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6771d1d681d2151a02508385 | 10.26434/chemrxiv-2024-dpqvv-v2 | 3-center-3-electron σ-Adduct Enables Silyl Radical Transfer Below the Minimum Barrier for Silyl Radical Formation | Transition-metal-catalyzed cleavage of the Si–H bond in silanes to yield silyl radicals requires substantial amounts of energy, which is commonly supplied by photons. For Rh(II) porphyrins, efficient hydrosilylation catalysis only becomes accessible upon site isolation in a MOF, and the formation of free silyl radicals likewise requires irradiation. Within the MOF, however, an uncommonly facile direct silyl radical transfer to olefin substrates is also possible, which makes thermal olefin hydrosilylation accessible at room temperature. The ability of MOF-supported Rh(II) metalloradicals to furnish an unprecedented 3-center-3-electron (3c-3e) Rh(II)-silane σ-adduct enables the assembly of a tri-component transition state that is comprised of Rh(II), silane and ethylene. The tri-component transition state bypasses the high-energy silyl radical species and enables silyl radical transfer with an activation free energy ~15 kcal∙mol–1 below the minimum energy barrier for silyl radical formation. We report direct observation of the 3c-3e silane σ-adduct, which is a stable species in the absence of light and olefins. Furthermore, a combination of experiments and quantum mechanical calculations show that direct silyl radical transfer to ethylene is promoted by the temporary oxidation of the transition structure by a proximal Rh(II) center. Thus, the crucial role of the MOF matrix is to fix the inter-Rh separation in our catalyst at a value large enough for 3c-3e silane adduct formation, but short enough for facile electron transfer. | Zihang Qiu; Paolo Cleto Bruzzese; Zikuan Wang; Hao Deng; Markus Leutzsch; Christophe Farès; Sonia Chabbra; Frank Neese; Alexander Schnegg; Constanze Neumann | Catalysis; Organometallic Chemistry; Nanoscience; Heterogeneous Catalysis; Bond Activation; Kinetics and Mechanism - Organometallic Reactions | CC BY 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6771d1d681d2151a02508385/original/3-center-3-electron-adduct-enables-silyl-radical-transfer-below-the-minimum-barrier-for-silyl-radical-formation.pdf |
61df103581f3fe82baa4f18c | 10.26434/chemrxiv-2022-qmnkv | Disclosing the role of C4-oxo substitution in the photochemistry of DNA and RNA pyrimidine monomers: Formation of photoproducts from the vibrationally-excited ground state | Oxo and amino substituted purines and pyrimidines have been suggested as protonucleobases participating in ancient pre-RNA forms. Considering electromagnetic radiation as a key environmental selection pressure in early Earth, the investigation of the photophysics of modified nucleobases is crucial to determine their viability as nucleobases’ ancestors and to understand the factors that rule the photostability of natural nucleobases. In this Letter, we combine femtosecond transient absorption spectroscopy and quantum mechanical simulations to reveal the photochemistry of 4-pyrimidinone, a close relative of uracil. Irradiation of 4-pyrimidinone with ultraviolet radiation populates the S1(pp*) state, which decays to the vibrationally-excited ground state in a few hundreds of femtoseconds. Analysis of the post-irradiated sample in water reveals the formation of a 6-hydroxy-5H-photohydrate and 3-(N-(iminomethyl)imino)propanoic acid as the primary photoproducts. 3-(N-(iminomethyl)imino)propanoic acid originates from the hydrolysis of an unstable ketene species generated from the C4-N3 photofragmentation of the pyrimidine core. | Eva Vos; Sean J. Hoehn; Sarah E. Krul; Carlos E. Crespo-Hernández; Jesús González-Vázquez; Inés Corral | Theoretical and Computational Chemistry; Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61df103581f3fe82baa4f18c/original/disclosing-the-role-of-c4-oxo-substitution-in-the-photochemistry-of-dna-and-rna-pyrimidine-monomers-formation-of-photoproducts-from-the-vibrationally-excited-ground-state.pdf |
6662de24418a5379b049b5a3 | 10.26434/chemrxiv-2024-34kvx | Real-Space Imaging of the Conformation and Atomic Structure of Individual β Cyclodextrins with Noncontact AFM | Glycans, consisting of covalently linked sugar units, are a major class of biopolymers essential to all known living organisms. To better understand their biological functions and further applications in fields from biomedicine to materials science, detailed knowledge of their structure is essential. However, due to the extraordinary complexity and conformational flexibility of glycans, state-of-the-art glycan analysis methods often fail to provide structural information with atomic precision. Here, we combine electrospray deposition in ultra-high vacuum with noncontact atomic force microscopy and theoretical calculations to unravel the structure of β-cyclodextrin, a cyclic glucose oligomer, with atomic-scale detail. Our results, established on the single-molecule level, reveal the different adsorption geometries and conformations of β-cyclodextrin. The cyclic arrangement of hydroxy groups on both faces of the molecule and the stabilizing H-bonds are imaged with atomic resolution, enabling the unambiguous assignment of the molecular structure and demonstrating the potential of the method for glycan analysis. | Márkó Grabarics; Benjamín Mallada; Shayan Edalatmanesh; Alejandro Jiménez-Martín; Martin Pykal; Martin Ondráček; Petra Kührová; Weston B. Struwe; Pavel Banáš; Stephan Rauschenbach; Pavel Jelínek; Bruno de la Torre | Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6662de24418a5379b049b5a3/original/real-space-imaging-of-the-conformation-and-atomic-structure-of-individual-cyclodextrins-with-noncontact-afm.pdf |
60c74333f96a00de5128675b | 10.26434/chemrxiv.8977673.v1 | Engaging Aldehydes in CuH-Catalyzed Reductive Coupling Reactions: Stereoselective Allylation from 1,3-Diene Pronucleophiles | Recently,
CuH-catalyzed reductive coupling processes involving carbonyl compounds and
imines has become an attractive alternative to traditional methods for
stereoselective addition to carbonyls due to the ability to use readily
accessible and stable olefin-derived pronucleophiles as surrogates for
organometallic reagents. However, the inability to use aldehydes, which traditionally
reduce too rapidly in the presence of copper hydride complexes to be viable
substrates, has been a major limitation. We show that by exploiting relative
concentration effects through slow addition, we can invert this intrinsic
reactivity and achieve the reductive coupling of 1,3-dienes with aldehydes.
Using this method, both aromatic and aliphatic aldehydes can be transformed to
valuable products with high levels of diastereo- and enantioselectivity and in
the presence of many useful functional groups. Furthermore, using a combination
of theoretical (DFT) and experimental methods, important mechanistic features
of this reaction related to stereo- and chemoselectivity were uncovered. | Chengxi Li; Kwangmin Shin; Richard Liu; Stephen L. Buchwald | Organic Synthesis and Reactions; Stereochemistry; Theory - Computational; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74333f96a00de5128675b/original/engaging-aldehydes-in-cu-h-catalyzed-reductive-coupling-reactions-stereoselective-allylation-from-1-3-diene-pronucleophiles.pdf |
662dc85a91aefa6ce19f9cfc | 10.26434/chemrxiv-2024-qvpz7 | Accelerating Dental Adhesive Innovations Through Active Learning and Bayesian Optimization | The discovery of new dental materials is typically a slow process due to high-dimensionality of the formulation space as well as the multiple competing objectives which must be optimized for a given application. Here, we lay out a strategy using active learning and Bayesian optimization that has led to the discovery of 3 new high-performing formulations for dental adhesives within 29 experiments. We utilize curated data from 91 experiments with 43 different components, to reduce the design space and incorporate domain knowledge into our search. The success of this machine learning approach can be adapted to a multitude of dental materials to allow for the fast and efficient discovery of optimal new formulations, leading to enhanced performance, reduced development times, and ultimately more cost-effective and innovative solutions in dental healthcare. | Ramsey Issa; Robert Sorenson; Taylor D. Sparks | Materials Science; Biocompatible Materials; Biological Materials; Composites; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662dc85a91aefa6ce19f9cfc/original/accelerating-dental-adhesive-innovations-through-active-learning-and-bayesian-optimization.pdf |
60d6017767d491d24a95eceb | 10.26434/chemrxiv-2021-jcwr3 | Investigating Tetrel based Neutral Frustrated Lewis Pairs for Hydrogen Activation | Tetrel Lewis acids are a prospective alternative to commonly employed neutral boranes in frustrated Lewis pair (FLP) chemistry. While cationic tetrylium Lewis acids, being isolobal and iso(valence)electronic, are a natural replacement to boranes, neutral tetrel Lewis acids allude as less trivial options due to the absence of a formally empty p orbital on the acceptor centre. Recently a series of intramolecular geminal FLPs (C2F5)3E-CH2-P(tBu)2 (E= Si, Ge, Sn) featuring neutral tetrel atoms as acceptor site, were reported for activation of small molecules including H2. In this work, through density functional theory computations, we elucidate the general mechanistic picture of H2 activation by this family of FLPs. Our findings reveal that the acceptor atom derives the required Lewis acidity utilizing the antibonding orbitals of its adjacent bonds with the individual contributions depending on the identity of the acceptor and the donor atoms. By varying the identity of the Lewis acid and Lewis base atoms and attached substituents, we unravel their interplay on the energetics of the H2 activation. We find that switching the donor site from P to N significantly affects the synchronous nature of the bond breaking/formations along the reaction pathway and as a result, N-bearing FLPs have a more favourable H2 activation profile than those with P. Our results are quantitatively discussed in detail within the framework of Activation Strain Model of reactivity along with the Energy Decomposition Analysis method. Finally, the reductive elimination decomposition route pertinent to the plausible extension of the H2 activation to catalytic hydrogenation by these FLPs is also examined | Pallavi Sarkar; Shubhajit Das; Swapan K. Pati | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d6017767d491d24a95eceb/original/investigating-tetrel-based-neutral-frustrated-lewis-pairs-for-hydrogen-activation.pdf |
60c7502f469df46acff44814 | 10.26434/chemrxiv.13003073.v1 | Synthesis of Axially Chiral 2,2’-Bisphosphobiarenes via a Nickel-Catalyzed Asymmetric Ullmann Coupling: General Access to Privileged Chiral Ligands without Optical Resolution | <div><p>We report an asymmetric Ullmann-type homocoupling of <i>ortho-</i>(iodo)arylphosphine oxides and <i>ortho</i>-(iodo)arylphosphonates that results in highly enantioenriched axially chiral bisphosphine oxides and bisphosphonates in good yields and excellent enantioselectivities. These products are readily converted to enantioenriched biaryl bisphosphines without need for chiral auxiliaries or optical resolution. This process provides a straightforward and practical route for the development of previously uninvestigated atroposelective biaryl bisphosphine ligands.</p></div> | Ziqing Zuo; Raphael Kim; Donald Watson | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7502f469df46acff44814/original/synthesis-of-axially-chiral-2-2-bisphosphobiarenes-via-a-nickel-catalyzed-asymmetric-ullmann-coupling-general-access-to-privileged-chiral-ligands-without-optical-resolution.pdf |
636d5775deff974544df4bf0 | 10.26434/chemrxiv-2022-19234 | Decarboxylative Bromooxidation of Indoles by a Vanadium Haloperoxidase | Halooxindoles are versatile building blocks for the construction of complex oxindole-containing targets of biological importance. Despite their synthetic value, catalytic methods to synthesize 3-halooxindoles from readily available starting materials has remained undisclosed. We recently discovered that the chloroperoxidase from Curvularia inaequalis (CiVCPO) is a viable catalyst for the decarboxylative bromooxidation of 3-carboxyindoles to furnish 3-bromooxindoles with excellent regio- and chemoselectivity. In addition to the development of the synthetic method, this study provides evidence of a bromide recycling mechanism for the indole oxidation event. A discussion of the reaction development, substrate scope, mechanistic insights, and reaction applicability will be discussed herein. | Clare E. Wells; Lauren P.T. Ramos; Lauren J. Harstad; Logan Z. Hessefort; Hyung Ji Lee; Manik Sharma; Kyle F. Biegasiewicz | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d5775deff974544df4bf0/original/decarboxylative-bromooxidation-of-indoles-by-a-vanadium-haloperoxidase.pdf |
677d78b76dde43c908a532a8 | 10.26434/chemrxiv-2025-93w58 | Optical Properties of New Donor–Acceptor Dyes for RNA Imaging: Insights from Ab Initio and H¨uckel’s Model Calculations | Optical properties of 11 donor–acceptor dyes based on pyridinium–indole, pyridinium–indolizine, isoquinolinium–indole, and isoquinolinium–indolizine motifs developed for RNA imaging are investigated using high-level quantum chemistry methods and semi-empirical H¨uckel’s model. The goal of this study is three-fold: (i) to develop and benchmark computational protocols that can be used for computational design and screening of novel dyes; (ii) to explain the trends in optical properties of the model dyes in terms of underlying charge distributions and connectivity; (iii) to propose a strategy for tuning their optical properties by structural modifications. We also present the results for a new dye designed to have red-shifted absorption and emission. | Goran Giudetti; Moon Jung Kim; Yida Li; Chao Zhang; Anna I. Krylov | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d78b76dde43c908a532a8/original/optical-properties-of-new-donor-acceptor-dyes-for-rna-imaging-insights-from-ab-initio-and-h-uckel-s-model-calculations.pdf |
60c74d650f50db8ce939702c | 10.26434/chemrxiv.12616268.v1 | Isogonal Weavings on the Sphere: Knots, Links, Polycatenanes | <p>We describe mathematical knots and links as piecewise linear – straight, non-intersecting sticks meeting at corners. Isogonal structures have all corners related by symmetry ("vertex" transitive). Corner- and stick-transitive structures are termed <i>regular</i>. We find no regular knots. Regular links are cubic or icosahedral and a complete account of these is given, including optimal (thickest-stick) embeddings. Stick 2-transitive isogonal structures are again cubic and icosahedral and also encompass the infinite family of torus knots and links. The major types of these structures are identified and reported with optimal embeddings. We note the relevance of this work to materials- and bio-chemistry.</p> | Michael O'Keeffe; Michael Treacy | Solid State Chemistry; Supramolecular Chemistry (Inorg.); Theory - Inorganic; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d650f50db8ce939702c/original/isogonal-weavings-on-the-sphere-knots-links-polycatenanes.pdf |
67785663fa469535b9ae7164 | 10.26434/chemrxiv-2025-tm6js | Designing A Bioinspired Degradation System for Forever Chemicals in Water Using Molecular Simulations | Per- and polyfluoroalkyl substances (PFAS), often termed “forever chemicals”, are resistant to natural biodegradation processes. PFAS poses many health risks and environmental challenges and is correlated with causing certain types of cancer, immune system disorders, and pollution. As a result, many approaches have been attempted to degrade PFAS and more similar substances but have been inefficient in degradation because of high cost, producing toxic byproducts, and high energy intensity. This research proposes a method of utilizing the fatty acid photodecarboxylase (5NCC), a photo enzyme that requires light to catalyze its reactions obtained from the Protein Data Bank, to degrade PFAS. Since the molecular characteristics of PFAS are similar to the protein’s natural ligand, palmitic acid (PLM), we suggest that PFAS is also degradable by the fatty acid photodecarboxylase (5NCC) protein. We produced the highest occupied molecular orbitals (HOMO), the lowest occupied molecular orbitals (LUMO), and molecular dynamic (MD) simulations of the 5NCC enzyme with a carboxylate PFAS ligand to assess binding affinity and examine if it can emulate the PLM ligand. These experimentations investigates the efficiency of carboxylate versions of a novel PFAS degradation system and represents a step forward in achieving sustainable solutions for the PFAS contamination global issue. | Danny Nguyen; Jesus Valdiviezo | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67785663fa469535b9ae7164/original/designing-a-bioinspired-degradation-system-for-forever-chemicals-in-water-using-molecular-simulations.pdf |
6775e1f36dde43c90806ea83 | 10.26434/chemrxiv-2025-jztr4 | Self-assembly versatility of fatty acid-amino acid conjugates | Fatty acids, as amphiphilic molecules, are widely recognized for their self-assembly behaviors, which are influenced by the hydrophilic and hydrophobic components of their structure. In biological systems, the conjugates of fatty acids with various biomolecules play important biological roles. In addition, synthetic conjugates of fatty acids with other molecules such as peptides can modulate their self-assembly properties, enabling the design of functional materials for diverse applications in drug delivery, biomedicine, and materials science. In this study, we explored the self-assembly behavior of a series of fatty acid-amino acid conjugates which were synthesized through N-acylation of glycine (Gly), threonine (Thr) and phenylalanine (Phe) respectively with Octanoic acid (OA). We at first determined the critical aggregation concentration (CAC) of the conjugates by using pyrene as the fluorescent probe. The CAC of the three conjugates varies which strongly depends on the amino acid residue. Transmission electron microscopy (TEM) further demonstrates that the conjugates self-assemble to both particle-like structures and fibrous structures. This study showcases the potential of fatty acid-amino acid conjugates as tunable amphiphiles and their potential applications in drug delivery, biomedicine, and material design. | Ali Wang; Shunqing Dong; Junjun Tan | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6775e1f36dde43c90806ea83/original/self-assembly-versatility-of-fatty-acid-amino-acid-conjugates.pdf |
60c74637337d6c4efae270ee | 10.26434/chemrxiv.11106347.v1 | Reversible Shifting of a Chemical Equilibrium by Light: The Case of Keto-Enol Tautomerism of a β-Ketoester | Manipulating the
equilibrium between a ketone and an enol by exposure to light opens up ample
opportunities in material chemistry and photopharmacology since it allows one
to reversibly control the content of the enol tautomer, which acts as a
hydrogen atom donor, with high spatio-temporal and energy resolution. Although
tautomerization of β-ketoesters or their analogs was studied in numerous
papers, their light-induced reversible tautomerization to give thermally stable
enols (photoenolization) is an unexplored area. To shed light on this “blind
spot”, we report an unprecedented property of diarylethene <b>2A</b> assembled from fragments of photoactive dithienylethene and a
β-ketoester as part of the cyclohexenone bridge. In a pristine state, the
tautomeric equilibrium of <b>2</b> is
almost completely shifted towards the ketone. Photocyclization of the
hexatriene system results in a new equilibrium system containing a significant
fraction of the enol tautomer, both in polar and non-polar solvents. Due to the
considerable spectral separation (35 nm), the keto-enol tautomerization process
could be observed visually. The tendency of <b>2A </b>to undergo light-induced enolization was proved by isolating a
related byproduct of photochemical 1,2-dyotropic rearrangement stabilized in the
enolic form. Our results provide a novel tool for controlling the keto-enol
tautomerism that might find use in the development of novel photocontrollable
processes. | Andrey Lvov; Anton Yadykov; Konstantin Lyssenko; Valerii Shirinian; Marat M. Khusniyarov | Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74637337d6c4efae270ee/original/reversible-shifting-of-a-chemical-equilibrium-by-light-the-case-of-keto-enol-tautomerism-of-a-ketoester.pdf |
