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67b356f3fa469535b9b9da76 | 10.26434/chemrxiv-2025-p3d20 | Catalytic Asymmetric Synthesis of Fused Polycyclic Tetrahydropyridazine through Inverse‐Electron‐Demand Aza-Diels-Alder Reaction of Olefins with Azoalkenes in Situ Generated from α‑Halogeno Hydrazones | An efficient inverse electron-demand aza-Diels-Alder reaction of different types of olefins and 1,2-diaza-1,3-dienes, which could be readily formed in situ from α-halogeno hydrazones and a base, has been successfully developed. With the developed approach, a wide range of fused polycyclic tetrahydropyridazines were smoothly obtained in up to 95% yield and ee up to 98% with dr >20:1 under optimal reaction conditions. A gram-scale experiment and further derivatizations of the polycyclic tetrahydropyridazine products were also conducted to verify the practicability of the methodology. | Shi-Wu Li; Wei Li; Zhifei Zhao | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b356f3fa469535b9b9da76/original/catalytic-asymmetric-synthesis-of-fused-polycyclic-tetrahydropyridazine-through-inverse-electron-demand-aza-diels-alder-reaction-of-olefins-with-azoalkenes-in-situ-generated-from-halogeno-hydrazones.pdf |
67a263a881d2151a022b9373 | 10.26434/chemrxiv-2025-zgm2v | Synthesis and Ring-Opening Polymerization of Lactones Derived from the Cotelomerization of Isoprene, Butadiene, and CO2 | Herein, we report ring-opening polymerizations and copolymerizations of substituted δ-lactones derived from isoprene, butadiene, and CO2. While the telomerization of CO2 with butadiene to form a disubstituted δ-lactone is well-established, the similar telomerization of isoprene with CO2—or cotelomerization of isoprene and butadiene with CO2—have been less studied. Our initial efforts focused on identifying the factors that govern yield and selectivity in the cotelomerization of isoprene, butadiene, and CO2. The most effective cotelomerization/hydrogenation reaction sequence was scaled-up, leading to mixtures of two isoprene-butadiene coupled lactones (3-ethyl-6-(prop-1-en-2-yl)tetrahydro-2H-pyran-2-one (EtPeP), and 3-ethyl-6-methyl-6-vinyltetrahydro-2H-pyran-2- one (EtVMeP) and the butadiene homocoupled lactone, 3-ethyl-6-vinyltetrahydro-2H-pyran-2-one (EtVP). The ratios of these three lactones varied depending on telomerization conditions and purification methods employed. Stepwise syntheses of pure EtVMeP and EtPeP via alternate routes were also carried out. The pure lactones as well as lactone mixtures were subjected to organocatalyzed ring-opening (co)polymerization (ROP) using triazabicyclodecene (TBD), yielding CO2-based copolymers with molar masses (Mn) ranging from 5.5 to 12.7 kDa and narrow dispersities (Đ = 1.3). Increasing the proportion of EtPeP relative to EtVP led to a notable increase in the glass transition temperature (Tg) of the copolymers, reaching -20.5 °C. While EtPeP underwent successful ring-opening polymerization, reactions with EtVMeP resulted in termination of the polymerization owing to the formation of a non-nucleophilic tertiary alkoxide chain end. Thus, small amounts of EtVMeP can have a deleterious effect on copolymerizations of lactone mixtures derived from cotelomerization. These results motivate further development in the selective synthesis of EtPeP via cotelomerization of butadiene and isoprene with CO2. | Ryan Anderson; Takuya Akiyama; Ian Tonks | Catalysis; Polymer Science; Organic Polymers; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a263a881d2151a022b9373/original/synthesis-and-ring-opening-polymerization-of-lactones-derived-from-the-cotelomerization-of-isoprene-butadiene-and-co2.pdf |
60c73f17bdbb895707a37ef3 | 10.26434/chemrxiv.7207448.v1 | Spermine-NBD as Fluorescent Probe for Studies of Polyamine Transport System in Leishmania Donovani | This study describes the synthesis of
fluorescent probes as potential substrates for the polyamine transport system
(PTS) of <i>Leishmania donovani</i>. A competitive
radioassay was used to determine the most efficient probe. We observed that the
conjugate spermine-nitrobenzofurazan (Spm-NBD) was able to compete with [<sup>3</sup>H]-spermidine
in <i>L. donovani</i> at a relevant IC<sub>50</sub>
of 60 µM.
<p><br /></p> | Raphael LABRUERE; Sébastien Pomel; Elodie Jagu; Jean-Christophe Cintrat; Philippe M. Loiseau; stéphanie Pethe | Bioorganic Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f17bdbb895707a37ef3/original/spermine-nbd-as-fluorescent-probe-for-studies-of-polyamine-transport-system-in-leishmania-donovani.pdf |
65149763ade1178b243d86e4 | 10.26434/chemrxiv-2023-95s19 | Enhancing FAIRdata by providing digital workflows from data generation to the publication of data: an open source approach described for cyclic voltammetry | Analytical data in chemistry and other disciplines is usually generated in different formats and lacks common data and metadata standards that are necessary for a FAIR handling of research data. In the work presented herein, we describe a workflow that uses non-standardized, in some cases proprietary data formats from cyclic voltammetry measurements coming from individual devices as an instructive example, to yield open, standardized data that are annotated with rich metadata. The presented workflow includes concepts, software and infrastructure that can be used to support the whole data life cycle from the measurement of data to the publication of data and metadata in repositories. Components used for this workflow were made available as open source, allowing the re-use of this approach in other laboratories. The methods described for cyclic voltammetry can be adapted and used for other measurements and experimental data collections, allowing for an easy way to integrate new methods for digitalized research and FAIR data management. | David Herrmann; Patrick Hodapp; Martin Starman; Pei-Chi Huang; Chia-Lin Lin; Lan Le; Jochen Klar; Claudia Bizzarri; Philipp Roese; Niklas Oppel; Tillmann G. Fischer; Pierre Tremouilhac; Laura Holzhauer; Sonja Herres-pawlis; Alexander Hoffmann; Tobias Seitz; Kirsten Zeitler; Alrik Dorn; Nicole Jung; Stefan Bräse | Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Electrochemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65149763ade1178b243d86e4/original/enhancing-fai-rdata-by-providing-digital-workflows-from-data-generation-to-the-publication-of-data-an-open-source-approach-described-for-cyclic-voltammetry.pdf |
65b98f4fe9ebbb4db950b170 | 10.26434/chemrxiv-2023-kzh7p-v2 | Amino- and Alkoxybenziodoxoles: Facile Preparation and Use as Arynophiles | We report here on the facile synthesis of amino- and alkoxy-λ3-iodanes supported by a benziodoxole (BX) template and their use as arynophiles. The amino- and alkoxy-BX derivatives can be readily synthesized by reacting the respective amines or alcohols with chlorobenziodoxole in the presence of a suitable base. Unlike previously known nitrogen- and oxygen-bound iodane compounds, which have primarily been employed as electrophilic group transfer agents or oxidants, the present amino- and alkoxy-BX reagents manifest themselves as nucleophilic amino and alkoxy transfer agents toward arynes. This reactivity leads to the aryne insertion into the N–I(III) or O–I(III) bond to afford ortho-amino- and ortho-alkoxy-arylbenziodoxoles, iodane compounds nontrivial to procure by existing methods. The BX group in these insertion products exhibits excellent leaving group ability, enabling diverse downstream transformations. | Kazuya Kanemoto; Ken Yoshimura; Koki Ono; Wei Ding; Shingo Ito; Naohiko Yoshikai | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b98f4fe9ebbb4db950b170/original/amino-and-alkoxybenziodoxoles-facile-preparation-and-use-as-arynophiles.pdf |
65c4bba766c138172935d9ac | 10.26434/chemrxiv-2024-bbrgt | Partial Density of States Representation for Accurate Deep Neural Network Predictions of X-ray Spectra | The performance of a Machine Learning (ML) algorithm for chemistry is highly contingent upon the architect’s choice of input representation. This work introduces the partial density of states (p-DOS) descriptor: a novel, quantum- inspired structural representation which encodes relevant electronic information for machine learning models seeking to simulate X-ray spectroscopy. p-DOS uses a minimal basis set in conjunction with a guess (non-optimised) electronic configuration to extract and then discretise the density of states (DOS) of the absorbing atom to form the input vector. We demonstrate that while the electronically-focused p-DOS performs well in isolation, optimal performance is achieved when supplemented with nuclear structural information imparted via a geometric representation. p-DOS provides a description of the key electronic properties of a system which is not only concise and computationally efficient, but also independent of molecular size or choice of basis set. It can be rapidly generated, facilitating its application with large training sets. Its performance is demonstrated using a wide variety of examples at the sulphur K-edge, including the prediction of ultrafast X-ray spectroscopic signal associated with photoexcited 2(5H)-thiophenone. These results highlight the potential for ML models developed using p-DOS to contribute to the interpretation and predic- tion of experimental results made possible by emergent cutting-edge technologies, especially X-ray free electron lasers. | Clelia Middleton; Basile Curchod; Thomas Penfold | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c4bba766c138172935d9ac/original/partial-density-of-states-representation-for-accurate-deep-neural-network-predictions-of-x-ray-spectra.pdf |
62005b950c0bf02f75e0e33a | 10.26434/chemrxiv-2022-s2m8f | Electroaffinity Labeling: A New Platform for Chemoproteomic-based Target Identification
| Target identification is a critical pillar within the drug discovery process that involves deconvoluting the protein target of a pharmacologically active small molecule ligand. While photoaffinity labeling strategies have become the benchmark for target deconvolution of small molecules owing to their reliance on external activation to induce covalent protein capture, the process of target identification remains one of the most technically challenging aspects of early drug discovery. Thus, there is a strong demand for new technologies that allow for controlled activation of chemical probes to covalently label their protein target. Here, we introduce an electroaffinity labeling (ECAL) platform which leverages the use of a small, redox-active diazetidinone (DZE) functional group to enable chemoproteomic-based target identification of pharmacophores within live cell environments. | Yu Kawamata; Keun Ah Ryu; Gary Hermann; Alexander Sandahl; Julien Vantourout; Aleksandra Olow; La-Tonya Adams; Eva Rivera-Chao; Lee Roberts; Rob Oslund; Olugbeminiyi Fadeyi; phil baran | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62005b950c0bf02f75e0e33a/original/electroaffinity-labeling-a-new-platform-for-chemoproteomic-based-target-identification.pdf |
63bffa6b5ad3ef722b968763 | 10.26434/chemrxiv-2022-09j0v-v2 | Boosting CO2 Photoreduction by π-π-Induced Preassembly between a Cu(I) Photosensitizer and a Pyrene-Appended Co(II) Catalyst | The design of a highly efficient system for CO2 photoreduction fully based on earth-abundant elements presents a challenge, which may be overcome by installing suitable interactions between photosensitizer and catalyst to expedite the intermolecular electron transfer. Herein we have designed a pyrene-decorated Cu(I) complex with a rare dual-emission behavior, aiming at additional π-interaction with a pyrene-appended Co(II) catalyst for visible-light-driven CO2-to-CO conversion. The results of 1H NMR titration, time-resolved fluorescence/absorption spectroscopies, quantum chemical simulations and photocatalytic experiments clearly demonstrate that the dynamic π-π interaction between sensitizer and catalyst is highly advantageous in photocatalysis by accelerating the intermolecular electron transfer rate up to 6.9 × 105 s-1, thus achieving a notable apparent quantum yield of 19% at 425 nm with near-unity selectivity. While comparable to most earth-abundant molecular systems, this value is over three-times of the pyrene-free system (6.0%) and far surpassing the benchmarking Ru(II) tris(bipyridine) (0.3%) and Ir(III) tris(2-phenylpyridine) (1.4%) photosensitizers under parallel conditions. | Jia-Wei Wang; Zizi Li; Zhi-Mei Luo; Yanjun Huang; Fan Ma; Stephan Kupfer; Gangfeng Ouyang | Inorganic Chemistry; Catalysis; Energy; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bffa6b5ad3ef722b968763/original/boosting-co2-photoreduction-by-induced-preassembly-between-a-cu-i-photosensitizer-and-a-pyrene-appended-co-ii-catalyst.pdf |
60c7538d567dfe004eec5efa | 10.26434/chemrxiv.13434143.v2 | Robust and Facile Automated Radiosynthesis of [18F]FSPG on the GE FASTlab | <p><i>Purpose</i>: (S)-4-(3-<sup>18</sup>F-Fluoropropyl)-ʟ-Glutamic Acid ([<sup>18</sup>F]FSPG) is a radiolabeled non-natural amino acid that is used for positron emission tomography (PET) imaging of the glutamate/cystine antiporter, system x<sub>C</sub><sup>-</sup>, whose expression is upregulated in many cancer types. To increase the clinical adoption of this radiotracer, reliable and facile automated procedures for [<sup>18</sup>F]FSPG production are required. Here, we report a cassette-based method to produce [<sup>18</sup>F]FSPG at high radioactivity concentrations from low amounts of starting activity.</p><p><i>Procedures</i>: An automated synthesis and purification of [<sup>18</sup>F]FSPG was developed for the GE FASTlab. Optimization of the reaction conditions and automated manipulations were performed by measuring the isolated radiochemical yield of [<sup>18</sup>F]FSPG and by assessing radiochemical purity using radioHPLC. Purification of [<sup>18</sup>F]FSPG was conducted by trapping and washing of the radiotracer on MCX SepPak catridges, followed by a reverse elution of [<sup>18</sup>F]FSPG in phosphate-buffered saline. Subsequently, the [<sup>18</sup>F]FSPG obtained from the optimized process was used to image an animal model of non-small cell lung cancer.</p><p><i>Results</i>: The optimized protocol produced [<sup>18</sup>F]FSPG in 38.4 ± 2.6% RCY and 96% radiochemical purity. Small alterations, including the implementation of a reverse elution and an altered hypercarb cartridge, lead to significant improvements in radiotracer concentration from <10 MBq/mL to >100 MBq/mL. The improved radiotracer concentration allowed for the imaging of up to 20 mice, starting with just 1.5 GBq of [<sup>18</sup>F]fluoride.</p><p><i>Conclusions: </i>We have developed a robust and facile method for [<sup>18</sup>F]FSPG radiosynthesis in high radiotracer concentration, RCP and RCY. This cassette-based method enabled the production of [<sup>18</sup>F]FSPG at radioactive concentrations sufficient to facilitate large-scale preclinical experiments with a single prep of starting activity. The use of cassettes for an ‘out the box’ synthesis on a synthesis module routinely used for clinical production make the method amenable to rapid and widespread clinical translation.</p> | Richard Edwards; Hannah Greenwood; Timothy Witney | Imaging Agents; Imaging | CC BY 4.0 | CHEMRXIV | 2020-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7538d567dfe004eec5efa/original/robust-and-facile-automated-radiosynthesis-of-18f-fspg-on-the-ge-fas-tlab.pdf |
611c6591b022df02bb93839b | 10.26434/chemrxiv-2021-9ql74 | Metal-Responsive Regulation of Enzyme Catalysis using Genetically Encoded Chemical Switches | The design of allosteric regulation in proteins to dynamically control function is a challenge in synthetic biology. To address this challenge, we developed an integrated computational and experimental workflow to incorporate a metal-responsive chemical switch into proteins. Pairs of bipyridinylalanine (BpyAla) residues were genetically encoded into two structurally distinct enzymes, a serine protease and firefly luciferase, so that metal coordination would bias the conformations of these enzymes, leading to reversible control of activity. MD-simulations guided rational BpyAla placement, significantly reducing experimental workload, and cell-free protein synthesis coupled with high-throughput experimentation enabled rapid prototyping of variants. Ultimately, this strategy yielded enzymes with a robust 20-fold dynamic range in response to divalent metals over 24 on/off switches, demonstrating the potential of this approach. We envision that this strategy of genetically encoding chemical switches into enzymes will complement other protein engineering and synthetic biology efforts, enabling new opportunities for applications where precise regulation of protein function is critical. | Yasmine S. Zubi; Kosuke Seki; Ying Li; Andrew Hunt; Bingqing Liu; Benoît Roux; Michael C. Jewett; Jared C. Lewis | Biological and Medicinal Chemistry; Catalysis; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611c6591b022df02bb93839b/original/metal-responsive-regulation-of-enzyme-catalysis-using-genetically-encoded-chemical-switches.pdf |
6627aaa721291e5d1d7a4c59 | 10.26434/chemrxiv-2024-91dbd-v2 | WS24: A diverse data set for predicting metal-organic framework stability in water and harsh environments with data-driven models | Metal-organic frameworks (MOFs) are porous materials with applications in gas separations and catalysis, but a lack of water stability often limits their practical use given the ubiquity of water in air and the environment. Consequently, it is useful to predict whether a MOF is water-stable before investing time and resources into synthesis. Existing heuristics for designing water-stable MOFs lack generality and artificially limit the diversity of explored chemistry due to narrowly defined criteria. Machine learning (ML) models offer the promise to improve generality of predictions but require diverse experimental MOF stability data to be trained. In an improvement on previous efforts, we enlarge the available training data for MOF water stability prediction by over 400%, adding 911 MOFs with water stability labels assigned through semi-automated manuscript analysis to curate the new data set WS24. The additional data is shown to improve ML model performance (test ROC-AUC > 0.8) over diverse chemistry for the prediction of both water stability and stability in harsher acidic conditions. We illustrate how the expanded data set and models can be used with previously developed activation stability models to carry out genetic algorithms to quickly screen ~10,000 MOFs from a space of hundreds of thousands for candidates with multivariate stability (i.e., for activation, in water, and in acid). Model analysis and genetic algorithm results uncover metal- and geometry-specific design rules for robust MOFs. The data set and ML models developed in this work, which we disseminate through an easy-to-use web interface, are expected to contribute toward the accelerated discovery of novel, water-stable MOFs for applications such as direct air gas capture and water treatment. | Gianmarco Terrones; Shih-Peng Huang; Matt Rivera; Shuwen Yue; Alondra Hernandez; Heather Kulik | Theoretical and Computational Chemistry; Nanoscience; Theory - Computational; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6627aaa721291e5d1d7a4c59/original/ws24-a-diverse-data-set-for-predicting-metal-organic-framework-stability-in-water-and-harsh-environments-with-data-driven-models.pdf |
66f467c712ff75c3a176a767 | 10.26434/chemrxiv-2024-ghclf-v2 | Enhanced mineral carbonation on surface functionalized MgO derived from mine tailings | The escalating demands of industrialization and development underscore the necessity for an efficient and scalable Carbon Capture and Storage (CCS) methodology. Mineral carbonation of MgO presents itself as a promising solution due to its considerable theoretical capacity for CO2 adsorption. However, the sluggish kinetics of the carbonation process pose a significant challenge. Consequently, a comprehensive understanding of the structural and chemical alterations occurring during carbonation is imperative for material design. In this
