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60c74f13842e651a82db378a | 10.26434/chemrxiv.11864934.v2 | Expanding the Family of Tetrahalide Iron Complexes: Synthesis, Structure and Biological Applications. | A
neutral octahedral mononuclear iron(II) tetrabromide complex, [Fe(Hampy)<sub>2</sub>Br<sub>4</sub>], that consists of equatorial bromide and
protonated aminopyrazinium axial ligands is successfully synthesised through
redox chemistry and analysed using X-ray crystallography. The iron(II)
oxidation state is balanced by the protonated pyrazinium nitrogen just outside
the coordination sphere. The biological properties of this and two other
related complexes are investigated using both Gram-negative and Gram-positive
bacteria as well as methicillin resistant strains. They all exhibit some
antimicrobial properties albeit at moderate to poor concentrations. However,
the tetrahalide complexes analysed exhibit excellent anti biofilm properties
well below cytotoxic levels. | Nusrat Abedin; Abdullah Hamed A Alshehri; Ali M A Almughrbi; Olivia Moore; Sheikh Alyza; Elizabeth Rusbridge; Naqash Masood; Biola Egbowon; Alan J. Hargreaves; Anthony Fitzpatrick; Felix Dafhnis-Calas | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f13842e651a82db378a/original/expanding-the-family-of-tetrahalide-iron-complexes-synthesis-structure-and-biological-applications.pdf |
6332341fba8a6d43695e3b14 | 10.26434/chemrxiv-2022-961zc | Advanced insights towards electrochemical urea synthesis: Strategic design and techno–commercial compatibility | The industrial production of urea involves two sequential steps, reaction of nitrogen and hydrogen to form ammonia followed by the reaction of the ammonia with carbon dioxide, so the process is capital expensive, massive energy consuming and complex synthesis process with multiple cycles to increase the production efficiency. The electrocatalytic C–N coupling reaction to specifically produce urea by simultaneous activation followed by co-reduction of carbon dioxide (CO2) and nitrogen sources (N2, NO2– or NO3–) at ambient condition presents a sustainable and eco-friendlier alternate route for urea production by a single step process. However, there are several challenges like adsorption capabilities of the reactants on the substrates followed by activation, suppression of hydrogen evolution reaction and finally effective C–N bond formation to specifically produce urea. In this work we showcase the road map of the electrocatalytic green urea production, with concise yet precise discussion on potential electrocatalyst, electrochemical working cell, mechanistic insight of urea synthesis, techno–commercial aspects and finally conclude with the future prospect of the green urea production. | Sourav Paul; Ashadul Adalder; Uttam Kumar Ghorai | Physical Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Electrocatalysis; Heterogeneous Catalysis; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6332341fba8a6d43695e3b14/original/advanced-insights-towards-electrochemical-urea-synthesis-strategic-design-and-techno-commercial-compatibility.pdf |
60c7563fbdbb8919ffa3a9a8 | 10.26434/chemrxiv.14219999.v1 | Multiplexed Flow Cytometric Approach for Detection of Anti-SARS-CoV-2 IgG, IgM and IgA Using Beads Covalently Coupled to the Nucleocapsid Protein | <p>Flow cytometry has emerged as a promising technique for detection of
SARS-CoV-2 antibodies. In this study, we described a new methodology to detect
simultaneously IgG, IgM and IgA of SARS-CoV-2 nucleocapsid protein in human
serum by flow cytometry. The Nucleocapsid protein was covalently bound on functional
beads surface applying sulfo-SMCC chemistry. BUV395 anti-IgG, BB515 anti-IgM,
biotinylated anti-IgA1/IgA2 and BV421 streptavidin were used as fluorophore
conjugated secondary antibodies. Serum and antibodies reaction conditions were
optimized for each antibody isotype detection and a multiplexed detection assay
was developed. This new cell-free multiplex approach based on flow cytometry was
able to efficiently discriminate COVID-19 negative and positive samples. The
simultaneous detection of IgG, IgM and IgA showed a sensibility of 88.5-96.2%
and specificity of 100%. The combined detection of antibody isotypes offers
greater spectrum for detection and monitoring of COVID-19 vaccines and seroconversion.
This novel strategy opens a new avenue for flow cytometry-based diagnosis.</p> | Ingrid Fatima Zattoni; Luciano F. Huergo; Edileusa C. M. Gerhardt; Jeanine M. Nardin; Alexia Marques Fernandes dos Santos; Fabiane Gomes de Moraes Rego; Geraldo Picheth; Vivian Rotuno Moure; Glaucio Valdameri | Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7563fbdbb8919ffa3a9a8/original/multiplexed-flow-cytometric-approach-for-detection-of-anti-sars-co-v-2-ig-g-ig-m-and-ig-a-using-beads-covalently-coupled-to-the-nucleocapsid-protein.pdf |
640f375de53eff1af3111098 | 10.26434/chemrxiv-2023-6m43n | A route for long-term DNA preservation through nanoconfinement in smectites | Traces of DNA found in sediments are shifting paradigms in the analysis of past and present ecosystems. DNA is an unstable polymer and conditions at which the millennial stabilization is achieved are unclear. Confinement of DNA in nanopores of clay minerals is a promising route for this long-term stabilization and storage. Using smectites with various layer charges, we measured adsorption capacity for DNA using UV spectroscopy and intercalation capacity using X-ray diffraction. We found that while the smectite adsorption capacity is large, the DNA intercalation, i.e. nanoconfinement, decreases as smectite charge increases. We show that low-charge smectites intercalate DNA at concentrations relevant to aqueous environments even at neutral pH but the nanoconfinement is minimal or absent in high-charge smectites. Different intercalation behaviour in NaCl and CaCl2 solutions imply different mechanisms driven by electrostatic forces. Our results demonstrate that DNA nanoconfinement in smectites is likely an important strategy for DNA preservation and that protocols targeting low-charge smectites might improve the success of ancient and modern DNA extraction even in hot and humid climates so far deemed unfavourable for DNA preservation. | Stanislav Jelavic; Bruno Lanson; Nathaniel Findling; Martine Lanson | Physical Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry; Interfaces; Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2023-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640f375de53eff1af3111098/original/a-route-for-long-term-dna-preservation-through-nanoconfinement-in-smectites.pdf |
671950f583f22e4214effa9d | 10.26434/chemrxiv-2024-lkpzf | Valence tautomerism, non-innocence, and emergent magnetic phenomena in lanthanide-organic tessellations | Coordination networks based on lanthanide ions entangle collective magnetic phenomena, otherwise only observed in inorganic 4f materials, and the tunable spatial and electronic structure engineering intrinsic to coordination chemistry. We discuss the use of 2D-structure-directing linear {LnII/IIII2} nodes to direct the formation of polymeric coordination networks. The equatorial coordination plasticity of {LnII/IIII2} results in broad structural diversity, including previously unobtainable tessellations containing motifs observed in quasicrystalline tilings. The new phases host also magnetic frustration, which is at the origin of enhanced magnetic refrigeration potential. Finally, careful redox matching of Ln node and frontier orbitals of the ligand scaffold has culminated in the discovery of quantitative valence tautomeric conversion in a molecule-based Ln material, opening up new avenues for combining exotic magnetic phenomena with an encoded switch. | Maja Dunstan; Kasper Steen Pedersen | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671950f583f22e4214effa9d/original/valence-tautomerism-non-innocence-and-emergent-magnetic-phenomena-in-lanthanide-organic-tessellations.pdf |
60f11397446ac38b1b90b1b4 | 10.26434/chemrxiv-2021-rlr12 | Diarylation of N- and O-nucleophiles through a metal-free cascade reaction | The arylation of heteroatom nucleophiles is a central strategy to reach diarylated compounds that are key building blocks in agrochemicals, materials and pharmaceuticals. Nucleophilic aromatic substitution is a classical tool for such arylations, and hypervalent iodine-mediated arylations are modern alternatives to achieve a wider scope of products. Herein, we combine the benefits of those strategies to enable an atom-efficient and transition metal-free functionalization of N- and O- nucleophiles with two structurally different aryl groups, to provide di- and triarylamines and diaryl ethers in one single step (> 100 examples). The core of this strategy is the unique reactivity discovered with certain fluorinated diaryliodonium salts, which unveils novel reaction pathways in hypervalent iodine chemistry. The method is suitable for aliphatic amines, anilines, ammonia and even water and tolerates a wide variety of functional and protecting groups. Furthermore, the retained iodine substituent is easily accessible for derivatization of the products. | Erika Linde; David Bulfield; Gabriella Kervefors; Nibadita Purkait; Berit Olofsson | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f11397446ac38b1b90b1b4/original/diarylation-of-n-and-o-nucleophiles-through-a-metal-free-cascade-reaction.pdf |
60cc0648461f566219476bd8 | 10.26434/chemrxiv-2021-tx6q4 | COVID-19: ABC System and LBP-like Function of ORF7a Activate Monocytes to Induce Diabetes | Lipopolysaccharide activates the natural immune system response in obese and diabetic patients’ adipose tissue and increases the risk of susceptibility and severity of COVID-19. In this study, bioinformatics techniques such as domain search and molecular docking were used to study the relationship between the ORF7a protein of the SARS-COV-2 virus and lipopolysaccharide. The results show that the transmembrane protein ORF7a has ABC transporter domains: ATP binding and ABC transmembrane domains. ORF7a also has lipopolysaccharide synthesized domains. It bound the lipopolysaccharide synthesized by ORF7a to CD14 molecule through lipopolysaccharide-binding protein (LBP) to activate CD14+ monocytes. The extracellular ORF7a with the N-terminus and C-terminus cut off has a similar function of LBP, binding and activating CD14+ monocytes with the help of two ATP-binding structures. We speculated that more lipopolysaccharides also activated CD14+ monocytes to release various inflammatory factors, damaging adipose and vascular endothelial tissue to induce diabetes and hypertension. | liu wenzhong; li hualan | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cc0648461f566219476bd8/original/covid-19-abc-system-and-lbp-like-function-of-orf7a-activate-monocytes-to-induce-diabetes.pdf |
63cbfb0b6bc5ca4b7b15a6a2 | 10.26434/chemrxiv-2023-89jlx | General access to cubanes: ideal bioisosteres of ortho-, meta-, and para-substituted benzenes | The replacement of benzene rings with sp3-hybridized bioisosteres in drug candidates generally improves pharmacokinetic properties while retaining biological activity. Rigid, strained frameworks such as bicyclo[1.1.1]pentane and cubane are particularly well-suited since the ring strain imparts high bond strength and thus metabolic stability on its C–H bonds. Cubane is the ideal bioisostere since it provides the closest geometric match to benzene. At present, however, all cubanes in drug design, like almost all benzene bioisosteres, act solely as substitutes for mono- or para-substituted benzene rings. This is due to the difficulty of accessing 1,3- and 1,2-disubstituted cubane precursors. The adoption of cubane in drug design has been further hindered by the incompatibility of cross-coupling reactions with the cubane scaffold, owing to a competing metal-catalyzed valence isomerization. Herein, we disclose expedient routes to 1,3- and 1,2-disubstituted cubane building blocks using a convenient cyclobutadiene precursor and a photolytic C–H carboxylation reaction, respectively. Moreover, we leverage the slow oxidative addition and rapid reductive elimination of copper to develop C–N, C–C(sp3), C–C(sp2), and C–CF3 cross-coupling protocols. Our research enables facile elaboration of all cubane isomers into drug candidates thus enabling ideal bioisosteric replacement of ortho-, meta-, and para-substituted benzenes. | Mario P. Wiesenfeldt; James. A. Rossi-Ashton; Ian B. Perry; Johannes Diesel; Olivia L. Garry; Florian Bartels; Susannah C. Coote; Xiaoshen Ma; Charles S. Yeung; David Jonathan Bennett; David W. C. MacMillan | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cbfb0b6bc5ca4b7b15a6a2/original/general-access-to-cubanes-ideal-bioisosteres-of-ortho-meta-and-para-substituted-benzenes.pdf |
60c74ea0f96a00c432287b14 | 10.26434/chemrxiv.12740801.v2 | Substructure-based Neural Machine Translation for Retrosynthetic Prediction | <p>This work presents a new template-free neural machine translation method for retrosynthetic reaction prediction by learning the chemical change at a substructural level. The proposed method effectively solves all the translation issues arising from SMILES-based representation of molecular structures.</p> | Umit Ucak; Taek Kang; Junsu Ko; Juyong Lee | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ea0f96a00c432287b14/original/substructure-based-neural-machine-translation-for-retrosynthetic-prediction.pdf |
65b9e3ade9ebbb4db9551b68 | 10.26434/chemrxiv-2024-8smwg | From Canonical to Unique: Extension of A Lipophilicity Scale of Amino Acids to Non-Standard Residues | The lipophilicity of amino acids plays a pivotal role in determining their physicochemical properties as it gives an estimate of solubility, binding propensity, and bioavailability. Herein, we applied the IEFPCM/MST implicit solvation model to compute the n-octanol/water partition coefficient as lipophilic descriptor for non-standard amino acids. Thus, extending our previous work on the hydrophobicity scale of amino acids. To this end, we employed two structural models, named Model 1 and 2, differentiated solely by their C-terminal capping groups using an N- or O- methyl substituent, respectively. Our findings revealed substantial similarities between the models, validating the lipophilicity values for the non-standard side chains. Differences were observed in fewer cases, indicating an effect of the capping group on the side chain hydrophobicity. This effect is expected as one model contains an hydrogen bond donor (Model 1) while the other one uses an hydrogen bond acceptor (Model 2). Overall, both models exhibit strong correlations with the experimental values, with Model 1 showing lower statistical errors. In addition, our predictions were able to correctly predict the experimental hydrophobicity change due to the number of acetylated lysines in peptide pairs determined by HPLC, suggesting that our scale can be employed for proteomics studies that include post-translational modifications beyond acetylation. | Antonio Viayna; Paulina Matamoros; David Blázquez-Ruano; William J. Zamora Ramírez | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b9e3ade9ebbb4db9551b68/original/from-canonical-to-unique-extension-of-a-lipophilicity-scale-of-amino-acids-to-non-standard-residues.pdf |
61aabd37772cb220154f89cc | 10.26434/chemrxiv-2021-dkb6l | OH binding energy as a universal descriptor of the potential of zero charge on transition metal surfaces | The potential of zero charge (U_PZC) is an important quantity of metal-water interfaces that are central in many electrochemical applications. In this work, we use ab initio molecular dynamics (AIMD) simulations to study a large number of (111), (100), (0001) and (211) and overlayers of transition metal-water interfaces in order to identify simple descriptors to predict their U_PZC. We find a good correlation between water coverage and the work function reduction Δφ which is defined by the difference of the work function in vacuum and in the presence of water. Furthermore, we determine the vacuum binding energies of H2O and *OH species as good descriptors for the prediction of water coverage and thereby of ∆φ. Our insights unify different facet geometries and mixed metal surfaces and thereby generalize recent observations. We further present a scheme to predict U_PZC based only on the *OH binding and the vacuum work function estimated from static DFT calculations. This formalism is applicable to all investigated metals and mixed metal surfaces including terrace and step geometries and does not require expensive AIMD simulations. To evaluate physical influences to U_PZC, we decompose ∆φ into its orientational (∆φ_orient) and electronic(∆φ_el) components. We find ∆φ_orient to be a facet dependent property and a major contributor to ∆φ on (211) surfaces, while ∆φ_sub strongly depends on the metal identity. | Sara Kelly; Hendrik Heenen; Nitish Govindarajan; Karen Chan; Jens Nørskov | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61aabd37772cb220154f89cc/original/oh-binding-energy-as-a-universal-descriptor-of-the-potential-of-zero-charge-on-transition-metal-surfaces.pdf |
62ea790515fdaebe2b211a8f | 10.26434/chemrxiv-2022-q51s2 | Synthesis and Characterization of a Calcium-Pyrazolonato
Complex. Observation of In-Situ Desolvation During MicroElectron Diffraction. | The synthesis and characterisation of a calcium pyrazolonato complex is reported. X-Ray diffraction (XRD) of single crystals revealed an octahedral geometry with two axial solvent ligands. Analysis of the bulk sample by means of microcrystal electron diffraction (micro-ED) measurement revealed a polymeric pentagonal bipyramidal coordination geometry joined via a central Ca2O2 ring with axial water ligands. During the micro-ED measurement, loss of water was observed resulting in a secondary structure with a polymeric distorted octahedral coordination
geometry joined via a central Ca2O2 ring. These findings
demonstrate that XRD and micro-ED methods can provide
complemetary data during structural determination, and that even electrophilic metals are susceptible to desolvation under micro-ED measurements. | Thomas Mies; Christian Schürmann; Sho Ito; Andrew J. P. White; Mark R. Crimmin; Anthony G. M. Barrett | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Ligands (Inorg.); Main Group Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ea790515fdaebe2b211a8f/original/synthesis-and-characterization-of-a-calcium-pyrazolonato-complex-observation-of-in-situ-desolvation-during-micro-electron-diffraction.pdf |
679b7ed66dde43c908f82432 | 10.26434/chemrxiv-2025-nn2x2 | Catalytically Competent Nickel(I)-Isocyanide Compounds | Nickel-catalyzed cross-coupling reactions have emerged as a powerful strategy to construct complex molecules. A salient feature of Ni catalysts is their ability to engage in one-electron chemistry involving paramagnetic Ni(I) and Ni(III) intermediates, which has led to development of cross-coupling reactions involving alkyl substrates; however, such reactions generally employ Ni(II) or Ni(0) complexes as pre-catalysts. Although highly desirable, well-defined and catalytically competent Ni(I) sources with exchangeable ancillary ligands are lacking. Here we report the synthesis, characterization, and catalytic activity of a family of thermally stable dinuclear Ni(I) complexes supported by commercially available isocyanides as a general solution to this problem. Two classes of Ni(I) isocyanide complexes showing high thermal and solid-state stability have been developed – coordinatively saturated homoleptic compounds and coordinatively unsaturated Ni(I)-halide compounds. The Ni(I) compounds exhibit rapid ligand substitution and are efficient catalysts in Kumada, Suzuki-Miyaura, and Buchwald-Hartwig cross-coupling reactions, suggesting their potential use as either Ni(I) catalysts or pre-catalysts. In addition, bromide-selective functionalization of polyhalogenated arenes with Grignard reagents was achieved for the first time under nickel catalysis. Finally, spectroscopic and mechanistic studies were performed to establish the general use of simple isocyanide ligands as spectator ligands for cross-coupling reactions, representing an untapped chemical space for new reaction discovery. | Sagnik Chakrabarti; Ju Byeong Chae; Katy Knecht; Nicholas Cedron; Liviu Mirica | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Redox Catalysis; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679b7ed66dde43c908f82432/original/catalytically-competent-nickel-i-isocyanide-compounds.pdf |
60c74aa3bdbb89d0a8a393fb | 10.26434/chemrxiv.12142383.v2 | Virtual Screening of Curcumin and Its Analogs Against the Spike Surface Glycoprotein of SARS-CoV-2 and SARS-CoV | COVID-19, a new pandemic caused by SARS-CoV-2, was first identified in 2019 in Wuhan, China. The novel corona virus SARS-CoV-2 and the 2002 SARS-CoV have 74 % identity and use similar mechanisms to gain entry into the cell. Both the viruses enter the host cell by binding of the viral spike glycoprotein to the host receptor, angiotensin converting enzyme 2 (ACE2). Targeting entry of the virus has a better advantage than inhibiting the later stages of the viral life cycle. The crystal structure of the SARS-CoV (6CRV: full length S protein) and SARS-CoV-2 Spike proteins (6M0J: Receptor binding domain, RBD) was used to determine potential small molecule inhibitors. Curcumin, a naturally occurring phytochemical in Curcuma longa, is known to have broad pharmacological properties. In the present study, curcumin and its derivatives were docked, using Autodock 4.2, onto the 6CRV and 6M0J to study their capability to act as inhibitors of the spike protein and thereby, viral entry. The curcumin and its derivatives displayed binding energies, ΔG, ranging from -10.98 to -5.12 kcal/mol (6CRV) and -10.01 to -5.33 kcal/mol (6M0J). The least binding energy was seen in bis-demethoxycurcumin with: ΔG = -10.98 kcal/mol (6CRV) and -10.01 kcal/mol (6M0J). A good binding energy, drug likeness and efficient pharmacokinetic parameters suggest the potential of curcumin and few of its derivatives as SARS-CoV-2 spike protein inhibitors. However, further research is necessary to investigate the ability of these compounds as viral entry inhibitors.<br /> | Ashish Patel; Malathi Rajendran; Suresh B Pakala; Ashish Shah; Harnisha Patel; Prashanthi Karyala | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aa3bdbb89d0a8a393fb/original/virtual-screening-of-curcumin-and-its-analogs-against-the-spike-surface-glycoprotein-of-sars-co-v-2-and-sars-co-v.pdf |
