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60c755529abda209a5f8e2f1 | 10.26434/chemrxiv.14075408.v1 | The Structure-Based Design of SARS-CoV-2 Nsp14 Methyltransferase Ligands Yields Nanomolar Inhibitors | COVID-19, caused by the SARS-CoV-2 virus, is
responsible for a global pandemic that has paralyzed the normal life in many
countries around the globe. Therefore, the preparation of both effective
vaccines and potential therapeutics has become a major research priority in the
biotechnology sector. Both viral proteins and selected host factors are
important targets for the treatment of this disease. Suitable targets for
antiviral therapy include i.a. viral methyltransferases, which allow the viral
mRNA to be efficiently translated and protect the viral RNA from the innate immune
system. In this study, we have focused on the structure-based design of the inhibitors
of one of the two SARS-CoV-2 methyltransferases, nsp14. This methyltransferase
catalyzes the transfer of the methyl group from <i>S</i>-adenosyl-<i>L</i>-methionine
(SAM) to cap the guanosine triphosphate moiety of the newly synthesized viral
RNA, yielding the methylated capped RNA and <i>S</i>-adenosyl-<i>L</i>-homocysteine (SAH). The crystal
structure of SARS-CoV-2 nsp14 is unknown; we have taken advantage of its high
homology to SARS-CoV nsp14 and prepared its homology model, which has allowed
us to identify novel SAH derivatives modified at the adenine nucleobase as
inhibitors of this important viral target. We have synthesized and tested the designed
compounds <i>in vitro</i> and shown that
these derivatives exert unprecedented inhibitory activity against this crucial enzyme.
The docking studies nicely explain the contribution of an aromatic part
attached by a linker to the position 7 of the 7-deaza analogues of SAH. Our
results will serve as an important source of information for the subsequent
development of new antivirals to combat COVID-19. | Tomáš Otava; Michal Šála; Fengling Li; Jindřich Fanfrlík; Kanchan Devkota; Paknoosh Pakarian; Pavel Hobza; Masoud Vedadi; Evzen Boura; Radim Nencka | Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755529abda209a5f8e2f1/original/the-structure-based-design-of-sars-co-v-2-nsp14-methyltransferase-ligands-yields-nanomolar-inhibitors.pdf |
60c757084c8919accbad4938 | 10.26434/chemrxiv.14347721.v1 | Conversion of Wood into Hierarchically Porous Charcoal in the 200-Gram-Scale Using Home-Built Kiln | Wood-to-charcoal
is crucial in developing new materials at the lab-scale for relevant
applications, such as pollutant removal from water. Unfortunately, laboratory carbonization methods
are costly and produce charcoal on the gram-scale. This work presents a
simple-to-build and simple-to-operate home-made kiln that carbonizes Eucalyptus
wood chips (yield of 30 ± 1%) and produces
charcoal on the 200-gram scale. Solid particles had the typical structure,
composition, and chemical behavior of charcoal obtained from wood. We believe
that his carbonization process eases the charcoal synthesis required for the
development of new charcoal-based materials. | Long Leonel; Pablo Arnal | Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757084c8919accbad4938/original/conversion-of-wood-into-hierarchically-porous-charcoal-in-the-200-gram-scale-using-home-built-kiln.pdf |
61b8a93ea53f1b6e739abe9f | 10.26434/chemrxiv-2021-d0szn | Blatter Radicals as Bipolar Materials for Symmetric Redox-Flow Batteries | Redox-active organic molecules are promising charge-storage materials for redox-flow batteries (RFBs), but material crossover between posolyte/negolyte and chemical degradation are limiting factors in the performance of all-organic RFBs. We demonstrate that the bipolar electrochemistry of 1,2,4-benzotriazin-4-yl (Blatter) radicals allows construction of batteries with symmetric electrolyte composition. Cyclic voltammetry shows that these radicals retain reversible bipolar electrochemistry also in the presence of water. The redox potentials of derivatives with a C(3)-CF3 substituent are least affected by water and, moreover, these compounds show >90% capacity retention after charge/discharge cycling in a static H-cell for seven days (ca. 100 cycles). Testing these materials in a flow regime at 0.1 M concentration of active material confirmed the high cycling stability under conditions relevant for RFB operation, and demonstrated that polarity inversion in a symmetric flow battery may be used to rebalance the cell. Chemical synthesis provides insight in the nature of the charged species by spectroscopy and (for the oxidized state) X-ray crystallography. The stability of these compounds in all three states of charge highlights the potential for application in symmetric organic redox-flow batteries. | Jelte Steen; Jules Nuismer; Vytautas Eiva; Albert Wiglema; Nicolas Daub; Johan Hjelm; Edwin Otten | Physical Chemistry; Organic Chemistry; Energy; Organic Synthesis and Reactions; Energy Storage; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b8a93ea53f1b6e739abe9f/original/blatter-radicals-as-bipolar-materials-for-symmetric-redox-flow-batteries.pdf |
64245da3647e3dca99b551db | 10.26434/chemrxiv-2023-j8hmc | Radiotherapy Enhancement by Ti3C2Tx MXenes | Radiotherapy is an integral part of cancer therapy. Due to the low tissue specificity of radiation, damage to tumor-surrounding healthy tissue remains a major concern. Radio-enhancers based on inorganic nanomaterials have attracted considerable attention in recent years. In addition to widely exploited metal and metal oxides nanoparticles, 2D materials may offer potential advantages due to their intrinsically high specific surface area.
Here, we report on the promising radio-enhancement properties of Ti3C2Tx MXenes. We show that Ti3C2Tx MXenes are readily internalized and well-tolerated by mammalian cells. In contrast to MXenes suspended in aqueous buffers which fully oxidize within days (yielding rice-grain shaped rutile nanoparticles), MXenes internalized by cells display slower oxidation rates, in line with cell-free experiments showing slower oxidation in cell media and lysosomal buffers compared to antioxidant-devoid dispersants. The MXenes show potent radio-enhancement properties with dose enhancement factors of up to 2.5 in human soft tissue sarcoma cells and no toxicity towards healthy human fibroblasts. Benchmarking against oxidized MXenes and commercial titanium dioxide nanoparticles indicates superior radio-enhancement properties of the intact 2D titanium carbide flakes. Taken together, this work provides direct evidence for the potent radio-enhancement properties of Ti3C2Tx MXenes rendering them a promising candidate material for radiotherapy enhancement.
| Monika Zimmermann; Lukas R.H. Gerken; Shianlin Wee; Vera M. Kissling; Anna Lena Neuer; Elena Tsolaki; Alexander Gogos; Maria R. Lukatskaya; Inge K. Herrmann | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64245da3647e3dca99b551db/original/radiotherapy-enhancement-by-ti3c2tx-m-xenes.pdf |
643e96aa83fa35f8f6d96e59 | 10.26434/chemrxiv-2023-0gzts | A Hammett’s analysis of the Substituent Effect in Functionalized Diketopyrrolopyrrole (DPP) Systems: optoelectronic properties and intramolecular charge transfer effects | Diketopyrrolopyrrole (DPP) systems have promising applications in different organic electronic devices. In this work, we investigated the effect of 20 distinct substituent groups on the optoelectronic properties of DPP-based derivatives as the donor (D)-material in an organic photovoltaics (OPV) device. For this purpose, we employed Hammett’s theory, which quantifies the electron-donating or -withdrawing properties of a given substituent group. Machine-Learning (ML)-based σ_m, σ_p, σ_m^0, σ_p^0, σ_p^+, σ_p^-, σ_I, and σ_R Hammett’s constants previously determined were used. Mono- (DPP-X1) and di-functionalized (DPP-X2) DPPs, where X is a substituent group, were investigated using density functional theory (DFT), time-dependent DFT (TDDFT), and ab initio methods. Several properties were computed using CAM-B3LYP and the second-order algebraic diagrammatic construction, ADC(2), ab initio wave function method, including the adiabatic ionization potential (IP_A), the electro affinity (EA_A), the HOMO-LUMO gaps (E_g), the maximum absorption wavelengths (λ_max), the first excited state transition 1S0 1S1 energies (∆E) (the optical gap), and exciton binding energies. From the optoelectronic properties and employing typical acceptor systems, the power conversion efficiency (PCE), open-circuit voltage (V_OC), and fill factor (FF) were predicted for a DPP-based OPV device. These photovoltaic properties were also correlated with the ML-based Hammett’s constants. Overall, good correlations between all properties and the different types of σ constants were obtained, except for the σ_I constants, which are related to inductive effects. This scenario suggests that resonance is the main factor controlling electron donation and withdrawal effects. We found that substituent groups with large σ values can produce higher photovoltaic efficiencies. It was also found that electron-withdrawing groups reduced E_g and ∆E considerably compared to the unsubstituted DPP-H. Moreover, for every decrease (increase) in the values of a given optoelectronic property of DPP-X1 systems, a more significant decrease (increase) in the same values was observed for the DPP-X2, thus showing that the addition of second substituent results in a more extensive influence on all electronic properties. For the exciton binding energies, an unsupervised machine learning algorithm identified groups of substituents characterized by average values (centroids) of Hammett’s constants that can drive the search for new DDP-derived materials. Our work presents a promising approach by applying Hammett’s theory on molecular engineering DPP-based molecules and other conjugated molecules for applications on organic optoelectronic devices. | Gabriel Monteiro-de-Castro; Itamar Borges Jr. | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643e96aa83fa35f8f6d96e59/original/a-hammett-s-analysis-of-the-substituent-effect-in-functionalized-diketopyrrolopyrrole-dpp-systems-optoelectronic-properties-and-intramolecular-charge-transfer-effects.pdf |
63c587c6c8362ca3fc6577fd | 10.26434/chemrxiv-2023-bf7lg | 2-Propanol Interacting with Co3O4(001):A combined AIMD and vSFS study | The interaction of 2-propanol with Co3O4(001) was studied by vibrational sum fre-quency spectroscopy (vSFS) and by ab initio molecular dynamics (AIMD) simulations of 2-propanol dissolved in a water film to gain insight at the molecular level into the pathways of catalytic oxidation. The experimental study has been performed under near ambient condition, where the presence of water vapor is unavoidable, resulting in a water film on the sample and thereby allowing us to mimic the solution-water interface. Both experiment and theory conclude that 2-propanol adsorbs molecularly. The lack of dissociation is attributed to the adsorption geometry of 2-propanol in which the O-H bond does not point towards the surface. Furthermore, the copresent water not only competitively adsorbs on the surface but also inhibits 2-propanol deprotonation. The calculations reveal that the presence of water deactivates the lattice oxygen, thereby reducing the surface activity. This finding sheds light on the multifaceted role of water at the interface for the electrochemical oxidation of 2-propanol in aqueous solution as recently reported. At higher temperatures 2-propanol remains molecularly adsorbedon Co3O4(001) until it desorbs with increasing surface temperature. | Amir H. Omranpoor; Anupam Bera; Denise Bullert ; Matthias Linke ; Soma Salamon ; Samira Weber ; Heiko Wende; Eckart Hasselbrink ; Eckhard Spohr; Stephane Kenmoe | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c587c6c8362ca3fc6577fd/original/2-propanol-interacting-with-co3o4-001-a-combined-aimd-and-v-sfs-study.pdf |
60c7509f702a9b528f18be0c | 10.26434/chemrxiv.13061717.v1 | Rerouting an Organocatalytic Reaction by Intercepting its Reactive Intermediates | Reactive intermediates are key to halting and promoting chemical transformations, however due to their elusive nature, they are seldom harnessed for reaction design. Herein, we describe studies aimed at stabilizing reactive intermediates in the N-heterocyclic carbene (NHC) catalytic cycle, which enabled fully shutting down the known benzoin coupling pathway, while rerouting its intermediates toward deuteration. The reversible nature of NHC catalysis and the selective stabilization of reaction intermediates facilitated clean hydrogen-deuterium exchange reactions of aromatic aldehydes by D<sub>2</sub>O, even for challenging electron withdrawing substrates. The addition of catalytic amounts of phenyl boronic acid was used to further stabilize highly reactive intermediates and mitigate the formation of benzoin coupling by-products. The mechanistic understanding at the foundation of this work resulted in unprecedented mild conditions with base and catalyst loadings as low as 0.1 mol%, and a scalable deuteration reaction applicable to a broad substrate scope with outstanding functional group tolerance. More importantly, adopting this approach enabled the construction of a machine-learning derived guideline for identifying the appropriate catalyst and conditions for different substrates based on a logistic regression classification model. Experimental studies combined with machine learning and computational methods shed light on the non-trivial mechanistic underpinnings of this reaction. | Santosh C. Gadekar; Vasudevan Dhayalan; Ashim Nandi; Inbal L. Zak; Shahar Barkai; Meital Shema Mizrachi; sebastian kozuch; anat milo | Physical Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7509f702a9b528f18be0c/original/rerouting-an-organocatalytic-reaction-by-intercepting-its-reactive-intermediates.pdf |
63e5c7a8fcfb27a31f81f877 | 10.26434/chemrxiv-2023-fvh63 | A linear C=Ge=C heteroallene with a di-coordinated germanium atom | Allenes (>C=C=C<) are classified as cumulated dienes that have a linear structure with an sp-hybridized central carbon atom. We have succeeded in synthesizing and isolating a stable 2-germapropadiene derivative with bulky silyl substituents. The 2-germapropadiene allene moiety adopts a linear structure both in the solid state and in solution. In addition, an X-ray diffraction electron-density-distribution analysis of this 2-germapropadiene revealed a linear C=Ge=C geometry with a formally sp-hybridized germanium atom bearing two orthogonal C=Ge pi-bonds. Based on detailed structural and computational studies, it can be concluded that the linear geometry of the isolated 2-germapropadiene most likely arises from the negative hyperconjugation of the silyl substituents at the terminal carbon atoms. The 2-germapropadiene reacts rapidly with nucleophiles, indicating that the linearly oriented germanium atom is highly electrophilic. | Koh Sugamata; Teppei Asakawa; Daisuke Hashizume; Mao Minoura | Organometallic Chemistry; Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e5c7a8fcfb27a31f81f877/original/a-linear-c-ge-c-heteroallene-with-a-di-coordinated-germanium-atom.pdf |
60c755984c89193682ad46e4 | 10.26434/chemrxiv.14135156.v1 | The Egg-Shaped Crystals That Should Not Be: A Brain-like Texture Combined with Single Crystallinity | We demonstrate here a unique metallo-organic material where the appearance and the internal crystal structure contradict. The egg-shaped (ovoid) crystals have a "brain-like" texture. Although these micro-sized crystals are monodispersed; like fingerprints the grainy surfaces are never alike. Remarkable, our X-ray and electron diffraction studies unexpectedly revealed that these structures are single crystals comprising a continuous coordination network of homochiral hexagonal and triangular channels. By applying different reaction condition, a series of isostructural and monodisperse crystals were obtained having a monodomain appearance. These results indicate that families of isostructural crystals following the established rules for crystal growth contain hidden gems to be discovered with fascinating multidomain morphologies.<br />
<br /> | vivek singh; Lothar Houben; linda shimon; Sidney Cohen; Ofra Golani; Yishay Feldman; Michal Lahav; Milko van der Boom | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Aggregates and Assemblies; Hybrid Organic-Inorganic Materials; Self-Assembly; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755984c89193682ad46e4/original/the-egg-shaped-crystals-that-should-not-be-a-brain-like-texture-combined-with-single-crystallinity.pdf |
64628b7bfb40f6b3eea50f70 | 10.26434/chemrxiv-2023-15vg7 | Catalytic materials enabled by a programmable assembly of synthetic polymers and engineered bacterial spores | Natural biological materials are formed by self-assembly processes and catalyze a myriad of reactions. Here, we report a programmable molecular assembly of designed synthetic polymers with engineered bacterial spores. This self-assembly process is driven by dynamic covalent bond formation on spore surface glycan and yields macroscopic materials that are structurally stable, self-healing, and recyclable. Molecular programming of polymer species shapes the physical properties of these materials while metabolically dormant spores allow for prolonged ambient storage. Incorporation of spores with genetically encoded functionalities enables operationally simple and repeated enzymatic catalysis. Our work lays an important foundation for scalable and programmable synthesis of robust materials for sustainable biocatalysis. | Masamu Kawada; Hyuna Jo; Alexis M. Medina; Seunghyun Sim | Catalysis; Polymer Science; Hydrogels; Polymer scaffolds; Biocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64628b7bfb40f6b3eea50f70/original/catalytic-materials-enabled-by-a-programmable-assembly-of-synthetic-polymers-and-engineered-bacterial-spores.pdf |
646edf9d4f8b1884b73c3112 | 10.26434/chemrxiv-2023-jgr4j | Dewar Pyridines: Conformationally Programmable Piperidine Isosteres | Bioisosteric replacement is an indispensable tool in the medicinal chemist’s arsenal to strike a fine balance in multiparameter optimization campaigns and to deliver the best molecules for further preclinical development. The piperidine heterocycle, a dominant fragment in drug discovery, is often targeted for such replacement in attempts to improve potency and ADME (absorption, distribution, metabolism, excretion) profile. In this manuscript we explore 4H-Dewar pyridines (4H-DP) as rigid programmable isosteres of equatorially and elusive axially substituted piperidines. These fragments are readily accessible via pyridine dearomatization without the need for expensive catalysts and reagents. A wide spectrum of available reactivities enables incorporation of 4H-DP in various structural contexts. Exit vector analysis (EVA) underscores topological similarity with the parent piperidine as well as complementarity with the previously reported bioisosteres. | Jan Petrovcic; Yaroslav Boyko D.; Alexander S. Shved; Giovanni Lenardon; Christophe Salome; Quentin Lefebvre; Thomas Fessard; David Sarlah | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646edf9d4f8b1884b73c3112/original/dewar-pyridines-conformationally-programmable-piperidine-isosteres.pdf |
61125cf7d800ad0f19434bf0 | 10.26434/chemrxiv-2021-p56dh | Off-target profiling of tofacitinib and baricitinib by machine learning: a focus on thrombosis and viral infection. | Objectives: There are no clear on-target mechanisms that explain the increased risk for thrombosis and viral infection or reactivation associated with Janus kinase (JAK) inhibitors. We aimed to identify and validate off-target binding effects of the JAK inhibitors baricitinib and tofacitinib using computational and experimental methods.
Methods: Potential biological targets of baricitinib and tofacitinib were predicted using two established computational methods. Targets related to thrombosis or viral infection/reactivation were experimentally validated using biochemical and cell-based in vitro assays.
Results: Overall, 98 targets were predicted by the computational methods (baricitinib n=41; tofacitinib n=58), of which 17 drug-target pairs were related to thrombosis (n=10) or viral infection/reactivation (n=7), and 11 were commercially available for in vitro analysis. Inhibitory activity was identified in vitro for four drug-target pairs – two related to thrombosis in the micromolar range (phosphodiesterase 10A [baricitinib], transient receptor potential cation channel subfamily M subtype 6 [tofacitinib]) and two related to viral infection/reactivation in the nanomolar range (Serine/threonine protein kinase N2 [baricitinib, tofacitinib]).