65df66bf66c1381729c5d592 | 10.26434/chemrxiv-2024-qpm6b | A simple software program for sorting biological sequences into unique groups. | In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein isomers, protein orthologs and polynucleotide sequences like DNA and RNA (1, 2). The program sorts the query sequences into unique groups. The output includes groups of sequences with unique permutation of the monomer units (amino acids and nucleotides) where the sequences of each group are identical but different from the sequences of every other group at least at one amino acid position or different in length by at least one monomeric unit. The algorithm has been implemented in the Visual Basic language which is a component of Microsoft’s Visual Studio (3). The entire code is made available as part of supplementary data in this communication. The user friendly program is available free of cost at Github.com (4), for downloading onto Windows-10 or higher operating systems. | Babu Bassa | Biological and Medicinal Chemistry; Chemical Education; Biochemistry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65df66bf66c1381729c5d592/original/a-simple-software-program-for-sorting-biological-sequences-into-unique-groups.pdf |
60c73fde567dfebf92ec3ad1 | 10.26434/chemrxiv.7523309.v1 | A DNA-Compatible [3+2] Nitrone–Olefin Cycloaddition Suitable for DEL Syntheses | The limited scope of DNA-compatible chemistry restricts the types of chemical features that can be incorporated into DNA-encoded libraries (DELs). Here, a method to synthesize DNA-conjugated polycyclic isoxazolidines via a [3+2] nitrone–olefin cycloaddition is described. The reaction is compatible with many olefin-containing substrates and diverse N-alkylhydroxylamines. The ability to perform subsequent DNA ligation and PCR amplification was also confirmed. This methodology facilitates the synthesis of DELs containing topographically complex compounds with under-explored chemical features. | Christopher Gerry; Zhenhua Yang; Michele Stasi; Stuart Schreiber | Combinatorial Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fde567dfebf92ec3ad1/original/a-dna-compatible-3-2-nitrone-olefin-cycloaddition-suitable-for-del-syntheses.pdf |
60d4abb4403d993fa9bc4fb1 | 10.26434/chemrxiv-2021-m5pnn-v2 | A Molecular Model of Secondary Battery Cycle-life Pointing Towards a Final Regularity Resembling Carnot-efficiency | A transition state theory-influenced ideal model of battery cycle-life is outlined and validated by example of the Panasonic NCR18650B Li-battery cell, which shows after 500 cycles a residual capacity of 68.2 % at 100 % depth of discharge (DoD) as by its datasheet. The ideal model, which bases on a minimum failure causality of one reaction event failing per half-cycle, overstates on the logarithmic scale by just 1.9 % for the conditions given, corresponding to an ideal cycle-life of 563 cycles. Generalization of the model towards DoD-ranges yields for the exemplary (70; 30) % and (100; 60) % margins the cycle-life values of 43252 and 23480, respectively. Because the model relies solely on natural constants, temperature(s) and C-rate(s), the conclusion is drawn that a thermodynamic final regularity similar to Carnot-efficiency governs secondary battery cycle-life; this is in contrast to hitherto academic consensus opinion attesting the matter a basically empiric nature. | Roland Hermann Pawelke | Physical Chemistry; Inorganic Chemistry; Energy; Electrochemistry; Electrochemistry - Mechanisms, Theory & Study; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d4abb4403d993fa9bc4fb1/original/a-molecular-model-of-secondary-battery-cycle-life-pointing-towards-a-final-regularity-resembling-carnot-efficiency.pdf |
6605d0cd9138d23161947865 | 10.26434/chemrxiv-2024-32z25-v2 | Calculating Apparent pKa Values of Ionizable Lipids in Lipid Nanoparticles | Creating new ionizable lipids for use in lipid nanoparticles (LNPs) is an active field of research. One of the critical properties for selecting suitable ionizable lipids is the apparent pKa value of the lipid as formulated in an LNP. We have developed a structure-based, computational methodology for the prediction of the apparent pKa value of ionizable lipids within LNPs. This methodology has been validated for the three most successful ionizable lipids to date which are present in the mRNA LNP COVID-19 vaccines COMIRNATY® (Pfizer/BioNTech) and Spikevax® (Moderna), and the siRNA LNP therapeutic Onpattro® (Alnylam). The calculation was also applied to Lipid A, a variant of the ionizable lipid used in COMIRNATY®. We believe that this new technology permits systematic computational prescreening of ionizable lipids to select the most promising candidates for synthesis and experimental testing, accelerating the formulation improvement process and reducing costs. | Nicholas B. Hamilton; Steve Arns; Mee Shelley; Irene Bechis; John C. Shelley | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Nanoscience; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6605d0cd9138d23161947865/original/calculating-apparent-p-ka-values-of-ionizable-lipids-in-lipid-nanoparticles.pdf |
674ee79b7be152b1d0c98fd1 | 10.26434/chemrxiv-2024-pzr6w-v2 | Multilayered Molybdenum Carbonitride MXene: Reductive Defunctionalization, Thermal Stability, and Catalysis of Ammonia Synthesis and Decomposition | Harnessing two-dimensional (2D) materials for catalytic applications is promising due to the high site utilization. Here, we synthesized a 2D molybdenum carbonitride of the MXene family, Mo2(C,N)Tx, and applied it as a catalyst for ammonia synthesis and decomposition, the essential reactions to establish NH3 as an energy vector. We determine the thermal stability limit of Mo2(C,N)Tx under H2 flow to be ca. 575 C. Exceeding this temperature results, under H2, in a transformation of the predominantly defunctionalized Mo2(C,N)Tx to a 3D Mo2(C,N) phase, which prevents the complete defunctionalization of Mo2(C,N)Tx while retaining its 2D morphology. Before this phase transformation occurs, the remaining Tx species reside in the interior layers of the mostly defunctionalized Mo2(C,N)Tx nanoplatelets, with the amorphous exterior being free from Tx groups, rendering the Mo2(C,N)Tx nanoplatelets chemically anisotropic in the direction orthogonal to the basal plane. The effect of this structure on catalytic properties is highlighted in the thermocatalytic synthesis and decomposition of NH3. In the latter reaction, Mo2(C,N)Tx shows similar gravimetric rates to a reference bulk β-Μο2Ν catalyst, which is ascribed to the presence of too narrow 2D pores (ca. 5.2 Å) with irregular shapes due to a disorder in the stacking of nanosheets in Mo2(C,N)Tx, limiting interlayer diffusion. A deactivation pathway in Mo-based MXenes was identified, and it relates to a precipitation of carbon vacancies to metallic molybdenum under NH3 decomposition conditions. While the ammonia decomposition reaction shows no dependence of the reaction rate on the specific H2 pretreatment of Mo2(C,N)Tx (500 or 575 C), the gravimetric ammonia formation rate increases appreciably with H2 pretreatment, viz., Mo2(C,N)Tx pretreated at 575 C outperforms by ca. four times both the reference β-Μο2Ν catalyst and Mo2(C,N)Tx pretreated at 500 C, explained by a smaller molecule size of the reactants H2 and N2 relative to NH3, and an increased accessibility and utilization of the interlayer space for ammonia synthesis. Overall, our study highlights the importance of addressing limitations due to small pore sizes in multilayered MXenes and the stability of carbon vacancies while simultaneously using optimized pretreatment conditions for surface defunctionalization to uncover the full potential of MXene-based heterogeneous catalysts. | Evgenia Kountoupi; Diana Piankova; Mikhail Agrachev; Zixuan Chen; Alberto Garbujo; Paula M. Abdala; Christoph R. Müller; Alexey Fedorov | Inorganic Chemistry; Catalysis; Solid State Chemistry; Spectroscopy (Inorg.); Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674ee79b7be152b1d0c98fd1/original/multilayered-molybdenum-carbonitride-m-xene-reductive-defunctionalization-thermal-stability-and-catalysis-of-ammonia-synthesis-and-decomposition.pdf |
67466f407be152b1d0f9cd75 | 10.26434/chemrxiv-2024-jb3fb | Influence of borohydrides pyrolysis conditions on closo-dodecaborane formation | Pyrolyses of tetraethylammonium and tetrabutylammonium borohydrides were performed. The obtained products were examined by 11B NMR spectroscopy. It was shown that formation of higher boranes is extremely sensitive to the presence of water vapor (2.7-2.8 kPa partial pressure). The pyrolysis conditions of Et4NBH4 and Bu4NBH4 suitable for synthesis of salts containing B3H8- and B12H122- were found and optimized. High-yield syntheses of Bu4NB3H8 and (Bu4N)2B12H12 with were developed. | Artem Mishchenko; Andriy Kozytskiy; Yulian Lishchenko; Radomyr Smaliy; Andrii Subota; Dmytro Leha; Nataliya Shtil; Andrey Mityuk; Maxim Nechayev; Yuliya Rassukana; Serhiy Ryabukhin | Inorganic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67466f407be152b1d0f9cd75/original/influence-of-borohydrides-pyrolysis-conditions-on-closo-dodecaborane-formation.pdf |
60c73d8dbb8c1a1f0a3d977d | 10.26434/chemrxiv.5844393.v1 | Programmable in vitro Co-Encapsidation of Guest Proteins Inside Protein Nanocages | Bioinspired self-sorting and self-assembling
systems using engineered versions of natural protein cages have been developed
for biocatalysis and therapeutic delivery. The packaging and intracellular delivery
of guest proteins is of particular interest for both <i>in vitro</i> and <i>in vivo</i> cell
engineering. However, there is a lack of platforms in bionanotechnology that
combine programmable guest protein encapsidation with efficient intracellular
uptake. We report a minimal peptide anchor for <i>in vivo</i> self-sorting of cargo-linked capsomeres of the Murine
polyomavirus (MPyV) major coat protein that enables controlled encapsidation of
guest proteins by <i>in vitro</i>
self-assembly. Using Förster resonance energy transfer (FRET) we demonstrate
the flexibility in this system to support co-encapsidation of multiple proteins.
Complementing these ensemble measurements with single particle analysis by
super-resolution microscopy shows that the stochastic nature of
co-encapsidation is an overriding principle. This has implications for the
design and deployment of both native and engineered self-sorting encapsulation
systems and for the assembly of infectious virions. Taking advantage of the
encoded affinity for sialic acids ubiquitously displayed on the surface of
mammalian cells, we demonstrate the ability of self-assembled MPyV virus-like
particles to mediate efficient delivery of guest proteins to the cytosol of
primary human cells. This platform for programmable co-encapsidation and
efficient cytosolic delivery of complementary biomolecules therefore has
enormous potential in cell engineering. | Noor H. Dashti; Rufika S. Abidin; Frank Sainsbury | Biocompatible Materials; Biological Materials; Controlled-Release Systems; Bioengineering and Biotechnology; Cell and Molecular Biology | CC BY NC 4.0 | CHEMRXIV | 2018-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d8dbb8c1a1f0a3d977d/original/programmable-in-vitro-co-encapsidation-of-guest-proteins-inside-protein-nanocages.pdf |
60c751fe4c8919d08dad4059 | 10.26434/chemrxiv.13238528.v1 | Unveiling Structural Disorders in Honeycomb Layered Oxide: Na2Ni2TeO6 | <b>Honeycomb
layered oxides have garnered tremendous research interest in a wide swath of
disciplines owing to not only the myriad physicochemical properties they
exhibit, but also due to their rich crystal structural versatility. Herein, a
comprehensive crystallographic study of a sodium-based Na<sub>2</sub>Ni<sub>2</sub>TeO<sub>6</sub>
honeycomb layered oxide has been performed using atomic-resolution transmission
electron microscopy, elucidating a plethora of atomic arrangement (stacking)
disorders in the pristine material. Stacking disorders in the arrangement
honeycomb metal slab layers (stacking faults) occur predominantly perpendicular
to the slabs with long-range coherence length and enlisting dislocations in
some domains. Moreover, the periodic arrangement of the distribution of alkali
atoms is altered by the occurrence of stacking faults. The multitude of
disorders innate in Na<sub>2</sub>Ni<sub>2</sub>TeO<sub>6</sub> envisage broad
implications in the material functionalities of related honeycomb layered oxide
materials and will bolster renewed interest in their material science.</b> | Titus Masese; Yoshinobu Miyazaki; Josef Rizell; Godwill Mbiti Kanyolo; Teruo Takahashi; Miyu Ito; Hiroshi Senoh; Tomohiro Saito | Ceramics; Composites; Magnetic Materials; Multilayers; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751fe4c8919d08dad4059/original/unveiling-structural-disorders-in-honeycomb-layered-oxide-na2ni2te-o6.pdf |
66552837418a5379b06ff85b | 10.26434/chemrxiv-2024-h9jd8 | High Electron Charge Carrier Mobility in the Nematic Phase of a Roof-Shaped Nematogen with Optimum Molecular Biaxiality | A roof-shaped molecule forming exclusively a nematic liquid crystals phase has been prepared based on a lead structure. The aspect ratio is designed to be almost optimum with respect to the molecular biaxiality. A broad nematic phase over more than 100 K is observed in which a transient biaxiality can be induced. In sandwich cells, TOF electron mobilities of up to 10-2 cm2V-1s-1are obtained, which are the highest found to date for nematic materials. The latter is attributed to the special self-assembly of the roof-shaped mesogens favouring the contacts between the aromatic units, which is confirmed by X-ray scattering, modelling and X-ray scattering simulation. The material is responsive to the applied electric field which results in the anomalous negative field dependence of the charge carrier mobilities. | Matthias Lehmann; Nikolai Scheuring; Dharmendra Pratap Singh; Richard Mandle | Organic Chemistry; Materials Science; Liquid Crystals; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66552837418a5379b06ff85b/original/high-electron-charge-carrier-mobility-in-the-nematic-phase-of-a-roof-shaped-nematogen-with-optimum-molecular-biaxiality.pdf |
613a29f78e38a36f464e0f90 | 10.26434/chemrxiv-2021-fh9gb | Ballistic ΔS=2 Intersystem Crossing in a Cobalt Cubane Following Ligand-Field Excitation Probed by Extreme Ultraviolet Spectroscopy | Femtosecond M2,3-edge X-ray absorption near-edge structure (XANES) spectroscopy is used to probe the excited-state dynamics of the cobalt cubane [CoIII4O4](OAc)4(py)4 (OAc = acetate, py = pyridine), a model for water oxidation catalysts. After ligand-field excitation, intersystem crossing to a metal-centered quintet occurs in 38 fs. 30% of the hot quintet undergoes ballistic back-ISC directly to the singlet ground stat, with the remainder relaxing to a long-lived triplet. | Yusef Shari'ati; Josh Vura-Weis | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613a29f78e38a36f464e0f90/original/ballistic-s-2-intersystem-crossing-in-a-cobalt-cubane-following-ligand-field-excitation-probed-by-extreme-ultraviolet-spectroscopy.pdf |
648c05f4e64f843f41dd46c7 | 10.26434/chemrxiv-2023-b0ss5 | Adenosine monophosphate assisted homogeneous silica coating of silver Nanoparticles in high-yield and their antibacterial activity | In this study, we propose a novel approach for the silica coating of silver nanoparticles based on surface modification with adenosine monophosphate (AMP). Upon AMP stabilization, the nanoparticles can be transferred into 2-propanol, promoting the growth of silica on the particle surfaces through the standard Stöber process. The obtained silica shells are uniform and homogeneous, and the method allows a high degree of control over shell thickness while minimizing the presence of uncoated NPs or the negligible presence of core-free silica NPs. In addition, AMP-functionalized AgNPs could be also coated with a mesoporous silica coating using cetyltrimethylammonium chloride (CTAC) as a template. Interestingly, the thickness of the mesoporous silica coating could be tightly adjusted by either the silica precursor concentration or varying the CTAC concentration while keeping constant the silica precursor concentration. Finally, the influence of the silica coating on the antimicrobial effect of AgNPs was studied on gram-negative bacteria (R. gelatinous and E. coli) and under different bacterial growth conditions, shedding light on their potential applications in different biological environments. | Carlos Fernández-Lodeiro; Reem Tambosi; Javier Fernández-Lodeiro; Adrián Fernández-Lodeiro; Silvia Nuti; Soufian Ouchane; Nouari Kébaïli; Jorge Pérez-Juste; Isabel Pastoriza-Santos; Carlos Lodeiro | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648c05f4e64f843f41dd46c7/original/adenosine-monophosphate-assisted-homogeneous-silica-coating-of-silver-nanoparticles-in-high-yield-and-their-antibacterial-activity.pdf |
60c755bc842e65731fdb438a | 10.26434/chemrxiv.13968620.v2 | Etching and Polymerization Reactions of Alkoxythiophenes in HKUST-1: Choosing Between Filled and Core-Shell MOF/Polymer Composite Structures | In an earlier report, we found that neat 3,4-ethylenedioxythiophene (EDOT) directly reacts with HKUST-1 to form a core-shell composite in which the HKUST-1 surface is coated with conjugated polymer, while unsubstituted thiophenes formed a filled composite where polythiophene is contained in the MOF's pores. In this work, we found that EDOT and 3-methoxythiophene (3MOT), which react in the neat form to form core-shell composites, can be loaded into HKUST-1 pores without reaction when dissolved in hexanes. To a lesser extent, 3-hexyloxythiophene (3HOT) can be loaded in the same way. These hexane-loaded composites can then be heated, resulting in the formation of a 'filled' composite. This finding allows us to choose to prepare either a core-shell or a filled composite by selecting reaction conditions. The process of heating with alkoxythiophenes results in a morphology change in the HKUST-1 material. Composites were characterized by nitrogen sorption measurements, powder X-ray diffraction, and vibrational spectroscopy.<br /> | William James; Colette M. Sullivan; Nicholas Marshall | Core-Shell Materials; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755bc842e65731fdb438a/original/etching-and-polymerization-reactions-of-alkoxythiophenes-in-hkust-1-choosing-between-filled-and-core-shell-mof-polymer-composite-structures.pdf |
662b5a9a91aefa6ce17a9373 | 10.26434/chemrxiv-2023-m2k87-v2 | Direct enthalpy measurement for hydrogenation of liquid organic hydrogen carriers by Differential Scanning Calorimetry under H2 pressure | In this contribution, we report the hydrogenation enthalpy direct measurement of well-studied Liquid Organic Hydrogen Carriers (LOHC) (Dibenzyltoluene, N-Ethylcarbazole, 2-Octanone) and of a new LOHC (Acetophenone) by differential scanning calorimetry (DSC) under H2 pressure. The obtained hydrogenation enthalpies showed good correspondence with DFT predictions and the literature. Moreover, multistep hydrogenation processes were investigated, evidencing that transfer hydrogenation occurred during the reaction. The study of bifunctional LOHC such as acetophenone and its derivatives showcased the potential of direct enthalpy measurement for rapid LOHC screening. Besides, a DFT correction factor for this specific bifunctional LOHC class was experimentally obtained, enabling more precise DFT predictions for similar systems. Kinetic parameters such as the activation energies for the catalytic Ru/Al2O3 system were also determined to be in the 45-60 kJ/mol range, compatible with the H2 adsorption on the Ru surface. The detrimental effect of steric hinderance was also observed. Finally, the reaction order in H2 was experimentally estimated to ~1 for all of the studied LOHCs. | Florian D'Ambra; Vicent Faucheux; Emmanuel Nicolas; Thibault Cantat; Gerard Gebel; Parviz HAJIYEV | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662b5a9a91aefa6ce17a9373/original/direct-enthalpy-measurement-for-hydrogenation-of-liquid-organic-hydrogen-carriers-by-differential-scanning-calorimetry-under-h2-pressure.pdf |
