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60c74df6f96a00d973287a2e | 10.26434/chemrxiv.12679226.v1 | Conformational Landscape Reduction of a Dynamic 29-Residue Peptide by a Perfluoroaromatic Small Molecule | Conformationally dynamic peptides and proteins display both important biochemical properties and present a challenge for computational modeling. Characterizing the accessible structural landscape represents one route to understand their function with molecular level detail. We characterize a self-labeling 29-residue peptide, MP01-Gen4, that undergoes structural alterations in the presence of a perfluoroaromatic reaction partner. Replica exchange molecular dynamics (REMD) shows MP01 to access a broad set of states, that microsecond-long explicit solvent simulations only minimally sample. REMD and structural network analysis find an altered and reduced conformational landscape when MP01 interacts non-covalently or is covalently attached to the perfluoroaromatic small molecule. Residues throughout the peptide, notably at the C-terminus, interact with the small molecule in conformational state-dependent manners. The results help explain and generate hypotheses for experimental observations including the importance of flexibility and the role of the N- and C-terminal regions, both of which are distant from the active cysteine. The simulations highlight the importance of substantial sampling in minimally stabilized, conformationally dynamic systems and supplies a case study for small molecule-mediated, peptide conformational changes.<br /> | ethan evans | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df6f96a00d973287a2e/original/conformational-landscape-reduction-of-a-dynamic-29-residue-peptide-by-a-perfluoroaromatic-small-molecule.pdf |
64ad5354ba3e99daefe70a18 | 10.26434/chemrxiv-2023-xw0pq-v2 | Fake it until you make it? Generative De Novo Design and Virtual Screening of Synthesizable Molecules | Computational techniques, including virtual screening, de novo design, and generative models, play an increasing role in expediting DMTA cycles for modern molecular discovery. However, computationally proposed molecules must be synthetically feasible for laboratory testing. In this perspective, we offer a succinct introduction to the subject, showcase typical workflows to integrate synthesis planning, synthesizability scoring, and molecule generation. Finally, we address limitations and opportunities for future research. | Megan Stanley; Marwin Segler | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ad5354ba3e99daefe70a18/original/fake-it-until-you-make-it-generative-de-novo-design-and-virtual-screening-of-synthesizable-molecules.pdf |
640e8128b5d5dbe9e82a821c | 10.26434/chemrxiv-2023-t5ppp | Computational Prediction of Metabolic alpha-Carbon Hydroxylation Potential of N-Nitrosamines: Overcoming Data Limitations for Carcinogenicity Assessment | Recent withdrawal of several drugs from the market due to N-nitrosamine impurities highlighted the necessity for computational approaches to assess the carcinogenicity risk of these impurities. However, current approaches are limited because robust animal carcinogenicity data is only available for a few simple nitrosamines, which do not represent the structural diversity of the many possible nitrosamine drug substance related impurities (NDSRIs). In this paper, we present a novel method that uses data on CYP-mediated metabolic hydroxylation of CH2 groups in non-nitrosamine xenobiotics to identify structural features that may also help in predicting the likelihood of metabolic alpha-carbon hydroxylation in N-nitrosamines. Our approach offers a new avenue for tapping into potentially large experimental datasets on xenobiotic metabolism to improve the risk assessment of nitrosamines. It is believed that alpha-carbon hydroxylation is the vital rate-limiting step in the metabolic activation of nitrosamines, and identifying structural features that influence this process may be valuable in evaluating their carcinogenic potential. This is particularly significant as information regarding the factors that influence the metabolic activation of NDSRIs is practically non-existent. We discovered hundreds of structural features that either promote or hinder hydroxylation, in contrast to the very few that have been identified so far from the small nitrosamine carcinogenicity dataset. While relying solely on -carbon hydroxylation prediction is insufficient for forecasting carcinogenic potency, the identified features can help in the selection of relevant structural analogs in read across studies and assist domain experts who, after considering other factors such as the reactivity of the resulting electrophilic diazonium species, can establish the acceptable intake limits for nitrosamine impurities. | Suman Chakravarti | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640e8128b5d5dbe9e82a821c/original/computational-prediction-of-metabolic-alpha-carbon-hydroxylation-potential-of-n-nitrosamines-overcoming-data-limitations-for-carcinogenicity-assessment.pdf |
6615344121291e5d1d75112f | 10.26434/chemrxiv-2024-ld5jn | Epitaxial Core/Shell Nanocrystals of (Europium-Doped) zirconia and hafnia | A careful design of nanocrystal architecture can strongly enhance the nanocrystal function. So far, this strategy faced a synthetic bottleneck in the case of refractory oxides. Here, we demonstrate the epitaxial growth of hafnia shells onto zirconia cores, and pure zirconia shells onto europium doped zirconia cores. The core/shell structures are fully crystalline. Upon shelling, the optical properties of the europium dopant are dramatically improved (featuring a more uniform coordination and a longer photoluminescence lifetime), indicating the suppression of non-radiative pathways. These results launch the stable zirconium and hafnium oxide hosts as alternatives for the established NaYF4 systems. | Carlotta Seno; Nico Reichholf; Francesco Salutari; Maria Chiara Spadaro; Yurii P. Ivanov; Giorgio Divitini; Alexander Gogos; Inge Herrmann; Jordi Arbiol; Philippe F. Smet; Jonathan De Roo | Materials Science; Inorganic Chemistry; Nanoscience; Core-Shell Materials; Optical Materials; Lanthanides and Actinides | CC BY 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6615344121291e5d1d75112f/original/epitaxial-core-shell-nanocrystals-of-europium-doped-zirconia-and-hafnia.pdf |
6628d98891aefa6ce14a6008 | 10.26434/chemrxiv-2024-5ctgg | Lewis Acid-Catalyzed Unusual (4+3) Annulation of para-Quinone Methides with Bicyclobutanes: Access to Oxabicyclo [4.1.1]octanes | Over the past few years, there has been a surge of interest in the chemistry of bicyclobutanes (BCBs). Although BCBs have been used to synthesize bicyclo[2.1.1]hexanes and bicyclo[3.1.1]heptanes, the synthesis of bicyclo[4.1.1]octanes has re-mained elusive. Herein, we report the first Lewis acid-catalyzed unexpected (4+3) annulation of para-quinonemethides (p-QMs) with BCBs allowing the synthesis of oxabicyclo[4.1.1]octanes proceeding under mild conditions. With 5 mol % of Bi(OTf)3, the reaction afforded the (4+3) annulated product in high regioselectivity and good functional group compatibility via a simultaneous Lewis acid activation of BCBs and p-QMs. The reaction is likely initiated by the 1,6-addition of Lewis acid activated BCBs to p-QMs followed by the C2-selective intramolecular addition of the phenol moiety to the generated cyclobutyl cation intermediate. Moreover, detailed mechanistic studies provided insight into the mechanism of the reaction. | Shiksha Deswal; Avishek Guin; A T Biju | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6628d98891aefa6ce14a6008/original/lewis-acid-catalyzed-unusual-4-3-annulation-of-para-quinone-methides-with-bicyclobutanes-access-to-oxabicyclo-4-1-1-octanes.pdf |
63eb3e439da0bc6b33e84d88 | 10.26434/chemrxiv-2023-5cp62 | High-throughput synthesis and machine learning assisted design of photodegradable hydrogels | Due to the large chemical space, the design of functional and responsive soft materials poses many challenges but also offers a wide range of opportunities in terms of the scope of possible properties. Herein we report an experimental workflow for miniaturized combinatorial high-throughput screening of functional hydrogel libraries. The data created from the analysis of the photodegradation process of more than 900 different types of hydrogel pads is used to train a machine learning (ML) model for automated decision making. Through iterative model optimization based on Bayesian Optimization we achieve a substantial improvement in response properties and thus expanded the scope of material properties obtainable within the chemical space of hydrogels in our study. We therefore demonstrate the potential of combining miniaturized high-throughput experiments with smart optimization algorithms for cost and time efficient optimization of materials properties. | Maximilian Seifermann; Patrick Reiser; Pascal Friederich; Pavel Levkin | Materials Science; Polymer Science; Hydrogels; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eb3e439da0bc6b33e84d88/original/high-throughput-synthesis-and-machine-learning-assisted-design-of-photodegradable-hydrogels.pdf |
657922f1fd283d7904dfb9a3 | 10.26434/chemrxiv-2023-88vng | Metal-ligand dual-site SAzyme with uricase-like mechanism for specific uric acid oxidation | In nature, coenzyme-independent oxidases have evolved in selective catalysis using isolated substrate-binding pockets. Single-atom artificial enzymes (SAzymes) are promising to simulating enzyme-like active centers, but owing to the lack of recognition sites, the specificity requiring in identifying multiple substrates simultaneously is a formidable task. Here we report an unprecedented metal (Ni)-ligand (3,3'-diaminobenzidine, DAB) dual-site SAzyme (Ni-DAB) that exhibited remarkably selectivity in uric acid (UA) oxidation. Experiments and theoretical calculations confirmed that like uricase Ni-DAB had an synergistic isolated dual sites, in which the Ni metal center and the C atom in the ligand served as the specific UA and O2 binding sites, respectively. As a potential application, a Ni-DAB-based biofuel cell using human urine was constructed. This work unlocks a new approach of synergistic isolated dual sites in boosting the selectivity of artificial enzymes. | Kaiyuan Wang; Qing Hong; Cai Zhu; Yuan Xu; Wang Li; Wenhao Chen; Xiang Gu; Xinghua Chen; Yanfeng Fang; Yanfei Shen; Songqin Liu; Yuanjian Zhang | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Biocatalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657922f1fd283d7904dfb9a3/original/metal-ligand-dual-site-s-azyme-with-uricase-like-mechanism-for-specific-uric-acid-oxidation.pdf |
60c752d4bdbb89e104a3a370 | 10.26434/chemrxiv.13184261.v2 | Understanding the Dipole Moment of Liquid Water from a Self-Attractive Hartree Decomposition | <p>The dipole moment of a single water molecule in liquid water has been a critical concept for understanding water’s dielectric properties. In this work, we investigate the dipole moment of liquid water through a self-attractive Hartree (SAH) decomposition of total electron density computed by density functional theory, on water clusters sampled from ab initio molecular dynamics simulation of bulk water. By adjusting one parameter that controls the degree of density localization, we reveal two distinct pictures of water dipoles that are consistent with bulk dielectric properties: a localized picture with smaller and less polarizable monomer dipoles, and a delocalized picture with larger and more polarizable monomer dipoles. We further uncover that the collective dipole-dipole correlation is stronger in the localized picture and is key to connecting individual dipoles with bulk dielectric properties. Based on these findings, we suggest considering both individual and collective dipole behaviors when studying the dipole moment of liquid water, and propose new design strategies for developing water models.</p> | Tianyu Zhu; Troy Van Voorhis | Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752d4bdbb89e104a3a370/original/understanding-the-dipole-moment-of-liquid-water-from-a-self-attractive-hartree-decomposition.pdf |
60c73ed80f50db1a203956de | 10.26434/chemrxiv.6998204.v2 | Acceptorless amine dehydrogenation and transamination using Pd-doped layered double hydroxides | <div>
<p>The synthesis, characterization,
and activity of Pd-doped layered double hydroxides (Pd-LDHs) for for
acceptorless amine dehydrogenation is reported. These multifunctional catalysts
comprise Brønsted basic and Lewis
acidic surface sites that stabilize Pd species in 0, 2+, and 4+ oxidation
states. Pd speciation and corresponding cataytic performance is a strong
function of metal loading. Excellent activity is observed for the oxidative
transamination of primary amines and acceptorless dehydrogenation of secondary
amines to secondary imines using a low Pd loading (0.5 mol%), without the need
for oxidants. N-heterocycles, such as indoline, 1,2,3,4-tetrahydroquinoline,
and piperidine, are dehydrogenated to the corresponding aromatics with high
yields. The relative yields of secondary imines are proportional to the calculated
free energy of reaction, while yields for oxidative amination correlate with the
electrophilicity of primary imine intermediates. Reversible amine
dehydrogenation and imine hydrogenation determine the relative imine:amine
selectivity. Poisoning tests evidence that Pd-LDHs operate heterogeneously,
with negligible metal leaching; catalysts can be regenerated by acid dissolution
and re-precipitation.</p>
</div>
<br /> | Diana Ainembabazi; Nan An; Jinesh Manayil; Karen Wilson; Adam Lee; Adelina Voutchkova-Kostal | Base Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed80f50db1a203956de/original/acceptorless-amine-dehydrogenation-and-transamination-using-pd-doped-layered-double-hydroxides.pdf |
60c752d60f50dba743397a6b | 10.26434/chemrxiv.13356842.v1 | Nature as a Treasure Trove for Anti-COVID-19: Luteolin and Naringenin from Indonesian Traditional Herbal Medicine Reveal Potential SARS-CoV-2 Mpro Inhibitors Insight from in Silico Studies | <div>Since the worldwide is currently facing the COVID-19 pandemic, there are no drugs or vaccines have been approved</div><div>for the treatment of SARS-CoV-2 infection. Therefore, there is an urgent need for in-depth research on emerging</div><div>human infectious coronaviruses. As part of our endeavour in combating this COVID-19 pandemic, in this paper, we</div><div>report on the discovery of an active antiviral small-molecule from Indonesian traditional herbal medicine used in Jamu</div><div>to inhibit 3CLpro of SARS-CoV-2 using in-silico approaches. As one of the mega biodiversity countries, Indonesia has</div><div>more than 1,180 species that can be prospected for medicine plants. Jamu, the Indonesian traditional herbal medicine,</div><div>is supposed to have similar potentials as those of traditional Chinese medicine (TCM). However, due to the lack of</div><div>scientific proof, Jamu is not recognised in the Guideline of COVID-19 Patients, particularly in Indonesia. Thus, in</div><div>this study, we performed virtual docking screening along with pharmacokinetic and DFT studies of selected 49</div><div>bioactive phytochemicals from several medicinal plants used in Jamu against the 3CLpro enzyme of SARS-CoV-2.</div><div>From the result, it was noted that from a set of 49 phytochemicals of medicinal plants used in Jamu, 2 phytochemicals,</div><div>i.e., Luteolin and Naringenin were identified as potential druggable inhibitors candidates of 3CLpro of SARS CoV-2.</div> | Wahyu Prasetyo; Triana Kusumaningsih; Maulidan Firdaus | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752d60f50dba743397a6b/original/nature-as-a-treasure-trove-for-anti-covid-19-luteolin-and-naringenin-from-indonesian-traditional-herbal-medicine-reveal-potential-sars-co-v-2-mpro-inhibitors-insight-from-in-silico-studies.pdf |
673c56a75a82cea2faa4462a | 10.26434/chemrxiv-2024-4r9m0 | Synthesis and development of an eco-friendly HPLC method for detection of Neratinib and its related Impurity H | Neratinib is a tyrosine kinase inhibitor prescribed for the treatment of breast cancer. The key step for the synthesis of neratinib involves the coupling of 4-N,N-dimethylaminocrotonic acid with 6-amino-4-[3-chloro-4-(2-pyridinyl methoxy)-anilino]-3-cyano-7-ethoxy quinolone. Several potential process related impurities are formed during the synthesis, including unreacted starting materials, and degradation products. These impurities are monitored by high-performance liquid chromatography (HPLC) and mass spectrometry (MS) to ensure the purity and quality of the final product. This study highlights the synthesis of neratinib impurity-H, and its detection by a new HPLC method. The HPLC method employed a C18 column (150 x 4.6 mm, 5μm) with a gradient flow of 1 ml min-1 of ethanol and phosphate buffer (pH 3.40) as a green solvent. The AGREE score confirmed the environmental benefits of using ethanol in the development of the liquid chromatographic method. | Sharada Prasanna Swain; Vivek Kumar; Satheesh Nanjappan | Analytical Chemistry; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673c56a75a82cea2faa4462a/original/synthesis-and-development-of-an-eco-friendly-hplc-method-for-detection-of-neratinib-and-its-related-impurity-h.pdf |
6454fb7427fccdb3ea888a8f | 10.26434/chemrxiv-2023-zq6zb | Silicon-based Solid-State Batteries: Electrochemistry and Mechanics to Guide Design and Operation | Solid-state batteries are promising alternatives to the incumbent lithium-ion technology however, they face a unique set of challenges that must be overcome to enable their widespread adoption. These challenges include solid-solid interfaces that are highly resistive, with slow kinetics, and a tendency to form interfacial voids leading to delamination which results in diminished cycle life. This modelling study probes the evolution of stresses at the solid electrolyte (SE) solid-solid interfaces, by linking the chemical and mechanical material properties to their electrochemical response, which can be used as a guide to optimise the design and manufacture of silicon (Si) based SSBs. A thin-film solid-state battery consisting of an amorphous Si negative electrode (NE) is studied, which exerts compressive stress on the SE, caused by the lithiation-induced expansion of the Si. By using a 2D chemo-mechanical model, continuum scale simulations are used to probe the effect of applied pressure and C-rate on the stress-strain response of the cell and their impacts on the overall cell capacity. A complex concentration gradient is generated within the Si electrode due to slow diffusion of Li through Si which leads to localised strains. To reduce the interfacial stress and strain at 100% SOC, operation at moderate C-rates with low applied pressure are desirable. Alternatively, the mechanical properties of the SE could be tailored to optimise cell performance. To reduce Si stress, a SE with a moderate Young’s modulus similar to that of lithium phosphorous oxynitride (~ 77 GPa) with a low yield strength comparable to sulfides (~ 0.67 GPa) should be selected. However, if the reduction in SE stress is of greater concern, then a compliant Young’s modulus (~ 29 GPa) with a moderate yield strength (1-3 GPa) should be targeted. This study emphasises the need for SE material selection and to consider other cell components in order to optimise the performance of thin film solid-state batteries. | Pooja Vadhva; Adam Boyce; Anisha Patel; Paul Shearing; Gregory Offer; Alexander Rettie | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6454fb7427fccdb3ea888a8f/original/silicon-based-solid-state-batteries-electrochemistry-and-mechanics-to-guide-design-and-operation.pdf |
633c2e76fee74e217e552635 | 10.26434/chemrxiv-2022-xcvxb | Tuning the Spin-Crossover Properties of FeII4L6 Cages via Ligand Modifications in the First and Second Coordination Spheres | The effects of modifications to the first and second coordination spheres of the metal centers in FeII-based cages on the spin-crossover properties is not well understood. Here, we report a family of FeII4L6 spin-crossover cages based on 2,2’-pyridylbenzimidazoles where subtle modifications to the coordination motif (first coordination sphere) and the linker type (second coordination sphere) of the organic ligand lowered the spin crossover temperature in CD3CN to a range between 430 K and 244 K. Comparing pairs of cages, CH3 substituents on either the coordination motif or phenylene linker lowered the spin-crossover temperature by 48 K, 91 K or 186 K, attributed to predominantly first, second coordination sphere effects and a combination of both, respectively. This study provides first insight into how ligand modifications in the first and second coordination sphere can be harnessed on the path towards the improved rational design of spin-crossover cages. | Tobias Paschelke; Eicke Trumpf; David Grantz; Malte Pankau; Niclas Grocholski; Christian Näther; Frank Sönnichsen; Anna McConnell | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c2e76fee74e217e552635/original/tuning-the-spin-crossover-properties-of-fe-ii4l6-cages-via-ligand-modifications-in-the-first-and-second-coordination-spheres.pdf |
66b5beb35101a2ffa8acaf91 | 10.26434/chemrxiv-2024-xv5mf | Application of tea leaves in the circular economy: A sustainable approach to remove synthetic dye from wastewater by alkali-activated spent tea leaves | Spent tea leaves (STL) were recycled and utilized to reduce water pollution caused by synthetic dyes. The current study used STL as a biosorbent to remove malachite green (MG) dye from aqueous solutions and fish aquarium wastewater. The dye removal efficiency was enhanced by alkali (NaOH) and thermal pretreatment and showed 98% removal efficiency. Biosorbent characteristics and dye removal mechanisms were established using BET-surface area, zeta-potential, SEM, and FTIR. An optimum adsorption capacity of 40.6 mgg-1 was obtained for MG. Equilibrium sorption data were analyzed by Langmuir and Freundlich isotherm. Sorption kinetics was determined by pseudo-first-order and pseudo-second-order kinetic models. Experimental data showed the best fit with Langmuir isotherm and the adsorption followed pseudo-second-order kinetics. The negative value of free energy (ΔG◦) and positive value of enthalpy (ΔH◦) changes obtained from the thermodynamic studies indicated the spontaneous and endothermic nature of the adsorption. In our previous study, the bioactive compound theaflavin was isolated from fresh black tea leaves to treat cancer. Also, the STL generated after the theaflavin extraction from the tea leaves or after the consumption of tea as a beverage can be used as a potential source of natural dye for the textile industries which could be a possible alternative to the harmful synthetic dyes. Taken together, our studies close the loop of circular economy in the application of tea leaves in therapeutics, textile industries, and waste management by reusing, recycling, and repurposing the product and its wastes through multiple generations. | Ritwija Bhattacharya; Lata Ramrakhiani; Aniruddha Mukhopadhyay; Pritha Bhattacharjee | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Wastes; Natural Resource Recovery | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b5beb35101a2ffa8acaf91/original/application-of-tea-leaves-in-the-circular-economy-a-sustainable-approach-to-remove-synthetic-dye-from-wastewater-by-alkali-activated-spent-tea-leaves.pdf |
60f1599fe0c60f6feee11ac3 | 10.26434/chemrxiv-2021-tw67z | Catalytic Carbochlorocarbonylation of Unsaturated Hydrocarbons via C–COCl Bond Cleavage | Here we report a palladium-catalysed intermolecular difunctionalisation of unsaturated C–C bonds with acid chlorides. Specifically, the C–COCl bond of an acid chloride is cleaved and added, with complete atom economy, across either strained alkenes or tethered alkynes to generate new acid chlorides. The transformation does not require exogenous carbon monoxide, operates under mild conditions, shows a good functional group tolerance, and occurs with excellent stereoselectivity. The intermolecular reaction tolerates both aryl- and alkenyl-substituted acid chlorides and is successful when carboxylic acids are transformed to the acid chloride in situ. The reaction also shows an example of temperature-dependent stereodivergence which, together with plausible mechanistic pathways, is investigated by DFT calculations. Moreover, we show that benzofurans can be formed in an intramolecular variant of the reaction. Finally, derivation of the products from the intermolecular reaction provides a highly stereoselective approach for the synthesis of tetrasubstituted cyclopentanes. | Elliott Denton; Yong Ho Lee; Sven Roediger; Philip Boehm; Maximillian Fellert; Bill Morandi | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f1599fe0c60f6feee11ac3/original/catalytic-carbochlorocarbonylation-of-unsaturated-hydrocarbons-via-c-co-cl-bond-cleavage.pdf |
60c7524f9abda27fd7f8ddc6 | 10.26434/chemrxiv.13099880.v2 | Transcription Factor Allosteric Regulation Through Substrate Coordination to Zinc | The development of new
synthetic biology circuits for biotechnology and medicine requires deeper
mechanistic insight on allosteric transcription factors (aTFs). Here we studied
the aTF UxuR, which is a dimer, with each monomer consisting of two structured
domains connected by a highly flexible linker region. In order to explore how
ligand binding to UxuR affects protein dynamics we performed molecular dynamics
simulations in the free protein and the aTF bound to the inducer D-fructuronate
or the structural isomer D-glucuronate. We then validated our results by constructing
a sensor plasmid for D-fructuronate in <i>E.