Conclusions: Previously unknown off-target interactions for the two JAK inhibitors were identified. The proposed pharmacological off-target effects include attenuation of pulmonary vascular remodeling, modulation of Hepatitis C viral response and hypomagnesemia. Off-target effects related to an increased risk of thrombosis or viral infection/reactivation for baricitinib and tofacitinib were not identified. Further clinical and experimental research is required to explain the observed thrombosis and viral infection/reactivation risk.
| Maria Luisa Faquetti; Francesca Grisoni; Petra Schneider; Gisbert Schneider; Andrea Burden | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2021-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61125cf7d800ad0f19434bf0/original/off-target-profiling-of-tofacitinib-and-baricitinib-by-machine-learning-a-focus-on-thrombosis-and-viral-infection.pdf |
66dfa858cec5d6c142a3c8d7 | 10.26434/chemrxiv-2024-w9fqr | Self-Strengthening Tough Elastomers Enabled by Dynamic Bottlebrush Mechanophores | Low activation efficiency of mechanosensitive groups in bulk materials challenges the expansion of practical applications of mechanochemistry. Here, we wish to report a topological approach to address this problem. Assembling dynamic mechanophores in a bottlebrush topology can increase the scission probability and unlock multiple rounds of activation. This concept is materialized via a new ring-opening polymerization reaction of cyclic carbonates followed by cross-linking with thermoplastic polyurethanes. The resulting elastomers, featuring advanced topology at the cross-linking points, display enhanced mechanosensitivity, high mechanical performance, and training-induced self-strengthening behavior without chemical amplification with a second component. | Jun-Jie Wang; Xing-Yuan Zhang; Qianyi Liu; Jun Wen; Rong Zhu | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dfa858cec5d6c142a3c8d7/original/self-strengthening-tough-elastomers-enabled-by-dynamic-bottlebrush-mechanophores.pdf |
60c75710ee301cb613c7b4a2 | 10.26434/chemrxiv.14369663.v1 | N-Phenylputrescine (NPP): A Natural Product Inspired Amine Donor for Biocatalysis | The synthesis of chiral amines in enantioenriched form is a keystone reaction in applied chemical
synthesis. There is a strong push to develop greener and more sustainable alternatives to the
metal-catalysed methods currently used in the pharmaceutical, agrochemical and fine chemical
industries. A biocatalytic approach using transaminase (TA or ATA) enzymes to convert
prochiral ketones to chiral amines with unparalleled levels of enantioselectivity is highly
appealing. However, the use of TA enzymes in synthesis is severely hampered by the unfavourable
thermodynamics associated with the amine donor/acceptor equilibrium. Several ‘smart’ amine
donors have been developed that leverage chemical and physical driving forces to overcome this
challenging equilibrium. Alongside this strategy, enzyme engineering is typically required to
develop TAs compatible with these non-physiological amine donors and the unnatural reaction
conditions they require. We herein disclose N-phenylputrescine (NPP) as a readily accessible
amine donor, inspired by the biosynthesis of the dipyrroloquinoline alkaloids. NPP is compatible
with a broad range of synthetically useful TA biocatalysts and performs across an unparalleled
variety of reaction conditions (pH and temperature). Synthetic applicability has been
demonstrated through the synthesis of the anti-diabetic drug sitagliptin, delivering the product
in excellent enantiopurity using just two equivalents of NPP<br /> | Catherine McKenna; Mária Štiblariková; Irene De Silvestro; Dominic Campopiano; Andrew Lawrence | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75710ee301cb613c7b4a2/original/n-phenylputrescine-npp-a-natural-product-inspired-amine-donor-for-biocatalysis.pdf |
60c747c1f96a0020dd286fa0 | 10.26434/chemrxiv.11768814.v1 | Promoting Nitrogen Electroreduction to Ammonia with Bismuth Nanocrystals and Potassium Cations in Water | We demonstrate that bismuth exhibits no measurable electrocatalytic activity for the nitrogen reduction reaction to ammonia in aqueous electrolyte solutions, contrary to several recent reports on the highly impressive rates of Bi-catalysed electrosynthesis of NH<sub>3</sub> from N<sub>2</sub>. | Jaecheol Choi; Hoang-Long Du; Manjunath Chatti; Bryan H. R. Suryanto; Alexandr Simonov; Douglas Macfarlane | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c1f96a0020dd286fa0/original/promoting-nitrogen-electroreduction-to-ammonia-with-bismuth-nanocrystals-and-potassium-cations-in-water.pdf |
66f5736d51558a15ef344070 | 10.26434/chemrxiv-2024-zrq0s | Distinct Valence States of the [4Fe4S] Cluster Revealed in the Hydrogenase CrHydA1 | Harnessing biological systems for the hydrogen economy requires a thorough understanding of the responsible iron-sulfur (FeS) cluster-containing proteins. This study focuses on the HydA1 hydrogenase of Chlamydomonas reinhardtii (CrHydA1), a simplistic and well-characterized [FeFe]-hydrogenase and employs electron paramagnetic resonance (EPR) spectroscopy for studying the complex paramagnetic states of its FeS cluster. We report the existence of two distinct cluster species arising from a single [4Fe4S]-cluster within the apo-form of the enzyme. Multi-frequency and variable-temperature pulsed EPR experiments revealed the interconversion of the two dominating species, characterized by their axial and rhombic EPR responses. The species interconvert depending on redox potentials and pH levels. Molecular dynamics simulations and quantum mechanical calculations identified two secondary-sphere residues, Arg227 and Lys228, as potential causes of the binary response of the [4Fe4S] cluster. These amino acids can adopt inner and outer conformations relative to the [4Fe4S] cluster, causing valence rearrangement and thus providing a plausible explanation for the observed spectroscopic differences. The dynamic behavior of these cluster species not only suggests a central role in the catalytic mechanisms of hydrogenases but also offers valuable insights for the analysis of other FeS-containing metalloproteins with comparable characteristics. | Melanie Heghmanns; Shalini Yadav; Sergius Boschmann; Victor Selve; Astrit Veliju; Claudia Brocks; Thomas Happe; Dimitrios Pantazis; Müge Kasanmascheff | Physical Chemistry; Biological and Medicinal Chemistry; Energy; Biophysics; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f5736d51558a15ef344070/original/distinct-valence-states-of-the-4fe4s-cluster-revealed-in-the-hydrogenase-cr-hyd-a1.pdf |
65fc6ce066c13817297ce414 | 10.26434/chemrxiv-2024-8d6zr | Development of a portable SERS tool to evaluate the effectiveness of washing methods to remove pesticide residue from fruit surface | Pesticides are commonly used to control pests and improve crop productivity in agriculture. Upon post-harvest, concerns have emerged regarding the potential harmful health effects resulting from the presence of pesticide residues. Analyzing these residues on crop surfaces is challenging due to their typically low concentration and potential interference from the complex matrix of the produce’s surface. To address this challenge, we developed a portable surface-enhanced Raman spectrometer (SERS)-based approach that offers a fast turnover rate, simplified protocol, on-site capability, and high sensitivity. Further, this new approach was used to investigate the efficacy of various washing methods to remove a fungicide (ferbam) from peach surfaces. Household washing methods were compared with the chlorine wash used in the food processing industry (25 mg/L, sodium hypochlorite). The 1- and 5-minute chlorine wash (25 mg/L) proved most effective in removing pesticide residues, compared to tap water, sodium bicarbonate, and vinegar-soaking methods. Among household washing agents, sodium bicarbonate and vinegar provided superior removal effectiveness compared to tap water. In addition, SERS analysis on the flesh and backside of the skin revealed negligible penetration of ferbam into peaches. This study not only introduces an innovative method for measuring pesticide residues but also contributes to our understanding of pesticide removal and penetration. This knowledge is crucial for the effective use of pesticides and mitigation of their exposure through food sources. | Lydia Freund; Huiyuan Guo; Jacqueline Mossa | Analytical Chemistry; Agriculture and Food Chemistry; Spectroscopy (Anal. Chem.); Food | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fc6ce066c13817297ce414/original/development-of-a-portable-sers-tool-to-evaluate-the-effectiveness-of-washing-methods-to-remove-pesticide-residue-from-fruit-surface.pdf |
60c74a97702a9b4a6d18b2a8 | 10.26434/chemrxiv.9938969.v3 | ‘Ring Breaker’: Neural Network Driven Synthesis Prediction of the Ring System Chemical Space | <p></p><p>Ring systems in
pharmaceuticals, agrochemicals and dyes are ubiquitous chemical motifs. Whilst
the synthesis of common ring systems is well described, and novel ring systems
can be readily computationally enumerated, the synthetic accessibility of
unprecedented ring systems remains a challenge. ‘Ring Breaker’ uses a
data-driven approach to enable the prediction of ring-forming reactions, for
which we have demonstrated its utility on frequently found and unprecedented
ring systems, in agreement with literature syntheses. We demonstrate the
performance of the neural network on a range of ring fragments from the ZINC and
DrugBank databases and highlight its potential for incorporation into computer
aided synthesis planning tools. These approaches to ring formation and
retrosynthetic disconnection offer opportunities for chemists to explore and
select more efficient syntheses/synthetic routes. </p><br /><p></p> | Amol Thakkar; Nidhal Selmi; Jean-Louis Reymond; Ola Engkvist; Esben Jannik Bjerrum | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Process Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Pharmaceutical Industry | CC BY 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a97702a9b4a6d18b2a8/original/ring-breaker-neural-network-driven-synthesis-prediction-of-the-ring-system-chemical-space.pdf |
60c75809567dfe0a2eec67a6 | 10.26434/chemrxiv.14491842.v1 | Biovalorisation of Brewer's Spent Grain (BSG) and Sensory Evaluation of BSG Bread | <div>
<div>
<div>
<p>Brewer’ spent grain (BSG) is the largest by-product of beer production,
generating over an approximate 38 billion kg annually. While the majority of BSG gets
repurposed as animal feed, its usage unfortunately remains very limited. Due to the
impressive nutritional profile of BSG, many studies have investigated its incorporation
in food products. However, its substitution at high levels tend to bring about
undesirable sensory changes. This paper looks at solid-state fermentation as a tool to
enhance the nutritional profile of BSG. The consumer acceptance of fermented BSG-
fortified bread was investigated, to understand the market value for fermented BSG
food products compared to its unfermented counterpart. Of the 8 koji starters studied,
M-1 (Aspergillus oryzae) brought about the greatest nutritional profile enhancement in
terms of total phenolic content and crude protein content, with an optimal fermentation
time of 4 days. No change in total dietary fibre content was observed after fermentation.
From the sensory evaluation, fermented BSG-fortified bread had the best nutritional
profile while having the poorest consumer acceptance. Despite the fact, this study
highlights that fermentation may yet be an important tool in bridging the gap of BSG
incorporation in food.
</p>
</div>
</div>
</div> | Luo Lin Goh; Ken Chi Lik Lee | Food | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75809567dfe0a2eec67a6/original/biovalorisation-of-brewer-s-spent-grain-bsg-and-sensory-evaluation-of-bsg-bread.pdf |
630781811945add389e67c36 | 10.26434/chemrxiv-2022-0hm0w | Photoinduced Acylations Via Azolium-Promoted Intermolecular Hydrogen Atom Transfer | Photoinduced hydrogen atom transfer (HAT) has been developed as a powerful tool to generate synthetically valuable radical species. The direct photoexcitation of ketones has been known to promote HAT or to generate acyl radicals through Norrish-type pathways, but these modalities remain severely limited by radical side reactions. We report herein a catalyst- and transition metal-free method for the acylation of C–H bonds that leverages the unique properties of stable, isolable acyl azolium species. Specifically, acyl azolium salts are shown to undergo an intermolecular and regioselective HAT upon LED irradiation with a range of substrates bearing active C–H bonds followed by C–C bond formation to afford ketones. Experimental and computational studies support photoexcitation of the acyl azoli-um followed by facile intersystem crossing to access triplet diradical species that promote selective HAT and radical-radical cross-coupling. | Karl Scheidt; Osvaldo Gutierrez; Joshua Zhu; Anthony Tam; Angel Renteria-Gomez; Achyut Gogoi | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630781811945add389e67c36/original/photoinduced-acylations-via-azolium-promoted-intermolecular-hydrogen-atom-transfer.pdf |
63f09b5bfcfb27a31ffda9fd | 10.26434/chemrxiv-2022-trrg5-v3 | Particle Size and Pore Size Selection on Ordered Mesoporous Silica | Controlling both particle size and pore size is critical when using mesoporous silica for fundamental studies. Pore size can be adjusted by modifying the reaction conditions during synthesis, but achieving a narrow particle size selection can be challenging. However, by allowing mesoporous silica to sediment in water, we can take advantage of the fact that particles of different sizes settle at different speeds in liquid. This approach enables us to obtain mesoporous silica particles with the exact pore size but different particle sizes or particles with varying pore sizes but the same particle size. This fine-tuning of particle size and pore size ensures precise control of the properties of mesoporous silica and is essential for many applications in various fields. | Tianyu Li | Nanoscience; Chemical Engineering and Industrial Chemistry; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f09b5bfcfb27a31ffda9fd/original/particle-size-and-pore-size-selection-on-ordered-mesoporous-silica.pdf |
621d17007c13f47c25627991 | 10.26434/chemrxiv-2022-vz360 | LabInform: A Modular Laboratory Information System
Built From Open Source Components | A framework for reproducible data analysis is only half the battle if it comes to reproducible
research. Additional essential requirements are a way to safely store both, raw data and metadata
and a method to uniquely refer to a dataset or any piece of information. Such unique identifier is
fully independent of the actual place the information referred to is stored and does not change over
time. Additionally, numeric IDs for samples and alike come in quite handy. A knowledge base and
an electronic lab notebook, both based on wiki software and thus easily accessible requiring only
a web browser and connection to the intranet, complete the system. Overarching design rules are
simplicity, robustness and sustainability, focussing on small-scale deployment of the system retaining
compatibility with future developments and community efforts. Key aspects in setting up the system
are its use of well-proven open-source tools combined with maximal modularity, resulting in a low
entry threshold and allowing to implement and develop it along the way of focussing on actual
research. | Till Biskup | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621d17007c13f47c25627991/original/lab-inform-a-modular-laboratory-information-system-built-from-open-source-components.pdf |
60c74c23bb8c1a8c7d3db37c | 10.26434/chemrxiv.12436457.v1 | Polymeric Encapsulation of a Ruthenium Polypyridine Complex for Tumor Targeted 1- and 2-Photon Photodynamic Therapy | Photodynamic
therapy is a medical technique, which is gaining increasing attention
to treat various types of cancer. Among the investigated classes of
photosensitizers, the use of Ru(II) polypyridine complexes is gaining
momentum. However, the currently investigated compounds generally show
poor cancer cell selectivity. As a consequence, high drug doses are
needed, which can cause side effects. To overcome this limitation, there
is a need for the development of a suitable drug delivery system to
increase the amount of PS delivered to the tumor. Herein, we report on
the encapsulation of a promising Ru(II) polypyridyl complex into
polymeric nanoparticles with terminal biotin groups. Thanks to this
design, the particles showed much higher selectivity for cancer cells in
comparison to non-cancerous cells in a 2D monolayer and 3D
multicellular tumor spheroid model. As a highlight, upon intravenous
injection of an identical amount of the Ru(II) polypyridine complex, an improved accumulation inside an adenocarcinomic human alveolar basal epithelial tumor
of a mouse by a factor of 8.7 compared to the Ru complex itself was
determined. The nanoparticles were found to have a high phototoxic
effect upon 1-photon (500 nm) or 2-photon (800 nm) excitation with an
eradication of an adenocarcinomic human alveolar basal epithelial tumor inside a mouse. Overall, this work describes, to the best of our knowledge, the first <i>in vivo</i>
study demonstrating the cancer cell selectivity of a very promising
Ru(II)-based PDT photosensitizer encapsulated into polymeric
nanoparticles with terminal biotin groups. | Johannes Karges; Jia Li; Leli Zeng; Hui Chao; Gilles Gasser | Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c23bb8c1a8c7d3db37c/original/polymeric-encapsulation-of-a-ruthenium-polypyridine-complex-for-tumor-targeted-1-and-2-photon-photodynamic-therapy.pdf |
60c74786567dfea99dec4822 | 10.26434/chemrxiv.11626068.v1 | QSPR Models for Predicting Critical Micelle Concentration of Gemini Cationic Surfactants Combining Machine-Learning Methods and Molecular Descriptors | <p>
A
data set of 231 diverse gemini cationic surfactants has been
developed to correlate the logarithm of critical micelle
concentration (cmc) with the molecular structure using a quantitative
structure-property relationship (QSPR) methods. The QSPR models were
developed using the Online CHEmical Modeling environment (OCHEM). It
provides several machine learning methods and molecular descriptors
sets as a tool to build QSPR models. Molecular descriptors were
calculated by eight different software packages including Dragon v6,
OEstate and ALogPS, CDK, ISIDA Fragment, Chemaxon, Inductive
Descriptor, SIRMS, and PyDescriptor. A total of 64 QSPR models were
generated, and one consensus model developed by using a simple
average of 13 top-ranked individual models. Based on the statistical
coefficient of QSPR models, a consensus model was the best QSPR
models. The model provided the highest R<sup>2</sup>
= 0.95, q<sup>2
</sup>=
0.95, RMSE = 0.16 and MAE = 0.11 for training set, and R<sup>2</sup>
= 0.87, q<sup>2</sup>
= 0.87, RMSE = 0.35 and MAE = 0.21 for test set. The model was freely
available at https://ochem.eu/model/8425670 and can be used for
estimation of cmc of new gemini cationic surfactants compound at the
early steps of gemini cationic surfactants development.</p> | Ely Setiawan; Mudasir Mudasir; Karna Wijaya | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74786567dfea99dec4822/original/qspr-models-for-predicting-critical-micelle-concentration-of-gemini-cationic-surfactants-combining-machine-learning-methods-and-molecular-descriptors.pdf |
60c750f0842e65267ddb3ae1 | 10.26434/chemrxiv.12950336.v2 | Oxygenate Reactions over PdCu and PdAg Catalysts: Distinguishing Electronic and Geometric Effects on Reactivity and Selectivity | We investigate PdCu and PdAg catalysts in the context of oxygenate upgrading for biofuels. To this end, we measure the rates of decarbonylation and hydrogenation of butyraldehyde, the reactive intermediate for the industrially relevant Guerbet condensation, and correlate the selectivity and reactivity with the properties of the catalysts via a range of characterization efforts. Data obtained from EXAFS and XANES show that the bulk of the catalyst metallic nanoparticles is enriched in Pd, while the surface is enriched in Cu and Ag. The data for PdCu show clear dominance of geometric (ensemble) effects on the selectivity. Conversely, the electronic (ligand) effects of alloying dominate over the reaction rate of the catalysts, as electron donation from Cu to Pd promotes the Cu and increases the desired (de)hydrogenation reactions. In contrast, in PdAg catalysts, the weaker electronic exchange, as indicated by Pd L edge XANES and theoretical calculations, is not sufficient to promote Ag, resulting in monotonic loss of activity with increasing Ag content and without selectivity improvement. We use the implications of these findings to provide valuable design principles for oxygenate catalysis and to discover a highly selective bifunctional catalyst system, comprised of a PdCu alloy catalyst and titanium dioxide for the upgrading of ethanol to longer-chain oxygenates.<br /> | Tanmayi Bathena; Truc Phung; Scott Svadlenak; Yu Liu; Lars Grabow; Konstantinos A Goulas | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750f0842e65267ddb3ae1/original/oxygenate-reactions-over-pd-cu-and-pd-ag-catalysts-distinguishing-electronic-and-geometric-effects-on-reactivity-and-selectivity.pdf |