60c74a144c8919979dad3187 | 10.26434/chemrxiv.12152679.v1 | Counter-Currently Operated Reactive Extractor with Additively Manufactured Enzyme Carrier Structure | The development of continuous flow reactors for heterogeneous chemical or biochemical reactions raises the question of efficient mixing and catalyst immobilization. Especially, in those cases where hybrid reactor concepts are aimed at, combining of reaction and extraction in one apparatus requires a solution for reaction and extraction phase distribution and immobilization concepts. Precisely designed structures inserted as reactor packings can be used to control the multiphase hydrodynamics and to act as a catalyst carrier simultaneously. However, the decision for the most suitable structure for specific reaction systems remains a challenge. While numerical simulations with computational fluid dynamics (CFD) has limitations regarding the complex interactions in multiphase flows, performing experiments using rapid prototyping (RP) offers the possibility of a fast fabrication and verification of tailor-made structures for specific flow characteristics, efficient mass transport and high conversion rates. Additionally, RP can be used to quickly approve results from CFD simulations in experiments. In the presented work the development of a counter-currently (CC) operated additively manufactured reactor (AMR) for the decarboxylation of ferulic acid (FA) to 2-metoxy-4-vinylphenol (MVP) along <i>in situ</i> extraction with <i>n-</i>heptane is shown. Here, the use and optimization of periodic open-cell structures (POCS) as a carrier for the enzyme phenolic acid decarboxylase and a distributor for the extraction phase is targeted. By rapid prototyping of transparent structures and their examination with respect to the induced flow characteristics of colored heptane, a structure could be optimized for the specific reaction system. The additive manufacturing of the POCS and its application in a CC AMR enabled 95% conversion of 5 mM FA in two hours and a MVP concentration in reaction phase below 0.5 mM. | Niclas Büscher; Claas Spille; John Kracht; Giovanni Sayogo; Ayad Dawood; Maria Maiwald; Dirk Herzog; Michael Schlüter; Andreas Liese | Fluid Mechanics; Reaction Engineering; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a144c8919979dad3187/original/counter-currently-operated-reactive-extractor-with-additively-manufactured-enzyme-carrier-structure.pdf |
663a6d1791aefa6ce166563e | 10.26434/chemrxiv-2024-5hxvv | Enantioselective Total Syntheses of (+)-Kasugamycin and (+)-Kasuganobiosamine Highlighting a Sulfamate-Tethered Aza-Wacker Cyclization Strategy | Here, we present the first enantioselective total syntheses of the natural products (+)-kasugamycin, a potent
antifungal antibiotic, and (+)-kasuganobiosamine, a compound that results from kasugamycin degradation. Salient features of these syntheses include a second-generation enantioselective preparation of a kasugamine derivative (much improved in efficiency relative to our first chiral-pool effort) and our laboratory’s sulfamate-tethered aza-Wacker cyclization. | Shyam Sathyamoorthi; Gour Mandal; Steven Kelley | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663a6d1791aefa6ce166563e/original/enantioselective-total-syntheses-of-kasugamycin-and-kasuganobiosamine-highlighting-a-sulfamate-tethered-aza-wacker-cyclization-strategy.pdf |
67d2ff416dde43c908a97ca1 | 10.26434/chemrxiv-2025-08n0x | Cytochrome C Facilitates Binding Between Lipid Bilayers and Citrate-Coated Gold Nanoparticles in Coarse-Grained Simulations | Characterization and prediction of the interactions between engineered nanoparticles (ENPs), proteins, and biological membranes is critical for advancing applications to nanomedicine and nanomanufacturing while mitigating nanotoxicological risks. In this work, we employ a coarse-grained dissipative particle dynamics (DPD) simulation to investigate the interactions among cytochrome c (CytC), lipid bilayers, and citrate-coated gold nanoparticles (AuNPs). We updated the DPD potential to accurately represent binding potentials between molecules, and validated the model relative to an all-atom representation. The DPD simulations successfully replicate experimental observations: CytC facilitates the binding of citrate-coated AuNPs to lipid bilayers composed of 90% dioleoylphosphatidylcholine (DOPC) mixed with 10\% stearoylphosphatidylinositol (SAPI) or 10% tetraoleoyl cardiolipin (TOCL)but not to pure 100% DOPC bilayers. In addition, the simulations reveal nuanced differences in binding preferences between CytC, the lipid bilayers, and the ENP, at a scale that is not presently directly observable in experiments. Specifically, we found that the surface coating of the nanoparticles---%viz variations in the CytC surface density---%affects the protein-mediated binding with the bilayers.Such a molecular-sensitive result underscores the utility of DPD simulations in simulating complex biological systems. | Yinhan Wang; Rigoberto Hernandez | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d2ff416dde43c908a97ca1/original/cytochrome-c-facilitates-binding-between-lipid-bilayers-and-citrate-coated-gold-nanoparticles-in-coarse-grained-simulations.pdf |
66d41474f3f4b05290c915f8 | 10.26434/chemrxiv-2024-tfsr7-v2 | Three-way data reduction based on essential information | In this article, the idea of essential information-based compression is extended to trilinear datasets. This basically boils down to identifying and labelling the essential rows (ERs), columns (ECs) and tubes (ETs) of such three-dimensional datasets that allow by themselves to reconstruct in a linear way the entire space of the original measurements. ERs, ECs and ETs can be determined by exploiting convex geometry computational approaches such as convex hull or convex polytope estimations and can be used to generate a reduced version of the data at hand. These compressed data and their uncompressed counterpart share the same multilinear properties and their factorisation (carried out by means of, e.g., Parallel Factor Analysis-Alternating Least Squares - PARAFAC-ALS) yield, in principle, indistinguishable results.
More in detail, an algorithm for the assessment and extraction of the essential information encoded in trilinear data structures is here proposed. Its performance was evaluated in both real-world and simulated scenarios which permitted to highlight the benefits that this novel data reduction strategy can bring in domains like multiway fluorescence spectroscopy and imaging. | Raffaele Vitale; Azar Azizi; Mahdiyeh Ghaffari; Nematollah Omidikia; Cyril Ruckebusch | Analytical Chemistry; Chemoinformatics; Imaging; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d41474f3f4b05290c915f8/original/three-way-data-reduction-based-on-essential-information.pdf |
61ed70ff8d70c3d2670b1160 | 10.26434/chemrxiv-2022-ckrjp | Regioselective access to orthogonal Diels-Alder C60 bis-adducts and tris-heteroadducts via avant-garde supramolecular mask strategy | The regioselective poly-functionalization of highly symmetric spherical Ih-C60 is extremely challenging and usually leads to the formation of regio-isomeric mixtures not amenable for HPLC purification. Recently, we have pioneered the regioselective functionalization of C60 fullerene under a supramolecular mask strategy, using tetragonal prismatic nanocapsules to encapsulate C60 and performing the Bingel tetrakis-cyclopropanation at the exposed fullerene surface through the four windows of the nanocapsule. Here, we describe an extension of the supramolecular mask strategy for the selective Diels-Alder (DA) functionalization of Ih-C60 using acenes. The supramolecular mask allows the chemo- and regioselective synthesis of e,e-bis-anthracene-C60 (functionalization at 90o) or the synthesis of trans-1-bis-pentacene-C60 (functionalization at 180o), only by changing the acene length. Moreover, the mask strategy allows to obtain unprecedented equatorial hetero-tris-functionalized-C60 adducts combining Diels-Alder with Bingel mask regiofunctionalization. Computational modelling revealed significant differences in the host-guest interactions and equilibrium established between the firstly formed anthracene- and pentacene-based monoadducts with the nanocapsule, respectively, which finally determine the observed orthogonal regioselectivity. The combination of Molecular Dynamics (MD) simulations and analysis of Frontier Molecular Orbital (FMO) involved in the Diels-Alder cycloadditions provide crucial insights to rationalize the regioselective control exerted by the supramolecular mask. | Míriam Pujals; Tània Pèlachs; Carles Fuertes-Espinosa; Teodor Parella; Marc Garcia-Borràs; Xavi Ribas | Organic Chemistry; Nanoscience; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ed70ff8d70c3d2670b1160/original/regioselective-access-to-orthogonal-diels-alder-c60-bis-adducts-and-tris-heteroadducts-via-avant-garde-supramolecular-mask-strategy.pdf |
679c4de981d2151a02a04763 | 10.26434/chemrxiv-2025-3sffc | Ruthenium(II) complexes with photoswitchable and photoejectable ligands | A ruthenium(II) complex with a photoswitchable arylazopyrazole ligand is reported. Under irradiation a combination of photoisomerisation and photoejection of the ligand occurs. | Kavisha A. Sarma; Isis A. Middleton; Man H. Chak; Jake P. Violi; Mohan Bhadbhade; Jonathon Beves | Inorganic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2025-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679c4de981d2151a02a04763/original/ruthenium-ii-complexes-with-photoswitchable-and-photoejectable-ligands.pdf |
66b768835101a2ffa8dbbb06 | 10.26434/chemrxiv-2024-5w7wp | Rethinking Polyiodides: The Role of Electron-Deficient Multicenter Bonds | Despite a bicentennial history, the interest in polyiodides and related systems still flourishes. The chemical puzzle provided by the intricate nature of chemical bonding in these polyanions remains challenging these days. The advent of the halogen bond and the spreading interest in supramolecular interactions of halogen-based systems promoted further recent interest. Research in the area of materials, where local bonding details eventually result in desired macroscopic properties, provided a further boost. Herein, we illustrate the consequences of contemplating a different bonding scheme for polyiodides, one making explicit use of electron-deficient multicenter bonds (EDMBs), an emerging concept in this area. We present a reinterpretation of polyiodide bonding using a revised approach to the Lewis dot formulas, leading to a clearer pen-and-paper understanding of their bonding. The model is general and can be applied to other related problems (here polyiodonium cations, other homo- and hetero-polyhalides). Our alternative narrative has a few interesting consequences on several traditional and currently hot topics, including the nature of basic building blocks for polyiodides, hypervalency vs. hypercoordination, the distinction between covalent bonds and supramolecular interactions, and the nature of secondary and halogen bonds. | Matteo Savastano; Hussien H. Osman; Ángel Vegas; Francisco Javier Manjón Herrera | Physical Chemistry; Inorganic Chemistry; Bonding; Physical and Chemical Properties; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b768835101a2ffa8dbbb06/original/rethinking-polyiodides-the-role-of-electron-deficient-multicenter-bonds.pdf |
649eb215ba3e99daef4a33c4 | 10.26434/chemrxiv-2023-ml4jd | Investigating Mass Transfer Around Spatially-Decoupled Electrolytic Bubbles | Electrolytic bubbles have a profound impact on mass transport in the vicinity of electrodes, greatly influencing the electrolyzer efficiency and cell overpotential. However, high spatio-temporal resolution experimental measurements of concentration fields around electrolytic bubbles, are challenging. In this study, a succession of spatially-decoupled electrolytic bubbles are simulated. The bubbles grow, and departing from a hydrophobic cavity at the center of a ring microelectrode. The gas-liquid interface is modeled using a moving mesh topology. A geometric cutting protocol is developed to handle topology changes during bubble departure. The simulated bubbles show good agreement with the bubble growth dynamics observed in experiments. The bubbles in this spatially-decoupled system outgrow the region of electrolyte that is saturated with dissolved hydrogen. This leaves the apex of the bubble interfaces exposed to an undersaturated region of the electrolyte which leads to an outward flux of hydrogen gas. This is shown to limit the gas evolution efficiency of bubbles despite the fact that they grow at a constant volumetric rate. By analyzing the distribution of the flux of dissolved hydrogen along the bubble interface along with the development of dissolve hydrogen concentration profiles around the bubble, we show that the magnitude of the outward diffusive flux at the apex of the bubble decreases with increasing electrolysis current. | Akash Raman; Carla Corina dos Santos Porto; Han Gardeniers; Cíntia Soares; David Fernández Rivas; Natan Padoin | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649eb215ba3e99daef4a33c4/original/investigating-mass-transfer-around-spatially-decoupled-electrolytic-bubbles.pdf |
60c75249469df4e01ef44b4b | 10.26434/chemrxiv.13008500.v2 | Automatic discovery of chemical reactions using imposed activation | Computational power and quantum chemical methods have improved immensely since computers were first applied to the study of reactivity, but the de novo prediction of chemical reactions has remained challenging. We show that complex reactions can be efficiently and autonomously predicted using chemical activation imposed by simple geometrical constraints. Our approach is demonstrated on realistic and challenging chemistry, such as a triple cyclization cascade involved in the total synthesis of a natural product and several oxidative addition reactions of complex drug-like molecules. Notably and in contrast with traditional hand-guided computational chemistry calculations, our method requires minimal human involvement and no prior knowledge of products or mechanisms. Imposed activation can be a transformational tool to screen for chemical reactivity and mechanisms as well as to study byproduct formation and decomposition.<br /> | Cyrille Lavigne; Gabriel dos Passos Gomes; Robert Pollice; Alan Aspuru-Guzik | Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75249469df4e01ef44b4b/original/automatic-discovery-of-chemical-reactions-using-imposed-activation.pdf |
635875afca86b8d57fc36848 | 10.26434/chemrxiv-2022-8wbgn | Synthesis and Characterization of Post-β-Carbon-Elimination Organopalladium Complexes | A unique family of N,N,π,C-palladacycles are synthesized from 8-aminoquinoline-coupled nopol derivatives through directed 1,2-migratory insertion of in situ generated arylpalladium(II) species followed by β-carbon elimination. These palladacycles have exceptional stability under air and moisture at room temperature, enabling successful isola-tion and characterization by X-ray crystallography, NMR, and high-resolution mass spectrometry. Computational studies shed light on the facile β-alkyl elimination step and the origins of the high stability of these post β-carbon-elimination complexes. | Taeho Kang; Yue Fu; Rei Matsuura; Anna Liu; Tanner Jankins; Arnold Rheingold; Jake Bailey; Milan Gembicky; Peng Liu; Keary Engle | Theoretical and Computational Chemistry; Organometallic Chemistry; Theory - Computational; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635875afca86b8d57fc36848/original/synthesis-and-characterization-of-post-carbon-elimination-organopalladium-complexes.pdf |
60e6500f0387b114dcca2dbc | 10.26434/chemrxiv-2021-f6rns | Unusually Strong Long-range Electronic Coupling Across Redox-Active Bridges in M3+/M4+ Mixed-Valence Complexes of Group 4 Congeners | Homobimetallic complexes of Group 4 metals, supported by the redox-active tetrakis(imino)pyracene (TIP) ligand were synthesized and isolated. The formation of these complexes resulted in LUMOs having significantly lower energies than the free ligand and the respective metal salts, MCl4 (M = Ti, Zr, Hf), whereby all three complexes were readily reduced by one electron using the mild reductant, Cp*2Fe (E0 = -0.59 V). Spectroscopic characterization and quantum chemical analyses of the reduced species revealed that the resulting complexes are delocalized, borderline Class II-III (Ti) and Class III (Zr, Hf) mixed valence complexes. All three complexes display surprisingly strong long-range electronic coupling between the metal centers, as M to M distances, rAB, are nearly 12 Å. The coupling strengths of Zr and Hf were significantly stronger than those observed for the Ti complex, suggesting that better orbital overlap between the ligand and 4d or 5d metal centers helps to relieve the instability of the 3+ oxidation state via delocalization. | Colby Seth Bell; Nathan J. DeYonker; Curtis E. Moore; Kensha Marie Clark | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Transition Metal Complexes (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e6500f0387b114dcca2dbc/original/unusually-strong-long-range-electronic-coupling-across-redox-active-bridges-in-m3-m4-mixed-valence-complexes-of-group-4-congeners.pdf |
669e5a1101103d79c5344c86 | 10.26434/chemrxiv-2024-xh80q | Carbon-Binder-Domain porosity extraction through lithium-ion battery electrode impedance data | In the field of 3-D resolved computational modelling of Lithium-ion battery electrodes, the arrangement and properties of the Carbon-Binder-Domain (CBD) play a critical role in the ion and electron transport properties through their impact on the electrode tortuosity factor. However, until now, the CBD porosity value -its main descriptor in terms of transport properties and occupied volume- has been determined through educated guesses due to the lack of an experimental approach. Here, we report a novel methodology is reported for the determination of the CBD internal porosity through the combination of computational modelling and experimental electrochemical impedance spectroscopy (EIS). The methodology is based on the creation of a calibration curve that relates tortuosity factor with CBD porosity through digital stochastic generation of electrode microstructures and diffusivity characterization. The curve is then compared to the EIS experimental results and analyzed through a transmission line model, yielding a good estimation of the parameters. In this work, the usefulness and the identified areas of limitation of this approach are demonstrated with three different formulations of LiNi0.3Mn0.3Co0.3O2 (NMC 111) cathodes. To the best of the authors’ knowledge, this is the first reported method for estimating CBD porosity. | Sergio Pinilla; Franco Zanotto; Diana Zapata-Dominguez; Tomas Garcia; Alejandro A. Franco | Theoretical and Computational Chemistry; Materials Science; Energy; Composites; Computational Chemistry and Modeling; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e5a1101103d79c5344c86/original/carbon-binder-domain-porosity-extraction-through-lithium-ion-battery-electrode-impedance-data.pdf |
647bc23f4f8b1884b7caa1b3 | 10.26434/chemrxiv-2023-dk5dx | Single-molecule electrochemical imaging resolves the midpoint potentials of individual fluorophores on nanoporous antimony-doped tin oxide | We report reversible switching of oxazine, cyanine, and rhodamine dyes by a nanoporous antimony-doped tin oxide electrode that enables single-molecule (SM) imaging of electrochemical activity. Since the emissive state of each fluorophore is modulated by electrochemical potential, the number of emitting single molecules follows a sigmoid function during a potential scan, and we thus optically determine the formal redox potential of each dye. We find that the presence of redox mediators (phenazine methosulfate and riboflavin) functions as an electrochemical switch on each dye’s emissive state and observe significantly altered electrochemical potential and kinetics. We are therefore able to measure optically how redox mediators and the solid-state electrode modulate the redox state of fluorescent molecules, which follows an electrocatalytic (EC’) mechanism, with SM sensitivity over a 900 µm2 field of view. Our observations indicate that redox mediator-assisted SM electrochemical imaging (SMEC) could be potentially used to sense any electroactive species. Combined with SM blinking and localization microscopy, SMEC imaging promises to resolve the nanoscale spatial distributions of redox species and their redox states, as well as the electron transfer kinetics of electroactive species in various bioelectrochemical processes. | Jin Lu; Matthew D. Lew | Analytical Chemistry; Electrochemical Analysis; Imaging; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647bc23f4f8b1884b7caa1b3/original/single-molecule-electrochemical-imaging-resolves-the-midpoint-potentials-of-individual-fluorophores-on-nanoporous-antimony-doped-tin-oxide.pdf |