coli</i> and performed site-directed mutagenesis. Our results show that zinc
coordination is necessary for UxuR function, since mutation to alanines
prevents expression de-repression by D-fructuronate. Analyzing the different complexes,
we found that the disordered linker regions allow the N-terminal domains to
display fast and large movements. When the inducer is bound, UxuR is able to
sample an open conformation with a more pronounced negative charge at the
surface of the N-terminal DNA binding domains. In opposition, in the free and
D-glucuronate bond forms the protein samples closed conformations, with a more
positive character at the surface of the DNA binding regions. These molecular
insights provide a new basis to better harness these systems for biological
systems engineering. | Beatriz Almeida; Jennifer Kaczmarek; Pedro Figueiredo; Kristala LJ Prather; Alexandra Carvalho | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7524f9abda27fd7f8ddc6/original/transcription-factor-allosteric-regulation-through-substrate-coordination-to-zinc.pdf |
66a28abd5101a2ffa809f6ed | 10.26434/chemrxiv-2023-m9d1z-v4 | Quantifying Stern Layer Water Alignment Prior to and During the Oxygen Evolution | While water's oxygen is the electron source in the industrially important oxygen evolution reaction, the strong absorber problem clouds our view of how the Stern layer water molecules orient themselves in response to applied potentials. Here, we report nonlinear optical measurements on nickel electrodes held at pH 13 indicating a disorder-to-order transition in the Stern layer water molecules prior to the onset of Faradaic current. A full water monolater (1.1 x 10^15 cm-2) aligns with oxygen atoms pointing towards the electrode at +0.8 V and the associated work is 80 kJ mol-1. Our experiments identify water flipping energetics as a target for understanding overpotentials, advance molecular electrochemistry, provide benchmarks for electrical double layer models, and serve as a diagnostic tool for understanding electrocatalysis. | Raiden Speelman; Franz Geiger | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.); Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a28abd5101a2ffa809f6ed/original/quantifying-stern-layer-water-alignment-prior-to-and-during-the-oxygen-evolution.pdf |
65bb592566c1381729b8b3cf | 10.26434/chemrxiv-2024-cdmm3 | Concerted two-proton-coupled electron transfer from piceatannol to electrogenerated superoxide in N,N-dimethylformamide | The reactivity of 4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]benzene-1,2-diol (piceatannol) toward electrochemically generated superoxide radical anion (O2•−) was investigated using electrochemistry and in situ controlled-potential electrolytic electron spin resonance (ESR) measurements in N,N-dimethylformamide with density functional theory (DFT) calculations. The quasireversible cyclic voltammogram of dioxygen/O2•−, modified in the presence of piceatannol, indicated that the electrogenerated O2•− was scavenged by piceatannol via proton-coupled electron transfer. Differences in the reactivities of piceatannol and 5-[(E)-2-(4-hydroxyphenyl)ethen-1-yl]benzene-1,3-diol (trans-resveratrol) toward O2•−, originating from the presence of the benzene-1,2-diol (catechol) moiety, were observed in the voltammograms and ESR measurements. The electrochemical and computational results show that the reaction mechanism is a concerted two-proton-coupled electron transfer (2PCET) via the catechol moiety of piceatannol. The stilbene moiety of piceatannol kinetically promotes 2PCET via its catechol moiety. These findings indicate that piceatannol is a better O2•− scavenger than catechol and trans-resveratrol. | Tatsushi Nakayama; bunji uno | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bb592566c1381729b8b3cf/original/concerted-two-proton-coupled-electron-transfer-from-piceatannol-to-electrogenerated-superoxide-in-n-n-dimethylformamide.pdf |
6230d4ad5cf719dbae54a50c | 10.26434/chemrxiv-2022-78g87 | Technical Note: Rayleigh Scattering of Sulfur Hexafluoride at 1.066 Microns | In this brief technical note, we measure the Rayleigh scattering of sulfur hexafluoride (SF6) at 1.066 microns using cavity ringdown spectroscopy to determine the difference in optical loss between Helium and SF6. By empirically verifying previous calculations, we provide further confidence in using SF6 as a calibration species for near-infrared scattering. The method can be readily extended to measuring other gases and wavelengths. | Manish Gupta; Michael Sullivan | Physical Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6230d4ad5cf719dbae54a50c/original/technical-note-rayleigh-scattering-of-sulfur-hexafluoride-at-1-066-microns.pdf |
60c75290469df4c59ff44bbd | 10.26434/chemrxiv.13315571.v1 | Xenon Gas Inhibits the Enzyme Furin In Vitro | Abstract: <br /><br /> Aims: <br /> Certain cancers, pathogenic infections, and other diseases are facilitated by the host enzyme furin, a calcium-dependent serine protease that is the most prominent member of the family of proprotein convertases. Furin and the other proprotein convertases modify certain other proteins to change them from their inactive to active forms. Previous attempts to find an effective, non-toxic furin inhibitor to treat diseases facilitated by furin have had only limited success, due to toxicity or large molecular size that impedes absorption of the molecule. This has placed increased importance on the development of small-molecule furin inhibitors. The object of this study was to consider the effect of the noble gas xenon as a furin inhibitor.<br /><br /><br /><br /> Methods:<br /><br /> This study uses a fluorometric furin inhibition assay to compare the enzymatic activity of recombinant human furin after exposure to 99.999% xenon gas, compared to the enzymatic activity of untreated recombinant human furin. <br /><br /> Results:<br /> Xenon exposure was found to decrease the in vitro enzymatic activity of recombinant human furin by 96-99%. Fluorescence measurements were taken for 24 hours and the enzyme inhibition persisted for the duration of the experiment. Further studies will be necessary to better characterize the exact duration of this inhibition.<br /><br /> Conclusions:<br /> These findings appear to be the first to report xenon as a furin inhibitor. The observed inhibition continued throughout the duration of the experiment. The effectiveness of xenon as a furin inhibitor, its favorable side effect profile, and its long history of safe use as an anesthetic, when used under direct medical supervision, make it a promising treatment for diseases facilitated by furin or its substrates. Further studies in cell culture or clinical trials may expand its clinical role for such diseases.<br /><br /> | David Beihl | Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2020-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75290469df4c59ff44bbd/original/xenon-gas-inhibits-the-enzyme-furin-in-vitro.pdf |
6301a69d521cb76401a075dc | 10.26434/chemrxiv-2022-gztrv | Carbodiimide-fueled assembly of π-conjugated peptides regulated by electrostatic interactions
| Peptides naturally have stimuli-adaptive structural conformations that are advantageous for endowing synthetic materials with dynamic functionalities. Here, we investigate a carbodiimide-based approach, combined with electrostatic modulation, to instruct π-conjugated peptides to self-assemble and be responsive to thermal disassembly cues upon consumption of the assembly trigger. Quaterthiophene-functionalized peptides are utilized as a model system herein to study the formation of kinetically trapped structures at non-equilibrium states. Peptides were designed to have aspartic acid at the termini to allow intramolecular anhydride formation upon adding carbodiimide, which consequentially reduces the electrostatic repulsion and facilitates assembly. We show that the carbodiimide-fueled assembly and subsequent thermally assisted disassembly can be modulated by the net charge of the peptidic monomers, suggesting an assembly mechanism that can be encoded by sequence design. This carbodiimide-based approach for the assembly of designer π-conjugated systems offers a unique opportunity to develop bioelectronic supramolecular materials with controllable formation of transient structures. | Zefan Yao; Yuyao Kuang; Phillip Kohl; Youli Li; Herdeline Ann Ardoña | Materials Science; Polymer Science; Nanoscience; Aggregates and Assemblies; Biopolymers; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6301a69d521cb76401a075dc/original/carbodiimide-fueled-assembly-of-conjugated-peptides-regulated-by-electrostatic-interactions.pdf |
64b8d0f7ae3d1a7b0d0834f7 | 10.26434/chemrxiv-2023-bnzgr-v2 | Simulation of Conformality of ALD Growth Inside Lateral Channels: Comparison Between a Diffusion-Reaction Model and a Ballistic Transport-Reaction Model | Atomic layer deposition (ALD) has found significant use in the coating of high-aspect-ratio (HAR) structures. Approaches to model ALD film conformality in HAR structures can generally be classified into diffusion-reaction (DR) models, ballistic transport-reaction (BTR) models and Monte Carlo simulations. This work compares saturation profiles obtained using a DR model and a BTR model. The saturation profiles were compared qualitatively and quantitatively in terms of half-coverage penetration depth, slope at half-coverage penetration depth and adsorption front broadness. The results showed qualitative agreement between the models, except for a section of elevated surface coverage at the end of the structure, `trunk', observed in the BTR model. Quantitatively, the BTR model produced deeper penetration into the structure, lower absolute values of the slope at half-coverage penetration depth and broader adsorption fronts compared to the DR model. These differences affect the values obtained when extracting kinetic parameters from the saturation profiles. | Jänis Järvilehto; Jorge Velasco; Jihong Yim; Christine Gonsalves; Riikka Puurunen | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.); Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b8d0f7ae3d1a7b0d0834f7/original/simulation-of-conformality-of-ald-growth-inside-lateral-channels-comparison-between-a-diffusion-reaction-model-and-a-ballistic-transport-reaction-model.pdf |
60c74a200f50dba0b23969fa | 10.26434/chemrxiv.12153594.v1 | Computational Models Identify Several FDA Approved or Experimental Drugs as Putative Agents Against SARS-CoV-2 | The outbreak of a novel human coronavirus (SARS-CoV-2) has evolved into global health emergency, infecting hundreds of thousands of people worldwide. We have identified experimental data on the inhibitory activity of compounds tested against closely related (96% sequence identity, 100% active site conservation) protease of SARS-CoV and employed this data to build QSAR models for this dataset. We employed these models for virtual screening of all drugs from DrugBank, including compounds in clinical trials. Molecular docking and similarity search approaches were explored in parallel with QSAR modeling, but molecular docking failed to correctly discriminate between experimentally active and inactive compounds. As a result of our studies, we recommended 41 approved, experimental, or investigational drugs as potential agents against SARS-CoV-2 acting as putative inhibitors of Mpro. Ten compounds with feasible prices were purchased and are awaiting the experimental validation.<br /> | Tesia Bobrowski; Vinicius Alves; Cleber
C. Melo-Filho; Daniel Korn; Scott S. Auerbach; Charles Schmitt; Eugene Muratov; Alexander Tropsha | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a200f50dba0b23969fa/original/computational-models-identify-several-fda-approved-or-experimental-drugs-as-putative-agents-against-sars-co-v-2.pdf |
61a76bdd57f827c7d4a2fa3f | 10.26434/chemrxiv-2021-b50gj | An efficient way to screen inhibitors of energy-coupling factor (ECF) transporters in bacteria uptake assay | Herein, we report a novel whole-cell screening assay using Lactobacillus casei as model microorganism to identify inhibitors of energy-coupling factor (ECF) transporters. This promising and underexplored target may have important pharmacological potential through modulation of vitamin homeostasis in bacteria and, importantly, it is absent in humans. The assay represents an alternative, cost-effective and fast solution to demonstrate the direct involvement of these membrane transporters in a native biological environment rather than using a low-throughput in vitro assay employing reconstituted proteins in a membrane bilayer system. Based on this new whole-cell screening approach, we demonstrated the optimization of a weak hit compound (2) into a small molecule (3) with improved in vitro and whole-cell activities. This study opens the possibility to quickly identify novel inhibitors of ECF transporters and optimize them based on structure–activity relationships. | Spyridon Bousis; Steffen Winkler; Jörg Haupenthal; Francesco Fulco; Eleonora Diamanti; Anna K. H. Hirsch | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2021-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a76bdd57f827c7d4a2fa3f/original/an-efficient-way-to-screen-inhibitors-of-energy-coupling-factor-ecf-transporters-in-bacteria-uptake-assay.pdf |
6661c2c921291e5d1d347359 | 10.26434/chemrxiv-2024-1fn78 | Vertical Ionization Energies, Generalized
Kohn-Sham Orbital Energies, and the Curious
Case of the Copper Oxide Anions | Are the vertical ionization energies from a bound electronic system, initially in its
ground state, equal to minus the corresponding exact Kohn-Sham orbital energies of
density functional theory (DFT)? This is known to be true for the first or lowest vertical
ionization energy. We show that the correction from time-dependent DFT arises from
the continuum and need not vanish. Recent work compared the experimental photoemission
thresholds of the molecules Cu2O−, CuO−, CuO−
2 , and CuO3− with minus
the corresponding orbital energies from a generalized gradient approximation (GGA)
and its global and range-separated hybrids with exact exchange, finding striking differences
which were attributed to self-interaction error, strong correlation, or both.
