crystalline Cu<sub>3–<i>x</i></sub>P forms
directly as a result of a high-temperature metathesis reaction between a tris(trimethylsilyl)phosphine
precursor and an NHC-CuBr precursor, the latter of which behaves as a source of
both carbene ligand and Cu<sup>+</sup>. To study the effect of the NHC surface ligands
on catalytic performance, we tested the electrocatalytic hydrogen evolving ability
of the NHC-ligated Cu<sub>3–<i>x</i></sub>P
nanocrystals and found they possess superior activity to analogous oleylamine-ligated
Cu<sub>3–<i>x</i></sub>P nanocrystals.
Density functional theory calculations suggest that the NHC ligands minimize
unfavorable electrostatic interactions between the copper phosphide surface and
H<sup>+</sup> during the first step of the hydrogen evolution reaction, which
likely contributes to the superior performance of NHC-ligated Cu<sub>3–<i>x</i></sub>P catalysts as compared to oleylamine-ligated
Cu<sub>3–<i>x</i></sub>P catalysts. | Bryce
A. Tappan; Keying Chen; Haipeng Lu; Shaama Mallikarjun Sharada; Richard Brutchey | Nanocatalysis - Catalysts & Materials; Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74706567dfed393ec472a/original/synthesis-and-electrocatalytic-her-studies-of-carbene-ligated-cu3-x-p-nanocrystals.pdf |
632dd3ea975e94cf5c863838 | 10.26434/chemrxiv-2022-9dftp | Programmed Heterocycle Synthesis Using Halomucononitriles as Zincke Nitrile Precursors | The isomeric imidazo[1,2-a]pyridines and pyrrolo[2,3-b]-pyridine (7-azaindole) heterocyclic cores are “privileged structures” due in part to their ability to interact with a multitude of different receptors, making them essential to the drug discovery process. Imidazo[1,2,-a]pyridine and 7-azaindole, though structurally related, are typically independently synthesized from 2-aminopyridine starting materials. Herein we report a method to convert primary amines, ubiquitous motifs found in pharmaceutical libraries, to either imidazo[1,2-a]pyridines or 7-alkyl azaindoles in two steps. Using halomucononitrile reagents, we can directly access 5-bromo-6-imino-1-alkyl-1,6-dihydropyridine-2-carbonitriles (pyridinimines) in a single step from primary amines (25–95% yield) through a cyclization of transient Zincke nitrile intermediates. We then demonstrate that these compounds can be readily converted to 7-alkylazaindoles using Sonogashira cross-coupling conditions (14 examples, up to 91% yield). Under oxidative conditions, the pyridinimines serve as directing groups for C–H functionalization reactions to afford imidazo[1,2-a]pyridines. We have studied the mechanism of the cyclization event using DFT calculations and propose this takes place via ketenimine intermediates. | Adam Zahara; Brandon Haines; Sidney Wilkerson-Hill | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632dd3ea975e94cf5c863838/original/programmed-heterocycle-synthesis-using-halomucononitriles-as-zincke-nitrile-precursors.pdf |
60c747414c8919e029ad2c78 | 10.26434/chemrxiv.11584458.v1 | Robust Aluminium and Iron Phosphinate Metal-Organic Frameworks for Efficient Removal of Bisphenol A | Herein, we introduce a new series of highly stable MOFs, constructed using Fe<sup>3+</sup> and Al<sup>3+</sup> metal ions and bisphosphinate linkers. The isoreticular design leads to ICR-2, ICR-4, ICR-6, and ICR-7 MOFs with a honeycomb arrangement of linear pores, surface areas up to 1360 m<sup>2</sup> g<sup>-1</sup>, and high solvothermal stability. In most cases, their sorption capacity is retained even after 24 h reflux in water. The choice of the linkers allows fine tuning of the pore sizes and the chemical nature of the pores. This feature can be utilized for optimization of host-guest interactions between molecules and pore walls. Water pollution by various endocrine disrupting chemicals has been considered as a global threat to public health. In this work, we proved that the chemical stability and the hydrophobic nature of the synthesized series of MOFs result in remarkable sorption properties of these materials for neurodisruptor bisphenol A.<br /> | Daniel Bůžek; Soňa Ondrušová; Jan Hynek; Petr Kovář; Kamil Lang; Jan Rohlíček; Jan Demel | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747414c8919e029ad2c78/original/robust-aluminium-and-iron-phosphinate-metal-organic-frameworks-for-efficient-removal-of-bisphenol-a.pdf |
6311c1853e2e36ae042858bd | 10.26434/chemrxiv-2022-pt7gj | Heterobifunctional Ligase Recruiters Enable Pan-Degradation of Inhibitor of Apoptosis Proteins | Proteolysis targeting chimeras (PROTACs) represent a new pharmacological modality to inactivate disease-causing proteins. PROTACs operate via recruiting E3 ubiquitin ligases, which enables the transfer of ubiquitin tags onto their target proteins leading to proteasomal degradation. However, several E3 ligases are validated pharmacological targets themselves, of which inhibitor of apoptosis (IAP) proteins are considered druggable in cancer. Here, we report three series of heterobifunctional PROTACs, which consist of an IAP antagonist linked to either von Hippel-Lindau- or cereblon-recruiting ligands. Hijacking E3 ligases against each other led to potent, rapid, and preferential depletion of cellular IAPs. In addition, these compounds caused complete X-chromosome-linked IAP knockdown, which was rarely observed for monovalent and homobivalent IAP antagonists. In cellular assays, degraders outperformed antagonists and showed potent inhibition of cancer cell viability. The hetero-PROTACs disclosed herein are valuable tools to facilitate studies of the biological roles of IAPs and will stimulate further efforts toward E3-targeting therapies. | Yuen Lam Dora Ng; Aleša Bricelj; Jacqueline A. Jansen; Arunima Murgai; Michael Gütschow; Jan Krönke; Christian Steinebach; Izidor Sosič | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6311c1853e2e36ae042858bd/original/heterobifunctional-ligase-recruiters-enable-pan-degradation-of-inhibitor-of-apoptosis-proteins.pdf |
67bc46e56dde43c9083fec32 | 10.26434/chemrxiv-2025-h4bgm | Lanthanide Selective Biomimetic Nanopores | Lanthanides serve as essential elements for modern technology, playing critical roles in batteries, wind turbines, portable electronics, and energy efficient lighting. However, purifying lanthanides from ores and recycling them from end-of-life consumer materials is costly and damaging to the environment due to inefficient separation technologies. Lanthanide-lanthanide ion separations are challenging due to similarity in their hydrated size, with commonly used methods limited to single stage selectivities of ~ 2-3. Here we present supramolecular membrane channel nanopores based on a pillar[5]arene scaffold with appended diphenylphosphine oxide (DPP) ligands that show high transport selectivity (~18:1) of the medium lanthanide, Europium (Eu3+), over all measured monovalent and divalent ions, including protons. These membrane channels also have high lanthanide-lanthanide transport selectivity with Eu3+/La3+ selectivity of >40 and Eu3+/Yb3+ selectivity of ~30. Molecular dynamics simulations indicate that the high selectivity observed is due to specific water-mediated interactions between the hydrated ions and the channel. Our findings could offer a promising avenue for efficient lanthanide separations, marking an important advancement towards a greener and more sustainable future. | Harekrushna Behera; Tyler Duncan; Laxmicharan Samineni; Hyeonji Oh; Ankit Jogdand; Arnav Karnik; Raman Dhiman; Aida Fica; Tzu-Yun Hsieh; Venkat Ganesan; Manish Kumar | Materials Science; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc46e56dde43c9083fec32/original/lanthanide-selective-biomimetic-nanopores.pdf |