study, we conduct a thorough structural and chemical investigation of the MgO (sourced from different mine tailings) carbonation process using electron microscopic techniques. Our findings demonstrate that treating MgO with polar solvents enhances its degree of carbonation significantly, offering a promising avenue for improvement. Moreover, we observe a particle size dependency in MgO carbonation and note that the inclusion of additional materials, such as Si-based compounds, further accelerates the carbonation. Density functional theory (DFT) calculations provide insight into surface functionalization as a result of solvent treatment and its mechanistic effect on the origin of the enhanced carbonation of polar solvent-treated MgO, revealing a stronger interaction between CO2 and the treated MgO (100) surface as compared to the non-polar solvent treated surfaces. These discoveries showcase an alternative approach for enhancing MgO carbonation, thereby offering a potential method for sequestering atmospheric CO2 more effectively using mine waste rich in MgO. | Rajeev Kumar Rai; Rui Serra-Maia; Yingjie Shi; Peter Psarras; Aleksandra Vojvodic; Eric A. Stach | Theoretical and Computational Chemistry; Materials Science; Geological Materials; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f467c712ff75c3a176a767/original/enhanced-mineral-carbonation-on-surface-functionalized-mg-o-derived-from-mine-tailings.pdf |
66831bb15101a2ffa810e976 | 10.26434/chemrxiv-2024-22xd4 | Probabilistic Deconvolution of the Distribution of Relaxation Times from Multiple Electrochemical Impedance Spectra | Electrochemical impedance spectroscopy (EIS) is widely used to study the properties of electrochemical materials and systems. However, analyzing EIS data remains challenging. Among various analysis methods, the distribution of relaxation times (DRT) has emerged as a novel non-parametric approach capable of providing timescale information. Among the various DRT inversion methods, those based on Gaussian processes (GP) are particularly promising because they provide uncertainty estimates for both EIS and DRT. However, current GP-based DRT implementations can only handle one spectrum at a time. This work extends these models to allow concurrent analysis of multiple impedance spectra as a function of experimental conditions. The new method, called the quasi-Gaussian process distribution of relaxation times, treats the DRT as a GP with respect to the experimental state and as a finite approximation of a positively constrained GP with respect to timescales. This new DRT inversion approach is validated against noise-corrupted artificial EIS data and applied to experimental data, allowing us to expedite EIS data analysis of multiple EIS data from a probabilistic perspective. | Adeleke Maradesa; Baptiste Py; Francesco Ciucci | Materials Science; Energy; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66831bb15101a2ffa810e976/original/probabilistic-deconvolution-of-the-distribution-of-relaxation-times-from-multiple-electrochemical-impedance-spectra.pdf |
66f3d17b51558a15ef0cd911 | 10.26434/chemrxiv-2024-vv8md | The temperature dependence of Mössbauer quadrupole splitting values: a quantum chemical analysis | The two key parameters extracted from Mössbauer spectroscopy, the isomer shift and the quadrupole splitting, have well-known temperature dependencies. While the values’ increase or decrease with sample temperature have long been established, the microscopic origins are less clear. For quantum chemical calculations – formally representing the situation at 0 K – significant discrepancies with experiment can arise depending on the temperature. Herein, we introduce an enesemble-based appraoch for capturing the temperature dependence of the quadrupole splitting. Our method is exemplified with [Fe(TPP)(2-MeHIm)]. We rationalise the temperature dependence by changes in the electric field gradient due to specific vibrational distortions. We use a normal mode fitting approach to isolate the specific collective nuclear movements that are associated with the changes in the quadrupole splitting. | Niklas von Rhein; Vera Krewald | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f3d17b51558a15ef0cd911/original/the-temperature-dependence-of-mossbauer-quadrupole-splitting-values-a-quantum-chemical-analysis.pdf |
66b1a23601103d79c5d7ccc1 | 10.26434/chemrxiv-2024-wxzt9 | Awakening the Sleeping Giant: Rediscovering Archimedes' Density Method for Fingerprinting of Multicomponent Alloys | If the matter is the manifestation of the God-particle, then density is its soul, as one cannot exist without the other. Hence, density inherently becomes mother of all properties of the matter. The Archimedes' density method presents a mathematically unsolvable, computationally non-recursive, and undecidable NP-Hard problem for non-binary alloys. Resolving underdetermined linear equations, discretizing infinite Probable Iso-density Compositions (PICs), solving NP-Hard problems, and achieving certainty from probabilities are key to its application. Non-binary alloy densities reveal multiple PIC series interconnected through "True Composition" (TC) in the Isopycnic Region (IR) of Vast Alloys Space (VAS), replicating as Concordant Compositions (CCs) similar to centromere replication during cell division. The Principle of Vernier coincidence in multiple dimensions echoes CCs as unique alloy fingerprints in geometrical superimposition. We modified Archimedes' equations for additional metals and developed Density Decoding System (DDS) (www.densityfingerprinting.com) to compute PICs using Successively increasing Predefined Imaginary Numerical values (SPIN-values) and standard metal densities, generating a real-time database. A perfectly symmetric C-band breaks the asymmetry of Density Genome fractals, visualizing Density Fingerprints to conclusively determine "True Composition" up to octonary alloys with absolute accuracy in polynomial time. The precision range of alloy density limits the chaotic Butterfly effect, creating a fractal composition space that enables self-authentication of True Compositions. The study uncovers the coexistence of chaos and order, the butterfly effect, the emergence of order from infinity, and the fractal nature of the composition space. The research reveals the manifestation of quantum-like phenomena in the classical realm of alloy compositions, challenging our understanding of the nature of matter. Our work unveils density as the genetic code for non-living matter, leading to a novel alloy classification into binary and non-binary alloys. Furthermore, it introduces the Density Fingerprinting and Density Genome framework, which enables comprehensive materials analysis, characterization, design, and discovery, marking a paradigm shift in our understanding about density and its pivotal role in shaping the future of material science. | Jai Hind Rathore; Pratibha Rathore; Bharati Rathore; Bhuvan Chandra Rathore | Theoretical and Computational Chemistry; Materials Science; Alloys; Theory - Computational; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b1a23601103d79c5d7ccc1/original/awakening-the-sleeping-giant-rediscovering-archimedes-density-method-for-fingerprinting-of-multicomponent-alloys.pdf |
60c7455d567dfe9552ec4455 | 10.26434/chemrxiv.8299544.v4 | A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network | <p>
</p><p>Deep learning methods applied to drug
discovery have been used to generate novel structures. In this study, we
propose a new deep learning architecture, LatentGAN, which combines an
autoencoder and a generative adversarial neural network for de novo molecular
design. We applied the method in two scenarios: one to generate random
drug-like compounds and another to generate target-biased compounds. Our
results show that the method works well in both cases: sampled compounds from
the trained model can largely occupy the same chemical space as the training
set and also generate a substantial fraction of novel compounds. Moreover, the drug-likeness
score of compounds sampled from LatentGAN is also similar to that of the
training set. Lastly, generated compounds differ from those obtained with a
Recurrent Neural Network-based generative model approach, indicating that both methods
can be used complementarily.</p><p>
</p> | Oleksii Prykhodko; Simon Viet Johansson; Panagiotis-Christos Kotsias; Josep Arús-Pous; Esben Jannik Bjerrum; Ola Engkvist; Hongming Chen | Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2019-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7455d567dfe9552ec4455/original/a-de-novo-molecular-generation-method-using-latent-vector-based-generative-adversarial-network.pdf |
65127c57ade1178b24220d4e | 10.26434/chemrxiv-2023-rsls2 | Identification of (+)-7R-Actinidine and its Biosynthetic Pathway in Rove beetles, Cafius spp. (Coleoptera: Staphylinidae) | Actinidine, a terpene alkaloid, is commonly found in various plants and insects. However, in recent years, it has been suggested that the presence of actinidine in these organisms may be due to artifacts resulting from heating during sample preparation and analysis. In this study, actinidine was successfully isolated and identified from rove beetles, specifically Cafius vestitus and Cafius pectoralis, using a nonheating extraction and purification method. Gas chromatography/mass spectrometry (GC/MS) and nuclear magnetic resonance analyses confirmed actinidine production by these rove beetle species. Additionally, employing a chiral column for GC/MS analysis revealed that the compound is (+)-7R-actinidine, marking its first discovery in natural products. To elucidate the actinidine biosynthesis pathway, D-glucose-1-13C and mevalolactone-2-13C were fed to C. vestitus. Results indicated that both compounds were incorporated into actinidine in the beetles, leading to the conclusion that C. vestitus accumulates (+)-7R-actinidine, which is derived from the mevalonic acid pathway. | Yu Takatani; Yuto Ohata; Takato Inoue; Naoki Mori | Organic Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Bioorganic Chemistry; Natural Products; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65127c57ade1178b24220d4e/original/identification-of-7r-actinidine-and-its-biosynthetic-pathway-in-rove-beetles-cafius-spp-coleoptera-staphylinidae.pdf |
62d91c204689332dde6342d2 | 10.26434/chemrxiv-2022-h5vlc | Sustainable Green Chemical Technology for Developments
in Process Industries | The environmental and climate issues facing across the world are widely recognized as serious problems. Therefore, green technologies and ecological sustainable development is need of the hour as the quality of life is worsening. We have had major progress in technology causing depletion of natural life sustaining resources, especially clean air and water. These problems are causing considerable environmental, economic and social impairment on a worldwide scale. Sustainable development implies that renewable resources should be used wherever possible and that non-renewable resources should be husbanded (e.g., reduced and recycled) to extend their viability for generations to come. The paper will present the trend towards sustainability and green technologies in the chemical process industry (CPI). A broad review of state-of-the-art green technologies in the understanding and application of sustainability with few case studies highlighting the economic benefits of adopting green processes from a chemical engineering viewpoint is addressed. Green technologies increasingly uses renewable resources; reduce wastes, pollutants, emissions; recover, reuse and recycle; reduce the pressure on natural resources and restore the balance of the eco-system and biosphere and ultimately help in providing "ecologically sustainable development". These technologies are, therefore, viable, cost-effective, environmentally advanced and most appropriate to the climatic, economical, geographical, ecological and social conditions of the country. This aim can only be achieved by developing new environmentally friendly, safe and non-toxic materials and their based innovative technologies. Therefore CPI must promote sustainable development by investing in green technologies and ensure increased adherence to safety, health and environmental standards.
Keywords: Green technologies, sustainable development, environmental, CPI, renewable resource | Kiran Patil | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing | CC BY 4.0 | CHEMRXIV | 2022-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d91c204689332dde6342d2/original/sustainable-green-chemical-technology-for-developments-in-process-industries.pdf |
66b62e6001103d79c55ea8c7 | 10.26434/chemrxiv-2024-k8qw2 | Local electronic correlation in multicomponent Møller-Plesset perturbation theory | We present in this contribution the first application of local correlation in the context of multicomponent methods. Multicomponent approaches allow for the targeted simulation of electrons together with other fermions (most commonly protons) as quantum particles. These methods have become increasingly popular over the last years, particularly for the description of nuclear quantum effects (in strong hydrogen bonds, proton tunneling, and many more). However, most implementations are still based on canonical formulations of wave function theory, which we know for decades to be computationally inefficient for capturing dynamical correlation effects. Local correlation approaches, particularly with the use of pair natural orbitals (PNOs), enable asymptotically linear scaling of computational costs with very little impact on the overall accuracy. In this context, the efficient use of density fitting approximations in the integrals calculation proves essential. We start by discussing our implementation of density-fitted NEO-MP2 and NEO-PNO-LMP2, upgrading the electronic correlation treatment up to PNO local coupled cluster. Several challenging examples are provided to benchmark the method in terms of accuracy as well as the computational cost scaling. Following appropriate protocols, anharmonic corrections to localized X-H stretches can be applied routinely with little computational overhead. | Lukas Hasecke; Ricardo A. Mata | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b62e6001103d79c55ea8c7/original/local-electronic-correlation-in-multicomponent-m-ller-plesset-perturbation-theory.pdf |
60c73cbfee301c551fc78482 | 10.26434/chemrxiv.14731455.v1 | Heck-Type Coupling of Fused Bicyclic Vinylcyclopropanes: Synthesis of 1,2-Dihydropyridines, 2,3-Dihydro-1H-Azepines, 1,4-Cyclohexadienes, 2H-Pyrans, and 1,3-Butadienes | Herein, we report a versatile approach for the
endocyclic ring-opening of bicyclic vinylcyclopropanes triggered by Heck
arylations. Key step for this transformation is a [1,3]-migratory shift of Pd
allowing the ring expansion of cyclopropanated pyrroles, piperidines, furans as
well as cyclopentadienes to grant access to the corresponding
1,2-dihydropyridines, 2<i>H</i>-pyrans,
2,3-dihydro-1<i>H</i>-azepines and
1,4-cyclohexadienes, respectively. Additionally, <i>gem</i>-disubstituted
cyclopropanated furans showed unexpected behavior by giving
diastereoselectively asymmetrically substituted dienes. Mechanistic studies and
theoretical calculations point towards a facile [1,3]-migratory shift
of Pd along the cyclopropane moiety, which can successfully compete with the usual
termination step of a Heck reaction via a <i>syn</i>-b-hydride elimination.<br /> | Nikolai Wurzer; Urszula Klimczak; Tobias Babl; Sebastian Fischer; Ricardo A. Angnes; Julia Rehbein; Oliver Reiser | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cbfee301c551fc78482/original/heck-type-coupling-of-fused-bicyclic-vinylcyclopropanes-synthesis-of-1-2-dihydropyridines-2-3-dihydro-1h-azepines-1-4-cyclohexadienes-2h-pyrans-and-1-3-butadienes.pdf |
64488bb9e4bbbe4bbf414f48 | 10.26434/chemrxiv-2023-q3983 | Regio- and stereospecific thiol-thioalkyne reaction facilitated by organic base | As an indispensable part of click chemistry, thiol-yne reactions are of great importance in organic and material synthesis. Nevertheless, efficient strategies for the addition of thiols onto internal alkynes with excellent regio- and stereocontrol are still scarce. Here we report the regio- and stereospecific hydrothiolation of electron-rich thioalkynes facilitated by organic base additive, which could proceed exceedingly fast under ambient atmosphere and room temperature, affording beta trans addition products in up to nearly quantitative yields. The dual nature of sulfur atom in attracting and donating electrons is supposed to be pivotal in determining the regio- and stereospecificity. This system tolerates a wide scope of thiols and thioalkynes, and shows great potential in polymer synthesis. In combination of its excellent performance in diverse environmentally benign solvents, especially in water/dimethyl sulfoxide mixtures that are usually used in bio-related research, applications of this newly established click reaction in diverse fields are highly expected. | shengtao ding; Yunxin Sun; Ningning Song; Yanchen Han | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64488bb9e4bbbe4bbf414f48/original/regio-and-stereospecific-thiol-thioalkyne-reaction-facilitated-by-organic-base.pdf |
6540584748dad23120bdd30d | 10.26434/chemrxiv-2023-2hg7c | Resilient wet adhesion of catechol analogs | The need for improved wet adhesives has driven research on mussel-inspired materials incorporating dihydroxyphenylalanine (Dopa) and related analogs of the parent catechol, but practical application of these functionalities is limited by their susceptibility to oxidation. Here, we investigate the molecular-level adhesion of the catechol analogs dihydroxybenzamide (DHB) and hydroxypyridinone (HOPO) as a function of pH. We find that the molecular structure of the catechol analogs influences their susceptibility to oxidation in alkaline conditions, with HOPO emerging as a particularly promising candidate for pH-tolerant adhesives for diverse environmental conditions. | George Degen; Syeda Tajin Ahmed; Parker Stow; Alison Butler; Roberto Andresen Eguiluz | Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6540584748dad23120bdd30d/original/resilient-wet-adhesion-of-catechol-analogs.pdf |
679c806cfa469535b9880641 | 10.26434/chemrxiv-2025-gl0qz | Low-entropy Supramolecular Crystals: Elucidating the
Inhomogeneity of Interfacial Water Molecules at Atomic Resolution | Water at interfaces plays crucial roles in various natural phenomena and in the
material sciences. Therefore, understanding the structure and hydrogen-bonding
network at such interfaces is essential. Recent advances in porous crystalline
materials, combined with single-crystal X-ray diffraction techniques, have enabled the
visualization of molecular structures on pore surfaces at atomic resolution. Herein, we
report the formation of a supramolecular porous crystal composed of a
resorcin[4]arene and a rigid cationic coordination complex, stabilized by hydrogen
bonds and noncovalent interactions. This low-entropy arrangement creates a porous
framework with anisotropic, information-rich surfaces, accommodating water
molecules to form multi-layered water channels. The analysis reveals clustering motifs
and hydrogen-bonding patterns in the water molecules at interfaces, supported by
molecular dynamics calculations and spectroscopy studies. These findings advance
our understanding of the structure–property relationship of water at interfaces in lowentropy
crystalline materials, offering insights into their behavior on complex surfaces. | Shinnosuke Horiuchi; Shota Ogura; Kazuya Otsubo; Yuka Ikemoto; Hisao Kiuchi; Go Watanabe; Osamu Takahashi; Mikihiro Hayashi; Eri Sakuda; Yasuhiro Arikawa; Keisuke Umakoshi; Yoshihisa Harada | Physical Chemistry; Materials Science; Analytical Chemistry; Hybrid Organic-Inorganic Materials; Interfaces; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679c806cfa469535b9880641/original/low-entropy-supramolecular-crystals-elucidating-the-inhomogeneity-of-interfacial-water-molecules-at-atomic-resolution.pdf |
60c74967842e6533b9db2d36 | 10.26434/chemrxiv.12058143.v1 | Systemic in Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server | <p>The emergence of the new
coronavirus (nCoV-19) has brought global impact on human health, whilst the
interaction between the virus and the host is the foundation of the disease.