Here we extend that work to include the local spin density approximation (LSDA), its
Perdew-Zunger self-interaction correction with Fermi-L¨owdin localized orbitals (LSDASIC),
a quasi-self-consistent locally scaled-down version of LSDA-SIC (QLSIC), and the Quantum Theory Project QTP02 range-separated hybrid functional, all but LSDA implemented
in a generalized Kohn-Sham approach. QTP02 impressively yields a near
equality for many sp-bonded molecules. But, for the copper oxide anions studied here,
none of the tested methods reproduces the experimental photoemission thresholds. | Chandra Shahi; Rohan Maniar; Jinliang Ning; Gabor I. Csonka ; John P. Perdew; Adrienn Ruzsinszky | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6661c2c921291e5d1d347359/original/vertical-ionization-energies-generalized-kohn-sham-orbital-energies-and-the-curious-case-of-the-copper-oxide-anions.pdf |
646bbfc0b3dd6a6530907e2f | 10.26434/chemrxiv-2023-60c90-v3 | CALPHAD Description of the Super-cooled Liquid from the
Mo-Nb-B System with the 2-State Model | In the present work, we assessed with the CALPHAD method via Thermo-Calc the super-cooled liquid
(SCL) that leads to the formation of metallic vitreous materials. This research aimed to improve the
database for thermodynamic calculations of SCLs in the computational study of materials, specifically
some subsystems of the Fe-Mo-Cr-Nb-B system, since its application as a metallic glass coating combines
exceptionally hardness, corrosion resistance and wear resistance. Thus, continuing the work of our group
that assessed the Fe-Nb-B system with the same methods and models, we described the liquid Mo with
the two-state phenomenological model as well as the binary liquids Mo-Nb and Mo-B. | THIAGO TAKAMURA YANAGUISSAVA; André Costa e Silva; Walter José Botta | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Alloys; Coating Materials; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646bbfc0b3dd6a6530907e2f/original/calphad-description-of-the-super-cooled-liquid-from-the-mo-nb-b-system-with-the-2-state-model.pdf |
623a24b2202c06565ddd76f0 | 10.26434/chemrxiv-2022-sdq2g | Recent Advances in Biologic Therapeutic N-Glycan Preparation Techniques and Analytical Methods for Facilitating Biomanufacturing Automation | Post-translational modification such as N-Glycosylation on biologics during the production of monoclonal antibody (mAb) based therapeutics is a critical quality attribute that dictates safety and efficacy. Variability is introduced in the cell culture process which influences, the glycosylation pattern which is known to be highly heterogenous and must be tightly controlled during the manufacturing process. Techniques have been developed for glycan screening through the use of new denaturation techniques; deglycosylation, fluorescent labeling, and analysis coupled to state-of-the-art tools consisting of multi attribute methods and multi attribute chromatography. In this review, we delve into advances within sample preparation techniques that allow for rapid and robust sample preparation as well as how these techniques are being used for innovative at-line high-throughput screening and PAT focused systems. Finally, we foresee how these advances will influence current manufacturing practices and enable bioprocess automation. The future state of biomanufacturing looks to decrease process costs while increasing process understanding and quality for novel biologic candidates and biosimilars | Erin Tiwold; Aron Gyorgypal; Shishir Chundawat | Organic Chemistry; Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Biochemical Analysis; Industrial Manufacturing; Quality Control | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623a24b2202c06565ddd76f0/original/recent-advances-in-biologic-therapeutic-n-glycan-preparation-techniques-and-analytical-methods-for-facilitating-biomanufacturing-automation.pdf |
60c73d77702a9b1f99189bad | 10.26434/chemrxiv.5830641.v1 | Chemical and Physical Properties of FSC Cigarette Papers and Physical Properties of the Cigarettes They Were Taken From: Results From a Small Product Survey of Cigarette Brand-Styles Sold in the USA | We undertook a small product survey in which we purchased a range of brand-styles at retail and sent them to commercial laboratories for dimensional and physical tests, including banded and nonbanded area porosities. Other analyses obtained used chemical, chromatographic, and spectrophotometric (FT-IR) techniques to identify main banding agents and additives used with them. One finding from this study was at least at the time the samples were collected, some companies used just one FSC paper for all products while others used multiple FSC papers.<br /> | John Lauterbach | Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d77702a9b1f99189bad/original/chemical-and-physical-properties-of-fsc-cigarette-papers-and-physical-properties-of-the-cigarettes-they-were-taken-from-results-from-a-small-product-survey-of-cigarette-brand-styles-sold-in-the-usa.pdf |
62afc00af70c211ecc34d0b1 | 10.26434/chemrxiv-2022-1ffmn | Fabrication and assembly of thermoplastic microfluidics; a review | Various fields within biomedical engineering have been afforded rapid scientific advancement through the incorporation of microfluidics. As literature surrounding biological systems become more comprehensive and many microfluidic platforms show potential for commercialization, the development of representative fluidic systems has become more intricate. This has brought increased scrutiny towards the material properties of microfluidic substrates. Thermoplastics have been highlighted as a promising material, given their material adaptability and commercial compatibility. This review provides a comprehensive discussion surrounding recent developments pertaining to thermoplastic microfluidic device fabrication. Existing and emerging approaches related to both microchannel fabrication and device assembly are highlighted, with consideration towards how specific approaches induce physical and/or chemical properties that are optimally suited for relevant real-world applications. | Amid Shakeri; Shadman Khan; Noor Abu Jarad; Tohid Didar | Materials Science; Nanoscience; Biocompatible Materials; Nanocatalysis - Catalysts & Materials; Nanofluidics; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62afc00af70c211ecc34d0b1/original/fabrication-and-assembly-of-thermoplastic-microfluidics-a-review.pdf |
662856e521291e5d1d87b234 | 10.26434/chemrxiv-2024-6www6 | Virtual Ligand-Assisted Optimization: A Rational Strategy for Ligand Engineering | Ligand engineering is one of the most important, but labor-intensive processes in the development of transition metal catalysis. Historically, this process has been streamlined by the invention of ligand descriptors such as Tolman’s electronic parameter and the cone angle. Analyzing reaction outcomes in terms of these parameters has enabled chemists to find important factors for designing optimal ligands. However, typical strategies for these analyses largely rely on regression approaches, which often requires many experimental data to understand non-intuitive trends. Here, we introduce the virtual ligand-assisted optimization (VLAO) method, a novel computational approach for ligand engineering. In this method, important features of ligands are identified by simple mathematical operations on equilibrium structures and/or transition states of interest, and derivative values of arbitrary objective functions with respect to ligand parameters are obtained. These derivative values are then used as a guiding principle to optimize ligands within the parameter space. The VLAO method was demonstrated in the optimization of monodentate and bidentate phosphine ligands including asymmetric quinoxaline-based ligands. In addition, we successfully found a highly selective ligand for the α-selective hydrogermylation of a terminal ynamide according to the suggested design principle by the VLAO method. These results would imply the potential utility of the VLAO method in optimizing wide variety of ligands in transition metal catalysis. | Wataru Matsuoka; Taihei Oki; Ren Yamada; Tomohiko Yokoyama; Shinichi Suda; Yu Harabuchi; Satoru Iwata; Satoshi Maeda | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662856e521291e5d1d87b234/original/virtual-ligand-assisted-optimization-a-rational-strategy-for-ligand-engineering.pdf |
60c7534a702a9bae8618c32a | 10.26434/chemrxiv.13473099.v1 | Exchange Bias in a Layered Metal–Organic Topological Spin Glass | <p><b>The discovery of conductive and magnetic two-dimensional (2D) materials is critical for the development of next generation spintronics devices. Coordination chemistry in particular represents a highly versatile, though underutilized, route toward the synthesis of such materials with designer lattices. Here, we report the synthesis of a conductive, layered 2D metal–organic kagome lattice, Mn<sub>3</sub>(C<sub>6</sub>S<sub>6</sub>), using mild solution-phase chemistry. Strong geometric<i> </i>spin frustration in this system mediates spin freezing at low temperatures, which results in glassy magnetic behavior consistent with a geometrically frustrated (topological) spin glass. Notably, the material exhibits a large exchange bias of 1625 Oe, providing the first example of exchange bias in a coordination solid or a topological spin glass. More generally, these results demonstrate the potential utility of geometrically frustrated lattices in the design of new nanoscale spintronic materials.</b></p> | Ryan Murphy; Lucy Darago; Michael Ziebel; Elizabeth A. Peterson; Edmond W. Zaia; Michael W. Mara; Daniel J. Lussier; David
K. Shuh; Jeffrey
J. Urban; Jeffrey B. Neaton; Jeffrey R. Long | Hybrid Organic-Inorganic Materials; Magnetic Materials; Coordination Chemistry (Inorg.); Magnetism; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7534a702a9bae8618c32a/original/exchange-bias-in-a-layered-metal-organic-topological-spin-glass.pdf |
67485a685a82cea2fa41bcc8 | 10.26434/chemrxiv-2024-4kl15-v2 | Plasma Decomposition of Ferrocene | Ferrocene (Fe(C5H5)2 or FeCp2) is a well-known precursor molecule for iron in vapor deposition of iron containing films by, e.g., chemical vapor deposition (CVD) processes. CVD processes often use the energy in plasma discharges to decompose precursor molecules, which allows lowering the substrate temperature for deposition on sensitive materials. Herein, we studied the plasma decomposition of ferrocene in a plasma CVD reactor using in situ optical emission spectroscopy (OES) and quadrupole mass spectrometry (QMS), coupled with in silico quantum chemical modeling. We suggest a plasma chemical decomposition model where FeCp2 is likely to undergo neutral decomposition, detaching both Cp ligands from the iron center, followed by fragmentation via C2H2 and C3H3 to C2, CH, H2 and H. | Pentti Niiranen; Felicia Andersson; Daniel Lundin; Lars Ojamäe; Henrik Pedersen | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67485a685a82cea2fa41bcc8/original/plasma-decomposition-of-ferrocene.pdf |
63ce5c7f66069408d33acc6c | 10.26434/chemrxiv-2022-m00xc-v3 | Modelling Anion Poisoning during Oxygen Reduction on Pt Near-Surface Alloys | Electrolyte effects play an important role on the activity of the oxygen reduction reaction (ORR) of Pt-based electrodes. Herein, we combine a computational model and rotating disk electrode measurements to investigate the effects from phosphate anion poisoning for the ORR on well-defined extended Pt surfaces. We construct a model including the poisoning effect from phosphate species on Pt(111) and Cu/Pt(111) based on density functional theory simulations. We have investigated the effect of adsorbed phosphate species at low overpotentials when tuning *OH binding energies. Our work shows that, regardless of the surface site blockage from phosphate, the trend in catalytic oxygen reduction activity is predominately governed by the *OH binding. | Amanda Schramm Petersen; Kim Degn Jensen; Hao Wan; Alexander Bagger; Ib Chorkendorff; Ifan E.L. Stephens; Jan Rossmeisl; María Escudero-Escribano | Physical Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ce5c7f66069408d33acc6c/original/modelling-anion-poisoning-during-oxygen-reduction-on-pt-near-surface-alloys.pdf |
66868e98c9c6a5c07a409e65 | 10.26434/chemrxiv-2024-tvns0 | An Anionic Mesoionic Carbene and its Transformation to Metallo-Mesoionic Carbenes: Synthesis, Properties and Catalysis | Neutral mesoionic carbenes (MICs) based on a 1,2,3-triazole core have had a strong impact on various branches of chemistry such as homogeneous catalysis, electrocatalysis, and photochemistry/photophysics over the past 15 years. We present here the first general route for the synthesis of anionic mesoionic carbenes (anMICs) based on a 1,2,3-triazole core and a borate backbone. The free anMIC is stable under an inert atmosphere at low temperatures, can be stored for several weeks, and can be coordinated to both main group and transition metal fragments. Analysis of donor properties by a battery of spectroscopic methods shows that these anMICs are extremely strong σ-donors, by-passing the donor properties of related strong donors such as MICs, N-heterocyclic carbenes, anionic N-heterocyclic carbenes and N-heterocyclic olefins. Intriguingly, they also display π-accepting properties. The room temperature conversion of the free anMICs leads to two equally interesting compound classes: an amide coordinated borane based on a MIC-borane backbone, and an amide coordinated metallo-MIC-borane. The metallo-MIC-borane is an interesting precursor for the synthesis of further amide-coordinated MIC-borane compounds, and the first example of a gold(I) complex is reported here. Gold(I) complexes of the anMIC ligands are potent catalysts for the hydroamination of alkynes without the need for any additional reagents. This report showcases a straightforward synthesis of anMIC ligands, and their conversion to two equally interesting compounds. The compounds have both exceptional donor properties, and a high potential in catalysis. We thus introduce three new categories of mesoionic compounds here with a huge potential for different branches of chemistry and beyond. | Richard Rudolf; Andrej Todorovski; Vera Lederer; Nicolas Neuman; Biprajit Sarkar | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Organometallic Compounds; Ligands (Organomet.); Main Group Chemistry (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66868e98c9c6a5c07a409e65/original/an-anionic-mesoionic-carbene-and-its-transformation-to-metallo-mesoionic-carbenes-synthesis-properties-and-catalysis.pdf |
6508921fb6ab98a41caed593 | 10.26434/chemrxiv-2023-73hdl | Carbodiimide-driven toughening of interpenetrated polymer networks | Recent work has demonstrated that temporary crosslinks in polymer networks generated by chemical “fuels” afford materials with large, transient changes in their mechanical properties. This can be accomplished in carboxylic-acid-functionalized polymer hydrogels using carbodiimides, which generate anhydrides with lifetimes on the order of minutes to hours. Here, the impact of the polymer architecture on the mechanical properties of materials was explored. Single networks (SNs) were compared to interpenetrated networks (IPNs). Notably, semi-IPN precursors that give IPNs on treatment with the carbodiimide gave much higher fracture energies (i.e., resistance to fracture) and superior resistance to compressive strain compared to other network structures. A precursor semi-IPN material featuring acrylic acid in only the free polymer chains yields, on treatment with carbodiimide, an IPN with a fracture energy of 2400 J/m2, a fourfold increase compared to an analogous semi-IPN precursor that yields a SN. This resistance to fracture enables the formation of macroscopic complex cut patterns, even at high strain, underscoring the pivotal role of polymer architecture in mechanical performance. | Chamoni W. H. Rajawasam; Corvo Tran; Jessica L. Sparks; William H. Krueger; C. Scott Hartley; Dominik Konkolewicz | Organic Chemistry; Polymer Science; Physical Organic Chemistry; Hydrogels; Organic Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6508921fb6ab98a41caed593/original/carbodiimide-driven-toughening-of-interpenetrated-polymer-networks.pdf |
67ae0f2cfa469535b92fae05 | 10.26434/chemrxiv-2025-kwdbd | FAST AND FLEXIBLE 3D MOLECULE DESIGN FRAMEWORK FOR NOVEL ORGANIC OPTOELECTRONIC MATERIALS | Organic optoelectronic materials (OOMs) are pivotal for advancing technologies such as organic photovoltaics and light-emitting diodes. Traditional methods for discovering new OOMs are inefficient and limited by chemical space exploration. We introduce O2-GEN, a novel framework leveraging a 3D pretraining backbone trained on a diverse dataset of over ten million molecules, enabling comprehensive exploration of chemical space. O2-GEN excels in generating fused-ring systems and conjugated fragment assemblies, achieving nearly 100% validity and novelty. It significantly outperforms existing models in speed and chemical structural validity, particularly for larger molecules. The framework supports both global and local generation modes, allowing for the creation of new molecules or modifications of existing structures. Additionally, O2-GEN integrates a property selector finetuned with density functional theory data, enabling precise multi-property screening. This framework offers a powerful tool for rational design and high-throughput screening of OOMs, with potential applications to drug discovery and energy materials. | Kele Xu ; Guojiang Zhao ; Zheng Cheng; Tianjiao Wan ; Ming Feng ; Shuqi Lu; Hongshuai Wang; Zijian Gao ; Qi Ou ; Liang Hu ; Dawei Feng ; Zifeng Zhao ; Zhifeng Gao | Materials Science; Energy; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae0f2cfa469535b92fae05/original/fast-and-flexible-3d-molecule-design-framework-for-novel-organic-optoelectronic-materials.pdf |
60c75835337d6c7df1e291db | 10.26434/chemrxiv.14524890.v1 | All Hands on Deck: Accelerating Ab Initio Thermochemistry via Wavefunction Approximations | <div>We accelerate the G4(MP2) composite model by fine-tuning the individual steps using resolution-of-identity and domain‐based local pair‐natural orbitals. The new variant, G4(MP2)-XP, has a low prediction error when tested on 1694 benchmark molecules. To showcase the method's relevance for large molecules, we determine and present a new reference value for the standard formation enthalpy of buckminsterfullerene. We expect G4(MP2)-XP to become the <i>de facto</i> method for rapid and accurate production of thermochemistry big data.</div> | Sambit Kumar Das; Salini Senthil; Sabyasachi Chakraborty; Raghunathan Ramakrishnan | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75835337d6c7df1e291db/original/all-hands-on-deck-accelerating-ab-initio-thermochemistry-via-wavefunction-approximations.pdf |
60c7514abb8c1ae3cd3dbc75 | 10.26434/chemrxiv.13143761.v1 | Molecular Simulations suggest Vitamins, Retinoids and Steroids as Ligands binding the Free Fatty Acid Pocket of SARS-CoV-2 Spike Protein | <p>Following our recent
identification of a fatty acid binding site in the SARS-CoV-2 spike protein (Toelzer
<i>et al., Science</i> eabd3255 (2020)), we investigate the binding of linoleate
and other potential ligands at this site using molecular dynamics simulations.
The results support the hypothesis that linoleate stabilises the locked form of
the spike, in which its interaction interface for the ACE2 receptor is occluded.
The simulations indicate weaker binding of linoleate to the partially open
conformation. Simulations of dexamethasone bound at this site indicate that it
binds similarly to linoleate, and thus may also stabilize a locked spike
conformation. In contrast, simulations suggest that cholesterol bound at this
site may destabilize the locked conformation, and in the open conformation, may
preferentially bind at an alternative site in the hinge region between the receptor
binding domain and the domain below, which could have functional relevance. We
also use molecular docking to identify potential ligands that may bind at the
fatty acid binding site, using the Bristol University Docking Engine (BUDE).