67d9d0e4fa469535b9b6830a | 10.26434/chemrxiv-2025-q3z8j | A comparative study of conductive 3D printing filaments for electrochemical sensing applications pretreated by alumina polishing, electrochemical activa-tion, and electrodeposition of Au nanoparticles | 3D printed electrochemical devices have gained tremendous attention recently because they are highly customizable platforms for analysis and energy storage that can be produced using simple, inexpensive components in a wide variety of settings. 3D printed electrochemical sensors, fabricat-ed from carbon-loaded conductive thermoplastics, enable decentralized production of electrochemi-cal devices that, if optimized, could be widely distributed. Achieving this goal requires a compre-hensive understanding
of the electrochemical behavior of these filaments. Here, we investigated how the electrochemical behavior of three commercial filaments was affected by alumina polishing, electrochemical activa-tion in 0.5 M NaOH, and electrodepositing Au nanoparticles (NPs). Our goal was to understand if/how a selection of commercial filaments responds to these commonly used pretreatments rather than perform an exhaustive study of all possible combinations of filaments and pretreatments. We characterized the physical properties of each filament/pretreatment using thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and Raman microscopy measurements. We then benchmarked the background electrochemical processes (capacitance and solvent window) and the peak potential separation (∆Ep) of two common outer-sphere redox species (ruthenium hexamine and ferrocene methanol) for each filament under each pretreatment (i.e., nine total conditions). We subsequently investigated how the filaments responded to inner-sphere redox couples that were sur-face sensitive (ferrocyanide oxidation), dependent on surface adsorption (dopamine oxidation), and sensitive to surface oxides (Fe2+ oxidation). We found that the electrode form factor (i.e., size, ge-ometry, and contact method) matters tremendously when evaluating a 3D printable material’s elec-trochemical properties because uncompensated resistance can lead to misinterpretations of the HET kinetics using voltammetric methods. We also observed that the selected filaments do not respond to pre-treatments identically, and that detailed characterization (especially electrochemical character-ization, including non-faradaic background processes) must be employed when evaluating fila-ments. and electrodepositing metal nanoparticles is a very effective method of producing high-quality sensing interfaces regardless of filament and is probably underutilized in the field. Im-portantly, the latter insights were only possible by using a well-controlled form factor that behaved according to theory towards outer-sphere electron transfer couples. | Shakir Ahmed; Enock Arthur; Kelly Orbzut; Ricoveer Shergill; Alexa Williams; Kelvin Wamalwa; Wanlu Li; Bhavik Patel; Glen O'Neil | Analytical Chemistry; Electrochemical Analysis | CC BY NC 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d9d0e4fa469535b9b6830a/original/a-comparative-study-of-conductive-3d-printing-filaments-for-electrochemical-sensing-applications-pretreated-by-alumina-polishing-electrochemical-activa-tion-and-electrodeposition-of-au-nanoparticles.pdf |
6544c96dc573f893f1b8fb34 | 10.26434/chemrxiv-2023-n79z2 | Capturing Histone Tails Motion using all-atom Replica-Exchange with Solute Tempering (REST2) Simulations | Full-length histone tails play a well characterized role in nucleosome core particles, and, as intrinsically disordered peptides, represent a current challenge for all-atom molecular dynamics simulations. Beyond the choice of the force field, the folding and the subsequent interactions with DNA landscape is complex and calls for a robust computational protocol capable of reproducibility. In this contribution, we assessed by a specifically tailored REST2-based simulation protocol the interaction between the four canonical histone tails and a DNA fragment from a canonical nucleosome core particles. We report contact maps obtained by clus- tering along several microseconds which prefigure plausible interactions between some of the positively-charged residues and DNA. Two major post-translational modifica- tions of lysines are also discussed. Our work thus contributes to pave the way toward a robust in silico predictive tool for DNA-histone tails interactions which remain ex- perimentally difficult to assess although of key importance in Biochemistry. | Natacha Gillet; Laleh Allahkaram; Elise Dumont | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6544c96dc573f893f1b8fb34/original/capturing-histone-tails-motion-using-all-atom-replica-exchange-with-solute-tempering-rest2-simulations.pdf |
60c74a25702a9ba74a18b23b | 10.26434/chemrxiv.12159207.v1 | An NADH-Inspired Redox Mediator Strategy to Promote Second-Sphere Electron and Proton Transfer for Cooperative Electrochemical CO2 Reduction Catalyzed by Iron Porphyrin | We present a bioinspired strategy for enhancing electrochemical carbon dioxide reduction catalysis by cooperative use of base-metal molecular catalysts with intermolecular second-sphere redox mediators that facilitate both electron and proton transfer. Functional synthetic mimics of the biological redox cofactor NADH, which are electrochemically stable and are capable of mediating both electron and proton transfer, can enhance the activity of an iron porphyrin catalyst for electrochemical reduction of CO<sub>2</sub> to CO, achieving a 13-fold rate improvement without altering the intrinsic high selectivity of this catalyst platform for CO<sub>2</sub> versus proton reduction. Evaluation of a systematic series of NADH analogs and redox-inactive control additives with varying proton and electron reservoir properties reveals that both electron and proton transfer contribute to the observed catalytic enhancements. This work establishes that second-sphere dual control of electron and proton inventories is a viable design strategy for developing more effective electrocatalysts for CO<sub>2</sub> reduction, providing a starting point for broader applications of this approach to other multi-electron, multi-proton transformations. | Peter T. Smith; Sophia Weng; Christopher Chang | Bioinorganic Chemistry; Electrochemistry; Small Molecule Activation (Inorg.); Electrocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a25702a9ba74a18b23b/original/an-nadh-inspired-redox-mediator-strategy-to-promote-second-sphere-electron-and-proton-transfer-for-cooperative-electrochemical-co2-reduction-catalyzed-by-iron-porphyrin.pdf |
673a9d62f9980725cf89abe1 | 10.26434/chemrxiv-2024-zvcb4-v3 | 3D2SMILES: Translating Physical Molecular Models into Digital DeepSMILES Notations Using Deep Learning | Physical molecular models are widely used in educational settings for teaching organic and other branches of chemistry, offering an intuitive understanding of molecular structures. Conversely, while less intuitive, virtual models provide additional functionalities, such as retrieving molecular names and other properties. Currently, to the best of our knowledge, there is a gap between 3D molecular models and their digital counterparts. This paper introduces a computer vision model designed to bridge this gap by converting images of physical molecular models into their digital DeepSMILES representations. This conversion facilitates further information retrieval, enhancing educational utility. We developed synthetic and real datasets to train our model and evaluated its performance across various dataset combinations. Additionally, we attempted to improve the model’s accuracy by multi-image input and beam search. We achieved 62.0% top1 accuracy and 80.3% top-3 accuracy with beam search and multi-image input on our validation set. We also explored the model’s characteristics, such as explainability by saliency maps, and examined its calibration. We also discussed the model’s limitations and directions for future research. | Wenqi Guo; Yiyang Du; Mohamed Shehata | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673a9d62f9980725cf89abe1/original/3d2smiles-translating-physical-molecular-models-into-digital-deep-smiles-notations-using-deep-learning.pdf |