65e8959566c13817295a0d0a | 10.26434/chemrxiv-2024-cmtnf | Simulation-Guided Conformational Space Exploration to Assess Reactive Conformations of a Ribozyme | Self-splicing ribozymes are small RNA enzymes that catalyze their own cleavage through a transphosphoesterification reaction. While this process is involved in some specific steps of viral RNA replication and splicing, it is also of importance in the context of the (putative) first autocatalytic RNA-based systems that could have preceded the emergence of modern life. The uncatalyzed phosphoesterbond formation is thermodynamically very unfavorable, and many experimental studies have focused on the understanding of the molecular features of catalysis in these ribozymes. However, chemical reaction paths are short-lived and not easily characterized by experimental approaches, so that molecular simulation approaches appear as an ideal tool to unveil the molecular details of the reaction. Here, we focus on the model hairpin ribozyme and highlight that identifying a relevant initial conformation for reactivity studies can be highly challenging due to limitations in both available X-ray and the force field accuracy, together with the necessity of extensive sampling. This is frequently overlooked in mixed quantum/classical studies that predominantly concentrate on the chemical reaction itself. These challenges stem from limitations in both available experimental structures (which are chemically altered to prevent self-cleavage) and the accuracy of force fields, together with the necessity for comprehensive sampling. We show that molecular dynamics simulations, combined with extensive conformational phase space exploration with Hamiltonian replica-exchange simulations, enable to characterize the relevant conformational basins of the minimal hairpin ribozyme in the ligated state, prior to self-cleavage. With all investigated force fields, we find that what is usually considered as a canonical reactive conformation with active site geometries and hydrogen-bond patterns that are optimal for the addition-elimination reaction with general acid/general base catalysis, is metastable and only marginally populated. The thermodynamically stable conformation appears to be consistent with the expectations of a mechanism that does not require the direct participation of ribozyme residues to the reaction. Our study therefore demonstrates that identifying the most pertinent reactant state conformation, holds equal importance alongside the accurate determination of the thermodynamics and kinetics of the chemical steps of the reaction. | Sélène Forget; Marie Juillé; Élise Duboué-Dijon; Guillaume Stirnemann | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Biophysics; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e8959566c13817295a0d0a/original/simulation-guided-conformational-space-exploration-to-assess-reactive-conformations-of-a-ribozyme.pdf |
658c9f1766c13817292b112f | 10.26434/chemrxiv-2023-cxbgr | Exploring mesoscopic mass transport effects on electrocatalytic selectivity | Electrocatalytic selectivity has shown a puzzling dependence on experimental parameters related to catalyst morphology or the reactor design. In this study, we explore the proposition that these effects are due to mesoscopic mass transport. Basis for the underlying mechanism is the kinetic competition that arises from exchanging surface-bound, yet volatile, reaction intermediates between the electrode and the bulk electrolyte. The electrocatalyst's morphology can be decisive in driving this competition since its surface area directly affects the probability that a diffusing species will return to the surface for continued reaction, rather than escape as an early partially-converted product. We argue that this competition is relevant for a number of technologically important reactions, including e.g. different products during the electrochemical CO2 reduction on Cu-based catalysts. Combining microkinetic and transport modeling in a multi-scale approach, we specifically explore and quantify this effect for various showcase examples in the experimental literature. Despite its simplicity, our model correctly reproduces selectivity trends with respect to electrode potential and catalyst roughness. Comparing against experimental data further establishes catalyst roughness as a descriptor that unifies the effects of meso-, micro- and atomic-scale morphology on selectivity through transport. The resulting insight provides an alternative or, at least, complementary explanation to changes in electrocatalytic selectivity that have otherwise been attributed to nano-structuring of active sites or electronic effects due to doping or alloying. | Hendrik H. Heenen; Hemanth S. Pillai; Karsten Reuter; Vanessa Jane Bukas | Theoretical and Computational Chemistry; Catalysis; Nanoscience; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY 4.0 | CHEMRXIV | 2023-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658c9f1766c13817292b112f/original/exploring-mesoscopic-mass-transport-effects-on-electrocatalytic-selectivity.pdf |
65201aefbda59ceb9a002fba | 10.26434/chemrxiv-2023-p6n7w | Accessibility Study of Porous Materials at the Single Particle Level as Evaluated within a Microfluidic Chip with Fluorescence Microscopy | Understanding the mass transfer phenomena taking place in solid catalysts, batteries, fuel cells, and adsorbents is essential to improve their performances. Uptake experiments of ultraviolet-active or fluorescent probes represent a direct way to directly provide an accessibility measure of porous particles. We propose a new method to evaluate the accessibility of functional porous materials at the single-particle level. A multiplexed microfluidic device and a fluorescence microscope are employed to assess the uptake of fluorescent molecules in porous particles over time. The device allows for performing multiple uptake experiments in parallel, enabling the comparison of different particles under the same conditions. We showcase the method by studying the diffusion and adsorption properties of a dye in different silica model particles. The approach allows for probing interparticle heterogeneity in accessibility and accessible surface area as well as the dependence of these parameters on electrostatic interactions between the particle and the probe molecules. | Alessia Broccoli; Luca Carnevale; Rafael Mayorga-González; Joren M. Dorresteijn; Bert M. Weckhuysen; Wouter Olthuis; Mathieu Odijk; Florian Meirer | Catalysis; Analytical Chemistry; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65201aefbda59ceb9a002fba/original/accessibility-study-of-porous-materials-at-the-single-particle-level-as-evaluated-within-a-microfluidic-chip-with-fluorescence-microscopy.pdf |
60c740a1567dfe73a3ec3bf0 | 10.26434/chemrxiv.7771217.v1 | Interpreting the Electrocatalytic Voltammetry of Homogeneous Catalysts by the Foot of the Wave Analysis and Its Wider Implications | <p>Mechanistic studies
of electrocatalytic reactions play a crucial role in developing efficient electrocatalysts
and solar-fuel devices. The foot of the wave analysis (FOWA) for cyclic
voltammetry, recently developed by Savéant and Costentin,
provides a powerful means to evaluate the performance of molecular
electrocatalysts. However, there is a considerable amount of confusion in the
community on how to interpret FOWA in multi-electron electrochemical reactions.
Herein, we further expand their earlier models from the Nernstian region to all
scenarios (i.e. including non-Nernstian behavior) and systematically examine
individual parameters, such as formal potentials and reaction rate constants,
to explore deeper insights and limitation. Detailed analysis from in-silico
voltammograms based on different mechanistic models reveals characteristic
features of FOWA traces for different kinetic phenomena, which is useful to diagnose
kinetic profiles and elucidate the limits of FOWA. The lessons learned from these
analyses are further used to reconcile the discrepancy of rate constants
determined by FOWA versus other methods, such as time-resolved spectroscopy, for
molecular electrocatalysts that catalyze proton reduction or the reduction of CO<sub>2</sub>
to CO. Such reconciliation demonstrates that electrochemical methods along with
FOWA can serve as an alternative tool to determine kinetic information and probe
mechanistic insights, which otherwise may be challenging and complicated to be
achieved by conventional methods. In addition, general guidelines and warnings
are also presented to avoid potential errors or mishandling when using FOWA. </p> | Vincent Wang; Ben A Johnson | Electrochemistry; Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a1567dfe73a3ec3bf0/original/interpreting-the-electrocatalytic-voltammetry-of-homogeneous-catalysts-by-the-foot-of-the-wave-analysis-and-its-wider-implications.pdf |
65087992b338ec988ab5a966 | 10.26434/chemrxiv-2023-dvf3r | Long-term Robustness and Failure Mechanisms of Electrochemical Stripping for Wastewater Ammonia Recovery | Nitrogen in wastewater has negative environmental, human health, and economic impacts but can be recovered to reduce costs and environmental impacts of wastewater treatment and chemical production. To recover ammonia/ammonium (TAN) from urine, we operated electrochemical stripping (ECS) for over a month, achieving 83.4% TAN removal and 73.0% TAN recovery. With two reactors, we recovered sixteen 500 mL batches (8 L total) of ammonium sulfate approaching commercial fertilizer concentrations and often having greater than 95% purity. While evaluating operation and maintenance needs, we identified pH, full-cell voltage, product volume, and water flux into the product as informative process monitoring parameters that can be inexpensively and rapidly measured. Characterization of fouled cation exchange and omniphobic membranes informs cleaning and reactor modifications to reduce fouling with organics and calcium/magnesium salts. To evaluate the impact of urine collection and storage on ECS, we conducted experiments with urine at different levels of dilution with flush water, extents of divalent cation precipitation, and degrees of hydrolysis. ECS effectively treated urine under all conditions, but minimizing flush water and ensuring storage until complete hydrolysis would enable energy-efficient TAN recovery. A preliminary cost assessment indicated that ECS-derived ammonium sulfate from urine was competitive with other nitrogen treatment technologies and commercially available fertilizer. Our experimental results and cost analysis motivate a multi-faceted approach to improving ECS’s technical and economic viability by extending component lifetimes, decreasing component costs, and reducing energy consumption through material, reactor, and process engineering. In sum, we demonstrated urine treatment as a foothold for electrochemical nutrient recovery from wastewater while supporting applicability of ECS to seven other wastewaters with widely varying characteristics. Our findings will facilitate scale-up and deployment of electrochemical nutrient recovery technologies, enabling a circular nitrogen economy that fosters sanitation provision, efficient chemical production, and water resource protection. | Anna Kogler; Neha Sharma; Diana Tiburcio; Meili Gong; Dean M. Miller; Kindle S. Williams; Xi Chen; William A. Tarpeh | Earth, Space, and Environmental Chemistry; Environmental Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65087992b338ec988ab5a966/original/long-term-robustness-and-failure-mechanisms-of-electrochemical-stripping-for-wastewater-ammonia-recovery.pdf |
614033dbd5f080ab0bc463e3 | 10.26434/chemrxiv-2021-tq1kw | Phase and facet-engineering of transition alumina leads to (hydro)thermally stable alumina-supported metal catalysts | Inherent thermal instability of gamma-alumina above 800-900 ⁰C leads to deactivation of noble metal-supported alumina catalysts used in automotive applications. This is typically solved by adding toxic (barium) and/or rare-earth (lanthanum, cerium) elements. We show that facet-dependent engineering of transition-alumina leads to (hydro)thermally stable supported metal catalysts in the absence of toxic and rare-earth additives. Since pure high-surface area theta-alumina can be prepared at 1,050-1,100 ⁰C directly from gamma-alumina (or boehmite), and because of its stable major (100) facet with very low surface energy of 597 mJ/m2, we succeeded in preparing ~0.07 wt% Rh and ~3 wt% Pd catalysts active in NO reduction and hydrocarbon oxidation that survive hydrothermal aging up to 1,100 ⁰C with little-to-no deactivation. | Konstantin Khivantsev; Ja-Hun Kwak; Nicholas Jaegers; Yong Wang; Janos Szanyi; Libor Kovarik | Catalysis; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614033dbd5f080ab0bc463e3/original/phase-and-facet-engineering-of-transition-alumina-leads-to-hydro-thermally-stable-alumina-supported-metal-catalysts.pdf |
6615de4991aefa6ce13767c7 | 10.26434/chemrxiv-2023-1fbv7-v3 | A Superstructure-Based Lignin Valorization Process Optimization Model for Lignocellulosic Biorefineries through Biological Upgrading | This study presents an optimization framework to identify economically viable pathways for lignin valorization in biorefineries that employ biological upgrading. The economic potential for converting lignin from hardwood, softwood, and herbaceous plants into valuable bioproducts is evaluated. The research indicates that the production of 2-pyrone-4,6-dicarboxylic acid (PDC) from hardwood is the most economically promising, with an estimated net present value (NPV) of $771.41 million and an internal rate of return (IRR) of 19.73% through dilute acid pretreatment, base catalyzed depolymerization, and PDC fermentation. Capital costs represent a large portion of the total expenses across all scenarios. Revenue from woody feedstocks is largely derived from lignin-based products, while for herbaceous plants, coproducts (fermentable sugars) are the main revenue contributors. The analysis provides insights for the development of lignin valorization biorefineries and guides the chemical industry toward a more sustainable use of renewable carbon sources. | Yajie Wu; Juan Manuel Restrepo-Flórez; Juliana Vasco-Correa | Chemical Engineering and Industrial Chemistry; Agriculture and Food Chemistry; Industrial Manufacturing | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6615de4991aefa6ce13767c7/original/a-superstructure-based-lignin-valorization-process-optimization-model-for-lignocellulosic-biorefineries-through-biological-upgrading.pdf |
6641ff9f21291e5d1d2230e1 | 10.26434/chemrxiv-2024-lljkf | Delayed Fluorescence and Amplified Chirality via Modified Substitution Position for Deep-red Circularly Polarized Organic Light Emitting-diodes | Developing easily accessible deep-red/near-infrared circularly polarized emitters for practical organic light-emitting diodes remains a significant challenge. Here, a practical strategy has been proposed for developing deep-red circularly polarized delayed fluorescent emitters based on a novel chiral acceptor platform. By changing triphenylamine (TPA) substitution position from para to meta, R/S-M-TBBTCN demonstrated thermally activated delayed fluorescence (TADF) properties with a delayed lifetime of 6.6 μs that R/S-P-TBBTCN doesn’t have. Furthermore, R/S-M-TBBTCN showed a 20 nm red-shift in emission and a 10-fold enhancement in asymmetry factor (glum), compared with R/S-P-TBBTCN. The solution-processed nondoped circularly polarized organic light-emitting diodes (CP-OLEDs) based on R-M-TBBTCN display deep-red emission and 2.2% external quantum efficiency. | Lixun Zhu; Dan Liu; Kaiwen Wu; Guohua Xie; Zheng Zhao; Ben Zhong Tang | Materials Science; Optical Materials | CC BY 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6641ff9f21291e5d1d2230e1/original/delayed-fluorescence-and-amplified-chirality-via-modified-substitution-position-for-deep-red-circularly-polarized-organic-light-emitting-diodes.pdf |
60c75255567dfe0b0bec5c3a | 10.26434/chemrxiv.13286312.v1 | Frustrated Flexibility in Metal-Organic Frameworks | <div><div><div><p>Stimuli-responsive flexible metal-organic frameworks (MOFs) remain at the forefront of porous materials research due to their enormous potential for various technological applications. Here, we introduce the concept of frustrated flexibility in MOFs, which arises from an incompatibility of intra-framework dispersion forces with the geometrical constraints of the inorganic building units. Controlled by appropriate linker functionalization with dispersion energy donating alkoxy groups, this approach results in a series of MOFs exhibiting a new type of guest- and temperature-responsive structural flexibility characterized by reversible loss and recovery of crystalline order under full retention of framework connectivity and topology. The stimuli-dependent phase change of the frustrated MOFs involves non-correlated deformations of their inorganic building unit, as probed by a combination of global and local structure techniques together with computer simulations. Frustrated flexibility may be a common phenomenon in MOF structures, which are commonly regarded as rigid, and thus may be of crucial importance for the performance of these materials in various applications.</p></div></div></div> | Roman Pallach; Julian Keupp; Kai Terlinden; Louis Frentzel-Beyme; Marvin Kloß; Andrea Machalica; Julia Kotschy; Suresh
K. Vasa; Philip A. Chater; Christian Sternemann; Michael T. Wharmby; Rasmus Linser; Rochus Schmid; Sebastian Henke | Hybrid Organic-Inorganic Materials; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75255567dfe0b0bec5c3a/original/frustrated-flexibility-in-metal-organic-frameworks.pdf |
6683dd095101a2ffa825e1e0 | 10.26434/chemrxiv-2024-bvslm-v2 | Rapid low-cost assembly of modular microvessel-on-a-chip with benchtop xurography | Blood and lymphatic vessels in the body are central to molecular and cellular transport, tissue repair, and pathophysiology. Several approaches have been employed for engineering microfabricated blood and lymphatic vessels in vitro, yet these approaches invariably require specialized equipment, facilities, and research training beyond the capabilities of most biomedical laboratories. Here we present xurography as an inexpensive, accessible, and versatile rapid prototyping technique for engineering cylindrical and lumenized microvessels. Using a benchtop xurographer, or a cutting plotter, we fabricated modular multi-layer poly(dimethysiloxane) (PDMS) -based microphysiological systems (MPS) that house endothelial-lined microvessels approximately 260μm in diameter embedded within a user-defined 3-D extracellular matrix (ECM). We validated the vascularized MPS (or vessel-on-a-chip) by quantifying changes in blood vessel permeability due to the pro-angiogenic chemokine CXCL12. Moreover, we demonstrated the reconfigurable versatility of this approach by engineering three different vessel-ECM arrangements, which were obtained by minor adjustments to one or two steps of the fabrication process. Several of these arrangements, such as ones that incorporate close-ended vessel structures and spatially distinct ECM compartments along the same microvessel, cannot be readily achieved with other microfabrication strategies. Therefore, we anticipate that our low-cost and easy-to-implement fabrication approach will facilitate wider accessibility of MPS with tunable vascular architectures and ECM components while reducing the turnaround time required for iterative designs. | Jonathan W. Song; Shashwat S. Agarwal; Marcos Cortes-Medina; Jacob C. Holter; Alex Avendano; Joseph W. Tinapple; Joseph M. Barlage; Miles M. Menyhert; Lotanna M. Onua | Biological and Medicinal Chemistry; Materials Science; Analytical Chemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6683dd095101a2ffa825e1e0/original/rapid-low-cost-assembly-of-modular-microvessel-on-a-chip-with-benchtop-xurography.pdf |
60c74691842e651b78db2845 | 10.26434/chemrxiv.11357726.v1 | Single-Step Modified Electrodes for Vitamin C Monitoring in Sweat | We demonstrate a flexible sensor for ascorbic acid detection in sweat based on single-step modified gold microelectrodes. The modification consists on the electrodeposition of alginate membrane with trapped CuO nanoparticles on top of the electrodes. The electrodes are fabricated at a thin polyimide support and the soft nature of the membrane can withstand mechanical stress far beyond the requirements for skin monitoring. We further show the efficient detection of ascorbic acid at the micromolar levels in both, a neutral buffer and acidic artificial sweat, at ultra-low applied potential (-5 mV). The effect of possible interfering species present in sweat is minimized, with no observable cross-reaction, thus maintaining a high degree of selectivity despite absence of enzymes in the fabrication scheme. This sensor is envisioned as a promising component of a wearable device for e.g. non-invasive monitoring of micronutrient loss through sweat. | Bergoi Ibarlucea; Arnau Perez Roig; Dmitry Belyaev; Larysa Baraban; Gianaurelio Cuniberti | Electrochemical Analysis; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74691842e651b78db2845/original/single-step-modified-electrodes-for-vitamin-c-monitoring-in-sweat.pdf |
614e04f57c08d583d14ef691 | 10.26434/chemrxiv-2021-z2n68 | Modified Born-Lande Equation to calculate Lattice Energy in a theoretical approach | Defects in ionic solid are very much common, which is increased with the rise in temperature. It causes the change in the value of many physical properties and varieties of physical parameters and the Lattice Energy is one such parameter to control the physical properties of the crystals.