BUDE docking successfully reproduces the linoleate complex and also supports
binding of dexamethasone at the spike fatty acid site. Virtual screening of a
library of approved drugs identifies vitamins D, K and A, as well as retinoid
ligands with experimentally demonstrated activity against SARS-CoV-2 replication
<i>in vitro</i>, as also potentially able to bind at this site. Our data
suggest that the fatty acid binding site of the SARS-CoV-2 spike protein may
bind a diverse array of candidate ligands. Targeting this site with small
molecules, including dietary components such as vitamins, which may stabilise its
locked conformation and represents a potential avenue for novel therapeutics or
prophylaxis for COVID-19.</p> | Deborah Shoemark; Charlotte Colenso; Christine Toelzer; Kapil Gupta; Richard Sessions; Andrew Davidson; Imre Berger; Christiane Schaffitzel; James Spencer; Adrian Mulholland | Biochemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2020-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7514abb8c1ae3cd3dbc75/original/molecular-simulations-suggest-vitamins-retinoids-and-steroids-as-ligands-binding-the-free-fatty-acid-pocket-of-sars-co-v-2-spike-protein.pdf |
60c74b8eee301c2b9ec79ead | 10.26434/chemrxiv.12349934.v1 | Characterization of Aqueous Lower Polarity Solvation Shells Around Amphiphilic TEMPO Radicals in Water | Solvation of the stable nitroxide radicals
2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo-TEMPO (TEMPONE) in water
and THF is studied. With electron paramagnetic resonance (EPR) spectroscopy at
X- and Q-band as well as spectral simulations, the existence of pure water
shells enclosing TEMPO in aqueous solution that lead to significantly reduced
local polarity at the nitroxide is shown. These aqueous lower polarity
solvation shells (ALPSS) offer TEMPO a local polarity that is similar to that
in organic solvents like THF. Furthermore, using double electron-electron
resonance (DEER) spectroscopy, local enrichment and inhomogenous distribution
without collisions of dissolved TEMPO in water is found that can be correlated
with potentially attractive interactions mediated through ALPSS. However, no
local enrichment of TEMPO is found in organic solvents such as THF. These
results are substantiated by MD and metadynamics simulations and physical
methods like DLS and MS. | Johannes Hunold; Jana Eisermann; Martin Brehm; Dariush Hinderberger | Interfaces; Physical and Chemical Processes; Physical and Chemical Properties; Self-Assembly; Solution Chemistry; Spectroscopy (Physical Chem.); Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b8eee301c2b9ec79ead/original/characterization-of-aqueous-lower-polarity-solvation-shells-around-amphiphilic-tempo-radicals-in-water.pdf |
60c74582469df44454f43519 | 10.26434/chemrxiv.10050515.v1 | The Evolution Pathway from Iron Compounds to Fe1(II)-N4 Sites Through Gas-Phase Iron During Pyrolysis | <div>
<div>
<div>
<p>Pyrolysis is indispensable for synthesizing highly active Fe-N-C catalysts for the oxygen reduction reaction (ORR)
in acid, but how Fe, N, and C precursors transform to ORR-active sites during pyrolysis remains unclear. This knowledge gap ob-
scures the connections between the input precursors and output products, clouding the pathway toward Fe-N-C catalyst improve-
ment. Herein, we unravel the evolution pathway of precursors to ORR-active catalyst comprised exclusively of single atom Fe1(II)-
N4 sites via in-temperature X-ray absorption spectroscopy. The Fe precursor transforms to Fe oxides below 300 °C, and then to
tetrahedral Fe1(II)-O4 via a crystal-to-melt-like transformation below 600 °C. The Fe1(II)-O4 releases a single Fe atom that flows
into the N-doped carbon defect forming Fe1(II)-N4 above 600 °C. This vapor phase single Fe atom transport mechanism is verified
by synthesizing Fe1(II)-N4 sites via “non-contact pyrolysis” wherein the Fe precursor is not in physical contact with the N and C
precursors during pyrolysis.
</p>
</div>
</div>
</div> | Jingkun Li; Li Jiao; Evan Wegener; Lynne K. LaRochelle Richard; Ershuai Liu; andrea Zitolo; Moulay-Tahar Sougrati; Sanjeev Mukerjee; Zipeng Zhao; Yu Huang; Fan Yang; Sichen Zhong; Hui Xu; A. Jeremy Kropf; Frederic Jaouen; Deborah J. Myers; Qingying Jia | Electrocatalysis; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74582469df44454f43519/original/the-evolution-pathway-from-iron-compounds-to-fe1-ii-n4-sites-through-gas-phase-iron-during-pyrolysis.pdf |
6604723d9138d23161785f22 | 10.26434/chemrxiv-2024-clzns | A DFT/MRCI Hamiltonian Parameterized Using Only Ab Initio Data: I. Valence Excited States | A new combined density functional theory and multi-reference configuration interaction (DFT/MRCI) Hamiltonian parameterized solely using benchmark ab initio electronic structure obtained from the QUEST databases is presented. This new formulation differs from all previous versions of the method in that the choice of the underlying exchange cor- relation (XC) functional employed to construct the one-particle (orbital) basis is considered, and a new XC functional, QTP17, is chosen for its ability to generate a balanced description of core and valence vertical excitation energies. The ability of the new DFT/MRCI Hamiltonian, termed QE8, to furnish accurate excitation energies is confirmed using benchmark quantum chemistry computations, and a mean absolute error of 0.16 eV is determined for the wide range of electronic excitations included the validation data set. In particular, the QE8 Hamiltonian dramatically improves the performance of DFT/MRCI for doubly-excited states. The performance of fast approximate DFT/MRCI methods, p-DFT/MRCI and DFT/MRCI(2), are also evaluated using the QE8 Hamiltonian and are found to yield excitation ener- gies in quantitative agreement with the parent DFT/MRCI method, with the two methods exhibiting a mean difference of 0.01 eV with respect to DFT/MRCI over the entire benchmark set. | Teagan Costain; Victoria Ogden; Simon Neville; Michael Schuurman | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6604723d9138d23161785f22/original/a-dft-mrci-hamiltonian-parameterized-using-only-ab-initio-data-i-valence-excited-states.pdf |
651451990065940912fd0933 | 10.26434/chemrxiv-2023-xdp95 | Switching it Up: New Mechanisms Revealed in Wurtzite-type Ferroelectrics | Wurtzite-type ferroelectrics have drawn increasing attention due to the promise of better performance and integration than traditional oxide ferroelectrics with semiconductors such as Si, SiC, and III-V compounds. However, wurtzite-type ferroelectrics generally require enormous electric fields, approaching breakdown, to reverse their polarization. The underlying switching mechanism(s), especially for multinary compounds and alloys, remains elusive. Here, we examine the switching behaviors in (Al,Sc)N alloys and new wurtzite-type multinary candidate compounds we recently computationally identified. We find that switching in these tetrahedrally-coordinated materials proceeds via a variety of non-polar intermediate structures and that switching barriers are dominated by the more electronegative of the cations. For (Al,Sc)N alloys, we find that the switching pathway changes from a collective mechanism to a lower-barrier mechanism enabled by inversion of individual tetrahedra with increased Sc composition. Our findings provide insights for future engineering and realization of wurtzite-type materials and open a door to understanding domain motion. | Cheng-Wei Lee; Keisuke Yazawa; Andriy Zakutayev; Geoff L. Brennecka; Prashun Gorai | Theoretical and Computational Chemistry; Materials Science; Alloys; Theory - Computational; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651451990065940912fd0933/original/switching-it-up-new-mechanisms-revealed-in-wurtzite-type-ferroelectrics.pdf |
6733f6457be152b1d0e25806 | 10.26434/chemrxiv-2024-hrc1c | Preparation of closo-decaborate by pyrolysis of tetraethylammonium borohydride: revision and optimization for large-scale production | Several methods for preparation of closo-decaborate (B10H102- as polyalkylammonium salts) – a key compound for synthesis of carborane – by pyrolysis of tetraethylammonium borohydride were examined. The studied reactions included variation of decomposition temperature, liquid medium, pressure and reaction time. The products were analyzed by 11B and 1H NMR spectroscopy, and, in some cases, by IR-spectroscopy. It was found that pyrolysis of Et4NBH4 in solid state as well as in suspension in silicone fluid led to the mixtures of (Et4N)2B10H10 and (Et4N)2B12H12. Pyrolysis of Et4NBH4 in n-decane or decalin resulted in Et4NB3H8 as a primary product; increase of reaction time in n-decane or both time and temperature in decalin yielded the mixture of (Et4N)2B10H10, (Et4N)2B12H12 and other compounds. It was shown that the degree of conversion of Et4NBH4 into Et4NB3H8 on time in n-decane at 174 °C and decalin at 180 °C linearly depended on time. Several methods for purification of (Et4N)2B10H10 or (Bu3NH)2B10H10 from other pyrolysis products were checked. A synthetic procedure for preparation of closo-decaborate from 60 g of Et4NBH4 was proposed, yielding 2.85 g of (Bu3NH)2B10H10 in one run. | Artem Mishchenko; Yulian Lishchenko; Andriy Kozytskiy; Kateryna Konysheva; Yulia Satska; Serhiy Ryabukhin; Dmytro Volochnyuk; Sergey Kolotilov; Yuliya Rassukana | Physical Chemistry; Inorganic Chemistry; Main Group Chemistry (Inorg.); Reaction (Inorg.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6733f6457be152b1d0e25806/original/preparation-of-closo-decaborate-by-pyrolysis-of-tetraethylammonium-borohydride-revision-and-optimization-for-large-scale-production.pdf |
65f73ca766c13817292fd20a | 10.26434/chemrxiv-2024-vdsh1 | Efficient Energy and Electron Transfer Photocatalysis with a Coulombic Dyad | Photocatalysis holds great promise for changing the way how value-added molecules are currently prepared. However, many photocatalytic reactions suffer from lousy quantum yields, hampering the transition from lab-scale reactions to large-scale or even industrial applications. Molecular dyads can be designed such that the beneficial properties of inorganic and organic chromophores are combined, resulting in milder reaction conditions and improved quantum yields of photocatalytic reactions. We have developed a novel approach for obtaining the advantages of molecular dyads without the time- and resource-consuming synthesis of these tailored photocatalysts. Simply by mixing a cationic ruthenium complex with an anionic pyrene derivative in water a salt bichromophore is produced owing to electrostatic interactions. The long-lived organic triplet state is obtained by static and quantitative energy transfer from the preorganized ruthenium complex. We exploited this so-called Coulombic dyad for energy transfer catalysis with similar reactivity and even higher photostability compared to a molecular dyad and reference photosensitizers in several photooxygenations. In addition, it was shown that this system can also be used to maximize the quantum yield of photoredox reactions. This is due to an intrinsically higher cage escape quantum yield after photoinduced electron transfer for purely organic compounds compared to heavy atom-containing molecules. The combination of laboratory-scale as well as mechanistic irradiation experiments with detailed spectroscopic investigations provided deep mechanistic insights into this easy-to-use photocatalyst class. | Matthias Schmitz; Maria-Sophie Bertrams; Arne C. Sell; Felix Glaser; Christoph Kerzig | Physical Chemistry; Inorganic Chemistry; Catalysis; Photocatalysis; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f73ca766c13817292fd20a/original/efficient-energy-and-electron-transfer-photocatalysis-with-a-coulombic-dyad.pdf |
60c74432ee301c4555c790fb | 10.26434/chemrxiv.9752807.v1 | The Mechanism of Rhodium Catalyzed Allylic C–H Amination | The mechanism of catalytic allylic C–H amination reactions promoted by Cp*Rh complexes is reported. Reaction kinetics experiments, stoichiometric studies, and DFT calculations demonstrate that allylic C–H activation to generate a Cp*Rh(π-allyl) complex is viable under mild reaction conditions. The role of external oxidant in the catalytic cycle is elucidated. Quantum mechanical calculations, stoichiometric reactions, and cyclic voltammetry<b></b>experiments support an oxidatively induced reductive elimination process of the allyl fragment with an acetate ligand. Lastly, evidences supporting the amination of an allylic acetate intermediate is presented. Both nucleophilic substitution catalyzed by Ag<sup>+</sup>that behaves as a Lewis acid catalyst and an inner-sphere amination catalyzed by Cp*Rh are shown to be viable for the last step of the allylic amination reaction. | Robert Harris; Jiyong Park; Taylor Nelson; Nafees Iqbal; Daniel Salgueiro; John Bacsa; Cora MacBeth; Mu-Hyun Baik; Simon Blakey | Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Reaction (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74432ee301c4555c790fb/original/the-mechanism-of-rhodium-catalyzed-allylic-c-h-amination.pdf |
61ab28dfa02d160db4e3858f | 10.26434/chemrxiv-2021-glt8v | A simple fragment-based method for van der
Waals corrections over density functional theory | Modelling intermolecular noncovalent interactions between large molecules remains a challenge for electron structure theory community. This is due to the high cost of calculating electron correlation energy. Fragment-based methods usually fare well in reducing the cost of computations in such systems while quantum Drude oscillators turn out to be a good model for van der Waals interactions. In this paper, we have developed a simple yet effective method based on oscillator methods for calculating van der Waals interactions between molecular fragments as a correction to low-cost DFT functional PBE. We have tested our method on S66X8 with significant success.
| Prasanta Bandyopadhyay; Priya Priya; Mainak Sadhukhan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2021-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ab28dfa02d160db4e3858f/original/a-simple-fragment-based-method-for-van-der-waals-corrections-over-density-functional-theory.pdf |
6557719edbd7c8b54b74af63 | 10.26434/chemrxiv-2023-3v2zv | Condensed Layer Deposition of Nanoscopic TiO2 Overlayers on High Surface Area Electrocatalysts | Encapsulating an electrocatalytic material with a semi-permeable, nanoscopic oxide overlayer offers a promising approach to enhancing its stability, activity, and/or selectivity compared to an unencapsulated electrocatalyst. However, applying nanoscopic oxide encapsulation layers to high surface area electrodes, such as nanoparticle-supported porous electrodes is a challenging task. This study demonstrates that the recently developed condensed layer deposition (CLD) method can be used for depositing nanoscopic (sub-10 nm thick) titanium dioxide (TiO2) overlayers onto high surface area platinized carbon foam electrodes. Characterization of the overlayers by transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) showed that the films are amorphous, while X-ray photoelectron microscopy confirmed that they exhibit a TiO2 stoichiometry. Electrodes were also characterized by hydrogen underpotential deposition (Hupd) and carbon monoxide (CO) stripping, demonstrating that the Pt electrocatalysts remain electrochemically active after encapsulation. Additionally, copper underpotential deposition (Cuupd) measurements revealed that TiO2 overlayers are effective at blocking Cu2+ from reaching the TiO2/Pt buried interface and were used to estimate that between 43-98% of Pt surface sites were encapsulated. Overall, this study shows that CLD is a promising approach for depositing nanoscopic protective overlayers on high surface area electrodes. | Daniela V. Fraga Alvarez; Zhexi Lin; Zixiao Shi; Amanda F. Baxter; Emily D. Wang; Dhruti Kuvar; Nafis Mahmud; Muftah H. El‐Naas; Héctor D. Abruña; David A. Muller; Daniel Esposito | Materials Science; Catalysis; Coating Materials; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6557719edbd7c8b54b74af63/original/condensed-layer-deposition-of-nanoscopic-ti-o2-overlayers-on-high-surface-area-electrocatalysts.pdf |
612f0454d5f080d1a0b7a5d3 | 10.26434/chemrxiv-2021-xpp8v | Following Molecular Mobility During Chemical Reactions: No Evidence for Active Propulsion | The measured changes in self-diffusion of small molecules during reactions have been attributed “boosted mobility”. We demonstrate the critical role of changing concentrations of paramagnetic ions on nuclear magnetic resonance (NMR) signal intensities, which lead to erroneous measurements of diffusion coefficients. We present simple methods to overcome this problem. The use of shuffled gradient amplitudes allows accurate diffusion NMR measurements, even with time-dependent relaxation rates caused by changing concentrations of paramagnetic ions. The addition of a paramagnetic relaxation agent allows accurate determination of both diffusion coefficients and reaction kinetics during a single experiment. We analyze a copper-catalyzed azide-alkyne cycloaddition ‘click’ reaction, for which boosted mobility has been claimed. With our methods, we accurately measure the diffusive behavior of solvent, starting materials and product, and find no global increase in diffusion coefficients during the reaction. We overcome NMR signal overlap using an alternative reducing agent to improve the accuracy of the diffusion measurements. The alkyne reactant diffuses slower as the reaction proceeds, due to binding to the copper catalyst during the catalytic cycle. The formation of this intermediate was confirmed by complementary NMR techniques and density functional theory calculations. Our work calls into question recent claims that molecules actively propel or swim during reactions, and establishes that time-resolved diffusion NMR measurements can provide valuable insight into reaction mechanisms. | Lucy Fillbrook; Jan-Philipp Günther; Günter Majer; Daniel O'Leary; William Price; Hal Van Ryswyk; Peer Fischer; Jonathon Beves | Physical Chemistry; Analytical Chemistry; Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612f0454d5f080d1a0b7a5d3/original/following-molecular-mobility-during-chemical-reactions-no-evidence-for-active-propulsion.pdf |
60c74f390f50db40a439737d | 10.26434/chemrxiv.12861017.v1 | Flow Control in a Laminate Capillary-Driven Microfluidic Device | Capillary-driven microfluidic devices are of significant interest for on-site analysis because they
do not require external pumps and can be made from inexpensive materials. Among capillary-driven devices,
those made from paper and polyester film are among the most common and have been used in a wide array
of applications. However, since capillary forces are the only driving force, flow is difficult to control, and
passive flow control methods such as changing the geometry must be used to accomplish various analytical
applications. This study presents several new flow control methods that can be utilized in a laminate
capillary-driven microfluidic device to increase available functionality. First, we introduce push and burst
valve systems that can stop and start flow. These valves can be opened by either pressing the channel or
inflowing other fluids to the valve region. Next, we propose flow control methods for Y-shaped channels
that enable more functions. In one example, we demonstrate the ability to accurately control concentration and in a second example, flow rate in the main channel is controlled by adjusting the geometry of the inlet
channel. Finally, the flow rate in the Y-shaped device as a function of channel height and fluid properties
such as viscosity and surface tension was examined. As in previous studies on capillary-driven channels,
the flow rate was affected by each parameter. The fluidic control tools presented here will enable new
designs and functions for low cost point of need assays across a variety of fields. | Ilhoon Jang; David S. Dandy; Brian J. Geiss; Charles Henry; Hyunwoong Kang; Simon Song | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f390f50db40a439737d/original/flow-control-in-a-laminate-capillary-driven-microfluidic-device.pdf |