The viral genome codes a cluster of proteins, each with a unique function in the
event of host invasion or viral development. Under current adverse situation, we
employ virtual screening tools in searching for drugs and nature products which
have been already deposited in the DrugBank in attempt to accelerate the drug
discovery process. This study provides an initial evaluation of current drug
candidates from various reports using our systemic in silico drug screening
based on structures of viral proteins and human ACE2 receptor. Besides, we
built an interactive online platform (<a href="https://shennongproject.com:11443/#/home">https://shennongproject.com:11443/#/home</a>)
for browsing these results with the visual display of small molecule docked on
its potential target protein, without installing any specialized structural software.
With continuous maintenance and incorporation of data from laboratory works, it
may serve not only as the assessment tool for the new drug discovery but also
an educational website to meet general interest from the public.</p> | Chi Xu; Zunhui Ke; Chuandong Liu; Zhihao Wang; Denghui Liu; Lei Zhang; Jingning Wang; Wenjun He; Zhimeng Xu; Yanqing Li; Yanan Yang; Zhaowei Huang; Panjing Lv; Xin Wang; Dali Han; Yan Li; Nan Qiao; Bing Liu | Chemoinformatics; High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74967842e6533b9db2d36/original/systemic-in-silico-screening-in-drug-discovery-for-coronavirus-disease-covid-19-with-an-online-interactive-web-server.pdf |
60c74ca2bb8c1a544b3db465 | 10.26434/chemrxiv.12504404.v1 | Natural Killer Cell Inspired AIE Nanoterminator for Blood-Brain-Barrier Crossing via Tight-Junction Modulation and NIR-II Gliomas Theranostics | Nature has always inspired
robotic designs and concepts. It is conceivable that biomimic nanorobots will
soon play a prominent role in medicine. In this paper, we developed a natural
killer cell-mimic AIE nanoterminator (NK@AIEdots) by coating natural kill cell
membrane on the AIE-active polymeric endoskeleton, PBPTV, a highly bright
NIR-II AIE-active conjugated polymer. Owning to the AIE and soft-matter
characteristics of PBPTV, as-prepared nanoterminator maintained the superior
NIR-II brightness (quantum yield ~8%) and good biocompatibility. Besides, they
could serve as tight junctions (TJs) modulator to trigger an intracellular
signaling cascade, causing TJs disruption and actin cytoskeleton reorganization
to form intercellular “green channel” to help themselves crossing Blood-Brain
Barriers (BBB) silently. Furthermore, they could initiatively accumulate to
glioblastoma cells in the complex brain matrix for high-contrast and
through-skull tumor imaging. The tumor growth was also greatly inhibited by
these nanoterminator under the NIR light illumination. As far as we known, The
QY of PBPTV is the highest among the existing NIR-II luminescent conjugated
polymers. Besides, the NK-cell biomimetic nanorobots will open new avenue for
BBB-crossing delivery. | Guanjun Deng; Xinghua Peng; Zhihong Sun; Wei Zheng; Jia Yu; Lulu Du; Huajie Chen; Ping Gong; Pengfei Zhang; Lintao Cai; Ben Zhong Tang | Bioorganic Chemistry; Supramolecular Chemistry (Org.); Aggregates and Assemblies; Biocompatible Materials; Biological Materials; Biodegradable Materials; Dyes and Chromophores; Nanostructured Materials - Materials; Optical Materials; Photosensitizers; Biopolymers; Conducting polymers; Drug delivery systems; Organic Polymers; Polymer scaffolds; Imaging; Microscopy; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Biophysical Chemistry; Photochemistry (Physical Chem.); Self-Assembly; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ca2bb8c1a544b3db465/original/natural-killer-cell-inspired-aie-nanoterminator-for-blood-brain-barrier-crossing-via-tight-junction-modulation-and-nir-ii-gliomas-theranostics.pdf |
66cd6f84a4e53c4876bcdebf | 10.26434/chemrxiv-2024-x6b9h | A Universal Strategy for Multi-Color Organic Circularly Polarized Afterglow Materials with High Dissymmetry Factor | Materials with pure organic circularly polarized afterglow (CPA) are notable for their multi-dimensional optical characteristics due to their time-dependent afterglow and polarization properties. These attributes endow them with exceptional appeal and value in the realms of information storage and anti-counterfeiting measures. Currently, there are limited studies on multi-color CPA materials with both high dissymmetry factor (glum) values and long lifetimes. Here, we propose a universal strategy to prepare multi-color CPA materials spanning from blue to red, with an ultralong emission lifetime of over 6 s and a glum of up to 100 (the highest glum was 1.90). This strategy leverages the mechanism of radiative energy transfer and selective reflection of cholesteric liquid crystals. Through multi-layered assembly, our method offers a simple and universal means of constructing organic CPA materials for multi-dimensional information encryption. | Chenjia Yin; Zi-Ang Yan; Honglong Hu; Ping Jiang; Zhuoran Xu; He Tian; Xiang Ma | Physical Chemistry; Photochemistry (Physical Chem.); Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cd6f84a4e53c4876bcdebf/original/a-universal-strategy-for-multi-color-organic-circularly-polarized-afterglow-materials-with-high-dissymmetry-factor.pdf |
60c73d91702a9beea7189bc2 | 10.26434/chemrxiv.5309668.v3 | Optimizing distributions over molecular space. An Objective-Reinforced Generative Adversarial Network for Inverse-design Chemistry (ORGANIC) | Molecular discovery seeks to generate chemical species tailored to very specific needs. In this paper, we present ORGANIC, a framework based on Objective-Reinforced Generative Adversarial Networks (ORGAN), capable of producing a distribution over molecular space that matches with a certain set of desirable metrics. This methodology combines two successful techniques from the machine learning community: a Generative Adversarial Network (GAN), to create non-repetitive sensible molecular species, and Reinforcement Learning (RL), to bias this generative distribution towards certain attributes. We explore several applications, from optimization of random physicochemical properties to candidates for drug discovery and organic photovoltaic material design. | Benjamin Sanchez-Lengeling; Carlos Outeiral; Gabriel L. Guimaraes; Alan Aspuru-Guzik | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2017-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d91702a9beea7189bc2/original/optimizing-distributions-over-molecular-space-an-objective-reinforced-generative-adversarial-network-for-inverse-design-chemistry-organic.pdf |
619a20ba47f47d723faba9bf | 10.26434/chemrxiv-2021-jcw85 | Incommensurate phase in Λ-cobalt (III) sepulchrate trinitrate governed by highly competitive N–H···O and C–H···O hydrogen bond networks | Phase transitions in molecular crystals are often determined by intermolecular interactions. The cage complex of [Co(C12H30N8)]3+·3NO3– is reported to undergo a disorder–order phase transition at Tc1 ≈ 133 K upon cooling. Temperature-dependent neutron and synchrotron diffraction experiments revealed satellite reflections in addition to main reflections in the diffraction patterns below Tc1. The modulation wave vector varies as function of temperature and locks in at Tc3 ≈ 98 K. Here, we demonstrate that the crystal symmetry lowers from hexagonal to monoclinic in the incommensurately modulated phases in Tc1 ˂ T ˂ Tc3. Distinctive levels of competitions: trade-off between longer N–H···O and shorter C–H···O hydrogen bonds; steric constraints to dense C-H···O bonds give rise to pronounced modulation of the basic structure. Severely frustrated crystal packing in the incommensurate phase is precursor to optimal balance of intermolecular interactions in the lock-in phase. | Somnath Dey; Andreas Schönleber; Sander van Smaalen; Wolfgang Morgenroth; Finn Krebs Larsen | Organic Chemistry; Analytical Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619a20ba47f47d723faba9bf/original/incommensurate-phase-in-cobalt-iii-sepulchrate-trinitrate-governed-by-highly-competitive-n-h-o-and-c-h-o-hydrogen-bond-networks.pdf |
66298d4721291e5d1da0df83 | 10.26434/chemrxiv-2024-s20bt | Paired Electrolysis Enables Reductive Heck Coupling of Unacti-vated (Hetero)Aryl Halides and Alkenes | The formation of carbon-carbon (C–C) bonds is a cornerstone of organic synthesis. Among various methods to construct Csp2–Csp3 bonds, the reductive Heck reaction between (hetero)aryl halides and alkenes stands out due to its potential efficiency and broad substrate availability. However, traditional reductive Heck reactions are limited by the use of pre-cious metal catalysts and/or limited aryl halide and alkene compatibility. Here, we present an electrochemically mediat-ed, metal- and catalyst-free reductive Heck reaction that tolerates both unactivated (hetero)aryl halides and diverse al-kenes such as vinyl boronates. Detailed electrochemical and deuterium-labeling studies support that this transformation likely proceeds through a paired electrolysis pathway, in which acid generated by the oxidation of N,N-diisopropylethylamine (DIPEA) at the anode intercepts an alkyl carbanion formed after radical-polar crossover at the cathode. As such, this approach offers a sustainable method for the construction of Csp2–Csp3 bonds from (hetero)aryl halides and alkenes, paving the way for the development of other electrochemically mediated olefin difunctionalization reactions. | Yihuan Lai; Phillip Milner | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66298d4721291e5d1da0df83/original/paired-electrolysis-enables-reductive-heck-coupling-of-unacti-vated-hetero-aryl-halides-and-alkenes.pdf |
60c747354c8919b621ad2c4d | 10.26434/chemrxiv.11538933.v1 | Towards Triptycene Functionalization and Triptycene-linked Porphyrin Arrays | 9,10-Diethynyltriptycene is investigated for its use as a rigid isolating unit in the synthesis of multichromophoric arrays. Sonogashira cross-coupling conditions are utilized to attach various porphyrins and boron dipyrromethenes (BODIPYs) to the triptycene scaffold. While there are previous examples of triptycene porphyrin complexes, this work reports the first example of a linearly connected porphyrin dimer, linked through the bridgehead carbons of triptycene. Symmetric and unsymmetric examples of these complexes are demonstrated and single crystal X-ray analysis of an unsymmetrically substituted porphyrin dimer highlights the evident linearity in these systems. Moreover, initial UV-Vis and fluorescence studies show the promise of triptycene as a linker for electron transfer studies, showcasing its isolating nature<br /> | Gemma Locke; Keith Flanagan; Mathias O.. Senge | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Small Molecule Activation (Organomet.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747354c8919b621ad2c4d/original/towards-triptycene-functionalization-and-triptycene-linked-porphyrin-arrays.pdf |
614972d47c08d53acb4a9c0d | 10.26434/chemrxiv-2021-f4sj8-v2 | Why Is Tetrahydrofuran a Good Solvent for Calcium Batteries? Insights From Ab Initio Molecular Dynamics Simulations | Calcium batteries are rapidly emerging as a potential, future energy storage technology; however, their advancement relies heavily on understanding of the liquid electrolyte component in terms of stability and interactions with a calcium metal anode. Tetrahydrofuran, a cyclic ether, is an experimentally common and promising solvent for the preparation of stable and efficient calcium electrolytes. However, insights into the reasons why are lacking, which could unveil key principles to electrolyte design. In this report, we provide a theoretical study employing ab initio molecular dynamics (AIMD) simulations of the interactions of Ca metal with the cyclic ether tetrahydrofuran (THF). The results show that the electrochemical breakdown and decomposition of THF at the Ca surface is highly orientation- and surface-site dependent, thereby significantly reducing the likelihood of its instability in a randomly organized bulk solvent. Likewise, in bulk electrolytes, its likelihood for breakdown is further diminished, in preference for coordination Ca2+ to form solvated structure. Hence, the finding that molecules require such strict conditions for their decomposition is an important selection and design principle for any solvent to prepare suitable calcium electrolytes. These findings are critical to the advancement of the calcium batteries. | Shreyas Pathreeker; Ian D. Hosein | Physical Chemistry; Energy; Energy Storage; Interfaces; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614972d47c08d53acb4a9c0d/original/why-is-tetrahydrofuran-a-good-solvent-for-calcium-batteries-insights-from-ab-initio-molecular-dynamics-simulations.pdf |
618e9422e0ea842e03949a4f | 10.26434/chemrxiv-2021-jwltx | Solvent-structured PEDOT:PSS surfaces: fabrication strategies and nanoscale properties | We present the preparation of nanostructured conducting PEDOT:PSS thin films by solvent vapor annealing (SVA), using the low boiling point solvent tetrahydrofuran (THF). An Atomic Force Microscopy (AFM) study allowed the observation of distinct nanostructure development as a function of solvent exposure time. Moreover, the nanostructures’ physical properties were evaluated by nanomechanical, nanoelectrical, and nano-FTIR measurements. In this way, we were able to differentiate the local response of the developed phases and to identify their chemical nature. The combination of these techniques allowed to demonstrate that exposure to THF is a facile method to effectively and selectively modify the surface nanostructure of PEDOT:PSS, and thereafter its final properties. Moreover, our nanoscale studies provided evidence about the molecular rearrangements that PEDOT:PSS suffers during nanostructure fabrication, a fundamental fact in order to expand the potential applications of this polymer in thermoelectric and optoelectronic devices. | Matteo Sanviti; Lars Mester; Rainer Hillenbrand; Angel Alegria; Daniel E. Martinez-Tong | Polymer Science; Conducting polymers; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618e9422e0ea842e03949a4f/original/solvent-structured-pedot-pss-surfaces-fabrication-strategies-and-nanoscale-properties.pdf |
64a9a44c6e1c4c986b098cca | 10.26434/chemrxiv-2023-gc2s8 | Stereoselective Polar Radical Crossover for the Functionalization of Strained-Ring Systems | Small ring systems have become essential motifs in drug discovery and medicinal chemistry. However, step-economic methods for their selective functionalization remains scarce. Here we present a one-pot strategy that merges a simple preparation of strained organoboron species species with the recently popularized polar radical crossover of borate derivatives to stereoselectively access tri-substituted azetidines, cyclobutanes and five-membered carbo- and heterocycles. | Florian Trauner; Rahma Ghazali; Jan Rettig; Christina M. Thiele; Dorian Didier | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a9a44c6e1c4c986b098cca/original/stereoselective-polar-radical-crossover-for-the-functionalization-of-strained-ring-systems.pdf |
60c73ed9469df4234ef42937 | 10.26434/chemrxiv.7127066.v1 | Inkjet-Printed Mesoporous TiO2 and Perovskite Layers for High Efficiency Perovskite Solar Cells | Inks for the inkjet-deposition of Titanium dioxide and hybrid organic inorganic perovskites were synthesized and then used to deposit films for high efficiency perovskite solar cell devices. The inkjet-printed titanium dioxide electron transport layer was optimized in reference to state-of-the-art spin-coated tio2 films. After observing that the printed TiO2 films perform at least as well as the spin-coated version, this charge transport layer was used as the anode for inkjet-printed perovskite absorber layers. Using printed TiO2 and perovskite, 14.1% power conversion efficiency was achieved. | Aron Huckaba; Yonghui Lee; Rui Xia; Sanghyun Paek; Victor Costa Bassetto; Emad Oveisi; Andreas Lesch; Sachin Kinge; Paul Dyson; Hubert Girault; Mohammad Khaja Nazeeruddin | Nanostructured Materials - Materials; Thin Films; Photovoltaics; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed9469df4234ef42937/original/inkjet-printed-mesoporous-ti-o2-and-perovskite-layers-for-high-efficiency-perovskite-solar-cells.pdf |
60c74431702a9bcfb318a768 | 10.26434/chemrxiv.9752216.v1 | The Effects of Enhancing the Crosslinking Degree in High Internal Phase Emulsion Templated Poly(dicyclopentadiene) Cured by Ring-Opening Metathesis Polymerization by a Crosslinking Comonomer | The effect of enhancing the crosslinking degree in polyHIPEs made from dicyclopentadiene by additionally using a crosslinking comonomer is described. Foams of 80% porosity with 10-40 w% comonomer content in the continous phase are prepared and show similar porosities and morphological characteristics as foams prepared with dicyclopentadiene alone. Assessing the mechanical properties reveals that the ductility is decreasing while the stiffness of the samples is increasing with increasing comonomer content. The foams containing the crosslinking comonomer take up at least five fold mass of toluene therby swelling to at least 30 v%. Upon drying of the swollen specimens, their initial shap and porosity are recovered. This feature distinguishes them from polyHIPEs made from dicyclopentadiene only.<br /> | Efthymia Vakalopoulou; Christian Slugovc | Organic Polymers; Polymer morphology; Polymer scaffolds | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74431702a9bcfb318a768/original/the-effects-of-enhancing-the-crosslinking-degree-in-high-internal-phase-emulsion-templated-poly-dicyclopentadiene-cured-by-ring-opening-metathesis-polymerization-by-a-crosslinking-comonomer.pdf |
66a5518d01103d79c5e93f8c | 10.26434/chemrxiv-2024-cvn76 | Direct (LC-)MS Identification of Regioisomers in C-H Activation by Partial Isotopic Labeling | C–H functionalization of complex substrates is highly enabling in total synthesis and in the development of late-stage drug candidates. Much work has been dedicated towards developing new methods as well as developing predictive modeling to accelerate route scouting. However, workflows to identify regioisomeric products are arduous, typically requiring chromatographic separation and/or nuclear magnetic resonance spectroscopy analysis. In addition, most reports focus on major products or do not assign regioisomeric products which biases predictive models constructed from such data. Herein, we present a novel approach to complex reaction analysis utilizing partial deuterium labels which enables direct product identification via liquid chromatography–mass spectrometry. When combined with spectral deconvolution, the method generates product ratios while circumventing chromatography altogether. Competitive kinetic isotope effects can also be determined. The resultant data is expected to be useful in the construction of predictive models across several dimensions including reaction selectivity, the impact of structure on mechanism, and mass spectral ionization patterns. | Christopher Sojdak; David Polefrone; Hriday Shah; Cassandra Vu; Brandon Orzolek; Pedro Jimenez Antenucci; Micah Valadez Bush; Marisa Kozlowski | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a5518d01103d79c5e93f8c/original/direct-lc-ms-identification-of-regioisomers-in-c-h-activation-by-partial-isotopic-labeling.pdf |