Considering the loss of ions from lattice points as random, the examination of each of the defects individually is going to be unpredictable, thus leading to almost nonattainment of the correct crystal structure with the theoretical calculations applying for available models. Here, in this present work, we have used some statistical methods and probabilistic approximation to introduce a novel idea of calculating the Madelung constant, and then Lattice Energy analytically.
To make the understanding more lucid, we have taken one of the very common crystals, very popular in the crystallographic community, NaCl crystal having 6:6 co-ordination number, for which a significant number of Schottky defects are observed.
During this study, we are bound to assume the random distribution of defects as Poisson distribution due to the fact that the number of defects is very less with respect to the total numbers of lattice points present in the crystal to calculate the Madelung Constant.
| Aakash Gupta; Debasis Jana | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614e04f57c08d583d14ef691/original/modified-born-lande-equation-to-calculate-lattice-energy-in-a-theoretical-approach.pdf |
67352815f9980725cf1a8432 | 10.26434/chemrxiv-2024-qwbgr | Tuning Hydrogen Bond Networks at Gold Electrodes: A Study of Potential-Dependent DMSO-Water Interfaces | Understanding the behavior of hydrogen bond (H-bond) networks at electrode interfaces is the first step towards optimizing electrochemical processes. This study investigates the potential-dependent interfacial environment of dimethyl sulfoxide (DMSO)‒water mixtures at gold electrodes using a combination of surface-enhanced infrared absorption spectroscopy (SEIRAS) and constant potential molecular dynamics (MD) simulations. SEIRAS provides in situ spectroscopic data on H¬¬ bonding populations and cosolvent enrichment at the interface, while MD simulations offer an atomistic view of H bond configurations and molecular orientations under applied potentials. Our results demonstrate that applied electrostatic potential influences the interfacial H¬¬ bonding environment. Negative potentials produce enrichment of DMSO and a reorientation of interfacial water molecules, which leads to a slight increase in H-bonded populations, particularly at lower DMSO concentrations. Conversely, positive potentials show a reduced impact on the H bond structure. The effects are different at higher DMSO concentrations where DMSO‒DMSO interactions dominate. Despite DMSO being electrically neutral, both experimental and simulation data reveal a measurable modulation of interfacial enrichment and H¬¬ bond populations as a function of potential. | Ziareena Al-Mualem; Alfredo Cardenas; Sulagna Hazarika; Hang Ren; Carlos Baiz | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67352815f9980725cf1a8432/original/tuning-hydrogen-bond-networks-at-gold-electrodes-a-study-of-potential-dependent-dmso-water-interfaces.pdf |
67b70ec381d2151a02450292 | 10.26434/chemrxiv-2025-trgrp | Design, Synthesis, and Structure–Activity Relationship Studies of 4-substituted Phenylpyrazolidinone Derivatives as Potent Ku70/80 Targeted DNA-PK Inhibitors | The Ku70-Ku80 (Ku) heterodimer complex plays a central role in the non-homologous end joining (NHEJ) double-strand break (DSB) repair pathway and the DNA damage response (DDR). Like DNA-PK, Ku is a promising drug target for cancer treatment when combined with radiotherapy or DSB-inducing agents. We have previously reported the first-in-class early-generation highly potent and specific Ku-DNA binding inhibitors (Ku-DBi’s) that block the Ku interaction with DNA and inhibit DNA-PK kinase activity. These early-generation Ku-DBi’s also inhibit cellular DNA-PK, NHEJ-catalyzed DSB repair, sensitize non-small cell lung cancer (NSCLC) cells to DSB-inducing agents, and potentiate the cellular effects of these agents via p53 phosphorylation through the activation of the ATM pathway. In this study, we report a comprehensive structure-activity relationship (SAR) around the initial X80 hit molecule to develop highly potent Ku-DBi’s. Early generation Ku-DBi’s display a potent Ku-DNA binding inhibitory activity with a range of 2 to 6 μM, and DNA-PK inhibitory activity in the nanomolar range of approximately 110 nM. Microscale thermophoresis assay shows that these compounds inhibit Ku70-Ku80 binding to DNA with a Kd value of 0.4-6.4 μM. The thermal stability analysis also supports the notion that these Ku-DBi’s bind to the Ku as measured by nano DSF, which is consistent with the observed SAR trends. These Ku-DBi’s may serve as candidate compounds for further modification and development as anticancer therapeutics in combination with radiotherapy or DSB-inducing agents to treat certain DNA repair-deficient cancers. | Narva Deshwar Kushwaha ; Pamela VanderVere-Carozza ; Tyler L. Vernon ; Pamela L. Mendoza-Munoz ; Jitender D. Gaddameedi ; Karim Ben Ali Gacem; Jean-Baptiste Charbonnier ; Navnath S. Gavande; John J. Turchi | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b70ec381d2151a02450292/original/design-synthesis-and-structure-activity-relationship-studies-of-4-substituted-phenylpyrazolidinone-derivatives-as-potent-ku70-80-targeted-dna-pk-inhibitors.pdf |
6514a35fa69febde9ece7088 | 10.26434/chemrxiv-2023-fj1m5 | ABCD Block Copolymers Using a Multistate Aluminum Complex | A ferrocene aluminum compound (salfan-H2)Al(OiPr) (salfan-H2 = 1,1’-di(2,4-bis-tert-butyl-salicylamino)ferrocene), with adjustable redox and protonation characteristics, has been synthesized and characterized, and serves as a switchable cata-lyst for ring-opening polymerization. Leveraging this versatile, multistate system, we have successfully synthesized a range of innovative copolymers, including AB diblock poly(styrene oxide-lactide) (PSO-PLA), ABC triblock poly(butyl lactone-styrene oxide-lactide) (PBBL-PSO-PLA), and ABCD tetrablock copolymers poly(ethoxy vinyl glycidyl ether-butyl lactone-styrene oxide-lactide) (PEVGE-PBBL-PSO-PLA). | Shiyun Lin; Maya Vasisht; Ramzi Massad; Hootan Roshandel; Yin-Pok Wong; Paula Diaconescu | Catalysis; Organometallic Chemistry; Polymer Science; Polymerization catalysts; Homogeneous Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6514a35fa69febde9ece7088/original/abcd-block-copolymers-using-a-multistate-aluminum-complex.pdf |
6666a6a2e7ccf7753a6a4038 | 10.26434/chemrxiv-2024-z9f59-v2 | Catalytic ‘Gelectrodes’ for Sustainable and Enhanced Oxygen Evolution Reaction | Development of cost-effective catalysts providing low overpotentials and enhanced electrochemical kinetics is a critical goal of contemporary research on electrochemical water splitting and other technologically significant processes. Translation to practical applications demands that they should also enable high current densities to be extracted. A simple strategy of encapsulating the active electrocatalyst in hydrogel polymer matrices is shown to provide a facile solution in several respects, especially regarding the last criterion. The concept is illustrated using two examples of ‘gelectrodes’ based on nanocomposites of cobalt oxyhydroxide and nickel-iron hydroxide with chitosan on nickel foam, and their efficient mediation of the oxygen evolution reaction (OER). Comparison with control systems show that significantly lower overpotentials and higher current densities with extended temporal stability can be achieved with the gelectrodes; the cobalt oxyhydroxide - chitosan and nickel-iron hydroxide - chitosan systems provide stable current densities up to 1.6 - 1.7 A cm-2 for the OER with alkaline aqueous electrolyte. This simple design strategy opens up a general route to technologically useful electrocatalyst performance. | Anu Bovas; T. P. Radhakrishnan | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666a6a2e7ccf7753a6a4038/original/catalytic-gelectrodes-for-sustainable-and-enhanced-oxygen-evolution-reaction.pdf |
67005687cec5d6c1422d73f0 | 10.26434/chemrxiv-2024-frkvj | Controlling Electrostatics to Enhance Conductivity in Structured Electrolytes | Solid-state electrolytes are currently being explored as a safe material capable of addressing consumer energy-storage demands. Solid polymer electrolytes, in particular, offer a high energy density and improved safety when compared to liquid-based electrolytes, but tend to have a significantly lower ionic conductivity. We hypothesize structured ionic liquids can enhance conductivity. Here, we explore the performance of these materials through coarse-grained molecular dynamics simulation. While we observe similar phase behavior (incorporating solid, smectic, and liquid phases) to that seen in experiments, we also observe significantly more mobility in the cationic species compared to the anionic species before the system reaches an arrest transition. We further discuss how the general results within this paper can guide further studies and target the design of new highly conductive solid electrolytes with the potential to enable the use of multivalent ionic species as ion conductors. | Logan Hennes; Chloe Behringer; Mohsen Farshad; Jennifer L. Schaefer; Jonathan K. Whitmer | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67005687cec5d6c1422d73f0/original/controlling-electrostatics-to-enhance-conductivity-in-structured-electrolytes.pdf |
651e47328bab5d2055abb5b0 | 10.26434/chemrxiv-2023-bwm63 | Switchable quaternary ammonium transformation leading to salinity-tolerance-conferring plant biostimulants | Since their discovery by Menshutkin in 1890, quaternary ammonium salts have been synthesized by alkylating tertiary amines, with the development of new synthetic methods having received limited attention. Here we describe a photoredox-catalyzed method for synthesizing quaternary ammonium salts that involves reacting α-haloalkylammonium salts with olefins. This chemistry enables selective and switchable alkylations and alkenylations that afford a variety of structurally new quaternary ammonium salts. The key to success is attributable to the photocatalytic generation of distonic α-ammonium radicals under both oxidative and reductive quenching conditions. Furthermore, during the course of our reaction-development-based chemical-screening campaign, we serendipitously discovered that the synthesized quaternary ammonium salts confer plants with salinity tolerance. The discovery of a novel class of salinity-tolerance-conferring molecule is expected to impact agrochemical development as salinity damage increasingly becomes a global problem. | Takumi Kinoshita; Yota Sakakibara; Tomoko Hirano; Kei Murakami | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Plant Biology; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651e47328bab5d2055abb5b0/original/switchable-quaternary-ammonium-transformation-leading-to-salinity-tolerance-conferring-plant-biostimulants.pdf |
657de69ae9ebbb4db90b7390 | 10.26434/chemrxiv-2023-v9kpm | Development of a cascade reaction to access complex tetrahydro-3,4'-biisoquinoline | C-3-functionalized tetrahydroisoquinolines (THIQs) structural motifs are found in numerous natural products such as the tetrahydroprotoberberine alkaloids (coralydine and corytenchirine) and the benzophenanthridine alkaloids (homochelidonine, norchelidonine and chelamine). These scaffolds are also highly valuable compounds in drug discovery. Therefore, in the past few years, there has been a growing interest in developing new methods for the synthesis of this building block. However, unlike C-1-functionalized tetrahydroisoquinolines which are easily accessible, construction of C-3-functionalized tetrahydroisoquinolines is highly challenging. Methodologies such as the Bischler-Napieralski cyclization/reduction sequence, radical cyclization approach, and palladium-catalysed aryl–aryl coupling/reduction reactions were mostly used. However, all of these methods require multi step synthesis and prefunctionalization of the substrate. Moreover, none of these strategies are of sufficiently general applicability, especially for the synthesis of tetrahydro-3,4'-biisoquinoline.
Herein, we have successfully developed an unprecedented cascade approach under mild conditions to access complex C-3-functionalized tetrahydroisoquinolines. The keystone of the present cascade process is the successive formation of two iminium intermediates resulting to the formation of 3 new bonds, therefore allowing creation of molecular complexity and diversity starting from simple substrates.