657118b3cf8b3c3cd7f29ba3 | 10.26434/chemrxiv-2023-6v70h | E-Selective Radical Difunctionalization of Unactivated Alkynes: Preparation of Functionalized Allyl Alcohols from Aliphatic Alkynes | Radical difunctionalization of aliphatic alkynes provides direct access to valuable multi-substituted alkenes, but achieving a high level of chemo- and stereo-control remains a formidable challenge. Herein we report a novel photoredox neutral alkyne difunctionalization through functional group migration followed by radical-polar crossover and energy transfer-enabled stereoconvergent isomerization of alkenes. In this sequence, a hydroxyalkyl and an aryl group are incorporated concomitantly into an alkyne, leading to diversely functionalized E-allyl alcohols. The scope of alkynes is noteworthy, and the reaction tolerates aliphatic alkynes containing hydrogen donating C-H bonds which are prone to intramolecular hydrogen atom transfer. The protocol features broad functional group compatibility, high product diversity and exclusive chemo- and stereoselectivity, thus providing a practical strategy for the elusive radical difunctionalization of unactivated alkynes. | Jie Wang; Xinxin Wu; Zhu Cao; Xu Zhang; Xinxin Wang; Jie Li; Chen Zhu | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657118b3cf8b3c3cd7f29ba3/original/e-selective-radical-difunctionalization-of-unactivated-alkynes-preparation-of-functionalized-allyl-alcohols-from-aliphatic-alkynes.pdf |
60c73edff96a000bcc285fe9 | 10.26434/chemrxiv.7176989.v1 | A Boronic Acid-Based Fluorescence Hydrogel for Monosaccharide Detection | <p>A
boronic acid-based anthracene fluorescent probe was functionalised with an
acrylamide unit to incorporate into a hydrogel system for monosaccharide
detection<i>. </i>In solution, the
fluorescent probe<b> </b>displayed a strong
fluorescence turn-on response upon exposure to fructose, and an expected trend
in apparent binding constants, as judged by a fluorescence response where D-fructose > D-galactose > D-mannose > D-glucose. The
hydrogel incorporating the boronic acid monomer demonstrated the ability to
detect monosaccharides by fluorescence with the same overall trend as the
monomer in solution with the addition of fructose resulting in a 10-fold
enhancement (≤ 0.25 M). <b><u></u></b></p> | Suying Xu; Adam Sedgwick; Souad Elfecky; Wenbo Chen; Ashley Jones; George Williams; Toby Jenkins; Steven Bull; John Fossey; Tony James | Supramolecular Chemistry (Org.); Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73edff96a000bcc285fe9/original/a-boronic-acid-based-fluorescence-hydrogel-for-monosaccharide-detection.pdf |
643d7a4e08c86922ff2cc417 | 10.26434/chemrxiv-2023-md55t | The Materials Experiment Knowledge Graph | Materials knowledge is inherently hierarchical. While high-level descriptors such as composition and structure are valuable for contextualizing materials data, the data must ultimately be considered in the context of its low-level acquisition details. Graph databases offer an opportunity to represent hierarchical relationships among data, organizing semantic relationships into a knowledge graph. Herein, we establish a knowledge graph of materials experiments whose construction encodes the complete provenance of each material sample and its associated experimental data and metadata. Additional relationships among materials and experiments further encode knowledge and facilitate data exploration. We illustrate the Materials Experiment Knowledge Graph (MEKG) using several use cases,
demonstrating the value of modern graph databases for
the enterprise of data-driven materials science. | Michael Statt; Brian Rohr; Dan Guevarra; Ja'Nya Breeden; Santosh Suram; John Gregoire | Materials Science; Catalysis; Energy; Thin Films; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d7a4e08c86922ff2cc417/original/the-materials-experiment-knowledge-graph.pdf |
60c74cadf96a009835287810 | 10.26434/chemrxiv.12510731.v1 | New Theoretical Insight into the Reaction Kinetics of Toluene and Hydroxyl Radicals | <p><a></a><a>Toluene’s removal mechanism in the atmosphere is mainly attributed to OH radical, which
includes major OH-addition and minor H-abstraction reactions. The cresols and RO2 derived from OHadducts reacting to O2 have significant impacts on the generation of secondary organic aerosols (SOA) and
O3. However, computed branching ratios of various OH-adducts at various theoretical levels are largely
inconsistent, mainly because previously reported barrier heights of OH-addition reaction showed a strong
method dependence. In the present study, we demonstrate that this reaction involves a nonnegligible
anharmonic effect (during the process of OH moving to the benzene ring), which has been overlooked by
previous studies. The reaction kinetics of toluene + OH was systematically studied by a high-level quantum
chemical method (CCSD(T)-F12/cc-pVQZ-F12//B2PLYP-D3/6-311++G(d,p)) combined with
RRKM/master equation simulations. The particle-in-a-box approximation was used to treat the
anharmonicity in this system. The final total rate coefficient is calculated to be 2.60 × 10−12 cm3 molecule−1
s−1 at 300 K and 1 atm. The main products for toluene + OH are computed as ortho-adducts (50.8%), benzyl
radical + H2O (21.1%), ipso-adduct (16.3%), para-adduct (6.1%), and meta-adduct (4.6%). Our results
indicate that both high level quantum chemical calculations for the crucial barrier heights and appropriate
treatments for the anharmonicity determine the accuracy of the final computed total rate coefficients and
branching ratios. Further analysis on the branching ratios of various reaction channels provides insight into
the atmosphere-initiated oxidation of toluene. </a></p> | Xiaoqing Wu; Can Huang; Shiyao Niu; Feng Zhang | Chemical Kinetics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cadf96a009835287810/original/new-theoretical-insight-into-the-reaction-kinetics-of-toluene-and-hydroxyl-radicals.pdf |
60c746dff96a004f2b286e1b | 10.26434/chemrxiv.11422521.v1 | Biosynthetic Incorporation of Site-Specific Isotopes in βLactam Antibiotics Enables Biophysical Studies | A biophysical understanding of the mechanistic, chemical, and physical
origins underlying antibiotic action and resistance is vital to the discovery
of novel therapeutics and the development of strategies to combat the growing
emergence of antibiotic resistance. The site-specific introduction of stable-isotope
labels into chemically complex natural products is particularly important for
techniques such as NMR, IR, mass spectrometry, imaging, and kinetic isotope
effects. Towards this goal, we developed a biosynthetic strategy for the
site-specific incorporation of <sup>13</sup>C-labels into the canonical
β-lactam carbonyl of penicillin G and cefotaxime, the latter via cephalosporin
C. This was achieved through sulfur-replacement with 1-<sup>13</sup>C-L-cysteine,
resulting in high isotope incorporations and mg-scale yields. Using <sup>13</sup>C
NMR and isotope-edited IR difference spectroscopy, we illustrate how these
molecules can be used to interrogate interactions with their protein targets, e.g.
TEM-1 β-lactamase. This method provides a feasible route to isotopically-labeled
penicillin and cephalosporin precursors for future biophysical studies. | Jacek Kozuch; Samuel Schneider; Steven Boxer | Biophysics; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746dff96a004f2b286e1b/original/biosynthetic-incorporation-of-site-specific-isotopes-in-lactam-antibiotics-enables-biophysical-studies.pdf |
60c74a59702a9b1f8d18b273 | 10.26434/chemrxiv.12192297.v1 | 2D Magnetic MOFs with Micron-Lateral Size by Liquid Exfoliation | The isolation in large amounts of high-quality flakes of 2D MOFs remains a challenge. In this work, we develop a liquid exfoliation procedure to obtain nanosheets for a whole family of Fe-based magnetic MOFs, MUV-1-X. High-quality crystalline layers with lateral sizes of 8 µm and thicknesses of 4 nm, which keep the structural integrity and magnetic properties, are obtained. | Guillermo Minguez Espallargas; Javier López-Cabrelles; Eugenio Coronado; Luis Leon-Alcaide | Hybrid Organic-Inorganic Materials; Magnetic Materials; Magnetism | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a59702a9b1f8d18b273/original/2d-magnetic-mo-fs-with-micron-lateral-size-by-liquid-exfoliation.pdf |
6523e71dbda59ceb9a2c14e2 | 10.26434/chemrxiv-2023-qbd0s | Mechanophotocatalysis | This proof-of-concept study establishes the viability and generality of mechanophotocatalysis, merging mechanochemistry and photocatalysis to enable solvent-minimized photocatalytic reactions. We demonstrate the transmutation of four archetypal solution-state photocatalysis reactions to a solvent-minimized environment driven by the combined actions of milling, light, and photocatalysts. The chlorosulfonylation of alkenes and the pinacol coupling of aldehydes and ketones were conducted under solvent-free conditions with competitive or superior efficiencies to their solution-state analogues. Furthermore, decarboxylative alkylations are shown to function efficiently under solvent-minimized conditions, while the photoinduced energy transfer promoted [2+2] cycloaddition of chalcone experiences a significant initial rate enhancement over its solution-state variant. This work serves as a platform for future discoveries in an underexplored field, validating that solvent-minimized photocatalysis is generalisable and competitive with solution-state photocatalysis. | Francis Millward; Eli Zysman-Colman | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6523e71dbda59ceb9a2c14e2/original/mechanophotocatalysis.pdf |
612fcec227d9061aae7b3d35 | 10.26434/chemrxiv-2021-197pf | Preventing bulky cation diffusion in lead halide perovskite solar cells | The impact on device stability of the bulky cation-modified interfaces in halide perovskite solar cells is not well-understood. We demonstrate the thermal instability of the bulky cation interface layers used in some of the highest performing solar cells to date. X-ray photoelectron spectroscopy and synchrotron-based grazing incidence X-ray scattering measurements reveal significant changes under thermal stress in the chemical composition and structure at the surface of these films. The changes impact charge carrier dynamics and device operation, as shown in transient photoluminescence, excitation correlation spectroscopy, and solar cells. The type of cation used for passivation affects the extent of these changes, where long carbon chains provide more stable interfaces and thus longer durability (more than 1000 hrs at 55ºC). Such findings highlight that annealing the treated interfaces before characterization is critical to enable reliable reporting of performances and to drive the selection between different cations. | Carlo Andrea Riccardo Perini; Esteban Rojas-Gatjens; Magdalena Rovello; Andres Felipe Castro Mendez; Juanita Hidalgo; Yu An; Ruipeng Li; Carlos Silva-Acuña; Juan-Pablo Correa-Baena | Materials Science; Hybrid Organic-Inorganic Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612fcec227d9061aae7b3d35/original/preventing-bulky-cation-diffusion-in-lead-halide-perovskite-solar-cells.pdf |
618e13ff9960f3cd08a91240 | 10.26434/chemrxiv-2021-3j2sz | Can substitutions affect the oxidative stability of lithium argyrodite solid electrolytes? | Lithium ion conducting argyrodites are among the most studied solid electrolytes due to their high ionic conductivities. A major concern in a solid-state battery is the solid electrolyte stability. Here we present a systematic study on the influence of cationic and anionic substitution on the electrochemical stability of Li6PS5X, using step-wise cyclic voltammetry, optical band gap measurements, hard X-ray photoelectron spectroscopy along with first-principles calculations. We observe that going from Li6PS5Cl to Li6+xP1-xMxS5I (M = Si4+, Ge4+), the oxidative degradation does not change. Considering the chemical bonding shows that the valence band edges are mostly populated by non-bonding orbitals of the PS43- units or unbound sulfide anions and that simple substitutions in these sulfide-based solid electrolytes cannot improve oxidative stabilities. This work provides insights on the role of chemical bonding on the stability of superionic conductors and shows that alternative strategies are needed for long-term stable solid-state batteries. | Ananya Banik; Yunsheng Liu; Saneyuki Ohni; Yannik Rudel; Alberto Jiménez-Solano ; Andrei Gloskovskii ; Nella Vargas-Barbosa; Yifei Mo; Wolfgang Zeier | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618e13ff9960f3cd08a91240/original/can-substitutions-affect-the-oxidative-stability-of-lithium-argyrodite-solid-electrolytes.pdf |
60c74da34c891950e5ad383e | 10.26434/chemrxiv.12643166.v1 | Biomimetic Design of a Robustly Stabilized Folded State Enabling Seed-Initiated Helical Supramolecular Polymerization Under Microfluidic Mixing | We have investigated the folding and assembly behavior of an alanine-based monomeric diamide and a cystine-based dimeric diamide bearing pyrene units and solubilizing alkyl chains at their C-termini andN-termini, respectively. In low-polarity solvents, the former molecule forms a folded 7-membered ring conformation with an intramolecular hydrogen bond, while the latter molecule forms a 14-membered ring through double intramolecular hydrogen bonds between two diamide units. Spectroscopic studies revealed that both folded states are thermodynamically unstable and eventually transform into more energetically stable supramolecular polymers. Importantly, compared to the alanine-based diamide, the cystine-based dimeric diamide exhibits a superior kinetic stability in the metastable folded state, as well asan increased thermodynamic stability in the aggregated state. Consequently, spontaneous transformation from the folded state into the aggregated state is retarded even under the conditions of rapid molecular diffusion. Accordingly, the initiation of supramolecular polymerization can be regulated via a seeding approach under microfluidic mixing conditions. Furthermore, the supramolecular polymer composed of the cystine-based dimeric diamide has a helical structure with an enhanced chiral excitonic coupling between the transition dipoles of the pyrene units. Taking advantage of the self-sorting behavior observed in a mixture of l-cysteine- and d-cysteine-based dimeric diamides, a two-step supramolecular polymerization from a racemic mixture was achieved by stepwise addition of the corresponding seeds. | Soichiro Ogi; Aiko Takamatsu; Kentaro Matsumoto; Shigehiro Yamaguchi | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74da34c891950e5ad383e/original/biomimetic-design-of-a-robustly-stabilized-folded-state-enabling-seed-initiated-helical-supramolecular-polymerization-under-microfluidic-mixing.pdf |
656806d45bc9fcb5c9b26bfd | 10.26434/chemrxiv-2023-b5x16 | Photocontrolled Stereoselective Cationic Polymerization | By virtue of noninvasive regulations by light, photocontrolled polymerizations have attracted considerable attention for the precision synthesis of macromolecules. However, a cationic polymerization with simultaneous photo-control and tacticity-regulation remains elusive and challenging to achieve. Herein, we introduce an asymmetric ion-pairing photoredox catalysis strategy, which allows for the development of a stereoselective cationic polymerization with light control for the first time. By employing a chiral ion pair photoredox catalyst (PC+/*A–) con-sisting of a photoredox active cationic part (PC+) and a sterically confined chiral anion (*A–) to deliver the stereochemical control, the stereoselective cationic polymerization of vinyl ethers with the assistance of photo control can be achieved with high isotactic selectivity (up to 91% m) at a remarkable low level of catalyst loading (50 ppm). | Zan Yang; Yun Liao; Zhengyi Zhang; Jianxu Chen; Xun Zhang; Saihu Liao | Catalysis; Polymer Science; Polymerization catalysts; Organocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656806d45bc9fcb5c9b26bfd/original/photocontrolled-stereoselective-cationic-polymerization.pdf |
60c743314c89191acaad25db | 10.26434/chemrxiv.8970755.v1 | Rational Design of Surface Modified TiO2 with Alkaline Earth Oxides (Mg2+, Ca2+) for the Oxygen Evolution Reaction | Photocatalytic
O<sub>2</sub> evolution reaction was performed TiO<sub>2</sub> rutile
surface-modified with alkaline earth oxides, namely CaO and MgO. From the
structural and surface characterization, modified systems do not show
significant differences with bare TiO<sub>2</sub>, indicating that the
integrity of the rutile phase is maintained after modification. However, the
charge carrier separation is strongly affected by the presence of small amounts
of alkaline-earth. Moreover, the<sub> </sub>O<sub>2</sub> evolution activity is
enhanced for Mg<sup>2+</sup> modified systems at low loadings. This improved performance
may be related to surface features such as higher ion dispersion and surface
hydroxylation, and the improved photonic efficiencies observed for low Mg<sup>2+</sup>
loading. First principles simulations indicate that surface aggregation is more
favourable for CaO-modifiers and may explain the greater degree of dispersion
of MgO at low loadings. Computed oxygen vacancy formation energies indicate
that the modified systems are reducible with moderate energy costs, relative to
unmodified rutile, so that Ti<sup>3+</sup> ions will be present. A model of
photoexcitation shows that modification promotes charge carrier separation;
electrons and holes localise at subsurface Ti sites and low-coordinated O sites
of the modifiers, respectively. Pathways to water oxidation at interfacial sites
of reduced MgO-modified rutile TiO<sub>2</sub> are identified, requiring
overpotentials of 0.75 V. In contrast, CaO-modified systems required
overpotentials in excess of 1 V for the reaction to proceed. | Ana I. Becerro; Stephen Rhatigan; Michael Nolan; Gerardo Colon | Electrocatalysis; Heterogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743314c89191acaad25db/original/rational-design-of-surface-modified-ti-o2-with-alkaline-earth-oxides-mg2-ca2-for-the-oxygen-evolution-reaction.pdf |
61fc672a0c0bf072b2ddd033 | 10.26434/chemrxiv-2022-q0692 | Structure and biosynthesis of desmamides A-C, lipoglycopeptides from the endophytic cyanobacterium Desmonostoc muscorum LEGE 12446 | Certain cyanobacteria of the secondary metabolite-rich order Nostocales can establish permanent symbioses with a large number of cycads, by accumulating in their coralloid roots and shifting their metabolism to dinitrogen fixa-tion. Here, we report the discovery of two novel lipoglycopeptides, desmamides A (1) and B (2), together with their aglycone desmamide C (3), from the nostocalean cyanobacterium Desmonostoc muscorum LEGE 12446 isolated from a cycad (Cycas revoluta) coralloid root. The chemical structures of the compounds were elucidated using a combination of 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy and Mass Spectrometry (MS). The desmamides are decapeptides, featuring O-glycosylation of tyrosine (in 1 and 2) and an unusual 3,5-dihydroxy-2-methyldecanoic acid residue. The biosynthesis of the desmamides was studied by substrate feeding experiments and bioinformatics. We describe herein the dsm biosynthetic gene cluster (BGC) and propose it to be associated with desmamide production. The discovery of this class of very abundant (>1.5% d.w.) bacterial lipoglycopeptides paves the way for exploration of their potential role in root endosymbiosis. | Sara Freitas; Raquel Castelo Branco; Arlette Wenzel-Storjohann; Vitor Vasconcelos; Deniz Tasdemir; Pedro Leão | Biological and Medicinal Chemistry; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fc672a0c0bf072b2ddd033/original/structure-and-biosynthesis-of-desmamides-a-c-lipoglycopeptides-from-the-endophytic-cyanobacterium-desmonostoc-muscorum-lege-12446.pdf |
60c73fe30f50db5197395878 | 10.26434/chemrxiv.7557224.v1 | Improving Atom Type Diversity and Sampling in Co-Solvent Simulations Using λ-Dynamics | <div>Here we present a novel co-solvent MD simulation method based on the lambda-dynamics simulation concept that aims to address a serious issue of current co-solvent simulation approaches, the limited chemical diversity of probe molecules ignoring the chemical
context of the pharmacophoric feature represented by a probe. The new concept significantly increases the chemical diversity of functional groups investigated during co-solvent simulations. Application to four different test cases highlights the utility of the new approach to identify binding preferences of different functional groups and to correctly rank ligand series that differ by their substitution patterns.</div> | Amr Mahmoud; Ying Yang; Markus Lill | Biophysics; Chemical Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe30f50db5197395878/original/improving-atom-type-diversity-and-sampling-in-co-solvent-simulations-using-dynamics.pdf |