614ca26218be85d6e82da623 | 10.26434/chemrxiv-2021-d0fg9 | Multifunctional Polyoxometalate-Platforms for Supramolecular Light-driven Hydrogen Evolution | Multifunctional supramolecular systems are a central research topic in light-driven solar energy conversion. Here, we report a polyoxometalate (POM)-based supramolecular dyad, where two platinum-complex hydrogen evolution catalysts are covalently anchored to an Anderson polyoxomolybdate anion. Supramolecular electrostatic coupling of the system to an iridium photosensitizer enables visible light-driven hydrogen evolution. Combined theory and experiment demon-strate the multifunctionality of the POM, which acts as photosensitizer / catalyst-binding-site and facilitates light-induced charge-transfer and catalytic turnover. Chemical modification of the Pt-catalyst site leads to increased hydrogen evolution reactivity. Mechanistic studies shed light on the role of the individual components and provide a molecular understanding of the interactions which govern stability and reactivity. The system could serve as a blueprint for multifunctional polyoxometalates in energy conversion and storage. | Salam Maloul; Matthias van den Borg; Carolin Müller; Linda Zedler; Alexander Mengele; Daniel Gaissmaier; Timo Jacob; Sven Rau; Benjamin Dietzek-Ivansic; Carsten Streb | Inorganic Chemistry; Catalysis; Energy; Spectroscopy (Inorg.); Supramolecular Chemistry (Inorg.); Photocatalysis | CC BY 4.0 | CHEMRXIV | 2021-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614ca26218be85d6e82da623/original/multifunctional-polyoxometalate-platforms-for-supramolecular-light-driven-hydrogen-evolution.pdf |
6633cd5a418a5379b04769c5 | 10.26434/chemrxiv-2024-lcmkj | Oxygen dimerization as a defect-driven process in bulk LiNiO2 | To explore the possibility of oxygen dimerization — particularly the formation of molecular oxygen-like species — in the bulk of LiNiO2 lithium ion cathodes materials at high states of charge, we conduct a redox-product structure search inspired by recent methodological developments for point defect structure prediction. We find that delithiated Li1 – x NiO2 (x = 1) has good kinetic stability towards decomposition into molecular oxygen and reduced transition metal oxides, but that defects can act as nucleation sites for oxygen dimerization. These results help reconcile conflicting reports on the formation of bulk molecular oxygen in LiNiO2 and other nickel-rich cathode materials, highlighting the role of defect chemistry in driving the bulk degradation of these compounds. | Alexander G. Squires; Lavan Ganeshkumar; Seán R. Kavanagh; Christopher N. Savory; David O. Scanlon | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6633cd5a418a5379b04769c5/original/oxygen-dimerization-as-a-defect-driven-process-in-bulk-li-ni-o2.pdf |
60c74005702a9b5587189ffc | 10.26434/chemrxiv.7586459.v1 | Supramolecular Organization and Evaporation of Polymeric Tin Trifluoroacetates | <div>
<div>
<div>
<p>Simple tin carboxylates make up a family of important industrial catalysts and precursors for deposition of SnO2 thin films. However, their structures remain disparately characterized, and tin trifluoroacetates have been particularly elusive. Here we report on a combined X-ray diffraction (XRD), gas phase electron diffraction (GED) and density functional theory (DFT) study into the structure and bonding of tin(II) and tin(IV) trifluoroacetates to understand their influence on thermal stability and volatility. Tin(II) bis(trifluoroacetate) (1′) eliminates trifluoroacetic anhydride upon sublimation to form the linear polymeric hexatin(II)-di-μ -oxy-octakis-μ-trifluoroacetate (1F ), which itself sublimes (1 Torr at 191 C) as a 1:1 mixture of 1 and ditin(II)-μ-oxy-bis-μ-trifluoroacetate (1′′). Tin(IV) tetrakis(trifluoroacetate) (2F) is also polymeric in the solid state, but evaporates as a monomer at low temperatures (1 Torr at 84 ◦C). Together they make a family of multifunctional Lewis acidic and basic building blocks for supramolecular organization of clusters and polymers in the solid state. Anomalous trends in the volatility of these trifluoroacetates and their hydrogenated derivatives can be rationalized by consideration of their modes of polymerization with respect to the thermodynamics of evaporation. Both 1F and 2F combine high thermal stability and volatility, and are demonstrated to be complementary, safe, and green potential precursors for chemical vapor deposition (CVD) or atomic layer deposition (ALD) of earth-abundant transparent conducting F-doped SnO2. </p>
<div><div><div>
<p> </p>
</div>
</div>
</div>
</div>
</div>
</div> | Goran Bacic; Conor
D. Rankine; Jason D. Masuda; Derek
A. Wann; Sean Barry | Coordination polymers; Inorganic Polymers; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling; Physical and Chemical Processes; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74005702a9b5587189ffc/original/supramolecular-organization-and-evaporation-of-polymeric-tin-trifluoroacetates.pdf |
64a63db69ea64cc16785deb9 | 10.26434/chemrxiv-2022-w5b99-v2 | An Automated and Lightweight Framework for Electrolyte Diagnostics using Quantitative Microelectrode Voltammetry | Voltammetry is a ubiquitous electroanalytical method that can be used to help probe sustainable electrochemical technologies. When conducted with a microelectrode (radius ca. μm), voltammetry enables special interrogation of electrolyte solutions by minimizing distortions and facilitating near-steady-state measurements. Methodologies aimed to evaluate the behavior of redox-active species often leverage well-established, physically-grounded expressions that can be extended to examine electrolyte solutions under non-ideal conditions (e.g., signal convolution from multiple redox events) by simulating the entire voltammogram. To characterize these analyte systems, we first develop closed-form expressions—building on previous work that utilizes oblate spheroidal coordinates—and establish a framework for rapidly evaluating electrolyte composition. We subsequently apply finite difference transient voltammogram models to assess the performance of this workflow. We then validate our findings using model, deterministically-prepared nonaqueous electrolyte solutions containing N-[2-(methoxyethoxy)ethyl]phenothiazine, finding the toolkit is particularly adept at rapidly (< 1 min) estimating the degree to which an electrolyte solution is charged (its “state-of-charge”) and remains intact (its “state-of-health”). Finally, we highlight potential extensions of this method towards advancing in situ or operando diagnostic methods within operating electrochemical devices. | Alexis M. Fenton, Jr.; Bertrand J. Neyhouse; Kevin M. Tenny; Yet-Ming Chiang; Fikile R. Brushett | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a63db69ea64cc16785deb9/original/an-automated-and-lightweight-framework-for-electrolyte-diagnostics-using-quantitative-microelectrode-voltammetry.pdf |
60c7460c4c891994b1ad2acf | 10.26434/chemrxiv.10453769.v1 | Light-Powered, yet Chemically Fueled, Dissipative DNA Systems with Transient Lifecycles | <div><div><div><p>Fuel-driven dissipative self-assemblies are gaining ground for creating life-like, active and adaptive materials with autonomous behavior. However, up to now there is a lack for simple external control mechanisms of the transient behavior of the steady-state properties, at best using high spatiotemporal resolution. Here, we introduce the first examples of an externally controlled, chemically fueled transient self-assembly system that is ultimately powered using different colors of light. We demonstrate this concept for the programming of the transient lifecycle behaviors of ATP-dissipating, enzymatically controlled, dynamic covalent DNA polymerizations using controlled photolysis of properly designed caged ATP derivatives. Multiple uncaging, as well as wavelength-orthogonal activation are achieved by storing caged fuels as latent energy sources inside the system. We anticipate that this approach can be generalize to other ATP-dissipating self-assemblies and other chemical fuels to achieve versatile spatiotemporal control.</p></div></div></div> | Jie Deng; Dominik Bezold; Henning J. Jessen; Andreas Walther | Polymerization (Polymers); Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7460c4c891994b1ad2acf/original/light-powered-yet-chemically-fueled-dissipative-dna-systems-with-transient-lifecycles.pdf |
6628d4af418a5379b093e12b | 10.26434/chemrxiv-2024-rn4m5 | Quantifying the Seasonal Variation of Environmental Pharmaceutical Residues | Pharmaceutical substances, among other contaminants drained from wastewater treatment process and entered into aqueous environments, exhibit significant seasonal dependencies in their environmental concentrations. Although measurement data on removal of pharmaceutical residues in wastewater treatment plants and their degradation in the environment thereafter are readily available, the complexity and uniqueness of the sampling scenarios makes general numerical estimation of these phenomena difficult. To gain quantitative insight on the mass balances of environmental pharmaceutical residues and their seasonal variations, measurement data of four pharmaceuticals were collected from the literature and an effort was undertaken to uniform them and parametrise them with as few variables as feasible. Temperature was found to be a commonly available parameter with a marked trendsetting effect, and the prospect of using it to characterise the variation was examined. Ways to reliably assess the effects of dilution and other advective phenomena on the measured concentrations were explored, and a simple method for using cross-comparisons of different pharmaceuticals to this end is presented. A corresponding fugacity model scenario was also constructed to provide a computational baseline for the mass balance. | Tuomas Nurmi; Toni Kiljunen | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Wastes | CC BY NC 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6628d4af418a5379b093e12b/original/quantifying-the-seasonal-variation-of-environmental-pharmaceutical-residues.pdf |
60c751d9702a9b6ede18c024 | 10.26434/chemrxiv.13221119.v1 | Virtual Repurposing of Ursodeoxycholate and Chenodeoxycholate as Lead Candidates Against SARS-Cov2-Envelope Protein: A Molecular Dynamics Investigation | Drug repurposing is an apt choice to combat the currently prevailing global threat of COVID-19, caused by SARS-Cov2 in absence of any specific medication/vaccine. The present work attempts to computationally evaluate binding affinities and effect of two widely used surfactant drugs i.e. chenodeoxycholate (CDC) and ursodeoxycholate (UDC) with the envelope protein of SARS-Cov2 (SARS-Cov2-E) using homology modelling, molecular docking and molecular dynamics simulations. A good quality homo-pentameric structure of SARS-Cov2-E was modelled from its homologue with more than 90% sequence identity followed by symmetric docking. The pentameric structure was embedded in a DPPC membrane and subsequently energy minimized. The minimized structure was used for blind molecular docking of CDC and UDC to obtain the best scoring SARS-Cov2-E–CDC/UDC complexes, which were subjected to 230ns molecular dynamics simulations in triplicates in DPPC membrane environment. Comparative analyses of structural and enthalpic properties and molecular interaction profiles from the MD trajectories revealed that, both CDC and UDC could stably bind to SARS-Cov2-E through H-bonds, water-bridges and hydrophobic contacts in the transmembraneresidues.T30 was observed to be a key residue for CDC/UDC binding. The polar functional groups of the bound CDC/UDC facilitated entry of a large number of water molecules into the channel and affected the H-bonding pattern between adjacent monomeric chains, loosening the compact transmembrane region of SARS-Cov2-E. These observations suggest the potential of CDC/UDC as repurposed candidates to hinder the survival of SARS-Cov2 by disrupting the structure of SARS-Cov2-E and facilitate entry of solvents/polar inhibitors inside the viral cell. | Reena Yadav; Chinmayee Choudhury; Yashwant Kumar; Alka Bhatia | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751d9702a9b6ede18c024/original/virtual-repurposing-of-ursodeoxycholate-and-chenodeoxycholate-as-lead-candidates-against-sars-cov2-envelope-protein-a-molecular-dynamics-investigation.pdf |
6123e55de65e2de7d51e8733 | 10.26434/chemrxiv-2021-qkjjr-v2 | On the Role of Heterojunctions of Core-Shell Heterostructures in Gas Sensing | Heterostructures made from semiconducting metal oxides (SMOX) are fundamental for the development of high-performance gas sensors. Yet, despite the recognition of their importance in real applications, the understanding of the transduction mechanism either related to the heterojunction, or simply to the core and shell materials is still lacking. A better understanding of the sensing response of heterostructured nanomaterials requires the engineering of heterojunctions with well-defined core and shell layers. Here, we introduce a series of prototypes nSMOX-CNT, pSMOX-CNT, and pSMOX-nSMOX-CNT and nSMOX-pSMOX-CNT hierarchical core-shell heterostructures (CSHS) permitting us to directly relate the sensing response to the SMOX shell, or to the p-n heterojunction. The carbon nanotubes are here used as highly conductive substrates permitting to operate the devices at relatively low temperature and are not involved in the sensing response. NiO and SnO2 are selected as representative p- and n-type SMOX, respectively, and the response of a set of samples is studied toward hydrogen considered as model analyte. The n,pSMOX-CNT CSHS exhibit response related to the n,pSMOX-shell layer. On the other hand, the pSMOX-nSMOX-CNT and nSMOX-pSMOX-CNT CSHS show sensing responses, which in certain cases are governed by the heterojunctions between nSMOX and pSMOX and strongly depends on the thickness of the SMOX layers. Due to the fundamental nature of this study, these findings are important for the development of next generation gas sensing devices. | Muhammad Hamid Raza; Roberto Di Chio; Kaveh Movlaee; Patrick Amsalem; Norbert Koch; Nicolae Barsan; Giovanni Neri; Nicola Pinna | Physical Chemistry; Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6123e55de65e2de7d51e8733/original/on-the-role-of-heterojunctions-of-core-shell-heterostructures-in-gas-sensing.pdf |
61b1079802d90d740a598dc5 | 10.26434/chemrxiv-2021-9srsx | Abiotic sugar synthesis from CO2 electrolysis | CO2 valorization is aimed at converting waste CO2 to value-added products. While steady progress has been achieved through diverse catalytic strategies, including CO2 electrosynthesis, CO2 thermocatalysis, and biological CO2 fixation, each of these approaches have distinct limitations. Inorganic catalysts only enable synthesis beyond C2 and C3 products with poor selectivity and with a high energy requirement. Meanwhile, although biological organisms can selectively produce complex products from CO2, their slow autotrophic metabolism limits their industrial feasibility. Here, we present an abiotic approach leveraging electrochemical and thermochemical catalysis to complete the conversion of CO2 to life-sustaining carbohydrate sugars akin to photosynthesis. CO2 was electrochemically converted to glycolaldehyde and formaldehyde using copper nanoparticles and boron-doped diamond cathodes, respectively. CO2-derived glycolaldehyde then served as the key autocatalyst for the formose reaction, where glycolaldehyde and formaldehyde combined in the presence of an alkaline earth metal catalyst to form a variety of C4 - C8 sugars, including glucose. In turn, these sugars were used as a feedstock for fast-growing and genetically modifiable Escherichia coli. Altogether, we have assembled a platform that pushes the boundaries of product complexity achievable from CO2 conversion while demonstrating CO2 integration into life-sustaining sugars. | Stefano Cestellos-Blanco; Sheena Louisia ; Michael Ross; Yifan Li; Tyler Detomasi; Jessica Cestellos Spradlin; Daniel Nomura; Peidong Yang | Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b1079802d90d740a598dc5/original/abiotic-sugar-synthesis-from-co2-electrolysis.pdf |
615b9b32be10746e0e922d92 | 10.26434/chemrxiv-2021-mcf3k | Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2 | Cepharanthine is a natural of plant origin, and recently demonstrated to have anti-SARS-CoV-2 activity. In order to evaluate the other natural analogues as a potential COVID-19 drug, a total of 24 compounds resembling cepharanthine were extracted from the KNApSAcK database, and their binding affinities to supposed target proteins, namely, spike protein and main protease of SARS-CoV-2, NPC1, and TPC2, were predicted via molecular docking simulations. Selected analogues were further evaluated by a cell-based SARS-CoV-2 infection assay, and the efficacies of cepharanthine (IC50 1.90 uM) and tetrandrine (IC50 10.37 uM) were demonstrated. From a comparison of the docking conformations of these compounds, the diphenyl ester moiety of the molecules was suggested for a putative pharmacophore of the cepharanthine-analogues. | Atsushi Hijikata; Clara Shionyu-Mitsuyama; Setsu Nakae; Masafumi Shionyu; Motonori Ota; Shigehiko Kanaya; Takatsugu Hirokawa; Shugo Nakajima; Koichi Watashi; Tsuyoshi Shirai | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615b9b32be10746e0e922d92/original/evaluating-cepharanthine-analogues-as-natural-drugs-against-sars-co-v-2.pdf |
62e890b43276f00a59575725 | 10.26434/chemrxiv-2022-v2tc6 | Prospects of ZnS and ZnO as smart semiconductor materials in light-activated antimicrobial coatings for mitigation of severe acute respiratory syndrome coronavirus-2 infection | We carried out theoretical and experimental analyses of ZnO and ZnS nanoparticles as smart semiconductor materials in light-activated antimicrobial coating for application in masks. We used low-cost hydrothermally processable precursors to direct the growth of the coatings on a cotton fabric. Both ZnO and ZnS coatings had high reactivities as disinfection agents in photocatalysis reactions for the degradation of a methylene blue dye solution. Also, these coatings showed excellent UV protection properties. For understanding at the molecular level, the broad-spectrum biological activities of the ZnO and ZnS coatings against Fusarium Oxysporum fungi, Escherichia coli bacteria, and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus and their variants, were investigated computationally. Hexagonal Zn6O6 and Zn6S6 clusters were used as models for the simulations through excited- and ground-state calculations. The theoretical findings show that changes in the local chemical environment in these excited systems have a profound impact on their physical and chemical properties and thus, can provide a better understanding to engineer new functional materials in light-activated antimicrobial coatings for mitigation of SARS-CoV-2 infection. | Victoria Benatto; João Paulo de Jesus; Alexandre de Castro; Letícia Assis; Teodorico Ramalho; Felipe A La Porta | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e890b43276f00a59575725/original/prospects-of-zn-s-and-zn-o-as-smart-semiconductor-materials-in-light-activated-antimicrobial-coatings-for-mitigation-of-severe-acute-respiratory-syndrome-coronavirus-2-infection.pdf |
60c754994c89199678ad4568 | 10.26434/chemrxiv.13688050.v1 | Modelling Molecular Emitters in Organic Light Emitting Diodes with the Quantum Mechanical Bespoke Force Field | <div><div><div><p>Combined molecular dynamics (MD) and quantum mechanics (QM) simulation procedures have gained popularity in modelling the spectral properties of functional organic molecules. However, the potential energy surfaces used to propagate long-time scale dynamics in these simulations are typically described using general, transferable force fields designed for organic molecules in their electronic ground states. These force fields do not typically include spectroscopic data in their training, and importantly there is no general protocol for including changes in geometry or intermolecular interactions with the environment that may occur upon electronic excitation. In this work, we show that parameters tailored for thermally activated delayed fluorescence (TADF) emitters used in organic light emitting diodes (OLEDs), in both their ground and electronically excited states, can be readily derived from a small number of QM calculations using the QUBEKit (QUantum mechanical BEspoke toolKit) software, and improve the overall accuracy of these simulations.</p></div></div></div> | Lupeng Yang; Joshua Horton; Michael C. Payne; Thomas Penfold; Daniel Cole | Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754994c89199678ad4568/original/modelling-molecular-emitters-in-organic-light-emitting-diodes-with-the-quantum-mechanical-bespoke-force-field.pdf |