679a580d6dde43c908dd8e0a | 10.26434/chemrxiv-2025-zrrlc | Scalable manufacturing of radiation-tolerant potentiometric electrodes: A systematic transition from laboratory to semi-automated fabrication | A “lab-to-fab” transition is described that enables the semi-automated production of thin-film potentiometric pH electrodes, designed for use in sterile single-use bioreactors. Manual methods of materials deposition and film casting are replaced with spray coating on a moving web and the production of membranes with a programmable dispenser operating at constant rates. These provide a greater degree of control over membrane thickness and a reduction in voltage spread between electrodes, which are evaluated in batches using a multichannel analyzer. Gamma-ray ionization of the pH electrodes introduces a predictable voltage drift that follows a log decay function on the day timescale; the voltage decay rate correlates with membrane thickness and can be modeled as a parallel diode–capacitor circuit. Batches of radiation-sterilized pH electrodes were tested in cell culture media and yielded mean pH values within 0.05 units relative to a commercial meter (ground truth) following a single-point calibration protocol. Quantitative uncertainty analysis attributes more than half of total error to variations caused by ionizing radiation, and yields novel insights into strategies for reducing uncertainty. | Bingyuan Zhao; Aiganym Yermembetova; Benson Tsai; Jialong Huang; Alexander Wei | Materials Science; Analytical Chemistry; Materials Processing; Thin Films; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679a580d6dde43c908dd8e0a/original/scalable-manufacturing-of-radiation-tolerant-potentiometric-electrodes-a-systematic-transition-from-laboratory-to-semi-automated-fabrication.pdf |
67040d44cec5d6c142767589 | 10.26434/chemrxiv-2024-3rzp4 | Kinetic Studies of Zirconium Catalyzed Ring-opening Copolymerization of Epoxide and Cyclic Anhydride | Zirconium(IV) isopropoxide complexes supported by the ligands 2-pyridylamino-N,N-bis(2-methylene-4,6-dimethylphenolate), L1, 2-pyridylamino-N,N-bis(2-methylene-4,6-tert-amylphenolate), L2, and N,N-dimethyl-N,N-bis(2-methylene-4,6-dimethylphenolate)ethylenediamine, L3 (1 – 3) when combined with cocatalyst, 4-dimethylaminopyridine (DMAP) or bis(triphenylphosphine)iminium chloride (PPNCl), were assessed for the ring-opening copolymerization (ROCOP) of cyclohexene oxide (CHO) and phthalic anhydride (PA). Complex 1, when combined with DMAP, resulted in the highest polyester conversions and selectivity demonstrating the best activity for CHO/PA ROCOP. Kinetic studies with complex 1 determined an overall second-order rate law with a first-order dependance in CHO and catalyst concentrations, and a zero-order dependance in PA concentration. Moderate molar mass polymers with narrow dispersities were obtained and the polymers showed decomposition temperatures above 180 C and glass transition temperatures of 43 C. | Kate Hanrahan; Cassie Meyers; Cyler Vos; Jian-Bin Lin; Christopher Kozak | Inorganic Chemistry; Catalysis; Polymer Science; Polymerization catalysts; Coordination Chemistry (Inorg.); Ligands (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67040d44cec5d6c142767589/original/kinetic-studies-of-zirconium-catalyzed-ring-opening-copolymerization-of-epoxide-and-cyclic-anhydride.pdf |
6322ff069cf6627c5f928c2a | 10.26434/chemrxiv-2022-993zl | Bioconjugation of Electron-Probe Au25 Nanocluster to Monoclonal Antibody | We report the first bioconjugation of Au25 nanocluster to a monoclonal antibody without protein engineering, in a step toward the development of high-resolution probes for cryogenic electron microscopy (cryo-EM) and tomography (cryo-ET). To achieve this, we improved the tryptophan (Trp)-selective bioconjugation step by using easy-to-analyze hydroxylamine (ABNOH) reagents in a pH-neutral buffer, instead of using N-oxyl radicals (ABNO) under acidic conditions as previously developed. This new protocol allowed for the application of Trp-selective bioconjugation to acid-sensitive proteins such as antibodies. We found that a two-step procedure, utilizing first Trp-selective bioconjugation for homogeneous introduction of azide groups to the protein and then strain-promoted azide-alkyne cycloaddition (SPAAC) to attach bicyclononyne (BCN)-presenting, redox-sensitive Au25 nanocluster, was key to successful immunogold synthesis. This procedure is scalable. The covalent labeling of the antibody with gold nanoclusters was confirmed by various analytical methods, including cryo-EM analysis of the Au25 nanocluster conjugates. In comparison with a non-homogenous variant prepared by lysine-selective bio-conjugation, Trp-selective conjugates exhibited both satisfactory gold cluster modification and minimal loss of antigen-binding ability. | Katarzyna Joanna Malawska; Shinjiro Takano; Kounosuke Oisaki; Haruaki Yanagisawa; Masahide Kikkawa; Tatsuya Tsukuda; Motomu Kanai | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Imaging; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322ff069cf6627c5f928c2a/original/bioconjugation-of-electron-probe-au25-nanocluster-to-monoclonal-antibody.pdf |
6744958f7be152b1d0b85d02 | 10.26434/chemrxiv-2024-zmdtq | Reaction Pathways for Electrochemical CO2 Reduction into Ethanol | Electrochemical CO2 reduction reaction (CO2RR) offers a promising route to storing chemical energy and producing valuable chemicals, while also contributing to carbon cycle closure. Despite significant advances in electrocatalytic CO2RR for multi-carbon products, challenges remain in optimizing catalysts for high selectivity and efficiency. Cu-based heterogeneous catalysts are among the most promising options; however, enhancing their catalytic efficiency and product selectivity remains complex due to several factors. One key challenge is that product selectivity heavily depends on the catalyst’s surface morphology, which impacts both Faradaic efficiency and overpotential requirements for target product formation. Additionally, the reaction pathways and intermediates for multi-carbon products are not yet fully understood, complicating efforts to achieve consistent multi-carbon yields. Variability introduced by the electrolyte environment, applied potential, and operating conditions further impacts selectivity and efficiency. This review aims to address these challenges by exploring the interplay between the surface structure of Cu-based catalysts and system parameters that shape reaction pathways for ethanol formation. Notably, we explore alternative pathways beyond the conventional mechanisms involving CHO, COH, and CO dimers. | Peshala Jayamaha; Lichang Wang | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6744958f7be152b1d0b85d02/original/reaction-pathways-for-electrochemical-co2-reduction-into-ethanol.pdf |
60c74b22f96a004032287583 | 10.26434/chemrxiv.12284330.v1 | Synthesis of Pentasubstituted 2-Aryl Pyrroles from Boryl and Stannyl Alkynes via One-Pot Sequential Ti-Catalyzed [2+2+1] Pyrrole Synthesis/Cross Coupling Reactions | <div>
<div>
<div>
<div>
<p>An efficient catalytic synthesis of 2-heteroatom-substituted
(9-BBN or SnR3) pyrroles via Ti-catalyzed [2+2+1] heterocoupling of heteroatom-substituted alkynes is reported. The resulting 2-boryl substituted pyrroles
can then be used in Suzuki reactions in a 1-pot sequential fashion, resulting in pentasubstituted 2-aryl pyrroles that are
inaccessible via previous [2+2+1] heterocoupling strategies. </p>
</div>
</div>
</div>
</div> | Yukun Cheng; Channing Klein; Ian Tonks | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b22f96a004032287583/original/synthesis-of-pentasubstituted-2-aryl-pyrroles-from-boryl-and-stannyl-alkynes-via-one-pot-sequential-ti-catalyzed-2-2-1-pyrrole-synthesis-cross-coupling-reactions.pdf |
6718c7ac83f22e4214e51430 | 10.26434/chemrxiv-2024-cc0bl | Non-Trivial Stimuli-Responsive Collective Behaviours Emerging from Microscopic Dynamic Complexity in Supramolecular Polymer Systems | Supramolecular polymers are composed of monomers that self-assemble non-covalently generating distributions of fibers in continuous exchange-and-communication with each other and the surrounding. Intriguing collective properties may emerge in such molecular-scale complex systems, following mechanisms often difficult to ascertain. Here we show how non-trivial collective behaviors may emerge in dynamical supramolecular polymer systems already at low-complexity levels. We combine minimalistic models, simulations, and advanced statistical analyses investigating how cooperative and non-cooperative supramolecular polymer systems respond to a specific stimulus: i.e., the addition of molecular sequestrators perturbing their equilibrium. Our data show how, while in a non-cooperative system all assemblies populating the system suffer uniformly the perturbation, in a cooperative system the larger/stronger assemblies survive at the expense of the smaller/weaker entities. Collective behaviors typical of larger-scale and more complex (social, economic, etc.) systems may thus emerge even in relatively simple self-assembling systems from the internal (microscopic) dynamic heterogeneity of their ensembles. | Martina Crippa ; Claudio Perego; Giovanni M. Pavan | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Self-Assembly; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6718c7ac83f22e4214e51430/original/non-trivial-stimuli-responsive-collective-behaviours-emerging-from-microscopic-dynamic-complexity-in-supramolecular-polymer-systems.pdf |
6572fb15cf8b3c3cd71943d3 | 10.26434/chemrxiv-2023-67t1w | Hexahydropyrrolo-[2,3-b]-indole Containing Alkaloids as a SARS-CoV-2 Inhibitors: An Integrated Multi-Target Based in-silico Approach | The discovery of potential drug molecules which can inhibit multiple targets at a single shot is extremely efficient in combating modern diseases. In continuation of this effort, this manuscript represents a multi-targeted based virtual screening approach aimed at identifying the most promising natural alkaloids based on Hexahydropyrrolo-[2,3-b]-indole backbone as a potential inhibitor against SARS-CoV-2. In this pursuit, eight traditional and understudied SARS-CoV-2 viral targets like the main protease (Mpro), RNA polymerase (RdRp), Envelope protein (Evp), Receptor binding domain (S-RBD), Human receptor angiotensin (hACE2), Spike protein, uridine specific endoribonuclease (nsp15) and capping protein (nsp16) are selected. The virtual screening of a series of naturally occurring alkaloids across these eight binding sites of SARS-CoV-2 proteins demonstrated great binding affinity. In fact, these sets of small natural product molecules highlight similar or greater binding affinity with multiple proteins compared to traditional-approved drugs like Ramdesivir, Nirmatrelvir and Molnupiravir. Based on the ADMET profiling, it can be verified that these sets of natural products exhibit the optimal pharmacokinetic parameters. Furthermore, analysis of the key amino acid-ligand interactions and time-dependent DFT calculation of top leads support the possibility of the multi-targeting capability of these moieties to fight persistently against the rapidly evolving SARS-CoV-2. | Debasish Mandal | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6572fb15cf8b3c3cd71943d3/original/hexahydropyrrolo-2-3-b-indole-containing-alkaloids-as-a-sars-co-v-2-inhibitors-an-integrated-multi-target-based-in-silico-approach.pdf |
60c74bb00f50db3b22396ca3 | 10.26434/chemrxiv.12370574.v1 | Scandium and Dimethylaminopyridine Catalyzed Dehydrative Coupling of Secondary Benzylic and Primary Alcohols to Synthesize Unsymmetrical Ethers | We developed a direct catalytic condensation of
benzylic alcohols and primary alcohols to synthesize unsymmetrical ethers in
one step, catalyzed by scandium triflate and p-dimethylaminopyridine (DMAP).
Preliminary experiments give some insight into the mechanism of the reaction,
though suggest that the process is quite complex. We suspect the rapid
formation of a dimer from a secondary benzylic alcohol via a carbocation intermediate
precedes unsymmetrical ether formation. Full experimental details and spectroscopic data are provided as supplementary information. | Julia Duncan; Lun Li; Vahid Mohammadrezaei; Laina Geary | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bb00f50db3b22396ca3/original/scandium-and-dimethylaminopyridine-catalyzed-dehydrative-coupling-of-secondary-benzylic-and-primary-alcohols-to-synthesize-unsymmetrical-ethers.pdf |
60c7436f337d6cbda7e26bd4 | 10.26434/chemrxiv.9158564.v1 | Metal-Free Photoredox-Catalyzed C–H/C–H Coupling of Arenes Enabled by Interrupted Pummerer Activation | <p>Aryl–aryl cross-coupling constitutes one of the most widely used procedures for the synthesis of high-value materials, ranging from pharmaceuticals to organic electronics and conducting polymers. The assembly of (hetero)biaryl scaffolds generally requires multiple steps; coupling partners must be functionalized before the key bond-forming event is considered. Thus, the development of selective C–H arylation processes in arenes, that side-step the need for prefunctionalized partners, is crucial for streamlining the construction of these key architectures. Here we report an expedient, one-pot assembly of (hetero)biaryl motifs using photocatalysis and two non-prefunctionalized arene partners. The approach is underpinned by the activation of a C–H bond in an arene coupling partner using the interrupted Pummerer reaction. A unique pairing of the organic photoredox catalyst and the intermediate dibenzothiophenium salts enables highly selective reduction in the presence of sensitive functionalities. The utility of the metal-free, one-pot strategy is exemplified by the synthesis of a bioactive natural product and the modification of complex molecules of societal importance.</p> | Miles Aukland; Mindaugas Šiaučiulis; Adam West; Gregory Perry; David Procter | Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436f337d6cbda7e26bd4/original/metal-free-photoredox-catalyzed-c-h-c-h-coupling-of-arenes-enabled-by-interrupted-pummerer-activation.pdf |
6604965c9138d2316179e9fd | 10.26434/chemrxiv-2024-rt7bs-v2 | Quantitative Characterization of Partitioning Stringency in SELEX | Maintaining stringent conditions in SELEX (Systematic Evolution of Ligands by EXponential enrichment) is crucial for obtaining high-affinity aptamers; however, excessive stringency greatly increases the risk of SELEX failure. The control of stringency remains a technical challenge reliant solely on intuition, largely due to the absence of a measure of stringency. Essentially, researchers increase or decrease stringency through its influencers without defining and quantitating it. This study was motivated by our insight that while stringency may not be easily definable via its multiple influencers, it can be delineated by its effect: increasing stringency leads to a decrease in the normalized quantity of binders at the output of partitioning. Building on this insight, we introduce a measure of stringency called the Binder-to-Nonbinder Ratio (BNR) and derive an expression for its experimental determination using a single experimental tool: quantitative PCR. The outcomes of our theoretical analysis and the result of SELEX experiments targeting three distinct protein targets underscore the importance of maintaining a BNR significantly greater than zero to avoid SELEX failure due to excessive stringency – a principle that we term the SELEX non-failure criterion. Utilizing BNR as a measure of stringency alongside this criterion will enable researchers to rationally control SELEX progress. | An Le; Eden Teclemichael; Svetlana Krylova; Sergey Krylov | Biological and Medicinal Chemistry; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6604965c9138d2316179e9fd/original/quantitative-characterization-of-partitioning-stringency-in-selex.pdf |
6264540f1033885748f83d79 | 10.26434/chemrxiv-2022-f3n93 | Lipid Isobaric Mass Tags via Aziridination for Probing Isomeric Structures and Accurate Quantification | Unsaturated lipids constitute a dominant portion of lipids in mammalian cells and often exist as a mixture of isomers. Knowing concentrations of lipids is essential for understanding their functions in physiology and diseases. Herein, a novel aziridination-based isobaric tag labeling strategy is developed for isomeric characterization and accurate quantification of unsaturated lipids. This strategy allows (i) determination of lipid double bond positional isomers, (ii) quantification of unsaturated lipids and lipid isomers, and (iii) improvement of ionization efficiencies of nonpolar lipids. The power of the method has been demonstrated in characterization and quantification of various categories of lipids such as fatty acids, phosphoglycerol lipids, cholesteryl esters and glycerides. Remarkably, 13 CE lipid isomers were identified and simultaneously quantified from human plasma without requiring the use of lipid standards. | Tingyuan Yang; Shuli Tang; Syuan-Ting Kuo; Dallas Freitas; Madison Edwards; Xin Yan | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6264540f1033885748f83d79/original/lipid-isobaric-mass-tags-via-aziridination-for-probing-isomeric-structures-and-accurate-quantification.pdf |
640a6656cc600523a3f114d6 | 10.26434/chemrxiv-2023-331cp | Instantaneous Degradation of Nerve Agent Simulants using Zirconium-based Metal-organic Polyhedra | Metal-organic polyhedra (MOPs) are discrete molecules made of metal ions/clusters and organic ligands, and their crystal packing leads to the generation of intrinsic and extrinsic porosity. Due to their structural versatility, porosity, and nanoscale size, MOPs are considered an attractive platform for catalysis. In this study, we report for the first time the use of three zirconium(IV)-based MOPs for the degradation of trace concentrations of the nerve agent simulant, dimethyl 4-nitrophenyl phosphate (DMNP). All three MOPs degraded DMNP instantaneously, with half-lives ranging from t1/2 = 17 to 130 s. The catalytic activity of MOPs is thought to be due to (1) their periodic packing resulting in long-range order that creates extrinsic porosity, allowing DMNP to diffuse in and interact with the pore surface and Lewis acids (Zr(IV) centers) of MOPs, and (2) the lability of Zr-Cp (Cp = cyclopentadienyl) bond, allowing Cp ligands to rearrange and make space for DMNP to interact with the Zr(IV). The catalytic activity of MOPs is not deteriorated by increasing the concentration of the nerve agent simulant nor in consecutive catalytic experiments, highlighting their robustness as catalysts. Our study showcases the promise of MOPs as one of the fastest active catalysts for the instantaneous degradation of nerve agents. | Kimia Kiaei; Andrzej Gładysiak; Kieran Brunson; Kye Hunter; Ava Thomas; Delaney Radke; Tim Zuehlsdorff; Kyriakos Stylianou | Inorganic Chemistry; Catalysis; Solid State Chemistry; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640a6656cc600523a3f114d6/original/instantaneous-degradation-of-nerve-agent-simulants-using-zirconium-based-metal-organic-polyhedra.pdf |
60c74c1c0f50dbfe56396da2 | 10.26434/chemrxiv.12429569.v1 | Identification of β-Strand Mediated Protein-Protein Interaction Inhibitors Using Ligand-Directed Fragment Ligation | β-Strand mediated
protein-protein interactions (PPIs) represent underexploited targets for
chemical probe development despite representing a significant proportion of
known and therapeutically relevant PPI targets. β-strand mimicry is challenging
given that both amino acid
side-chains and backbone hydrogen-bonds are typically required for
molecular recognition, yet these are oriented along perpendicular vectors. This
paper describes an alternative approach using GKAP/SHANK1 PDZ as a model and
dynamic ligation screening to identify small-molecule replacements for tranches
of peptide sequence. A peptide truncation of GKAP functionalized at the N- and
C-termini with acylhydrazone groups was used as an anchor. Reversible
acylhydrazone bond exchange with a library of aldehyde fragments in the
presence of the protein as template and <i>in
situ</i> screening using a fluorescence anisotropy (FA) assay identified
peptide hybrid hits with comparable affinity to the GKAP peptide binding
sequence. Identified hits were validated using FA, ITC, NMR and X-ray
crystallography to confirm selective inhibition of the target PDZ-mediated PPI
and mode of binding. These analyses together with molecular dynamics
simulations demonstrated the ligands make transient interactions with an