63e25dfb1f23f0032d47a746 | 10.26434/chemrxiv-2023-cv3hv | Lab-on-a-Bead: Polymeric Natural Deep Eutectic Solvents as a Versatile Platform for (Bio)sensor Design | Natural polymers offer not only low-cost, wide availability, biocompatibility, and biodegradability but also a rich chemical functionality towards custom modifications and new applications. Among those, sodium alginate (ALG) offers a number of competitive advantages, including the possibility to form beads by a simple process call spherification as well as their modification by a wide number of processes, including the possibility to mixing the alginate solution with deep eutectic solvents (DES). Thus, and considering the capacity of DES to stabilize enzymes, the main objective of this work was to design and fabricate a new PODES (using ALG as one of the components, ALGPODES) and to deploy this material as a new phase to develop colorimetric biosensors. The formed beads displayed a narrow size distribution (2.9 0.1 mm) and a permeable structure with large internal cavities (25-100 m). The applicability of these beads towards analytical applications (lab-on-a-bead) was demonstrated by integrating three sensing platforms and by their application in real food samples. | Federico Gomez; Ezequiel Vidal; Graciela Zanini; Claudia Domini; Maria Silva; Carlos Garcia | Catalysis; Analytical Chemistry; Biochemical Analysis; Redox Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e25dfb1f23f0032d47a746/original/lab-on-a-bead-polymeric-natural-deep-eutectic-solvents-as-a-versatile-platform-for-bio-sensor-design.pdf |
617ede8292abe02704300fa1 | 10.26434/chemrxiv-2021-pnbt0 | Albumin nanoparticles loaded with hemin as peroxidase mimics for immunoassay | Contemporary immunoassays commonly used in clinical diagnostics mostly utilize enzymes, such as horseradish peroxidase, for signal generation. Numerous research is dedicated to the development of artificial peroxidase-mimicking catalysts with lower cost, high activity, better operational stability, and tunable properties. Herein we synthesized hemin-loaded bovine serum albumin (BSA) nanoparticles and applied them as catalytic labels (nanozymes) in colorimetric immunoassay of anti-tetanus antibodies. Hemin is a key part of the peroxidase catalytic center, possessing peroxidase like-activity. Albumin nanoparticles were loaded with multiple hemin molecules and decorated with Streptococcal protein G. Resulting nanozymes possessed good colloidal stability and allowed for antibody detection in blood serum. The sensitivity of antibody detection was sufficient for the assessment of post-vaccination immunity. | Pavel Khramtsov; Maria Bochkova; Valeria Timganova; Dmitriy Kiselkov; Svetlana Zamorina; Mikhail Rayev | Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617ede8292abe02704300fa1/original/albumin-nanoparticles-loaded-with-hemin-as-peroxidase-mimics-for-immunoassay.pdf |
60c753b2567dfe1ba9ec5f6c | 10.26434/chemrxiv.13530977.v1 | “Simple” AIEgens for Non-doped Solution-Processed OLEDs with Emission Close to Pure Red in sRGB Gamut | <p>Herein, two
red luminogens with aggregation-induced emission (AIE) characteristics based on
simple D–A structures with high performance in the film state are explored. Efficient
non-doped solution-processed organic light emitting
diodes (OLEDs) are
fabricated and emit bright red electroluminescence at 652 nm and 711 nm, respectively. Most importantly,
they exhibit CIE coordinates of (0.63, 0.36) and
(0.64, 0.35), respectively, which are close to that of primary red color (0.63,
0.34) according to the digital television standard.</p> | Tianfu Zhang; Zhicong Zhou; Zheng Zheng; Jianyu Zhang; Ying Yu,; Jacky W. Y. Lam; jonathan E. halpert; Ben Zhong Tang | Organic Compounds and Functional Groups; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753b2567dfe1ba9ec5f6c/original/simple-ai-egens-for-non-doped-solution-processed-ole-ds-with-emission-close-to-pure-red-in-s-rgb-gamut.pdf |
6476412f4f8b1884b78ec317 | 10.26434/chemrxiv-2023-nm4vk | Core-Ionization Spectrum of Liquid Water | We present state-of-the-art calculations of the core-ionization spectrum of water. The values of experimentally derived solvation shifts in the core 1sO ionization energy of water vary from -1.3 to -2.8 eV due to difficulties in assessing the effect of the surface potential. This provides a motivation to obtain a robust theoretical value of the shift. Here we develop theoretical protocols based on coupled-cluster theory and electrostatic embedding. Our value of the solvent-induced shift of the core 1sO ionization energy of water is -1.51 eV. The computed absolute position and the width of the 1sO in photoelectron spectrum of water are 538.75 eV and 1.44 eV, respectively, agree well with the best experimental values. | Sourav Dey; Sarai Folkestad; Alexander Paul; Henrik Koch; Anna Krylov | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6476412f4f8b1884b78ec317/original/core-ionization-spectrum-of-liquid-water.pdf |
648317cdbe16ad5c57b15958 | 10.26434/chemrxiv-2023-w9rr0 | Role of vacancies in structural thermalization of binary and high-entropy alloys | Vacancy assisted atomic self-diffusion is a major structural thermalization mechanism in bulk metal alloys. Depending on alloy composition, the local atomic environments might stabilize vacancies to such extent that the vacancies become trapped and the atomic self-diffusion part of the thermalization process stalls. The consequence is that such alloys get kinetically trapped in disordered structures. In this study, we investigate equimolar AgAu, CuPt, AgPdPtIr, and AgAuCuPdPt alloy thermalizing using Metropolis Monte Carlo simulations in two approaches, one where the alloy structure changes through vacancy migration and one where the structure changes by swapping atomic pairs. By comparing the two approaches, we find that the vacancy is less effective at thermalizing alloys with more elements (i.e. AgPdPtIr and AgAuCuPdPt), more heterogeneous configurational energy distributions (i.e. CuPt and AgPdPtIr), and strong interactions between certain elements, e.g. Ir-Ir interactions in AgPdPtIr. In the case of AgPdPtIr, the vacancy cannot thermalize Ir-Ir neighbors even when the vacancy is mobile, because the vacancy has difficulty breaking individual Ir-Ir pairs apart. | Henrik Kristoffersen; Jack K. Pedersen; Jan Rossmeisl | Physical Chemistry; Materials Science; Alloys; Physical and Chemical Properties; Structure | CC BY NC 4.0 | CHEMRXIV | 2023-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648317cdbe16ad5c57b15958/original/role-of-vacancies-in-structural-thermalization-of-binary-and-high-entropy-alloys.pdf |
60c73dd5ee301ca0c8c7864b | 10.26434/chemrxiv.6195176.v1 | Chimera: Enabling Hierarchy Based Multi-Objective Optimization for Self-Driving Laboratories | <div><div>We introduce Chimera, a general purpose achievement scalarizing function (ASF) for multi-objective optimization problems in experiment design. Chimera combines concepts of a priori scalarizing with ideas from lexicographic approaches. It constructs a single merit-based function which implicitly accounts for a provided hierarchy in the objectives. The performance of the suggested ASF is demonstrated on several well-established analytic multi-objective benchmark sets using different single-objective optimization algorithms. We further illustrate the performance and applicability of Chimera on two practical applications: (i) the auto-calibration of a virtual robotic sampling sequence for direct-injection, and (ii) the inverse-design of a system for efficient excitation energy transport. The results indicate that Chimera enables a wide class of optimization algorithms to rapidly find solutions. The presented applications highlight the interpretability of Chimera to corroborate design choices on tailoring system parameters. Additionally, Chimera appears to be applicable to any set of n unknown objective functions, and more importantly does not require detailed knowledge about these objectives. We recommend the use of Chimera in combination with a variety of optimization algorithms for an efficient and robust optimization of multi-objective problems.</div></div><div><br /></div> | Florian Häse; Loic Roch; Alan Aspuru-Guzik | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence; Reaction Engineering; Quasiparticles and Excitations; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd5ee301ca0c8c7864b/original/chimera-enabling-hierarchy-based-multi-objective-optimization-for-self-driving-laboratories.pdf |
65e9b69fe9ebbb4db92bb2db | 10.26434/chemrxiv-2024-tbqxj | Straightforward, Sustainable and Scalable Access to 3,4-Perylenedicarboxylic Monoanhydride | Perylene dyes are a cornerstone of modern research and technology in fields rang- ing from printed (opto)eletronics to bioimaging. Most known compounds are bisimide derivatives prepared from perylenetetracarboxylic dianhydride (PTCDA), essentially a chemical commodity. On the contrary, there are comparatively fewer reports on perilenedicarboxylic monoimide derivatives not due to lack of performance but due to the challenging access to the key intermediate 3,4-perylenedicarboxylic monoanhy- dride (PDCMA). As we detail, reported synthetic pathways are both costly, resource intensive and associated with extremely poor green metrics. We show a new two-step straightforward, sustainable, efficient and organic solvent free preparation of PDCMA based on a combination of solventless and in-water reactions. | Anita Zucchi; Sara Mattiello; Mauro Sassi; Luca Beverina | Organic Chemistry; Organic Synthesis and Reactions; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e9b69fe9ebbb4db92bb2db/original/straightforward-sustainable-and-scalable-access-to-3-4-perylenedicarboxylic-monoanhydride.pdf |
60c743ec0f50dbafd6395fdb | 10.26434/chemrxiv.9691730.v1 | Validation of Slow Off-Kinetics of Sirtuin Rearranging Ligands (SirReals) by Means of the Label-Free Electrically Switchable Nanolever Technology | Recently, we have discovered the sirtuin rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD+-dependent lysine deacetylase Sirt2. In previous studies, using a biotinylated SirReal analogue in combination with biolayer interferometry, we observed a slow dissociation rate of the inhibitor-enzyme complex, which had been postulated to be the key to the high affinity and selectivity of SirReals. However, for the attachment of biotin to the SirReal core, we introduced a triazole as a linking moiety, which was shown by X-ray co-crystallography to interact with Arg97 of the cofactor binding loop. This study now is directed to answer the question, whether the observed long residence time of the SirReals is induced mainly by triazole incorporation or is an inherent characteristic of the SirReal inhibitor core. Therefore, we used the novel label-free switchSENSE® technology, based on electrically switchable DNA nanolevers, to validate that the long residence time of the SirReals is caused by the core scaffold.<br /> | Matthias Schiedel; Herwin Daub; Aymelt Itzen; Manfred Jung | Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ec0f50dbafd6395fdb/original/validation-of-slow-off-kinetics-of-sirtuin-rearranging-ligands-sir-reals-by-means-of-the-label-free-electrically-switchable-nanolever-technology.pdf |
672da9515a82cea2fa786821 | 10.26434/chemrxiv-2024-6vqxf | Sulfur-locked multiple resonance emitters for high performance orange-red/deep-red OLEDs | Herein, an innovative concept for a paradigm shift in orange-red/deep-red multiple resonance (MR) emitters is proposed by linking the outer phenyl groups in a classical MR framework through intramolecular sulfur (S) locks. Endowed with the planar architectural feature of the MR mother core, the proof-of-concept S-embedded emitters S-BN and 2S-BN also exhibit considerable flatness, which proves critical in avoiding the direct establishment of potent charge transfer states and inhibiting the non-radiative decay process. The emission maxima of S-BN and 2S-BN are 594 nm and 671 nm, respectively, and both have a high photoluminescence quantum yield of approximately 100%, a rapid radiative decay rate of around 107 s-1, and a remarkably high reverse intersystem crossing rates of about 105 s−1. In addition, 2S-BN is the first example of a single boron deep red MR emitter. Notably, unprecedented maximum external quantum efficiencies of 39.9% (S-BN, orange-red) and 29.3% (2S-BN, deep-red) were also achieved in typical planar organic light-emitting diode structures with ameliorated efficiency roll-offs. | Yexuan Pu; Qian Jin; Yuewei Zhang; Chenglong Li; Lian Duan; Yue Wang | Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Optics; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672da9515a82cea2fa786821/original/sulfur-locked-multiple-resonance-emitters-for-high-performance-orange-red-deep-red-ole-ds.pdf |
650846c7b6ab98a41ca9f8f3 | 10.26434/chemrxiv-2023-dbc9d | Modular Synthesis of Congested b2,2-Amino Acids via the Merger of Photocatalysis and Oxidative Functionalisations | b-Amino acids are privileged scaffolds present in numerous bioactive compounds, as well as versatile synthons in organic chemistry. b2- or b3-amino acids can be readily synthesised, however, access to b2,2-analogues is limited by challenges associated with building the quaternary centre. Herein, we report a two-step protocol for the modular synthesis of b2- and -quaternary b2,2-amino acid derivatives from readily available feedstocks such as carbonyl compounds, malononitrile, and -amino acids. The key steps are: 1) a photocatalytic decarboxylative radical hydroalkylation reaction that enables the facile construction of the a-quaternary centre, and 2) an oxidative esterification converting the malononitrile motif into the targeted ester moiety. This versatile approach grants selective access to b-amino esters, b-amino amides, or N-protected b-amino acids bearing bulky substituents on the a-position. Additionally, we demonstrated that this synthesis can be effectively scaled up via continuous-flow technology. | Khadijah Anwar; Luca Capaldo; Ting Wan; Timothy Noël; Adrián Gómez-Suárez | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650846c7b6ab98a41ca9f8f3/original/modular-synthesis-of-congested-b2-2-amino-acids-via-the-merger-of-photocatalysis-and-oxidative-functionalisations.pdf |
6491c655853d501c00334bf1 | 10.26434/chemrxiv-2023-zzj3f | Total Synthesis of Neohomohalichondrin B | The total synthesis of neohomohalichondrin B has been achieved using a de novo sequence that enabled a highly convergent pathway to access the C38-C55 thioester fragment. The highlights of this synthesis include: (i) a tandem base-induced hydrolysis and rearrangement to access the C47-C50 tetrahydrofuran, and (ii) a Ni(I)/Ni(II)-mediated ketone coupling and acid-catalyzed cyclization sequence to access the C44 spiroketal and complete carbon framework of the left half fragment. The total synthesis of neohomohalichondrin B was completed following coupling of the left half thioester with a C1-C37 macrolactone iodide, according to our method for the unified synthesis of halichondrins. This synthetic strategy may facilitate an improved method to prepare other members of the halichondrin family, and analogues thereof. | Harry Aitken; Rachelle Quach; Yoshito Kishi | Organic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6491c655853d501c00334bf1/original/total-synthesis-of-neohomohalichondrin-b.pdf |
60c74781567dfe1be5ec481d | 10.26434/chemrxiv.11691780.v1 | Β-Galactosidase-Catalyzed Fluorescent Reporter Labeling of Living Cells for Sensitive Detection of Cell Surface Antigens | The ability to detect cell surface proteins using
fluorescent dye-labeled antibodies is crucial for the reliable identification
of many cell types. However, the different types of cell surface proteins used to
identify cells are currently limited in number because they need to be
expressed at high levels to exceed background cellular autofluorescence,
especially in the shorter wavelength region. Herein, we report on a new method
(CLAMP: quinone methide-based <u>c</u>atalyzed signa<u>l</u> <u>amp</u>lification)
in which the fluorescence signal is amplified by an enzymatic reaction that strongly
facilitates the detection of cell surface proteins on living cells. We used β-galactosidase
as an amplification enzyme and designed a substrate for it, called MUGF, which contains
a fluoromethyl group. Upon removal of the galactosyl group in MUGF by β-galactosidase labeling
of the target cell surface proteins, the resulting quinone methide
group-containing product was found to be both cell membrane permeable and reactive
with intracellular nucleophiles, thereby providing fluorescent adducts. Using this
method, we successfully detected
several cell surface proteins including programmed death ligand 1 protein,
which is difficult to detect using conventional fluorescent dye-labeled antibodies. | Katsuya Noguchi; Takashi Shimomura; Yuya Ohuchi; Munetaka Ishiyama; Masanobu Shiga; Takeshi Mori; Yoshiki Katayama; Yuichiro Ueno | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74781567dfe1be5ec481d/original/galactosidase-catalyzed-fluorescent-reporter-labeling-of-living-cells-for-sensitive-detection-of-cell-surface-antigens.pdf |
6617632991aefa6ce1505d28 | 10.26434/chemrxiv-2023-8n7tq-v4 | Turning Green Waste into Gold: A Novel Approach to Sustainable Organic Fertilization for Enhanced Maize Yield in Comparison to NPK Fertilizer. | Abstract: Inorganic fertilizers have long been recognized for their adverse environmental impacts, prompting a quest for sustainable alternatives. This study delves into the rapid conversion of residual plant biomass into organic fertilizer, presenting an eco-friendly and cost-effective solution. The effects of this novel fertilizer on maize growth, development, and yield were meticulously compared to traditional NPK 20:10:5 fertilizers and rabbit manure. Three unique organic fertilizers were synthesized from a blend of eleven types of residual dry plant biomass, incorporating calcium hydroxide, clay soil, and thiourea for optimized maize application. The most promising formulation demonstrated significant nutrient content, including Total nitrogen (2.18%), Total phosphorus (1.80%), Total potassium (3.77%), and Total Carbon (37.40%), with a pH of 5. Impressively, maize plants treated with this synthesized fertilizer reached a maximum height of 171.45 cm, outperforming both NPK fertilizer (134.0 cm) and rabbit manure (121.92 cm). Moreover, maize yield was significantly enhanced with the synthesized fertilizer, particularly with fertilizer C boasting a weight of 287.38 g. Notably, this fertilizer exhibited both rapid and slow nutrient release dynamics, with 11% thiourea incorporation yielding superior results. Additionally, post-harvest soil analysis revealed higher residual organic matter content with the synthesized fertilizer, coupled with controlled nutrient release patterns (N ≈ 91.25%, P ≈ 76.11%, K ≈ 90.64%). This underscores the potential of utilizing agricultural plant residues in organic fertilization practices, offering a sustainable approach to soil enrichment and crop production. | Mathew Gideon; Emmanuel Kambai Duniya ; Mamman Abakeyah James | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Agriculture and Food Chemistry; Environmental Science; Industrial Manufacturing; Natural Resource Recovery | CC BY 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6617632991aefa6ce1505d28/original/turning-green-waste-into-gold-a-novel-approach-to-sustainable-organic-fertilization-for-enhanced-maize-yield-in-comparison-to-npk-fertilizer.pdf |