| MOMAR TOURE; Saul Jaime-Figueroa; George Burslem; Philipp Cromm; Gaspard Hedouin; Craig Crews | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657de69ae9ebbb4db90b7390/original/development-of-a-cascade-reaction-to-access-complex-tetrahydro-3-4-biisoquinoline.pdf |
60c74d9fbb8c1adb913db612 | 10.26434/chemrxiv.12640781.v1 | Automated Design of Macrocycles for Therapeutic Applications: from Small Molecules to Peptides and Proteins | <div>Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have </div><div>improved affinity, are able to bind to extended protein interfaces and otherwise have favorable </div><div>properties. Macrocyclization of a known binder molecule has the potential to stabilize its bioactive </div><div>conformation, improve its metabolic stability, cell permeability and in certain cases oral </div><div>bioavailability. Herein, we present an in silico approach that automatically generates, evaluates and </div><div>proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the </div><div>three-dimensional (3D) conformation of the linear molecule in complex with a target protein as </div><div>starting point, this approach identifies attachment points, generates linkers, evaluates the </div><div>conformational landscape of suitable linkers and their geometric compatibility and ranks the resulting </div><div>molecules with respect to their predicted conformational stability and interactions with the target </div><div>protein. As we show here with several prospective and retrospective case studies, this procedure can </div><div>be applied for the macrocyclization of small molecules and peptides and even PROTACs and proteins.</div><div>The presented approach is an important step towards the enhanced utilization of macrocycles and</div><div>cyclic peptides as attractive therapeutic modalities.</div> | Daniel Sindhikara; Michael Wagner; Paraskevi Gkeka; Stefan Guessregen; Garima Tiwari; Gerhard Hessler; Engin Yapici; Ziyu Li; Andreas Evers | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d9fbb8c1adb913db612/original/automated-design-of-macrocycles-for-therapeutic-applications-from-small-molecules-to-peptides-and-proteins.pdf |
60c747cd337d6c3cffe27402 | 10.26434/chemrxiv.11798763.v1 | Hysteresis in the Gas Sorption Isotherms of Metal-Organic Cages Accompanied by Subtle Changes in Molecular Packing | Structural deformation in response to gas sorption is rarely observed for porous molecular solids, when compared to porous framework materials. Here, we describe the effect of chemical modification on the exterior of lantern-type metal-organic cages on the emergence and then disappearance of cooperative gas uptake. The results suggest that supramolecular design of ligands can be used to reveal this behaviour. | Gavin Craig; Patrick Larpent; Hinano Urabe; alexandre legrand; Mickaele Bonneau; Shinpei Kusaka; Shuhei Furukawa | Coordination Chemistry (Inorg.); Ligands (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747cd337d6c3cffe27402/original/hysteresis-in-the-gas-sorption-isotherms-of-metal-organic-cages-accompanied-by-subtle-changes-in-molecular-packing.pdf |
6746ec285a82cea2fa1458b8 | 10.26434/chemrxiv-2024-bkn81 | Scrambled RGD hexameric peptide hydrogel supports efficient self-assembly and cell activity | Amino acid sequence is crucial in controlling peptide-based hydrogel formation, whereby changing the position of a single amino acid can significantly alter the gel’s properties. Herein, we report the gelation kinetics and cell viability of scrFmoc-GFFRDG (where we have scrambled the RGD-based gel hexapeptide; Fmoc-GFFRGD). The scrambled sequence showed improved gelation properties compared to the original Fmoc-GFFRGD sequence with scrFmoc-GFFRDG forming a gel in under 10 minutes, significantly faster than the 2-hour gelation time, and at a concentration eight times lower than the original Fmoc-GFFRGD sequence. We also examined the combination of the two gelators in a ratio of 1:1, final concentration of 0.4% (w/v). Interestingly, the stiffness of hybrid hydrogel was ~3 kPa, whereas individually, neither gelator at the same concentration exceeded 0.5 kPa. The cell-adhesion motif RGD improves the ability of the peptides to promote attachment of cells due to integrin recognition. However, when fibroblasts were cultured on the hydrogels, the scrFmoc-GFFRDG yielded a higher level of alpha-SMA expression in cells than those cultured on Fmoc-GFFRGD, suggesting a microenvironment conducive to myofibroblast transitions. This study provides a new outlook on how a well-known scrambled peptide motif (RDG) can fine-tune hydrogel assembly and cell culture applications. | Karrar Al Taief; Stephanie Nemec; Isis Middleton; Kristopher Kilian; Pall Thordarson | Organic Chemistry; Nanoscience; Supramolecular Chemistry (Org.); Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6746ec285a82cea2fa1458b8/original/scrambled-rgd-hexameric-peptide-hydrogel-supports-efficient-self-assembly-and-cell-activity.pdf |
66a4039801103d79c5c8f00e | 10.26434/chemrxiv-2024-cm32m | From C-F Activation to Catalytic Regioselective Double Hydrodefluorination of Pyridines with a Nickel Complex | The nickel(0) complex [Ni(iPrPN)(COD)] (iPrPN = 2-[(N-diisopropylphosphino)methylamino]pyridine, COD = 1,5-cyclooctadiene) has been found an efficient precatalyst for the hydrodefluorination of pyridines employing HBPin. Substituted 2,6-difluoropyridines were doubly hydrodefluorinated selectively at the 2 and 6 positions at room tem-perature employing 5 mol% of catalyst loading. Mechanistic studies for the hydrodefluorination of 2,6-difluoropyridine allowed to identify COD decoordination followed by C-F activation of the fluorinated pyridine as the catalyst entry pathway to the cycle and the [Ni(iPrPN)(COD)] complex as the catalyst resting-state. | Roger Nunez; Victor Duran Arroyo; Rebeca Arevalo | Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Bond Activation; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a4039801103d79c5c8f00e/original/from-c-f-activation-to-catalytic-regioselective-double-hydrodefluorination-of-pyridines-with-a-nickel-complex.pdf |
63e7e8e81d2d1840634f9917 | 10.26434/chemrxiv-2023-fjtf1 | Photochemical synthesis of acyl fluorides using copper-catalyzed fluorocarbonylation of alkyl iodides | Acyl fluorides are important reagents in organic synthesis due to their unique balance between reactivity and stability. Here, we report a copper-catalyzed carbonylative coupling strategy to synthesize acyl fluorides under photoirradiation. Various alkyl halides were transformed in high yields into corresponding acyl fluorides by using a commercially available copper catalyst (CuBrSMe2) and a readily available fluoride salt (KF) at room temperature and mild CO pressure (6 atm) under blue light irradiation. A radical fluorocarbonylation mechanism is proposed based on experimental data. | Pinku Tung; Neal Mankad | Organic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e7e8e81d2d1840634f9917/original/photochemical-synthesis-of-acyl-fluorides-using-copper-catalyzed-fluorocarbonylation-of-alkyl-iodides.pdf |
60c74c200f50db296b396db8 | 10.26434/chemrxiv.12424658.v1 | Protein-Controlled Actuation of Dynamic Nucleic Acid Networks Using Synthetic DNA Translators | Integrating dynamic DNA nanotechnology with protein-controlled actuation will expand our ability to process molecular information. We have developed a strategy to actuate strand displacement reactions using DNA-binding proteins by engineering synthetic DNA translators that convert specific protein-binding events into trigger inputs through a programmed conformational change. We have constructed synthetic DNA networks responsive to two different DNA-binding proteins, TATA-binding protein and Myc-Max, and demonstrated multi-input activation of strand displacement reactions. We finally achieved protein-controlled regulation of a synthetic RNA and of an enzyme through artificial DNA-based communication, showing the potential of our molecular system in performing further programmable tasks. | ALESSANDRO BERTUCCI; Alessandro Porchetta; Erica Del Grosso; Tania Patiño; Andrea Idili; Francesco Ricci | Nanodevices; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c200f50db296b396db8/original/protein-controlled-actuation-of-dynamic-nucleic-acid-networks-using-synthetic-dna-translators.pdf |
678f34c881d2151a020c02ed | 10.26434/chemrxiv-2025-6c23s-v2 | One-pot Chemoselective Aerobic Cascade Synthesis of Allyl-Aryl Sulfoxides Enabled by Photoinduced Na2 - Eosin Y and TEMPO | Allylic sulfoxides are ubiquitous in medicine as well as in catalysis. Chemoselective synthesis of allyl-aryl sulfoxides is challenging due to competitive isomerizatio and overoxidation of allylic C-H as well as sulfur. Herein, we have accomplished an unprecedented, metal-free one-pot protocol for the aerobic cascade synthesis of allyl-aryl sulfinyls from Morita–Baylis–Hillman allyl bromides and thiols under visible light photocatalysis through a radical pathway. The most interesting part of this methodology is the selective and controlled oxidation of in situ formed allyl-aryl sulfides by merging sub-stoichiometric oxidizing agent TEMPO and visible light photocatalysis where overoxidation was completely excluded. This approach provides an efficient one-step access to biologically relevant and synthetically important molecules. | Trinadh Ballanki; Aishwarya Subramanian; Baby Viswambharan | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678f34c881d2151a020c02ed/original/one-pot-chemoselective-aerobic-cascade-synthesis-of-allyl-aryl-sulfoxides-enabled-by-photoinduced-na2-eosin-y-and-tempo.pdf |
60c7529dbdbb89d788a3a2ff | 10.26434/chemrxiv.11869692.v5 | RetroXpert: Decompose Retrosynthesis Prediction Like A Chemist | <div>Retrosynthesis is the process of recursively decomposing target molecules into available building blocks. It plays an important role in solving problems in organic synthesis planning. To automate the retrosynthesis analysis, many retrosynthesis prediction methods have been proposed.</div><div>However, most of them are cumbersome and lack interpretability about their predictions.</div><div>In this paper, we devise a novel template-free algorithm, RetroXpert, for automatic retrosynthetic expansion by automating the procedure that chemists used to do.</div><div>Our method disassembles retrosynthesis into two steps: i) we identify the potential reaction center within the target molecule through a graph neural network and generate intermediate synthons; and ii) we predict the associated reactants based on the obtained synthons via a reactant generation model. </div><div>While outperforming the state-of-the-art baselines by a significant margin, our model also provides chemically reasonable interpretation.</div> | Chaochao Yan; Qianggang Ding; Peilin Zhao; Shuangjia Zheng; Jinyu Yang; Yang Yu; Junzhou Huang | Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7529dbdbb89d788a3a2ff/original/retro-xpert-decompose-retrosynthesis-prediction-like-a-chemist.pdf |
60c73ed9469df429cef4294b | 10.26434/chemrxiv.7130795.v1 | Revealing Quantum Mechanical Effects in Enzyme Catalysis with Large-Scale Electronic Structure Simulation | <div><div><div><p>Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.</p></div></div></div> | Zhongyue Yang; Rimsha Mehmood; Mengyi Wang; Helena W. Qi; Adam H. Steeves; Heather Kulik | Computational Chemistry and Modeling; Theory - Computational; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed9469df429cef4294b/original/revealing-quantum-mechanical-effects-in-enzyme-catalysis-with-large-scale-electronic-structure-simulation.pdf |
60c74601f96a001b32286c9f | 10.26434/chemrxiv.9722528.v2 | A General Techno-Economic Model for Evaluating Emerging Electrolytic Processes | <p>Increasing societal concern about carbon emissions and the concomitant emergence of inexpensive renewable resources provide growing impetus for the electrification of the chemical industry. While there have been notable recent advances in the science and engineering of electrolytic processes, there are comparatively few engineering economic studies that outline the technical specifications needed to approach feasibility. Here we introduce an open-source techno-economic framework to connect system performance and price goals to the constituent materials property sets with a goal of quantifying the economic potential of existing and conceptual electrolytic processes. To validate the outputs and demonstrate the versatility of this toolkit, we explore three contemporary electrolyses of varying technology readiness levels. Specifically, we first benchmark our model results against the Department of Energy hydrogen analysis model, then evaluate the impact of mass transport and catalyst performance on the electrochemical reduction of carbon dioxide, and chart a pathway to low-cost electrolytic production of phenol from guaiacol. As this model is based on generalized mass balances and electrochemical equations common to a number of electrochemical processes, it serves as an adaptable toolkit for researchers to evaluate new chemistries and reactor configurations as well as to back-translate system targets to interdependent materials-level property requirements.<br /></p> | Michael Orella; Steven M. Brown; McLain Leonard; Yuriy Román-Leshkov; Fikile Brushett | Industrial Manufacturing; Reaction Engineering; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74601f96a001b32286c9f/original/a-general-techno-economic-model-for-evaluating-emerging-electrolytic-processes.pdf |
64e603373fdae147faa82f71 | 10.26434/chemrxiv-2023-n2v3r | Thermally Activated Delayed Fluorescence in a Deep Red Dinuclear Iridium(III) Complex: a Hidden Mechanism for Short Luminescence Lifetimes | The high luminescence efficiency of cyclometallated iridium(III) complexes, including those widely used in OLEDs, is typically attributed solely to the formally spin-forbidden phosphorescence process being facilitated by spin-orbit coupling with the Ir(III) centre. In this work, we provide unequivocal evidence that an additional mechanism can also participate, namely a thermally activated delayed fluorescence (TADF) pathway. TADF is well-established in other materials, including in purely organic compounds, but has never been observed in iridium complexes. Our findings may transform the design of iridium(III) complexes by including an additional, faster fluorescent radiative decay pathway. We discover it here in a new dinuclear complex, 1, of the form [Ir(N^C)2]2(u-L), where N^C represents a conventional N^C-cyclometallating ligand, and L is a bis-N^O-chelating bridging ligand derived from 4,6-bis(2-hydroxyphenyl)-pyrimidine. Complex 1 forms selectively as the rac diastereoisomer upon reaction of [Ir(N^C)2(u-Cl)]2 with H2L under mild conditions, with none of the alternative meso isomer being separated. Its structure is confirmed by X-ray diffraction. Complex 1 displays deep-red luminescence in solution or in polystyrene film at room temperature (λem = 643 nm). Variable-temperature emission spectroscopy uncovers the TADF pathway, involving thermally activated re-population of S1 from T1. At room temperature, TADF reduces the photoluminescence lifetime in film by a factor of around 2, to 1 s. The TADF pathway is associated with a small S1–T1 energy gap ΔEST of approximately 50 meV. Calculations that take into account the splitting of the T1 sublevels through spin-orbit coupling perfectly reproduce the experimentally observed temperature-dependence of the lifetime over the range 20 – 300 K. A solution-processed OLED comprising 1 doped into the emitting layer at 5 wt. % displays red electroluminescence, λEL = 625 nm, with an EQE of 5.5% and maximum luminance of 6300 cd m–2. | Piotr Pander; Andrey Zaytsev; Amit Sil; Glib Baryshnikov; Farhan Siddique; J.A. Gareth Williams; Fernando B Dias; Valery Kozhevnikov | Materials Science; Inorganic Chemistry; Organometallic Compounds; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e603373fdae147faa82f71/original/thermally-activated-delayed-fluorescence-in-a-deep-red-dinuclear-iridium-iii-complex-a-hidden-mechanism-for-short-luminescence-lifetimes.pdf |
625579e7ef2ade874b2ca57c | 10.26434/chemrxiv-2022-xndvx | Potential-dependent Pt(111)—water interface: Tackling the challenge of a consistent treatment of electrochemical interfaces | The interface between an electrode and an electrolyte is the location where electro- chemical processes for countless technologically important applications occur. Though its high relevance and the intense efforts devoted to its elucidation, an atomic-level description of the interfacial structure and especially the dynamics of the electric double layer is still amiss. Here, we present reactive force field molecular dynamics simulations of electrified Pt(111)|water interfaces, shedding light on the orientation of water molecules in the vicinity of the Pt(111) surface, considering the influence of potential, adsorbates and ions simultaneously. We obtain a shift of the water’s preferred orientation in the surface oxidation potential region, breaking with the so far proclaimed strict correlation to the free charge density. Further, the course of the entropy and the intermolecular ordering in the interfacial region complements the characterization. Our work contributes to the ongoing understanding process of electric double layers and in particular of the structure of the electrified Pt(111)|water interface and aims at providing insights into electrochemical processes occurring there. | Laura Braunwarth; Christoph Jung; Timo Jacob | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625579e7ef2ade874b2ca57c/original/potential-dependent-pt-111-water-interface-tackling-the-challenge-of-a-consistent-treatment-of-electrochemical-interfaces.pdf |
620f25cc0aec1ab99921a024 | 10.26434/chemrxiv-2022-6853j | Temperature-Regulated Regiodivergent Synthesis via Alkene Migratory Hydroalkylation | An approach for reliable and predictable carbon-carbon or carbon-heteroatom bond formation that produces either regioisomer starting from the same raw materials, also known as a regiodivergent methodology, is highly desirable. Altering the chemical reaction variables, including catalysts, ligands, solvents, or other additives, were the predominant strategy for the implementation of regiodivergent features in metal-catalysed organic synthesis. The achievement of switchable selectivity using quickly and conveniently controlled physical variables constitutes a desirable goal with an intriguing method of attainment. Herein, we report our discovery that temperature-regulated switchable site-selectivity can be achieved in alkene (migratory) functionalization. Judicious selection of reaction temperatures, one of the most easily changed variables, led to protocols that provide the regiodivergent alkylation products starting from a single alkene substrate. This protocol allows for the convenient synthesis of α- and β-branched protected amines, both of which are substantially important to the pharmaceutical chemistry and biochemistry fields. In addition, enantioenriched β-branched alkyl amines could be accessed in a catalytic asymmetric variant manner. This work may inspire more research interests in metal-catalysed regiodivergent reaction discovery using easily changed physical variables. | Jia-Wang Wang; De-Guang Liu; Zhe Chang; Zhen Li; Yao Fu; Xi Lu | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2022-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620f25cc0aec1ab99921a024/original/temperature-regulated-regiodivergent-synthesis-via-alkene-migratory-hydroalkylation.pdf |
61b7eafad10aa5821310935d | 10.26434/chemrxiv-2021-cw1l0 | Influence of Halide Substitution and External Stimuli on Ion Transport in Inverted MAPb(I1-xBrx)3 Perovskite Solar Cells | The coupled electronic-ionic response in various MAPb(I1-xBrx)3-based inverted perovskite solar cells (PSCs) is studied in-operando by impedance spectroscopy (IS) under varied AM1.5G light intensities and electrical biases. We show that the concentration of Br- in the composition significantly alters the capacitance and resistive response of the PSC under external stimuli. For example, we observed that the low frequency capacitance does not increase proportionally with light intensity, instead it is highly dependent on the amount of Br- in the composition. We found that the recombination resistance (Rrec) has a linear inverse relationship with light intensity in MAPbI3 and MAPbBr3 whereas, the mixed compositions show deviation. Interestingly, the deviation of Rrec from linearity also scales with the increase in Br- concentration. Upon applying an electrical bias, a large deviation of Rrec from linearity was observed all mixed halide compositions exhibited a non-linear inverse trend. We further report the diffusion coefficient (D) for each MAPb(I1-xBrx)3 composition under different light intensity. Notably, the D values decreased on changing the composition from MAPbI3 (10-7 cm2 s-1) to MAPb(I0.8Br0.2)3 and MAPbBr3 (10-8 cm2 s-1). On the other hand, mixed compositions containing more than 20% Br- concentration show faster diffusion kinetics. Overall, our results emphasize on the complex and intertwined nature of electronic and ionic response in PSC that is tunable by changing the halide composition. | Hamza Javaid; Christie L.C. Ellis; Emily C. Smith; Yao Liu; Monojit Bag; D. Venkataraman | Materials Science; Hybrid Organic-Inorganic Materials; Thin Films; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b7eafad10aa5821310935d/original/influence-of-halide-substitution-and-external-stimuli-on-ion-transport-in-inverted-ma-pb-i1-x-brx-3-perovskite-solar-cells.pdf |
60f8fd76880443d606e2cb75 | 10.26434/chemrxiv-2021-l6cp8 | Cationic-Palladium Catalyzed Regio- and Stereoselective Dicarbo-functionalization of Unsymmetrical Internal Alkynes | Reported is the discovery of an approach to regio- and stereoselective syn-1,2-dicarbofuctionalization of unsymmetrical alkynes. A cationic Pd-catalyzed three-component coupling of two distinct carbon-bearing functionalities aryl diazonium salts and aryl boronic acids/olefins with unsymmetrical alkynes enables accessing to all-carbon substituted unsymmetrical olefins. The transformation features broad scope with labile functional group tolerance building a novel chemical space of structural diversity (82 molecules) and is scalable. The cationic Pd species plays crucial; notably, density functional theory (DFT) studies establish this observation. Synthetic versatility of the modifiable carboxylate bearing highly-substituted olefins is also presented. | Shubham Dutta; Shashank Shandilya; Shengwen Yang; Manash Protim Gogoi; Vincent Gandon; Akhila K. Sahoo | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f8fd76880443d606e2cb75/original/cationic-palladium-catalyzed-regio-and-stereoselective-dicarbo-functionalization-of-unsymmetrical-internal-alkynes.pdf |
6440131d7be842788de9706d | 10.26434/chemrxiv-2023-xctsg | N-Heterocyclic Carbenes - the Design Concept for Densely Packed and Thermally Ultra-Stable Aromatic Self-Assembled Monolayers | Self-assembled monolayers (SAMs) of N-heterocyclic carbenes (NHCs) on metal substrates are currently one of the most promising systems in context of molecular-scale engineering of surfaces and interfaces, crucial for numerous applications. Interest in NHC SAMs is mainly driven by their assumingly higher thermal stability compared to thiolate SAMs most broadly used at the moment. Most of the NHC SAMs utilize imidazolium as an anchoring group for linking molecules to the metal substrate via carbene C atom. It is well established in the literature that standing up and stable NHC SAMs are built only when using bulky side groups attached to nitrogen heteroatoms in imidazolium moiety, which, however, leads to monolayers exhibiting much lower packing density compared to thiolate SAMs. Here, by combined X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and temperature-programmed secondary ion mass spectrometry analysis, we demonstrate that using NHCs with small methyl side groups in combination with simple solution-based preparation leads to the formation of aromatic monolayers exhibiting at least double surface density, upright molecular orientation, and ultra-high thermal stability compared to the NHC SAMs reported before. These parameters are crucial for most applications, including, in particular, molecular and organic electronics, where aromatic SAMs serve either as a passive element for electrode engineering or as an active part of organic field effect transistors and novel molecular electronics devices. | Mateusz Wróbel; Daria Cegiełka; Andika Asyuda,; Krzysztof Kozieł; Michael Zharnikov; Piotr Cyganik | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Self-Assembly; Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6440131d7be842788de9706d/original/n-heterocyclic-carbenes-the-design-concept-for-densely-packed-and-thermally-ultra-stable-aromatic-self-assembled-monolayers.pdf |