668ddd8fc9c6a5c07ad117b9 | 10.26434/chemrxiv-2024-tkb28 | Mechanical Tuning of Fluorescence Lifetime and Bandgap in an Elastically Flexible Molecular Semiconductor Crystal | Despite superior transport properties, lack of mechanical flexibility is a major drawback of crystalline molecular semiconductors compared to their polymer analogues. Here we report single crystals of an organic semiconductor that are not only flexible but exhibit systematic tuning of bandgaps, fluorescence lifetime, and emission wavelengths upon elastically bending. Spatially resolved fluorescence lifetime imaging and confocal fluorescence microscopy reveal systematic trends in the lifetime decay across the bent crystal region along with shifts in the emission wavelength. From the outer arc to the inner arc of the bent crystal, a significant decrease in the lifetime of ~1.9 ns was observed, with a gradual bathochromic shift of ~10 nm in the emission wavelength. For the crystal having a bandgap of 2.73 eV, the directional stress arising from bending leads to molecular reorientation effects and variations in the extent of intermolecular interactions– which are correlated to the lowering of bandgap and the evolution of the projected density of states. The systematic changes in the interactions quantified using electron density topological analysis in the compressed inner arc and elongated outer arc region are correlated to the non-radiative decay processes, thus rationalizing the tuning of fluorescence lifetime. Such mechanical tuning of band gaps and photophysical properties may pave the way to innovative technologies in the micro-fabrication of flexible organic functional materials such as semiconductors and organic light-emitting diodes. | Arif Hassan Dar; Atiqur Rahman; Srijan Mondal; Argha Barman; Monika Gupta; Pramit K. Chowdhury; Sajesh P. Thomas | Physical Chemistry; Spectroscopy (Physical Chem.); Structure; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668ddd8fc9c6a5c07ad117b9/original/mechanical-tuning-of-fluorescence-lifetime-and-bandgap-in-an-elastically-flexible-molecular-semiconductor-crystal.pdf |
60c75314469df4c9eaf44cad | 10.26434/chemrxiv.13385351.v1 | Synthesis and Molecular Properties of Partially Fluorinated DNTTs | 1,2,3,4-Tetrafluoro-dinaphthothienothiophene
(F4DNTT) and 1,2,3,4,8,9,10,11-octafluoro-dinaphthothienothiophene
(F8DNTT) were synthesized via bisthiomethyl alkene intermediates which
were accessible by McMurry coupling or Wittig olefination of partially
fluorinated naphthalene precursors. DFT-based electronic structure
calculations, X-ray absorption spectroscopy (NEXAFS) and UV/Vis
measurements were used for HOMO/LUMO gap determination and to analyse
the electronic structures of the partially fluorinated DNTTs. Reduced
exciton binding was observed in thin films | Matthias W Tripp; Daniel Bischof; Maximilian Dreher; Gregor Witte; Ulrich Koert | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75314469df4c9eaf44cad/original/synthesis-and-molecular-properties-of-partially-fluorinated-dnt-ts.pdf |
60c7563e469df4e238f452a2 | 10.26434/chemrxiv.14219816.v1 | Oscillation in Excited State Lifetimes with Size of Sub-Nanometer Neutral (TiO2)n Clusters Observed with Ultrafast Pump-Probe Spectroscopy | <div>Neutral titanium oxide clusters of up to 1 nm in diameter (TiO<sub>2</sub>)<sub>n</sub>, with n < 10, are produced in a laser vaporization source and subsequently ionized by a sequence of femtosecond laser pulses. Using 400 nm pump, 800 nm probe lasers, the excited state lifetimes of neutral (TiO<sub>2</sub>)<sub>n</sub> clusters are measured. All clusters exhibit a rapid relaxation lifetime of ~30 fs, followed by a sub-picosecond lifetime that we attribute to carrier recombination. The excited state lifetimes oscillate with size, with even numbered clusters possessing longer lifetimes. Density functional theory calculations show the excited state lifetimes are correlated with electron-hole pair localization or polaron-like formation in the excited states of neutral clusters. Thus, structural rigidity is suggested as a feature for extending excited state lifetimes in titania materials.</div> | Jacob Garcia; Lauren Heald; ryan shaffer; Scott Sayres | Catalysts; Photocatalysis; Clusters; Photochemistry (Physical Chem.); Quantum Mechanics; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7563e469df4e238f452a2/original/oscillation-in-excited-state-lifetimes-with-size-of-sub-nanometer-neutral-ti-o2-n-clusters-observed-with-ultrafast-pump-probe-spectroscopy.pdf |
60c75306567dfe49c9ec5da3 | 10.26434/chemrxiv.13379126.v1 | A Rocking-Chair Proton Battery with Conducting Redox Polymer Active Materials and a Protic Ionic Liquid Electrolyte | <p>Rechargeable
batteries that use redox-active organic compounds are currently considered as
an energy storage technology for the future. Conducting redox polymers (CRPs) are
organic materials being both electronically conducting and resilient to
dissolution. While insolubility is an advantageous property for active battery
materials, it complicates the processing necessary for fabricating electrodes,
including electrode formulation and layer formation. Here we employ a
post-deposition electro-polymerization (PDP) method, which allows for solution-processing
to be used for electrode layer formation. The polymerization conditions are optimized
and the underlying mechanism is studied with the final aim to produce high
performance CRPs as energy storage materials. We show that quinizarin (Qz) and
naphthoquinone (NQ) based CRPs can reach their theoretical capacity thorough
optimization of the polymerization conditions. Combining the two CRPs, with the
Qz-CRP as cathode and the NQ-CRP as anode, and a protic ionic liquid
electrolyte, yields a 0.8 V proton rocking-chair battery. The conducting additive-free
all-organic proton battery exhibits a capacity of 62 mAh/g and a capacity retention
of 80% after 500 cycles using rapid potentiostatic charging and galvanostatic
discharge at 4.5 C. </p> | huan Wang; Rikard Emanuelsson; Christoffer Karlsson; Patric Jannasch; Maria Strømme; Martin Sjödin | Organic Polymers; Polymerization (Polymers); Polymer morphology; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75306567dfe49c9ec5da3/original/a-rocking-chair-proton-battery-with-conducting-redox-polymer-active-materials-and-a-protic-ionic-liquid-electrolyte.pdf |
63d3c2d910cb6a14c0e88bfa | 10.26434/chemrxiv-2023-g4qpb | Basis for accurate protein pKa prediction with
machine learning | pH regulates protein structures and the resulting functions in many biological processes via protonation and deprotonation of ionizable side chains where the titration equilibra is determined by pKa. To accelerate pH-dependent molecular mechanism research in life science or industrial protein and drug designs, fast and accurate pKa prediction is crucial. Here we present a theoretical pK data set PHMD549, which was successfully applied to four distinct machine learning methods, including DeepKa that was proposed in our previous work. To reach a valid comparison, EXP67S was selected as the test set. Encouragingly, DeepKa was improved significantly and outperforms other state-of-the-art methods, except for the constant-pH molecular dynamics, which was utilized to create PHMD549. More importantly, DeepKa reproduced experimental pKa orders of acidic dyads in five enzyme catalytic sites. Apart from structural proteins, DeepKa was found applicable to intrinsically disordered peptides. Further, in combination with solvent exposures, it's revealed that DeepKa offers the most accurate prediction under the challenging circumstance that hydrogen bonding or salt bridge interaction is partly compensated by desolvation for a buried side chain. Finally, our benchmark data qualify PHMD549 and EXP67S as the basis for future developments of protein pKa prediction tools driven by artificial intelligence. In addition, DeepKa built on PHMD549 has been proved an efficient protein pKa predictor and thus can be applied immediately to, for example, pKa database construction, protein design, drug discovery and so on. | Zhitao Cai; Tengzi Liu; Qiaoling Lin; Jiahao He; Xiaowei Lei; Fangfang Luo; Yandong Huang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d3c2d910cb6a14c0e88bfa/original/basis-for-accurate-protein-p-ka-prediction-with-machine-learning.pdf |
60c751cdf96a0044d02880ab | 10.26434/chemrxiv.13210979.v1 | Cellular Fucosylation Inhibitors Based on Fluorinated Fucose-1-Phosphates | <a>Fucosylation
of glycans impacts a myriad of physiological and pathological processes. Inhibition
of fucose expression emerges as a potential therapeutic avenue for example in
cancer, inflammation, and infection. In this study, we found that protected 2-fluorofucose
1-phosphate efficiently inhibits cellular fucosylation with a four to seven
times higher potency than known inhibitor 2FF, independently of the anomeric
stereochemistry. Nucleotide sugar analysis revealed that both the α- and β-GDP-2FF anomers are
formed inside the cell. In conclusion, we developed A2FF1P and B2FF1P as potent
new tools for studying the role of fucosylation in health and disease</a> and they are potential therapeutic candidates. | Johan Pijnenborg; eline visser; Marek Noga; Emiel Rossing; Raisa Veizaj; Dirk J. Lefeber; Christian Büll; Thomas Boltje | Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751cdf96a0044d02880ab/original/cellular-fucosylation-inhibitors-based-on-fluorinated-fucose-1-phosphates.pdf |
66c4ae7a20ac769e5f2b2ea5 | 10.26434/chemrxiv-2024-vwww7 | Harnessing the Reactivity of Nitroarene Radical Anions to Create Quinoline N-oxides by Electrochemical Reductive Cyclization | Electrochemical reduction of 2-allyl-substituted nitroarenes using a simple, undivided electrochemical cell with non-precious electrodes to generate nitroarene radical anions was developed. The reactivity of ArNO2 radical anion can be controlled to participate in 1,5-HAT reactions to construct quinoline N-oxides bearing aryl-, heteroaryl-, alkenyl-, benzyl-, sulfonyl-, or carboxyl groups. | Haoran Zhu; Victoria Geldchen; Adam Drumheller; Tom Driver | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c4ae7a20ac769e5f2b2ea5/original/harnessing-the-reactivity-of-nitroarene-radical-anions-to-create-quinoline-n-oxides-by-electrochemical-reductive-cyclization.pdf |
60c7509f567dfe0f14ec58cb | 10.26434/chemrxiv.13061402.v1 | Quantitative Interpretation Explains Machine Learning Models for Chemical Reaction Prediction and Uncovers Bias | <div><div><div><p>Organic synthesis remains a stumbling block in drug discovery. Although a plethora of machine learning models have been proposed as solutions in the literature, they suffer from being opaque black-boxes. It is neither clear if the models are making correct predictions because they inferred the salient chemistry, nor is it clear which training data they are relying on to reach a prediction. This opaqueness hinders both model developers and users. In this paper, we quantitatively interpret the Molecular Transformer, the state-of-the-art model for reaction prediction. We develop a framework to attribute predicted reaction outcomes both to specific parts of reactants, and to reactions in the training set. Furthermore, we demonstrate how to retrieve evidence for predicted reaction outcomes, and understand counterintuitive predictions by scrutinising the data. Additionally, we identify ”Clever Hans” predictions where the correct prediction is reached for the wrong reason due to dataset bias. We present a new debiased dataset that provides a more realistic assessment of model performance, which we propose as the new standard benchmark for comparing reaction prediction models.</p></div></div></div> | David Peter Kovacs; William McCorkindale; Alpha Lee | Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7509f567dfe0f14ec58cb/original/quantitative-interpretation-explains-machine-learning-models-for-chemical-reaction-prediction-and-uncovers-bias.pdf |
6482e4b2e64f843f418a5d61 | 10.26434/chemrxiv-2023-t7s9b | Restore high-resolution NMR spectra from inhomogeneous magnetic fields using neural network | High-resolution nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical tool with wide application. However, the conventional shim technique may not guarantee the homogeneity of the magnetic field when the experimental conditions are unfavorable. In this study, we proposed a data post-processing method called Restore High-resolution Unet (RH-Unet), which uses a convolutional neural network to restore distorted NMR spectra that have been acquired in inhomogeneous magnetic fields. The method generates feature-label pairs from singlet peak regions and ideal Lorentzian line shape and trains a RH-Unet model to map low resolution spectra to high resolution spectra. The method was applied to different samples, and showed superior performance than the REFDCON method incorporated in Bruker Topspin software. The proposed method provides a simple and fast way to obtain high resolution NMR spectra in inhomogeneous fields, which can facilitate the application of NMR spectroscopy in various fields. | Xiongjie Xiao; Qianqian Wang; Xu Zhang; Bin Jiang; Maili Liu | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6482e4b2e64f843f418a5d61/original/restore-high-resolution-nmr-spectra-from-inhomogeneous-magnetic-fields-using-neural-network.pdf |
60c73dd5337d6c249de26248 | 10.26434/chemrxiv.6168980.v1 | Benchmark of ReaxFF Force Field for Subcritical and Supercritical Water | <div><div><div><p>Water in the subcritical and supercritical states has remarkable properties that make it an excellent solvent for oxidation of hazardous chemicals, waste separation, and green synthesis. Molecular simulations are a valuable complement to experiments in order to understand and improve the relevant sub- and super-critical reaction mechanisms. Since water molecules under those conditions can act not only as solvent but also as reactant, dissociative force fields are specially interesting to investigate theseprocesses. In this work, we evaluate the capacity of the ReaxFF force field to reproduce the microstructure, hydrogen bonding, dielectric constant, diffusion, and proton transfer of sub- and super-critical water. Our results indicate that ReaxFF is able to simulate water properties in these states in very good quantitative agreement with existing experimental data, with the exception of the static dielectric constant which is reproduced only qualitatively.</p></div></div></div> | Hegoi Manzano; Weiwei Zhang; Adri C. T. van Duin; Muralikrishna Raju; Jorge S. Dolado; Iñigo Lopez Arbeloa | Hydrology and Water Chemistry; Computational Chemistry and Modeling; Solution Chemistry; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd5337d6c249de26248/original/benchmark-of-reax-ff-force-field-for-subcritical-and-supercritical-water.pdf |
6231d85921e2d0de84a5a3a8 | 10.26434/chemrxiv-2022-q98mf | The Effect of Particle Size and Composition on the Optical and Electronic Properties of CdO and CdS Rocksalt Nanoparticles | Quantum confinement like behaviour in CdO and CdS nanoparticles is demonstrated through explicit evGW-BSE many-body perturbation theory calculations on 0.6-1.4 nanometre particles of these materials. However, while the lowest optical excited-state, exciton, and the highest occupied and lowest unoccupied quasiparticle states in such nanoparticles are predicted to be delocalised, they are found to be delocalised over the surface of the particle only and not the whole particle volume. The electronic and optical properties of CdO and CdS rocksalt nanoparticles are predicted to differ dramatically from their structurally analogous MgO counterparts, where the lowest exciton and highest occupied and lowest unoccupied quasiparticle states are strongly localised, in contrast. This difference in behaviour between MgO and CdO/CdS is explained in terms of the more polarisable, less ionic, bonding in CdO and CdS. The effect on the optical and fundamental gaps of the particles due to the presence of amine capping agents on the particles’ surface is explored and predicted to be relatively small. However, the highest occupied and lowest unoccupied quasiparticle states are found to consistently shift to more shallow values when increasing the surface density of capping agents. An explanation of this shift, finally, is proposed in terms of the dipole field induced by the aligned dipoles of the capping agents. | Martijn Zwijnenburg | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Quasiparticles and Excitations | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6231d85921e2d0de84a5a3a8/original/the-effect-of-particle-size-and-composition-on-the-optical-and-electronic-properties-of-cd-o-and-cd-s-rocksalt-nanoparticles.pdf |
621d00ecdaa4fb36e37aae84 | 10.26434/chemrxiv-2022-rgvwg | Tetraanionic arachno-Carboranyl Ligand Imparts Strong Axiality to Terbium(III) Single-Molecule Magnets | A family of fully sandwiched arachno-lanthanacarborane complexes formulated as {6-[µ-1,2-[o-C6H4(CH2)2]-1,2-C2B10H10]2Ln}{Li5(THF)10} (Ln = Tb, Dy, Ho, Er, Y) is successfully synthesized, where the “carbons-adjacent” carboranyl ligand (arachno-C2B10H104−) bears four negative charges and coordinates to the central lanthanide ions using the hexagonal 6C2B4 face. Thus, the central lanthanide cations are pseudo-twelve-coordinate and have an approximate local D6h symmetry or hexagonal-prismatic geometry. As the crystal field effect imparted by this geometry is still unknown, we thoroughly investigated the magnetic properties of this series of complexes and found the crystal field imposed by this ligand causes a relation of Tb > Dy > Ho > Er for the energy gaps between the ground and the first excited states, which is of striking resemblance to the ferrocenophane and phthalocyanine ligands despite that the latter two ligands give disparate local coordination geometries. Moreover, the effective energy barrier to magnetization reversal of 445(10) K, observable hysteresis loop up to 4K and the relaxation time of the yttrium diluted sample reaching 193(17) seconds at 2 K under an optimized field for the Tb analogue of this family of arachno-lanthanacarborane complexes, render a new benchmark for Tb3+ based single-molecule magnets. | Peng-Bo Jin; Ke-Xin Yu; Qian-Cheng Luo; Ye-Ye Liu; Yuan-Qi Zhai; Yan-Zhen Zheng | Inorganic Chemistry; Organometallic Chemistry; Lanthanides and Actinides; Magnetism; Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621d00ecdaa4fb36e37aae84/original/tetraanionic-arachno-carboranyl-ligand-imparts-strong-axiality-to-terbium-iii-single-molecule-magnets.pdf |
677049de81d2151a023712db | 10.26434/chemrxiv-2024-jzxfs | Expanding the Toolbox for Supramolecular Chemistry: Probing Host-Guest Interactions with in situ FTIR Spectroscopy for Struc-tural and Dynamic Insights | Association constant (Ka) measurements provide fundamental information on host-guest interactions in supramolecular chemistry and other areas of science. Many techniques can be used to measure Ka values, with NMR spectroscopy often providing useful information on time-averaged interactions or changes in geometry due to perturbations in chemical shifts. Here we report the use of in situ FTIR spectroscopy to measure the Ka values of supramolecular host-guest complexes across three classes of host-guest complexes using different types of interactions including hydrogen bonding and halogen bonding. This approach can be performed with minimal sample preparation, does not require deuterated solvents, can measure asso-ciation based on changes in host or guest vibrations, and benefits from a much shorter timescale than NMR spectroscopy. Due to its fast timescale, FTIR spectroscopy also provides details on host/guest conformational changes, such as the presence of unsymmetrical host conformation that are not in the ideal binding conformation until treatment with a suitable guest, which would otherwise not be observed in more common time-averaged NMR measurements. Using this approach, we demonstrated the capabilities and challenges of this technique to investigate host-guest interactions of three anion receptors that use hydrogen or halogen bonding with both mono- and polyatomic anions. In addition to directly observing how host-guest interactions impact bonding within the individual molecules, we also demonstrate that global fitting of the FTIR spectra is an effective and robust approach to measure Ka values of these host-guest complexes. We anticipate that this method will provide a new and useful approach to investigating the dynamics and specific interactions across abroad areas of science. | Shiva Moaven; Douglas Vander Griend; Darren Johnson; Michael Pluth | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Spectroscopy (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677049de81d2151a023712db/original/expanding-the-toolbox-for-supramolecular-chemistry-probing-host-guest-interactions-with-in-situ-ftir-spectroscopy-for-struc-tural-and-dynamic-insights.pdf |