61f75aea0716a8b43741e1cf | 10.26434/chemrxiv-2021-0d01d-v2 | Reaction of irbesartan with nitrous acid produces irbesartan oxime derivatives, rather than N-nitrosoirbesartan | In October 2021, a number of batches of irbesartan and irbesartan hydrochlorothiazide finished products were recalled from the US market, due to the presence of unacceptable level of the probably carcinogenic nitrosamine N-nitrosoirbesartan. Nevertheless, there is no revealing of the exact structure of this hypothetical N-nitrosoirbesartan. In the current study, we performed a set of 10 reactions of irbesartan with nitrous acid under various conditions and found no trace of this hypothetical N-nitrosoirbesartan by a sensitive and accurate LC-MS method with limit of detection (LOD) of 30 ppb. With the use of LC-PDA/UV-high resolution MSn as well as 1D/2D NMR, the reaction products formed are found to be the two isomeric oxime derivatives of irbesartan, with the Z-isomer as the predominant product. Furthermore, no trace of this hypothetical N-nitrosoirbesartan can be detected in representative commercial batches of irbesartan. Despite of the fact that in silico evaluation suggests that the two irbesartan oximes may be controlled as regular impurities, analysis of representative irbesartan commercial batches by the LC-MS method indicates that the oximes are not detected (LOD: 30 ppb). | Jinsheng Lin; Qiang Zhou; Ru Jia; Wentao Liu; Huacui Hou; Jian Ma; Dan Li; Nuo Chen; Wenbin Chen; Jian Ye; Wenping Hu; Wenquan Zhu; Min Li | Organic Chemistry; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f75aea0716a8b43741e1cf/original/reaction-of-irbesartan-with-nitrous-acid-produces-irbesartan-oxime-derivatives-rather-than-n-nitrosoirbesartan.pdf |
62e3e661cf661245c3ba63a4 | 10.26434/chemrxiv-2022-gg3g5 | Site-selective Electrochemical Oxidation of Glucosides | Quinuclidine-mediated electrochemical oxidation of glycopyranosides provides C3-ketosaccharides with excellent selectivity. The method is a versatile alternative to Pd-catalyzed oxidation, and to photochemical oxidation, and is complementary to the TEMPO-mediated C6-selective oxidation. Contrary to the electrochemical oxidation of methylene and methine groups, the reaction does not require oxygen. | Marios Kidonakis; Augustin Villotet; Martin Witte; Sebastian Beil; Adriaan Minnaard | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2022-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e3e661cf661245c3ba63a4/original/site-selective-electrochemical-oxidation-of-glucosides.pdf |
65cca35fe9ebbb4db9573403 | 10.26434/chemrxiv-2024-hg1wn | Spectral tuning and emission enhancement through lanthanide coordination in a dual Vis-NIR emissive cyanide-bridged heterometallic Ru(II)-Er(III) complex | Owing to their unique luminescent properties and photosensitizing capability, cyanoruthenium(II) complexes with diimine lig-ands are the subject of intense research striving for routes for tuning their electronic properties and improving their emission quantum yield. In this work, we describe the first example of a heterometallic d-f cyanide-bridged Ru(II)-Er(III) assembly ob-tained by the direct reaction of trivalent erbium salt with the neutral [Ru(bipy)2(CN)2] metalloligand. This strategy allows for accommodating inorganic negatively charged anions, such as nitrate and oxalate, in the coordination sphere of the lanthanide ion. As a result, a dimeric tetranuclear discrete molecular architecture is obtained, where the two constituting monomeric Ru(II)-CN-Er(III) units are bridged by an oxalate anion coordinating two Er(III) ions in a bis-bidentate fashion. Strikingly, this heter-ometallic compound shows intense dual emission in the visible and near-infrared spectral ranges under single-wavelength exci-tation both in solution and in the crystalline state. The effect of Er(III) coordination through a cyanide bridge is thoroughly dis-cussed, also with the support of DFT calculations, to highlight the factors that induce the observed spectral hypsochromism and, more importantly, the remarkable tenfold-increased emission quantum yield of the [Ru(bipy)2(CN)2] moiety in the visible range. We show that the described coordination mode induces an energy raise of the emissive 3MLCT state and even a more pronounced lifting of the non-emissive Ru(II) 3MC states, suppressing thermal deactivation channels. Furthermore, thanks to the reduced number of water molecules and quenching groups surrounding the lanthanide ion in the molecular architecture, rel-atively intense erbium emission at 1.5 μm telecom wavelength is detected through the sensitization from the Ru(II) metallolig-and. We suggest that this compound can find applications as efficient solid-state dual emitter and luminescent chemical sensor. | Dimitrije Mara; Zhiwang Cai; Silvia Bonabello; Stefano Penna; Rik Van Deun; Paola Deplano; Luciano Marchiò; Luca Pilia; Flavia Artizzu | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cca35fe9ebbb4db9573403/original/spectral-tuning-and-emission-enhancement-through-lanthanide-coordination-in-a-dual-vis-nir-emissive-cyanide-bridged-heterometallic-ru-ii-er-iii-complex.pdf |
613f62a4b817b44b741ba97d | 10.26434/chemrxiv-2021-v36v1 | Assessing the importance of cation size in the tetragonal-cubic phase transition in lithium garnet electrolytes. | Lithium garnets are promising solid-state electrolytes for next generation lithium-ion batteries. These materials have high ionic conductivity, a wide electrochemical window and stability with Li metal. However, lithium garnets have a maximum limit of 7 lithium atoms per formula unit (e.g. La3Zr2Li7O12), before the system transitions from a cubic to a tetragonal phase with poor ionic mobility. This arises from full occupation of the Li sites. Hence, the most conductive lithium garnets have Li between 6-6.55 Li per formula unit, which maintains the cubic symmetry and the disordered Li sub-lattice.
The tetragonal phase, however, forms the highly conducting cubic phase at higher temperatures, thought to arise from increased cell volume and entropic stabilisation permitting Li disorder. However, little work has been undertaken in understanding the controlling factors of this phase transition, which could enable enhanced dopant strategies to maintain room temperature cubic garnet at higher Li contents.
Here, a series of nine tetragonal garnets were synthesised and analysed via variable temperature XRD to understand the dependence of site substitution on the phase transition temperature. Interestingly the octahedral site cation radius was identified as the key parameter for the transition temperature with larger or smaller dopants altering the transition temperature noticeably. A site substitution was, however, found to make little difference irrespective of significant changes to cell volume.