62d87c443787f166eabf21ef | 10.26434/chemrxiv-2022-jtt63-v2 | A quantum-chemical analysis on the Lewis acidity of diaryl-halonium ions | Cyclic diaryliodonium compounds like iodolium derivatives have increasingly found use as noncovalent Lewis acids in the last years. They are more stable than acyclic systems and are markedly more Lewis acidic. Herein, this higher Lewis acidity is analyzed and explained via quantum-chemical calculations and energy decomposition analyses. Its key origin is the change in energy levels and hybridization of iodine’s orbitals, leading to both more favorable electrostatic interaction and better charge transfer. Both of the latter seem to contribute in similar fashion, while hydrogen bonding as well as steric repulsion with the phenyl rings play at best a minor role. In comparison to iodolium, bromolium and chlorolium are less Lewis acidic the lighter the halogen, which is predominantly based on less favorable charge-transfer interactions. | Raphael Robidas; Dominik Reinhard; Stefan M. Huber; Claude Legault | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d87c443787f166eabf21ef/original/a-quantum-chemical-analysis-on-the-lewis-acidity-of-diaryl-halonium-ions.pdf |
60c7463bee301c812ac79494 | 10.26434/chemrxiv.9860753.v2 | Thermal Decomposition Kinetics of Glyphosate (GP) and its Metabolite Aminomethylphosphonic Acid (AMPA) | Glyphosate (GP) is a widely used herbicide worldwide, yet accumulation of GP and its main byproduct, aminomethylphosphonic acid (AMPA), in soil and water has raised concerns about its potential effects to human health. Thermal treatment processes are one option for decontaminating material containing GP and AMPA, yet the thermal decomposition chemistry of these compounds remains poorly understood. Here, we have revealed the thermal decomposition mechanism of GP and AMPA by applying computational chemistry and reaction rate theory methods. <br /> | Milad Narimani; Gabriel da Silva | Environmental Science; Soil Science; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7463bee301c812ac79494/original/thermal-decomposition-kinetics-of-glyphosate-gp-and-its-metabolite-aminomethylphosphonic-acid-ampa.pdf |
60c747d54c8919726ead2e19 | 10.26434/chemrxiv.11809077.v1 | A Variation of Favorskii Rearrangement Mechanism Under Weakly Acidic Conditions: The Case of Clobetasol Propionate Degradation in Solution | This paper describes our efforts in proposing a novel mechanism for the
formation of the major degradant of clobetasol propionate under weakly acidic
conditions through a comprehensive investigation. In the proposed mechanism, the
key Favorskii intermediate plays a critical role. This variation of the
original Favorskii rearrangement, which proceeds only under alkaline conditions, has
not been reported before. This mechanism enriches the understanding of
the degradation chemistry of corticosteroids containing the α-haloketone
moiety on their 17-position. | Yun Tian; Haoran Zhang; Zach Zhu; Li Chen; Evelyn Wang; Jianyang Jin; Dan Li; Wenquan Zhu; Min Li; Lei Fu | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747d54c8919726ead2e19/original/a-variation-of-favorskii-rearrangement-mechanism-under-weakly-acidic-conditions-the-case-of-clobetasol-propionate-degradation-in-solution.pdf |
676468d96dde43c908a610ff | 10.26434/chemrxiv-2024-vjk7p | pyGlobOpt: Parallel Global Optimization Software for Nanoclusters, Materials, and Beyond | With the ever-increasing demand for atomistic structures representative of real-life systems as well as the ad-vent of exascale computers, it has now become necessary and possible to use advanced global optimization (GO) techniques to intelligently sample the potential energy surface (PES). Given the previous studies demonstrating the relative efficiency of the artificial bee colony (ABC) swarm intelligence algorithm for chemical systems, we turn to focus on maximizing the potential of this tool. This is achieved by producing a new software; pyGlobOpt is the first ABC algorithm tool that has an asynchronously parallel implementation, in practice this means that the number of concurrent sample geometries we are able to evaluate is only lim-ited to the size of computer available to us. Furthermore, pyGlobOpt interfaces directly with the atomistic simulation environment providing a huge array of potential energetic evaluators at our disposal to drive our algorithm. In this work, we show the implementation of GO algorithm and demonstrate its utility in a num-ber of examples, including the recovery of a Buckminster fullerene from a random distribution of C atoms and cluster distribution on the surface. | Małgorzata Z. Makoś; Julian Holland; Difan Zhang; Loukas Kollias; Mal-Soon Lee; Roger Rousseau; Chris-Kriton Skylaris; Vassiliki-Alexandra Glezakou | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676468d96dde43c908a610ff/original/py-glob-opt-parallel-global-optimization-software-for-nanoclusters-materials-and-beyond.pdf |
674a48e55a82cea2fa74ba87 | 10.26434/chemrxiv-2024-5gz7f | Mechanochemical Synthesis of Dynamic Hybrid Polymer Networks using Whole Biomass | Whole plant biomass from non-agricultural sources and waste biomass from processing agricultural products are promising feedstocks for biopolymer production because they are abundant and do not compete with food production. However, their processing steps are notoriously tedious with the final materials often displaying inferior performance and limited scope in their properties. Here, we report a strategy to integrate whole-cell spirulina, a green-blue algae, into mechanically robust hybrid biomass-polyimine networks by leveraging mechanochemistry. This strategy provides a greener synthetic approach to conventional solution-phase methods for polyimine synthesis, and it simultaneously overcomes persistent constraints encountered in biomass processing and derivatization. The hybrid algae-based materials retain recyclability imparted by the underlying dynamic covalent polymer matrix and display enhanced mechanical properties compared to their all-synthetic equivalents. These advantageous properties are attributed to differences in morphology between 1) the all-synthetic material and the hybrid materials and 2) their respective synthetic methods (solution-phase vs mechanochemical). Substituting spirulina with alternative biomass sources such as waste agricultural products also yields robust hybrid materials, thus highlighting the generality of this mechanochemical approach. | Meng Jiang; Emily Bird; Woojung Ham; Joshua Worch | Polymer Science; Biopolymers; Cellulosic materials; Polymer scaffolds; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674a48e55a82cea2fa74ba87/original/mechanochemical-synthesis-of-dynamic-hybrid-polymer-networks-using-whole-biomass.pdf |
60c74faff96a0059ca287cb5 | 10.26434/chemrxiv.12931703.v1 | π-Extended Helical Nanographenes: Synthesis and Photophysical Properties of Naphtho[1,2-a]pyrenes | A mild and efficient synthesis of a broad scope of substituted naphtho[1,2-<i>a</i>]pyrene derivatives was accomplished in good yields using an InCl<sub>3</sub>/AgNTf<sub>2</sub>-mediated two-fold alkyne benzannulation reaction. HPLC enantiomeric separation was achieved and the interconversion barriers have been determined. The ECD spectra of two derivatives were recorded and interpreted through TD-DFT calculations. Raman spectra were also recorded and predicted through DFT calculations. | Paban Sitaula; Ryan Malone; Giovanna Longhi; Sergio Abbate; Eva Gualtieri; Andrea Lucotti; Matteo Tommasini; Roberta Franzini; Claudio Villani; Vincent J. Catalano; Wesley Chalifoux | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74faff96a0059ca287cb5/original/extended-helical-nanographenes-synthesis-and-photophysical-properties-of-naphtho-1-2-a-pyrenes.pdf |
60c746bfbdbb897e79a38c63 | 10.26434/chemrxiv.11385906.v1 | SuFEx-Enabled High-Throughput Medicinal Chemistry | <p>Optimization of small-molecule probes or drugs is a lengthy, challenging and resource-intensive process. Lack of automation and reliance on skilled medicinal chemists is cumbersome in both academic and industrial settings. Here, we demonstrate a high-throughput hit-to-lead process based on the biocompatible SuFEx click chemistry. A modest high-throughput screening hit against a bacterial cysteine protease SpeB was modified with a SuFExable iminosulfur oxydifluoride [RN=S(O)F2] motif, rapidly diversified into 460 analogs in overnight reactions, and the products directly screened to yield drug-like inhibitors with 300-fold higher potency. We showed that the improved molecule is drug-like and biologically active in a bacteria-host coculture. Since these reactions can be performed on a picomole scale to conserve reagents, we anticipate our methodology can accelerate the development of robust biological probes and drug candidates.</p> | Seiya Kitamura; Qinheng Zheng; Jordan L. Woehl; angelo solan; Emily Chen; Nicholas Dillon; Mitchell Hull; Miyako Kotaniguchi; Shinichi Kitamura; Victor Nizet; K. Barry Sharpless; Dennis Wolan | Biochemistry; Chemical Biology; 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/60c746bfbdbb897e79a38c63/original/su-f-ex-enabled-high-throughput-medicinal-chemistry.pdf |
60c7436e702a9b068c18a5c8 | 10.26434/chemrxiv.7959110.v2 | Systematic Exploration of the Mechanical Properties of 13,621 Inorganic Compounds | In order to better understand the mechanical properties of crystalline materials, we performed a large-scale exploration of the elastic properties of 13,621 crystals from the Materials Project database, including both experimentally synthesized and hypothetical structures. We studied both their average (isotropic) behavior, as well as the anisotropy of the elastic properties: bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio, and linear compressibility. We show that general mechanical trends, which hold for isotropic (noncrystalline) materials at the macroscopic scale, also apply “on average” for crystals. Further, we highlight the importance of elastic anisotropy and the role of mechanical stability as playing key roles in the experimental feasibility of hypothetical compounds. We also quantify the frequency of occurrence of rare anomalous mechanical properties: 3% of the crystals feature negative linear compressibility, and only 0.3% have complete auxeticity. | Siwar Chibani; François-Xavier Coudert | Elastic Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436e702a9b068c18a5c8/original/systematic-exploration-of-the-mechanical-properties-of-13-621-inorganic-compounds.pdf |
6627c33021291e5d1d7c0c5c | 10.26434/chemrxiv-2024-f52p7 | Terahertz Signatures of the Methane Replacement Reaction in Hydroquinone Clathrates | We report a comprehensive experimental and computational study into the low-frequency vibrational dynamics of hydroquinone clathrate during in situ gas loading, in order to monitor the replacement of carbon dioxide with methane in the atomic-level pores of the material. Specifically, terahertz time-domain spectroscopy is utilized, as the terahertz modes are highly-sensitive to the identity and structure of the enclathrated guest molecules. Through the use of ab initio simulations, it was clearly determined that the replacement reaction does not go to completion, and instead we observe the formation of a heterogenous material, with the methane molecules occupying approximately one third of the available adsorption sites. Additionally, while the structure of the methane-hydroquinone clathrate system has been previously determined, our observations suggest that the reported symmetry is incorrect due to methane molecules weakly-interacting with the framework, resulting in dynamic disorder (as opposed to positional disorder) of the guests, unlike the related carbon dioxide clathrate system that is fully-ordered. This work puts us on the path to quantitatively tracking gas loading in porous materials using terahertz spectroscopy. | Katharine Bancroft; Saheed Ajibade; Johanna Koelbel; Michael Ruggiero; Daniel Mittleman | Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6627c33021291e5d1d7c0c5c/original/terahertz-signatures-of-the-methane-replacement-reaction-in-hydroquinone-clathrates.pdf |
67c9a69181d2151a0252bb0b | 10.26434/chemrxiv-2025-jr3p6-v2 | Catalyst Phylogenetic Tree: A Visualization Tool for Exploring Catalyst Research and Development from Tabular Data | The rise of data-driven catalyst design has led to an increasing availability of curated catalyst datasets. These datasets likely contain historical trends that could guide research, but extracting such trends from high-dimensional, high-volume data remains challenging, limiting broader use beyond data scientists. This study proposes a catalyst phylogenetic tree, a pipelined method for visualizing vast catalyst datasets to provide an overview of their evolution. It groups catalysts by distinct elemental combinations, termed catalyst sets, and maps their physicochemical distances onto a phylogenetic tree. Applied to two publicly available datasets on oxidative coupling and dry reforming of methane, this method successfully identified catalyst lineages with similar designs emerging across different eras, as well as the standard catalyst designs for each lineage. This approach can be extended beyond catalyst data to various materials, maximizing the value of literature-based data curation and accelerating research and development across diverse fields. | Sunao Nakanowatari; Toshiaki Taniike | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c9a69181d2151a0252bb0b/original/catalyst-phylogenetic-tree-a-visualization-tool-for-exploring-catalyst-research-and-development-from-tabular-data.pdf |
66e43e3a12ff75c3a138bca8 | 10.26434/chemrxiv-2024-41295 | Crossover Operators for Molecular Graphs with an Application to Virtual Drug Screening | Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for searching over spaces of graphs. These operators are based on introducing small cuts into graphs and rejoining the resulting induced subgraphs of two parents. This form of cut-and-join crossover can be restricted in a consistent way to preserve local properties such as vertex-degrees (valency), or bond-orders, as well as global properties such as graph-theoretic planarity. In contrast to crossover on strings, cut-and-join crossover on graphs is powerful enough to ergodically explore chemical space even in the absence of mutation operators. Extensive benchmarking shows that the offspring of molecular graphs are again plausible molecules with high probability, while at the same time crossover drastically increases the diversity compared to initial molecule libraries. Moreover, desirable properties such as favorable indices of synthesizability are preserved with sufficient frequency that candidate offsprings can be filtered efficiently for such properties. As an application we utilized the cut-and-join crossover in REvoLd, a GA-based system for computer-aided drug design. In optimization runs searching for ligands binding to four different target proteins we consistently found candidate molecules with binding constants exceeding the best known binders as well as candidates found in make-on-demand libraries. Taken together, cut-and-join crossover operators constitute a mathematically simple and well-characterized approach to recombination of molecules that performed very well in real-life CADD tasks. | Nico Domschke; Bruno Schmidt; Thomas Gatter; Richard Golnik; Paul Eisenhuth; Fabian Liessmann; Jens Meiler; Peter F Stadler | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e43e3a12ff75c3a138bca8/original/crossover-operators-for-molecular-graphs-with-an-application-to-virtual-drug-screening.pdf |
60c742a69abda2816af8c04a | 10.26434/chemrxiv.8317127.v1 | Isomerization of the Isoprene Hydroxy Nitrates and Formation of Orthonitrite Compounds | Atmospheric oxidation of isoprene produces significant yields of eight unique nitrate 11 compounds, each with a β- or δ-hydroxy group. These isoprene hydroxy nitrates (ISOPNs) 12 significantly impact upon global NOx budgets, O3 levels, and aerosol formation. 13 Uncertainties exist, however, in our understanding of ISOPN chemistry, particularly in their 14 yields from the reaction of isoprene peroxyl radicals with NO. This study describes novel 15 isomerization reactions of the ISOPNs, identified through the application of computational 16 chemistry techniques. These reactions produce saturated polycyclic orthonitrite compounds 17 via attack of the R–NO2 group on the vinyl moiety. For the δ-hydroxy nitrates, low-energy 18 isomerization pathways exist to six-membered ring compounds that are around 5 kcal mol-1 19 exothermic. These reactions proceed with barriers around 15 kcal mol-1 below the 20 respective peroxyl radical + NO reactants and yield orthonitrites that can further isomerize 21 to β-hydroxy ISOPNs. Moreover, the δ-hydroxy nitrates can directly interconvert with their β 22 substituted counterparts via NO3 group migration, with barriers that are lower yet. It follows 23 that β-hydroxy nitrates may be stabilized in the δ-hydroxy form, and vice versa. Moreover, 24 the lowest-energy pathway for dissociation of the δ-hydroxy ISOPNs is for the formation of 25 β-hydroxy alkoxyl radicals, and because of this established branching fractions between the 26 various isoprene peroxyl radicals may require re-evaluation. The results presented here also 27 suggest that ISOPNs may be stabilized to some extent in their saturated orthonitrite forms, 28 which has implications for both the total nitrate yield and for their subsequent removal by 29 OH, O3, and photolysis.<br /><br /> | Gabriel da Silva | Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742a69abda2816af8c04a/original/isomerization-of-the-isoprene-hydroxy-nitrates-and-formation-of-orthonitrite-compounds.pdf |
6794bc0cfa469535b9cb8766 | 10.26434/chemrxiv-2025-rg620 | Mechanistic insight into the light absorption and charge carrier separation in photoelectrochemical performance of oxygen-doped g-C3N4 and oxygen-vacancy-enriched Mn3O4 nanocomposites | With the increasing awareness of the universal need to access clean and renewable energy resources, semiconductor photoelectrocatalysis has emerged as an efficient way to utilize light photons and produce hydrogen. Among different materials used for photoelectrocatalysis, graphitic carbon nitride (g-C3N4) is a promising photoelectrode; but possesses some drawbacks. Also, most researchers are focused on the anodic application of g-C3N4-based materials; while its cathodic performance has remained less investigated. In the present study, a g-C3N4-based nanocomposite made of oxygen-doped g-C3N4 nanosheets, and oxygen-vacancy-containing Mn3O4 nanoparticles with a size range of 20-30 nm was synthesized as photocathode through a facile method and carefully characterized. The internal electric field in the interface enhanced the charge carrier separation compared to both g-C3N4 and oxygen-doped g-C3N4, with an impressive cathodic photocurrent density of the resulting nanocomposite (-5.28 mA.cm-²) higher than those of g-C3N4 (-2.51 mA.cm-²) and oxygen-doped g-C3N4 (-5.05 mA.cm-²) at -1 V vs. Ag/AgCl at pH=7. The bandgap of the oxygen-doped g-C3N4, oxygen-vacancy-enriched Mn3O4, and the resulting nanocomposite were approximately 1.5 eV, 1.4 eV, and 1.6 eV, respectively, and the light absorption ranges for the materials were clearly expanded to the visible region. The specific surface area of the nanocomposite was obtained by BET analysis to be 224.65 m2.g-1, representing a remarkable rise in comparison with oxygen-doped graphitic carbon nitride, contributing to the high photoelectrochemical performance of the nanocomposite electrode. In this platform, the oxygen-vacancy-enriched Mn3O4 also serves as an effective co-catalyst, eliminating the need to use precious materials such as platinum particles. | Elahe Zandy; Alborz Bakhtiari; Hamid Reza Madaah Hosseini | Materials Science; Nanoscience; Energy; Carbon-based Materials; Nanostructured Materials - Materials; Photosensitizers | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6794bc0cfa469535b9cb8766/original/mechanistic-insight-into-the-light-absorption-and-charge-carrier-separation-in-photoelectrochemical-performance-of-oxygen-doped-g-c3n4-and-oxygen-vacancy-enriched-mn3o4-nanocomposites.pdf |
67d49c7c81d2151a0269228b | 10.26434/chemrxiv-2025-5s46n | A Graph Theory-Based Algorithm for the Reduction of Atmospheric Chemical Mechanisms | The atmospheric chemistry of volatile organic compounds (VOC) has a major influence on atmospheric pollutants and particle formation. Accurate modeling of this chemistry is essential for air quality models. Complete representations of VOC oxidation chemistry are far too large for spatiotemporal simulations of the atmosphere, necessitating reduced mechanisms. We present Automated MOdel REduction version 2.0 (AMORE 2.0), an algorithm for the reduction of any VOC oxidation mechanism to a desired size by removing, merging, and rerouting sections of the graph representation of the mechanism. We demonstrate the algorithm on isoprene (398 species) and camphene (100,000 species) chemistry. We remove up to 95% of isoprene species while improving upon prior reduced isoprene mechanisms by 53-67% using a multi-species metric. We remove 99% camphene species while accurately matching camphene secondary organic aerosol production. This algorithm will bridge the gap between large and reduced mechanisms, helping to improve air quality models. | Forwood Wiser; Siddhartha Sen; Zhizhao Wang; Julia Lee-Taylor; Kelley Barsanti; John Orlando; Daniel Westervelt; Daven Henze; Arlene Fiore; Alexander Berman; Reese Carter; V. Faye McNeill | Chemical Engineering and Industrial Chemistry; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d49c7c81d2151a0269228b/original/a-graph-theory-based-algorithm-for-the-reduction-of-atmospheric-chemical-mechanisms.pdf |
60c749ae4c8919c90aad3102 | 10.26434/chemrxiv.12097908.v1 | Autonomous Titration for Chemistry Classrooms: Preparing Students for Digitized Chemistry Laboratories | <div>
<div>
<div>
<div>
<p>The digitalization of the economy is one of the drivers of the fourth industrial revolution. This
trend is already heavily permeating biology laboratories and rapidly moving into chemistry as
well. Notably, automated laboratories enhance process quality and intensification while freeing
researchers from repetitive tasks. With these societal changes in place, students need to be
prepared for the advanced digitization of chemistry and science by teaching fundamental
chemistry concepts in combination with emerging Industry 4.0 technologies, including
programming and automation. We describe an undergraduate classroom exercise at the
interface of chemistry, computer science and engineering based on the development of an
autonomous titration platform. Following an inquiry learning ansatz, the exercise focuses on
standard titration experiments which are first executed manually, then automatically and finally
in full autonomy by a student-designed robotic platform. We demonstrate that the exercise
introduced in this work enables students to learn fundamental concepts in analytical chemistry,
naturally integrates basic aspects of programming and automation, and as a consequence
promotes and reinforces the detailed understanding of experimental processes and
measurements. The exercise is designed in a collaborative active learning framework to
encourage complex critical thinking and creative problem solving and thus prepares students for
the next-generation chemistry laboratories.