unoccupied basic patch through electrostatic interactions, establishing
proof-of-concept that this unbiased approach to ligand discovery represents a
powerful addition to the armory of tools that can be used to identify PPI
modulators. | Zsófia Hegedüs Zsófia Hegedüs; Fruzsina Hobor; Deborah K. Shoemark; sergio Celis; Lu-Yun Lian; Chi Trinh; Richard Sessions; Thomas Edwards; Andrew Wilson | Supramolecular Chemistry (Org.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c1c0f50dbfe56396da2/original/identification-of-strand-mediated-protein-protein-interaction-inhibitors-using-ligand-directed-fragment-ligation.pdf |
60c7589b567dfed514ec68ab | 10.26434/chemrxiv.14567472.v1 | N-Heterocyclic Iod(az)olium Salts - Potent Halogen Bond Donors in Organocatalysis | Herein we describe the first systematic investigation of cyclic iodonium salts (iodoliums and iodazoliums) and their performance as XB-donors in a variety of benchmark reactions. It was found that further <i>N</i>-alklyation of the <i>N</i>-heterocycle has a significant influence on their XB-donor capability. These novel dicationic species show a reactivity which is comparable or even better than the best so far described iodine(I) and iodine(III) compounds throughout the investigated reaction set. <br /> | Andreas Boelke; Thomas Kuczmera; Enno Lork; Boris Nachtsheim | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Acid Catalysis; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7589b567dfed514ec68ab/original/n-heterocyclic-iod-az-olium-salts-potent-halogen-bond-donors-in-organocatalysis.pdf |
672e88fe7be152b1d07b09f5 | 10.26434/chemrxiv-2023-z007q-v2 | Versatile sulfidation of a metal-organic framework via heterolytic splitting of organo sulfides at distorted Zr-nodes | The sulfidation of metal oxides is critical to the creation of catalyst active sites for industrially-relevant reactions, but occurs at high temperatures for refractory oxides like zirconia. Here, we investigate sulfidation of the structurally-well-defined, Zr-based metal-organic framework (MOF) NU-1000 as a model system. Sulfidation with H2S and alkane thiols occurred readily at room temperature after thermal distortion of the Zr6 clusters in NU-1000. The sulfidation occurred via heterolytic S-H bond cleavage over frustrated Lewis-acid/Lewis-base pairs in the form of under-coordinated Zr(IV) sites and a terminal O(-II) site formed during the thermal distortion. In situ synchrotron based structural analysis, spectroscopic characterization, and computational studies provide evidence that thiols react with distorted Zr6 nodes to form stable bridging Zr-S-Zr bonds and a terminal hydroxo. This study provides insight into the surface structures responsible for the sulfidation of high-valent metal oxides and also suggests a promising strategy for introducing S-bearing moieties to otherwise sulfur-resistant MOF nodes. | Qining Wang; Simon M. Vornholt; Patrick Melix; Filip Formalik; Zhihengyu Chen; Luke M. Tufaro; Jian Liu; Boris V. Kramar; Zhiwei Wang; Lin X. Chen; Randall Q. Snurr; Karena W. Chapman; Justin M. Notestein; Joseph T. Hupp | Inorganic Chemistry; Bonding; Frustrated Lewis Pairs; Small Molecule Activation (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672e88fe7be152b1d07b09f5/original/versatile-sulfidation-of-a-metal-organic-framework-via-heterolytic-splitting-of-organo-sulfides-at-distorted-zr-nodes.pdf |
66a345e35101a2ffa816c76c | 10.26434/chemrxiv-2024-n04fm | Spatial and Temporal Visualization of Polymorphic Transformations in Pharmaceutical Tablets | X-ray Diffraction Computed Tomography (XRD-CT) represents a cutting-edge method for non-destructive material analysis, offering the unique capability of providing molecular-level information with spatial resolution. In this study, we have applied XRD-CT to investigate pharmaceutically relevant tablets that have been subjected to a range of compression pressures typical in tablet manufacturing. By employing XRD-CT to pharmaceutical tablets, we reveal material changes without tablet destruction, thereby avoiding potential phase transformations during sample preparation that could lead to errors in the interpretation of the processes that have occurred. Utilizing a pressure-sensitive marker, glycolide, we have tracked changes within tablet structures induced by compression, pinpointing locations where glycolide undergoes pressure-induced transformation. Additionally, we conducted a follow-up study with analysis one month later, observing an in-situ hydrolysis reaction of glycolide within the tablets. Through the complementary use of electron diffraction, we have elucidated the structure of the hydrolysis product, further enhancing our understanding of temporal changes in the tablets. | Julia Gasol-Cardona; Martin Ward; Olof Gutowski; Jakub Drnec; Christian Jandl; Danny Stam; Andrew Maloney; Daniel Markl; Stephen Price; Iain Oswald | Physical Chemistry; Materials Science; Physical and Chemical Properties; Structure; Materials Chemistry; Crystallography | CC BY 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a345e35101a2ffa816c76c/original/spatial-and-temporal-visualization-of-polymorphic-transformations-in-pharmaceutical-tablets.pdf |
616601f2cada1f7fc4d43cc5 | 10.26434/chemrxiv-2021-zfvc9 | Carbodiphosphorane-Catalyzed Hydroboration of Ketones and Imines | We report the use of a cyclic carbodiphosphorane catalyst for ketone and imine hydroboration reactions. To our knowledge, this represents the first use of a carbodiphosphorane as an organocatalyst. The carbodiphospohorane shows superior catalytic activity compared to other neutral carbon nucleophiles tested. | Cara Aversa-Fleener; Daniel Chang; Allegra Liberman-Martin | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Catalysis; Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616601f2cada1f7fc4d43cc5/original/carbodiphosphorane-catalyzed-hydroboration-of-ketones-and-imines.pdf |
60c757ca469df4060cf45519 | 10.26434/chemrxiv.14462376.v1 | Ni-Catalyzed Aryl Sulfide Synthesis through an Aryl Exchange Reaction | A Ni-catalyzed aryl sulfide synthesis through an aryl exchange reaction between aryl sulfides and a variety of aryl electrophiles was developed. By using 2-pyridyl sulfide as a sulfide donor, this reaction achieved the synthesis of aryl sulfides without using odorous and toxic thiols. The use of a Ni/dcypt catalyst capable of cleaving and forming aryl–S bonds was important for the aryl exchange reaction between 2-pyridyl sulfides and aryl electrophiles, which include aromatic esters, arenol derivatives, and aryl halides. Mechanistic studies revealed that Ni/dcypt can simultaneously undergo oxidative additions of aryl sulfides and aromatic esters, followed by ligand exchange between the generated aryl–Ni–SR and aryl–Ni–OAr species to furnish aryl exchanged compounds. | Ryota Isshiki; Miki B. Kurosawa; Kei Muto; Junichiro Yamaguchi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757ca469df4060cf45519/original/ni-catalyzed-aryl-sulfide-synthesis-through-an-aryl-exchange-reaction.pdf |
61e632fd77a4164aa5d4c3bf | 10.26434/chemrxiv-2022-c69w8 | Sterically Frustrated Aromatic Enes with Various Colors Originating from Multiple Folded and Twisted Conformations in Crystal Polymorphs | Overcrowded ethylenes composed of 10-methyleneanthrone and two bulky aromatic rings contain a twisted carbon-carbon double (C=C) bond as well as a folded anthrone unit. As such, they are unique frustrated aromatic enes (FAEs). Various colored crystals of these FAEs, obtained using different solvents, correspond to multiple metastable conformations of the FAEs with various twist and fold angles of the C=C bond, as well as various dihedral angles of attached aryl units with respect to the C=C bond. The relationships between color and these parameters associated with conformational features around the C=C bond were elucidated using experimental and theoretical studies. Owing to the fact that they are separated by small energy barriers, the variously colored conformations in the FAE crystal change in response to various external stimuli, such as mechanical grinding, hydrostatic pressure and thermal heating. | Tomohiko Nishiuchi; Seito Aibara; Takuya Yamakado; Ryo Kimura; Shohei Saito; Hiroyasu Sato; Takashi Kubo | Organic Chemistry; Materials Science; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e632fd77a4164aa5d4c3bf/original/sterically-frustrated-aromatic-enes-with-various-colors-originating-from-multiple-folded-and-twisted-conformations-in-crystal-polymorphs.pdf |
65e045e966c1381729d53b1b | 10.26434/chemrxiv-2024-t7861 | Targeted Degradation of Antigen-Specific Pathogenic Autoantibodies That Cause Heart Failure | Autoantibodies are the causative agents in a wide range of autoimmune diseases. Existing approaches to the depletion of such autoantibodies include therapies that deplete the whole antibody repertoire or immunoadsorption, which although antigen-specific is costly and time-consuming. Here, we report the first pharmacological strategy for the antigen-specific depletion of autoantibodies. Specifically, we synthesized a synthetic bifunctional molecule (β-MoDE-A) capable of selectively depleting antibodies against the beta-1 adrenergic receptor (β1AR) in vitro and in vivo. β-MoDE-A contains a motif that mimics the anti-β1AR binding epitope linked to a ligand for the asialoglycoprotein receptor, which re-routes pathogenic autoantibodies to the liver for degradation. We demonstrate that β-MoDE-A is effective in mediating ternary complex formation and endocytosis of anti-β1AR antibodies in vitro and depletes these antibodies in vivo in a mouse model. The novel drug platform represented by this approach provides the first example of an antigen-specific extracellular degrader of an individual pathogenic IgG species of any isotype or subclass, but without any potential for broad-based immunosuppression. | Edward deRamon; David McDonald; David Spiegel | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e045e966c1381729d53b1b/original/targeted-degradation-of-antigen-specific-pathogenic-autoantibodies-that-cause-heart-failure.pdf |
678fd4ff81d2151a0225f793 | 10.26434/chemrxiv-2025-09kqv | Machine Learning Reveals Amine Type in Polymer Micelles Determines mRNA Binding, In Vitro, and In Vivo Performance for Lung-Selective Delivery | Cationic micelles, composed of amphiphilic block copolymers with polycationic coronas, offer a customizable platform for mRNA delivery. Here, we present a library of 30 cationic micelle nanoparticles (MNPs) formulated from diblock copolymers with reactive poly(pentafluorophenol acrylate) backbones modified with a diverse set of amines. This library systematically varies in nitrogen-based cationic functionalities, exhibiting a spectrum of properties that encompass varied degrees of alkyl substitution (A1-A5), piperazine (A6), oligoamine (A7), guanidinium (A8), hydroxylation (A9-A10) that vary in sidechain volume, substitution pattern, hydrophilicity, and pKa to assess parameter impact on mRNA delivery. In vitro delivery assays using GFP+ mRNA across multiple cell lines reveal that amine sidechain bulk and chemical structure critically affect performance. Using machine learning analysis via SHapley Additive exPlanations (SHAP) on 3,780 experimental data points, we mapped key relationships between amine chemistry and performance metrics, finding that amine-specific binding efficiency was a major determinant of mRNA delivery efficacy, cell viability, and GFP intensity. Micelles with stronger mRNA binding capabilities (A1 and A7) have higher cellular delivery performance, whereas those with intermediate binding tendencies deliver a higher amount of functional mRNA per cell (A2 and A10). This indicates that balancing the binding strength is crucial for performance. Micelles with hydrophobic and bulky pendant groups (A3, A4, and A5) tend to induce necrosis during cellular delivery, highlighting the significance of chemical optimization. A cationic amphiphile identified as A7 displaying a primary and secondary amine, consistently demonstrates the highest GFP expression across various cell types and in vivo achieving high delivery specificity to lung tissue upon intravenous administration. Moreover, we established a strong correlation between in vitro and in vivo performance using Multitask Gaussian Process models, linking amine properties directly to both delivery efficacy and biodistribution. This correlation underscores the predictive power of in vitro models for anticipating in vivo outcomes and highlights chemical amine-dependent optimization as crucial for advancing mRNA delivery vehicle development. Overall, this innovative study integrates advanced data science with experimental design demonstrating the pivotal role of chemical amine identity for targeted mRNA delivery to the lungs. | Sidharth Panda; Ella Eaton; Praveen Muralikrishnan; Erin Stelljes; Davis Seelig; Michael Leyden; Alexandria Gilkey; Jackson Barnes; David Morrissey; Sapna Sarupria; Branden Moriarity; Theresa Reineke | Biological and Medicinal Chemistry; Polymer Science; Nanoscience; Drug delivery systems; Polyelectrolytes - Polymers; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678fd4ff81d2151a0225f793/original/machine-learning-reveals-amine-type-in-polymer-micelles-determines-m-rna-binding-in-vitro-and-in-vivo-performance-for-lung-selective-delivery.pdf |
659daf8a66c138172916c188 | 10.26434/chemrxiv-2024-xklj4 | Steviol Rebaudiosides bind to four different sites of the human sweet taste receptor (T1R2/T1R3) complex explaining confusing experiments | Sucrose provide sweetness and energy when it binds to both the Venus fly trap domains (VFD) of heterodimeric sweet taste receptor (T1R2/T1R3),1 while non-caloric sweeteners (Sucralose, Aspartame, Neotame, Saccharin, Acesulfame-K (Ace-K), Suosan, SC-45647, Fructose, and D-Tryptophan) bind only at the VFD of T1R2 (VFD2) to provide high-intensity sweetness.2 Here, we address the binding mechanism of various steviol glycosides (Rebaudioside B (RebB), RebM, RebD, Rubusoside (Rubu), RebC), artificial sweeteners (Neohesperidin dihydrochalcone (NHDC), acesulfame K, S-819, Amiloride, and Perillartine), and negative allosteric modulator (Lactisole) at four distinct binding sites, VFD2, VFD3, transmembrane domain 2 (TMD2) and TMD3 by performing binding experiments and computational docking studies. Our docking results find multiple binding sites for the tested ligands including the radio labelled ligands, which provides an explanation of the mixed data of the radio-ligand binding experiments. We predict different preferred binding sites depending on ligand modifications of steviol glycosides. Thus, Rubu binds best at VFD3, while RebB binds best at TMD3, while the others prefer VFD2. We also observed G protein-coupled receptor (GPCR) allostery using the label free Frequency Locking Optical Whispering Evanescent Resonator (FLOWER) method. We show experimentally that the C20 carboxy terminus of the Gα protein can bind to the intracellular region of either TMD2 or TMD3, which can alter GPCR affinity to the high-affinity state for steviol glycosides. These studies provide a mechanistic understanding of the structure and function of this heterodimeric sweet taste receptor that can guide rational structure-based design of novel non-caloric sweeteners aimed at enabling lower sugar usage levels while retaining the sweet taste. This may provide the basis for novel therapeutic applications for treatment of obesity and related metabolic dysfunctions such as diabetes. | Shuang Hao; Brian Guthrie; Soo-Kyung Kim; Sergej Balanda; Jan Kubicek; Babar Murtaza; Naim Khan; Pouyan Khakbaz; Judith Su; William Goddard | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Food; Cell and Molecular Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659daf8a66c138172916c188/original/steviol-rebaudiosides-bind-to-four-different-sites-of-the-human-sweet-taste-receptor-t1r2-t1r3-complex-explaining-confusing-experiments.pdf |
64d9e012dfabaf06ff3fbb70 | 10.26434/chemrxiv-2023-hrxsl | Design and synthesis of bioreductive prodrugs of class I histone deacetylase inhibitors and their biological evaluation in virally transfected acute myeloid leukemia cells | Although histone deacetylase (HDAC) inhibitors show promise in treating various types of hematologic malignancies, they have some limitations, including poor pharmacokinetics and off-target side effects, which may be a reason to exclude many of them from further drug development. Prodrug design has shown promise as an approach to improve pharmacokinetic properties and also to improve target tissue specificity. In the present work, several bioreductive prodrugs for class I HDACs were designed and synthesized based on known selective HDAC inhibitors. The zinc-binding group of the HDAC inhibitors was masked with various nitroarylmethyl residues to make them substrates of nitroreductase (NTR). The developed prodrugs showed very weak HDAC inhibitory activity compared to their parent inhibitors. The prodrugs were also tested against wild-type and NTR-transfected THP1 cells. Cellular assays showed that both 2-nitroimidazole-based prodrugs 5 and 6 were best activated by the NTR prodrug system and exhibited potent activity against NTR-THP1 cells. Compound 6 showed the highest cellular activity (GI50 = 77 nM) and also exhibited a moderate selectivity window. Moreover, activation of the prodrug by NTR was confirmed by LC-MS analysis, which showed the release of the parent inhibitor after incubation of prodrug 6 with E. coli NTR. Thus, compound 6 can be considered as a novel prodrug selective for class I HDACs with good bioreductive properties, which could be used as a good starting point for increasing selectivity and for further optimization. | Wolfgang Sippl; Mohamed Abdelsalam; Mariia Zmyslia ; Karin Schmidtkunz; Anita Vecchio; Sebastian Hilscher; Hany S. Ibrahim ; Mike Schutkowski; Manfred Jung; Claudia Jessen-Trefzer | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d9e012dfabaf06ff3fbb70/original/design-and-synthesis-of-bioreductive-prodrugs-of-class-i-histone-deacetylase-inhibitors-and-their-biological-evaluation-in-virally-transfected-acute-myeloid-leukemia-cells.pdf |
655ea118cf8b3c3cd7e73374 | 10.26434/chemrxiv-2023-wttkj | Decoding the Broadband Emission of Two-Dimensional Pb-Sn Halide Perovskites through High-Throughput Exploration | Unlike single-component two-dimensional (2D) metal halide perovskites (MHPs) exhibiting sharp excitonic photoluminescence (PL), a broadband PL emerges in mixed Pb-Sn 2D lattices. Two physical models –self-trapped exciton and defect-induced Stokes-shift – have been proposed to explain this unconventional phenomenon. However, both explanations provide limited rationalizations without consideration of the formidable compositional space, and thus, the fundamental origin of broadband PL remains elusive. Herein, we established our high-throughput automated experimental workflow to systematically explore the broadband PL in mixed Pb-Sn 2D MHPs, employing PEA (phenethylammonium) as a model cation known to work as a rigid organic spacer. Spectrally, the broadband PL becomes further broadened with rapid PEA2PbI4 phase segregation with increasing Pb concentrations during early-stage crystallization. Counterintuitively, MHPs with high Pb concentrations exhibit prolonged PL lifetimes despite high defect densities. Hyperspectral microscopy identifies substantial PEA2PbI4 phase segregation in those films, hypothesizing that the establishment of charge transfer excitons by the phase segregation upon crystallization is responsible for the extraordinary behavior; at high-Pb compositions, this far outperforms the leverage of defect-induced emission, thereby resulting in distinctive PL properties. Our high-throughput approach allows us to reconcile the controversial prior models describing the origin of the broadband emission in 2D Pb-Sn MHPs, shedding light on how to comprehensively explore the fundamentals and functionalities of the complex materials systems. | Elham Foadian; Jonghee Yang; Yipeng Tang; Summer B. Harris; Christopher M. Rouleau; Syed Joy; Kenneth R. Graham; Benjamin J. Lawrie; Bin Hu; Mahshid Ahmadi | Physical Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Photochemistry (Physical Chem.); Physical and Chemical Properties; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655ea118cf8b3c3cd7e73374/original/decoding-the-broadband-emission-of-two-dimensional-pb-sn-halide-perovskites-through-high-throughput-exploration.pdf |
60c75799bb8c1a615d3dc891 | 10.26434/chemrxiv.14428091.v1 | Mechanically Robust Hydrophobized Double Network Hydrogels for Water Purification | Water swollen polymer
networks are attractive for applications ranging from tissue regeneration to
water purification. For water purification, charged polymers provide excellent
ion separation properties. However, many ion exchange membranes (IEMs) are brittle,
necessitating the use of thick support materials that ultimately decrease throughput.