| Mark Stockham; Alice Griffiths ; Bo Dong; Peter Slater | Inorganic Chemistry; Energy; Electrochemistry; Solid State Chemistry; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613f62a4b817b44b741ba97d/original/assessing-the-importance-of-cation-size-in-the-tetragonal-cubic-phase-transition-in-lithium-garnet-electrolytes.pdf |
66dee56151558a15ef817371 | 10.26434/chemrxiv-2024-5pspg | Continuous Tuning of Intersystem Crossing Times in Rose Bengal Water/Methanol Solutions | We use femtosecond transient broadband absorption spectroscopy (TAS) to characterize rose bengal in water/methanol solutions and reveal a continuous tunability of intersystem crossing (ISC) times by changing the mole fraction of the solvents. We find that the transients of excited state absorptions (ESA) in rose bengal at ~430 nm can be attributed to transitions from the singlet state S1, with decay times of 74 ps via ISC in pure water and up to 405 ps in pure methanol. TA measurements at near-infrared wavelengths on the other hand reveal the rise of an ESA at ~1080 nm from the triplet state T1 with time constants of 68 ps and 491 ps in pure water and methanol respectively, strongly supporting the associated UV-Vis TAS data. Solvent mixtures show a quasi-linear rise of the ISC times with increasing mole fractions of methanol and indicate that rose bengal in varying solvent mixtures can be used as a model system to study their influence on excited state photophysics. | Onno Strolka; Pascal Rauthe; Tim Muschik; Philipp Frech; André Niebur; Andreas-Neil Unterreiner; Jannika Lauth | Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dee56151558a15ef817371/original/continuous-tuning-of-intersystem-crossing-times-in-rose-bengal-water-methanol-solutions.pdf |
6114c41eabc9e235146ba6b1 | 10.26434/chemrxiv-2021-6rqb2 | Facile and Divergent Optimization of Chromazonarol Enabled the Identification of Simplified Drimane Meroterpenoids as Novel Pharmaceutical Leads | The coverage of drimane hydroquinones chemical space was expanded by the facile construction of the focused libraries of (+)-chromazonarol relevant natural products, isomers and analogues for advance as pharmaceutical leads. Through the synergistic interaction of the programmable synthesis and bioactivity-guided screening, the structure-activity relationship of (+)-chromazonarol relevant (non)-natural products was delineated. The first divergent derivatization of (+)-chromazonarol demonstrated that the phenolic hydroxyl group is one inviolable requirement for antifungal effect. Pin-point modification of (+)-yahazunol manifested the position of hydroxyl group was crucial for both antifungal and anti-tumor activities. (+)-Albaconol, (+)-neoalbaconol and two yahazunol isomers (24 and 25) were witnessed to be the novel pharmaceutical leads. The probable macromolecular targets were estimated to deliver new information about the biological potential resident in (+)-yahazunol relevant products. This work also featured the first synthesis of (+)-albaconol and (+)-neoalbaconol, the first biological exploration of (+)-dictyvaric acid and an improved preparation of (+)-8-epi-puupehedione and a promising pelorol analogue. | Xia Wang; Nvdan Hu; Wenlong Kong; Baoan Song; Shengkun Li | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6114c41eabc9e235146ba6b1/original/facile-and-divergent-optimization-of-chromazonarol-enabled-the-identification-of-simplified-drimane-meroterpenoids-as-novel-pharmaceutical-leads.pdf |
6738a6c05a82cea2fa4d8c9b | 10.26434/chemrxiv-2024-xkkbf | Stacked all-graphite microfluidic microbial fuel cells | In this work, three high-surface-area graphite plates were structured by micromilling and incorporated directly microfluidic microbial fuel cells. All MFCs were run individually to verify their high-power outputs and substrate conversion efficiencies. Then the MFCs grew electroactive biofilms with an average 35 µm thickness. They were connected in different stacked configurations to increase raw outputs. In a parallel configuration, the internal resistance was as low as 480 Ω, resulting in outputs in power (595 µW) and current (1.4 mA), which are impressive by microfluidic standards. Adjusting the flow conditions enabled the parallel stack to reach over 70% acetate utilization. A series stack was used to successfully power an environmental multisensor (temperature, humidity) and a wristwatch. We discuss staked systems that could reproduce the results of an 850 L pilot MFC system. | LInlin Liu; Marc-Antoine Bansept; Changhong Cao; Denis Boudreau; Jesse Greener | Energy; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6738a6c05a82cea2fa4d8c9b/original/stacked-all-graphite-microfluidic-microbial-fuel-cells.pdf |
6585ddc19138d23161476eb1 | 10.26434/chemrxiv-2023-9cw9v | One size does not fit all: revising traditional paradigms for QSAR-based virtual screenings. | Traditional best practices for Quantitative Structure Activity Relationship (QSAR) modeling recommend dataset balancing and balanced accuracy (BA) as the key desired objective of model development. This study challenges the conventional norms by recommending the use of models with the highest positive predictive value (PPV) built for imbalanced training sets as preferred tools in virtual screening campaigns for drug discovery. As proof of concept, we developed QSAR models for five expansive datasets with different ratios of active and inactive molecules and assessed model performance using BA, PPV, and other metrics. We demonstrated that PPV-oriented models used in virtual screening have at least 30% higher first-batch hit rate as compared to all other models. These findings suggest that QSAR models trained on imbalanced datasets for the highest PPV are preferred tools for virtual screening campaigns in drug discovery. | James Wellnitz; Sankalp Jain; Joshua Hochuli; Travis Maxfield; Eugene Muratov; Alexander Tropsha; Alexey Zakharov | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6585ddc19138d23161476eb1/original/one-size-does-not-fit-all-revising-traditional-paradigms-for-qsar-based-virtual-screenings.pdf |
63f4b1c3fcfb27a31f2a7018 | 10.26434/chemrxiv-2023-77sx8 | Transition Moments Beyond the Electric-Dipole Approximation: Visualization and Basis Set Requirements | In the simulation of X-ray absorption spectroscopy, the validity of the electric dipole approximation comes into question. Three different schemes exist to go beyond thisapproximation: the first scheme is based on the full semi-classical light-matter inter-action, whereas the latter two schemes, referred to as the generalized length and velocity representation, are based on truncated multipole expansions. Even though these schemes have been successfully implemented in several quantum chemistry codes,their basis set requirements remained largely unknown. Here, we assess the basis set requirements of the full interaction operator and the generalized length and velocity representations. These three schemes were applied in the calculation of radial distributions of transition moment densities corresponding to the 1s1/2 and 7s1/2 7p1/2transition in the radium atom, representative of core and valence excitations, respectively. We have performed calculations with the dyall.aeXz (X=2,3,4) basis sets at the four-component relativistic TD-HF level of theory and compared them withequivalent finite-difference calculations. We find that the full interaction is extremelystable with respect to the choice of basis set, already being converged with dyall.ae2z.With respect to truncated interaction, we find that the length representation electric multipoles is the easiest to converge, requiring the dyall.ae2z basis for low-order multipoles and the dyall.ae4z basis at higher orders. The magnetic multipole moments follow a similar trend, although they are more diffcult to converge. The velocity representation electric multipoles are the most difficult to converge: at high orders, thedyall.ae3z and dyall.ae4z basis sets introduce artificial peaks and oscillations, which increase the overall error. These artifacts are associated with linear dependence issues in the small component space of the larger basis sets. The full interaction operator,however, does not suffer from these problems, and we therefore recommend its use in the simulation of x-ray spectroscopy. | Martin van Horn; Nanna List; Trond Saue | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f4b1c3fcfb27a31f2a7018/original/transition-moments-beyond-the-electric-dipole-approximation-visualization-and-basis-set-requirements.pdf |