65a25ddee9ebbb4db90f8bc7 | 10.26434/chemrxiv-2023-zjdhn-v3 | Catalytic Antioxidant Activity of Two Diterpenoid Polyphenols of Rosemary, Carnosol and Isorosmanol, against Lipid Oxidation in the Presence of Cysteine Thiol | Lamiaceae herbs such as rosemary have excellent antioxidant properties, and lipidic diterpenoid constituents, such as carnosol, are known as characteristic components to exhibit strong antioxidant activity. This study investigates the effect of thiol compounds on the antioxidant properties of diterpenoid polyphenols. The results concerning the antioxidant activity of polyphenols in the presence of thiol showed that two polyphenols, namely carnosol and isorosmanol, enhanced antioxidant capacity against the radical-induced oxidation of lipids. Further examination of the mechanism revealed that both polyphenols exhibit excellent catalytic antioxidant activity by using the thiol group as a reduction source. Using density functional theory calculations, we attempted to explain why only these two polyphenols exhibit catalytic antioxidant properties. The calculation results and the assumed reaction mechanism suggested that the orthoquinones produced in the antioxidant reactions of carnosol and isorosmanol are more unstable than the others, and that the regioselectivity of their reactions with thiols contributes to their catalytic antioxidant properties. | Hayate Higashino; Asuka Karatsu; Toshiya Masuda | Agriculture and Food Chemistry; Food | CC BY 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a25ddee9ebbb4db90f8bc7/original/catalytic-antioxidant-activity-of-two-diterpenoid-polyphenols-of-rosemary-carnosol-and-isorosmanol-against-lipid-oxidation-in-the-presence-of-cysteine-thiol.pdf |
6582f23e9138d231611cafbf | 10.26434/chemrxiv-2023-2j2p0 | Substituent effects on the equilibria between cyclopropylcarbinyl, bicyclobutonium, homoallyl, and cyclobutyl cations | The cyclopropylcarbinyl (CPC) and bicyclobutonium (BCB) structures of the C4H7+ cation have been proposed as intermediates in various synthetic transformations forming cyclopropylcarbinyl, cyclobutyl, or homoallyl products. It has recently been recognized that such cations, when generated from chiral electrophiles, are themselves chiral and can react with nucleophiles stereospecifically. However, the CPC and BCB cations are in equilibrium with each other and with other related structures such as the cyclobutyl (CB) and homoallyl (HA) cations, from which stereospecificity is not guaranteed. Currently, the effect of substitution on the composition of cation mixtures containing CPC/BCB/CB/HA cations is not understood, precluding the prediction and control of the major products generated from such cations. Using Density Functional Theory and DLPNO-CCSD(T) calculations, we have studied the electronic and steric effects on the equilibria between mono- and polysubstituted C4H7+ cations. Our results indicate that electron-donating groups at the C1 position favor CPC structures, while BCB/CB structures are favored for the C2 position and HA structures for the C3/C4 positions. Electron-withdrawing groups yield shallower potential energy surfaces where many related structures are energetically accessible. Strong Hammett correlations (σ+) are observed for the various substituent effects, which appear to be additive in nature. In addition, BCB cations with more substituents are energetically destabilized compared to CPC cations, except with donating substituents at the C2 position. This work provides a predictive model for the major structures observed in mixtures of CPC/BCB/CB/HA cations, for given substituent patterns. | Sean Larmore; Pier Alexandre Champagne | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6582f23e9138d231611cafbf/original/substituent-effects-on-the-equilibria-between-cyclopropylcarbinyl-bicyclobutonium-homoallyl-and-cyclobutyl-cations.pdf |
63abf8a9e8047ae08ff8223a | 10.26434/chemrxiv-2022-xp2fr | No Transition Metals Required – Oxygen Promoted Synthesis of Imines from Primary Alcohols and Amines under Ambient Conditions | The synthesis of imines denotes a cornerstone in organic chemistry. The use of alcohols as renewable substituents for carbonyl-functionality represents an attractive opportunity. Consequently, carbonyl moieties can be in situ generated from alcohols upon transition-metal catalysis under an inert atmosphere. Alternatively, bases can be utilized under aerobic conditions. In this context, we report the synthesis of imines from benzyl alcohols and anilines, promoted by KOtBu under aerobic conditions at room temperature in the absence of any transition-metal catalyst. We present a detailed investigation of the radical mechanism underlying the reaction revealing a complex reaction network, which supports the experimental findings. | Daniel Himmelbauer; Radu Talmazan; Stefan Weber; Jan Pecak; Antonio Thun-Hohenstein; Maxine-Sophie Geissler; Lukas Pachmann; Marc Pignitter; Maren Podewitz; Karl Kirchner | Organic Chemistry; Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63abf8a9e8047ae08ff8223a/original/no-transition-metals-required-oxygen-promoted-synthesis-of-imines-from-primary-alcohols-and-amines-under-ambient-conditions.pdf |
633a1bddea6a229197065606 | 10.26434/chemrxiv-2022-k2k13-v2 | Transfer of an Aluminium Atom: An Avenue to Aluminium Heterocycles | Synthetic chemistry targets building up molecular complexity using simple substrates through simple processes. We disclose an unprecedented Al-atom transfer strategy for the synthesis of aluminium heterocycles with high atom economy. This strategy involves an effective cycloaddition of a free carbazolyl-aluminylene with unsaturated hydrocarbons, followed by facile cleavage of the N-Al bond. The aluminylene formally behaves as an [Al+] cation transfer reagent in a two-step manner, and the only byproduct is a carbazolide salt that can be utilized to regenerate the aluminylene. The carbazolyl Al-heterocycles show unique luminescent properties, one of which exhibits dual emission. Our approach not only has a significant impact on the future design of single-atom addition reactions, but also paves the way for emissive materials based on Al-heterocycles. | Xin Zhang; Hongyu Wang; Xiaofang Lan; Yanbo Mei; David Ruiz; Liu Leo Liu | Inorganic Chemistry; Organometallic Chemistry; Bonding; Main Group Chemistry (Inorg.); Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633a1bddea6a229197065606/original/transfer-of-an-aluminium-atom-an-avenue-to-aluminium-heterocycles.pdf |
60c74580567dfe7c16ec4485 | 10.26434/chemrxiv.10045931.v1 | Self-Limiting Electrospray Deposition for the Surface Modification of Additively Manufactured Parts | Electrospray deposition
(ESD) is a spray coating process that utilizes a high voltage to atomize a
flowing solution into charged microdroplets. These self-repulsive droplets
evaporate as they travel to a target substrate, depositing the solution solids.
Our previous research investigated the conditions necessary to minimize charge
dissipation and deposit a thickness-limited film that grows in area over time
through self-limiting electrospray deposition (SLED). Such sprays possess the
ability to conformally coat complex three-dimensional objects without changing
the location of the spray needle or orientation of the object. This makes them
ideally suited for the post-processing of materials fabricated through additive
manufacturing (AM), opening a paradigm of independent bulk and surface
functionality. Having demonstrated three-dimensional coating with film
thickness in the range of 1-50 µm on a variety of conductive objects, in this
study we employed model substrates to quantitatively study the technique’s limits
with regard to geometry and scale. Specifically, we examined the effectiveness
of thickness-limited ESD for coating recessed features with gaps ranging from
50 µm to 1 cm, as well as the ability to coat surfaces hidden from the
line-of-sight of the spray needle. This was then extended to the coating of
hydrogel structures printed by AM, demonstrating that coating could be
conducted even into the body of the structures as a means to create hydrophobic
surfaces without affecting the absorption-driven humidity response. | Dylan A. Kovacevich; Lin Lei; Daehoon Han; Christianna Kutznetsova; Howon Lee; Jonathan Singer | Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74580567dfe7c16ec4485/original/self-limiting-electrospray-deposition-for-the-surface-modification-of-additively-manufactured-parts.pdf |
6601648ae9ebbb4db97bcea6 | 10.26434/chemrxiv-2024-7w489 | Structure-based Design of CBP/EP300 Degraders: When Coopera-tivity Overcomes Affinity | Here we present the development of dCE-2, a structurally novel PROTAC targeting the CREB-binding protein (CBP) and E1A-associated protein (EP300) – two homologous multidomain enzymes crucial for enhancer-mediated transcription. The design of dCE-2 was based on the crystal structure of an in-house bromodomain (BRD) inhibitor featuring as acetyl-lysine mimic a 3-methyl cinnoline discovered by high-throughput fragment docking. Our study shows that, despite its modest binding affinity to CBP/EP300-BRD, dCE-2 remarkable protein degradation activity stems from its excellent cooperativity, which we demonstrate by the characterisation of its ternary complex formation both in vitro and in cellulo. Molecular dynamics simulations indicate that in aqueous solvent this active degrader populates both folded and extended conformations which are likely to promote cell permeabil-ity and ternary complex formation, respectively. | Ivan Cheng-Sanchez; Katherine Gosselé; Leonardo Palaferri; Eleen Laul; Gionata Riccabella; Rajiv Bedi; Yaozong Li; Anna Müller; Amedeo Caflisch; Cristina Nevado | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6601648ae9ebbb4db97bcea6/original/structure-based-design-of-cbp-ep300-degraders-when-coopera-tivity-overcomes-affinity.pdf |
60c7560a0f50db3c7939800a | 10.26434/chemrxiv.14199335.v1 | Quantitative Structure–property Relationship Modelling for the Prediction of Singlet Oxygen Generation by Heavy-Atom-Free BODIPY Photosensitizers | Heavy-atom-free sensitizers forming long-living triplet excited states via the spin-orbit charge transfer intersystem crossing (SOCT-ISC) process have recently attracted attention due to their potential to replace costly transition metal complexes in photonic applications. The efficiency of SOCT-ISC in BODIPY donor-acceptor dyads, so far the most thoroughly investigated class of such sensitizers, can be finely tuned by structural modification. However, predicting the triplet state yields and reactive oxygen species (ROS) generation quantum yields for such compounds in a particular solvent is still very challenging due to a lack of established quantitative structure-property relationship (QSPR) models. Herein, we analyzed the available data on singlet oxygen generation quantum yields (F?) for a dataset containing > 70 heavy-atom-free BODIPY in three different solvents (toluene, acetonitrile, and tetrahydrofuran). In order to build reliable QSPR model, we synthesized a series of new BODIPYs containing different electron donating aryl groups in the meso position, studied their optical and structural properties along with the solvent dependence of singlet oxygen generation, which confirmed the formation of triplet states via the SOCT-ISC mechanism. For the combined dataset of BODIPY structures, a total of more than 5000 quantum-chemical descriptors was calculated including quantum-chemical descriptors using Density Functional Theory (DFT), namely M06-2X functional. QSPR models predicting F? values were developed using multiple linear regression (MLR), which perform significantly better than other machine learning methods and show sufficient statistical parameters (R = 0.88 ? 0.91 and q2 = 0.62 ? 0.69) for all three solvents. A small root mean squared error of 8.2% was obtained for F? values predicted using MLR model in toluene. As a result, we proved that QSPR and machine learning techniques can be useful for predicting F? values in different media and virtual screening of new heavy-atom-free BODIPYs with improved photosensitizing ability.<br /> | Andrey A. Buglak; Asterios Charisiadis; Aimee Sheehan; Christopher
J. Kingsbury; Mathias O.. Senge; Mikhail A. Filatov | Photochemistry (Org.); Dyes and Chromophores; Photosensitizers; Drug Discovery and Drug Delivery Systems; Photochemistry (Physical Chem.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7560a0f50db3c7939800a/original/quantitative-structure-property-relationship-modelling-for-the-prediction-of-singlet-oxygen-generation-by-heavy-atom-free-bodipy-photosensitizers.pdf |
65a56d97e9ebbb4db93a556c | 10.26434/chemrxiv-2024-g4jbr | Ultrasonic or Microwave Modified Continuous Flow Chemistry for The Synthesis of Tetrahydrocannabinol: Observing Effects Of Various Solvents And Acids | Synthesizing tetrahydrocannabinol is a lengthy process with minimal yields and little applicability on an industrial scale. To close the gap between bench chemistry and industry process chemistry, this paper introduces a small-scale flow chemistry method that utilizes a microwave or ultrasonic medium to produce major tetrahydrocannabinol isomers. This process produces excellent yields and minimal side products, which leads to more efficient large-scale production of desired cannabinoids. | Giovanni Ramirez; Tesfay Tesfatsion; Maite Docampo-Palacios; Ivan Cruces; Adam Hellmann; Alex Okhovat; Monica Pittiglio; Kyle Ray; Westley Cruces | Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a56d97e9ebbb4db93a556c/original/ultrasonic-or-microwave-modified-continuous-flow-chemistry-for-the-synthesis-of-tetrahydrocannabinol-observing-effects-of-various-solvents-and-acids.pdf |
61deaea0e7b75191b297900d | 10.26434/chemrxiv-2022-k5m14 | Performance of GFN1-xTB for periodic optimization of Metal Organic Frameworks | Tight-binding approaches bridge the gap between force field methods and Density Functional Theory (DFT). Density Functional Tight Binding (DFTB) has been employed for a wide range of systems containing up to ca. 5000 atoms, and has an accuracy comparable to DFT but is 2-3 orders of magnitude faster. The efficiency of DFTB comes via pre-computed integrals, which are parameterized for each pair of atoms, and the requirement for this parameterization has previously prevented widespread use of DFTB for Metal-Organic Frameworks. The GFN-xTB (Geometries, Frequencies, and Non-covalent interactions Tight Binding) method provides parameters for elements up to Z≤86. We have therefore employed GFN-xTB to periodic optimizations of the Computation Ready Experimental (CoRE) database of MOF structures. We find that 75% of all cell parameters remain within 5% of the reference (experimental) value and that bonds containing metal atoms are typically well conserved with a mean average deviation of 0.187Å. Therefore GFN-xTB provides the ability to calculate MOF structures more accurately than force fields, and ca. 2 orders of magnitude faster than DFT. We therefore propose that GFN-xTB is a suitable method for screening of hypothetical MOFs (Z ≤ 86), with the advantage of accurate binding energies for adsorption applications. | Maryam Nurhuda; Carole Perry; Matthew Addicoat | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61deaea0e7b75191b297900d/original/performance-of-gfn1-x-tb-for-periodic-optimization-of-metal-organic-frameworks.pdf |
64788e6ebe16ad5c5748dcec | 10.26434/chemrxiv-2023-s446n | Comprehensive Mapping of Electrophilic Small Molecule-Protein Interactions in Human Cells | Covalent chemistry is a versatile approach for expanding the ligandability of the human proteome. Activity-based protein profiling (ABPP) can infer the specific residues modified by electrophilic compounds through competition with broadly reactive probes. Nonetheless, the extent to which such residue-directed ABPP platforms fully assess the protein targets of electrophilic compounds in human cells remains unclear. Here, we introduce a complementary approach that directly identifies proteins showing stereoselective reactivity with focused libraries of stereochemically-defined, alkynylated electrophilic compounds. Integration of protein- and cysteine-directed ABPP data from compound-treated human cancer cells revealed generally well-correlated target maps and highlighted specific features, such as protein size and the proteotypicity of cysteine-containing peptides, that help to explain gaps in each ABPP platform. The integrated ABPP strategy furnished stereoselective, high-engagement covalent ligands for > 300 structurally and functionally diverse human proteins, including compounds that modulate enzymes by canonical (active-site cysteine) and non-canonical (isotype-restricted and non-catalytic cysteines) mechanisms. | Benjamin Cravatt; Evert Njomen; Rachel Hayward; Kristen DeMeester; Daisuke Ogasawara; Melissa Dix; Tracey Nguyen; Paige Ashby; Gabriel Simon; Stuart Schreiber; Bruno Melillo | Biological and Medicinal Chemistry; Organic Chemistry; Stereochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64788e6ebe16ad5c5748dcec/original/comprehensive-mapping-of-electrophilic-small-molecule-protein-interactions-in-human-cells.pdf |
60c7507b0f50db259639758b | 10.26434/chemrxiv.13013057.v1 | Data-Driven Many-Body Models with Chemical Accuracy for CH4/H2O Mixtures | <div>
<div>
<div>
<p>Many-body potential energy functions (PEFs) based on the TTM-nrg and MB-nrg
theoretical/computational frameworks are developed from coupled cluster reference
data for neat methane and mixed methane/water systems. It is shown that that the
MB-nrg PEFs achieve subchemical accuracy in the representation of individual many-body effects in small clusters and enables predictive simulations from the gas to the
liquid phase. Analysis of structural properties calculated from molecular dynamics
simulations of liquid methane and methane/water mixtures using both TTM-nrg and
MB-nrg PEFs indicates that, while accounting for polarization effects is important for
a correct description of many-body interactions in the liquid phase, an accurate representation of short-range interactions, as provided by the MB-nrg PEFs, is necessary
for a quantitative description of the local solvation structure in liquid mixtures.
</p>
</div>
</div>
</div> | Marc Riera; Alan Hirales; Raja Ghosh; Paesani Lab | Computational Chemistry and Modeling; Physical and Chemical Properties; Statistical Mechanics; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7507b0f50db259639758b/original/data-driven-many-body-models-with-chemical-accuracy-for-ch4-h2o-mixtures.pdf |
60c743b30f50db0fc6395fa7 | 10.26434/chemrxiv.8040737.v4 | A New Computational Interface for Catalysis | This manuscript outlines the utility and power of our computational catalysis interface. This interface has been developed by our group and used extensively to study metal, ceramic, and zeolite catalyst systems. | Pavlo Kravchenko; Craig Plaisance; David Hibbitts | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b30f50db0fc6395fa7/original/a-new-computational-interface-for-catalysis.pdf |
60c749f5842e650331db2e4b | 10.26434/chemrxiv.12123126.v1 | Disentangling Viral Entry Kinetics Using Lipid Bilayers Coating Silica Nanoparticles | <div>
<div>
<div>
<p>Enveloped viruses infect cells via fusion between the viral envelope and a cellular
membrane. This membrane fusion process is driven by viral proteins, but slow stochastic protein
activation dominates fusion kinetics, making it challenging to probe the role of membrane
mechanics in viral entry directly. We have used bilayer-coated silica nanoparticles to restrict the
deformability of lipid membranes in a controllable manner. These bilayer-coated nanoparticles
are then used in a single-particle fusion assay with infectious influenza virus. We observe that as
we vary the free energy of membrane deformation by changing nanoparticle size, we obtain a
corresponding response in fusion kinetics and apparent fusion protein stoichiometry. We thus
directly measure the effect of membrane deformability on the free-energy barrier to membrane
fusion by influenza, overcoming the masking effect of slow protein activation kinetics.