62584fb1742e9f3ae05d3a0f | 10.26434/chemrxiv-2021-4s6lc-v3 | Magnetic Exchange Interactions in Binuclear and Tetranuclear Iron (III) Complexes Described by Spin-Flip DFT and Heisenberg Effective Hamiltonians | Low-energy spectra of single-molecule magnets (SMMs) are often described by Heisenberg Hamiltonians. Within this formalism, exchange interactions between magnetic centers determine the ground-state multiplicity and energy separation between the ground and excited states. In this contribution, we extract exchange coupling constants (J) for a set of iron (III) binuclear and tetranuclear complexes from all-electron calculations using non-collinear spin-flip time-dependent density functional theory (NC-SF-TDDFT). For 12 binuclear complexes with J-values ranging from -6 to -132 cm−1, our benchmark calculations using the short-range hybrid ωPBEh functional and 6-31G(d,p) basis set agree well with the experimentally derived values (mean absolute error of 4.7 cm−1). For the tetranuclear SMMs, the
computed J constants are within 6 cm−1 from the experimentally derived values. We explore the range of applicability of the Heisenberg model by analyzing bonding patterns in these Fe(III) complexes using natural orbitals (NO), their occupations, and the number of effectively unpaired electrons. The results illustrate the efficiency of the spin-flip protocol for computing the exchange couplings and the utility of the NO analysis in assessing the validity of effective spin Hamiltonians. | Saikiran Kotaru; Sven Kähler; Maristella Alessio; Anna I. Krylov | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62584fb1742e9f3ae05d3a0f/original/magnetic-exchange-interactions-in-binuclear-and-tetranuclear-iron-iii-complexes-described-by-spin-flip-dft-and-heisenberg-effective-hamiltonians.pdf |
60c743be0f50db9feb395fc9 | 10.26434/chemrxiv.9642008.v1 | Emissive Single-Crystalline Boroxine-Linked Colloidal Covalent Organic Frameworks | The synthesis of periodic two-dimensional (2D) polymers and characterization of their optoelectronic behaviors are challenges at the forefront of polymer chemistry and materials science. Recently, we showed that layered 2D polymers known as 2D covalent organic frameworks (COFs) can be synthesized as single crystals by preparing COF particles as colloidal suspensions. Here we expand this approach from the condensation of boronic acids and catechols to the dehydrative trimerization of polyboronic acids. The resulting boroxine-linked colloids are the next class of 2D COFs to be obtained as single‑crystalline particles, as demonstrated here for four 2D COFs and one 3D COF. Colloidal stabilization enables detailed structural analysis by synchrotron X-ray diffraction and high-resolution transmission electron microscopy. Solution fluorescence spectroscopy revealed that the COF crystallites are highly emissive compared to their respective monomer solutions. Excitation‑emission matrix fluorescence spectroscopy indicated that the origin of this enhanced emission can be attributed to through-space communication of chromophores between COF sheets. These observations will motivate the development of colloidal COF systems as a platform to organize functional aromatic systems into precise and predictable assemblies with emergent properties. | Austin Evans; Ioannina Castano; Alexandra Brumberg; Lucas
R. Parent; Amanda Corcos; Rebecca Li; Nathan C. Flanders; David J. Gosztola; Nathan Gianneschi; Richard Schaller; William Dichtel | Physical Organic Chemistry; Organic Polymers; Polymerization (Polymers); Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743be0f50db9feb395fc9/original/emissive-single-crystalline-boroxine-linked-colloidal-covalent-organic-frameworks.pdf |
60c755d3337d6c01dbe28cfb | 10.26434/chemrxiv.14170202.v1 | Pathway Complexity in Supramolecular Porphyrin Self-Assembly at an Immiscible Liquid|Liquid Interface | <p>Nanostructures
that are inaccessible through spontaneous thermodynamic processes may be formed
by supramolecular self-assembly under kinetic control. In the past decade, the
dynamics of pathway complexity in self-assembly have been elucidated through
kinetic models based on aggregate growth by sequential monomer association and
dissociation. Immiscible liquid|liquid interfaces are an attractive platform to
develop well-ordered self-assembled nanostructures, unattainable in bulk
solution, due to the templating interaction of the interface with adsorbed
molecules. Here, we report time-resolved <i>in situ</i> UV/vis spectroscopic
observations of the self-assembly of zinc(II) meso-tetrakis(4-carboxyphenyl)porphyrin
(ZnTPPc) at an immiscible aqueous|organic interface. We show that the
kinetically favoured metastable J-type nanostructures form quickly, but then
transform into stable thermodynamically favoured H-type nanostructures.
Numerical modelling revealed two parallel and competing cooperative pathways
leading to the different porphyrin nanostructures. These insights demonstrate
that pathway complexity is not unique to self-assembly processes in bulk
solution, and equally valid for interfacial self-assembly. Subsequently, the
interfacial electrostatic environment was tuned using a kosmotropic anion
(citrate) in order to control the influence the pathway selection. At high
concentrations, interfacial nanostructure formation was forced completely down
the kinetically favoured pathway and only J-type nanostructures were obtained.
Furthermore, we found by atomic force microscopy (AFM) and scanning electron
microscopy (SEM) that the J- and H-type nanostructures obtained at low and high
citric acid concentrations, respectively, are morphologically distinct, which
illustrates the pathway-dependent material properties.</p> | Iván Robayo-Molina; Andrés F. Molina-Osorio; Luke Guinane; Syed A.M. Tofail; Micheal D. Scanlon | Chemical Kinetics; Interfaces; Self-Assembly; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755d3337d6c01dbe28cfb/original/pathway-complexity-in-supramolecular-porphyrin-self-assembly-at-an-immiscible-liquid-liquid-interface.pdf |
60c75628f96a0051a9288a02 | 10.26434/chemrxiv.14199236.v1 | Zirconia Nanotube Coatings - UV-Resistant Superhydrophobic Surfaces | Surface modifications influence material interactions such as wettability, imparting
hydrophobicity or hydrophilicity. Mainstream research focused on enhancing product shelf-life,
directs attention towards superhydrophobic surfaces (SHS). SHS offer several benefits for outdoor applications such as self-cleaning, anti-soiling, anti-mist etc. In this manuscript, we explore
the possibility of combining structural and chemical modifications to metal substrates in order to
create superhydrophobic metal oxide surfaces. ZrO2-nanotubes are evaluated with regard to their
application as transparent UV-stable superhydrophobic coatings. Nanostructured oxide surfaces
are created via single-step electrochemical anodization. The absence of HF acid-based pre-etching
steps offer a safe and alternatively a green synthesis route. Anodized oxides are modified using
octadecylphosphonic acid self-assembled monolayers, demonstrate superhydrophobicity and are
evaluated for their mechanical stability under a jet of water, chemical stability under indirect
sunlight irradiation in air/water and direct UV exposure. Zirconia nanotubular films were
evaluated for optical transparency using light microscopy and surface wettability of the different
zirconia-composites was compared to the model system-titania. Structural and compositional
differences of the SAM layer upon time dependent decay were analyzed with X-ray photoelectron
spectroscopy. <br /> | Swathi Naidu Vakamulla Raghu; Manuela S Killian; Khajidkhand Chuluunbandi | Coating Materials; Nanostructured Materials - Materials; Electrochemistry; Photovoltaics; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75628f96a0051a9288a02/original/zirconia-nanotube-coatings-uv-resistant-superhydrophobic-surfaces.pdf |
6229c607011b5821cdc46968 | 10.26434/chemrxiv-2022-1tmlj | Side chain interactions govern the response of polypeptide alpha-helices under mechanical stress and prevent the formation of beta-sheets | Secondary a-helix and b-sheet structures are key scaffolds around which the rest of the residues condense during protein folding. They are crucial for proteins to adopt their correct native structure. Despite their key role in numerous processes to maintain life, little is known about their properties under force. Their stability under mechanical stress, as constantly experienced in the turbulent environment of cells, is however essential. Here, we designed and synthesized two pH-responsive polypeptides, poly(L-glutamic acid) and poly(L-lysine), for optimal interfacing with an AFM single-molecule force spectroscopy set-up to probe the mechanical unfolding of a-helix and b-sheet secondary motifs. The force experiments, supported by simulations, reveal a superior mechanical stability of the poly(L-Lysine) a-helix, which we attribute to hydrophobic interactions of the alkyl side chains. Most importantly, our results show that these interactions play a key role in inhibiting the formation of a metastable b-sheet-like structure when the polypeptide is subjected to mechanical deformations, which might have important implications in the mechanism behind polyQ diseases. | Marie Asano; Damien Sluysmans; Nicolas Willet; Colin Bonduelle; Sébastien Lecommandoux; Anne-Sophie Duwez | Physical Chemistry; Polymer Science; Nanoscience; Biopolymers; Biophysical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6229c607011b5821cdc46968/original/side-chain-interactions-govern-the-response-of-polypeptide-alpha-helices-under-mechanical-stress-and-prevent-the-formation-of-beta-sheets.pdf |
65a0314ae9ebbb4db9f2b753 | 10.26434/chemrxiv-2024-qp2rs | How Low can you Go? Nanoscale Membranes for Efficient Water Electrolysis | Motivated by the need to lower the cost of hydrogen (H2) production by water electrolysis, significant research efforts are focused on making proton (H+) exchange membrane (PEM) water electrolyzers more efficient and capable of operating at higher current densities. These aims can be met by making H+ conducting membranes thinner, which has the effect of lowering ohmic drops across the membrane that represent the largest efficiency loss at high current densities (>2 A cm-2). However, decreasing membrane thickness below 50 microns is not trivial due to trade-offs between membrane resistance, H2 cross-over (safety), membrane degradation, and manufacturing throughput. Herein, descriptions of key processes, limitations, and trade-offs that arise in thin membranes are provided that can be used to guide the design of ultrathin (i.e., sub-micron thick), low-resistance membrane materials that have potential to transform the field of clean H2 production. | Lucas A. Cohen; Matthew S. Weimer; Kyungmin Yim; Jingjing Jin; Daniela V. Fraga Alvarez; Arrelaine A. Dameron; Christopher B. Capuano; Ryan J. Ouimet; Serafina Fortiner; Daniel V. Esposito | Energy; Energy Storage; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a0314ae9ebbb4db9f2b753/original/how-low-can-you-go-nanoscale-membranes-for-efficient-water-electrolysis.pdf |
654a7790c573f893f104119d | 10.26434/chemrxiv-2023-plj1t-v2 | Chemistry of Cyclo-[2n]-Carbon: A Many-Particle Quantum Mechanics Investigation | Direct observations of cyclo-[2n]-carbon molecules (C10, C14, C16 and C18) experimentally prepared by atom manipulation technique raised immense attraction in the general chemistry society. The cyclic π-conjugated systems, namely in-plane and out-plane, construct dual aromaticity for odd n while dual anti-aromaticity for even n. In this work, we performed electronic structure investigation into cyclo-[2n]-carbon with n = 3 ~ 9 by comparing results obtained by density functional theory (DFT) and density matrix renormalization group (DMRG) method. By using Huckel molecular orbital (HMO) theory and the particle in a ring model, the electronic feature of such innovative carbon allotrope was clearly and chemically presented. Comparison showed that DFT results are considered to be incorrect for C6, which has a unique bonding structure among all cyclo-[2n]-carbon. The bond length alternating (BLA) phenomenon results from difference in electron correlation intensity and spatial distribution observed in pairs of bonding and anti-bonding orbitals. Therefore, results suggested that the dual anti-aromaticity in cyclo-[2n]-carbon with even n should be attributed to electron correlation effect, instead of decreased geometric symmetry, which actually exists in all cyclo-[2n]-carbon molecules and does not point out the essence. | Xi Chen; Xueyuan Yan; Zihan Liu; Tao Yuan; Caijie Bu; Yunlong Shang; Han Xiao; Yong Wu; Haiyan Wei; Jiawei Xu | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Clusters; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2023-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654a7790c573f893f104119d/original/chemistry-of-cyclo-2n-carbon-a-many-particle-quantum-mechanics-investigation.pdf |
67563498f9980725cf75d90e | 10.26434/chemrxiv-2024-trlwc | Deep-red to NIR Solution-Processed OLEDs of Donor-Decorated Quinoxaline-based TADF Aggregates | We report the use of an extended -conjugated electron-deficient “pyrazino[2,3-g]quinoxaline (PQ)” as a strong, planar acceptor in a donor-acceptor thermally activated delayed fluorescence emitter design to achieve deep-red to NIR emission. A pair of multi-donor-acceptor (multi-D-A) emitters, 4DMAC-TPPQ and 4PXZ-TPPQ, using PQ as the strong acceptor and dimethylacridine (DMAC) and phenoxazine (PXZ) as strong donors, respectively, emit at 650 and 762 nm in toluene, which is significantly red-shifted in comparison to the parent compound TPPQ (PL = 456 nm). Both compounds show aggregation-induced emission enhancement in THF:water mixtures. Both compounds are TADF as doped films in 4,4′-bis(N-carbazolyl)-1,1′-biphenyl (CBP) and as neat films. The emission of the neat film is similar to that in toluene with PL of 654 and 770 nm for 4DMAC-TPPQ and 4PXZ-TPPQ, respectively. Solution-processed organic light-emitting diodes (SP-OLEDs) of neat 4DMAC-TPPQ showed electroluminescence (EL) at 685 nm and EQEmax of 0.3%, while the device with 4PXZ-TPPQ emitted at EL of 780 nm and showed an EQEmax of 0.04%. The OLEDs with 4PXZ-TPPQ showed the most red-shifted emission amongst those employing TADF emitters containing a quinoxaline-type acceptor. | Abhishek Kumar Gupta; David Cordes; Alexandra Slawin; Stuart Warriner; Ifor Samuel; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67563498f9980725cf75d90e/original/deep-red-to-nir-solution-processed-ole-ds-of-donor-decorated-quinoxaline-based-tadf-aggregates.pdf |
6448069de4bbbe4bbf3d8191 | 10.26434/chemrxiv-2023-whjvj | Techno-economic analysis of a CO2 direct air capture-cooling tower hybrid process at a geothermal facility | Direct air capture (DAC) of CO2 can play a crucial role in global efforts to manage atmospheric concentrations of CO2, but the current cost-of-capture is prohibitively high. In this work we present a new DAC concept whereby cooling towers at geothermal power plants are hybridized to capture CO2 at very low cost. The system design is elegant in its ability to overcome key technical challenges and highlights the potential for using existing infrastructure to lower DAC cost and land footprint, and secure utilities and public confidence. The techno-economic analysis suggests a cost-of-capture of $100 per metric tonne of CO2 is feasible, allowing geothermal facilities to increase their net profit by $29 per metric tonne of CO2 captured — or $6 million per year — under the 45Q tax credit. If deployed at geothermal facilities in the United States, a net reduction of 270 million tonne CO2 per year is possible by 2050. | Fabian Rosner; Alexandre Schamberger; Hanna Breunig | Energy; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.); Power | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6448069de4bbbe4bbf3d8191/original/techno-economic-analysis-of-a-co2-direct-air-capture-cooling-tower-hybrid-process-at-a-geothermal-facility.pdf |
60c757abee301c2898c7b5d9 | 10.26434/chemrxiv.14038736.v2 | Computational Insights into Intramolecular Cross-Coupling of Quaternary Borate Salts | Cross-coupling reactions for C-C bond formation represent a cornerstone of organic synthesis. In most cases, they make use of transition metals, which has several downsides. Recently, metal-free alternatives relying on electrochemistry have gained interest. One example of such a reaction is the oxidation of tetraorganoborate salts that initiates aryl-aryl and aryl-alkenyl couplings with promising selectivities. This work investigates the mechanism of this reaction computationally using density functional and coupled-cluster theory. Our calculations reveal a distinct difference between aryl-alkenyl and aryl-aryl couplings: While C-C bond formation occurs irreversibly and without an energy barrier if an alkenyl residue is involved, many intermediates can be identified in aryl-aryl couplings. In the latter case, intramolecular transitions between reaction paths leading to different products are possible. Based on the energy differences between these intermediates, we develop a kinetic model to estimate product distributions for aryl-aryl couplings.<br /> | Florian Matz; Arif Music; Dorian Didier; Thomas C. Jagau | Computational Chemistry and Modeling; Kinetics and Mechanism - Organometallic Reactions; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757abee301c2898c7b5d9/original/computational-insights-into-intramolecular-cross-coupling-of-quaternary-borate-salts.pdf |
648f4a4bbe16ad5c571eb5ae | 10.26434/chemrxiv-2023-c0hgg | Analysis: A Figure of Merit for Efficiency Roll-off in Thermally Activated Delayed Fluorescent Organic Light-Emitting Diodes | Organic light-emitting diodes (OLEDs) are a revolutionary self-emitting display technology that has been successfully commercialized in mobile phones and TVs. The injected charges form both singlet and triplet excitons, and for high efficiency it is important to enable dark triplets to emit light. Currently materials that harvest triplets by thermally activated delayed fluorescence (TADF) are a very active field of research as an alternative to phosphorescent emitters which frequently employ heavy metal atoms. Whilst excellent progress has been made, there is a severe decrease of efficiency as the drive current is increased, i.e. efficiency roll-off, in most TADF OLEDs. At present much of the literature suggests that efficiency roll-off should be reduced by minimising the energy difference between singlet and triplet excited states in order to maximise the rate of conversion of triplets to singlets via reverse intersystem crossing (kRISC). We analyse the efficiency roll-off in a wide range of TADF OLEDs and find that neither of these parameters fully accounts for the reported efficiency roll-off. By considering the dynamic equilibrium between singlets and triplets in TADF materials, we propose new figures of merit (FOMs) for efficiency roll-off and discuss their correlation with reported data of TADF OLEDs. Our new FOMs will guide the design and development of TADF-OLEDs with lower efficiency roll-off. This will also lead to improved efficiency of TADF OLEDs at realistic display operating conditions and help expand the use of TADF materials to applications that require high brightness, such as lighting, augmented reality, and lasing. | Stefan Diesing; Le Zhang; Eli Zysman-Colman; Ifor Samuel | Physical Chemistry; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2023-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648f4a4bbe16ad5c571eb5ae/original/analysis-a-figure-of-merit-for-efficiency-roll-off-in-thermally-activated-delayed-fluorescent-organic-light-emitting-diodes.pdf |
611bc572ac8b494f2244e206 | 10.26434/chemrxiv-2021-gznvz | Towards reliable three-electrode cells for lithium–sulfur batteries | Three-electrode measurements are valuable to the understanding of the electrochemical processes in a battery system. However, their application in lithium–sulfur chemistry is difficult due to the complexity of the system and thus rarely reported. Here, we present a simple three-electrode cell format with relatively good life time and minimum interference with the cell operation. | Yu-Chuan Chien; Daniel Brandell; Matthew J. Lacey | Inorganic Chemistry; Energy; Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611bc572ac8b494f2244e206/original/towards-reliable-three-electrode-cells-for-lithium-sulfur-batteries.pdf |