To this end, a series of double network
hydrogels (DNHs), synthesized with varied composition to decrease water content,
are examined as robust membrane materials for water purification. One network
contains fixed anionic charges, while the other comprises a copolymer with
different ratios of hydrophobic ethyl acrylate (EA) and hydrophilic dimethyl
acrylamide (DMA) repeat units. Characterizing water content and mechanical
performance in free standing DNH films reveals a ~5× decrease in water content, while increasing ultimate stress and strain
by ~3.5× and ~4.5× for 90:5
EA:DMA relative to pure DMA. Salt transport properties relevant to water
purification, including permeability, solubility, and diffusivity, are measured
and show improved performance upon reducing water content. Overall, the ability
to simultaneously reduce water content, increase mechanical integrity, and
decrease salt transport rates highlights the potential of DNHs for membrane applications. | Marshall Allen; Rahul Sujanani; Alyssa Chamseddine; Benny Freeman; Zachariah Page | Materials Processing; Hydrogels; Polyelectrolytes - Polymers; Polymerization (Polymers); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75799bb8c1a615d3dc891/original/mechanically-robust-hydrophobized-double-network-hydrogels-for-water-purification.pdf |
60c75651469df4cc43f452cd | 10.26434/chemrxiv.13284416.v2 | Enantioselective Access to Dialkyl Amines and Alcohols via Ni-Catalyzed Reductive Hydroalkylations | Chiral dialkyl amines and alcohols are ubiquitous in pharmaceuticals, pesticides, natural products and fine chemicals,
yet difficult to access due to the challenge to differentiate between the spatially and electronically similar alkyl groups. Herein, we
report a nickel-catalyzed enantioselective reductive hydroalkylation of enamides and enolates with alkyl halides to afford enantioenriched α-branched aliphatic amines and alcohols in good yields with excellent levels of enantioselectivity. The operationally simple
protocol provides a straightforward access to chiral dialkyl amine and alcohol derivatives from simple starting materials with great
functional group tolerance. | Shan Wang; Tian-Yi Zhang; Jian-Xin Zhang; Huan Meng; Bi-Hong Chen; Wei Shu | Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75651469df4cc43f452cd/original/enantioselective-access-to-dialkyl-amines-and-alcohols-via-ni-catalyzed-reductive-hydroalkylations.pdf |
62a4bf9e769c5e76674bfb02 | 10.26434/chemrxiv-2022-hfzzr | Lipidomic Comparison of 2D and 3D Colon Cancer Cell Culture Models | Altered lipid metabolism is one of the hallmarks of cancer. Cellular proliferation and de novo synthesis of lipids are related to cancer progression. In this study, we evaluated the lipidomic profile of two-dimensional (2D) monolayer and multicellular tumor spheroids from the HCT 116 colon carcinoma cell line. We utilized serial trypsinization on the spheroid samples to generate three cellular populations representing the proliferative, quiescent, and necrotic regions of the spheroid. This analysis enabled a comprehensive identification and quantification of lipids produced in each of the spheroid layer and 2D cultures. We show that lipid subclasses associated with lipid droplets form in oxygen-restricted and acidic regions of spheroids and are produced at higher levels than in 2D cultures. Additionally, sphingolipid production, which is implicated in cell death and survival pathways, is higher in spheroids relative to 2D cells. Finally, we show that increased numbers of lipids comprised of polyunsaturated fatty acids (PUFAs) are produced in the quiescent and necrotic regions of the spheroid. The lipidomic signature for each region and cell culture type highlights the importance of understanding the spatial aspects of cancer biology. These results provide additional lipid biomarkers in the tumor microenvironment that can be further studied to target pivotal lipid production pathways. | Fernando Tobias; Amanda B Hummon | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2022-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a4bf9e769c5e76674bfb02/original/lipidomic-comparison-of-2d-and-3d-colon-cancer-cell-culture-models.pdf |
66a3716501103d79c5bec1a4 | 10.26434/chemrxiv-2024-bglq8 | Direct Synthesis of Polyesterether from Ethylene glycol | We report here a new method of making polyesterether from ethylene glycol. The reaction is catalysed by a ruthenium com-plex and liberates H2 gas and H2O as by-products. Preliminary mechanistic studies suggest that the reaction proceeds by the dehydrogenation of ethylene glycol to glycoaldehyde which can subsequently react with another ethylene glycol to make a hemiacetal intermediate. Hemiacetal intermediate can either dehydrogenate to make ester or dehydrate to make ether result-ing in the formation of polyesterether. Investigation into the polymerization of other diols has also been conducted that shows that diols with lower number of carbons between both the alcohol groups (propylene glycol, glycerol, and 1,3-propanediol) lead to the formation of polyesterether whereas α,ω-diols containing higher number of carbons (1,6-hexanediol, and 1,10-decanediol) lead to the formation of polyester. | Garima Saini; Pavel Kulyabin; Angus McLuskie; Niklas von Wolff; Amit Kumar | Catalysis; Organometallic Chemistry; Polymer Science; Organic Polymers; Polymerization (Polymers); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a3716501103d79c5bec1a4/original/direct-synthesis-of-polyesterether-from-ethylene-glycol.pdf |
60c74c020f50db94a6396d61 | 10.26434/chemrxiv.12415166.v1 | A Non-alternant Aromatic Belt: Methylene-bridged [6]Cycloparaphenylene Synthesized from Pillar[6]arene | The synthesis, structure, and properties of <a>methylene-bridged [6]cycloparaphenylene ([6]CPP), a non-alternant aromatic belt,</a> are described. This belt-shaped methylene-bridged [6]CPP, in which each phenylene unit is tethered to its neighbors by methylene bridges, was constructed through six-fold intramolecular nickel-mediated aryl-aryl coupling of <a>triflate-functionalized pillar[6]arene </a>in 15% isolated yield. <a>Compared with the analogous [6]CPP, the methylene bridges co-planarize neighboring paraphenylene units and enhance the degree of </a>p-conjugation, resulting in a significant decrease in energy gap. Moreover, the incorporation of small molecules in the defined pocket of methylene-bridged [6]CPP makes it an attractive supramolecular architecture. Methylene-bridged [6]CPP is characterized by high internal strain energy reaching 110.2 kcal·mol<sup>–1</sup>, attributed to its restricted structure. This work not only exhibits an efficient strategy to construct a new family of aromatic belt, but also showcases their properties, which combine the merits of CPPs and pillararenes. | Yuanming Li; Yasutomo Segawa; Akiko Yagi; Kenichiro Itami | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c020f50db94a6396d61/original/a-non-alternant-aromatic-belt-methylene-bridged-6-cycloparaphenylene-synthesized-from-pillar-6-arene.pdf |
638c586c92f084781826bfa9 | 10.26434/chemrxiv-2022-zm9hv-v2 | Algorithm for Analytic Nuclear Energy Gradients of State Averaged DMRG-CASSCF Theory with Newly Derived Coupled-Perturbed Equations | We present an algorithm for evaluating analytic nuclear energy gradients of the state-averaged density matrix renormalization group complete-active-space self-consistent field (SA-DMRG-CASSCF) theory, based on the newly derived coupled-perturbed (CP) DMRG-CASSCF equations. The Lagrangian for the conventional SA-CASSCF analytic gradient theory is extended to the SA-DMRG-CASSCF variant that can fully consider a whole set of constraints on the parameters of multi-root canonical matrix product states (MPSs) formed at all the DMRG block configurations. An efficient algorithm to solve the CP-DMRG-CASSCF equations for determining the multipliers was developed. The complexity of the resultant analytic gradient algorithm is overall the same as that of the unperturbed SA-DMRG-CASSCF algorithm. In addition, a reduced-scaling approach was developed to directly compute the SA reduced density matrices (SA-RDMs) and their perturbed ones without calculating separate state-specific RDMs. As part of our implementation scheme, we neglect the term associated with the constraint on the active orbitals in terms of the active-active rotation in the Lagrangian. Thus, errors from the true analytic gradients may be caused in this scheme. The proposed gradient algorithm was tested with the spin-adapted implementation by checking how accurately the computed analytic energy gradients reproduce numerical gradients of the SA-DMRG-CASSCF energies using a common number of renormalized basis. The illustrative applications show that the errors are sufficiently small when using a typical number of the renormalized basis, which is required to attain adequate accuracy in DMRG's total energies. | Tsubasa Iino; Toru Shiozaki; Takeshi Yanai | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638c586c92f084781826bfa9/original/algorithm-for-analytic-nuclear-energy-gradients-of-state-averaged-dmrg-casscf-theory-with-newly-derived-coupled-perturbed-equations.pdf |
61555055aade365c84c74af4 | 10.26434/chemrxiv-2021-2v7kh-v3 | A SHORT COMMUNICATION ON INHIBITORY AGENTS AGAINST SARS-COV2: VIRTUAL SCREENING AND DRUG REPURPOSING STUDIES | <div>Severe Acute Respiratory Syndrome (SARS-CoV2) infected about 93 million people and killed over two million worldwide. The disease transmits very quickly, therefore; due to its severity and widespread the World Health Organization has declared this menace as ‘Global Pandemic’. An urgent need was felt to manage this disease through aggressive and efficient research process all over the globe. That’s why drug re-purposing of 212 chemical entities (CEs) against SARS-COV2 was found to be one of the efficient ways in finding new indications of already discovered drugs amisdst of the discovery of a new drug. Results of this study revealed that out of 212 CEs, only Etodolac forms a hydrogen (H)-bond with a relatively low energy and active central fragment, demonstrating more significant interaction with SARS-CoV2 viral proteins. Other CEs exhibit good pharmacokinetics properties with the least acute toxicity through ADMET analysis. We also discovered other therapeutic applications of these CEs through Molinspiration. Etodolac, a non-steroidal anti-inflammatory drug forms H-bonding with 5.6 kcal/mol binding energy with active residues of this receptor. This drug created H-bonding with PHE326 and PRO328, with pyridine group, and was found more suitable to control SARS-CoV2.</div> | Muniba Pervez; Muhammad Bilal; Fahad Hassan Shah; Robaica Khan; Maham Chaudhry; Sajid Asghar; Sajid Khan Sadozai; Ayesha Sajjad; Zulekha Mughal; Song Ja Kim; Kashif Iqbal; Saad Salman | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61555055aade365c84c74af4/original/a-short-communication-on-inhibitory-agents-against-sars-cov2-virtual-screening-and-drug-repurposing-studies.pdf |
64de7ef600bbebf0e6581368 | 10.26434/chemrxiv-2023-x014j | Ultra-high Dielectric Strength and Capacitive Energy Density of Thin Entangled Glassy Polymer Films | The influence of high-intensity electric fields on the stability of polymeric materials is a problem of interest in the design of next-generation energy storage and electronic devices, and for understanding the limits of stability of polymer films exposed to large electric fields generally. Here, we show that the dielectric strength of entangled glassy polymer films increases sharply as an inverse power-law of the film thickness h for “ultrathin” films below a micron in thickness. The dielectric strength enhancement in these polymer films can reach values as large as ≈ 2 GV/m in films thinner than 100 nm, but this large “finite-size” effect depends strongly on the polymer mass and sample aging time. Our enhanced dielectric breakdown with confinement can be consistently interpreted within a working model in which dielectric breakdown is taken to be an electric field-induced analog of previously reported mechanical yield enhancement in the same thickness range of glassy polymer films. As a proof of principle regarding applications, we utilized ultra-thin glassy polymer films of the type studied in our paper to fabricate polymeric nanocapacitors having ultra-high discharge energy densities (Udmax) as large as 27 J/cm3 and having efficiencies greater than 80 %. These efficiency values at comparable charge densities are significantly higher than those of competing ferroelectric polymer materials, and we anticipate that our observations will inspire the creation of practical high-energy density nanocapacitor devices for advanced energy storage applications. | Maninderjeet Singh; Roushanak Nejat; Jack Douglas; Alamgir Karim | Polymer Science; Nanoscience; Energy; Organic Polymers; Nanodevices; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64de7ef600bbebf0e6581368/original/ultra-high-dielectric-strength-and-capacitive-energy-density-of-thin-entangled-glassy-polymer-films.pdf |
6478f1694f8b1884b7adec0a | 10.26434/chemrxiv-2023-xf58t | Experimental Phase Diagram and Its Temporal Evolution for Submicron 2-Methylglutaric Acid and Ammonium Sulfate Aerosol Particles | Liquid–liquid phase separation (LLPS) in aerosol particles is important for the climate system due to its potential to impact heterogeneous chemistry, cloud condensation nuclei, and new particle growth. Our group and others have shown a lower separation relative humidity for submicron particles, but whether the suppression is due to thermodynamics or kinetics is unclear. Herein, we characterize the experimental LLPS phase diagram of submicron 2-methylglutaric acid and ammonium sulfate aerosol particles and compare it to that of supermicron-sized particles. Surprisingly, as the equilibration time of submicron-sized aerosol particles was increased to 60 min, the experimental phase diagram converges with the results for supermicron-sized particles. Our findings indicate that nucleation kinetics are responsible for the observed lower separation relative humidities in submicron aerosol particles. Therefore, experiments and models that investigate atmospheric processes of Aitken and accumulation mode organic aerosol particles may need to consider the temporal evolution of aerosol LLPS. | Qishen Huang; Kiran Pitta; Kayla Constantini; Emily-Jean Ott; Andreas Zuend; Miriam Freedman | Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6478f1694f8b1884b7adec0a/original/experimental-phase-diagram-and-its-temporal-evolution-for-submicron-2-methylglutaric-acid-and-ammonium-sulfate-aerosol-particles.pdf |
60ce1ef1e21133ea62dfc625 | 10.26434/chemrxiv-2021-6kd0t | Using Data Science to Guide Aryl Bromide Substrate Scope Analysis in a Ni/Photoredox-Catalyzed Cross-Coupling with Acetals as Alcohol-Derived Radical Sources | Ni/photoredox catalysis has emerged as a powerful platform for C(sp2)–C(sp3) bond formation. In principle, these reactions enable access to the same product scaffolds, but it can be hard to discern which method to employ because non-standardized sets of aryl bromides are used in scope evaluation. Herein we report a Ni/photoredox-catalyzed alkylation of aryl halides where benzaldehyde di(alkyl) acetals serve as alcohol-derived radical sources. We describe the integration of data science techniques, including DFT featurization, dimensionality reduction, and hierarchical clustering, to delineate a diverse and succinct collection of aryl bromides that is representative of the chemical space of the substrate class. By superimposing the scope examples from published Ni/photoredox methods on this chemical space, we identify areas of sparse coverage and high/low yields, enabling comparisons between prior art and this method. We demonstrate that the systematically-selected scope of aryl bromides can be used to quantify population-wide reactivity trends with supervised ML. | Stavros Kariofillis; Shutian Jiang; Andrzej Żurański; Shivaani Gandhi; Jesus Martinez Alvarado; Abigail Doyle | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ce1ef1e21133ea62dfc625/original/using-data-science-to-guide-aryl-bromide-substrate-scope-analysis-in-a-ni-photoredox-catalyzed-cross-coupling-with-acetals-as-alcohol-derived-radical-sources.pdf |
60c741ea0f50db044c395be1 | 10.26434/chemrxiv.8168354.v1 | Automatic Retrosynthetic Pathway Planning Using Template-free Models | <div><div><div><p>We present
an attention-based Transformer model for automatic retrosynthesis route planning.
Our approach starts from <a></a><a>reactants
prediction of single-step organic reactions for gi</a>ven products, <a>followed by Monte Carlo tree search-based
automatic retrosynthetic pathway prediction</a>. Trained on two datasets from the United States patent
literature, our models achieved a top-1 prediction accuracy of over 54.6% and 63.0% with more than 95% and 99.6% validity rate
of SMILES, respectively, which is the best up to now to our knowledge. We also
demonstrate the application potential of our model by successfully performing
multi-step retrosynthetic route planning for four case products, i.e.,
antiseizure drug Rufinamide, a novel allosteric activator, an inhibitor of
human acute-myeloid-leukemia cells and a complex intermediate of drug
candidate. Further, by using heuristics Monte Carlo tree search, we achieved
automatic retrosynthetic pathway searching and successfully reproduced published
synthesis pathways. In summary, our model has achieved the state-of-the-art
performance on single-step retrosynthetic prediction and provides a novel
strategy for automatic retrosynthetic pathway planning.