</p>
</div>
</div>
</div> | Ana M. Villamil
Giraldo; Peter Kasson | Nanostructured Materials - Nanoscience; Biophysics; Microbiology; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749f5842e650331db2e4b/original/disentangling-viral-entry-kinetics-using-lipid-bilayers-coating-silica-nanoparticles.pdf |
64188040aad2a62ca10f597b | 10.26434/chemrxiv-2023-t1sqg | Hydrogel crosslinking via thiol-reactive pyridazinediones | Thiol-reactive Michael acceptors are commonly used for the formation of chemically crosslinked hydrogels. In this paper, we address the drawbacks of many Michael acceptors by introducing pyridazinediones as new crosslinking agents. Through the use of pyridiazinediones and their mono- or di-brominated analogues, we show that the mechanical strength, swelling ratio, and rate of gelation can all be controlled in a pH sensitive manner. Moreover, we demonstrate that the degradation of pyridazinedione-gels can be induced by the addition of thiols, thus providing a route to responsive or dynamic gels. We anticipate that our results will provide a valuable and complementary addition to the existing toolkit of crosslinking agents, allowing researchers to tune and rationally design the properties of biomedical hydrogels. | Calise Bahou; Richard Spears; Angela Ramirez Rosales; Lea Rochet; Lydia Barber; Vijay Chudasama; Christopher Spicer | Biological and Medicinal Chemistry; Organic Chemistry; Bioengineering and Biotechnology; Chemical Biology; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64188040aad2a62ca10f597b/original/hydrogel-crosslinking-via-thiol-reactive-pyridazinediones.pdf |
60c741ebf96a00418128652b | 10.26434/chemrxiv.8184218.v1 | Decay Associated Fourier Spectroscopy: Visible to Shortwave Infrared Time-Resolved Photoluminescence Spectra | We describe and implement an interferometric approach to decay associated photoluminescence spectroscopy, which we term decay associated Fourier spectroscopy (DAFS). In DAFS, the emitted photon stream from a substrate passes through a variable path length Mach-Zehnder interferometer prior to detection and timing. The interferometer encodes spectral information in the intensity measured at each detector enabling simultaneous spectral and temporal resolution. We detail several advantages of DAFS, including wavelength-range insensitivity, drift-noise cancellation, and optical mode retention. DAFS allows us to direct the photon stream into an optical fiber, enabling the implementation of superconducting nanowire single photon detectors for energy-resolved spectroscopy in the shortwave infrared spectral window (λ=1-2 μm). We demonstrate the broad applicability of DAFS, in both the visible and shortwave infrared, using two Förster resonance energy transfer pairs: a pair operating with conventional visible wavelengths and a pair showing concurrent acquisition in the visible and the shortwave infrared regime. | Timothy Atallah; Anthony Sica; Ashley Shin; Hannah Friedman; Justin Caram | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ebf96a00418128652b/original/decay-associated-fourier-spectroscopy-visible-to-shortwave-infrared-time-resolved-photoluminescence-spectra.pdf |
6631a92391aefa6ce1d9f149 | 10.26434/chemrxiv-2024-wwwb9 | Ligand-induced self-assembly of twisted two-dimensional halide perovskites | Two-dimensional (2D) halide perovskites (HPs) are now an emerging materials system that exhibits intriguing optoelectronic functionalities. Conventionally, they have been synthesized with linear and/or planar molecular spacers, rendering nominal modifications in optoelectronic properties. In contrast, lower dimensional HPs (0D and 1D) have been accommodating to the incorporation of bulky molecular spacers, leaving fundamental insights to remain elusive in their application for unconventional 2D HP structures. Herein, by implementing a high-throughput autonomous exploration workflow, crystallization behaviors of 2D HPs based on bulky 3,3-diphenylpropylammonium (DPA) spacer are comprehensively explored. Counterintuitive to the conventional HP chemistry, synthesis of 2D DPA2PbI4 HP is indeed feasible when the steric hindrance is mediated by minute incorporation of 3D HPs. Furthermore, a Moiré superlattice is observed from the DPA2PbI4 flakes, indicating the spontaneous formation of twisted stacks of 2D HPs – the first time to the best our knowledge. We hypothesize that the unconventional van der Waals surface of DPA2PbI4 facilitates the self-assembly of the twisted stacks of 2D HPs. This work exemplifies how high-throughput experimentation can discover unconventional material systems where the synthetic principle lies beyond the conventional chemical intuition. Furthermore, these findings provide hints on how to ‘chemically’ manipulate the twist stacking in 2D HPs, thus rendering a straightforward way for bespoke realization of functionalities in exotic materials systems via bottom-up approach. | Jonghee Yang; Addis S. Fuhr; Kevin M. Roccapriore; Bogdan Dryzhakov; Bin Hu; Bobby G. Sumpter; Sergei V. Kalinin; Mahshid Ahmadi | Physical Chemistry; Energy; Self-Assembly; Structure; Robotics; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6631a92391aefa6ce1d9f149/original/ligand-induced-self-assembly-of-twisted-two-dimensional-halide-perovskites.pdf |
6479b01fe64f843f41322645 | 10.26434/chemrxiv-2023-6w94r | Selective Activation of TRPC6 Ion Channel by Metallated Type-B Polyprenylated Polycyclic Acylphloroglucinols | The selective modulation of TRPC6 ion channels has emerged as a promising therapeutic approach for treating neuro-degenerative diseases and depression. Here, we present a significant advancement in this field by demonstrating the se-lective activation of TRPC6 using a metallated type-B PPAP, designated as PPAP53. The success of PPAP53 is attributed to the utilization of the 1,3-diketone motif present in PPAPs for metal coordination. The metallated PPAPs exhibit water solubility and equipotent activity compared to hyperforin, which is a natural product and considered the gold standard in the field. Notably, and in sharp contrast to type-A PPAPs, type-B PPAPs possess unique properties such as synthetic ac-cessibility in gram scale, facile derivatization, being thermally stable and stable against photochemical oxidation. Our detailed investigations reveal that PPAP53 selectively binds to the C-terminus of TRPC6. Although cryo electron micros-copy has resolved the majority of the TRPC6 structure, the binding site in the C-terminus remained unresolved. To ad-dress this issue, we employed state-of-the-art artificial intelligence-based protein structure prediction algorithms, includ-ing AlphaFold2, ColabFold, and trRosetta, to predict the missing C-terminus region. Our computational results, validated against experimental data, indicate that PPAP53 binds to the 777LLKL780-region of the C-terminus, thus providing critical insights into the binding mechanism of PPAP53 with TRPC6. | Philipp Peslalz; Frank Kraus; Flavia Izzo; Anton Bleisch; Yamina El Hamdaoui; Ina Schulz; Andreas Kany; Anna Hirsch; Kristina Friedland; Bernd Plietker | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6479b01fe64f843f41322645/original/selective-activation-of-trpc6-ion-channel-by-metallated-type-b-polyprenylated-polycyclic-acylphloroglucinols.pdf |
60c74c37469df40b05f44043 | 10.26434/chemrxiv.12451208.v1 | Chromate Conversion Coating and Alternatives as Corrosion-Resistant Treatments for Metal Parts | <p>Chromate conversion coating is an efficacious and
fast means of protecting metal parts from corrosion, but problematic in that it
uses the toxic and carcinogenic chromic acid as the reagent. This short report covers some key considerations and alternatives.</p> | Isaac Omari; Johanne Penafiel; J Scott McIndoe | Electrochemistry; Inorganic Acid/Base Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c37469df40b05f44043/original/chromate-conversion-coating-and-alternatives-as-corrosion-resistant-treatments-for-metal-parts.pdf |
60c75346567dfed37dec5e30 | 10.26434/chemrxiv.13370285.v2 | Influence of a Single Ether Bond on Assembly, Orientation, and Miscibility of Phosphocholine Lipids at the Air-Water Interface | How does a small change in the structure of a phospholipid affect its
supramolecular assembly? In aqueous suspensions, the substitution of one
ester linkage in DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) by
an ether linkage alters its phase behaviour completely. To unravel the
effect of replacing a phospholipid’s ester linkage by an ether linkage
in lipid monolayers, we characterized pure monolayers of the model lipid
DPPC and its sn-2 ether analogue PHPC
(1-palmitoyl-2-O-hexadecyl-sn-glycero-3-phosphocholine) as well as
mixtures of both by measurements of surface pressure – molecular area
(π–A_mol) isotherms. In addition, we used infrared reflection absorption
spectroscopy (IRRAS) and epifluorescence microscopy to study lipid condensation, lipid chain
orientation, headgroup hydration, and lipid miscibility in all samples. | Matthias Hoffmann; Simon Drescher; Christian Schwieger; Dariush Hinderberger | Biophysical Chemistry; Physical and Chemical Properties; Self-Assembly; Spectroscopy (Physical Chem.); Structure; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75346567dfed37dec5e30/original/influence-of-a-single-ether-bond-on-assembly-orientation-and-miscibility-of-phosphocholine-lipids-at-the-air-water-interface.pdf |
66ec651f12ff75c3a1d81ae7 | 10.26434/chemrxiv-2024-l9608 | Synthesis and Electrochemical Studies of Nickel Complexes with a Flexidentate Bipyridine-aza-crown Ether Ligand | Bipyridine ligands have been extensively employed in nickel catalysis, with ligand modifications focused on steric or electronic tuning. In this work, we explore modifications designed to modulate the coordination mode using a 2,2'-bipyridine derivative with an appended aza-crown ether macrocycle capable of flexidentate binding to nickel. A series of complexes varying in charge from neutral to dicationic demonstrates the flexibility of the macrocycle, with bipyridine-aza-crown ether denticity changing from к4 to к6 upon sequential abstraction of chloride ligands. The changes in binding mode can be reversed by addition of chloride ion. Comparisons between the macrocycle-containing ligand and an analogous ligand with a non-macrocyclic diethylamine donor provide insight into the role of the crown ether, including in electrochemical reductions probed via cyclic voltammetry. | Sebastian Acosta-Calle; Elsa Huebsch; Jenna Halenda; Zoe Stuart; Chun-Hsing Chen; Alexander Miller | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Electrochemistry; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ec651f12ff75c3a1d81ae7/original/synthesis-and-electrochemical-studies-of-nickel-complexes-with-a-flexidentate-bipyridine-aza-crown-ether-ligand.pdf |
65cebfff66c1381729be393a | 10.26434/chemrxiv-2024-hr1hf | High-performance multi-GPU analytic RI-MP2 energy gradients | This article presents a novel algorithm for the calculation
of analytic energy gradients from second order Møller Plesset perturbation theory within the Resolution-of-the-Identity approximation (RI-MP2) which is designed to achieve high performance on multi-GPU clusters. The algorithm uses GPUs for all major steps of the calculation, including integral generation, formation of all required intermediate tensors, solution of the Z-vector equation and gradient accumulation. The implementation in the EXtreme Scale Electronic Structure System (EXESS) software package includes a tailored, highly efficient, multi-stream scheduling system to hide CPU-GPU data transfer latencies and allows nodes with 8 A100 GPUs to operate at over 80% of theoretical peak floating-point performance. Comparative performance analysis shows a significant reduction in computational time relative to traditional multi-core CPU-based methods, with our approach achieving up to a 95-fold speedup over the single-node performance of established software such as Q-Chem and ORCA. Additionally, we demonstrate that pairing our implementation with the molecular fragmentation framework in EXESS can drastically lower the computational scaling of RI-MP2 gradient calculations from quintic to sub-quadratic, enabling further substantial savings in runtime while retaining high numerical accuracy in the resulting gradients. | Ryan Stocks; Elise Palethorpe; Giuseppe Maria Junior Barca | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cebfff66c1381729be393a/original/high-performance-multi-gpu-analytic-ri-mp2-energy-gradients.pdf |
6557e156dbd7c8b54b7aefa5 | 10.26434/chemrxiv-2023-tkcd9 | An Anode-Free Sodium All-Solid-State Battery | Anode-free batteries possess the optimal cell architecture due to their reduced weight, volume, and cost. However, their implementation has been limited by unstable anode morphological changes and anode-liquid electrolyte interface reactions. An electrochemically stable solid electrolyte can solve these issues by enabling the deposition of dense sodium metal. Furthermore, a novel type of aluminum current collector can achieve intimate solid-solid contact with the solid electrolyte which allows highly reversible sodium plating and stripping at both high areal capacities and current densities, previously unobtainable with conventional aluminum foil. A sodium anode-free all-solid-state battery full-cell is demonstrated with stable cycling for several hundred cycles. This cell architecture serves as a future direction for other battery chemistries to enable low-cost, high-energy-density, and fast charging batteries. | Grayson Deysher; Jin An Sam Oh; Yu-Ting Chen; Baharak Sayahpour; So-Yeon Ham; Diyi Cheng; Phillip Ridley; Ashley Cronk; Sharon Wan-Hsuan Lin; Kun Qian; Long Hoang Bao Nguyen; Jihyun Jang; Ying Shirley Meng | Materials Science; Energy; Ceramics; Energy Storage; Power; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6557e156dbd7c8b54b7aefa5/original/an-anode-free-sodium-all-solid-state-battery.pdf |
63ce9d531fb2a87c4addbfaa | 10.26434/chemrxiv-2023-r52zg | Development of a Low-Cost Multi-Wavelength Inline Detector for Slug Detection in Continuous Flow | Herein we describe our expansion upon previously published low-cost inline detectors. Using an Adafruit AS7341 10-channel light/colour sensor, a Raspberry Pi, and a white LED we were able to simultaneously monitor infrared and multiple visible spectrum absorption wavelengths. This allowed even challenging colourless slugs within a colourless carrier solvent to be detected and characterised as they progressed through a flow reactor. The sensor data is displayed in graphical form in real-time and stored on the device for reference afterwards. | Daniel Maddox; James E. P. Davidson; Lucie Guetzoyan; Lee Walmsley | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2023-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ce9d531fb2a87c4addbfaa/original/development-of-a-low-cost-multi-wavelength-inline-detector-for-slug-detection-in-continuous-flow.pdf |
66ccd86720ac769e5fea1fba | 10.26434/chemrxiv-2024-f67jg | Leveraging Flexible Pipette-based Tool Changes to Transform Liquid Handling Systems into Dual-Function Sample Preparation and Imaging Platforms | In this study, we present an advanced system that integrates simultaneous pipetting and in-situ imaging using the Opentron OT-2 liquid handling robot. This system enables real-time monitoring and characterization of dynamic processes, such as hydrogel crosslinking, without any manual intervention. The platform’s modular design maintains cost-effectiveness and high-throughput capabilities while expanding the versatility of the OT-2 robot by incorporating imaging functionalities into the experimental workflow using a pick-and-place apparatus. Due to its modular architecture, based on an OT-2 robot, the system can be adapted for a wide range of laboratory applications at an affordable cost. This real-time imaging solution offers a practical approach to laboratory automation, leading to more efficient and data-driven experimentation. Although ionically crosslinked hydrogels were used as a proof-of-concept, this platform has potential applications across various materials systems, including crystallization dynamics, polymerization kinetics, and drug delivery system development. | Mohammad Nazeri; Jeffrey Watchorn; Sheldon Mei; Alex Zhang; Christine Allen; Frank Gu | Materials Science; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ccd86720ac769e5fea1fba/original/leveraging-flexible-pipette-based-tool-changes-to-transform-liquid-handling-systems-into-dual-function-sample-preparation-and-imaging-platforms.pdf |