65087fc599918fe5372f8e76 | 10.26434/chemrxiv-2023-x82fz | Machine Learning of Reactive Potentials | In the past two decades, machine learning potentials (MLPs) have driven significant developments in chemical, biological and material sciences. The construction and training of MLPs enables fast and accurate simulations and analysis on thermodynamic and kinetic properties. This review focuses on the applications of MLPs to reaction systems with consideration of bond breaking and formation. We review the development of MLP models, primarily with neural network and kernel-based algorithms, and recent applications of reactive MLPs (RMLPs) to systems at different scales. We will show how RMLPs are constructed and how they speed up the calculation of reactive dynamics and facilitate study of reaction trajectories, reaction rates, free energy calculations, and many other calculations. Different data sampling strategies applied in building RMLPs are also discussed with a focus on how to collect structures for rare events and how to further improve the performance with active learning. | Yinuo Yang; Shuhao Zhang; Kavindri Ranasinghe; Olexandr Isayev; Adrian Roitberg | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65087fc599918fe5372f8e76/original/machine-learning-of-reactive-potentials.pdf |
63607930ecdad5caaff4f734 | 10.26434/chemrxiv-2022-t5qqx | Digitizing Chemical Discovery with a Bayesian Explorer for Interpreting Reactivity Data | Interpretating the outcome of chemistry experiments consistently is slow and often introduces unwanted hidden bias. This difficulty limits the scale of collectable data and often leads to exclusion of negative results, which severely limits progress in the field. What is needed is a way to standardise the discovery process and accelerate the interpretation of high dimensional data aided by the expert chemist’s intuition. We demonstrate a digital Oracle that reasons about chemical reactivity using probability. By doing >500 reactions covering a large space and retaining both the positive and negative results the Oracle was able to rediscover eight historically important reactions including the Aldol condensation, Buchwald-Hartwig amination, Heck, Mannich, Sonogashira, Suzuki, Wittig and Wittig-Horner reactions. This new paradigm for decoding reactivity validates and formalizes the expert chemist’s experience and intuition, providing a quantitative criterion of discovery scalable to all available experimental data. | Leroy Cronin; S. Hessam Mehr; Dario Caramelli | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63607930ecdad5caaff4f734/original/digitizing-chemical-discovery-with-a-bayesian-explorer-for-interpreting-reactivity-data.pdf |
6697eb71c9c6a5c07a8a9d3e | 10.26434/chemrxiv-2024-nggx1 | Deoxytrifluoromethylation/Aromatization of Cyclohexan(en)ones to Access Highly Substituted Trifluoromethyl Arenes | Trifluoromethyl arenes (Ar–CF3) are amongst the commonly encountered fluorinated substructures in pharmaceutical, agrochemical, and material sciences. However, predominant methods to access Ar–CF3 possess several limitations, including harsh conditions, lack of availability of substrates, and poor regioselectivity, which combined restrict access to desirable highly functionalized Ar–CF3-containing compounds. To expand the scope of accessible Ar–CF3-based molecules, we present an innovative and orthogonal deoxyfluoroalkylation/aromatization approach that exploits readily accessible and programable cyclohexan(en)one substrates, which undergo a reliable 1,2-addition reaction with the Ruppert-Prakash reagent (TMSCF3) followed by aromatization to deliver highly functionalized Ar–CF3 compounds in a one/two-pot sequence. This general strategy enables access to highly substituted Ar–CF3-containing molecules that are difficult, expensive, and/or impossible to access by current synthetic methods. | Pankaj Bhattarai; Mohammed Khalifa Abd El Gaber; Suvajit Koley; Ryan Altman | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6697eb71c9c6a5c07a8a9d3e/original/deoxytrifluoromethylation-aromatization-of-cyclohexan-en-ones-to-access-highly-substituted-trifluoromethyl-arenes.pdf |
6167160b8b620df2b94e443d | 10.26434/chemrxiv-2021-wt2ck | Principal Component Analysis (PCA) and Statistical Tests Using Factoshiny and R Commander. | Spreadsheets are commonly used for data handling. However, in huge data sets, spreadsheets cannot do statistical tests, such as one-way ANOVA, boxplot, plot of means, principal component analysis (PCA). Most of the students had never worked with programming software such as MATLAB, Phyton, Octave and R project. Hence, in this lab experiment, students analyzed large data sets using R Commander and Factoshiny plugins. Commander and Factoshiny are packages which gives graphical user interface (GUI). GUI plugins allows students with no programming knowledge to run statical tests quickly and easily without having to type a single command line. The class was divided into three parts. First, students analyzed a red wine data set (1599 samples, 11 physicochemical variables, and one qualitative variable) to find correlations between wine quality (qualitative variable) and its physicochemical variables (quantitative variable). Second, they analyzed a white wine data set (4898 samples, 11 physicochemical variables, and one qualitative variable) to find correlations between white wine quality and its physicochemical variables. Third, they analyzed a red wine and white wine data set and found correlations between wine's physicochemical variables and their quality and type. Statistical tests and PCA were carried out using R Commander and Factoshiny, respectively. Due to the graphical interface and simplicity of these two plugins, the class can be concluded in 200 min. | Endler Marcel Borges; Matheus Fernandes Filgueiras | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6167160b8b620df2b94e443d/original/principal-component-analysis-pca-and-statistical-tests-using-factoshiny-and-r-commander.pdf |
65cf72b866c1381729cad96a | 10.26434/chemrxiv-2024-rg406 | Development of Robust Redox-Active Lyotropic Liquid Crystal Structures for Bioelectrodes | The fabrication of stable and highly performing enzyme-based electrodes is key for the effective generation of biodevices and bioelectronics, such as electrochemical biosensors. In this context, redox-active lyotropic liquid crystals based on 3D nanomaterials, known as lipid cubic phases (LCP), hold great potential due to the large specific surface area and the possibility to be functionalized. In this study, we functionalized a monoolein (MO) LCP matrix by incorporating an amphiphilic redox shuttle within its matrix with the aim to enhance the electrochemical performance of a glucose oxidase (GOx) based electrode and we investigated the stability of the overall system. The use of dodecyl(ferrocenylmethyl)dimethylammonium bromide (Fc12-Br) resulted in an electroactivity loss with time of the resulting Fc12-Br/MO electrode, probably due to the formation of a passivating layer between the bromide counterions and the electrode surface. Hence, bromine (Br-) was replaced with hexafluorophosate (PF6-), leading to Fc12-PF6/MO. Both structures were used for GOx entrapment and the resulting electro-activity towards glucose was assessed. Though the sensitivity obtained with the Fc12-Br/MO/GOx and Fc12-PF6/MO/GOx systems was comparable, the latter showed superior stability over time, with more than 80% activity retained for > 20 days. Moreover, when the concentration of the Fc12 redox shuttle within the cubic phase was increased by 10, a 4 times greater current density was generated. Consequently, the Fc12-PF6/MO electrode shows superior stability and performance than previously reported redox lyotropic LCP systems, thus paving the way for promising applications in enzyme-based biodevices. | Wanli Liu; Jodie L. Hann; Joshua S. White; Adam Milsom; Stephen Williams; Leide P. Cavalcanti; Iris S. Nandhakumar; Emily R. Draper; Simon E. Lewis; Mirella Di Lorenzo; Adam M. Squires | Physical Chemistry; Materials Science; Liquid Crystals; Biophysical Chemistry; Self-Assembly; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cf72b866c1381729cad96a/original/development-of-robust-redox-active-lyotropic-liquid-crystal-structures-for-bioelectrodes.pdf |
654c97a1dbd7c8b54be7ee00 | 10.26434/chemrxiv-2023-bqlfd | Second Quantization-based Symmetry-Adapted Perturbation Theory: Generalizing Exchange Beyond Single Electron Pair Approximation | This paper presents a general second-quantized form of a permutation operator interchanging $n$ pairs of electrons between interacting subsystems in the framework of the symmetry-adapted perturbation theory (SAPT). We detail the procedure for constructing this operator through the consecutive multiplication of single-pair permutation operators. This generalised form of the permutation operator has enabled the derivation of universal formulae for $S^{2n}$ approximations of the exchange energies in the first- and second-order of the interaction operator. We present the expressions for corrections of the $S^4$ approximations, and assess its efficacy on a selection of systems anticipated to exhibit a slowly converging overlap expansion. Additionally, we outline a method to sum the overlap expansion series to infinity in second-quantization, up to the second order in $V$. This new approach offers an alternative to the existing formalism based on the density-matrix formulations. When combined with a symbolic algebra program for automated derivations, it paves the way for advancements in SAPT theory, particularly for intricate wavefunction theories. | Bartosz Tyrcha; Filip Brzęk; Piotr Zuchowski | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654c97a1dbd7c8b54be7ee00/original/second-quantization-based-symmetry-adapted-perturbation-theory-generalizing-exchange-beyond-single-electron-pair-approximation.pdf |
60ed8b1e338e925d4d0aa690 | 10.26434/chemrxiv-2021-p517f | Nickel-catalyzed enantioselective annulation/alkynylation and Sonogashira reaction to form C(sp3)-C(sp) and C(sp2)-C(sp) bonds, respectively | While traditional Sonogashira reaction requires a palladium catalyst and a copper co-catalyst, some recent variants were reported being promoted by single transition metals. Here we report a single nickel-catalyzed tandem Heck-Sonogashira annulation/alkynylation for enantioselectively constructing C(sp3)-C(sp) bond. In addition, using the same catalytic system, Sonogashira C(sp2)-C(sp) cross-coupling has also been achieved. The alkynylations described in this report are important for the three reasons: 1. C(sp3)/(sp2)-C(sp) bonds exist in many bioactive natural products and drug molecules as well as their key synthetic intermediates; 2. There was no precedent for single nickel-catalyzed Sonogashira reaction owing to the difficulties caused by strong coordination of nickel to the triple bond to inactivate the catalyst; 3. Isolation and characterization of single-crystal structure of a resting state intermediate, di-phosphine chelated σ-alkyl-NiII-I complex, which provided crucial evidence to support the mechanistic postulation and guided DFT calculations. | chen hui; Liao xuebin; Tian Boxue ; Yao Licheng; Gu Buming; Zhang Yixuan ; Liu Yahu A | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ed8b1e338e925d4d0aa690/original/nickel-catalyzed-enantioselective-annulation-alkynylation-and-sonogashira-reaction-to-form-c-sp3-c-sp-and-c-sp2-c-sp-bonds-respectively.pdf |
672a49e87be152b1d013e180 | 10.26434/chemrxiv-2024-22jrq | Data Science-Driven Discovery of Optimal Conditions and a Condition-Selection Model for the Chan-Lam Coupling of Primary Sulfonamides | Secondary N-arylsulfonamides are common in pharmaceutical compounds owing to their valuable physicochemical properties. Direct N-arylation of primary sulfonamides presents a modular approach to this scaffold but remains a challenging disconnection for transition metal-catalyzed cross coupling broadly, including the Chan-Lam (CL) coupling of nucleophiles with (hetero)aryl boronic acids. Although the CL coupling reaction typically operates under mild conditions, it is also highly substrate-dependent and prone to over-arylation, limiting its generality and predictivity. To address these gaps, we employed data science tools in tandem with high-throughput experimentation to study and model the CL N-arylation of primary sulfonamides. To minimize bias in training set design, we applied un-supervised learning to systematically select a diverse set of primary sulfonamides for high-throughput data collection and modeling, resulting in a novel dataset of 3,904 reactions. This workflow enabled us to identify broadly applicable, highly selective conditions for the CL coupling of aliphatic and (hetero)aromatic primary sulfonamides with complex organoboron coupling partners. We also generated a regression model that not only successfully identifies high-yielding conditions for the CL coupling of various sulfonamides, but also sulfonamide features that dictate reaction outcome. | Shivaani Gandhi; Giselle Brown; Santeri Aikonen; Jordan Compton; Paulo Neves; Jesus Martinez Alvarado; Iulia Strambeanu; Kristi Leonard; Abigail Doyle | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Machine Learning; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a49e87be152b1d013e180/original/data-science-driven-discovery-of-optimal-conditions-and-a-condition-selection-model-for-the-chan-lam-coupling-of-primary-sulfonamides.pdf |
67b8de7d81d2151a027c75f2 | 10.26434/chemrxiv-2025-r7vwq | Electrochemically Resolved Acoustic Emissions from Li-ion Batteries | New methods of operando non-destructive evaluation (NDE) are needed to better assess the health and safety of Li-ion batteries. Monitoring acoustic emissions (AEs) is a popular NDE method in structural engineering, but has not yet provided reliable assessments when applied to batteries. Here, we show that various electro-chemo-mechanical processes in battery electrodes (graphite and nickel-manganese-cobalt oxides, NMC) can be reproducibly identified by electrochemically resolved AEs, after eliminating electromagnetic interference and applying wavelet-based signal processing. First, we perform “acousto-voltammetry” to correlate acoustic activity with specific electrochemical processes, such as ethylene gas generation and NMC particle fracture, as confirmed by gas detection and ex-situ SEM imaging, respectively. Next, we show that AEs can be distinguished using wavelet-transform features. Electrochemically resolved AEs provide a new window into quantitatively monitoring battery degradation, offering insights into electro-chemo-mechanical processes and potential advantages over conventional methods to improve metrics for state-of-health, remaining useful life, and safety risks. | Yash Samantaray; Daniel A. Cogswell; Alexander E. Cohen; Martin Z. Bazant | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b8de7d81d2151a027c75f2/original/electrochemically-resolved-acoustic-emissions-from-li-ion-batteries.pdf |
660eb4b721291e5d1d0c54aa | 10.26434/chemrxiv-2024-9ggdm-v2 | Photoredox Catalyzed Strain-Release Driven Synthesis of Functionalized Spirocyclobutyl Oxindoles | Spirocyclobutyl oxindoles have garnered substantial attention in drug discovery and pharmaceuticals owing to their wide range of biological activities. Strain-release in small-ring compounds is a powerful strategy to enable efficient access to complex molecules. In this study, we have successfully realized a photoredox-catalyzed strain-release radical spirocyclization approach to attain functionalized spirocyclobutyl oxindoles. A diverse array of radicals, such as sulfonyl, phosphonyl, and trifluoromethyl, were added efficiently to the strained C-C bond of bicyclobutanes (BCBs) to afford a library of spirocyclobutyl oxindoles. Furthermore, the obtained products could be transformed into valuable building blocks. The observed reactivity and selectivity have been rationalized based on density functional theory calculations. | Tushar Singha; Nakul Abhay Bapat; Subrat Kumar Mishra; Durga Prasad Hari | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660eb4b721291e5d1d0c54aa/original/photoredox-catalyzed-strain-release-driven-synthesis-of-functionalized-spirocyclobutyl-oxindoles.pdf |
655cb742dbd7c8b54bb571f5 | 10.26434/chemrxiv-2023-335gp | Unraveling Motion in Proteins by Combining NMR Relaxometry and Molecular Dynamics Simulations: A Case Study on Ubiquitin | Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of molecular systems in the picosecond to nanosecond timescales. As these methods cannot provide an atomically resolved view of the motion of atoms, functional groups, or domains giving rise to such signals, relaxation techniques have been combined with molecular dynamics (MD) simulations to obtain mechanistic descriptions and gain insights into the functional role of side chain or domain motion. In this work, we present a comparison of five computational methods which permit the joint analysis of MD simulations and NMR relaxation experiments. We discuss their relative strengths and areas of applicability, and demonstrate how they may be utilized to interpret the dynamics in MD simulations with the small protein ubiquitin as test system. We focus on the aliphatic side chains given the rigidity of the backbone of this protein. We find encouraging agreement between experiment, Markov state models built in the χ1/χ2 rotamer space of isoleucine residues, explicit rotamer jump models, and a decomposition of the motion using ROMANCE. These methods allow us to ascribe the dynamics to specific rotamer jumps. Simulations with eight different force fields and three different water models highlight how the different metrics may be employed to pinpoint force field deficiencies. Furthermore, the presented comparison offers a perspective on the utility of NMR relaxation to serve as validation data for the prediction of kinetics by state-of-the-art biomolecular force fields. | Candide Champion; Marc Lehner; Albert A. Smith; Fabien Ferrage; Sereina Riniker | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655cb742dbd7c8b54bb571f5/original/unraveling-motion-in-proteins-by-combining-nmr-relaxometry-and-molecular-dynamics-simulations-a-case-study-on-ubiquitin.pdf |
60c7484e469df467e2f439c3 | 10.26434/chemrxiv.11888022.v1 | Fe-N-C Nanozyme with Both Accelerated and Inhibited Biocatalytic Activities Capable of Accessing Drug-Drug Interaction | <p>Emerged as a cost-effective
and robust enzyme mimic, nanozymes have drawn increasing attention with broad
applications ranging from cancer therapy to biosensing. Developing nanozymes with
both accelerated
and inhibited biocatalytic
properties in a biological context is highly envisioned for
perusing more advanced functions of natural enzymes, such as in drug-drug
interaction, but remains challenging. By re-visiting the well-known Fe-N-C electrocatalyst
that has a heme-like Fe-N<sub>x</sub> coordination active center, herein, we
report that the Fe-N-C with a minimum graphitization had an even superior cytochrome
P450 (CYP)-like biocatalytic activity. Moreover, the drug metabolization by the
Fe-N-C upon co-existence of other foods and drugs demonstrated a trend of inhibition
similar to CYP, indicating its great potential as a replacement for <a>drug dosing guide and outcome prediction</a>. Beyond boosting
the enzyme-like activity, this work would open a new vista of nanozymes with inhibited
behavior for keeping up more demanding applications, enabled by further mimicking
the molecular structure of enzymes.</p> | Yuan Xu; Jing Xue; Qing Zhou; Yongjun ZHENG; Xinghua Chen; Songqin Liu; Yanfei Shen; Yuanjian Zhang | Carbon-based Materials; Analytical Chemistry - General; Biocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7484e469df467e2f439c3/original/fe-n-c-nanozyme-with-both-accelerated-and-inhibited-biocatalytic-activities-capable-of-accessing-drug-drug-interaction.pdf |