</p><div>
<div><div><p><br /></p></div></div><div><div>
</div>
</div>
</div><br /><p></p></div></div></div> | Kangjie Lin; Jianfeng Pei; Luhua Lai; Youjun Xu, | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ea0f50db044c395be1/original/automatic-retrosynthetic-pathway-planning-using-template-free-models.pdf |
63a613d5e8047a86b2f39aa4 | 10.26434/chemrxiv-2022-4k3wh | Solution Aggregate Structures of Donor Polymers Determine the Morphology and Processing Resiliency of Non-Fullerene Organic Solar Cells | The solution-state aggregation of conjugated polymers is critical to the morphology and device performance of bulk heterojunction (BHJ) organic solar cells (OSCs). However, tuning the polymer solution-state aggregation for optimal film morphology remains challenging due to a lack of understanding of polymer aggregates in the solution-state. Herein, we demonstrate that polymer solution-state aggregate structure significantly impacts the BHJ film morphology and processing temperature resiliency of OSCs. Using X-ray scattering and imaging techniques, we ascertain that the donor polymer PM7 forms a combination of large fibrillar aggregates and network-like aggregates comprised of single polymer chains while its derivatives PM7 D1 and D2 are mainly composed of polymer network-like aggregates in solution. Upon increasing the solution temperature, large fibrillar aggregates dissolve while polymer network-like aggregates maintain their network structures. Surprisingly, regardless of the polymer system, we show that OSCs fabricated from polymer network-like aggregates yield favorable BHJ morphology comprised of small domains with face-on preferred molecular orientation while large fibrillar aggregates lead to poor film morphologies consisting of large domains without preferential molecular orientation. Due to their stability with temperature, polymer network-like aggregates are resilient to processing temperature variation whereas fibrillar aggregates are sensitive to processing temperature. Overall, this work highlights the critical role of solution-state aggregation of polymers, especially their aggregate structures, in achieving OSCs with favorable morphology and high processing resiliency. | Azzaya Khasbaatar; Andrew Cheng; Austin L. Jones; Justin J. Kwok; Sang Kyu Park; Jessica K. Komar; Oliver Lin; Nicholas E. Jackson; Qian Chen; John R. Reynolds; Ying Diao | Materials Science; Chemical Engineering and Industrial Chemistry; Aggregates and Assemblies; Thin Films; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a613d5e8047a86b2f39aa4/original/solution-aggregate-structures-of-donor-polymers-determine-the-morphology-and-processing-resiliency-of-non-fullerene-organic-solar-cells.pdf |
64a6a697ba3e99daef9cb044 | 10.26434/chemrxiv-2023-d2d3k | Unprecedented selective synthesis of imines by photo-oxidative coupling under N2O atmosphere | The synthesis of imines was unprecedently performed using nitrous oxide (N2O) as a highly selective oxidative agent for the photocatalytic homo-coupling of amines. In a similar way, unsymmetrical imines were produced through cross-coupling of amines with alcohols. Promisingly, this greenhouse gas showed excellent performances towards the target reactions when photocatalytically activated at atmospheric pressure, with silver photodeposited on titanium dioxide as catalyst. Relevantly, reactions under N2O atmosphere exhibited high conversion rates and turn-over frequencies, and higher selectivities than the ones carried out under a dioxygen atmosphere. Mechanisms for both reactions were proposed with release of nitrogen and water as benign by-products. | Oriane DELAUNAY; Audrey Denicourt-Nowicki; Alain Roucoux | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a6a697ba3e99daef9cb044/original/unprecedented-selective-synthesis-of-imines-by-photo-oxidative-coupling-under-n2o-atmosphere.pdf |
64285a16a029a26b4cbf81c3 | 10.26434/chemrxiv-2023-plz39 | Autonomous alignment and self-healing in multilayer soft electronics using dynamic polymers with immiscible backbones | Self-healing soft electronic and robotic devices can recover autonomously from some forms of external damage, analogous to human skin. While current self-healing devices employ a single type of dynamic polymer network for all functional layers to ensure strong interlayer adhesion, this approach requires the manual alignment of layers to ensure functional healing. Here, we use two dynamic polymers, which have immiscible backbones but identical dynamic bonds, to maintain interlayer adhesion while enabling autonomous realignment of functional components during healing. We show that these dynamic polymers exhibit a weakly interpenetrating and adhesive interface, whose width is tunable. Moreover, when multi-layer laminates of these polymers are misaligned after damage, these structures autonomously realign during healing to minimize interfacial area—a phenomena that is also observed in simulations. We demonstrate the broader utility of this strategy by fabricating composite devices with conductive, dielectric, and magnetic particles that functionally heal after damage, enabling thin film pressure sensors, magnetically assembled soft robots, and underwater circuit assembly. | Christopher Cooper; Samuel Root; Lukas Michalek; Shuai Wu; Jian-Cheng Lai; Muhammad Khatib; Solomon Oyakhire; Renee Zhao; Jian Qin; Zhenan Bao | Materials Science; Polymer Science; Composites; Multilayers; Thin Films; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64285a16a029a26b4cbf81c3/original/autonomous-alignment-and-self-healing-in-multilayer-soft-electronics-using-dynamic-polymers-with-immiscible-backbones.pdf |
65dcbddbe9ebbb4db94f5165 | 10.26434/chemrxiv-2024-rc3dw | Determination of particle number concentration for biological particles using AF4-MALS: Dependencies on light scattering model and refractive index | Determining accurate counts and size distributions for biological particles (bioparticles) is crucial in wide-ranging fields, but current ensemble methods to this end are susceptible to bias from polydispersity in size. This bias can be mitigated by incorporating a separation step prior to characterization. For this reason, asymmetrical flow field-flow fractionation (AF4) with on-line multiangle light scattering (MALS) has become an important platform for determining particle size. AF4-MALS has been used to report particle concentration, particularly for complex biological particles, yet the impact of light scattering models and particle refractive indices (RI) have not been quantitatively assessed. Here, we develop an analysis workflow using AF4-MALS to simultaneously separate and determine particles sizes and concentrations. The impacts of the MALS particle counting model used to process data and the chosen RI value(s) on particle counts are systematically assessed for polystyrene latex (PSL) particles and bacterial outer membrane vesicles (OMVs) in the 20-500 nm size range. Across spherical models, PSL and OMV particle counts varied up to 13% or 200%, respectively. For the coated-sphere model used in the analysis of OMV samples, the sphere RI value greatly impacts particle counts. As the sphere RI value approaches the RI of the suspending medium, the model becomes increasingly sensitive to the light scattering signal-to-noise ultimately causing erroneous particle counts. Overall, this work establishes the importance of selecting appropriate MALS models and RI values for bioparticles to obtain accurate counts and provides an AF4-MALS method to separate, enumerate, and size polydisperse bioparticles. | Christine L. Plavchak; Allison Z. Werner; Elizabeth Betz; Davinia Salvachua; Gregg Beckham; S. Kim Ratanathanawongs Wiliams | Analytical Chemistry; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dcbddbe9ebbb4db94f5165/original/determination-of-particle-number-concentration-for-biological-particles-using-af4-mals-dependencies-on-light-scattering-model-and-refractive-index.pdf |
63ead79b9da0bc6b33e1a0be | 10.26434/chemrxiv-2023-fszz8 | Model for humidity-mediated diffusion on aluminum surfaces and its role in accelerating atmospheric aluminum corrosion | Bare aluminum metal surfaces are highly reactive, which leads to the spontaneous formation of a protective oxide surface layer. Because many subsequent corrosive processes are mediated by water, the structure and dynamics of water at the oxide interface are anticipated to influence corrosion kinetics. Using molecular dynamics simulations with a reactive force field, we model the behavior of aqueous aluminum metal ions in water adsorbed onto aluminum oxide surfaces across a range of ion concentrations and water film thicknesses corresponding to increasing relative humidity. We find that the structure and diffusivity of both the water and the metal ions depends strongly on the humidity of the environment and the relative height within the adsorbed water film.Aqueous aluminum ion diffusion rates in water films corresponding to a typical indoor relative humidity of 30% are found to be more than two orders of magnitude slower than self-diffusion of water in the bulk limit. Connections between metal ion diffusivity and corrosion reaction kinetics are assessed parametrically with a reductionist model based on a 1D continuum reaction-diffusion equation. Our results highlight the importance of incorporating the properties specific to interfacial water in predictive models of aluminum corrosion. | Jeremy Scher; Stephen Weitzner; Yue Hao; Tae Wook Heo; Stephen Castonguay; Sylvie Aubry; Susan Carroll; Matthew Kroonblawd | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Interfaces; Physical and Chemical Processes; Transport phenomena (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ead79b9da0bc6b33e1a0be/original/model-for-humidity-mediated-diffusion-on-aluminum-surfaces-and-its-role-in-accelerating-atmospheric-aluminum-corrosion.pdf |
60c742b49abda277fdf8c092 | 10.26434/chemrxiv.7903388.v4 | Minimally Empirical Double Hybrid Functionals Trained Against the GMTKN55 Database: revDSD-PBEP86-D4, revDOD-PBE-D4, and DOD-SCAN-D4 | We present a family of minimally empirical double-hybrid DFT functionals parametrized against the very large and diverse GMTKN55 benchmark. The very recently proposed wB97M(2) empirical double hybrid (with 16 empirical parameters) has the lowest WTMAD2 (weighted mean absolute deviation over GMTKN55) ever reported at 2.19 kcal/mol. However, our xrevDSD-PBEP86-D4 functional reaches a statistically equivalent WTMAD2=2.22 kcal/mol, using just a handful of empirical parameters, and the xrevDOD-PBEP86-D4 functional reaches 2.25 kcal/mol with just opposite-spin MP2 correlation, making it amenable to reduced-scaling algorithms. In general, the D4 empirical dispersion correction is clearly superior to D3BJ. If one eschews dispersion corrections of any kind, noDispSD-SCAN offers a viable alternative. Parametrization over the entire GMTKN55 dataset yields substantial improvement over the small training set previously employed in the DSD papers. | Golokesh Santra; Nitai Sylvetsky; Gershom Martin | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742b49abda277fdf8c092/original/minimally-empirical-double-hybrid-functionals-trained-against-the-gmtkn55-database-rev-dsd-pbep86-d4-rev-dod-pbe-d4-and-dod-scan-d4.pdf |
60c74d970f50db2125397077 | 10.26434/chemrxiv.12636974.v1 | Electrochemically Induced In-Situ Generated Co(OH)2 Nanoplates to Promote the Volmer Process Toward Efficient Alkaline Hydrogen Evolution Reaction | <p>Hydrogen production via alkaline water electrolysis
is of significant interest. However, the additional water dissociation step
makes the Volmer step a relatively more sluggish kinetics and consequently
leads to a slower reaction rate than that in acidic solution. Herein, we
demonstrate an effective strategy that Co(OH)<sub>2</sub> can promote the
Volmer process by accelerating water dissociation and enhance the
electrocatalytic performance of CoP toward alkaline hydrogen evolution
reaction. The Co(OH)<sub>2</sub> nanoplates are electrochemically induced
in-situ generated to form a nanotree-like structure with porous CoP nanowires,
endowing the hybrid electrocatalyst with superior charge transportation, more
exposed active sites, and enhanced reaction kinetics. This strategy may be
extended to <a></a><a>other phosphides and chalcogenides </a>and
provide insight into the design and fabrication of efficient alkaline HER
catalysts.</p> | Hong Liu; Jian-Jun Wang; Li-Wen Jiang; Yuan Huang; Bing Bing Chen; Jian-Qiu Zhou | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d970f50db2125397077/original/electrochemically-induced-in-situ-generated-co-oh-2-nanoplates-to-promote-the-volmer-process-toward-efficient-alkaline-hydrogen-evolution-reaction.pdf |
60c755ec567dfe4ed1ec6392 | 10.26434/chemrxiv.14185442.v1 | Development of a 3D Printable and Highly Stretchable Ternary Organic-Inorganic Nanocomposite Hydrogel | This work describes the synthesis and detailed characterization of a ternary hybrid hydrogel comprising a thermogelling hydrogel containing laponite clay nanoparticles, in which an additional polymer network is polymerized by free radical polymerization. The precursor hydrogel can be effectively 3D printed and after curing, interesting mechanical properties are obtained.<br /> | Chen Hu; Malik Salman Haider; Lukas Hahn; Mengshi Yang; Robert Luxenhofer | Composites; Elastic Materials; Hybrid Organic-Inorganic Materials; Materials Processing; Hydrogels; Polymer scaffolds; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755ec567dfe4ed1ec6392/original/development-of-a-3d-printable-and-highly-stretchable-ternary-organic-inorganic-nanocomposite-hydrogel.pdf |
67dd676481d2151a0251a7ae | 10.26434/chemrxiv-2025-4q7p4 | Two-way mechanism of designer biomolecular condensate catalysts | Condensates formed via liquid-liquid phase separation provide a chemically versatile environment for catalysis through dynamic molecular interactions. We present designed biomolecular condensates, formed by LLPS of minimalistic histidine-containing peptides, catalyzing ester hydrolysis with two distinct mechanisms. Zn2+-dependent condensates activate a coordinating water molecule at the active site, formed by Zn2+-histidine coordination, enabling nucleophilic attack. In the absence of Zn2+, catalysis is driven by intermolecular low-barrier hydrogen bonds between histidine residues, facilitating nucleophile formation. Combined computational and experimental evidence reveals the molecular basis of these catalytic pathways, demonstrating the functionality of biomolecular condensates in catalysis and nanotechnology. These findings establish a foundation for exploring new mechanisms of metal-free emergent catalysis within complex liquid assemblies, expanding the potential of LLPS-based systems in green chemistry and advanced materials. | Tlalit Massarano; Yuqin Yang; Avigail Baruch Leshem; Ori Eran; Xiaoyu Wang; Hao Dong; Ayala Lampel | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Aggregates and Assemblies; Catalysts; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd676481d2151a0251a7ae/original/two-way-mechanism-of-designer-biomolecular-condensate-catalysts.pdf |
65c4ebdb9138d23161b09bbc | 10.26434/chemrxiv-2023-kfp6p-v3 | Elucidating the lithiation process in Fe3–δO4 nanoparticles by correlating magnetic and structural properties | Due to their high potential energy storage magnetite (Fe3O4) nanoparticles have become appealing for anode materials in lithium-ion batteries. However, the details of the lithiation process are still not completely understood. Here, we investigate chem- ical lithiation in 70 nm cubic shaped magnetite nanoparticles with varying degree of lithiation x = 0, 0.5, 1, 1.5. The induced changes on the structural and magnetic properties were investigated by using X-ray techniques along with electron microscopy and magnetic measurements. The results indicate that a structural transformation from spinel to rock salt phase occurs above a critical limit for the lithium concentra- tion (xc), which is determined to be between 0.5< xc≤1 for Fe3–δO4. Magnetization measurements clearly shows the formation of the LiFeO2 phase with its distinct anti- ferromagnetic behaviour below its Need temperature. Upon lithiation, magnetization measurements reveal exchange bias in the hysteresis loops with an asymmetry, which can be attributed to the formation of mosaic-like LiFeO2 subdomains. The combined characterization techniques enabled us to unambiguously identify the phases and their distribution involved in the lithiation process. Correlating magnetic and structural properties opens the path to increase the understanding of the processes involved in a variety of non-magnetic applications of magnetic materials. | Seda Ulusoy; Mikhail Feygenson; Thomas Thersleff; Toni Uusimäki; Mario Valvo; Alejandro Gomez Roca; Josep Nogues; Peter Svedlindh; German Salazar-Alvarez | Nanoscience; Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c4ebdb9138d23161b09bbc/original/elucidating-the-lithiation-process-in-fe3-o4-nanoparticles-by-correlating-magnetic-and-structural-properties.pdf |
62df50e57f3aa65708f73d87 | 10.26434/chemrxiv-2022-4ns3r | Structure-dependent Photoluminescence from MA1-xFAxPbI3 with Evidence of Defect-suppression on FA-substitution | We present temperature-dependent photoluminescence (PL) spectra from MA1-xFAxPbI3 for x = 0.02, 0.15, 0.2, and 0.6 over the temperature range of ~12-300 K. These results show remarkable changes across the structural phase transitions together with presence of multiple peaks, prominently in the low temperature regime, that can be associated with different crystallographic phases apparently coexisting at low temperatures. We propose that the persistent dominant presence of the PL signal associated with the high temperature tetragonal/cubic phase in each case even at the lowest temperature can only originate from a structural relaxation at the surface of the grains of the low temperature phase, making the surface electronic structure close to that of the high temperature phases. Since the bandgap is smaller for the surface related phase, the photoexcited energy is significantly transferred to the surface region before deexcitation, giving rise to the dominance of this PL feature. Our results show that with an increasing FA content, this transfer of energy becomes more efficient with a complete suppression of the PL features of the low temperature bulk phase, while the x-ray diffraction shows a phase pure low temperature phase alone. Additionally, we show that the lowest energy PL feature that appears only at a critical low temperature is not associated with any crystallographic transition, but correlates well with the plastic crystal-like transition arising from the three-fold rotations of the MA unit around its C-N axis as determined by prior quasi-elastic neutron scattering studies. This suggests that the MA rotations suppress the formation of self-trapped excitonic features via electron-phonon interactions, while the feature begins to appear with increasing intensity as the MA rotations are frozen with a decreasing temperature below a certain temperature. This interpretation allows us to estimate the polaronic contribution to the stability of the self-trapped exciton in these systems to be around ~35 ± 3 meV. Interestingly, the PL spectrum progressively shows a suppression of contributions from the low temperature phases and the self-trapped exciton with an increasing FA content, leading to a single peak PL feature at all temperatures for the highest FA content sample investigated in this work. | Ashutosh Mohanty; D. D. Sarma | Materials Science; Energy; Hybrid Organic-Inorganic Materials; Optical Materials; Photovoltaics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62df50e57f3aa65708f73d87/original/structure-dependent-photoluminescence-from-ma1-x-f-ax-pb-i3-with-evidence-of-defect-suppression-on-fa-substitution.pdf |
60c73e8a702a9b5353189d82 | 10.26434/chemrxiv.6993404.v1 | Computational Strategies to Probe CH Activation in Dioxo-Dicopper Complexes | Our work addresses the long-standing question of the preferred mechanism of CH activation in dioxodicopper
complexes, with implications for [Cu2O2]2+
-containing enzymes as well as homogeneous and
heterogeneous catalysts, which are capable of performing selective oxidation. Using density functional theory
(DFT), we show that the two proposed mechanisms, one-step oxo-insertion and two-step radical
recombination, have very distinct and measurable responses to changes in the electrophilicity of N-donors in
the catalyst. Using energy decomposition analysis, we calculate the electronic
interactions that contribute to transition state stabilization, and the effect of N-donors on these interactions.
The analysis shows that oxo-insertion, by virtue of possessing a late and charged transition state, is highly
sensitive to N-donor electrophilicity and barriers decrease with more electron-withdrawing N-donors. On the
other hand, the radical pathway possesses an early transition state and is therefore relatively insensitive to N-donor
variations. One possible strategy, going forward, is the design and execution of complementary
experiments to deduce the mechanism based on the presence or absence of N-donor dependence. We adopt
an alternative approach where DFT results are contrasted with prior experiments via Hammett relationships.