614df7884853d2d47cb120f5 | 10.26434/chemrxiv-2021-pmcfv | Elucidating the formation and structural evolution of platinum single-site catalysts for hydrogen evolution reaction | Platinum single-site catalysts (SSCs) are a promising technology for the production of hydrogen from clean energy sources. They have high activity and maximal platinum-atom utilisation. However, the bonding environment of platinum during operation is poorly understood. In this work, we use operando, synchrotron-X-ray absorption spectroscopy to study the platinum bonding in SSCs. First, we synthesise an atomically dispersed platinum complex with aniline and chloride ligands onto graphene and characterise it with ex-situ electron microscopy, X-ray diffractometry, X-ray photoelectron spectroscopy, X-ray absorption near edge structure spectroscopy (XANES), and extended X-ray absorption fine structure spectroscopy (EXAFS). Then, by operando EXAFS and XANES, we show that as a negatively biased potential is applied, the Pt-N bonds break first followed by the Pt-Cl bonds. The platinum is reduced from platinum(II) to metallic platinum(0) by the onset of the hydrogen-evolution reaction at 0 V. Furthermore, we observe an increase in Pt-Pt bonding, indicating the formation of platinum agglomerates. Together, these results indicate that while aniline is used to prepare platinum SSCs, the single-site complexes are decomposed and platinum agglomerates at operating potentials. This work is an important contribution to the understanding of the bonding environment and the evolution of the molecular structure of platinum complexes in SSCs. | Peng Tang; Hyeon Jeong Lee; Kevin Hurlbutt; Po-Yuan Huang; Sudarshan Narayanan; Chenbo Wang; Diego Gianolio; Rosa Arrigo; Jun Chen; Jamie Warner; Mauro Pasta | Materials Science; Catalysis; Catalysts; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614df7884853d2d47cb120f5/original/elucidating-the-formation-and-structural-evolution-of-platinum-single-site-catalysts-for-hydrogen-evolution-reaction.pdf |
60c740a44c89194935ad219a | 10.26434/chemrxiv.7797533.v1 | Aromaticity and Antiaromaticity in the Excited States of Porphyrin Nanorings | Aromaticity can be a useful concept for predicting the behavior of excited states. Here we show that π-conjugated porphyrin nanorings exhibit size-dependent excited-state global aromaticity and antiaromaticity, for rings containing up to eight porphyrin subunits, although they have no significant global aromaticity in their neutral singlet ground states. Applying Baird’s law, odd rings ([4n] π-electrons) are aromatic in their excited states, whereas the excited states of even rings ([4n+2] π-electrons) are antiaromatic. These predictions are borne out by density functional theory (DFT) studies of the nucleus-independent chemical shift in the T1 triplet state of each ring, which reveal the critical importance of the triplet delocalization to the emergence of excited-state aromaticity. The singlet excited states (S1) are explored by measurements of the radiative rate and fluorescence peak wavelength, revealing a subtle odd-even alternation as a function of ring size, consistent with symmetry-breaking in antiaromatic excited states. | Martin Peeks; Juliane Gong; Kirstie McLoughlin; Takayuki Kobatake; Renee Haver; Laura Herz; Harry L. Anderson | Physical Organic Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a44c89194935ad219a/original/aromaticity-and-antiaromaticity-in-the-excited-states-of-porphyrin-nanorings.pdf |
653b12b748dad23120713793 | 10.26434/chemrxiv-2023-1rzqx | Photophysical Studies of Helicate and Mesocate Double-Stranded Dinuclear Ru(II) Complexes | The metal-ligand charge transfer (3MLCT) and the phosphorescence-quenching metal-centered (3MC) states of the helicate and mesocate conformers of a double- stranded dinuclear polypyridylruthenium(II) complex have been investigated using ultrafast transient absorption spectroscopy. At 294 K, transient signals of the helicate decayed significantly slower than the mesocate, whereas at 77 K, no clear contrast in kinetics was observed. Contributions to excited-state decay from high-lying 3MLCT states were identified at both temperatures. Spectroscopic data (294 K) suggest that the 3MC state of the helicate lies above the 3MLCT and the reverse is true for the mesocate; this was further validated by DFT calculations. The stabilization of the 3MC state relative to the 3MLCT state in the mesocate was explained by a reduction in ligand field strength due to distortion near the ligand bridge which causes further deviation from octahedral geometry compared to the helicate. This work illustrates how minor structural differences can significantly influence excited state dynamics. | Xinyue Xu; Samuel Marlton; Kate Flint; Rohan Hudson; Richard Keene; Christopher Hall; Trevor Smith | Physical Chemistry; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653b12b748dad23120713793/original/photophysical-studies-of-helicate-and-mesocate-double-stranded-dinuclear-ru-ii-complexes.pdf |
6351a88aaca19814fbde3fcd | 10.26434/chemrxiv-2022-lf9dc | Size-dependent Thermal Shifts to MOF Nanocrystal Optical Gaps Induced by Dynamic Bonding
| Conventional semiconductor nanocrystals exhibit wide-ranging optical behavior, whereas the size-dependent photophysical properties of metal-organic framework (MOF) nanocrystals remains an open research frontier. Here, we present size- and temperature-dependent optical absorption spectra of common MOFs with particle sizes ranging from tens of nanometers to several microns. All materials exhibit optical gaps that decrease at elevated temperatures, which we attribute to the dynamic nature of MOF metal-linker bonds. Accordingly, whereas the labile titanium-carboxylate bonds of MIL-125 give rise to bandgaps that redshift by ~600 meV over 300 K, the more rigid zinc-imidazolate bonds of ZIF-8 produce a redshift of only ~10 meV. Furthermore, smaller particles induce far larger decreases to optical gaps. Taken together, these results suggest MOF bonding becomes more flexible with smaller nanocrystal sizes, offering a powerful tool for manipulating optical behavior through composition, temperature, and dimensionality. | Kevin Fabrizio; Carl Brozek | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.); Spectroscopy (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6351a88aaca19814fbde3fcd/original/size-dependent-thermal-shifts-to-mof-nanocrystal-optical-gaps-induced-by-dynamic-bonding.pdf |
60c74afdbdbb895bcaa3948b | 10.26434/chemrxiv.12273122.v1 | Tracking Charge Transfer to Residual Metal Clusters in Conjugated Polymers for Photocatalytic Hydrogen Evolution | Semiconducting polymers are versatile materials for solar energy conversion and have gained popularity as photocatalysts for sunlight-driven hydrogen production. Organic polymers often contain residual metal impurities such as palladium (Pd) clusters that are formed during the polymerization reaction, and there is increasing evidence for a catalytic role of such metal clusters in polymer photocatalysts. Using transient optical spectroscopies on nanoparticles of F8BT, P3HT, and the dibenzo[b,d]thiophene sulfone homopolymer, P10, we demonstrate how differences in the timescale of electron transfer to Pd clusters translate into hydrogen evolution activity optima at extremely different residual Pd concentrations. For F8BT nanoparticles with common Pd concentrations of >1000 ppm (>0.1 wt. %), we find that residual Pd clusters quench photogenerated excitons via energy and electron transfer on the fs – ns timescale, thus outcompeting reductive quenching via the electron donor diethylamine in the solution phase. We spectroscopically identify reduced Pd clusters in our F8BT nanoparticles from the µs timescale onwards and show that the predominant location of long-lived electrons gradually shifts to the F8BT polymer when the Pd content is lowered. However, a low yield of long-lived electrons limits the hydrogen evolution activity of F8BT. P10, on the other hand, exhibits a substantially higher hydrogen evolution activity, which we demonstrate results from higher yields of long-lived electrons compared to F8BT due to more efficient reductive quenching. Surprisingly, and despite the higher performance of P10, long-lived electrons reside on the P10 polymer rather than on the Pd clusters in P10 particles, even at very high Pd concentrations of 27,000 ppm (2.7 wt. %). We show that these long-lived electrons in P10 react orders of magnitude slower at lower Pd levels, which suggests that their transfer to Pd sites constitutes a kinetic bottleneck and thus reveals a direction towards further improvements for this already very performant material. In contrast, long-lived electrons in F8BT already reside on Pd clusters before the typical timescale of hydrogen evolution. This comparison illustrates that P10 exhibits efficient reductive quenching but slow electron transfer to residual Pd clusters, whereas the opposite is the case for F8BT. We discuss possible reasons for this pronounced difference in the predominant location of long-lived electrons in F8BT and P10. Our results suggest that the development of even more efficient polymer photocatalysts should target materials that combine both rapid reductive quenching and rapid charge transfer to a metal-based co-catalyst. | Michael Sachs; Hyojung Cha; Jan Kosco; Catherine M. Aitchison; Laia Francàs; Sacha Corby; Chao-Lung Chiang; Anna A. Wilson; Robert Godin; Alexander Fahey-Williams; Andrew
I. Cooper; Seb Sprick; Iain McCulloch; James R Durrant | Photochemistry (Org.); Organic Polymers; Photocatalysis; Energy Storage; Fuels - Energy Science; Chemical Kinetics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74afdbdbb895bcaa3948b/original/tracking-charge-transfer-to-residual-metal-clusters-in-conjugated-polymers-for-photocatalytic-hydrogen-evolution.pdf |
62ab2ccd20a4ed9ef740f330 | 10.26434/chemrxiv-2022-mw4gp | Mixed-Reference Spin-Flip Time-Dependent
Density Functional Theory for Accurate X-ray
Absorption Spectroscopy | It is demonstrated that the challenging core hole-particle (CHP) orbital relaxation for core
electron spectra can be readily achieved by the mixed-reference spin-flip (MRSF)-TDDFT.
With the additional scalar relativistic effects on K-edge excitation energies of 24 second- and
17 third-row molecules, the particular ∆CHP-MRSF(R) exhibited near perfect predictions
with RMSE ∼ 0.5 eV, featuring a median value of 0.3 and and an interquartile range of 0.4.
Overall, the CHP effect is 2 ∼ 4 times stronger than relativistic ones, contributing more than 20 eV in the cases of sulfur and chlorine third-row atoms. Such high precision allows to explain the splitting and spectral shapes of O, N and C atom K-edges in the ground state of thymine with atom as well as orbital specific accuracy. The same protocol with a double hole particle relaxation also produced remarkably accurate K-edge spectra of core to valence hole excitation energies from the first (nO8π∗) and second (ππ∗) excited states of thymine, confirming the assignment of 1s → n excitation for the experimentally observed 526.4 eV peak. Regarding both accuracy and practicality, therefore, MRSF-TDDFT provides a promising protocol for core electron spectra both of ground and excited electronic states alike. | Woojin Park; Marc Alías-Rodríguez; Daeheum Cho; Seunghoon Lee; Miquel Huix-Rotllant; Cheol Ho Choi | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ab2ccd20a4ed9ef740f330/original/mixed-reference-spin-flip-time-dependent-density-functional-theory-for-accurate-x-ray-absorption-spectroscopy.pdf |
66b4416201103d79c52446d3 | 10.26434/chemrxiv-2024-m9m2w | Near-Ambient Temperature Spin Crossover Controlled via the Self-Assembly of Chiral and Racemic Polymorphs in Triazolylimine [Fe2L3](BF4)4 Helicates | Three new chiral spin crossover (SCO) dinuclear triple helicates of type [Fe2L3](BF4)4 are reported exhibiting a robust magnetic behaviour that is resistant to the effect of temperature scan rate, moisture, and light. The selective formation of racemic aggregates upon crystallization of a solution of the respective racemic complexes was associated with the helical torsion, intermetallic distance and the spatial arrangement of the enantiomers and anions. Torsional stress and hydrogen bonding interactions were related to the potential spring-like movement inherent to helically chiral systems as well as to the efficacy of cooperativity transmission. These unique structural dynamics were correlated to the display of a chirality-dependent semi-abrupt profile observed for each enantiopure aggregate. This study highlights how the molecular shape of helically chiral compounds can be altered to modulate the magnetic behaviour towards a robust and near-ambient SCO system. | Feng Li; James Flood; Matthew Wallis; Joseph Tadros; Yuto Nakashima; Daniel Fanna; Janice Aldrich-Wright; Leonard Lindoy; Shinya Hayami | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Supramolecular Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b4416201103d79c52446d3/original/near-ambient-temperature-spin-crossover-controlled-via-the-self-assembly-of-chiral-and-racemic-polymorphs-in-triazolylimine-fe2l3-bf4-4-helicates.pdf |
64c8b9a7658ec5f7e58bc5e8 | 10.26434/chemrxiv-2023-5gbb6-v2 | Expanding the Structural Diversity at the Phenylene Core of Ligands for the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Development of Highly Potent Hypoxia-Inducible Factor-1alpha (HIF-1alpha) Stabilizers | Hypoxia-inducible factor-1α (HIF-1α) constitutes the principal mediator of cellular adaptation to hypoxia in humans. HIF-1α protein level and activity is tightly regulated by the ubiquitin E3 ligase von Hippel-Lindau (VHL). Here, we performed a structure-guided and bioactivity-driven design of new VHL inhibitors. Our iterative and combinatorial strategy focused on chemical variability at the phenylene unit and encompassed further points of diversity. The exploitation of tailored phenylene fragments and the stereoselective installation of the benzylic methyl group provided potent VHL ligands. Three high-resolution structures of VHL-ligand complexes were determined and bioactive conformations of these ligands were explored. The most potent inhibitor (30) exhibited dissociation constants lower than 40 nM, independently determined by fluorescence polarization and surface plasmon resonance and an enhanced cellular potency, as evidenced by its superior ability to induce HIF-1α transcriptional activity. Our work is anticipated to inspire future efforts towards HIF-1α stabilizers and new ligands for proteolysis-targeting chimeras. | Lan Phuong Vu; Claudia Diehl; Ryan Casement; Adam Bond; Christian Steinebach; Nika Strasek; Alesa Bricelj; Andrej Perdih; Gregor Schnakenburg; Izidor Sosic; Alessio Ciulli; Michael Gutschow | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c8b9a7658ec5f7e58bc5e8/original/expanding-the-structural-diversity-at-the-phenylene-core-of-ligands-for-the-von-hippel-lindau-vhl-e3-ubiquitin-ligase-development-of-highly-potent-hypoxia-inducible-factor-1alpha-hif-1alpha-stabilizers.pdf |
63da6e497972289ce2b08db6 | 10.26434/chemrxiv-2023-1qbb5 | HOAX: A Hyperparameter Optimization Algorithm Explorer for Neural Networks | Computational chemistry has become an important tool to predict and understand molecular properties and reactions. Even though recent years have seen a significant growth in new algorithms and computational methods that speed up quantum chemical calculations, the bottleneck for trajectory-based methods to study photoinduced processes is still the huge number of electronic structure calculations. In this work, we present an innovative solution, in which the amount of electronic structure calculations is drastically reduced, by employing machine learning algorithms and methods borrowed from the realm of artificial intelligence. However, applying these algorithms effectively requires finding optimal hyperparameters, which remains a challenge itself. Here we present an automated user-friendly framework, HOAX, to perform the hyperparameter optimization for neural networks, which bypasses the need for a lengthy manual process. The neural network generated potential energy surfaces (PESs) reduces the computational costs compared to the ab initio-based PESs. We perform a comparative investigation on the performance of different hyperparameter optimiziation algorithms, namely grid search, simulated annealing,genetic algorithm, and bayesian optimizer in finding the optimal hyperparameters necessary for constructing the well-performing neural network in order to fit the PESs of small organic molecules. Our results show that this automated toolkit not only facilitates a straightforward way to perform the hyperparameter optimization but also the resulting neural networks-based generated PESs are in reasonable agreement with the ab initio-based PESs. | Albert Thie; Maximillian F.S.J. Menger; Shirin Faraji | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da6e497972289ce2b08db6/original/hoax-a-hyperparameter-optimization-algorithm-explorer-for-neural-networks.pdf |
64ab2913ba3e99daefca17a1 | 10.26434/chemrxiv-2023-mncbr | Comparative Quantum-Classical Dynamics of
Natural and Synthetic Molecular Rotors Show How Vibrational Synchronization
Modulates the Photoisomerization Quantum Efficiency | We use quantum-classical trajectories to investigate the origin of the different photoisomerization
quantum efficiency observed in the dim-light visual pigment Rhodopsin and in the light-driven
biomimetic molecular rotor para-methoxy N-methyl indanylidene-pyrrolinium (MeO-NAIP) in
methanol. The results reveal that effective light-energy conversion requires, in general, an
auxiliary molecular vibration (called promoter) that does not correspond to the rotary motion but
that synchronizes with it at specific times. They also reveal that Nature has designed Rhodopsin
to exploit two mechanisms working in a vibrationally coherent regime. The first uses a wag
promoter to ensure that ca. 75% of the absorbed photons lead to unidirectional rotations. The
second mechanism ensures that the same process is fast enough to avoid directional randomization.