</p>
</div>
</div>
</div>
</div> | Florian Häse; Teresa Tamayo-Mendoza; Carmen Boixo; Jonathan Romero; Loic Roch; Alan Aspuru-Guzik | Chemical Education - General; Analytical Apparatus; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749ae4c8919c90aad3102/original/autonomous-titration-for-chemistry-classrooms-preparing-students-for-digitized-chemistry-laboratories.pdf |
6706dd9812ff75c3a1fd018f | 10.26434/chemrxiv-2024-rxkf4 | On-Demand Access to Palladium Oxidative Addition Complexes (OACs) from a Stable Organopalladate Salt | Palladium oxidative addition complexes (OACs) are state-of-the-art catalysts for many C¬–C and C–heteroatom cross-coupling reac-tions, but altering the OAC ancillary ligand identity (i.e., phosphine, N-heterocyclic carbene) often requires a bespoke synthesis. This has limited the modularity and accessibility of these ideal catalysts. We report a simple admixture approach combining a bench-stable or-ganopalladate salt with a mono- or bidentate ligand to generate OACs within minutes at room temperature. High yields across a suite of canonical cross-coupling reactions demonstrates the “on-demand” Pd OAC strategy can function as a drop-in replacement for isolated OACs as well as several other contemporary Pd precatalysts. Characterization of a previously unknown OAC coordinated by a single NHC ligand also highlights how this approach can circumvent decomposition of thermally sensitive OACs that are difficult to access directly from oxidation addition reactions. | Aidan Looby; Lalu Venigalla; Wenjun Hou; Mengyuan Xiao; Yongqing Yang; Hao Chen; Brad Carrow | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Transition Metal Complexes (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706dd9812ff75c3a1fd018f/original/on-demand-access-to-palladium-oxidative-addition-complexes-oa-cs-from-a-stable-organopalladate-salt.pdf |
6533e5cec3693ca993ced462 | 10.26434/chemrxiv-2023-ltkj1 | Selective C(sp3)–H Arylation/Alkylation of Alkanes Enabled by Paired Electrocatalysis | We report a combination of electrocatalysis and photoredox catalysis to perform selective C(sp3)–H arylation/alkylation of alkanes for the first time, in which a binary catalytic system based on earth-abundant iron and nickel is applied. Reaction selectivity between two-component C(sp3)–H arylation and three-component C(sp3)–H alkylation is tuned by modulating the applied current and light source. Importantly, an ultra-low anodic potential (~0.23 V vs. Ag/AgCl) is applied in this protocol, thus enabling compatibility with a variety of functional groups (> 70 examples). The robustness of the method is further demonstrated on a preparative scale and applied to late-stage diversification of natural products and pharmaceutical derivatives. | Long Zou; Siqi Xiang; Rui Sun; qingquan lu | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6533e5cec3693ca993ced462/original/selective-c-sp3-h-arylation-alkylation-of-alkanes-enabled-by-paired-electrocatalysis.pdf |
60c7453f469df4db67f434a0 | 10.26434/chemrxiv.9999548.v1 | Theoretical Examination of Efficiency of Anthocyanidins as Sensitizers in Dye-Sensitized Solar Cells | After experimental studies on the application of anthocyanidins as sensitizers in dye-sensitized solar cells (DSSCs) we have used computational methods to further elucidate the data obtained in the experimental study. In this study structural effects and electronic contributions of four anthocyanidins, cyanidin (Cy), delphinidin (Dp), malvidin (Mv) and pelargonidin (Pg), to improve the efficiency of DSSCs were investigated, using quantum chemical method, the density functional theory (DFT), to calculate parameters such as frontier molecular orbitals, band gap energies, reactivity descriptors.<br /> | Ibrahim Olasegun Abdulsalami; Banjo Semire; Issa Adewale Bello | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453f469df4db67f434a0/original/theoretical-examination-of-efficiency-of-anthocyanidins-as-sensitizers-in-dye-sensitized-solar-cells.pdf |
60c9e3b11fd5336b7156ac7a | 10.26434/chemrxiv.14776458.v1 | Selective Catalysis for the Reductive Amination of Furfural Towards Furfurylamine by the Graphene-Co-Shelled Cobalt Nanoparticles | <p>Amines with
functional groups are widely used in the manufacture of pharmaceuticals,
agricultural chemicals, polymers, and surfactants; so far, amines are mostly
produced via petrochemical routes, which <a></a><a>motivates the
sustainable production of amines from renewable resources</a>, such as
biomass. Unfortunately, the reductive amination of biomass-derived platforms is
now suffering from challenges, e.g. poor <a></a><a>selectivity </a>and
carbon balances, because of the restriction of homogenous catalyst. For this
reason, we developed an eco-friendly, simplified, and highly effective procedure
for the preparation of non-toxic heterogeneous catalyst based on the earth-abundant
metals (i.e., cobalt), whose catalytic activity on furfural or other biomass-derived
platforms were proved to be broadly available. The corresponding conversion rate
and few of side products were also determined so as to optimized the reaction
conditions, suggesting that the prepared cobalt-supported catalyst enables easy
substitution of –NH<sub>2 </sub>moiety towards functionalized and structurally
diverse molecules, even under very mild industrially viable and scalable
conditions. More surprisingly, the cobalt-supported catalyst could also be expediently
recycled by magnetic bar and still remained the excellent catalytic activity
after reusing up to eight times; on another hands, the gram-scale reductive
amination catalyzed by the same catalyst exhibited the similar yield of target
products in comparison to its smaller scale, which was comparable to the
reported heterogeneous noble-based catalysts. And also, results from a series
of analytic technologies involving XRD, XPS, TEM/Mapping and <i>in-suit</i> FTIR revealed that the structural
features of catalyst are closely in relation to its catalytic mechanisms; in
simple terms, <a></a><a>the outer graphitic shell is activated by the
electronic interaction between the inner </a><a></a><a>metallic </a>nanoparticles
and the carbon layer as well as the induced charge redistribution.
In conclusion, this newly developed catalysts enable the synthesis of amines
from biomass-derived platforms with satisfied selectivity and carbon balance,
providing a cost-effective and sustainable access to the widely application of reductive
amination.</p> | Xiuzheng Zhuang; Jianguo Liu; Shurong Zhong; Longlong Ma; 修政 庄 | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b11fd5336b7156ac7a/original/selective-catalysis-for-the-reductive-amination-of-furfural-towards-furfurylamine-by-the-graphene-co-shelled-cobalt-nanoparticles.pdf |
60c75070702a9b6ad618bd8b | 10.26434/chemrxiv.13040810.v1 | Quantifying Uncertainties in Solvation Procedures for Modeling Aqueous Phase Reaction Mechanisms | <div>Computational quantum chemistry modeling provides fundamental chemical and physical insights into solvated reaction mechanisms across many areas of chemistry, especially in homogeneous and heterogeneous renewable energy catalysis. Such reactions may depend on explicit interactions with ions and solvent molecules that are non-trivial to characterize. Rigorously modeling explicit solvent effects with molecular dynamics usually brings steep computational costs while the performance of continuum solvent models such as polarizable continuum model (PCM), nonlocal solvent models with charge asymmetry (CANDLE), conductor-like screening model for real solvents (COSMO-RS) and effective screening medium method with the reference interaction site model (ESM-RISM) are less well understood for reaction mechanisms. Here, we revisit a fundamental aqueous phase hydride transfer reaction, carbon dioxide (CO2) reduction by sodium borohydride (NaBH4), as a test case to evaluate how different solvent models perform in aqueous phase charge migrations that would be relevant in general to renewable energy catalysis mechanisms. For this system, quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations almost exactly reproduced energy profiles from all-QM simulations, and the Na+ counterion in the QM/MM simulations plays an insignificant role over ensemble averaged trajectories that describe the reaction pathway.</div><div>However, solvent models used on static calculations gave much more variability in data depending on whether the system was modeled using explicit solvent shells and/or the counter ion. We pinpoint this variability due to unphysical descriptions of charge-separated states in the gas phase (i.e., self-interaction errors), and we show that using more accurate hybrid functionals and/or explicit solvent shells will lessens these errors and allow more reliable results to be obtained.</div><div>This work closes with recommended procedures for treating solvation in future computational efforts in studying renewable energy catalysis mechanisms.</div> | alex maldonado; Satoshi Hagiwara; Tae Hoon Choi; Frank Eckert; Kathleen Schwarz; Ravishankar Sundararaman; Minoru Otani; John Keith | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75070702a9b6ad618bd8b/original/quantifying-uncertainties-in-solvation-procedures-for-modeling-aqueous-phase-reaction-mechanisms.pdf |
61751dfe0f3eeb03006e5229 | 10.26434/chemrxiv-2021-kgcx5 | Mechanochemical Nucleophilic Substitution of Alcohols via Isouronium Intermediates | An expansion of the solvent-free synthetic toolbox is essential for advances in the sustainable chemical industry. Mechanochemical reactions offer a superior safety profile and reduced amount of waste compared to conventional solvent-based synthesis. Herein we report a new mechanochemical method for nucleophilic substitution of alcohols using fluoro-N,N,N′,N′-tetramethylformamidinium hexafluorophosphate (TFFH) and K2HPO4 as an alcohol-activating reagent and a base, respectively. Alcohol activation and reaction with a nucleophile were performed in one milling jar via reactive isouronium intermediates. Nucleophilic substitution with amines afforded alkylated amines in 40–91% yields. The complete stereoinversion occurred for the SN2 reaction of (R)- and (S)-ethyl lactates. Substitution with halide anions (F−, Br−, I−) and oxygen-centered (CH3OH, PhO−) nucleophiles was also tested. Application of the method to the synthesis of active pharmaceutical ingredients (APIs) has been demonstrated. | Tatsiana Dalidovich; Jagadeesh Varma Nallaparaju; Tatsiana Shalima; Riina Aav; Dzmitry G. Kananovich | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61751dfe0f3eeb03006e5229/original/mechanochemical-nucleophilic-substitution-of-alcohols-via-isouronium-intermediates.pdf |
66f238ffcec5d6c14204501e | 10.26434/chemrxiv-2024-m9ss2 | Chlorination and Oxygenation of Carbon Electrodes for Covalent Attachment of Thiol-Terminated Molecules | This study investigated the reactivity of two carbon electrodes (glassy carbon - GC and carbon powder - CP), with iodine monochloride for surface chlorination and subsequent covalent attachment of thiol-terminated molecules, (6-mercaptohexyl)ferrocene and benzene-1,2,4,5-tetrathiol. X-ray photoelectron spectroscopy analysis revealed that the iodine monochloride treatment resulted in chlorination and iodination of both carbon electrodes, with post-reaction GC exhibiting significant Cl:C ratios. However, chlorination of either carbon electrode did not enhance reactivity with thiol-terminated molecules. For GC, inherent or anodized surface oxide groups were found to be equally effective for covalent attachment of thiol-terminated molecules through Michael addition as chlorine-termination through nucleophilic aromatic substitution. In contrast, CP, despite its lower surface reactivity, could directly tether (6-mercaptohexyl)ferrocene without pretreatment or chlorination. Furthermore, a tetrathiolate bridge was successfully employed to covalently attach a molybdenum complex to anodized GC. | Xin Zheng; Igor L. Bolotin; Beria Tanriover; Kumuditha Rathnayake; Erik J. Askins; Jordi Cabana; Neal P. Mankad; Ksenija D. Glusac | Physical Chemistry; Materials Science; Inorganic Chemistry; Carbon-based Materials; Electrochemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f238ffcec5d6c14204501e/original/chlorination-and-oxygenation-of-carbon-electrodes-for-covalent-attachment-of-thiol-terminated-molecules.pdf |
60d9a819e2113346a9e12170 | 10.26434/chemrxiv-2021-grnzt | Hidden Lewis acidity: Studies on the medium and structure dependent fluorescence of zinc(II) complexes | Three new zinc(II) coordination units [Zn(1–3)] based on planar-directing tetradentate Schiff base-like ligands H2(1–3) were synthesized. Their solid-state structures were investigated by single crystal X-ray diffraction, showing the tendency to overcome the square-planar coordination sphere by axial ligation. Affinity in solution towards axial ligation has been tested by extended spectroscopic studies, both in the absorption and emission mode. The electronic spectrum of the pyridine complex [Zn(1)(py)] has been characterized by multiconfiguration pair-DFT to validate the results of extended TD-DFT studies. Green emission of fluorescence-silent solutions of [Zn(1–3)] in chloroform could be switched on in the presence of potent Lewis-bases. While interpretation in terms of an equilibrium of stacked/non-fluorescent and destacked/fluorescent species is in line with precedents from literature, the sensitivity of [Zn(1–3)] was greatly reduced. Results of a computation-based structure search allow to trace the hidden Lewis acidity of [Zn(1–3)] to a new stacking motif, resulting in a strongly enhanced stability of the dimers. | Hannah Kurz; Gerald Hörner; Oskar Weser; Giovanni Li Manni; Birgit Weber | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Ligand Design; Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d9a819e2113346a9e12170/original/hidden-lewis-acidity-studies-on-the-medium-and-structure-dependent-fluorescence-of-zinc-ii-complexes.pdf |
679d46db81d2151a02b76442 | 10.26434/chemrxiv-2025-9xjh5 | Examining the Influence of Graph Representation on Property Prediction of Polymorphic Organic Molecular Crystals | Organic semiconductors (OSCs) can exhibit polymorphism, which may impact the physichochemical properties of the material, including the bandgap. With the advent of machine learning, graph neural networks have been used to predict the bandgap of OSCs. However, these frameworks struggle with differentiating between polymorphs. Here, we examine the performance of two graph representations, one including incorporation of angular information and one including only edge and node information, on two datasets, the Organic Materials Database (OMDB) and Organic Crystals in Electronic and Light-Oriented Technologies (OCELOT). We find that incorporating angle featurization improves the performance of the model on both databases. We also test the models on two cases: the polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY) and an augmented version of the PAH101 dataset. We find that angular featurization significantly improves the ability of the model to differentiate between polymorphs in the prediction of the bandgap. | Dana O'Connor; Paola Buitrago | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679d46db81d2151a02b76442/original/examining-the-influence-of-graph-representation-on-property-prediction-of-polymorphic-organic-molecular-crystals.pdf |
657fa2609138d23161e86b31 | 10.26434/chemrxiv-2023-27mjd | Cooperative Fe/Co Catalyzed Remote Desaturation for the Synthesis of Unsaturated Amide Derivatives | Unsaturated amides represent common functional groups found in natural products and bioactive molecules, serving as versatile synthetic building blocks. Here, we report an iron(II)/cobalt(II) dual catalytic system for the syntheses of distally unsaturated amide derivatives. The transformation proceeds through an iron nitrenoid-mediated 1,5-hydrogen atom transfer (1,5-HAT) mechanism. Subsequently, the radical intermediate undergoes hydrogen atom abstraction from the vicinal methylene by a cobaloxime catalyst, efficiently yielding β,γ- or γ,δ-unsaturated amide derivatives under mild conditions. The efficiency of Co-mediated HAT is tunable by varying different auxiliaries, highlighting the generality of this protocol. Remarkably, this desaturation protocol is also amenable to practical scalability, enabling the synthesis of unsaturated carbamates and ureas which can be readily converted into various valuable molecules. | Yanjun Wan; Emmanuel Ramirez; Ayzia Ford; Harriet K. Zhang; Jack R. Norton; Gang Li | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657fa2609138d23161e86b31/original/cooperative-fe-co-catalyzed-remote-desaturation-for-the-synthesis-of-unsaturated-amide-derivatives.pdf |
661419ab418a5379b0686693 | 10.26434/chemrxiv-2024-0bhgz-v2 | Monomer Architecture as a Mechanism to Control the Self-Assembly of Oligomeric Diblock Peptide-Polymer Amphiphiles | Diblock oligomeric peptide-polymer amphiphiles (PPAs) are biohybrid materials that offer versatile functionality by integrating the sequence-dependent properties of peptides with the synthetic versatility of polymers. Despite their potential as biocompatible materials, the rational design of PPAs for assembly into multi-chain nanoparticles remains challenging due to the complex intra- and intermolecular interactions emanating from the polymer and peptide segments. To systematically explore the impact of monomer architecture on nanoparticle assembly, PPAs were synthesized with a random coil peptide (XTEN2) and oligomeric alkyl acrylates with unique side chains: ethyl, tert-butyl, n-butyl, and cyclohexyl. Experimental characterization using electron and atomic force microscopies demonstrated that tail hydrophobicity impacted accessible morphologies. Moreover, characterization of different assembly protocols (i.e., bath sonication and thermal annealing) revealed that certain tail architectures provide access to kinetically trapped assemblies. All-atom molecular dynamics simulations of micelle structure formation unveiled key interactions and differences in hydration states, dictating PPA assembly behavior. These findings highlight the complexity of PPA assembly dynamics and serve as valuable benchmarks to guide the design of PPAs for a variety of applications including catalysis, mineralization, targeted sequestration, antimicrobial activity, and cargo transportation | Benjamin Allen; Sabila Pinky; Emily Beard ; Abigail Gringeri; Nicholas Calzadilla ; Matthew Sanders; Yaroslava Yingling ; Abigail Knight | Theoretical and Computational Chemistry; Polymer Science; Nanoscience; Biopolymers; Polymer morphology; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661419ab418a5379b0686693/original/monomer-architecture-as-a-mechanism-to-control-the-self-assembly-of-oligomeric-diblock-peptide-polymer-amphiphiles.pdf |
6276ed6843d1f00dee23ed6d | 10.26434/chemrxiv-2022-ck2ll | Structure-Reactivity Relationships of Buchwald-Type Phosphines in Nickel-Catalyzed Cross-Couplings | The dialkyl-ortho-biaryl class of phosphines, commonly known as Buchwald-type ligands, are among the most important phosphines in Pd-catalyzed cross-coupling catalysis. These ligands have also recently been applied to select Ni-catalyzed cross-coupling methodologies. However, little is known about their structure-reactivity relationships (SRRs) with Ni, and limited examples of well-defined, catalytically relevant Ni complexes with Buchwald-type ligands exist. In this work, we report the analysis of Buchwald-type phosphine SRRs in four representative Ni-catalyzed cross-coupling reactions. Our study was guided by data-driven classification analysis, which together with organometallic studies of structurally characterized Ni(0) and Ni(II) complexes and density functional theory allowed us to rationalize reactivity patterns in catalysis. Overall, we expect that this study will serve as a platform for further exploration of this ligand class in organonickel chemistry, as well as in the development of new Ni-catalyzed cross-coupling methodologies. | Samuel Newman-Stonebraker; Jason Wang; Philip Jeffrey; Abigail Doyle | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6276ed6843d1f00dee23ed6d/original/structure-reactivity-relationships-of-buchwald-type-phosphines-in-nickel-catalyzed-cross-couplings.pdf |