The remarkable agreement between experimental and calculated trends for oxo-insertion with
imidazole N-donor catalysts presents compelling evidence in favor of the one-step pathway for CH activation. | Zhenzhuo Lan; Shaama Mallikarjun Sharada | Computational Chemistry and Modeling; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e8a702a9b5353189d82/original/computational-strategies-to-probe-ch-activation-in-dioxo-dicopper-complexes.pdf |
61e9c54adeeafa865a2434a2 | 10.26434/chemrxiv-2022-h5krl | ANN-based Drug-isolate-fold-change model predicting the resistance profiles of HIV-1 protease inhibitors | : Drug resistance is a primary barrier to effective treatments of HIV/AIDS. Calculating quantitative relations between genotype and phenotype observations for each inhibitor with cell-based assays requires time and money consuming experiments. Machine learning models are good options for tackling these problems by generalizing the available data with suitable linear or nonlinear mappings. The main aim of this paper is to construct drug isolate fold change (DIF)-based artificial neural network (ANN) models for estimating the resistance potential of molecules inhibiting the HIV-1 protease (PR) enzyme. Throughout the study, seven of eight protease inhibitors (PIs) have been included in the training set and the remaining ones in the test set. Using the 7-in 1-out procedure, eight ANN models have been produced to measure the learning capacity of models from the descriptors of the inhibitors. The mean value of eight ANN models for unseen inhibitors is and 95% confidence interval (CI) is Predicting the fold change resistance for hundreds of isolates allowed for robust comparison of drug pairs. These eight models have predicted the drug resistance tendencies of each inhibitor pair with the mean 2D correlation coefficient 0.933 and 95% CI A classification problem has been created to predict the ordered relationship of the PIs and the mean accuracy, sensitivity and specificity values are obtained as 0.954, 0.791 and 0.791, respectively. The currently derived ANN models can accurately predict the drug resistance tendencies of PI pairs, and this observation could help test new inhibitors with various isolates. | Huseyin Tunc; Serdar Durdagi; Murat Sari; Seyfullah Kotil | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e9c54adeeafa865a2434a2/original/ann-based-drug-isolate-fold-change-model-predicting-the-resistance-profiles-of-hiv-1-protease-inhibitors.pdf |
668434995101a2ffa82d736d | 10.26434/chemrxiv-2024-8kgf0 | Salt-Free CatAnionic Vesicular Nanoreactor from Dithiocarbamate: Michael Addition of Nitroolefins in Aqueous Vesicle System | The salt-free CatAnionic vesicle was previously generated by mixing cationic and anionic amphiphiles, and removing the salt that occurred as a side product from the mixture. In this study, we report a new strategy to produce the salt-free CatAnionic vesicle of N,N-dialkylamonium N,N dialkyldithiocarbamate (AmDTC) through a one-step condensation between secondary amine and carbon disulfide. Both dialkylammonium cationic and dithiocarbamate anionic amphiphiles were generated concurrently during the condensation. The AmDTC was dispersed in water, resulting in the spontaneous formation of salt-free CatAnionic vesicles. Among several AmDTCs, the N,N-didodecylamonium N,N-didodecyldithiocarbamate (AmDTC-C12C12) showed high stability and was applied as a vesicular nanoreactor for the Michael addition in water. Michael addition in an aqueous system between nitroolefins and 1,3-dicarbonyl compounds afforded the desired twenty-three Michael adducts, with yields ranging from 65% to 92%. It is hypothesized that the AmDTC-C12C12 serves as a vesicular nanoreactor and plays a role in catalysis at the dithiocarbamate functional group. Preparative-scale and one-pot Michael addition by in situ generation of AmDTC-C12C12 vesicle afforded the Michael adducts also in good yields. The AmDTC-C12C12 vesicular nanoreactor was applied for the synthesis of (±)-baclofen with 54% yields over three steps. The reusability of the AmDTC-C12C12 was demonstrated and allowed the reuse of the CatAnionic vesicle up to seven cycles. Finally, chemical recycling was demonstrated by converting AmDTC-C12C12 to N,N-didodecylammonium chloride by simple acidification. | Panassilp Authai; Witsanu Sombat; Voravee P. Hoven; Tirayut Vilaivan; Panuwat Padungros | Catalysis; Nanocatalysis - Reactions & Mechanisms; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668434995101a2ffa82d736d/original/salt-free-cat-anionic-vesicular-nanoreactor-from-dithiocarbamate-michael-addition-of-nitroolefins-in-aqueous-vesicle-system.pdf |
64f9dbf7b6ab98a41c040d24 | 10.26434/chemrxiv-2023-vskk8 | Rotaxane-Like Dysprosium(III) Triiodide Single-Molecule Magnets with Tunable Air Stability and Record Energy Barrier | High-performance and air-stable single-molecule magnets (SMMs) can offer great convenience for the fabrication of information storage devices. However, the controversial requisition of high stability and magnetic axiality is hard to balance for lanthanide based SMMs. Here we show a family of rotaxane-like dysprosium(III) triiodide complexes possessing hexagonal-bipyramidal (pseudo-D6h symmetry) local coordination geometry with tunable air stability and effective energy barrier for magnetization reversal (Ueff). The three complexes share the common formulae of [Dy(18-C-6)L2][I3] (18-C-6 = 1,4,7,10,13,16-hexaoxacyclooctadecane; L = I, 1; L = OtBu 2 and L = 1-AdO 3). 1 is highly unstable in the air. 2 can survive in the air for less than one hour, while 3 remains unchanged in the air for more than one week. This is roughly in accordance to the percentage of buried volumes of the axial ligands. More strikingly, 2 and 3 show progressive enhancement of Ueff and 3 exhibits a record high Ueff of 2427(19) K, which significantly contributes to the 100 seconds blocking temperature up to 11 K for yttrium-diluted sample, setting a new benchmark for air-stable SMMs. | Yan-Zhen Zheng; Wen-Jie Xu; Qian-Cheng Luo; Zi-Han Li; Yuan-Qi Zhai | Inorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f9dbf7b6ab98a41c040d24/original/rotaxane-like-dysprosium-iii-triiodide-single-molecule-magnets-with-tunable-air-stability-and-record-energy-barrier.pdf |
6548dee648dad231202f13c7 | 10.26434/chemrxiv-2023-8g4g4 | Field Desorption Mass Spectrometric Analysis of Ethylene Polymerization Initiated by the Anthracenide Yttrium Complex, (C5H5)Y(C14H10)(THF)2. | Yttrium anthracenide complex CpY(C14H10)(THF)2 (1) catalyzes ethylene polymerization under mild conditions. The initiation polymerization step has been modeled by a reaction of 1 and of its Lu analog (3) with t-BuCN, resulting in the formation of mono-insertion products CpLn(-C14H10-(t-Bu)C=N-)(THF)2 (Ln= Y(5), Lu (6)). Crystal structures of 1, CpY(C14H10)(1,4-dioxane)2 (2) and 6 have been determined by the X-ray diffraction analysis. Field desorption mass spectrometry (FD MS) has been used to analyze polymerization products (oligoethylene and its copolymer with pent-1-ene) formed on 1 under various conditions. The thorough analysis of FD MS data enabled us to detect end groups and to suggest a plausible mechanism for ethylene polymerization. The proposed mechanism explains formation of all detected polymer species. | Daniil Bardonov; Mikhail Minyaev; Dmitrii Roitershtein | Organometallic Chemistry; Polymer Science; Catalysis; Polymerization (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6548dee648dad231202f13c7/original/field-desorption-mass-spectrometric-analysis-of-ethylene-polymerization-initiated-by-the-anthracenide-yttrium-complex-c5h5-y-c14h10-thf-2.pdf |
66f116e1cec5d6c142eb9bf7 | 10.26434/chemrxiv-2024-3mtxb | Dipeptidic Phosphonates: Potent Inhibitors of Pseudomonas aeruginosa Elastase B Showing Efficacy in a Murine Keratitis Model | The ubiquitous opportunistic pathogen Pseudomonas aeruginosa is responsible for severe infections and notoriously known for acquiring antimicrobial resistance. Inhibiting the bacterium’s extracellular elastase, LasB – a zinc-dependent protease – presents a promising strategy to mitigate its virulence. Within this medicinal chemistry–driven hit-to-lead optimization campaign, a new series of highly potent dipeptidic phosphonates is designed and synthesized following a structure–based drug discovery approach. In vitro and in vivo evaluation reveal beneficial pharmacokinetic profiles, excellent selectivity over human off-targets and good tolerability in murine toxicity studies. Ultimately, the scaffold presented herein demonstrates promising in vivo efficacy in a murine Pseudomonas aeruginosa keratitis model in combination with the antibiotic meropenem. | Alexander Felix Kiefer; Christian Schütz; Colya Englisch; Dominik Kolling; Samira Speicher; Andreas Martin Kany; Roya Shafiei; Noran Abdel Wadood; Ahmad Aljohmani; Niklas Wirschem; Ravindra Jumde ; Andreas Klein; Asfandyar Sikandar; Yu-Mi Park; Gabriela Krasteva-Christ; Daniela Yildiz; Ahmed Saad Abdelsamie; Katharina Rox; Jesko Köhnke; Rolf Müller; Markus Bischoff; Jörg Haupenthal; Anna Katharina Herta Hirsch | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f116e1cec5d6c142eb9bf7/original/dipeptidic-phosphonates-potent-inhibitors-of-pseudomonas-aeruginosa-elastase-b-showing-efficacy-in-a-murine-keratitis-model.pdf |
6363dbf718a8ccae675d2ac8 | 10.26434/chemrxiv-2022-n1g60 | Machine Learning Potentials for Metal-Organic Frameworks using an Incremental Learning Approach | Computational modeling of physical processes in metal-organic frameworks (MOFs) is highly challenging. The intrinsic length and time scales often stretch far beyond the nanometer and picosecond range due to e.g. large spatial heterogeneities or complex phase transitions. Machine learning potentials (MLPs) can extend the applicability of density functional theory (DFT) towards such challenging systems, but the generation of a representative training set of atomic configurations still poses a major challenge. In this work, we present an incremental learning scheme that constructs accurate and transferable MLPs based on a minimal number of DFT evaluations. Key to the approach is a combination of an active learning scheme that generates systematically improved MLPs with efficient and parallelized enhanced sampling protocols that explore increasingly larger portions of the phase space and learn physical interactions on-the-fly. The method requires a single atomic structure and a collective variable as input, after which the incremental learning approach constructs accurate interatomic potentials based on as few as 1000 single point DFT evaluations, even for flexible frameworks with multiple structurally different phases. The accuracy of the obtained potentials is extensively validated in terms of structural and mechanical properties across a wide range of thermodynamic conditions, yielding thermodynamically transferable MLPs. Finally, it is demonstrated how the incremental learning approach shows great potential to train universal MLPs for a larger set of materials. A proof of principle based on 10 well-known aluminum- and zirconium-based MOFs is shown. The proposed incremental learning approach is universally applicable and may induce a paradigm shift in both the accuracy as well as the time and length scale of computational models for framework materials. | Sander Vandenhaute; Maarten Cools-Ceuppens; Simon DeKeyser; Toon Verstraelen; Veronique Van Speybroeck | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6363dbf718a8ccae675d2ac8/original/machine-learning-potentials-for-metal-organic-frameworks-using-an-incremental-learning-approach.pdf |
6731b093f9980725cfce7488 | 10.26434/chemrxiv-2024-7kf7h | Theory-driven Discovery of Thermally Stable Mechanophore for Self-strengthening Materials | Mechanophores that readily undergo bond cleavage upon mechanical stimuli normally contain a highly strained ring or reactive unit with weak bonds, which are usually thermally unstable. Here, we propose a general theory-driven procedure for selecting thermally stable radical-type mechanophore which can be used in self-strengthening materials. First, following our previous work, it is confirmed that a conformational motif called “node” along the force transduction direction enhances the force effect by generating a severe distortion on the breaking covalent bond. Molecules possessing bridged rings are ideal candidates to have a “node”, as the bridged structure helps to fix the key dihedral angle. Our computational exploration then focused on camphanediol and pinanediol, which do not have highly strained ring or intrinsically weak covalent bond, but a node ensured by a small dihedral angle. Our simulations predicted that polymer chains including these molecular skeletons easily undergo a C−C bond homolysis under relatively low tensile force and efficiently generate mechanoradicals. Subsequently, our automated reaction path exploration calculations unveiled the fate of the mechanoradicals by enumerating their possible reaction channels, and suggested that camphanediol can generate long-lived radicals, which can be utilized to develop self-strengthening materials. Therefore, we prepared double-network (DN) hydrogels containing camphanediol moiety and found that these novel DN hydrogels do have a good self-strengthening performance. Moreover, thanks to the present design guideline not assuming strained rings or weak bonds, such a camphanediol-containing DN hydrogel showed a good thermal and UV stability. | Julong Jiang; Zhi Jian Wang; Ruben Staub; Yu Harabuchi; Alexandre Varnek; Jian Ping Gong; Satoshi Maeda | Theoretical and Computational Chemistry; Polymer Science; Hydrogels; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6731b093f9980725cfce7488/original/theory-driven-discovery-of-thermally-stable-mechanophore-for-self-strengthening-materials.pdf |
6772c20bfa469535b944d40e | 10.26434/chemrxiv-2024-2xp0x-v2 | Analysis of variants of non-adiabatic ring polymer molecular dynamics for calculating excited state dynamics | The non-adiabatic ring polymer molecular dynamics (NRPMD) method, which combines the path-integral ring polymer molecular dynamics framework for the nuclei with the Meyer-Miller-Stock-Thoss mapping of the electronic states, is a powerful tool for simulating non-adiabatic dynamics including nuclear quantum effects. However, challenges arise in utilizing NRPMD associated with zero-point energy leakage between the electronic and nuclear degrees of freedom and ambiguities in how to apply the method under non-equilibrium conditions. Here, we explore several variants of NRPMD and compare their performance using a set of benchmark systems for excited-state electronic population dynamics. Within this context, we adopt an idea from recent work on the linearized semi-classical initial value representation and derive a new NRPMD correlation function for the population of the electronic states in terms of a trace-less operator and the identity operator. The in-depth analysis of the different choices when utilizing NRPMD provides new insight into the practical implementation of the method and related techniques. | Ziying Cao; Joshua Kretchmer | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772c20bfa469535b944d40e/original/analysis-of-variants-of-non-adiabatic-ring-polymer-molecular-dynamics-for-calculating-excited-state-dynamics.pdf |
66ef3cb6cec5d6c142c9bf80 | 10.26434/chemrxiv-2024-tjmgp | Enhanced Aluminium Passivation properties of lithium nonafluoro-tert-butoxide: Designing Electrolyte Additives for High-Voltage 4.8 V LiNi0.5Mn1.5O4-graphite batteries | LiNi0.5Mn1.5O4 (LNMO) cathodes offer high energy density in Li-ion batteries due to their higher operational potential than conventional cathode materials. However, their practical application in Li-ion batteries is limited by the active metal (e.g., Mn) dissolution, which irreversibly compromises the graphite anode of a Li-ion battery. In this work, lithium nonafluoro-tert-butoxyborate (LiONFtb) has been tested as an additive in LNMO-graphite system. The electrochemical stability analysis of the LiONFtb salt on the aluminium current collector revealed a new passivation mechanism, without the formation of cracks and pits, which are otherwise commonly observed in the case of LiPF6-containing electrolytes. Adding 1 wt% LiONFtb to the commercial LiPF6-based electrolyte is demonstrated to improve the high voltage stability of the electrolyte in LNMO-Li half-cell. The LiONFtb additive was also found to promote better Li+ de-/intercalation behaviour in graphite-Li half-cell. The long-term cycling of the LNMO-graphite full cell with the 1% LiONFtb additive electrolyte demonstrated higher initial discharge capacity (121 mAh/g) and higher capacity retention (62%) than the LiPF6 containing electrolyte (105 mAh/g and 9.2%, respectively) after 100 cycles. The post-cycling analysis reveals that the LiONFtb additive helps to retain the morphology of the LNMO particles and reduces the Mn dissolution during cycling. The positive influence of the LiONFtb additive on reducing the cathode particle cracking and active metal dissolution makes it a viable electrolyte additive candidate for next-generation high-voltage Li-ion batteries. | Binayak Roy; Urbi Pal; Jason John; Cuong Nguyen; Craig Forsyth; Patrick Howlett; Douglas MacFarlane | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ef3cb6cec5d6c142c9bf80/original/enhanced-aluminium-passivation-properties-of-lithium-nonafluoro-tert-butoxide-designing-electrolyte-additives-for-high-voltage-4-8-v-li-ni0-5mn1-5o4-graphite-batteries.pdf |
6377d3eabe365e64f6248f53 | 10.26434/chemrxiv-2022-prr2h | Revealing the Impact of Molecular Weight on Mixed Conduction in Glycolated Polythiophenes Through Electrolyte Choice | Developing material design guidelines for organic mixed ionic–electronic conductors (OMIECs) is critical to enable high efficacy mixed transport within bioelectronics. One important feature which has yet to be thoroughly explored is the role of molecular weight on OMIEC performance. In this work, we examined a series of prototypical glycolated polythiophene materials (P3MEEET) with systematically increasing molecular weights within organic electrochemical transistors (OECTs) – a common testbed for investigating mixed transport. We find that there is improved performance beyond an intermediate molecular weight, however, this relationship is electrolyte dependent. Operando analysis suggests that the enhanced mobility at higher molecular weights may be negated by significant swelling when operated in NaCl due to disruption of intercrystallite charge percolation. The role of molecular weight is revealed through operation in KTFSI, as doping occurs through cation expulsion, preventing detrimental swelling and maintaining percolative pathways. These findings demonstrate the importance of both molecular weight and electrolyte composition to enhance the performance of OMIECs. | Joshua Tropp; Dilara Meli; Ruiheng Wu; Bohan Xu; Samuel Hunt; Jason Azoulay; Bryan Paulsen; Jonathan Rivnay | Materials Science; Carbon-based Materials; Materials Processing; Thin Films; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6377d3eabe365e64f6248f53/original/revealing-the-impact-of-molecular-weight-on-mixed-conduction-in-glycolated-polythiophenes-through-electrolyte-choice.pdf |
64454cd6df78ec501544c35d | 10.26434/chemrxiv-2023-svc4t | Rotational transitions of COH+ and He: New interaction potential, bound states, scattering and pressure broadening cross-sections | We present new calculations of a metastable isomer of HCO+, i.e. COH+ in collision with He. The COH+ has been suggested as an alternative molecular hydrogen tracer, which makes it of great interest for astrophysical studies. COH+ was first observed in astronomical space towards SgrB2 with the observation of J=1→0, J=2→1 and J=3→2 lines. Calculations are based on new ab initio potential energy surfaces (PES) of charged complex COH+-He using the CCSD(T) in conjunction with aug-cc-pVQZ basis set. The PES has a well depth of -836.5 cm−1 towards H-end at the
COH+−He distance (R) of 2.9 ˚A in linear orientation. To test the new PES, the calculations of the bound-state are carried out and pressure broadening cross-sections of COH+ with He collisions are computed for kinetic energies up to 150 cm−1 using the accurate close-coupling method. Further,
the pressure broadening and shift coefficients have been calculated from the corresponding real and imaginary parts of cross-sections for the first six rotational transitions. The data obtained is found to be in the same order as the HCO+-He system. Further, we have computed the rate coefficients
and compared the results with the reported COH+-He and HCO+-He data. The results generated by this study is believed to be useful for both laboratory and future astrophysical research. | Ritika .; Apoorv Kushwaha; T. J. Dhilip Kumar | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64454cd6df78ec501544c35d/original/rotational-transitions-of-coh-and-he-new-interaction-potential-bound-states-scattering-and-pressure-broadening-cross-sections.pdf |
65136d470065940912f124c8 | 10.26434/chemrxiv-2023-p1507-v2 | Is the functional response of a receptor determined by the thermodynamics of ligand binding? | Although strong binding to the target protein is a prerequisite, it is not enough to be an effective drug. To produce a particular functional response, drugs need to regulate the targets’ signal transduction pathways, either blocking the proteins’ functions or modulating their activities by changing the conformational equilibrium. The routinely calculated binding free energy of a compound to its target is a good predictor of affinity but may not always predict efficacy. While the time scales for the protein conformational changes are prohibitively long to be routinely modeled via physics-based simulations, thermodynamic principles suggest that binding free energies of the ligands with different receptor conformations may infer their efficacy if the functional response of the receptor is determined by thermodynamics. However, while this hypothesis was proposed in the past, it has not been thoroughly validated and is seldom used in practice for ligand efficacy prediction. We present an actionable protocol and a comprehensive validation study to show that binding thermodynamics provides indeed a strong predictor for the efficacy of a ligand. We apply the absolute-binding free energy perturbation (ABFEP) method to ligands bound to active and inactive states of eight G protein–coupled receptors (GPCRs) and a nuclear receptor. By comparing the resulting binding free energies, we can determine with a very high accuracy whether a ligand acts as an agonist or an antagonist. We find that carefully designed restraints are often necessary to efficiently model the corresponding conformational ensembles for each state and provide a procedure for setting up these restraints. Our method achieves excellent performance in classifying ligands as agonists or antagonists across the various investigated receptors, all of which are important drug targets. | Martin Vögele; Bin W. Zhang; Jonas Kaindl; Lingle Wang | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65136d470065940912f124c8/original/is-the-functional-response-of-a-receptor-determined-by-the-thermodynamics-of-ligand-binding.pdf |
60c745c49abda22043f8c63e | 10.26434/chemrxiv.10260494.v1 | Exchange-Biasing in a Dinuclear Dysprosium(III) Single-Molecule Magnet with a Large Energy Barrier for Magnetization Reversal | A dichlorido-bridged
dinuclear dysprosium(III) single-molecule magnet [Dy<sub>2</sub>L<sub>2</sub>(<i>µ</i>-Cl)<sub>2</sub>(THF)<sub>2</sub>] has been made using a diamine-bis(phenolate)
ligand, H<sub>2</sub>L. Magnetic studies show an energy barrier for
magnetization reversal (<i>U</i><sub>eff</sub>)
around 1000 K. Exchange-biasing effect is clearly seen in magnetic hysteresis with steps up to 4 K. <i>Ab</i> initio calculations exclude the
possibility of pure dipolar origin of this effect leading to the conclusion
that super-exchange <i>via</i> the chloride bridging ligands is important. | Tian Han; Marcus
J. Giansiracusa; Zi-Han Li; You-Song Ding; Nicholas F. Chilton; Richard E. P. Winpenny; Yan-Zhen Zheng | Magnetism | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c49abda22043f8c63e/original/exchange-biasing-in-a-dinuclear-dysprosium-iii-single-molecule-magnet-with-a-large-energy-barrier-for-magnetization-reversal.pdf |
662b70bf21291e5d1dc4b64b | 10.26434/chemrxiv-2024-kzf8v | Mechanochemical synthesis of corannulene flanked N-heterocyclic carbene (NHC) precursors and preparation of their metal complexes | The synthesis of new compounds is an important pillar of organic chemistry with implications in adjacent fields. In this regard, over the last decades huge efforts have been made not only to produce new molecular entities but also to develop more efficient sustainable synthetic methodologies due to the increasing concerns over environmental sustainability. In this context, we have developed synthetic routes to novel corannulene-flanked imidazolium bromide NHC precursors both in the solid state and solution phases. Our work presents a comprehensive comparative study of mechanochemical routes and conventional solution-based methods. The green metrics comparison performed for both routes reveals ball-milling generation of these compounds to be an environmentally greener technique to produce such precursors compared to conventional solvent-based methods. In addition, we have demonstrated proof-of-concept of the herein reported corannulene flanked NHCs to be robust ligands to transition metals and their ligand substitution reactions. | Gavin Hum; Ezzah M. Muzammil; Yongxin Li; Felipe Garcia; Mihaiela C. Stuparu | Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Coordination Chemistry (Organomet.); Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662b70bf21291e5d1dc4b64b/original/mechanochemical-synthesis-of-corannulene-flanked-n-heterocyclic-carbene-nhc-precursors-and-preparation-of-their-metal-complexes.pdf |
60c74392842e656e63db22b8 | 10.26434/chemrxiv.9252692.v1 | A 9-Connected Zirconium-Based Metal-Organic Framework for Ammonia Capture | <p>Construction of
multifunctional metal-organic frameworks (MOFs) with asymmetric connectivity have
the potential to expand the scope of their utilization. Herein, we report a
robust 9-connected microporous Zr-based MOF, <b>NU-300</b>, assembled from asymmetric tri-carboxylate ligands and Zr<sub>6</sub>
nodes. As indicated by single-crystal X-ray diffraction analysis, there exist
uncoordinated carboxylate groups in the structure of <b>NU-300</b> that can participate in ammonia (NH<sub>3</sub>) sorption
through acid-base interactions which yield high uptake of NH<sub>3</sub> at low
pressure regions (<0.01 bar). <i>In situ </i>infrared
(IR) spectroscopy shows the interactions between Brønsted acidic sites and NH<sub>3</sub>,
which suggests that <b>NU-300</b> can be
used as a sorbent for NH<sub>3</sub> capture at low pressures.</p> | Yongwei Chen; Xuan Zhang; Kaikai Ma; Zhijie Chen; Xingjie Wang; Julia Knapp; Selim Alayoglu; Fenfen Wang; Qibin Xia; Zhong Li; Timur Islamoglu; Omar Farha | Coordination Chemistry (Inorg.); Polymers; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74392842e656e63db22b8/original/a-9-connected-zirconium-based-metal-organic-framework-for-ammonia-capture.pdf |
60c74f17469df4aa39f44613 | 10.26434/chemrxiv.12846629.v1 | A Single-Step Synthesis of Azetidine-3-Amines | <div>
<p>The azetidine group is frequently encountered within
contemporary medicinal chemistry where it is viewed as a privileged structure.