It is found that MeO-NAIP in methanol is incapable of exploiting the above mechanisms resulting
into a 50% quantum efficiency loss. However, when the solvent is removed, MeO-NAIP rotation
is predicted to synchronize with a ring-inversion promoter leading to a 30% increase of quantum
efficiency and, therefore, biomimetic behavior. | Alejandro Blanco-Gonzalez; Madushanka Manathunga; Xuchun Yang; Massimo Olivucci | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ab2913ba3e99daefca17a1/original/comparative-quantum-classical-dynamics-of-natural-and-synthetic-molecular-rotors-show-how-vibrational-synchronization-modulates-the-photoisomerization-quantum-efficiency.pdf |
66718587c9c6a5c07ac01ad7 | 10.26434/chemrxiv-2024-t4bz9 | Multipurpose DIY Spectrophotometer for Teaching Analytical Chemistry | Spectroscopy is an integral part of chemical research, and the operation of any spectroscopic instrument is critical in chemical education. This study presents a low-cost, do-it-yourself (DIY) style spectrophotometer system that can be adapted for UV-Vis, fluorimetry, and atomic emission applications. The DIY system is constructed with commonly available hardware and 3D-printed parts, totaling less than $50. Python code is also provided to process the color spectrum image into intensity vs. wavelength data, similar to any commercial-level instrument. The functionality of the DIY spectrometer is demonstrated with the absorption of KMnO₄, fluorescence of fluorescein, and atomic emission of LiCl, NaCl, BaCl₂, and SrCl₂. All the collected spectra show accurate results compared to a commercial instrument or existing literature. The goal of this project is to provide a hands-on platform for undergraduate students to see and modify the individual components of a spectrophotometer, which will enhance their understanding of the underlying principles. | Yuguang Li; Gina Delmonache; Pratahdeep Gogoi; Xiaoli Ge; Xingyu Wang ; Rachel Snider; Timothy Cook; Ziyun Wang | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66718587c9c6a5c07ac01ad7/original/multipurpose-diy-spectrophotometer-for-teaching-analytical-chemistry.pdf |
619b3e242e10ad29e5521577 | 10.26434/chemrxiv-2021-plssb-v2 | Stable dinitrile end-capped closed-shell non-quinodimethane as donor, acceptor and additive of organic solar cells | Non-fullerene acceptors exhibit great potential to improve photovoltaic performances of organic solar cells. However, it is important to further enhance chemical stability and device durability for future commercialization, especially for Y6-series small molecule acceptors with 2-(3-oxo-2,3-dihydroinden-1-ylidene)malononitrile (IC) type as ending group. In this work, an IC-free photovoltaic material YF-CN consisting of 2-fluoren-9-ylidenepropanedinitrile terminal was designed and synthesized by stille coupling. YF-CN exhibited closed-shell chemical structure with enhanced photostability and improved morphological compatibility with the binary PCE10:Y6 blend. The moderate energy level makes YF-CN could serve as a multifunctional material, such as donor, acceptor and the third component. When adding YF-CN as second donor into PCE10:Y6 system, an improved power conversion efficiency of 12.03% was achieved for as-cast device. Importantly, the ternary PCE10:YF-CN:Y6-devices showed enhanced storage durability maintaining 91% of initial PCE after the 360 hours. This work provides new perspective to understand the open-shell character of donor and closed-shell structure of acceptors, respectively, as well as promising design concept of stable IC-free acceptors for organic solar cells. | Liang weixuan; Liu Peng; Zhang Yiheng; Zhu weiya; Tao Xinyang; He Zhicai; Li Yuan | Materials Science; Energy; Photovoltaics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619b3e242e10ad29e5521577/original/stable-dinitrile-end-capped-closed-shell-non-quinodimethane-as-donor-acceptor-and-additive-of-organic-solar-cells.pdf |
60c75584bb8c1a84623dc3ff | 10.26434/chemrxiv.14122901.v1 | Deep Learning Combined with IAST to Screen Thermodynamically Feasible MOFs for Adsorption-Based Separation of Multiple Binary Mixtures | This study demonstrates the coupling of a multipurpose multilayer perceptron (MLP) model that predicts single-component adsorption for a various molecules with ideal adsorption solution theory (IAST). The resulting computational framework predicts MOF separations properties for various binary mixtures at various compositions and pressures. The accuracy of the MLP+IAST framework was sufficiently high so that, for a given separation, MOFs in the 90th percentile from MLP+IAST-based screening contain ~87% of MOFs in the 95th percentile one would obtain from molecular simulation-based screening. Clustering algorithms were shown effective to identify so-called "privileged" MOFs that were high-performing for multiple separations. Free energy calculations were performed to determine privileged MOFs that were likely to be accesses synthetically, at least from a thermodynamic perspective. | Ryther Anderson; Diego Gómez-Gualdrón | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75584bb8c1a84623dc3ff/original/deep-learning-combined-with-iast-to-screen-thermodynamically-feasible-mo-fs-for-adsorption-based-separation-of-multiple-binary-mixtures.pdf |
65c37ad5e9ebbb4db9d89d0d | 10.26434/chemrxiv-2024-l0vll | Isolation, Identification, and Characterization of a Serine Protease with Anti-nociceptive Activity from the Gut Bacterium, Faecalibacterium prausnitzii | Inflammatory bowel disease (IBD) induces hyperexcitability in dorsal root ganglion (DRG) nociceptors, which contributes to abdominal pain. Proteases modulate the excitability of nociceptive neurons via activation of cell-surface protease-activated receptors. Recent findings indicate that serine proteases from Faecalibacterium prausnitzii, a bacterial strain found in the colonic microbiota of healthy individuals, can directly signal to the DRG neurons and reduce excitability, which may suppress abdominal pain. Herein we identify an anti-nociceptive serine protease from F. prausnitzii by heterologous expression and purification of multiple putative anti-nociceptive serine proteases followed by clamp electrophysiology experiments. A single serine protease, Clp-fp, from F. prausnitzii reduced DRG neuronal excitability via activation of protease-activated receptor-4, thereby recapitulating the effect of F. prausnitzii culture supernatants. The identification and characterization of a potentially analgesic serine protease from a commensal gut bacterium makes possible the further exploration of new treatments for IBD-related abdominal pain. | Manasa Ramachandra; Corey Baker; Taylor Alward; Lorena Ucciferri; Josh Innis; Shu-Mei He; Prameet Sheth; Alan Lomax; Avena Ross | Biological and Medicinal Chemistry; Catalysis; Biochemistry; Microbiology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c37ad5e9ebbb4db9d89d0d/original/isolation-identification-and-characterization-of-a-serine-protease-with-anti-nociceptive-activity-from-the-gut-bacterium-faecalibacterium-prausnitzii.pdf |
60c7418c337d6c6647e268f0 | 10.26434/chemrxiv.8063120.v1 | Access to Fe(II) Bis(σ-B-H) Aminoborane Complexes via Protonation of a Borohydride Complex and Dehydrogenation of Amine-Boranes | We
report on the first synthesis and structural characterization of the iron based
aminoborane complexes. These species are formed upon protonation of a borohydride complex by ammonium salts.<br /> | Nikolaus Gorgas; Berthold Stöger; Luis F. Veiros; Karl Kirchner | Organic Synthesis and Reactions; Coordination Chemistry (Inorg.); Organometallic Compounds; Small Molecule Activation (Inorg.); Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7418c337d6c6647e268f0/original/access-to-fe-ii-bis-b-h-aminoborane-complexes-via-protonation-of-a-borohydride-complex-and-dehydrogenation-of-amine-boranes.pdf |
64b15019b605c6803bb2a7ac | 10.26434/chemrxiv-2023-s6qg4 | A light touch: solar photocatalysis detoxifies oil sands process-affected waters prior to significant treatment of naphthenic acids or acid extractable organics | The toxicity of oil sands process-affected water (OSPW) has been associated to its dissolved organics, a complex mixture of naphthenic acid fraction components (NAFCs). Here, we evaluated solar treatment with buoyant photocatalysts (BPCs) as a candidate passive advanced oxidation process (P-AOP) for OSPW remediation, according to both analytical chemistry and standard rainbow trout (Oncorhynchus mykiss) and fathead minnow (Pimephales promelas) whole effluent toxicity (WET) bioassays. Solar photocatalysis with BPCs fully degraded naphthenic acids (NAs) and acid extractable organics (AEO) in 3 different OSPW samples, however fish toxicity was eliminated well before concentrations of dissolved organics had significantly diminished, within <2 days of sunlight exposure for all OSPWs. Classical NAs and AEO, traditionally considered among the principal toxicants in OSPW, were not correlated with OSPW toxicity herein. Instead, petroleomic mass spectrometry (MS) analysis revealed low polarity organosulfur NAFCs – O2S− and OS+ (putatively naphthenic sulfoxides), together composing <10% of the total AEO – were correlated with WET outcomes, and apparently accounted for the majority of waters’ toxicity, as described by a physiologically-based model (PBM) of tissue partitioning. These results demonstrate that complete elimination of OSPW toxicity per standard WET bioassays is achievable without significant changes to overall concentrations of dissolved organics, suggesting that most AEO are toxicologically benign, and toxicity may instead be driven by only a small subset of NAFCs, which are preferentially photocatalytically treated. These findings have implications for OSPW release, for which a less extensive but more selective treatment may be required than previously expected. | Timothy M. C. Leshuk; Zachary W. Young; Brad Wilson; Zi Qi Chen; Danielle Smith; Greg Lazaris; Mary Gopanchuk; Sean McLay; Corin Seelemann; Theo Paradis; Asfaw Bekele; Rodney Guest; Hafez Massara; Todd White; Warren Zubot; Daniel J. Letinski; Aaron D. Redman; D. Grant Allen; Frank Gu | Catalysis; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Water Purification; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b15019b605c6803bb2a7ac/original/a-light-touch-solar-photocatalysis-detoxifies-oil-sands-process-affected-waters-prior-to-significant-treatment-of-naphthenic-acids-or-acid-extractable-organics.pdf |
661736d9418a5379b09667f2 | 10.26434/chemrxiv-2024-1dlt9-v3 | Machine-Learning Discovered Crystallization Model for Two
Dimensional Covalent Organic Frameworks: Towards Precise Control of the Crystal Quality | The rational molecular design and experimental condition optimizations for two-dimensional co-valent organic frameworks (2D COFs) call for a crystallization model capable of capturing exper-imental time and size scales. However, accurately describing their crystallization process remains a significant challenge due to the presence of non-classical pathways. Here, we demonstrate the implementation of a machine-learning approach, overcoming the difficulties associated with bot-tom-up model derivation. The resulting model, referred to as NEgen1, establishes correlations among the induction time, nucleation rate, growth rate, material parameters, and common solu-tion synthesis conditions for 2D COFs that belong to the nucleation-elongation category. NEg-en1 represents the emergence of practical crystallization models for 2D COFs, enabling the direct calculation of their crystallization processes in both experimental times and sizes. The results elu-cidate the detailed competition between the nucleation and growth dynamics in solution, which has been inappropriately apprehended via classical, empirical models with assumptions invalid for 2D COFs. Importantly, we demonstrate the potential application of the NEgen1 model in opti-mizing the synthesis conditions, which has predominantly relied on empirical knowledge to date. The identification of conditions superior to those routinely used experimentally reveals a promis-ing strategy of gradually increasing monomer addition speed for growing large 2D COF crystals while maintaining a reasonable synthesis time. These results highlight the potential for systemati-cally improving the crystal quality of 2D COFs for wider applications. | Jiaxin Tian; Haoyuan Li | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Physical and Chemical Processes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661736d9418a5379b09667f2/original/machine-learning-discovered-crystallization-model-for-two-dimensional-covalent-organic-frameworks-towards-precise-control-of-the-crystal-quality.pdf |
673196b6f9980725cfcc7691 | 10.26434/chemrxiv-2024-n8wc5 | STD and WLOGSY NMR Based Fingerprinting Reveals Subtle and Biologically Relevant Differences in Short Linear Motif Binding | Interactions between Short Linear Motifs (SLiMs) and a partner domain are commonly exploited as simplified functional models of transient Protein-Protein Interactions (PPI) for characterizing interfacial associations between partner proteins. In this study, we report the use of a ligand-observed NMR approach, where through unambiguous assignment of 1H resonances of two closely related SLiMs, whilst bound to their partner domain (HopTPR2A ), we could assign STD and WLOGSY NMR signals to specific regions in the peptide backbone. These data revealed subtle alterations in magnetization transfer, resulting from changes in the binding mode of each SLiM respectively. The ability to detect and compare these changes at sub-residue resolution, provided differing fingerprints of SLiM binding. This approach therefore represents a broadly accessible method for identifying binding hot spots and interrogating the impact of structural variations on SLiM-domain interaction stability, and by extension transient PPIs. | Marwaan Rylands; Daniel Kusza; David Clarke; Beatriz de la Torre; Fernando Albericio; Adrienne Edkins; Clinton Veale | Physical Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673196b6f9980725cfcc7691/original/std-and-wlogsy-nmr-based-fingerprinting-reveals-subtle-and-biologically-relevant-differences-in-short-linear-motif-binding.pdf |
67cba4d281d2151a029372cd | 10.26434/chemrxiv-2025-b40mr | A one-pot RT-LAMP diagnostic assay for SARS-CoV-2 from saliva samples | Results of efforts to diagnose infections with SARS-CoV-2 using a sampling method that was less invasive than the nasopharyngeal swab led to the rapid adoption of anterior nasal swabs. Saliva was also shown to have potential as a sample matrix and, like anterior nasal swabs, could be obtained non-invasively (e.g., passive drool). However, due to its inherent complexity and heterogeneity across patient populations (e.g., presence of mucins and RNases), saliva was largely disregarded as point-of-care diagnostics were being developed and broadly implemented. For molecular diagnostic approaches (e.g., RT-PCR or RT-LAMP), these matrix effects from saliva could lead to undesirable false positives or false negatives. The opportunity to address these challenges by normalizing the performance of saliva could enable important applications of molecular tests, particularly at the point-of-care. Towards these goals, we developed a one-pot RT-LAMP assay for the colorimetric detection of SARS-CoV-2 from saliva samples. The assay is performed in five steps: (i) a patient collects a passive saliva sample, (ii) the sample is placed on a heat block for 10 minutes at 95 °C, (iii) the undiluted sample is added to the one-pot RT-LAMP assay, (iv) the RT-LAMP reaction tube is place on a heat block for 40 minutes at 65 °C, and, (v) immediately post-amplification, the reaction tube is inverted to observe the colorimetric output. We demonstrated the clinical performance of our assay using a panel of 127 patient samples. Our assay had an overall accuracy of 98%, with a sensitivity of 88% and a specificity of 100%. These results indicate excellent diagnostic agreement with the gold standard, RT-PCR, and highlight the potential to improve the clinical utility of saliva for point-of-care testing of SARS-CoV-2 and other respiratory viruses. | Andrea C. Mora; Allison J. Tierney; Alexandra K. Sogn; Paul T. Lawrence; Elizabeth Tzavaras; Mabi L. Singh; Gustavo Mahn Arteaga; Fiorenzo G. Omenetto; Athena Papas; Charles R. Mace | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Bioengineering and Biotechnology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cba4d281d2151a029372cd/original/a-one-pot-rt-lamp-diagnostic-assay-for-sars-co-v-2-from-saliva-samples.pdf |
6712575f12ff75c3a1cac2fd | 10.26434/chemrxiv-2024-lf3nr | Noncovalent Interactions in Density Functional Theory: All the Charge Density We Do Not See | Exact determination of the electronic density of molecules and materials would provide direct access to accurate bonded and non-bonded interatomic interactions by virtue of the Hellman-Feynman theorem. However, density-functional approximations (DFA) -- the workhorse methods for the electronic structure of atomistic systems -- only provide approximate and sometimes unreliable electron densities. Here we show that long-range van der Waals (vdW) dispersion interactions can visibly modify the charge density, scale nontrivially with system size, and in some cases cause polarization of charge density that exceeds that of the underlying semi-local density functional. We use the fully-coupled Many-Body Dispersion model to compute the vdW charge density by an appropriate real-space projection of the collective fluctuations of optimally-tuned coupled harmonic oscillators that constitute the model. Our analysis highlights the potential unreliability of post-hoc methods for vdW dispersion interactions, has implications for detecting interacting regions in large (bio)molecules, and enables the construction of more accurate DFAs and machine-learned force fields based on the electron density. | Almaz Khabibrakhmanov; Matteo Gori; Carolin Müller; Alexandre Tkatchenko | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6712575f12ff75c3a1cac2fd/original/noncovalent-interactions-in-density-functional-theory-all-the-charge-density-we-do-not-see.pdf |
60c74ec4bdbb8909cca39c3b | 10.26434/chemrxiv.12798545.v1 | 3D Printed Tetrakis(triphenylphosphine)palladium (0) Impregnated Stirrer Devices for Suzuki-Miyaura Cross-Coupling Reactions | 3D printed materials can be readily modified to
create bespoke structures that incorporate a range of catalysts at the point of
printing. In this present study we report on the design and 3D printing of
tetrakis (triphenylphosphine) palladium (0) impregnated 3D printed stirrer
devices that were used to catalyze a Suzuki-Miyaura reaction between biaryl
compounds in a batch-based approach. It was shown that the devices themselves
are reusable, easy to use, air-stable, give access to an array of biaryl
compounds in excellent yields and lead to low levels of palladium loss into the
reaction. Simple modification of the device’s design by size reduction, meant
that they could also be used to reduce the time of the Suzuki-Miyaura reaction
by microwave enhanced heating. At the end of the reaction, devices can simply be
removed from the flask, washed and reused, analogous to stirrer bead workflows.