65ce4507e9ebbb4db96f0381 | 10.26434/chemrxiv-2024-2pmnk | High-Throughput Liquid Chromatography- Vacuum Differential Mobility Spectrometry-Mass Spectrometry for the Analysis of Isomeric Drugs of Abuse in Human Urine | The use of differential mobility spectrometry at low pressure coupled to liquid chromatography-mass spectrometry (LC-vDMS-MS) was investigated for the analysis of thirteen drugs of abuse (DoA) including: cocaine, ecgonine methyl ester, cocaethylene, benzoylecgonine, norcocaine, tramadol, isomeric pairs of metabolites; O-desmethyl-cis-tramadol and N-desmethyl-cis-tramadol, and cannabinoids; Δ9-tetrahydrocannabinol, Δ9-tetrahydrocannabidiol, 11-hydroxy-Δ9-tetrahydrocannabinol, 11-nor-9carboxy-Δ9-tetrahydrocannabinol, 11-nor-9carboxy-Δ9-tetrahydrocannabinol glucuronide. Different parameters were optimized for isomeric separation, such as LC mobile phase composition (20-100% methanol acetonitrile and isopropanol, flow rate: 8-100 µL/min) and DMS separation voltage. Methanol and acetonitrile significantly affected the compensation voltage of the analytes and improved DMS separation. A short trap/elute LC-vDMS-SIM/MS screening method of 1 min was developed to quantify 11 drugs of abuse (except THC/CBD), in addition to a 4 min LC-vDMS-SIM/MS method to identify and quantify 5 cannabinoids including the isomers THC/CBD and three THC metabolites. The signal responses were linear over a concentration range of 0.005-10 µg/ml for the DoA and 1-1000 ng/ml for cannabinoids. The intra- and inter-day precision were better than 12.2% and accuracy better than 115%. Urine samples from subjects who tested positive for THC and/or cocaine during roadside drug testing were evaluated to assess the performance of the methods LC-vDMS-SIM/MS and LC-MRM/MS. Results show that the developed LC-vDMS-SIM/MS method presents similar performance to LC-MRM/MS with improved sample throughput. | Maria Fernanda Cifuentes Girard; Patrick Knight; Gérard Hopfgartner | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY 4.0 | CHEMRXIV | 2024-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ce4507e9ebbb4db96f0381/original/high-throughput-liquid-chromatography-vacuum-differential-mobility-spectrometry-mass-spectrometry-for-the-analysis-of-isomeric-drugs-of-abuse-in-human-urine.pdf |
6749be76f9980725cf74410f | 10.26434/chemrxiv-2024-twhrl | Structure of a Supramolecular Water Copolymer | The use of water as a solvent to facilitate supramolecular polymerization is well documented, however, it is rare that water acts as a monomer that undergoes polymerization. We report the copolymerization of water with a saddle-shaped porphyrinoid macrocycle, carpyridine, which allows for linearly stacked, eclipsed columns within formed 2D nanosheets. Self-assembling carpyridine monomers from solutions with different extents of wetness allow for the formation of nanosheets on surface that appear identical by microscopy. Structural analysis through electron diffrac-tion reveals fundamental changes in the local organization. Under dry conditions, carpyridine stacks are formed through π–π interactions between curved surfaces whereas in solutions containing greater quantities of water, a hy-drogen-bonded water-to-carpyridine-core network is propagated throughout perfectly linear columns. The observed wet phase can be interconverted to a dry one through vapor annealing, indicating an accessible energy surface of polymorphism. | Joseph F. Woods; Kai Zhang; Joëlle Peterschmitt; Olivier Blacque; Céline Besnard; Gustavo Santiso-Quinones; Laura Samperisi; Andreas Vargas Jentzsch; Michel Rickhaus | Organic Chemistry; Polymer Science; Supramolecular Chemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6749be76f9980725cf74410f/original/structure-of-a-supramolecular-water-copolymer.pdf |
639267547b7c9162bde930fe | 10.26434/chemrxiv-2022-7wqj3 | Computational Material Database of Free-Standing 2D Perovskites | Inspired by the recent developments in the free-standing 2D complex oxide perovskite membranes and bulk 2D halide perovskite photoabsorbers, here, we put forward a new computational material database that has screened the stabilities and physical properties of 5,112 free-standing 2D nanostructures for 213 ABX3 cubic perovskites in 3 crystallographic orientations and 4 thicknesses, each with 2 different types of terminating surface chemistries. Our screening results show that many ABX3 compounds may form free-standing 2D structures that are both chemically and dynamically stable. Generally, the optimized 2D structures exhibit a shrinkage of the in-plane B-X bond lengths that are compensated by the elongation of the bonds normal to the 2D plane. As a result, the electron density distributions along the out-of-plane directions are strongly perturbed leading to a complex structural-dependent variation in the space-charge polarizations in these free-standing 2D perovskites. However, the out-of-plane ionic contributions to the dielectric permittivity are completely suppressed because of the structural confinement effect. The dominant contribution to the ionic dielectric permittivity thus comes from the in-plane optical phonons, the change in the frequencies of which from their bulk counterparts exhibits a complex dependency with the structures and chemistries of the 2D structures. Furthermore, without considering surface passivations and structural defects, the majority of the free-standing 2D perovskites exhibit metallic behavior. In particular, transition metal halides show exclusive spin-polarization at the Fermi level, which may be harnessed for applications such as nano spin-polarizer. Finally, unsupervised machine learning is further applied to discover the intriguing chemical and structural patterns among the computationally screened free-standing 2D perovskite structures, allowing us to reveal in a fully `data-driven' manner, the dependence of the energetic stabilities upon the surface termination, ionic radii and the layer thicknesses of these nanostructures. With fully open-sourced data and analysis code, we anticipate the current work can inspire the future theoretical and experimental works in the developments of free-standing 2D perovskites to harness their ubiquitous properties for new applications in nanoelectronics, sensing, energy harvesting and many others. | Jack Yang; Sean Li | Theoretical and Computational Chemistry; Materials Science; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639267547b7c9162bde930fe/original/computational-material-database-of-free-standing-2d-perovskites.pdf |
66290afe418a5379b0986b69 | 10.26434/chemrxiv-2024-0m8dm | Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer | The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry-based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of QC, it typically falls behind learning new techniques, instruments, or software. Considering how important QC is in a core setting where data is generated for non-mass spectrometry experts and confidence in delivered results is paramount, we have created this quick-start guide focusing on off-the-shelf QC materials and relatively easy to use QC software. We hope that by providing a background on the different levels of QC, different materials and their uses, describing QC design options, and highlighting some current QC software, that implementing QC in a core setting will be easier than ever. There continues to be development in each of these areas (such as new materials and software), and the current generation of QC mass spectrometry-based proteomics is more than capable of conveying confidence in results as well as minimizing laboratory downtime by guiding experimental, technical, and analytical troubleshooting from sample to results. | Benjamin Neely; Yasset Perez-Riverol; Magnus Palmblad | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Biochemistry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66290afe418a5379b0986b69/original/quality-control-in-the-mass-spectrometry-proteomics-core-a-practical-primer.pdf |
60c75121f96a00c6ee287f5e | 10.26434/chemrxiv.13122830.v1 | Shuttle Arylation by Rh(I) Catalyzed Reversible Carbon–Carbon Bond Activation of Unstrained Alcohols | The advent of transfer hydrogenation and borrowing hydrogen reactions paved the way to manipulate simple alcohols in previously unthinkable manners and circumvent the need for hydrogen gas. Analogously, transfer hydrocarbylation could greatly increase the versatility of tertiary alcohols. However, this reaction remains unexplored because of the challenges associated with the catalytic cleavage of unactivated C–C bonds. Herein, we report a rhodium(I)-catalyzed shuttle arylation cleaving the C(sp<sup>2</sup>)–C(sp<sup>3</sup>) bond in unstrained triaryl alcohols via a redox-neutral <i>β</i>-carbon elimination mechanism. A selective transfer hydrocarbylation of substituted (hetero)aryl groups from tertiary alcohols to ketones was realized, employing benign alcohols as latent <i>C</i>-nucleophiles. All preliminary mechanistic experiments support a reversible <i>β</i>-carbon elimination/migratory insertion mechanism. In a broader context, this novel reactivity offers a new platform for the manipulation of tertiary alcohols in catalysis. | Marius D. R. Lutz; Valentina C. M. Gasser; Bill Morandi | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75121f96a00c6ee287f5e/original/shuttle-arylation-by-rh-i-catalyzed-reversible-carbon-carbon-bond-activation-of-unstrained-alcohols.pdf |
65f9f4239138d23161d0598e | 10.26434/chemrxiv-2024-d0832 | Computed vs Experimental Energy Barriers in Solution: Influence of the type of the density functional approximation. | Mechanistic investigations at the Density Functional Theory (DFT) level of organic and organometallic reactions in solution are now broadly accessible and routinely implemented to complement experimental investigations. The selection of an appropriate functional among the plethora of developed ones is the first challenge on the way to reliable energy barrier calculations. To provide guidelines for the choice of an initial and reliable computational level, the performances of commonly used non-empirical (PBE, PBE0, PBE0-DH) and empirical density functionals (BLYP, B3LYP, B2PLYP) were evaluated relative to experimental activation enthalpies. Most reactivity databases to assess density functional performances are primarily based on high level calculations, here a set of experimental activation enthalpies of organic and organometallic reactions performed in solution were selected from the literature. As a general trend, the non-empirical functionals outperform the empirical ones. The most accurate energy barriers are obtained with hybride PBE0 and double-hybrid PBE0-DH density functionals, both providing similar performance. Regardless of the functional under consideration, the addition of the GD3-BJ empirical dispersion correction does not enhance the accuracy of computed energy barriers. | Aurore E. F. Denjean; Jordan Rio; Ilaria Ciofini; Marie-Eve L. Perrin; Pierre-Adrien Payard | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f9f4239138d23161d0598e/original/computed-vs-experimental-energy-barriers-in-solution-influence-of-the-type-of-the-density-functional-approximation.pdf |
6338ab80975e94054f900d80 | 10.26434/chemrxiv-2022-nc91f | Phosphorus(V) Fluoride Exchange (PFEx): Multidimensional Click Chemistry from Phosphorus(V) Connective Hubs | We report catalytic Phosphorus Fluoride Exchange (PFEx) as the latest advance in connective click-reaction technology. Emulating Nature, PFEx reaches into the biological world and creates stable tetrahedral P(V)- connections through efficient phosphorus-fluoride exchange chemistry. We showcase PFEx through the coupling of P(V)-F hubs with aryl alcohols, alkyl alcohols, and amines, delivering stable, multidimensional P(V)-O and P(V)- N connected products. The reactivity profile of P-F hubs surpasses that of their P-Cl counterparts, both in reaction performance, rate, and outcome, qualifying PFEx as a true click reaction. The rate of PFEx transformations is significantly enhanced by Lewis amine base catalysis [e.g., 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD)]. When using substrates comprising multiple P-F bonds, selective, serial exchange reactions are realized through judicious catalyst selection. Synthesis of the final products (in up to 4 steps) allows controlled projections to be deliberately installed along 3 of the 4 tetrahedral axes departing the P(V) central hub. The unique reactivity window of PFEx allows for selective, modular click-reactions to be performed in series (e.g., SuFEx-PFEx-CuAAC) to rapidly generate complex multidimensional molecules, rendering PFEX a perfect addition to the click chemistry toolbox. | Shoujun Sun; Christopher J. Smedley; Joshua A. Homer; Qing-Qing Cheng; K. Barry Sharpless; John E. Moses | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6338ab80975e94054f900d80/original/phosphorus-v-fluoride-exchange-pf-ex-multidimensional-click-chemistry-from-phosphorus-v-connective-hubs.pdf |
6244ab267ffb6352bff0d68a | 10.26434/chemrxiv-2022-n4cq4 | Lipid Expansion Microscopy | Strategies to visualize cellular membranes with light microscopy are restricted by the diffraction limit of light, which far exceeds the dimensions of lipid bilayers. Here, we describe a method for super-resolution imaging of metabolically labeled phospholipids within cellular membranes. Guided by the principles of expansion microscopy, we develop an approach featuring cell-permeable reagents that enables direct chemical anchoring of bioorthogonally labeled phospholipids into a hydrogel network and is capable of tunable, isotropic expansion, thus facilitating super-resolution imaging of cellular membranes. We apply this method, termed lipid expansion microscopy, to visualize organelle membranes with precision, including a unique class of membrane-bound structures known as nuclear invaginations. As it is compatible with standard confocal microscopes, lipid expansion microscopy will be widely applicable for super-resolution imaging of phospholipids and cellular membranes in numerous physiological contexts. | Brittany M White; Amanda N Conwell; Kane Wu; Jeremy M Baskin | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6244ab267ffb6352bff0d68a/original/lipid-expansion-microscopy.pdf |
6502f746b338ec988a77049a | 10.26434/chemrxiv-2023-nps5t-v2 | Electrochemical Synthesis of Unnatural Amino Acids Embedding 5- and 6-Membered Heteroaromatics | Using a commercially available potentiostat, the electrochemical synthesis of unnatural amino acids bearing heteroaromatics on the lateral chain has been accomplished. This strategy exploits the side-chain decarboxylative arylation of aspartic/glutamic acid, a reaction that becomes challenging with electron-rich coupling partners such as 5- and 6-membered heteroaromatics. These rings are underrepresented in unnatural amino acids, therefore it allowed a wider exploration of the chemical space, also given the abundance of the aryl bromides employable in this reaction | Elena Bombonato; Valerio Fasano; Daniel Pecorari; Luca Fornasari; Massimo Marcaccio; Paolo Ronchi | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6502f746b338ec988a77049a/original/electrochemical-synthesis-of-unnatural-amino-acids-embedding-5-and-6-membered-heteroaromatics.pdf |
60c745a09abda22807f8c5ea | 10.26434/chemrxiv.10072799.v1 | Force Field Partial Charges with Restrained Electrostatic Potential 2 (RESP2) | <p>Many molecular simulation force fields represent the charge
distributions of molecules with atom-centered partial charges, so simulations
with these force fields require that partial charges be assigned to the
molecules of interest. The restrained
electrostatic potential (RESP) approach is a highly regarded and widely used
method of assigning partial charges to varied organic compounds. RESP uses gas-phase
HF/6-31G* as the underlying quantum chemical method, intending the resulting
overpolarization of molecules to approximate the self-polarization that occurs
in the condensed phase setting. However, it is far from clear that this
fortuitous overpolarization is optimal or consistent across all compounds. In
order to reach a higher level of accuracy, we propose a next generation of this
approach, termed RESP2. In RESP2, the charges are derived from higher-level quantum
chemical calculations carried out for both gas and aqueous phase, the latter
using a continuum solvent model. The polarity of the final charges is tuned by
a mixing parameter, δ, which scales the relative contributions of the gas- and
aqueous-phase charges. We find that simply substituting RESP2 charges for RESP
charges in the context of regular LJ parameters does not lead to clear
improvement in liquid-state densities and heats of vaporization but does
improve the accuracy of observables expected to depend most strongly on the
accuracy of the charge model, i.e., dielectric constants and molecular dipole
moments. However, when Lennard-Jones (LJ) parameters are optimized in the
context of RESP charges, based on liquid properties, significant improvement in
accuracy can be achieved, even with a sharply reduced set of LJ types. <a>We argue that RESP2 with </a>δ≈0.6 (60% aqueous and 40% gas-phase charges) is an accurate and robust method of generating
atom-centered partial charges. The present study also highlights the value of optimizing
LJ parameters along with the electrostatic model and
suggests that a small set of LJ types can be a good starting point for a
systematic re-optimization of this important nonbonded term.</p> | Michael Schauperl; Paul Nerenberg; Hyesu Jang; Lee-Ping Wang; Christopher I. Bayly; David Mobley; Michael Gilson | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745a09abda22807f8c5ea/original/force-field-partial-charges-with-restrained-electrostatic-potential-2-resp2.pdf |
60c74dcdee301c854dc7a383 | 10.26434/chemrxiv.12662240.v1 | Simplified Computational Model for Generating Biological Networks | <p>A method to generate and simulate biological networks is discussed. An expanded Wooten-Winer-Weaire bond switching methods</p><p>is proposed which allows for</p><p>a distribution of node degrees in the network while conserving the mean average node degree.</p><p>The networks are characterised in terms of their polygon structure and assortativities (a measure</p><p>of local ordering). A wide range of experimental images are analysed and the underlying networks</p><p>quantified in an analogous manner. Limitations in obtaining the network structure are discussed.</p><p>A "network landscape" of the experimentally observed and simulated networks is constructed from the underlying metrics.</p><p>The enhanced bond switching algorithm is able to generate networks spanning the full range of experimental observations.</p> | Matthew Bailey; David Ormrod Morley; Mark Wilson | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dcdee301c854dc7a383/original/simplified-computational-model-for-generating-biological-networks.pdf |
60c73fdfbb8c1a30493d9c5d | 10.26434/chemrxiv.7530854.v1 | Electronic or steric effects: Detailed DFT investigations of titanium amino based Kaminsky type olefin catalysts | We report detailed Density Functional Theory (DFT) investigations of a series of structurally similar titanium (IV) chelating σ-aryl catalysts. Particular attention was paid to the electronic charges of the Ti, C ipso of the substituted aryl group and the benzylic CH<sub>2</sub> and C<i><sub>ipso</sub></i> atoms. The Bader and NBO derived charges were compared with the recently reported polymerisation results by Chan. We found a strong correlation between the relative energies of one of the computed isomers and the activity of the catalyst. Neither NBO nor Bader charges could be convincingly correlated to the observed activity. | Jörg Saßmannshausen | Computational Chemistry and Modeling; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdfbb8c1a30493d9c5d/original/electronic-or-steric-effects-detailed-dft-investigations-of-titanium-amino-based-kaminsky-type-olefin-catalysts.pdf |
60e0509d9bb5dde1a3909d49 | 10.26434/chemrxiv-2021-3xfds | Quantum chemical calculations to trace back reaction paths for the prediction of reactants | The long-due development of a computational method for the ab initio prediction of chemical reactants that provide a target compound has been hampered by the combinatorial explosion that occurs when reactions consist of multiple elementary reaction processes. To address this challenge, we have developed a quantum chemical calculation method that can enumerate the reactant candidates from a given target compound by combining an exhaustive automatic reaction path search method with a kinetics method for narrowing down the possibilities. Two conventional name reactions were then assessed by tracing back reaction paths using this new method to determine whether the known reactants could be identified. Our method is expected to be a powerful tool for the prediction of reactants and the discovery of new reactions. | Yosuke Sumiya; Yu Harabuchi; Yuuya Nagata; Satoshi Maeda | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e0509d9bb5dde1a3909d49/original/quantum-chemical-calculations-to-trace-back-reaction-paths-for-the-prediction-of-reactants.pdf |
60c749dcf96a001eb328733a | 10.26434/chemrxiv.12055395.v2 | Signal Amplification by Reversible Exchange for COVID-19 Antiviral Drug Candidates | <p></p><p>Several drug candidates have been proposed and tested as
the latest clinical treatment for the coronavirus pneumonia (COVID-19).