64fb460b99918fe5379813ca | 10.26434/chemrxiv-2023-q704t | Singlet-to-Triplet Cross-Effect Dynamic Nuclear Polarization | A new kind of cross-effect (CE) dynamic nuclear polarization (DNP) using biradicals with exchange couplings larger than the g-anisotropy or g-difference is proposed. The strongly coupled biradicals can be described with a combination of singlet S0 and triplet T(0,±1) states. Despite being invisible to w irradiation and spectral detection for the singlet state, S0↔T0 singlet-triplet transition by hyperfine couplings can occur driving nuclear spin flip for cross-effect DNP process. The T0 state population and spin alignment order can be generated by selectively saturating one of the T0↔ T(±1) transitions. Introducing dipolar couplings and frequency differences between the two electrons can remove the degeneracy between the two triplet transitions enabling selective saturation to obtain singlet-to-triplet cross-effect (ST-CE) DNP. | Zhehong Gan | Theoretical and Computational Chemistry; Physical Chemistry; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fb460b99918fe5379813ca/original/singlet-to-triplet-cross-effect-dynamic-nuclear-polarization.pdf |
62d4eca05819875b4944b4ca | 10.26434/chemrxiv-2022-nxb0c-v2 | Simplifying electrode design for lithium-ion rechargeable cells | In the race to improve lithium-ion cell manufacturing, societal impact is a chief concern as significant resources are required to meet increasing demands. Modified cell designs which employ foils and textiles may offer a scalable path to realizing sustainability. Here we demonstrate one possibility for a simplified lithium-ion energy storage device that utilizes a pre-lithiated aluminum foil anode and a carbon fiber cathode, potentially avoiding energy and cost-intensive production steps. | Tianye Zheng; Steven Boles | Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d4eca05819875b4944b4ca/original/simplifying-electrode-design-for-lithium-ion-rechargeable-cells.pdf |
66c8b149f3f4b05290dc2c29 | 10.26434/chemrxiv-2024-qd9kk | Catalytic coupling of 1,4-benzenedimethanol with ethanol for alcohol upgradation | We report here a catalytic method to upgrade 1,4-benzenedimethanol to 3-(4-(hydroxymethyl)phenyl)propan-1-ol via coupling of 1,4-benzenedimethanol with ethanol using a ruthenium catalyst. Through systematic optimization of catalytic conditions, a high TON of 400,000 has been achieved. Based on previous studies and those reported herein, we suggest that the reaction proceeds via a hydrogen-borrowing mechanism in a Guerbet-style process. | Chandrika Ghosh; Amit Kumar | Catalysis; Organometallic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c8b149f3f4b05290dc2c29/original/catalytic-coupling-of-1-4-benzenedimethanol-with-ethanol-for-alcohol-upgradation.pdf |
60c75456ee301cbe4bc7af4c | 10.26434/chemrxiv.13647920.v1 | Ab Initio Metadynamics Calculations Reveal Complex Interfacial Effects in Acetic Acid Deprotonation Dynamics | Acid-base reactions play a central role in solution chemistry, with carboxylic acids being particularly important in atmospheric chemical processes. In this work, we harness metadynamics calculations with Born-Oppenheimer molecular dynamics (BOMD) simulations to understand deprotonation dynamics of acetic acid (CH<sub>3</sub>COOH) in both bulk and air-water interfacial environments. Collective variables are carefully chosen in our well-tempered metadynamics simulations to capture the deprotonation process in various aqueous configurations. Our findings show that the free energy barrier for deprotonation of acetic acid at the air-water interface is lower than in the bulk, in accordance with the available experimental data. Furthermore, our well-tempered metadynamics calculations suggest that the variations in free energy are primarily due to intricate solvation shell effects. | Sohag Biswas; Bryan Wong | Computational Chemistry and Modeling; Theory - Computational; Chemical Kinetics; Interfaces; Physical and Chemical Processes; Quantum Mechanics; Solution Chemistry; Statistical Mechanics; Structure; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75456ee301cbe4bc7af4c/original/ab-initio-metadynamics-calculations-reveal-complex-interfacial-effects-in-acetic-acid-deprotonation-dynamics.pdf |
60c75793702a9b15d318cb0c | 10.26434/chemrxiv.12725276.v2 | Teaching a Neural Network to Attach and Detach Electrons from Molecules | <p></p><p>Physics-inspired Artificial Intelligence (AI) is at the forefront
of methods development in molecular modeling and computational chemistry. In
particular, interatomic potentials derived with Machine Learning algorithms
such as Deep Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum
mechanical (QM) methods in areas traditionally dominated by empirical force
fields and allow performing massive simulations. The applicability domain of DNN
potentials is usually limited by the type of training data. As such, transferable
models are aimed to be extensible in the description of chemical and conformational
diversity of organic molecules. However, most DNN potentials, such as the AIMNet
model we proposed previously, were parametrized for neutral molecules or closed-shell
ions due to architectural limitations. In this work, we extend machine learning
framework toward open-shell anions and cations. We introduce AIMNet-NSE (Neural
Spin Equilibration) architecture, which being properly trained, could predict
atomic and molecular properties for an arbitrary combination of molecular
charge and spin multiplicity. This model explores a new dimension of
transferability by adding the charge-spin space. The AIMNet-NSE model is
capable of reproducing reference QM energies for cations, neutrals, and anions
with errors of about 2-3 kcal/mol, compared to the reference QM simulations.
The spin-charges have errors ~0.01 electrons for small organic molecules containing
nine chemical elements {H, C, N, O, F, Si, P, S and Cl}. <a>The
AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization
potential, electron affinity, and conceptual Density Functional Theory
quantities like electronegativity, hardness, and condensed Fukui functions with
a speed up to 10<sup>4</sup> molecules per second on a single modern GPU.</a> We
show that these descriptors, along with learned atomic representations, could
be used to model chemical reactivity through an example of regioselectivity in
electrophilic aromatic substitution reactions.</p><p></p> | Roman Zubatyuk; Justin Smith; Benjamin T. Nebgen; Sergei Tretiak; Olexandr Isayev | Physical Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75793702a9b15d318cb0c/original/teaching-a-neural-network-to-attach-and-detach-electrons-from-molecules.pdf |
674484035a82cea2fac1d9df | 10.26434/chemrxiv-2023-9wnb8-v2 | DNA Mimic Foldamer Recognition of a Chromosomal Protein | Helical aromatic oligoamide foldamers bearing anionic side chains that mimic the overall shape and charge surface distribution of DNA were synthesized. Their interactions with chromosomal protein Sac7d, a non-sequence-selective DNA-binder that kinks DNA, were investigated by Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC), Circular Dichroism spectroscopy (CD), melting curve analysis, Atomic Force Microscopy (AFM), and Nuclear Magnetic Resonance (NMR), as well as by single crystal X-ray crystallography. The foldamers were shown to bind to Sac7d better than a DNA duplex of comparable length. The interaction is diastereoselective and takes place at the DNA binding site. Crystallography revealed that the DNA mimic foldamers have a binding mode of their own and that they can bind to Sac7d without being kinked. | Deepak Deepak; Jiaojiao Wu; Valentina Corvaglia; Lars Allmendinger; Michael Scheckenbach; Philip Tinnefeld; Ivan Huc | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674484035a82cea2fac1d9df/original/dna-mimic-foldamer-recognition-of-a-chromosomal-protein.pdf |
61f11b1f8d70c397a10e44d8 | 10.26434/chemrxiv-2021-pgxq1-v2 | Olefin-surface interactions: a key activity parameter in silica-supported olefin metathesis catalysts | Molecularly defined and classical heterogenous Mo-based metathesis catalysts are shown to display dis-tinct and unexpected reactivity patterns for the metathesis of long-chain α-olefins at low temperatures (< 100 °C). Namely, catalysts based on supported Mo oxo species, whether prepared via wet impregnation or surface organometallic chemistry (SOMC), exhibit strong activity dependencies on the α-olefin chain length, with slower reaction rates for longer substrate chain lengths. In contrast, molecular and support-ed Mo alkylidenes are highly active and do not display such dramatic dependence on chain length. State-of-the-art 2D solid-state NMR analyses of post-metathesis catalysts, complemented by FTIR and molecular dynamics calculations, evidence that the activity decrease observed for supported Mo oxo catalysts relates to the strong adsorption of internal olefin metathesis products due to interactions with surface Si-OH groups. Overall, this study shows that in addition to the nature and the number of active sites, the metathesis rates and overall catalytic performance depend on product desorption, even in the liquid phase with non-polar substrates. This study further highlights the role of support and active site composition and dynamics on activity as well as the need to consider adsorption in catalyst design. | Zachariah Berkson; Moritz Bernhardt; Simon Schlapansky; Mathis Benedikter; Michael Buchmeiser; Gregory Price; Glenn Sunley; Christophe Copéret | Physical Chemistry; Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f11b1f8d70c397a10e44d8/original/olefin-surface-interactions-a-key-activity-parameter-in-silica-supported-olefin-metathesis-catalysts.pdf |
616650b1a3d2c919f0d4f5fa | 10.26434/chemrxiv-2021-9q5xr | Immunotargeting of Nanocrystals by SpyCatcher Conjugation of Engineered Antibodies | Inorganic nanocrystals such as quantum dots (QDs) and upconverting nanoparticles (UCNPs) are uniquely suited for quanti-tative live-cell imaging and are typically functionalized with ligands to study specific receptors or cellular targets. Antibod-ies (Ab) are among the most useful targeting reagents owing to their high affinities and specificities, but common nanocrys-tal labeling methods may orient Ab incorrectly, be reversible or denaturing, or lead to Ab-NP complexes too large for some applications. Here, we show that SpyCatcher proteins, which bind and spontaneously form covalent isopeptide bonds with cognate SpyTag peptides, can conjugate engineered Ab to nanoparticle surfaces with control over stability, orientation, and stoichiometry. Compact SpyCatcher-functionalized QDs and UCNPs may be labeled with short-chain variable fragment Ab (scFv) engineered to bind urokinase-type plasminogen activator receptors (uPAR) that are overexpressed in many human can-cers. Confocal imaging of anti-uPAR scFv-QD conjugates shows the Ab mediates specific binding and internalization by breast cancer cells expressing uPAR. Time-lapse imaging of photostable scFv-UCNP conjugates show that Ab binding caus-es uPAR internalization with a ∼20-minute half-life on the cell surface, and uPAR is internalized to endolysosomal com-partments distinct from general membrane stains and without significant recycling to the cell surface. The controlled and stable conjugation of engineered Ab to NPs enables targeting of diverse receptors for live-cell study of their distribution, trafficking, and physiology. | Cassio Pedroso; Victor Mann; Kathrin Zuberbühler; Markus-Frederik Bohn; Jessica Yu; Virginia Altoe; Charles Craik; Bruce Cohen | Biological and Medicinal Chemistry; Nanoscience; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616650b1a3d2c919f0d4f5fa/original/immunotargeting-of-nanocrystals-by-spy-catcher-conjugation-of-engineered-antibodies.pdf |
60c75854bb8c1aaf843dc9e5 | 10.26434/chemrxiv.14410967.v2 | Phosphorene–Fullerene Nanostructures: A First-Principles Study | Hybrid materials formed by carbon fullerenes and layered materials have emerged due to their advantages for several technological applications, and phosphorene arises as a promising two-dimensional semiconductor for C60 adsorption. However, the properties of phosphorenefullerene hybrids remain mainly unexplored. In this work, we employed density functional theory to obtain structures, adsorption energies, electronic/optical properties, binding (AIM, NBO), and energy decomposition analyses (ALMO-EDA) of nanostructures formed by phosphorene and fullerenes (C24 to C70). We find fullerenes form covalent and non-covalent complexes with phosphorene depending on the molecular size, showing remarkable stability even in solution. Two classes of covalent complexes arise by cycloaddition-like reactions: the first class, where short-range effects (charge-transfer and polarization) determines the stability; and the second one, where short-range effects decay to avoid steric repulsion, and balanced longrange forces (electrostatics and dispersion) favors the stability. Otherwise, high-size fullerenes (C50 to C70) only form non-covalent complexes due to strong repulsion at shorter intermolecular distances and lack of dissociation barriers. In terms of electronic properties, fullerenes act as mild p-dopants for phosphorene, increasing its polar character and ability to acquire induced dipole moments (polarizability). Also, small energy-bandgap fullerenes (<0.8 eV) largely increase the phosphorene metallic character. We also note fullerenes retain their donor/acceptor properties upon adsorption, acting as active sites for orbital-controlled interactions and maximizing the phosphorene light absorbance at the UV-Vis region. Finally, we strongly believe our study will inspire future experimental/theoretical studies focused on phosphorene-fullerene uses for storage, anode materials, sensing, phosphorene bandgap engineering, and optoelectronics.<br /> | Diego Cortes-Arriagada; Daniela E. Ortega | Aggregates and Assemblies; Alloys; Carbon-based Materials; Composites; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Optical Materials; Photosensitizers; Thin Films; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75854bb8c1aaf843dc9e5/original/phosphorene-fullerene-nanostructures-a-first-principles-study.pdf |
66907948c9c6a5c07a06c8b0 | 10.26434/chemrxiv-2024-d26cx | Nickel-Catalyzed Arylative Telomerization of Isoprene | Developing new transformations of bulk chemicals is an important approach to expand the reaction boundary of current chemistry. Instead of traditional hydroarylation of dienes, we herein demonstrated a nickel-catalyzed arylative telomerization of isoprene with high chemo- and regioselectivities. By utilizing a bulky mono-phosphine ligand, a range of structurally diverse aryl substituted
terpenes was created efficiently under redox-neutral conditions. Preliminary mechanistic studies suggest this telomerization proceeds through an oxidative cyclometallation of isoprene with Ni(0) species followed by arylation with organoboron reagents. This work not only
offers a new transformation of isoprene, but also provides a complementary approach for the creation of unnatural monoterpenoids. | Xiao-Yu Wang; Bing-Zhi Chen; Su-Yang Xu; Xue-Ting Li; Yan Liu; Ding-Wei Ji; Qing-An Chen | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66907948c9c6a5c07a06c8b0/original/nickel-catalyzed-arylative-telomerization-of-isoprene.pdf |
60c74020337d6c5bbee2664c | 10.26434/chemrxiv.7634849.v1 | Synthesis of Simplified Azasordarin Analogs as Potential Antifungal Agents | A new series of simplified azasordarin analogs was synthesized using as key steps a Diels-Alder reaction to generate a highly substituted bicyclo[2.2.1]heptane core, followed by a subsequent nitrile alkylation. Several additional strategies were investigated for the generation of the key tertiary nitrile or aldehyde thought to be required for activity at the fungal protein eukaryotic elongation factor 2. This new series also features a morpholino glycone previously reported in semisynthetic sordarin derivatives with broad spectrum antifungal activity. Despite a lack of activity against <i>C. albicans </i>for these early de novo analogs, the synthetic route reported here permits more comprehensive modifications of the bicyclic core, and SAR studies that were not heretofore possible. | Yibiao Wu; Chris Dockendorff | Natural Products; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74020337d6c5bbee2664c/original/synthesis-of-simplified-azasordarin-analogs-as-potential-antifungal-agents.pdf |
65eff684e9ebbb4db9853ae1 | 10.26434/chemrxiv-2024-mw90x | What leads to direct epoxidation? An exhaustive DFT investigation of electrophilic oxygen mediated epoxidation of ethylene on Ag(100) | Extensive research has contributed to a better understanding of the commercially important epoxidation reaction. Selectivity, a crucial aspect of this reaction, has re- ceived significant attention in both experimental and theoretical investigations. How- ever, a consensus regarding the role of electrophilic oxygen in epoxidation is yet to be reached. The present study is a theoretical examination of the prerequisites necessary for direct epoxidation to occur on the Ag(100) surface, at varied monolayer concentra- tions. Additionally, the study investigates the characteristics of various oxygen species interacting with ethylene to promote the direct epoxidation pathway. Based on the effective charges and projected density of states (pDOS) analysis, three oxygen vari- ants were identified on the Ag(100) surface: atomic oxygen, dissociatively adsorbed molecular oxygen, and O3 . The investigation reveals that all oxygen species, despite their physical and electronic differences, are electrophilic and undergo direct epoxida- tion. This work provides insights into the complex nature of epoxidation reaction and discusses electronic factors influencing the selective oxidation route on different Ag-O complexes. | Aathira Nair; Kavita Joshi | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eff684e9ebbb4db9853ae1/original/what-leads-to-direct-epoxidation-an-exhaustive-dft-investigation-of-electrophilic-oxygen-mediated-epoxidation-of-ethylene-on-ag-100.pdf |
60c747bb842e656d08db2a02 | 10.26434/chemrxiv.10029599.v2 | A Mechanistic Understanding of Non-Classical Crystal Growth in Hydrothermally Synthesized Sodium Yttrium Fluoride Nanowires | Sodium yttrium fluoride (NaYF<sub>4</sub>) is an upconverting material with many potential
uses in chemistry, materials science, and biology that can be synthesized hydrothermally
in both cubic (α) and hexagonal (β) crystallographic polymorphs. Understanding the
mechanisms underlying the phase conversion between the cubic and hexagonal polymorphs is of great interest to help inform future efforts to synthesize atomically-precise
quantum materials with well-defined sizes and morphologies. In this work, we use
a combination of analytical transmission electron microscopy (TEM),
scanning transmission electron microscopy (STEM), powder X-ray diffraction (XRD),
in situ liquid cell TEM, atom probe tomography (APT), and extended x-ray absorption
fine structure (EXAFS) measurements to show evidence suggesting that the hexagonal
NaYF<sub>4</sub> nanowires form through a non-classical crystal growth mechanism involving the formation and subsequent oriented attachment of mesocrystals consisting of cubic (α) plase units. EXAFS spectroscopy also suggests
that substitutional Yb<sup>3+</sup> point defects within NaYF<sub>4</sub> are distributed evenly throughout
the crystal lattice without clustering, and also that they may exhibit selective substitution into one
of the two possible trivalent yttrium sites in the unit cell for hydrothermally synthesized NaYF<sub>4</sub>. | Alex Bard; Xuezhe Zhou; Xiaojing Xia; Guomin Zhu; Matthew Lim; Seung Min Kim; Matthew Johnson; Justin Kollman; Matthew Marcus; Steven Spurgeon; Daniel Perea; Arun Devaraj; Jaehun Chun; James De Yoreo; Peter Pauzauskie | Aggregates and Assemblies; Ceramics; Nanostructured Materials - Materials; Optical Materials; Microscopy; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Lanthanides and Actinides; Solid State Chemistry; Structure; Surface; Crystallography; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747bb842e656d08db2a02/original/a-mechanistic-understanding-of-non-classical-crystal-growth-in-hydrothermally-synthesized-sodium-yttrium-fluoride-nanowires.pdf |
60c740d1337d6c80c8e26791 | 10.26434/chemrxiv.7836584.v1 | Tissue Scaffolds with Nanoscale Hybrid Coating Shining New Lights on Multi-Modal Bone Targeted Therapeutics | <p>The challenging post-surgery management of bone
metastasis sees the needs for multi-functional bone scaffolds that offer multi-modal
therapeutic functions. Through a nature-inspired layer-by-layer assembly
process, we developed a unique multi-functional tissue scaffold that consists
of porous polyurethane substrate and nanoscale chitosan/ graphene oxide hybrid coating.