60c741ea842e656719db1fa5 | 10.26434/chemrxiv.8170859.v1 | Self-Immolative Bottlebrush Polypentenamers and their Macromolecular Metamorphosis | The complete depolymerization of a polypentenamer bottlebrush backbone and the kinetic principles involved are discussed. The deconstruction of the bottlebrush occurs from end-to-end in a self-immolative fashion producing individual linear grafts. The phenomenon paints a clearer picture on the original bottlebrush design. Architecture transformations from bottlebrush to linear to star polymers through facile means is explored.<br /> | William Neary; Justin Kennemur | Polymer brushes; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ea842e656719db1fa5/original/self-immolative-bottlebrush-polypentenamers-and-their-macromolecular-metamorphosis.pdf |
610a686c3b558f7388f6aecd | 10.26434/chemrxiv-2021-lph4p | Molecular stabilization of chemically exfoliated bare MnPS3 layers | Transition metal chalcogenophosphates of general formula MPX3 have attracted recent interest in the field of 2D materials due to the possibility of tuning
their properties when reaching the 2D limit. Several works address this challenge by dry mechanical exfoliation. However, only a few of them use a scalable
approach. In this work, we apply a general chemical protocol to exfoliate MnPS3. The method uses in a first step chemical intercalation and liquid phase
exfoliation, followed in a second step by the addition of molecules used as capping agents on the inorganic layers. Therefore, molecules of different nature
prompts the quality of the exfoliated material and its stabilization in aqueous solution, opening the possibility of using these functionalized layers in several
fields. Here we illustrate this possibility in electrochemistry. Thus, we show that when polyethylenimine is used as capping agent, it is possible to reach a
compromise between the stability of high quality MnPS3 flakes in aqueous suspension and their optimum performance as an electrocatalytic system for HER
activity. | Ramon Torres-Cavanillas; Isaac Brotons-Alcazár; Alicia Forment-Aliaga; Eugenio Coronado; Marc Morant-Giner; Samuel Mañas-Valero; Martin Cvik | Materials Science; Inorganic Chemistry; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Electrochemistry | CC BY 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610a686c3b558f7388f6aecd/original/molecular-stabilization-of-chemically-exfoliated-bare-mn-ps3-layers.pdf |
60c73d4b469df44562f42693 | 10.26434/chemrxiv.5531038.v1 | Charge Transfer Initializes Photoexcited YOYO-1 Intramolecular Rotation and Fluorescent Quenching | YOYO-1 is a commonly used cyanine dye for DNA
staining that is fluorescently bright in DNA but very dim in water. The major
assumption of its excited electron decay pathway is thermal relaxation via the
rotation at a bridging methine that connects the two moieties of the molecule,
i.e. photo-isomerization. In this report, we use femtosecond transient
absorption spectroscopy to directly measure the excited electron decay, the
hole refill, and the hot ground state rise and decay. The data suggest that the
first step of the photo-isomerization involves a charge transfer to quench the
holes and vibrational activation of the molecules to a hot ground state. | Jixin Chen; Lei Wang; Joseph R. Pyle | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4b469df44562f42693/original/charge-transfer-initializes-photoexcited-yoyo-1-intramolecular-rotation-and-fluorescent-quenching.pdf |
62212c67c6bb55b0117bb350 | 10.26434/chemrxiv-2022-50gnd | Bridging Database Analysis with Microrheology to Reveal Super-Hydrodynamic Conductivity Scaling Regimes in Ionic Liquids | Ion transport through electrolytes critically impacts the performance of batteries and other electrochemical devices. Many frameworks used to predict and tune ion transport, such as the Nernst-Einstein model, assume hydrodynamic transport mechanisms, and hence focus on maximizing electrolyte conductivity by minimizing bulk viscosity. However, the emergence of solid-state electrolytes illustrates that selective, non-hydrodynamic ion transport provides promising avenues for enhancing ionic transport in electrolytes. Increasingly, selective ion transport mechanisms, such as hopping, are proposed for concentrated electrolytes, including ionic liquid-derived materials. Yet viscosity-conductivity scaling relationships in ionic liquids are still often analyzed with hydrodynamic models. Here, we report a data-centric analysis of how well hydrodynamic transport models describe the scaling between viscosity and conductivity in neat ionic liquids by merging three databases to bridge physical properties and chemical descriptors. With this expansive data set, we constrained our scaling analysis using ion sizes defined using simulated molecular volumes, as opposed to prior approaches that estimate sizes from activity coefficients or rely on ad-hoc estimates. Remarkably, we find that many commonly studied ionic liquids exhibit positive deviations from the Nernst-Einstein model, implying that ions move faster than hydrodynamic limitations should allow. We experimentally verify these positive deviations in a common class of ionic liquids using microrheology and conductivity measurements. Our results highlight overlooked super-hydrodynamic regimes in ionic liquid viscosity-conductivity scaling and point to opportunities to understand mechanisms of correlated ion motion in ionic liquids. We further show data science and machine learning tools can improve predictions of conductivity from molecular properties, including demonstrating predictions can be made using only computational features. Our findings reveal that many ionic liquids exhibit super-hydrodynamic viscosity-conductivity scaling, which could be harnessed to influence the behavior of electrochemical devices. | Ryan Cashen; Megan Donoghue; Abigail Schmeiser; Matthew Gebbie | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Machine Learning; Energy Storage; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62212c67c6bb55b0117bb350/original/bridging-database-analysis-with-microrheology-to-reveal-super-hydrodynamic-conductivity-scaling-regimes-in-ionic-liquids.pdf |
645547f907c3f0293744ac66 | 10.26434/chemrxiv-2023-6vmqd | Investigating the Structure-Activity Relationship of Laulimalides Marine Macrolides as Promising Inhibitors for SARS-CoV-2 Main Protease (Mpro) | SARS-CoV-2, the new coronavirus variant is a world-wide health crisis. Over spans of human history, preparations derived from natural products have always been recognized as a preliminary source of medications. Taking into account the SARS-CoV-2 main protease (Mpro) as the essential element of the viral cycle and as a main target, herein we highlight a computer-aided comprehensive virtual screening for a focused chemical list of 14 laulimalides marine macrolides against SARS-CoV-2 main protease (Mpro) using a set of integrated modern computational techniques including molecular docking (MDock), molecule dynamic simulations (MDS) and structure-activity relationships (SARs) as well. Indeed, computational studies had disclosed two promising macrolides [laulimalides LA4 (6) and LA18 (13)] based on their remarkable ligand-protein energy scores and relevant binding affinities with the SARS-CoV-2 (Mpro) pocket residues. Consequentially, the two compounds were further investigated thermodynamically though deciphering their MD simulations at 100 ns, where they showed noticeable stability within the accommodated (Mpro) pockets. Moreover, in-deep SARs studies suggested the crucial roles of the C-23 subistituted side chain and the C-20 methoxy as essential pharmacophoric structural features for activity. Such interesting outcomes are highly recommending further in vitro/vivo examinations regarding those marine macrolides and open a gate towards developing more effective antivirals drug leads. | Alaa M. Elgohary; Abdo A. Elfiky; Florbela Pereira; Mariam I. Gamal El-Din; Mohamed A. Tammam; Mohamed Sebak; Sherif I. Hamdallah ; Emad Shehata; Amr El-Demerdash | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645547f907c3f0293744ac66/original/investigating-the-structure-activity-relationship-of-laulimalides-marine-macrolides-as-promising-inhibitors-for-sars-co-v-2-main-protease-mpro.pdf |
61f321ebe4d9b8f15bfa4fbc | 10.26434/chemrxiv-2022-px0fd | Insights into the active catalyst formation in
palladium catalyzed coupling reaction from
di-nuclear palladium acetate: A DFT study | We explored the formation of active palladium catalyst species by degradation of Pd-acetate dimer with the addition of phosphine ligands (PH3 and PPh3 ) with