65e5b6839138d23161a2d109 | 10.26434/chemrxiv-2024-06jcc-v2 | Synthesis and Cytotoxic Activity of Madecassic Acid-Silybin Conjugate Compounds in Liver Cancer Cells | Madecassic acid – isolated from the medicinal herb Centella asiatica – and its derivatives exhibit cytotoxic activity against the HepG2 liver cancer cell line. Silybin, a natural compound from Silybum marianum, is well-known as a hepatoprotective agent. This paper describes the synthesis of madecassic acid-silybin conjugate compounds and evaluation of their cytotoxic activity against a range of liver cancer cell lines. Depending on the reaction conditions, the direct conjugation products of 2,3,23-triacetylmadecassic acid and silybin were found to be either an ester at position 7 of silybin (40%) and its 2,3-dehydrated derivative (20%), a 2,3-dehydrated ester at position 3 of silybin (42%), or an ester at position 3 of silybin with madecassic acid. We have also used linkers such as glycine, β-alanine and 11-aminoundecanoic acid. For further diversification, 2,3,23-triacetylmadecassic acid was dehydrated to form the Δ5,6-compound, and was converted to amide derivatives on reaction with glycine or β-alanine, and finally condensed with silybin to afford esters at position 3 of silybin. In total, sixteen new conjugates have been synthesized. The conjugates were tested in vitro for their cytotoxic effect on HepG2 cells using the MTT assay. Results confirmed the conjugated compounds demonstrated a stronger cytotoxic effect versus those of the parent compounds. Of these compounds, the most promising conjugate, compound 8, was evaluated for cytotoxic activity on the Hep3B, Huh7, and Huh7R liver cancer cell lines and also for induction of apoptosis. This compound caused a rapid and significant induction of caspase 3 activity in HepG2 cells and induced cell cycle arrest in S phase, effects distinct from the activity of madecassic acid. This is the first study on the synthesis and the cytotoxicity of the madecassic acid-silybin conjugates, and of their testing against liver cancer cell lines and provides evidence for a distinct biological profile versus madecassic acid alone. | Chien Van Tran; Thao Thi Phuong Tran; Anh The Nguyen; Loc Van Tran; Ninh Thi Pham; Luu Thi Nguyen; Dung Thi Nguyen; Michelle Garrett; Nga Thi Nguyen; Thao Thi Do; Christopher Serpell; Sung Van Tran | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e5b6839138d23161a2d109/original/synthesis-and-cytotoxic-activity-of-madecassic-acid-silybin-conjugate-compounds-in-liver-cancer-cells.pdf |
60c7463e4c89190c06ad2af8 | 10.26434/chemrxiv.11211245.v1 | Radical C‒N Borylation of Aromatic Amines Enabled by a Pyrylium Reagent | Herein, we report a radical borylation of aromatic amines through a homolytic C(sp2)‒N bond cleavage. This method capitalizes on a simple and mild activation via a pyrylium reagent (ScPyry-OTf) thus priming the amino group for reactivity. The combination of terpyridine and a diboron reagent triggers a radical reaction which cleaves the C(sp2)‒N bond and forges a new C(sp2)‒B bond. The unique non-planar structure of the pyridinium intermediate, provides the necessary driving force for the aryl radical formation. The method permits borylation of a wide variety of aromatic amines indistinctively of the electronic environment.<br /> | Yuanhong Ma; Yue Pang; jan niski; Markus Leutzsch; Josep Cornella | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7463e4c89190c06ad2af8/original/radical-c-n-borylation-of-aromatic-amines-enabled-by-a-pyrylium-reagent.pdf |
6104d0c88804435bbee4afe2 | 10.26434/chemrxiv-2021-l3gc0-v2 | Hypervalent Carbon Atoms in a Ferrocene Dication Derivative - [Fe(Si2C5H2)2]2+ | Pentacoordinate carbon atoms are theoretically predicted
here in a ferrocene dication derivative in both staggered-
[Fe(Si2C5H2)2]2+ (1; C2h) and eclipsed-[Fe(Si2C5H2)2]2+ (2; C2v) forms for the first time. Relative energy difference between these two ranges from -40.34 to 2.47 kJ/mol at different levels. The planar tetracoordinate carbon atom in the ligand Si2C5H2 becomes a hypervalent pentacoordinate carbon upon complexation. | Venkatesan S. Thimmakondu | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bonding; Coordination Chemistry (Inorg.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6104d0c88804435bbee4afe2/original/hypervalent-carbon-atoms-in-a-ferrocene-dication-derivative-fe-si2c5h2-2-2.pdf |
65fae84366c138172964a7e2 | 10.26434/chemrxiv-2024-sc4fj | Low-cost, syringe based ion-selective electrodes for the evaluation of potassium in food products and pharmaceuticals | Over the years, ion-selective electrodes (ISEs) have become routine means of analysis for industrial, environmental, and clinical applications, allowing for rapid, non-invasive, and easy disease monitoring and diagnostics. Their enormous advantages include wide dynamic range, ease of operation and low detector cost. Sets of ion-selective electrodes selective towards various ions can easily be assembled into an electronic tongue system. The additional information gained from other electrodes can help overcome the ISE’s inherent limitations, such as the need for recalibration in more complex samples of variable ionic strength. In this work we developed low-cost ion-selective electrodes made from disposable syringes equipped with plasticized PVC membranes. To characterize the system we have chosen well-studied ionophore valinomycin, and the results in model solutions were comparable to standard ISE electrodes fabricated using commercial bodies. However, quantification of potassium in real samples showed, as expected, that measurement in complex, more concentrated solutions of higher ionic strength, such as beetroot soup, tomato-based food products, and dried fruits, are reproducible but subject to relative error up to 76 %. To overcome this limitation, we have constructed an electronic tongue based on the low-cost syringe electrodes. Different compositions of the array were tested with a series of multivariate algorithms. We have shown that adding a single type of electrode coupled with an ensemble random forest model allows us to quantify potassium in a wide range of food products, and pharmaceutical supplements without recalibration. Compared to a quantification of potassium using a standard calibration curve, the root mean square error of prediction was almost six times lower. We have also shown how the array can be designed to achieve comparable analytical performance using less selec-tive ionophores, such as dibenzo-18-crown-6 instead of valinomycin. | Elzbieta Jarosinska; Julia Wojnowska; Martyna Durka; Marta Podrażka; Emilia Witkowska Nery | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fae84366c138172964a7e2/original/low-cost-syringe-based-ion-selective-electrodes-for-the-evaluation-of-potassium-in-food-products-and-pharmaceuticals.pdf |
671f357898c8527d9e999ac6 | 10.26434/chemrxiv-2024-vxw92 | Mechanistic Insights into Atom-Economical Bromoalkynylation of Ynamides: 1,3-Alkynyl Migration Explored through ¹³C Kinetic Isotope Effects, XPS, and DFT Analysis | Difunctionalization of ynamides, whether through an intermolecular approach or in an atom-economical manner, continues to pose a significant challenge. This work presents a simpler method for such unprecedented functionalization through a highly regio- and stereoselective bromoalkynylation. The developed strategy, which requires a Pd(II) catalyst and no additive, has a broad scope and high functional-group tolerance and provided access to fifty value-added -bromo ynenamides. In addition to late-stage functionalization, the synthetic potential of this method was demonstrated through rapid access to previously challenging -skeletons. A unique 1,3-alkynyl migration, which was enabled by carbopalladation, offers a platform for the development of atom-economical reactions. Experimental evidence, such as from Hammett plot analysis, XPS studies, and 13C kinetic isotope effect measurements, supported by density functional theory computations enabled a comprehensive understanding of the mechanism. | Tapas R. Pradhan; Gisela A. González-Montiel; Alina Dzhaparova; Eunseok Park; Paul Ha-Yeon Cheong; Jin Kyoon Park | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671f357898c8527d9e999ac6/original/mechanistic-insights-into-atom-economical-bromoalkynylation-of-ynamides-1-3-alkynyl-migration-explored-through-13c-kinetic-isotope-effects-xps-and-dft-analysis.pdf |
672318a87be152b1d08a6cf3 | 10.26434/chemrxiv-2024-5w5rp-v2 | Highly Efficient Crystallization Studies through Machine Learning and Automation | Crystallization is an important process in a broad range of industries, though studies on this topic remain complicated. Recently, machine learning has been applied to resolve complex issues in chemistry and material science. Here we present a machine learning model integrated into a robotic platform to effectively propose and automatically perform crystallization experiments for organic small molecules. The model was pretrained on around 140000 simulated data generated by a kinetic model, and fine-tuned by over 7000 experimental data obtained on the automated workstation. The improved prediction accuracy and working efficiency of our integrated platform were presented in case studies compared with the traditional approach by humans. A feature contribution analysis demonstrates that this model provides a holistic data-based perspective of promoting and inhibiting influences to crystallization. This work thereby demonstrates the feasibility of applying machine learning techniques to solid-state studies to reduce cost, boost efficiency and deepen understanding. | Zi Li; Wenbo Fu; Bochen Li; Jia Yao; Jiuchuang Yuan; Michael Bellucci; Guangxu Sun; Zhengtian Song; Shi Liu; Zhu Lang; Jian Ma; Shuhao Wen; Qun Zeng | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Machine Learning; Chemoinformatics - Computational Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672318a87be152b1d08a6cf3/original/highly-efficient-crystallization-studies-through-machine-learning-and-automation.pdf |
666fd9f05101a2ffa8c21071 | 10.26434/chemrxiv-2024-8kkgv | Chemical and Redox Non-Innocence in Low‐Valent Molybdenum β-Diketonate Complexes: Novel Pathways for CO2 and CS2 Activation | The investigation of fundamental properties of low-valent molybdenum complexes bearing anionic ligands is crucial for elucidating the molybdenum’s role in critical enzymatic systems involved in the transformation of small molecules, including the nitrogenase’s iron molybdenum cofactor, FeMoco. The β-diketonate ligands in [Mo(acac)3] (acac = acetylacetonate), one of the earliest low-valent Mo complexes reported, provide a robust anionic platform to stabilize Mo in its +III oxidation state. This complex played a key role in demonstrating the potential of low-valent molybdenum for small molecule activation, serving as the starting material for the preparation of the first reported molybdenum dinitrogen complex. Surprisingly however, given this fact and the widespread use of β-diketonate ligands in coordination chemistry, only a very limited number of low-valent Mo β-diketonate complexes have been reported. To address this gap, we explored the redox behavior of homoleptic molybdenum tris-β-diketonate complexes, employing a tertiary butyl substituted diketonate ligand (dipivaloylmethanate, tBudiket) to isolate and fully characterize the corresponding Mo complexes across three consecutive oxidation states (+IV, +III, +II). We observed marked reactivity of the most reduced congener with heterocumulenes CE2 (E = O, S), yet with very distinct outcomes. Specifically, CO2 stoichiometrically carboxylates one of the β-diketonate ligands, while in the presence of excess CS2, catalytic reductive dimerization to tetrathiooxalate occurs. Through the isolation and characterization of reaction products and intermediates, we demonstrate that the observed reactivity results from the chemical non-innocence of the 𝛽-diketonate ligands, which facilitates the formation of a common ligand-bound intermediate, tBuMo(II)·CE2 (E = O, S). The stability of this proposed intermediate dictates the specific reduction products observed, highlighting the relevance of the chemically non-innocent nature of 𝛽-diketonate ligands. | Fabio Masero; Victor Mougel | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666fd9f05101a2ffa8c21071/original/chemical-and-redox-non-innocence-in-low-valent-molybdenum-diketonate-complexes-novel-pathways-for-co2-and-cs2-activation.pdf |
60c74ac9567dfe52deec4e1b | 10.26434/chemrxiv.12245270.v1 | Naturally Occurring Anthraquinones as Potential Inhibitors of SARS-CoV-2 Main Protease: A Molecular Docking Study | <i>Background:</i> The novel coronavirus (COVID-19) has quickly spread
throughout the globe, affecting millions of people. The World Health Organization
(WHO) has recently declared this infectious disease as a pandemic. At present, several
clinical trials are going on to identify possible drugs for treating this
infection. SARS-CoV-2 M<sup>pro</sup> is one of the most critical drug targets
for the blockage of viral replication.
<i>Method:</i> The blind molecular docking
analyses of natural anthraquinones with SARS-CoV-2 M<sup>pro</sup> were carried
out in an online server, SWISSDOCK, which is based on EADock DSS docking
software.
<i>Results: </i>Blind molecular docking studies
indicated that several<i> </i>natural antiviral anthraquinones
could prove to be effective inhibitors for SARS-CoV-2 M<sup>pro</sup> of
COVID-19 as they bind near the active site having the catalytic dyad, HIS41 and
CYS145 through non-covalent forces. The anthraquinones showed less inhibitory
potential as compared to the FDA approved drug, remdesivir.<i></i>
<p><b><i>Conclusion:</i></b><i> </i>Among the natural anthraquinones<i>, </i>alterporriol Q could be the most potential inhibitor of SARS-CoV-2 M<sup>pro</sup>
among the natural anthraquinones studied here, as its ∆<i>G</i> value differed from that of remdesivir only by 0.51 kcal/ mol. The
uses of these alternate compounds might be favorable for the treatment of the
COVID-19.</p> | Sourav Das; Atanu Singha Roy | Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ac9567dfe52deec4e1b/original/naturally-occurring-anthraquinones-as-potential-inhibitors-of-sars-co-v-2-main-protease-a-molecular-docking-study.pdf |
63cbafb91fb2a81f93db71f2 | 10.26434/chemrxiv-2023-trsps | Ab initio chemical kinetics of Isopropyl acetate oxidation with OH radicals | Global reactivity descriptors of Isopropyl acetate (IPA) and thermo-kinetics aspects of its oxidation via the ground state (X2Π) and the first excited state (A2Σ+) •OH radicals have been studied computationally using the moderate ab initio composite method, restricted open-shell complete basis setquadratic Becke3 (ROCBSQB3), the accurate thermo-kinetic density functional method (DFT) M06-2X/cc-pVTZ and the time-dependent density functional TDDFT-M06-2X/cc-pVTZ//M06-2X/cc-pVTZ levels. Ten oxidation pathways have been investigated all of them are exothermic. The potential energy diagram has been sketched using different pre- and post-reactive complexes for all reactions. Rate constants calculations were obtained directly by connecting the separated reactants with different transition states and via an effective approach using the unimolecular Rice-Ramsperger-Kassel-Marcus (RRKM) and the transition state (TST) theories. The results indicate that the reaction of IPA with •OH radicals occurs in the ground state rather than the excited state and the rate constants obtained directly and from the effective approach are the same which confirmed the accuracy of the estimated pre-reactive complexes and the reaction mechanism. Rate constants and branching ratios show that H- atom abstraction from iso C-H (C2 atom) bond is the most kinetically preferable route up to 1000 K, while at higher temperature H-atom abstraction from the out-plane CH3 group (C3 atom) became the most dominant route with the high competition with that of in-plane CH3 group (C4 atom). | Mohamed Abdel-Rahman; Mohamed Mahmoud; Abolfazl Shiroudi; Mohamed Shibl | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cbafb91fb2a81f93db71f2/original/ab-initio-chemical-kinetics-of-isopropyl-acetate-oxidation-with-oh-radicals.pdf |
62b511a9b7bbed01dc8e2e01 | 10.26434/chemrxiv-2022-w700h-v2 | Plasmonic Nanoscale Temperature Shaping on a Single Titanium Nitride Nanostructure | Arbitrary shaping of temperature fields at the nanometer scale is an important goal in nanotechnology; this is challenging due to diffusive nature of heat transfer. In the present work, we have numerically demonstrated that spatial shaping of nanoscale temperature fields can be achieved by plasmonic heating of a single titanium nitride (TiN) nanostructure. A key feature of TiN is its low thermal conductivity (k_TiN = 29 [W m−1K−1]) compared with ordinary plasmonic metals such as Au (k_Au = 314 [W m−1K−1]). When localized surface plasmon resonance of a metal nanostructure is excited, light intensity will be converted to heat power density in the nanostructure via the Joule heating effect. For a gold nanoparticle, nonuniform spatial distributions of the heat power density will be disappeared due to the high thermal conductivity of Au; the nanoparticle surface will be entirely isothermal. In contrast, the spatial distributions of the heat power density can be clearly transcribed into temperature fields on a TiN nanostructure because heat dissipation is suppressed. In fact, we have revealed that highly localized temperature distributions can be selectively controlled around the TiN nanostructure in the several tens of nm spatial resolution depending on excitation wavelength. The present results indicate that the arbitrary temperature shaping at the nanometer scale can be achieved by designing the heat power density in TiN nanostructures in plasmonic heating, leading to unconventional thermofluidics and thermal chemical biology. | Mamoru Tamura; Takuya Iida; Kenji Setoura | Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b511a9b7bbed01dc8e2e01/original/plasmonic-nanoscale-temperature-shaping-on-a-single-titanium-nitride-nanostructure.pdf |
671ad3231fb27ce12480ceb7 | 10.26434/chemrxiv-2024-1lj6h | Supramolecular Assembly of Hypervalent Iodine Macrocycles and Alkali Metals | This study explores the solution- and solid-state assembly of phenylalanine based hypervalent iodine macrocycles (HIMs) with lithium and sodium cations. The metal cation binding of HIMs was evaluated by addition of lithium tetrakis(pentafluorophenyl)borate ethyl etherate (Li)BARF and sodium tetrakis[3,5-bis(trifluoromethyl)phenyl] borate (Na)BARF. The relatively electron rich, outwardly projected carbonyl oxygens of the HIM co-crystalize with the cations into bent supramolecular architectures. Both crystal structures show a pattern of assembly between HIM and metal cation in 2:1 ratio. While association with sodium leads to a polymer-like network, the lithium crystal structure was limited to dimeric assemblies of HIM. In the lithium coordinating complex, the oxygen-lithium-oxygen bond angle is approximately 98.83°, displaying a closer arrangement of two HIMs. In contrast, the sodium complex exhibits a more open orientation of two HIMs with an oxygen-sodium-oxygen bond angle close to 167.98°. Lastly, a comparative study of association constants and binding energies for phenylalanine based HIM with (Li)BARF and (Na)BARF are presented. | Krishna Pandey; Lucas Orton; Grayson Venus; Waseem Hussain; Toby Woods; Lichang Wang; Kyle Plunkett | Organic Chemistry; Materials Science; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Aggregates and Assemblies | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671ad3231fb27ce12480ceb7/original/supramolecular-assembly-of-hypervalent-iodine-macrocycles-and-alkali-metals.pdf |
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