However, the introduction of an azetidine can be synthetically challenging. Herein,
a straight-forward one step synthesis of azetidine-3-amines, starting from a bench
stable, commercial material is presented. The reaction tolerates functional
groups commonly encountered in biological-, medicinal- and agro-chemistry, and
proceeds in moderate-to-high yield with secondary amines, and moderate-to-low
yield with primary amines. The methodology compares favorably to recent alternative
procedures and can be utilized in “any-stage” functionalization, including late-stage
azetidinylation of approved drugs and other compounds with pharmacological
activity.</p>
</div> | Brian J Wang; Matthew Duncton | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f17469df4aa39f44613/original/a-single-step-synthesis-of-azetidine-3-amines.pdf |
6169a43acada1f73e0d72eef | 10.26434/chemrxiv-2021-gx4mr | Eukaryotic catecholamine hormones influence the chemotactic control of Vibrio campbellii by binding to the coupling protein CheW | In addition to their well-known role as stress-associated catecholamine hormones in animals and humans, epinephrine (EPI) and norepinephrine (NE) act as interkingdom signals between eukaryotic hosts and bacteria. However, the molecular basis of their effects on bacteria is not well understood. In initial phenotypic studies utilizing Vibrio campbellii as a model organism, we characterized the bipartite mode of action of catecholamines, which consists of promotion of growth under iron limitation, and enhanced colony expansion on soft agar. In order to identify the molecular targets of the hormones, we designed and synthesized tailored probes for chemical proteomic studies. As the catechol group in EPI and NE acts as iron chelator and is prone to form a reactive quinone moiety, we devised a photoprobe based on the adrenergic agonist phenylephrine (PE), which solely influenced colony expansion. Using this probe, we identified CheW, located at the core of the chemotaxis signaling network, as a major target. In vitro studies confirmed that EPI, NE, PE, as well as labetalol, a clinically applied antagonist, bind to purified CheW with affinity constants in the sub-micromolar range. In line with these findings, exposure of V. campbellii to these adrenergic agonists affects the chemotactic control of the bacterium. This study highlights a previously unknown effect of eukaryotic signaling molecules on bacterial motility. | Angela Weigert Muñoz; Elisabeth Hoyer; Kilian Schumacher; Marianne Grognot; Katja Taute; Stephan Hacker; Stephan Sieber; Kirsten Jung | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6169a43acada1f73e0d72eef/original/eukaryotic-catecholamine-hormones-influence-the-chemotactic-control-of-vibrio-campbellii-by-binding-to-the-coupling-protein-che-w.pdf |
60c74610567dfe42deec4577 | 10.26434/chemrxiv.10565588.v1 | In-situ Activation of a Highly Volatile and Thermally Stable Indium(III) Triazenide Precursor for Epitaxial Growth of Indium Nitride by Atomic Layer Deposition | Indium nitride (InN) is characterised by its superb electron mobility making it a ground-breaking material for high frequency electronics. The difficulty of depositing highquality crystalline InN currently impedes its broad implementation in electronic devices. Herein, we report a new highly volatile and thermally stable In(III) triazenide precursor and demonstrate its ability to deposit high-quality epitaxial hexagonal InN by atomic layer deposition (ALD). The new triazenide precursor was found to sublime at 80 °C and thermogravimetric analysis showed single step volatilisation with an onset temperature of 145 °C and negligible residual mass. Strikingly, two temperature intervals were observed when depositing InN films. In the high temperature interval, the precursor underwent thermal decomposition inside the ALD reaction chamber to produce a more reactive indium compound whilst retaining self-limiting growth behaviour. Stochiometric InN films with very low levels of impurities were grown epitaxially on 4H-SiC. This new triazenide precursor now enables ALD of InN for semi-conductor applications.<br /> | Nathan O'Brien; Polla Rouf; Rouzbeh Samii; Karl Rönnby; Sydney C. Buttera; Ivan G. Ivanov; Vadim Kessler; Lars Ojamäe; Henrik Pedersen | Materials Processing; Thin Films; Nanofabrication; Coordination Chemistry (Inorg.); Ligands (Inorg.); Main Group Chemistry (Inorg.); Organometallic Compounds; Reaction (Inorg.); Coordination Chemistry (Organomet.); Ligand Design; Ligands (Organomet.); Main Group Chemistry (Organomet.); Interfaces; Physical and Chemical Processes; Physical and Chemical Properties; Surface; Thermodynamics (Physical Chem.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74610567dfe42deec4577/original/in-situ-activation-of-a-highly-volatile-and-thermally-stable-indium-iii-triazenide-precursor-for-epitaxial-growth-of-indium-nitride-by-atomic-layer-deposition.pdf |
6452783f27fccdb3ea6e78d8 | 10.26434/chemrxiv-2022-41f04-v3 | Neural potentials of proteins extrapolate beyond training data | We evaluate neural network (NN) coarse-grained (CG) force fields compared to traditional CG molecular mechanics force fields. We conclude NN force fields are able to extrapolate and sample from unseen regions of the free energy surface when trained with limited data. Our results come from 88 NN force fields trained on different combinations of clustered free energy surfaces from 4 protein mapped trajectories. We used a statistical measure named total variation similarity (TVS) to assess the agreement between free energy surfaces of mapped atomistic simulations and CG simulations from the trained NN force fields. Our conclusions support the hypothesis that constructing force fields on one region of the protein free energy surface can indeed extrapolate to unexplored regions. Additionally, the force matching error was found to only be weakly correlated with a force field's ability to reconstruct the correct free energy surface. | Geemi P. Wellawatte; Glen M. Hocky; Andrew D. White | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6452783f27fccdb3ea6e78d8/original/neural-potentials-of-proteins-extrapolate-beyond-training-data.pdf |
65cf840d66c1381729cc143e | 10.26434/chemrxiv-2024-mxr86 | Terahertz Spectroscopy Unambiguously Determines the Orientation of Guest Water Molecules in a Structurally Elusive Metal-Organic Framework | Porous materials, particularly metal-organic frameworks (MOFs), hold great promise for ad- vanced applications, with one of the most exciting being passive water harvesting. In order to realize such goals, it is crucial to understand in detail the structures of these host-guest com- plexes. MIL-53(Al) is an exceptionally well-studied MOF, which exhibits a phase transition upon guest capture – in this case, water – resulting in a dramatic change in the pore volume. Despite extensive studies, the structure of the water-loaded narrow-pore phase, MIL-53(Al)-np remains controversial, particularly with respect to the positions of the adsorbed water molecules within the framework. We use terahertz (THz) spectroscopy, coupled with powder X-ray diffraction (PXRD) and density functional theory simulations, to unambiguously resolve this controversy. We show that the low frequency (< 100 cm−1) vibrational spectrum depends on weak long-range forces, which are extremely sensitive to the orientation of the adsorbed water molecules. This enables us to definitively determine the correct structure of MIL-53(Al)-np, while highlighting the extreme sensitivity of THz spectroscopy to the bulk structure of porous crystals, suggesting its potential as a robust complement to X-ray diffraction for precise characterization of host-guest complexes. | Saheed Ajibade; Luca Catalano; Johanna Kolbel; Daniel Mittleman; Michael Ruggiero | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Spectroscopy (Physical Chem.); Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cf840d66c1381729cc143e/original/terahertz-spectroscopy-unambiguously-determines-the-orientation-of-guest-water-molecules-in-a-structurally-elusive-metal-organic-framework.pdf |
60c743b1702a9b165018a666 | 10.26434/chemrxiv.8241887.v2 | Investigating the Effect of Positional Isomerism on the Assembly of Zirconium Phosphonates Based on Tritopic Linkers | We report on the use of a novel tritopic phosphonic linker, 2,4,6-tris[3-(phosphonomethyl)phenyl]-1,3,5-triazine, for the synthesis of a layered zirconium phosphonate, named UPG-2. Comparison with the structure of the permanently porous UPG-1, based on the related linker 2,4,6-tris[4-(phosphonomethyl)phenyl]-1,3,5-triazine, reveals that positional isomerism disrupts the porous architecture in UPG-2 by preventing the formation of infinitely extended chains connected through Zr-O-P-O-Zr bonds. The presence of free, acidic P-OH groups and an extended network of hydrogen bonds makes UPG-2 a good proton conductor, reaching values as high as 5.7x10<sup>-4</sup> S cm<sup>-1</sup>.<br /> | Marco Taddei; Stephen J. I. Shearan; Anna Donnadio; Mario Casciola; Riccardo Vivani; Ferdinando Costantino | Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b1702a9b165018a666/original/investigating-the-effect-of-positional-isomerism-on-the-assembly-of-zirconium-phosphonates-based-on-tritopic-linkers.pdf |
6194107778db4e4f3710a67e | 10.26434/chemrxiv-2021-tth3p | User-friendly, magnetically sealed plug-and-play sensor module for online electrochemical sensing for fluidic devices | The growth in fluidic devices, such as organ-on-chip (OOC) technology, comes with a need for growth in sensing capabilities of key biomolecules to help elucidate changes during the time course of experiments. We developed an on-line, easy-to-assemble, 3D-printed electrochemical sensor module that is magnetically sealed for ease of assembly. The sensor module includes a plug-and-play format for electrochemical sensors made in finger-tight fittings to allow for a wide selection of experimental set-ups and target molecules. Here, we report the feasibility of the sensor module as well as demonstrate its use for electrochemical sensing with integrated thermoplastic electrodes (TPEs). The sensor module withstood over 300 kPa of backpressure and demonstrated reliable performance with TPEs when using cyclic voltammetry (CV) and amperometry under flow conditions. CVs using the ferri/ferrocyanide (K3/4[Fe(CN)6]) redox system demonstrate that the sensor module does not hinder the expected linear response with respect to analyte concentration. Further CVs and amperometry demonstrated the use of the sensor module under flow conditions. Such success in device design and usability is promising for future work using the on-line sensor module with a variety of applications. | Amanda Roley; Kaylee Clark; Alec Richardson; Brandaise Martinez; Stuart Tobet; Charles Henry; Alec Richardson | Analytical Chemistry; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6194107778db4e4f3710a67e/original/user-friendly-magnetically-sealed-plug-and-play-sensor-module-for-online-electrochemical-sensing-for-fluidic-devices.pdf |
627abfb543d1f0b3a427d02b | 10.26434/chemrxiv-2022-ldblr | Formation of Nanostructured Silicas through the Fluoride Catalysed Self-Polymerization of Q-type Silsesquioxane Cages | Octa(dimethylsiloxy)silsesquioxane (Q8M8H) undergoes rapid self-polymerization in the presence of a fluoride catalyst to form complex 3D porous structural network materials with specific surface areas up to 650 m2g-1. This establishes a new method to bio-derived high inorganic content soft silicas with potential applications in filtration, carbon capture, catalysis, or hydrogen source. | Nai-hsuan Hu; Cory Sims; Kathryn Haver; Joseph Furgal | Materials Science; Polymer Science; Nanoscience; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Inorganic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627abfb543d1f0b3a427d02b/original/formation-of-nanostructured-silicas-through-the-fluoride-catalysed-self-polymerization-of-q-type-silsesquioxane-cages.pdf |
64c7e2e1658ec5f7e5808425 | 10.26434/chemrxiv-2023-dcg9d | Reinforcement learning prioritizes general applicability in reaction optimization | Reaction conditions that are generally applicable to a wide variety of substrates are highly desired. While many approaches exist to evaluate the general applicability of developed conditions, a universal approach to efficiently discover such conditions during optimizations de novo is rare. In this work, we report the design, implementation, and application of reinforcement learning bandit optimization models to identify generally applicable conditions in a variety of chemical transformations. Performance benchmarking on existing datasets statistically showed high accuracies for identifying general conditions. A palladium-catalyzed imidazole C–H arylation reaction and an aniline amide coupling reaction were investigated experimentally to demonstrate utilities of our learning model in practice. | Jason Y. Wang; Jason M. Stevens; Stavros K. Kariofillis; Mai-Jan Tom; Jun Li; Jose E. Tabora; Marvin Parasram; Benjamin Shields; David Primer; Bo Hao; David Del Valle; Stacey DiSomma; Ariel Furman; G. Greg Zipp; Sergey Melnikov; James Paulson; Abigail Doyle | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c7e2e1658ec5f7e5808425/original/reinforcement-learning-prioritizes-general-applicability-in-reaction-optimization.pdf |
60c75438bdbb898ceda3a5ea | 10.26434/chemrxiv.13633280.v1 | Calculating Vacuum Metal Infiltration Rate and Depth of BN-Al Composite Materials | <p>For the first
time, the metal infiltration depth and infiltration rate of the BN-Al composite
prepared by metal infiltration have been calculated and studied. The
calculation results show that the infiltration depth gradually increases with
the increase of time, and the final infiltration depth can reach 0.21 m. As
time increases and voids decrease, the infiltration rate gradually decreases.
The maximum impregnation rate is 0.65cm·min<sup>-1</sup>. This calculation and
research provide a positive idea for the calculation and prediction of metal
infiltration in void media in the future study.</p> | Chao Wang; Zhefu Li; Mengge Dong; Lu Zhang; Jianxing Liu; Xiaozhou Cao; Xiangxin Xue | Composites | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75438bdbb898ceda3a5ea/original/calculating-vacuum-metal-infiltration-rate-and-depth-of-bn-al-composite-materials.pdf |
60c74cd4842e65cb2adb3366 | 10.26434/chemrxiv.12550868.v1 | Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase | <div>
<div>
<div>
<p>Glycerol-3-phosphate dehydrogenase is a biomedically important enzyme that plays a crucial
role in lipid biosynthesis. It is activated by a ligand-gated conformational change that is necessary
for the enzyme to reach a catalytically competent conformation capable of efficient transition state
stabilization. While the human form (hlGPDH) has been the subject of extensive structural and
biochemical studies, corresponding computational studies to support and extend the experimental
observations have been lacking. We perform here detailed empirical valence bond and Hamiltonian replica exchange molecular dynamics simulations of wild-type hlGPDH and its
variants, as well as providing a novel crystal structure of the binary hlGPDH·NAD R269A variant
where the enzyme is present in the open conformation. We estimated the activation free energies
for the hydride transfer reaction in wild-type and substituted variants of hlGPDH and investigated
the effect of mutations on the catalysis from a detailed structural study. Our structural data and simulations also illustrate the critical role of the R269 side chain in facilitating the closure of
hlGPDH into a catalytically competent conformation, through modulating the flexibility of a key
catalytic loop (292-LNGQKL-297), thus rationalizing a tremendous 41,000-fold decrease
experimentally in the turnover number, kcat, upon truncating this residue. Taken together, our data
highlight the importance of this ligand-gated conformational change in catalysis, a feature that can
be exploited both for protein engineering and for the design of novel allosteric inhibitors targeting
this biomedically important enzyme.</p></div></div></div> | Anil Ranu Mhashal; Adrian Romero-Rivera; Lisa S. Mydy; Judith R. Cristobal; Andrew M. Gulick; John Richard; Shina Caroline Lynn Kamerlin | Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cd4842e65cb2adb3366/original/modeling-the-role-of-a-flexible-loop-and-active-site-side-chains-in-hydride-transfer-catalyzed-by-glycerol-3-phosphate-dehydrogenase.pdf |
60c759a6f96a000616289063 | 10.26434/chemrxiv.12757943.v3 | A hidden catalysis: metal-, and organocatalyst-free one-pot assembly of chiral aza-tricyclic molecules | <p></p><p> Development of a rapid synthesis of complex
molecules from simple building blocks under a metal-and organocatalyst-free
condition is both conceptually and chemically challenging. Here, we developed a
hidden catalysis that allow the straightforward assembly of enantiopure
aza-tricyclic molecules containing six contiguous stereocenters from <a>aminophenols, α,β-unsaturated aldehydes </a>and α-amino
acids. <a>Without using a metal or an organocatalyst, our
approach relies on a temporary formation of a spiroimidazolidinone intermediate
and its participation in a sequential aza-Michael/Michael reaction as both a
substrate and a catalyst</a> under an iminium/enamine catalysis. The formation
of the putative iminium intermediate was supported by spectroscopic data and its
interruptive reduction derivative was isolated and fully characterized. Whereas
a conventional catalyst is always present and does not undergo a permanent
chemical change in a classic catalysis, the spiroimidazolidinone intermediate is
conceptualized as a sub-catalyst as it is only temporary produced from
precursors and catalyzes its own consumption. This unique substrate-catalyst
(sub-catalyst) dual role of the spiroimidazolidinone induces a substantial steric
discrimination in the transition state and an excellent overall
diastereoselectivity (>20:1 dr). It allows the use of an amino acid
precursor as the sole chirality genesis and avoids the use of transition metals
or organocatalysts. An enantiomer of an aza-tricyclic
imidazolidinone can be prepared from a commercially available amino acid
precursor. The aqueous-based reaction is practical and scalable for multi-gram
synthesis. The success of implementing this sub-catalysis concept in the
synthesis will pave the way for many efficient chiral catalyst-free
preparations of chiral complex molecules.<br /></p><br /><p></p> | Dung Do | Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759a6f96a000616289063/original/a-hidden-catalysis-metal-and-organocatalyst-free-one-pot-assembly-of-chiral-aza-tricyclic-molecules.pdf |
672fa4c4f9980725cfad3421 | 10.26434/chemrxiv-2024-lj0fb | Surface-Functionalized Layered Double Hydroxides (LDHs) Nanoplatelets for Enhanced Thermal Stability of Plasticized Polyvinyl Chloride (PVC) films | Surface and interfacial engineering of additives is crucial for enhancing the compatibility between inorganic additives and polymer matrices. Thermal stabilizers are particularly prevalent in polyvinyl chloride (PVC) compounding. Recently, layered double hydroxidehydroxide (LDH) structures have been explored as a new class of efficient and environmentally-friendly stabilizers. This study uses oleic acid (OA) as a bio-sourced surface-active agent for improved compatibility between MgAlZn-CO3 LDH and the PVC matrix. Scanning electron microscopy (SEM) results indicated that OA substantially influences the distribution of LDHs throughout PVC matrix. Additionally, Raman spectroscopy confirmed that the incorporation of OA enhances the HCl absorption capability of LDHs, leading to an over two-fold increase in the static thermal stability of PVC. Correspondingly, color stability of PVC compounds with the modified LDH also improves significantly. The surface-functionalized LDH developed in this work exhibits tremendous potential as a highly potent and yet environmentally-friendly stabilizer for PVC processing as well as for PVC recycling and its circular economy. | Hossein Ipakchi; Kushal Panchal; Roozbeh Mafi; Li Xi | Materials Science; Polymer Science; Materials Processing; Organic Polymers; Polymer blends; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672fa4c4f9980725cfad3421/original/surface-functionalized-layered-double-hydroxides-ld-hs-nanoplatelets-for-enhanced-thermal-stability-of-plasticized-polyvinyl-chloride-pvc-films.pdf |
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