an automated reaction search employing Density Functional Theory calculations followed by kinetic studies with stochastic simulation analysis. Our reaction search starting from dimeric form, considered a resting state of the catalyst, produced similar monomeric species by sequential ligand addition as found in the experimental investigation of the active catalytic species in Heck reactions. We analyzed the bonding in the Pd-acetate dimer and the role of Pd in the stability of the dimeric species. We implemented the Gillespie Stochastic Simulation Algorithm and applied it to the degradation reaction path. This algorithm can give more insights into multi-channel reaction paths. The energetics of the degradation path is reasonably achievable in the experimental reaction conditions that make dimeric species a potential catalytic precursor in the Pd-acetate catalyzed coupling reactions. | Saikat Roy; Anakuthil Anoop | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f321ebe4d9b8f15bfa4fbc/original/insights-into-the-active-catalyst-formation-in-palladium-catalyzed-coupling-reaction-from-di-nuclear-palladium-acetate-a-dft-study.pdf |
64be6a4cae3d1a7b0d409649 | 10.26434/chemrxiv-2023-2v99z | A simple HPLC-fluorescence screening method for rapid determination of oleuropein in olive leaves; cross validation with an UPLC-MS-UV method and analysis of leaves of French olive varieties | ABSTRACT Olive leaves are an abundant but under-exploited by-product of the olive oil industry, comprising 10 % of the total mass processed for olive oil. They are a rich source of oleuropein, the most abundant polyphenol in olive leaves, whose bioactive properties are widely documented. If olive leaves are to be seriously considered as a readily-available source of oleuropein, simple analytical methods are needed to identify varieties and growing conditions conducive to its formation. HPLC-fluorescence detection and UPLC-UV-MS methods on different instruments were developed and cross-validated using blank (oleuropein-free) leaves produced in-house to establish matrix standards in the concentration range 0.4 to 4.8 mg/g. For the HPLC-FLD method, mean repeatability and intermediate precision were respectively 3.64% and 4.76% relative standard deviation; the coefficient of determination was generally >0.9999 and linearity was demonstrated by the Fischer test. There was a close linear relationship (R2 > 0.999) between back-calculated concentrations of both spiked placebos and authentic standards. Analysis of the same spiked placebos by the three chromatographic methods showed no significant differences in the validation results as confirmed by ANOVA. Cross-validation of the three methods indicate that selective quantification can equally be carried out on standard HPLC equipment available to most laboratories or by more sophisticated UPLC-MS techniques in larger structures. The determination of oleuropein in “Olivière” olive variety is reported here for the first time, and leaves collected in 2022 contained about 40 mg/g oleuropein, almost twice the amount found in Picholine and three times more than in other varieties. | MARY KELLY; Morgane Carrara; Lauren Griffin; Delphine Margout | Analytical Chemistry; Agriculture and Food Chemistry; Analytical Chemistry - General; Food | CC BY 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64be6a4cae3d1a7b0d409649/original/a-simple-hplc-fluorescence-screening-method-for-rapid-determination-of-oleuropein-in-olive-leaves-cross-validation-with-an-uplc-ms-uv-method-and-analysis-of-leaves-of-french-olive-varieties.pdf |
66c48451f3f4b052906ca4c9 | 10.26434/chemrxiv-2024-5tfzd | Accelerated mechanochemical bond scission and stabilization against heat and light in carbamoyloxime mechanophores | Current approaches to the discovery of mechanochemical reactions in polymers are limited by the interconnection of the zero-force and force-modified potential energy surfaces, since most mechanochemical reactions are force-biased thermal reactions. Here, carbamoyloximes are developed as a mechanophore class in which the mechanochemical reaction rates counterintuitively increase together with the thermal stability. All carbamoyloxime mechanophores undergo force-induced homolytic bond scission at the N–O bond and their mechanochemical scission rate increases with the degree of substitution on the α-substituent. Yet, carbamoylaldoximes react to both heat and light with a pericyclic syn elimination while carbamoylketoximes undergo thermal decomposition at high temperature and photochemical homolytic scission only from the triplet state. Thereby, the mechanochemical and thermal reaction trajectories are separated and the thermal stability increases alongside the mechanochemical reaction kinetics. This approach may play an important role in the future of systematic mechanochemical reaction discovery. | Simay Aydonat; Davide Campagna; Sourabh Kumar; Sonja Storch; Tim Neudecker; Robert Göstl | Theoretical and Computational Chemistry; Organic Chemistry; Polymer Science; Photochemistry (Org.); Organic Polymers; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c48451f3f4b052906ca4c9/original/accelerated-mechanochemical-bond-scission-and-stabilization-against-heat-and-light-in-carbamoyloxime-mechanophores.pdf |
6557cb1a2c3c11ed719b9291 | 10.26434/chemrxiv-2023-cck1b-v2 | Physics Constrained Multi-objective Bayesian Optimization to Accelerate 3D Printing of Thermoplastics | Vat photopolymerization (VPP) of thermoplastics faces an issue of unpredictable printability due to the involved competing photopolymerization and dissolution reactions. The printing outcome largely depends on physicochemical properties of monomers and their compositions in resins, which also greatly determine the material properties, e.g., strength/toughness and phase transition temperature (Tg). Thus, a methodology for optimizing the resin formulation is of paramount importance in realizing highly printable thermoplastics with balanced strength/toughness and target Tg while remaining largely underexplored. Herein, we introduce a multi-objective Bayesian optimization (MOBO) algorithm with two physics informed constraints (printability and Tg) to optimize two conflicting properties: tensile strength (σT) and toughness (UT). The two constraints are formulated as two machine learning (ML) models, which are trained with weight ratios of the six input monomers and physics informed (PI) descriptors derived from their physiochemical parameters. Dimensional reduction analysis reveals that the algorithm avoids recommendation of the monomer ratios that do not pass the two constraints. The printing failure rate is reduced from 16% in the background experiments to 3% in the recommended experiments. Within only 36 iterations (72 samples), the MOBO algorithm successfully identifies five sets of ratios leading to Pareto optimal of σT and UT. Due to the constraint in Tg they show appropriate Tg for shape memory application. The partial dependence analysis indicates that σT and UT depend on both the ratios and physiochemical features of the monomers. These results underscore capability of such a smart decision-making algorithm—with constraints that are not fully understood but can be informed by prior knowledge—in planning the experiments from the vast design space, thus holding a great promise for broader applications in materials and manufacturing. | Kianoosh Sattari; Yuchao Wu; Zhenru Chen; Alireza Mahjoubnia; Changhua Su; Jian Lin | Materials Science; Polymer Science; Materials Processing; Organic Polymers | CC BY NC 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6557cb1a2c3c11ed719b9291/original/physics-constrained-multi-objective-bayesian-optimization-to-accelerate-3d-printing-of-thermoplastics.pdf |
60c74b07f96a004793287546 | 10.26434/chemrxiv.12279833.v1 | Improving Printability of a Thermoresponsive Hydrogel Biomaterial Ink by Nanoclay Addition | As a promising biofabrication technology, extrusion-based bioprinting has gained significant attention in the last decade and major advances have been made in the development of bioinks. However suitable synthetic and stimuli-responsive bioinks are underrepresented in this context. <a>In this work, we described a hybrid system of nanoclay Laponite XLG and thermoresponsive block copolymer poly(2-methyl-2-oxazoline)-<i>b</i>-poly(2-<i>n</i>-propyl-2-oxazine) (PMeOx-<i>b</i>-PnPrOzi) as a novel biomaterial ink, and discussed its critical properties relevant for extrusion-based bioprinting, including viscoelastic properties and printability.</a> <a>The hybrid hydrogel retains the thermogelling properties but is strengthened by the added clay (over 5 kPa of storage modulus, and 240 Pa of yield stress). Importantly, the shear-thinning character is further enhanced, which, in combination with very rapid viscosity recovery (~1 s) and structure recovery (~10 s) is highly beneficial for extrusion-based 3D printing. Accordingly, various 3D patterns could be printed with markedly enhanced resolution and shape fidelity compared to the biomaterial ink without added clay.</a> | Chen Hu; Lukas Hahn; Mengshi Yang; Alexander Altmann; Philipp Stahlhut; Jürgen Groll; Robert Luxenhofer | Biocompatible Materials; Composites; Materials Processing; Drug delivery systems; Hydrogels; Organic Polymers; Polymer scaffolds | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b07f96a004793287546/original/improving-printability-of-a-thermoresponsive-hydrogel-biomaterial-ink-by-nanoclay-addition.pdf |