Chloroquine, hydroxychloroquine, ritonavir/lopinavir, and favipiravir are
proved to be effective after treatment. The hyperpolarization technique
presents an ability to further understand the roles of these drugs at the
molecular scale and applications in nuclear magnetic resonance/magnetic
resonance imaging (NMR/MRI). This technique may provide new opportunities in
diagnosis and biomedical research to cope with COVID-19. Signal amplification by reversible
exchange (SABRE)-based
hyperpolarization studies on large-sized drug candidates were carried out. We
observed hyperpolarized proton signals from whole structures, due to the unprecedented
long-distance polarization transfer by <i>para</i>-hydrogen. We also found that
the optimum magnetic field for the maximum polarization transfer yield was dependent
on the molecular structure. Therefore, future research on isotope labelling and
polarization transfer on long T1 time nuclei including clinical perspectives can
help us overcome this worldwide pandemic.</p><p></p> | HyeJin Jeong; Sein Min; Heelim Chae; Sara Kim; Gunwoo Lee; Sung Keon Namgoong; Keunhong Jeong | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749dcf96a001eb328733a/original/signal-amplification-by-reversible-exchange-for-covid-19-antiviral-drug-candidates.pdf |
634d1019dfbd2b3aa3590a35 | 10.26434/chemrxiv-2022-dtb1t | Azide click chemistry on magnetotactic bacteria: a versatile technique to attach a cargo | Adding biomolecules to living organisms and cells is the basis for creating living materials or biohybrids for robotic systems. Bioorthogonal chemistry allows covalently modifying biomolecules with functional groups not natively present under biological conditions and is therefore applicable to microorganisms and cells. Click chemistry is a biorthogonal chemistry approach that allows the study and manipulation of living entities. Incorporating the bioorthogonal click-chemistry handle, azide groups, into living microorganisms has been achieved by metabolic labeling, i.e., by culturing cells or organisms in a modified culture media having a specific natural molecular building block (e.g., amino acid, nucleotide, carbohydrate) modified with a tagged chemical analog. Here we explore the effect of the azide group incorporation into the magnetotactic bacteria Magnetospirillum gryphiswaldense (MSR-1) by adding a modified amino acid, 3-Azido-D-Alanine, during their cultivation. We show the existence of a concentration limit to effectively incorporate the azide group while maintaining the magnetic properties of the cells. We use this modification to explore the combination with versatile single-cell tagging methods. | Paul Soto; Mila Sirinelli-Kojadinovic; Maximilien Rouzaud; Damien Faivre | Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634d1019dfbd2b3aa3590a35/original/azide-click-chemistry-on-magnetotactic-bacteria-a-versatile-technique-to-attach-a-cargo.pdf |
64f19b5579853bbd78d9b6a7 | 10.26434/chemrxiv-2023-5rn0w | Gas Separating Metal-Organic Framework Membrane Films on Large Area 3D-Printed Tubular Ceramic Scaffolds | Polycrystalline metal-organic framework (MOF) membrane films prepared on ceramic supports can separate gases with high energy efficiency. They generally exhibit very high permeance and selectivity but suffer from cost issues through the required ceramic supports. Increasing the area and reducing the ceramic component to a minimum could be a strategy to enabling neat membrane of MOFs. In a rapid prototyping approach using 3D-printed porous scaffolds with a double helical channel geometry, we dramatically increase the active membrane area-to-volume ratio. Following stereolithographic printing and de-binding of a ceramic slurry, an adapted sintering protocol was employed to sinter commercially available alumina slurries into porous scaffolds. The 3D-printed scaffolds were optimized at a porosity of 40%, with satisfying mechanical stability. Furthermore, synthetic procedures yielding omnidirectional, homogeneous coatings on the outside and inside of the tubular scaffolds were developed. Membrane films of ZIF-8 and HKUST-1 covering a huge 50 cm² membrane area were produced in this way by applying a counter-diffusion methodology. Gas separation performance was evaluated for H2, CO2, N2 and CH4, in single-gas measurements and on their binary gas mixtures. | Surjyakanta Rana; Roman Sajzew; Oksana Smirnova; Josef B. Slowik; Ayisha Komal; José J. Velázquez; Ralf Wyrwa; Dušan Galusek; Ingolf Voigt; Lothar Wondraczek; Alexander Knebel | Inorganic Chemistry; Chemical Engineering and Industrial Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Industrial Manufacturing; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f19b5579853bbd78d9b6a7/original/gas-separating-metal-organic-framework-membrane-films-on-large-area-3d-printed-tubular-ceramic-scaffolds.pdf |
66a52715c9c6a5c07a26b95c | 10.26434/chemrxiv-2024-3bm54 | Structural optimization of oxaprozin for selective inverse Nurr1 agonism | Nuclear receptor related 1 (Nurr1, NR4A2) is a ligand-sensing transcription factor with neuroprotective and anti-inflammatory roles widely distributed in the CNS. Pharmacological Nurr1 modulation is considered a promising experimental strategy in Parkinson's and Alzheimer's disease but target validation is incomplete. While significant progress has been made in Nurr1 agonist development, inverse agonists blocking the receptor's constitutive activity are lacking. Here we report comprehensive structure-activity relationship elucidation of oxaprozin which acts as moderately potent and non-selective inverse Nurr1 ago-nist and RXR agonist. We identified structural determinants selectively driving RXR agonism or inverse Nurr1 agonism of the scaffold enabling the development of selective inverse Nurr1 agonists with enhanced potency and strong efficacy. | Sabine Willems; Romy Busch; Felix Nawa; Marco Ballarotto; Felix F. Lillich; Till Kasch; Úrsula López-García; Julian A. Marschner; Lorena A. Rüger; Beatrice Renelt; Julia Ohrndorf; Silvia Arifi; Daniel Zaienne; Ewgenij Proschak; Jörg Pabel; Daniel Merk | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a52715c9c6a5c07a26b95c/original/structural-optimization-of-oxaprozin-for-selective-inverse-nurr1-agonism.pdf |
60c7504c702a9b17a918bd43 | 10.26434/chemrxiv.13017161.v1 | Analyzing Mechanisms in Co(I) Redox Catalysis Using a Pattern Recognition Platform | Redox catalysis has been broadly utilized in electrochemical synthesis due to its kinetic advantages over direct electrolysis. The appropriate choice of redox mediator can avoid electrode passivation and overpotential, which strongly inhibit the efficient activation of substrates in electrolysis. Despite the benefits brought by redox catalysis, establishing the precise nature of substrate activation remains challenging. Herein, we determine that a Co(I) complex bearing two <i>N</i>,<i>N</i>,<i>N</i>-tridentate ligands acts as a competent redox catalyst for the reduction of benzyl bromide substrates. Kinetic studies combining electroanalytical techniques with multivariable linear-regression analysis were conducted, disclosing an outer-sphere electron-transfer mechanism, which occurs in concert with C–Br bond cleavage. Furthermore, we apply a pattern recognition platform to distinguish between mechanisms in the activation of benzyl bromides, found to be dependent on the ligation state of the cobalt(I) center and ligand used. | Tianhua Tang; Christopher Sandford; Shelley D. Minteer; Matthew Sigman | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7504c702a9b17a918bd43/original/analyzing-mechanisms-in-co-i-redox-catalysis-using-a-pattern-recognition-platform.pdf |
60c7432f9abda275c6f8c153 | 10.26434/chemrxiv.8966048.v1 | Parallel Charge-Transfer Mechanisms Allow for Diversifying the Choices for Photoredox Catalysts | Photochemistry provides access to reactive intermediates that are often inaccessible by any other means. Most organic molecules, however, are colorless ultraviolet absorbers. Therefore, photocatalysts absorbing in the visible spectral region are essential for transferring the required energy and charges to make challenging chemical transformations possible. A selection of a photocatalyst for driving oxidative or reductive reactions is crucial and is commonly based on their electrochemical potentials as well as the potentials of the starting materials. This selection, however, sometimes proves limiting and misleading, especially when the thermodynamic driving forces of the charge-transfer steps are relatively small. Here, we show that porphyrinoids with differences in their electrochemical potentials exceeding 0.5 V can photocatalyze the same model reaction of N-alkyl-2,4,6-triphenylpyridinium salt with alkynyl p-tolylsulfone to form the same alkylated alkynyl product in similar yields. Our studies reveal that switching between parallel reaction pathways makes the attainment of these conversion efficiencies possible. Electron-rich catalysts drive the formation of alkyl radicals principally via a photoinduced electron transfer to the pyridinium ion and a sequential hole transfer recovers their ground states, i.e., PET-HT mechanism. Conversely, a photoinduced hole transfer dominates the initial formation of the reduced forms of electron-deficient porphyrins that then transfer electrons to the pyridinium salt to release the same alkyl radicals, i.e., PHT-ET mechanism. This discovery demonstrates a paradigm where reaction mechanism adjust to the electronic properties of catalysts and opens doors for transformative diversification and broadening of the applicability of photochemical transformations.<br /><br /> | Katarzyna Goliszewska; Katarzyna Rybicka-Jasińska; John A. Clark; Valentine I. Vullev; Dorota Gryko | Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7432f9abda275c6f8c153/original/parallel-charge-transfer-mechanisms-allow-for-diversifying-the-choices-for-photoredox-catalysts.pdf |
64060db26642bf8c8f11319a | 10.26434/chemrxiv-2023-hq4xp | A Short and Facile [3+2] Addition Protocol Towards construction of Levuglandin Skeleta | The design and development of a simple and economical route for the construction of levuglandin skeleton from readily available isopropenyl acetate and methyl oleate has been reported. The key step involves a regio-controlled
elimination of the hydroxy group resulting in the formation of a cyclobutene derivative. Oxidative cleavage of the cyclobutene derivative gives levuglandin framework in three steps. The intriguing chemistry of elimination resulting in
the inseparable mixture of regioisomeric cyclobutenes has been discussed. | Pradeep Deota; Deepak Singh; Gaurang Bhatt | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64060db26642bf8c8f11319a/original/a-short-and-facile-3-2-addition-protocol-towards-construction-of-levuglandin-skeleta.pdf |
60c748ce702a9b55ae18b058 | 10.26434/chemrxiv.11833323.v2 | 3D Convolutional Neural Networks and a CrossDocked Dataset for Structure-Based Drug Design | One of the main challenges in drug discovery is predicting protein-ligand binding affinity. Recently, machine learning approaches have made substantial progress on this task. However, current methods of model evaluation are overly optimistic in measuring generalization to new targets, and there does not exist a standard dataset of sufficient size to compare performance between models. We present a new dataset for structure-based machine learning, the CrossDocked2020 set, with 22.5 million poses of ligands docked into multiple similar binding pockets across the Protein Data Bank and perform a comprehensive evaluation of grid-based convolutional neural network models on this dataset. We also demonstrate how the partitioning of the training data and test data can impact the results of models trained with the PDBbind dataset, how performance improves by adding more, lower-quality training data, and how training with docked poses imparts pose sensitivity to the predicted affinity of a complex. Our best performing model, an ensemble of 5 densely connected convolutional newtworks, achieves a root mean squared error of 1.42 and Pearson R of 0.612 on the affinity prediction task, an AUC of 0.956 at binding pose classification, and a 68.4% accuracy at pose selection on the CrossDocked2020 set. By providing data splits for clustered cross-validation and the raw data for the CrossDocked2020 set, we establish the first standardized dataset for training machine learning models to recognize ligands in non-cognate target structures while also greatly expanding the number of poses available for training. In order to facilitate community adoption of this dataset for benchmarking protein-ligand binding affinity prediction, we provide our models, weights, and the CrossDocked2020 set at https://github.com/gnina/models. | Paul Francoeur; Tomohide Masuda; David R. Koes | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748ce702a9b55ae18b058/original/3d-convolutional-neural-networks-and-a-cross-docked-dataset-for-structure-based-drug-design.pdf |
6595d2c19138d231612241e9 | 10.26434/chemrxiv-2024-wq0q6 | ZrH-Catalyzed Semi-Reduction of Esters Enabled by an Imine/Enamine Trap | Semi-reductive transformations of esters remains an underdeveloped but valuable class of functional group interconversions. For example, few strategies exist for the catalytic partial reduction of esters to aldehydes, and the direct catalytic semi-reductive imination/enamination of esters is absent from synthetic strategy. Here, we describe the development of a highly selective method for the interconversion of esters to imines, enamines, aldehydes or amines through an amine-intercepted ZrH-catalyzed reduction. This protocol employs Cp2ZrCl2 as an inexpensive catalyst in combination with hydrosilanes and simple unprotected amines. The in situ formation of imines and enamines effectively preserves an aldehyde oxidation level throughout the course of the reaction. A variety of aryl and aliphatic esters are directly transformed to imines and enamines in up to 99% yield or aldehydes in up to 84% yield, with little-to-no reduction to the corresponding alcohols. The utility of this method for the efficient preparation of nitrogen-containing products is also presented, including single-flask multicomponent reactions and the direct reductive amination of esters. These findings further demonstrate the utility of oxophilicity-driven ZrH catalysis for unconventional chemical transformations. | Rebecca Kehner; Liela Bayeh-Romero | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6595d2c19138d231612241e9/original/zr-h-catalyzed-semi-reduction-of-esters-enabled-by-an-imine-enamine-trap.pdf |
60c747c9337d6ccdb7e273fb | 10.26434/chemrxiv.11787534.v1 | Taking Lanthanides out of Isolation: Tuning the Optical Properties of Metal-Organic Frameworks | <div>Metal organic frameworks (MOFs) are increasingly used in applications that rely on the optical and electronic properties of these materials. These applications require a fundamental understanding on how the structure of these materials, and in particular the electronic interactions of the metal node and organic linker, determines these properties. </div><div><br /></div><div>Herein, we report a combined experimental and computational study on two families of lanthanide-based MOFs: Ln-SION-1 and Ln-SION-2. Both comprise the same metal and ligand but with differing structural topologies. In the Ln-SION-2 series the optical absorption is dominated by the ligand and using different lanthanides has no impact on the absorption spectrum. The Ln-SION-1 series shows a completely different behavior in which the ligand and the metal node do interact electronically. By changing the lanthanide in Ln-SION-1, we were able to tune the optical absorption from the UV region to absorption that includes a large part of the visible region. For the early lanthanides we observe intraligand (electronic) transitions in the UV region, while for the late lanthanides a new band appears in the visible. DFT calculations showed that the new band in the visible originates in the spatial orbital overlap between the ligand and metal node. Our quantum calculations indicated that Ln-SION-1 with late lanthanides might be (photo)conductive. Experimentally, we confirm that these materials are weakly conductive and that with an appropriate co-catalysts they can generate hydrogen from a water solution using visible light. Our experimental and theoretical analysis provides fundamental insights for the rational design of Ln-MOFs with the desired optical and electronic properties.</div> | Samantha L. Anderson; Davide Tiana; Christopher Ireland; Gloria Capano; Maria Fumanal; Andrzej Gładysiak; Stavroula Kampouri; Aiman Rahmanudin; Néstor Guijarro; Kevin Sivula; Kyriakos Stylianou; Berend Smit | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c9337d6ccdb7e273fb/original/taking-lanthanides-out-of-isolation-tuning-the-optical-properties-of-metal-organic-frameworks.pdf |
61782a246c5aa02bad251686 | 10.26434/chemrxiv-2021-px470 | Dimethoxytriazine-Triazole Linked Mesoporous Silica Hybrid Sorbent for Cationic Dyes Adsorption | Organic dye has always been considered one of the most serious water pollutants. Therefore, the great significance nowadays is to synthesis effective adsorbent Materials for removal of these contaminants. Herein, we prepared successfully a novel sorbent based on dimethoxy-triazine/triazole groups functionalized via a 1,3-dipolar cycloaddition click reaction on mesoporous silica SBA-15. The resulting sample denoted DMT-Tr-SBA-15 was characterized by FTIR spectra, X-ray photoelectron spectroscopy (XPS), solid-state 13C NMR spectroscopy and nitrogen adsorption/desorption isotherm. The resulting hybrid silica material was evaluated as a sorbent for adsorption of four cationic dyes in aqueous media showed high adsorption efficiency and a fast removal rate. The adsorption properties were monitored versus time; the after 40 min and using a 40 mg/L of adsorbent was reached. The maximum adsorption capacity for methylene blue at room temperature and neutral pH was 4.59 mmol g-1. These results indicate the great potential of clickable mesoporous silica to diversify the active sites for adsorption, thus demonstrating a significant interest for environmental applications. | Ali Saad; Khouloud Jlassi; Manef Abderrabba; Mohamed CHEHIMI | Materials Science; Earth, Space, and Environmental Chemistry; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Environmental Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61782a246c5aa02bad251686/original/dimethoxytriazine-triazole-linked-mesoporous-silica-hybrid-sorbent-for-cationic-dyes-adsorption.pdf |
61e87c3ceab6ef004ce7352e | 10.26434/chemrxiv-2022-93cff | Analytical Approaches for Porous Media Geothermal Power Calculations | Geothermal electricity generation may play a role in reducing greenhouse gas emissions and addressing climate change in a cost-effective manner. Reservoir equations for pressure and temperature must be coupled to a power cycle model to calculate electricity generation from a geothermal power plant. This work focuses on sedimentary basin geothermal power production, which relies on flow through porous and permeable aquifers in sedimentary basins. Previous work has used numerical reservoir simulators, but we introduce analytical reservoir solutions for reservoir impedance, wellbore heat loss, and reservoir heat depletion in this work. The reservoir impedance and wellbore heat loss solutions are combined with a power cycle model to calculate electricity generation. The reservoir heat depletion solution provides insight into the reservoir lifetime because electricity generation decreases with reservoir temperature. We compare the analytical and numerical approaches and discuss their implications for geothermal electricity generation from sedimentary basins. Both approaches have merits, and the comparison herein can guide those who want to understand geothermal electricity production. | Daniel T. Birdsell; Benjamin M. Adams; Jonathan D. Ogland-Hand; Jeffrey M. Bielicki; Mark R. Fleming; Martin O. Saar | Energy; Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry; Energy Storage; Power | CC BY 4.0 | CHEMRXIV | 2022-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e87c3ceab6ef004ce7352e/original/analytical-approaches-for-porous-media-geothermal-power-calculations.pdf |
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