Alternative layers of drug laden chitosan and graphene oxide nanosheets were
held together through strong electrostatic interaction, giving rise to a robust
multilayer architecture with control over structural element orientation and
chemical composition at nanoscale. For the first time, proof-of-concept on
combining pH-controlled co-delivery of multiple therapeutic agents and
photothermal therapy have demonstrated, in the context of malignant bone cancer
treatment. Our scaffold system can be tailored to the patient’s specific needs
through loading of bespoke therapeutic agents and offering on-demand photothermal
therapy. The methodology can also be generalized to create functional surfaces
for a wide range of biomedical devices as well as for applications beyond healthcare
technology.</p> | Zhijun Guo; Nan Jiang; Jessical moore; Colin McCoy; Monika Ziminska; Cormac Rafferty; Andrew Hamilton; Yubao Li; Li Zhang; Songsong Zhu; Gianluca Sarri; dan Sun | Biocompatible Materials; Biological Materials; Nanostructured Materials - Materials; Bioengineering and Biotechnology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740d1337d6c80c8e26791/original/tissue-scaffolds-with-nanoscale-hybrid-coating-shining-new-lights-on-multi-modal-bone-targeted-therapeutics.pdf |
669779055101a2ffa89cd4ba | 10.26434/chemrxiv-2024-rlsf8 | Molecular alloying drives valence change in a van der Waals antiferromagnet | Bespoke van der Waals (vdW) crystals provide control over the generation, confinement, and transport of charge, spin, light, and heat within and between atomically precise two-dimensional (2D) layers. We report a novel functionality in vdW crystals by actuating valence changes in a metal-organic antiferromagnet through molecular alloying. The quadratic net materials Cr(pyz)2Br2 and Cr(pyz)2I2 (pyz = pyrazine) are aliovalent, with different Cr(III) and Cr(II) oxidation states due to disparate crystal field potentials induced by I– and Br–. Applying isotropic pressure compresses the layers in Cr(pyz)2I2 significantly (16% at 1.5 GPa), but no Cr valence change is induced by mechanical strengthening of the axial crystal field. However, the alloyed, solid solutions Cr(pyz)2I2–xBrx exhibit quantitative, hysteretic, and tunable Cr(II) ⇄ Cr(III) interconversions with concomitant charge injection into the organic scaffold. This valence change, driven by the larger chemical pressure exerted by Br– over I–, manifests drastic changes to the magnetization and electrical conductivity, which varies by up to five orders of magnitude across the transition. The use of reticular coordination chemistry addresses a current gap in vdW and 2D materials science, where electronic structure engineering via valence change events has remained elusive. The concept of molecular alloying in vdW crystals expands the functionalities for future magnetoelectronics with drastically different electronic and magnetic states interchangeable by mild external stimuli. | Frédéric Aribot; Laura Voigt; Maja A. Dunstan; Wenjie Wan; James N. McPherson; Mariusz Kubus; Nathan J. Yutronkie; Charles J. McMonagle; Marco Coletta; Anna S. Manvell; Anton Viborg; Siena Wong; Kirstine A. Stampe; Volodymyr Baran; Anatoliy Senyshyn; Manh Duc Le; Helen C. Walker; Amit Chanda; Felix Trier; Nini Pryds; Fabrice Wilhelm; Michael R. Probert; Niels B. Christensen; Euan K. Brechin; Andrei Rogalev; Kasper S. Pedersen | Physical Chemistry; Materials Science; Inorganic Chemistry; Magnetic Materials; Coordination Chemistry (Inorg.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669779055101a2ffa89cd4ba/original/molecular-alloying-drives-valence-change-in-a-van-der-waals-antiferromagnet.pdf |
6122751251cfec491e978ca8 | 10.26434/chemrxiv-2021-lh8jp | Photo-induced degradation of PFASs: Excited-state mechanisms from real-time time-dependent density functional theory | Per- and polyfluoroalkyl substances (PFASs) are hazardous, carcinogenic, and bioaccumulative contaminants found in drinking water sources. To mitigate and remove these persistent pollutants, recent experimental efforts have focused on photo-induced processes to accelerate their degradation; however, the mechanistic details of these promising degradation processes remain unclear. To shed crucial insight on these electronic-excited state processes, we present the first study of photo-induced degradation of explicitly-solvated PFASs using excited-state, real-time time-dependent density functional theory (RT-TDDFT) calculations. Furthermore, our large-scale RT-TDDFT calculations show that these photo-induced excitations can be highly selective by enabling a charge-transfer process that only dissociates the C–F bond while keeping the surrounding water molecules intact. Collectively, the RT-TDDFT techniques used in this work (1) enable a new capability for probing photo-induced mechanisms that cannot be gleaned from conventional ground-state DFT calculations and (2) provide a rationale for understanding ongoing experiments that are actively exploring photo-induced degradation of PFAS and other environmental contaminants. | Sharma Yamijala; Ravindra Shinde; Kota Hanasaki; Zulfikhar Ali; Bryan Wong | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Photochemistry (Physical Chem.); Quasiparticles and Excitations | CC BY 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6122751251cfec491e978ca8/original/photo-induced-degradation-of-pfa-ss-excited-state-mechanisms-from-real-time-time-dependent-density-functional-theory.pdf |
60f91c95d03b3db7eb023362 | 10.26434/chemrxiv-2021-q8whq-v2 | Molecular scale chemical imaging of the orientation of an on-surface coordination complex by tip-enhanced Raman spectroscopy | Metal-organic coordination structures at interfaces play an essential role in many biological and chemical systems. Understanding the molecular specificity, orientation and spatial distribution of the coordination complexes at the nanometer scale is of great im-portance for effective molecular engineering of nanostructures and fabrication of functional devices with controllable properties. However, fundamental properties of such coordination systems are still rarely studied directly. In this work, we present a spectro-scopic approach on the basis of tip-enhanced Raman spectroscopy (TERS) to investigate a cobalt(II) tetraphenyl-porphyrine (CoTPP) coordination species on the scale of a single molecule under ambient conditions. Coordination species anchored on gold surfaces modified with pyridine thiol self-assembled monolayers can be spectroscopically distinguished and mapped with ca. 2 nm resolution. In addition, in combination with density functional theory simulations, the adsorption configuration and molecular ori-entation of the coordination complexes are also revealed using TERS imaging. | Zhen-Feng Cai; Li-Qing Zheng; Yao Zhang; Renato Zenobi | Physical Chemistry; Nanoscience; Interfaces; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f91c95d03b3db7eb023362/original/molecular-scale-chemical-imaging-of-the-orientation-of-an-on-surface-coordination-complex-by-tip-enhanced-raman-spectroscopy.pdf |
663a34f4418a5379b0aba4b1 | 10.26434/chemrxiv-2024-z0bgc | Surface chemistry in atomic layer deposition of AlN thin films from Al(CH3)3 and NH3 studied by mass spectrometry | Aluminum nitride (AlN) is a semiconductor with a very wide band gap and a potential dielectric material. Deposition of thin AlN films is routinely done by several techniques, including atomic layer deposition (ALD). In this study, we deposited AlN using ALD with trimethylaluminum (TMA) as the Al precursor and ammonia (NH3) with and without plasma activation as the N precursor in the temperature range from 100 to 400 °C while monitoring the surface reactions using mass spectrometry. Our results, combined with recent quantum chemical modelling, suggest that the surface chemistry of the deposition process is chemisorption of TMA followed by reductive elimination of the methyl groups to render mono methyl aluminum species. The NH3 chemisorption is done by ligand exchange to form CH4 and an -NH2 terminated surface. | Pamburayi Mpofu; Houyem Hafdi; Pentti Niiranen; Jonas Lauridsen; Oscar Alm; Tommy Larsson; Henrik Pedersen | Physical Chemistry; Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Physical and Chemical Processes; Surface; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663a34f4418a5379b0aba4b1/original/surface-chemistry-in-atomic-layer-deposition-of-al-n-thin-films-from-al-ch3-3-and-nh3-studied-by-mass-spectrometry.pdf |
64e7b1c63fdae147fabf71f2 | 10.26434/chemrxiv-2023-jgc8g | Orchestrating nimble experiments across interconnected labs | Advancements in artificial intelligence (AI) for science are continually expanding the value proposition for automation in materials and chemistry experiments. The advent of hierarchical decision-making also motivates automation of not only the individual measurements but also the coordination among multiple research workflows. In a typical lab or network of labs, workflows need to independently start and stop operation while also sharing resources such as centralized or multi-functional equipment. A new paradigm in instrument control is needed to realize the combination of independence with respect to periods of operation and interdependence with respect to shared resources. We present Hierarchical Experimental Laboratory Automation and Orchestration with asynchronous programming (HELAO-async), which is implemented via the Python asyncio package by abstracting each resource manager and experiment orchestrator as a FastAPI server. This framework enables coordinated workflows of adaptive experiments, which will elevate Materials Acceleration Platforms (MAPs) from islands of accelerated discovery to the AI emulation of team science. | Dan Guevarra; Kevin Kan; Yungchieh Lai; Ryan Jones; Lan Zhou; Phillip Donnelly; Matthias Richter; Helge Stein; John Gregoire | Materials Science; Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e7b1c63fdae147fabf71f2/original/orchestrating-nimble-experiments-across-interconnected-labs.pdf |
6577390dfd283d7904c66378 | 10.26434/chemrxiv-2023-t446q | Optimal ionomer interaction resolved by operando X-ray Absorption Spectroscopy and gas sorption analysis | To bridge the gap between oxygen reduction electrocatalysts development and their implementation in real proton exchange membrane fuel cell electrodes, an important aspect to be understood is the interaction between the carbon support, the active sites, and the proton conductive ionomer as it greatly affects the local transportations to the catalyst surface. To gain a deeper understanding of the catalyst-ionomer interaction, three Pt/C catalysts were prepared with the same polyol method using three different carbon support: low surface area Vulcan carbon, high surface area Ketjenblack carbon and in-house developed ordered mesoporous carbon. The Pt/C catalysts supported on ordered mesoporous carbon derived from biomass showed the best performance under the gas diffusion electrode configuration. Through a unique approach of operando X-ray Absorption Spectroscopy (XAS) combined with gas sorption analysis, we were able to demonstrate the beneficial effect of mesopore presence for optimal ionomer-catalyst interaction at both molecular and structural level. | Mengnan Wang; Jiaguang Zhang; Silvia Favero; Hui Luo; Luke Higgins; Ifan.E.L. Stephens ; Maria-Magdalena Titirici | Catalysis; Energy; Electrocatalysis; Fuel Cells; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6577390dfd283d7904c66378/original/optimal-ionomer-interaction-resolved-by-operando-x-ray-absorption-spectroscopy-and-gas-sorption-analysis.pdf |
620ee98249bd322010543de9 | 10.26434/chemrxiv-2022-vpq96 | Exhaustive catalytic ortho-alkoxylation of azobenzenes: flexible access to functionally diverse yellow-light-responsive photoswitches | We develop the first method for catalytic, exhaustive ortho-alkoxylation of azobenzene photoswitches. Alkoxylation is known to improve the photoswitch properties that control azobenzenes' success in chemical biology or materials sciences: e.g. better completeness of both E→Z and Z→E photoisomerisations, and >100 nm red-shifting of photoresponse. Our method enables straightforward late-stage diversification of photoswitches with interesting functional handles. We showcase four applications, using it to rationally tune lipophilicity, prepare isotopic tracers for metabolism studies, install full water solubility without ionic charges, and efficiently access previously difficult mixed-substituent photoswitches. We also identified a previously unstudied mixed-substituent tetra-ortho-family, difluoro-dialkoxy-azobenzenes, whose photoresponse can outperform previous 'gold standard' tetrafluoro-, dichloro-difluoro-, and tetrachloro-azobenzenes in significant ways. We thus expect that both the scaffolds we showcase and the method we develop will impact broadly on photochemistry and photopharmacology. | Adrian Müller-Deku; Oliver Thorn-Seshold | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2022-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620ee98249bd322010543de9/original/exhaustive-catalytic-ortho-alkoxylation-of-azobenzenes-flexible-access-to-functionally-diverse-yellow-light-responsive-photoswitches.pdf |
60c756704c89192caaad4854 | 10.26434/chemrxiv.14216561.v1 | Synergistic Use of FTIR Spectroscopy and TG to Elucidate the Solid State THCA Decarboxylation Reaction Kinetics in THCA Standard and Cannabis Flower | <p>The decarboxylation of
Δ9-tetrahydrocannabinolic acid (THCA) plays pivotal role in the potency of
medical cannabis and its extracts. However, the literature data point out
substantial variations in the process reaction rate and conversion efficacy due
to variability of the temperature, heat transfer efficacy, raw material
attributes, consequently resulting in incomplete decarboxylation, cannabinoid
content decrease due to decomposition, evaporation, and possible side
reactions. Our present work aims to draw attention to mid-infrared (MIR)
spectroscopy for in-situ monitoring and decipher the THCA decarboxylation
reaction in the solid state. The initial TG/DTG curves of THCA, for a first
time outlined the solid-solid decarboxylation dynamics, defined the endpoint of
the process and the temperature of the maximal conversion rate, which aided in
the design of the further IR experiments. Temperature controlled IR
spectroscopy experiments were performed on both THCA standard and cannabis
flower by providing detailed band assignment and conducting spectra-structure
correlations, based on the concept of functional groups vibrations. Moreover, a
multivariate statistical analysis was employed to depict the spectral regions
of utmost importance for the THCA→THC interconversion process. The principal
component analysis model was reduced to two PCs, where PC1 explained 94.76% and
98.21% of the total spectral variations in the THCA standard and in the plant
sample, respectively. The PC1 plot score of the THCA standard, as a function of
the temperature, neatly complemented to the TG/DTG curve and enabled
determination of rate constants for the decarboxylation reaction undertaken on
several temperatures. Consequently, a progress in elucidation of kinetic models
of THCA decarboxylation, fitting experimental data for both, solid state
standard substance and a plant flower, was achieved. The results open the horizon
to promote an appropriate process analytical technology (PAT) in the outgrowing
medical cannabis industry.</p> | Olga Gigopulu; Nikola Geskovski; Gjoshe Stefkov; Veronika Stoilkovska Gjorgievska; Irena Slaveska Spirevska; Christian Huck; Petre Makreski | Analytical Chemistry - General; Chemoinformatics; Spectroscopy (Anal. Chem.); Pharmaceutical Industry; Process Control | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756704c89192caaad4854/original/synergistic-use-of-ftir-spectroscopy-and-tg-to-elucidate-the-solid-state-thca-decarboxylation-reaction-kinetics-in-thca-standard-and-cannabis-flower.pdf |
63e53c7ffcfb27a31f7dd8d4 | 10.26434/chemrxiv-2023-gcmkh | Comparing the emission reduction effectiveness of continuous monitoring to periodic Optical Gas Imaging surveys for methane emissions at oil and gas production sites | Periodic methane emission screening using Optical Gas Imaging (OGI), or other short duration emission detection methods, is used at oil and gas facilities to detect and mitigate leaks and large emission events. Use of continuous monitoring systems can provide more rapid detection of emission events than periodic screening and, if responses to the detection of large emission events is rapid, the use of continuous emission monitoring can reduce the frequency of periodic screening required to achieve a targeted level of emission reductions. A hypothetical case study of oil and gas production sites in the Permian Basin shows that the deployment of one continuous sensor per site with a rapid response to only the single largest emission event occurring across 100 sites would allow screening frequency to be cut in half (quarterly to semi-annual), while preserving an equivalent amount of emission reductions. | Colette Schissel; Qining Chen; Erin Tullos; Arvind Ravikumar; David Allen | Energy; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e53c7ffcfb27a31f7dd8d4/original/comparing-the-emission-reduction-effectiveness-of-continuous-monitoring-to-periodic-optical-gas-imaging-surveys-for-methane-emissions-at-oil-and-gas-production-sites.pdf |
6537df6187198ede072cb5ac | 10.26434/chemrxiv-2023-lbdrm | Exploration of elastic moduli of molecular crystals via database screening by pretrained neural network potential | This paper presents the database screening of elastic moduli of molecular crystals using a pretrained neural network potential. The calculated elastic moduli were sufficiently consistent with experiment values, better than Hartree-Fock calculations. The database screening suggested crystals with large and small moduli. | Takuya Taniguchi | Theoretical and Computational Chemistry; Materials Science; Elastic Materials; Machine Learning; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6537df6187198ede072cb5ac/original/exploration-of-elastic-moduli-of-molecular-crystals-via-database-screening-by-pretrained-neural-network-potential.pdf |
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