678fb52581d2151a021ef616 | 10.26434/chemrxiv-2025-pszwj | Generalised Fault Diagnostics of Polymer Electrolyte Fuel Cells Using Machine Learning | The ongoing threat of global warming necessitates a shift towards clean energy sources to meet rising demands while reducing carbon emissions. Polymer electrolyte fuel cells (PEFCs) represent a promising technology for both mobile and stationary applications but their poor operational lifetimes and frequent faults are barriers to their commercial ubiquity. Thus, detecting and addressing faults rapidly is crucial to extend PEFC lifetimes and enhance their viability for alternative electricity generation. White-box and black-box models are widely used to diagnose PEFC faults; this work introduces a novel black-box approach using multifrequency Walsh function perturbation signals to diagnose polymer electrolyte membrane PEFC faults. This method improves signal-to-noise ratios in the electrical response of the fuel cell, increasing measurement accuracies without causing cell damage from excessive perturbation amplitudes. Using the voltage response of the PEFC as the diagnostic variable, dense neural networks (DNNs), 1-dimensional convolutional neural networks (1D-CNNs), and support vector machines (SVMs) were investigated for fault classification. Initial testing revealed that all models could accurately detect normal, drying, and starvation conditions in an individual PEFC, with the 1D-CNN and SVMs achieving 100% diagnostic accuracy. When tested on data from a different PEFC, the models exhibited poor generalisation abilities; nevertheless, combining data from multiple PEFCs significantly improved diagnostic accuracy, with the 1D-CNN displaying superior generalisation performance, particularly when trained with only a small portion of new data. The network’s convolutional architecture facilitates effective parameter sharing and local connectivity, enhancing computational efficiency and reducing errors. Thus, it emerges as the most suitable model for the diagnostic framework, capable of managing varying datasets from different PEFCs while maintaining high accuracies. | Greg D’Silva; Eashaal Mahmood; Rhodri Jervis; Shangwei ZHOU | Energy; Fuel Cells | CC BY 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678fb52581d2151a021ef616/original/generalised-fault-diagnostics-of-polymer-electrolyte-fuel-cells-using-machine-learning.pdf |
61ad0d977ce05654ff8a3f2d | 10.26434/chemrxiv-2021-c5q8b | Chemical vapor deposition of sp2-boron nitride films on Al2O3 (0001), (11𝟐0), (1𝟏02) and (10𝟏0) substrates | Thin films of boron nitride in its sp2-hybridized form (sp2-BN) have potential use in UV-devices and dielectrics. Here, we explore chemical vapor deposition (CVD) of sp2-BN on various cuts of sapphire; Al2O3(112̅0), Al2O3(11̅02), Al2O3(11̅00) and Al2O3 (0001) using two CVD processes with different boron precursors; triethylborane (TEB) and trimethylborane (TMB). Fourier transform infrared spectroscopy (FTIR) showed that sp2-BN grows on all the sapphire substrates, using X-ray diffraction (XRD), 2θ/ω diffractograms showed that only Al2O3(112̅0) and Al2O3(0001) renders crystalline films and using phi(ɸ)-scans the growth of rhombohedral polytype (r-BN) films on these substrates is confirmed. These films are found to be epitaxially grown on an AlN interlayer with a higher crystalline quality for the films grown on the Al2O3(112̅0) substrate which is determined using omega(ω)-scans. Our study suggests that Al2O3(112̅0) is the most favorable sapphire substrate to realize the envisioned applications of r-BN films. | Sachin Sharma; Laurent Souqui; Henrik Pedersen; Hans Högberg | Physical Chemistry; Materials Science; Coating Materials; Thin Films; Surface; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ad0d977ce05654ff8a3f2d/original/chemical-vapor-deposition-of-sp2-boron-nitride-films-on-al2o3-0001-1120-1102-and-1010-substrates.pdf |
641987dd2bfb3dc2511da0a0 | 10.26434/chemrxiv-2023-2zb3k | Novel ultrahard carbon allotropes from crystal chemistry and first principles: rhombohedral ene-C21 and yne-C24 | Rhombohedral ene-C21 and yne-C24, characterized by the presence of C=C and C=C bonds, respectively, inserted into the 9R diamond polytype C18, are proposed as novel ultrahard carbon allotropes from crystal chemistry and first principles. Like 9R C18, they belong to the cfe topology characteristic of layered SiC polytypes. With ultrahard properties approaching those of diamond and lonsdaleite, ene-C21 and yne-C24 are dynamically stable with phonon signatures identifying C=C and C=C high frequency vibrations similar to molecular allene and acetylene. The electronic band structures correspond to insulating C18, metallic ene-C21 and semiconducting yne-C24. | Samir F. Matar; Vladimir L. Solozhenko | Theoretical and Computational Chemistry; Materials Science; Carbon-based Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641987dd2bfb3dc2511da0a0/original/novel-ultrahard-carbon-allotropes-from-crystal-chemistry-and-first-principles-rhombohedral-ene-c21-and-yne-c24.pdf |
61d4345675c5722662022016 | 10.26434/chemrxiv-2021-87t1c-v2 | Identifying signatures of thermal and
non-thermal reaction pathways in plasmon
induced H2 + D2 exchange reaction | In this work we demonstrate a strategy for identifying experimental signatures of thermal and non-thermal effects in plasmon mediated heterogeneous catalytic chemistry, a topic widely debated and discussed in the literature. Our method is based on monitoring the progress of plasmon-induced (or thermally-driven) reaction, carried out in a closed system, all the way to equilibrium. Initial part of evolution of the reaction provides information about kinetics, whereas at later times the equilibrium
concentrations provide information about effective temperature at the reaction sites. Combining these two pieces of information we estimate the activation energies. Using this strategy on H 2 (g) + D 2 (g) <-->2 HD(g) isotope exchange reaction, catalyzed by Au nanoparticles under thermally-driven and light-induced conditions, we estimate the activation energies to be 0.75 ± 0.02 eV and 0.21 ± 0.02 eV, respectively. These vastly different activation energies observed are interpreted as a signature of different reaction
pathways followed by the system under thermally-driven and light-induced conditions. | Amaraja Taur; Saurabh Kumar Singh; Pranav Ravindra Shirhatti | Physical Chemistry; Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2022-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d4345675c5722662022016/original/identifying-signatures-of-thermal-and-non-thermal-reaction-pathways-in-plasmon-induced-h2-d2-exchange-reaction.pdf |
6712c34bcec5d6c1428ba031 | 10.26434/chemrxiv-2024-5nvjs | Advancing Sustainable Ammonia Production via Solventless, Robust, and Thermally Conductive Absorbents | Sorption-based low-pressure green ammonia synthesis using supported metal halide salts enables efficient interconversion between hydrogen and ammonia, allowing the high hydrogen density and well-established transportation network of ammonia to be used for green energy storage. Magnesium chloride supported on silica gel (MgCl2/SiO2) sorbent has been the subject of much investigation owing to its high capacity, selectivity, and reversibility at temperatures close to reactor conditions; however, MgCl2/SiO2 suffers from low thermal conductivity, which complicates absorber design at larger scales and prolongs absorption-desorption cycle times. We present a scalable, solventless method for supporting MgCl2 on thermally conductive aluminum fibers (MgCl2/Al) - a thermally conductive ammonia sorbent with a high working capacity of 220 mgNH3/gabsorbent. Although the solventless synthesis causes variance in initial-cycle pressure drop and capacity, we show that this stabilizes after cycling. The high thermal conductivity of MgCl2/Al allows for rapid absorption-desorption cycles, enabling easier scale-up. MgCl2/Al also maintains its cyclic capacity up to 50 cycles without any signs of degradation. | Tejas Nivarty; William Straub; Chinomso Onuoha; Michael Manno; Jeffrey Schott; Mahdi Malmali; Alon McCormick | Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Reaction Engineering; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6712c34bcec5d6c1428ba031/original/advancing-sustainable-ammonia-production-via-solventless-robust-and-thermally-conductive-absorbents.pdf |
66266475418a5379b0628d73 | 10.26434/chemrxiv-2024-5vhzx | Evaluation of a fluorescence–based screening assay for the detection of silyl hydrolase activity | This study reports the development of fluorometric assays for the detection and quantification of silyl hydrolase activity, using silicatein as a model enzyme. These assays employed a series of organosilane substrates containing either the mycophenolate or umbelliferone moieties, which become fluorescent upon hydrolysis of a scissile Si–O bond. Amongst these substrates, the mycophenolate-derived molecule MycoF, emerged as the most promising candidate due to its relative stability in aqueous media, which resulted in good differentiation between the enzyme-catalysed and uncatalysed background hydrolysis. The utility of MycoF was also demonstrated in the detection of enzyme activity in cell lysates and was found to be capable of rapid identification of a positive ‘hit’ with assay times as low as 15 min. These fluorogenic substrates were also suitable for use in quantitative kinetic assays, as demonstrated by the acquisition of their Michaelis-Menten parameters. | Jason Z. He; Yuqing Lu; Neha Jain; David G. Churchill; Lu Shin Wong | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Bioorganic Chemistry; Biochemical Analysis; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66266475418a5379b0628d73/original/evaluation-of-a-fluorescence-based-screening-assay-for-the-detection-of-silyl-hydrolase-activity.pdf |
60c758c1469df431f5f4573c | 10.26434/chemrxiv.14096603.v3 | The Temperature Dependence of Fundamental Photophysical Properties of [Eu(MeOH-d4)9]3+ Solvates and [Eu.DOTA(MeOH-d4)]- Complexes | The trivalent lanthanide ions show optical transitions between energy levels within the 4f shell. All these transitions are formally forbidden according to the quantum mechanical selection rules used in molecular photophysics. Nevertheless, highly luminescent complexes can be achieved, and terbium(iii) and europium(iii) ions are particularly efficient emitters. This report started when an apparent lack of data in the literature led us to revisit the fundamental photophysics of europium(iii). The photophysical properties of two complexes – [Eu.DOTA(MeOH-d4)]- and [Eu(MeOH-d4)9]3+ – were investigated in deuterated methanol at five different temperatures. Absorption spectra showed decreased absorption cross sections as the temperature was increased. Luminescence spectra and time-resolved emission decay profiles showed a decrease in intensity and lifetime as a temperature was increased. Having corrected the emission spectra for the actual number of absorbed photons and differences in non-radiative pathways, the relative emission probability was revealed. These were found to increase with increasing temperature. The transition probability for luminescence was shown to increase with temperature, while the transition probability for light absorption decreased. The changes in transition probabilities were correlated to a change in the symmetry of the absorber or emitter, with an average increase in symmetry lowering absorption cross section and access to more asymmetric structures increasing the emission rate constant. Determining luminescence quantum yields and the Einstein coefficient for spontaneous emission allowed us to conclude that lowering symmetry increases both. Further, it was found that collisional self-quenching is an issue for lanthanide luminescence, when high concentrations are used. Finally, detailed analysis revealed results that show the so-called ‘Werts’ method’ for calculating radiative lifetimes and intrinsic quantum yields are based on assumption that does not hold for the two systems investigated here. We conclude that we are lacking a good theoretical description of the intraconfigurational f-f transition, and that there are still aspects of fundamental lanthanide photophysics to be explored.<br /> | Nicolaj Kofod; Lea Gundorff Nielsen; Thomas Just Sørensen | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758c1469df431f5f4573c/original/the-temperature-dependence-of-fundamental-photophysical-properties-of-eu-me-oh-d4-9-3-solvates-and-eu-dota-me-oh-d4-complexes.pdf |
64d10d43dfabaf06ffdec0bf | 10.26434/chemrxiv-2023-61nh6-v2 | Shear Thickening Behavior in Injectable Tetra-PEG Hydrogels Cross-Linked via Dynamic Thia-Michael Addition Bonds | Injectable poly(ethylene glycol, PEG)-based hydrogels were reversibly crosslinked through thia-conjugate addition bonds and demonstrated to shear thicken at low shear rates. Crosslinking bond exchange kinetics and dilute polymer concentrations were leveraged to tune hydrogel plateau moduli (from 60 - 650 Pa) and relaxation times (2 - 8 seconds). Under continuous flow shear rheometry, these properties affected the onset of shear thickening and the degree of shear thickening achieved before a flow instability occurred. The changes in viscosity were reversible whether the shear rate increased or decreased, suggesting that chain stretching drives this behavior. Given the relevance of dynamic PEG hydrogels under shear to biomedical applications, their injectability was investigated, and injection forces were found to increase with higher polymer concentrations and slower bond exchange kinetics. Altogether, these results characterize the nonlinear rheology of dilute, dynamic covalent tetra-PEG hydrogels and offer insight to the mechanism driving their shear thickening behavior. | Anne Crowell; Thomas FitzSimons; Eric Anslyn; Kelly Schultz; Adrianne Rosales | Materials Science; Polymer Science; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d10d43dfabaf06ffdec0bf/original/shear-thickening-behavior-in-injectable-tetra-peg-hydrogels-cross-linked-via-dynamic-thia-michael-addition-bonds.pdf |
63f62a5f897b18336ff4dd10 | 10.26434/chemrxiv-2023-1pm0d | Substrate Specific Closed-loop Optimization of Carbohydrate Protective Group Chemistry Using Bayesian Optimization and Transfer Learning | A new way of performing reaction optimization within carbohydrate chemistry is presented. This is done by performing closed-loop optimization of regioselective benzoylation of unprotected glycosides using Bayesian optimization. Both 6-O- monobenzoylations and 3,6-O-dibenzoylations of three different monosaccharides are optimized. A novel transfer learning approach, where data from previous optimizations of different substrates is used to speed up the optimizations, has also been developed. The optimal conditions found by the Bayesian Optimization algorithm provide new insight into substrate specificity, as the conditions found are significantly different. In most cases, the optimal conditions include Et3N and benzoic anhydride, a new reagent combination for these reactions, discovered by the algorithm, demonstrating the power of this concept to widen the chemical space. Further, the developed procedures include ambient conditions and short reaction times. | Natasha Videcrantz Faurschou; Rolf Hejle Taaning; Christian Marcus Pedersen | Theoretical and Computational Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f62a5f897b18336ff4dd10/original/substrate-specific-closed-loop-optimization-of-carbohydrate-protective-group-chemistry-using-bayesian-optimization-and-transfer-learning.pdf |
60c73cc9702a9ba934189aa7 | 10.26434/chemrxiv.14770740.v1 | A Ball Milling Enabled Cross-Electrophile Coupling | <div><div><div><p>The nickel-catalyzed cross-electrophile coupling of aryl (pseudo)halides and alkyl (pseudo)halides enabled by ball-milling is herein described. Under a mechanochemical manifold, the reductive C–C bond formation was achieved in the absence of bulk solvent and air/moisture sensitive set-ups, in reaction times of 2 hours. The mechanical action provided by ball milling permits the use of a range of zinc sources to turnover the catalytic cycle of nickel. A library of 28 cross- electrophile coupled building blocks has been constructed to exemplify this technique.</p></div></div></div> | Andrew Jones; William I. Nicholson; Jamie Leitch; Duncan Browne | Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9702a9ba934189aa7/original/a-ball-milling-enabled-cross-electrophile-coupling.pdf |
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