This makes the overall process of setting up multiple reactions simpler by
obviating the need to weigh out catalysts for reactions and the device, once
used, can be simply removed from the reaction media at the end of the reaction. | Matthew Penny; Zenobia Rao; Ahtsham Ishaq; Rumintha Thavarajah; Stephen Hilton | Organic Synthesis and Reactions; Catalysts; Multilayers; Nanostructured Materials - Materials; Fluid Mechanics; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ec4bdbb8909cca39c3b/original/3d-printed-tetrakis-triphenylphosphine-palladium-0-impregnated-stirrer-devices-for-suzuki-miyaura-cross-coupling-reactions.pdf |
6384cdc40058eb2e03680994 | 10.26434/chemrxiv-2022-6nhtt | Osmotic pressure induced toxicity by aggregation of citrate-coated silver nanoparticles inside HepG2 cells | The effects of 10nm citrate-coated silver nanoparticles (AgNPs) to hepatocellular carcinoma (HepG2) cells were investigated to elucidate toxicity mechanisms. Cell viability, oxidative stress, protein expression, and cell morphology were assessed to determine the toxicity of AgNPs at various dose levels. 10nm citrate-coated AgNPs were found to be toxic to HepG2 cells at a dose of > 1.0 ppm and their LD50 was determined to be 3.0 ppm. Oxidative stress levels in the cells were found to increase with the dose of AgNPs and HepG2 cells can withstand high level of reactive oxygen species before cell death. The expressions of heat shock proteins and tubulin proteins were most significantly affected by the presence of AgNPs of 5.0 ppm. The AgNPs were observed to penetrate the cells treated with a dose of 5.0 ppm by transmission electron microscopy. Furthermore, the agglomeration of AgNPs in HepG2 cells was found and generated osmotic pressure that is likely another pathway to be responsible for the toxicity of AgNPs. | Pamela Ubaldo; Henok Abshiro; Franklin Cavender; Jay Means; Dale Hales; Lichang Wang | Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Biophysical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6384cdc40058eb2e03680994/original/osmotic-pressure-induced-toxicity-by-aggregation-of-citrate-coated-silver-nanoparticles-inside-hep-g2-cells.pdf |
6410a1287290f69f8ef8ca02 | 10.26434/chemrxiv-2023-twxlq | Understanding the limits to Short-range order Suppression in Many-Component Disordered Rock Salt Lithium-ion Cathode Materials | Suppressing unfavourable short-range ordering in disordered rock salt lithium-ion cathode materials is seen as a key research goal on their route to commercialisation. In this study we use cluster-expansion-driven Monte Carlo simulations of a model 3d-transition metal disordered rock salt oxyfluoride system to investigate the effect of many component cation substitution on the suppression of short- range ordering in disordered rock salt cathode materials. We confirm that many-cation substitution is effective in suppressing short-range ordering, but has diminishing returns on increasing the number of component transition metals, or alternatively, increasing the size of the long-range lithium diffusion network as the number of transition metals increases. We particularly emphasize the critical role of lithium excess and fluorine content in the success of the “high-entropy” cation substitution strategy: short-range ordering is strongly influenced by cation-anion bonding preferences, underscoring the need to consider the full composition of the target system when designing high entropy lithium-ion cathode materials. | Alexander G. Squires; David O. Scanlon | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6410a1287290f69f8ef8ca02/original/understanding-the-limits-to-short-range-order-suppression-in-many-component-disordered-rock-salt-lithium-ion-cathode-materials.pdf |
60c74cc9bdbb895d5aa3987f | 10.26434/chemrxiv.12517457.v1 | Orbital Energies and Nuclear Forces in DFT: Interpretation and Validation | The bonding and antibonding character of individual Molecular Orbitals has been previously shown to be related to their orbital energy derivatives with respect to nuclear coordinates, known as Dynamical Orbital Forces. Albeit usually derived from Koopmans' theorem, in this work we show a more general derivation from conceptual DFT, which justifies application in a broader context. The consistency of the approach is validated numerically for valence orbitals in Kohn-Sham DFT. Then, we illustrate its usefulness by showcasing applications in aromatic and antiaromatic systems and in excited state chemistry. Overall, Dynamical Orbital Forces can be used to interpret the results of routine ab initio calculations, be it wavefunction or density based, in terms of forces and occupations. | Rubén Laplaza; Julia Contreras-Garcia; Patrick Chaquin; Carlos Cardenas; Paul W. Ayers | Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Quantum Mechanics; Quasiparticles and Excitations; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cc9bdbb895d5aa3987f/original/orbital-energies-and-nuclear-forces-in-dft-interpretation-and-validation.pdf |
657b61fc66c1381729302e62 | 10.26434/chemrxiv-2023-t7c5s | Biosourced Spherical Microbeads from Brewer’s Spent Grain for Sustainable Personal Hygiene Products | Many countries have recently banned the production and importation of petrochemical plastic mi- crobeads for use as exfoliating agents in personal care products. Plastic particles in products of this nature are too small to be retrieved during wastewater treatment and they accumulate in the environment, negatively impacting living organisms and ecosystems. Sustainable alternatives that offer comparable mechanical properties to synthetic plastic microbeads could be developed using biowaste material. Brewer’s spent grain (BSG), the primary residue of the brewery industry, is shown herein to be a promising starting material in the development of biodegradable, non-toxic microbeads. After dilute acid hydrolysis, pretreated lignocellulosic pulp from BSG is solubilized using an aqueous system of NaOH and ZnO. Solid microbeads may then be formed by dropping the resulting solution into an acid bath, filtering, and drying. The conditions of each step required opti- mization to successfully produce spherical microbeads with a mean diameter as small as 1.25 mm, a homogeneous size distribution, and an average hardness of 199 MPa. The beads also demonstrated superior cleansing abilities to commercially available natural exfoliating particles. BSG microbeads are therefore a promising option for use as a physical exfoliating agent in various personal hygiene products. | Amy McMackin; Vincent Banville; Sébastien Cardinal | Polymer Science; Agriculture and Food Chemistry; Biopolymers; Cellulosic materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657b61fc66c1381729302e62/original/biosourced-spherical-microbeads-from-brewer-s-spent-grain-for-sustainable-personal-hygiene-products.pdf |
6437c1da1d262d40ea6034f7 | 10.26434/chemrxiv-2023-fj1vv | Excited State Deactivation via Solvent to Chromophore
Proton Transfer in Isolated 1:1 Molecular Complex:
Experimental Validation by Measuring the Energy Barrier
and Kinetic Isotope Effect | We have experimentally demonstrated conclusive evidence of solvent-to-chromophore excited state proton
transfer (ESPT) as a deactivation mechanism in a binary complex isolated in the gas phase. The above was achieved by determining the energy barrier of the ESPT processes, qualitatively analysing the quantum tunnelling rates and evaluating the kinetic isotope effect. The 1:1 complexes of 2,2’-pyridylbenzimidazole (PBI) with H2O, D2O and NH3, produced in a supersonic jet-cooled molecular beam, were characterised spectroscopically. The vibrational frequencies of the complexes in the S1 electronic state were recorded using a resonant two-colour two-photon ionization method coupled to a Time-ofFlight mass spectrometer set-up. In the PBI-H2O, the ESPT energy barrier of 43110 cm-1 was measured using UV-UV hole-burning spectroscopy. The exact reaction pathway was experimentally determined by isotopic substitution of the tunnelling proton (in PBI-D2O) and increasing the width of the proton transfer barrier (in PBI-NH3). In both cases, the energy barrier was significantly increased to > 1030 cm-1 in the PBI-D2O and to > 868 cm-1 in PBI-NH3. The heavy atom in PBI-D2O decreased
the zero-point energy in the S1 state significantly, resulting in the elevation of the energy barrier. Secondly, the solvent-to-chromophore proton tunnelling was found to decrease drastically upon deuterium substitution. In the PBI-NH3 complex, the solvent molecule formed a preferential hydrogen bonding with the acidic (PBI)N-H group. This led to the formation of a weak hydrogen bonding between the ammonia and the pyridyl-N atom, thus, increasing the proton transfer barrier width (H2NH‧‧‧Npyridyl(PBI)). The above resulted in increased barrier height and decreased quantum tunnelling rate in the excited state. The experimental investigation, aided by computational investigations, demonstrated conclusive evidence of a novel
deactivation channel of an electronically excited biologically relevant system. The variation observed for the energy barrier and the quantum tunnelling rate by substituting NH3 in place of H2O can be directly correlated to the drastically different photochemical and photo-physical reactions of biomolecules under various microenvironments. | Saurabh Khodia; Ramesh Jarupula; Simran Baweja; Md Shabeeb; Bhavika Kalal; Surajit Maity | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6437c1da1d262d40ea6034f7/original/excited-state-deactivation-via-solvent-to-chromophore-proton-transfer-in-isolated-1-1-molecular-complex-experimental-validation-by-measuring-the-energy-barrier-and-kinetic-isotope-effect.pdf |
60c75230337d6c1e84e286c0 | 10.26434/chemrxiv.13265555.v1 | Modeling Molecules Under Pressure with Gaussian Potentials | <div>
<div>
<div>
<p>The computational modeling of molecules under high pressure is a growing research
area that augments experimental high-pressure chemistry. Here, a new electronic structure method for modeling atoms and molecules under pressure, the <i>Gaussians On Sur</i><i>ace Tesserae Simulate HYdrostatic Pressure</i> (GOSTSHYP) approach, is introduced. In
this method, a set of Gaussian potentials is distributed evenly on the van der Waals surface of the investigated chemical system, leading to a compression of the electron density
and the atomic scaffold. Since no parameters other than the pressure need to be specified, GOSTSHYP allows straightforward geometry optimizations and <i>ab initio</i> Molecular Dynamics simulations of chemical systems under pressure for non-expert users.
Calculated energies, bond lengths and dipole moments under pressure fall within the
range of established computational methods for high-pressure chemistry. A Diels-Alder
reaction and the cyclotrimerization of acetylene showcase the ability of GOSTSHYP
to model pressure-induced chemical reactions. The connection to mechanochemistry is
pointed out. </p>
</div>
</div>
</div> | Maximilian Scheurer; Andreas Dreuw; Evgeny Epifanovsky; Martin Head-Gordon; Tim Stauch | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75230337d6c1e84e286c0/original/modeling-molecules-under-pressure-with-gaussian-potentials.pdf |
60c751ad702a9b864b18bfbe | 10.26434/chemrxiv.12382595.v3 | Approximately self-consistent ensemble density functional theory: toward inclusion of all correlations | Recent theory developments in ensemble density functional theory (EDFT) promise to bring decades of work for ground-states to the practical resolution of excited-states - provided newly-discovered "density-driven correlations" can be dealt with and adequate effective potentials can be found. This Letter introduces simple theories for both; and shows that EDFT using these theories outperforms ΔSCF DFT and time-dependent DFT for low-lying gaps in most of the small atoms and molecules tested, even when all use the same density functional approximations. It thus establishes EDFT as a promising tool for low-cost studies of excited states; and provides a clear route to practical EDFT implementation of arbitrary functional approximations.<br /><br /> | Tim Gould | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751ad702a9b864b18bfbe/original/approximately-self-consistent-ensemble-density-functional-theory-toward-inclusion-of-all-correlations.pdf |
66dc499b51558a15ef5471c9 | 10.26434/chemrxiv-2024-jlg7m | Spontaneous Chemical Capping with Bis(trifluoromethanesulfonyl)imide-Based Additive for Photoabsorbers in Perovskite Solar Cells | The improvement in the performance of perovskite photoabsorbers plays a crucial role in the development of perovskite solar cells (PSCs). Thus far, salts based on bis(trifluoromethanesulfonyl)imide (TFSI) have been developed as additives for perovskite photoabsorbers and have improved the quality of the perovskite layers. However, the effects of TFSI anions require clarification because most TFSI-based additives are multifunctional; both the counter cation and TFSI anion improve the quality of the perovskite layers. Therefore, we synthesized a novel methylammonium bis(trifluoromethanesulfonyl)imide (MATFSI) and revealed the chemical capping effects of TFSI-based additives on the perovskite layer. MATFSI includes the same cation as the co-additive MA chloride, which is used to create narrow-bandgap perovskite layers. Hence, the use of the MATFSI additive can reveal the effect of the TFSI anion, independent of its counter cation. MATFSI addition resulted in the spontaneous coating of the TFSI moiety on the perovskite layer during its deposition process, and facilitated the crystal growth of the perovskite layer; thus, TFSI chemical capping effectively hampered defect formation in the perovskite layer. Hence, the optimal MATFSI addition improved the photovoltaic (PV) performance of the PSCs. Notably, the resulting perovskite surface that was chemically capped with TFSI displayed high wettability to water droplets, yet exhibited improved PV performance stability against humidity, which contradicts the overarching opinion in this research field. Parameter-differentiated contact angle (PDCA) measurements indicated that the high wettability of water droplets was attributed to the formation of active hydrogen bonds derived from the TFSI capping on the outer perovskite surface; moreover, the improvement in stability against humidity could be attributed to the low dispersion energy of the CF3 moiety in the TFSI capping. The insights obtained in this study could assist in improving perovskite additives and highlight the effectiveness of the simple PDCA method, which offers insights that conventional contact angle measurements cannot provide. | Naoyuki Nishimura; Ryuzi Katoh; Hiroyuki Kanda; Takurou N. Murakami | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dc499b51558a15ef5471c9/original/spontaneous-chemical-capping-with-bis-trifluoromethanesulfonyl-imide-based-additive-for-photoabsorbers-in-perovskite-solar-cells.pdf |
64ee94293fdae147fa1a61fc | 10.26434/chemrxiv-2023-dz9v9-v2 | Nickel-Catalyzed C(sp3)−O Hydrogenolysis via a Remote Concerted Oxidative Addition and its Application to Degradation of a Bisphenol A-Based Epoxy Resin | In this work, we developed a nickel-catalyzed transfer hydrogenolysis of 1-aryloxy-3-amino-2-propanols, which is a model compound of amine-cured bisphenol A (BPA)-based epoxy resin. Mechanistic investigation revealed that the hydroxy group acts as the hydrogen donor to generate α-aryloxy ketone, which undergoes an unprecedented remote concerted oxidative addition of the C(sp3)−O bond as suggested by DFT calculation. Successful application of this method was demonstrated by the degradation of a diamine-cured BPA-based epoxy resin, where BPA was directly recovered from the resin. | Yumeng Liao; Kohei Takahashi; Kyoko Nozaki | Organic Chemistry; Catalysis; Organometallic Chemistry; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ee94293fdae147fa1a61fc/original/nickel-catalyzed-c-sp3-o-hydrogenolysis-via-a-remote-concerted-oxidative-addition-and-its-application-to-degradation-of-a-bisphenol-a-based-epoxy-resin.pdf |
658651eb9138d231614f3061 | 10.26434/chemrxiv-2023-5tndz | Membrane-Free Electrochemical Production of Acid and Base Solutions Capable of Processing Ultramafic Rocks | Chemical transformations that are effected by sequential addition of acid and base can be performed in closed-loop processes powered by electricity if the acid and base are produced electrochemically from water. Conventional methods of electrochemical acid-base production utilize ion exchange membranes (IEMs) to inhibit proton (H^+) and hydroxide (OH^–) recombination, but these components lead to high resistive losses, low current densities, and poor tolerance for polyvalent metal ions, which compromise energy efficiency and scalability. Here we use an ion transport model to guide the design of an acid-base co-generating system that inhibits recombination via competitive transport of the supporting electrolyte and masking H^+ as HSO4^–, which enables the use of a simple porous separator instead of IEMs. Using the H2 oxidation reaction (HOR) and H2 evolution reaction (HER) for H^+ and OH^– production, we demonstrate steady-state co-generation of acid and base solutions at useful concentrations in the presence of polyvalent impurities with lower energy demand and higher current density than state-of-the-art reported IEM-based systems. Cells can be stacked by combining HER and HOR electrodes into a bipolar gas diffusion electrode, which recirculates H2 with near-unity efficiency. The acid and base outputs of the cell are capable of extracting alkalinity from olivine and serpentine in the form of Mg(OH)2 and Mg(OH)2 * 2 MgSiO3, which are shown to be competent for removing CO2 from dilute streams to form Mg carbonates. | Benjamin Charnay; Yuxuan Chen; Rishi Agarwal; Jason Misleh; Gage Wright; Ethan Sauve; Wei Lun Toh; Yogesh Surendranath; Matthew Kanan | Physical Chemistry; Inorganic Chemistry; Energy; Electrochemistry; Solution Chemistry; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658651eb9138d231614f3061/original/membrane-free-electrochemical-production-of-acid-and-base-solutions-capable-of-processing-ultramafic-rocks.pdf |
60c7578dee301c1b91c7b57a | 10.26434/chemrxiv.14371331.v2 | Active Machine Learning for Chemical Dynamics Simulations. I. Estimating the Energy Gradient | Ab initio molecular dymamics (AIMD) simulation studies are a direct
way to visualize chemical reactions and help elucidate non-statistical dynamics that does not follow the intrinsic reaction coordinate. However,
due to the enormous amount of the ab initio energy gradient calculations
needed for AIMD, it has been largely restrained to limited sampling and
low level of theory (i.e., density functional theory with small basis sets).
To overcome this issue, a number of machine learning (ML) methods have
been employed to predict the energy gradient of the system of interest.
In this manuscript, we outline the theoretical foundations of a novel ML
method which trains from a varying set of atomic positions and their
energy gradients, called interpolating moving ridge regression (IMRR),
and directly predicts the energy gradient of a new set of atomic positions.
Several key theoretical findings are presented regarding the inputs used to
train IMRR and the predicted energy gradient. A hyperparameter used to
guide IMRR is rigorously examined as well. The method is then applied to
three bimolecular reactions studied with AIMD, including HBr+ + CO2,
H2S + CH, and C4H2 + CH, to demonstrate IMRR’s performance on different chemical systems of different sizes. This manuscript also compares
the computational cost of the energy gradient calculation with IMRR vs.
ab initio, and the results highlight IMRR as a viable option to greatly
increase the efficiency of AIMD. | Kazuumi Fujioka; Rui Sun | Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7578dee301c1b91c7b57a/original/active-machine-learning-for-chemical-dynamics-simulations-i-estimating-the-energy-gradient.pdf |
60c750650f50db5fe8397575 | 10.26434/chemrxiv.13031843.v1 | Twistable Dipolar Aryl Rings as Electric Field Actuated Conformational Molecular Switches | The ability to control the chemical conformation of a system via external stimuli is a promsing route for developing molecular switches. For eventual deployment as viable sub-nanoscale components that are compatible with current electronic device technology, conformational switching should controllable by a local electric field (i.e. E-field gateable) and accompanied by a rapid change in conduction. In organic chemical systems the degree of π-conjugation is linked to the degree of electronic delocalisation, and thus largely determines the conductivity. Here, by means of accurate first principles calculations, we study the prototypical biphenyl based molecular system in which the dihedral angle between the two rings determines the degree of conjugation. In order to make this a gateable system we create a net dipole by asymmetrically functionalising one ring with electronegative substituents (F, Br and CN) with different polarisabilities. In this way, the application of an E-field interacts with the dipolar system to influence the dihedral angle, thus controlling the conjugation. For all three considered substituents we consider a range of E-fields, and in each case extract conformational energy profiles. Using this data we obtain the minimum E-field required to induce a barrierless switching event for each system. We further extract the estimated switching speeds, the conformational probabliities at finite temperatures, and the effect of applied E-field on electronic structure. Consideration of these data allow us to assess which factors are most important in the design of efficient gateable electrical molecular switches. | Kílian Jutglar Lozano; Raul Santiago; Jordi Ribas; Stefan Bromley | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750650f50db5fe8397575/original/twistable-dipolar-aryl-rings-as-electric-field-actuated-conformational-molecular-switches.pdf |
60c75575ee301cb9bfc7b1a6 | 10.26434/chemrxiv.14069480.v1 | Computer-Aided Drug Designing of Ocimum Basilicum Compounds as Therapeutic Agents Against RdRp of SARS-CoV2 | <div>The prevailing situation of the world is challenging due to COVID-19 pandemic that is caused by SARS-CoV2. To combat with this emerging pandemic by reducing disease severity and infection, the need of hour is to develop an effective vaccine and antiviral candidates as therapeutic agents against SARS-CoV2. This study was developed for the identification of potential anti-viral agents, from Ocimum basilicum against RdRp of SARS-CoV2. In this concern, nevadensin, ursolic acid, β-Sesquiphellandren, apigenin, nerolidol, nonyl acetate and geranyl acetate were screened out of fifty-seven compounds from Ocimum basilicum based on their best docking scores. The docking results were also compared with already clinically used drugs (Remdesivir and Ribavirin) against RdRp of SARS-CoV2. Molecular docking was performed using MOE software. The ADMET analysis and drug likeliness were also performed for all screened compounds by using admetSAR, pkCSM and SwissADME. Cumulatively, the optimum binding energies of screened compounds indicated their potential for drug development against SARS-CoV2. It appears promising that nevadensin exhibited a good docking score and high binding affinity towards RdRp of SARS-CoV2. Therefore, it may represent the potential to inhibit COVID-19. Hence, Ocimum basilicum nutraceuticals could be effective therapeutic candidates for the treatment and prevention of COVID-19. </div><div><br /></div> | Mehwish Shafiq; Rashid Saif; Laraib Ali; Tuba Ahmad; Anood Sohail | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75575ee301cb9bfc7b1a6/original/computer-aided-drug-designing-of-ocimum-basilicum-compounds-as-therapeutic-agents-against-rd-rp-of-sars-co-v2.pdf |
60c74981469df424b6f43be6 | 10.26434/chemrxiv.12068307.v1 | Photo-Electrochemical Properties of CuO–TiO2 Heterojunctions for Glucose Sensing | <p>Electrochemical sensors for monitoring
biochemical substances are attracting considerable attention. These devices are
usually based on enzymes that are sensitive and very specific. Still, the activity
of those enzymes is lost with changes in temperature or pH. Non-enzymatic
electrochemical sensors – fabricated <i>via</i>
the modification of the electrode surface with metal oxide nanoparticles – are
a judicious answer. In this study, we investigated the photo-electrochemical properties
of CuO–TiO<sub>2</sub> heterojunctions for glucose sensing in alkaline media. A
combination of high-resolution (scanning) transmission electron microscopy,
spatially resolved electron energy-loss spectroscopy, energy-dispersive X-ray
spectroscopy and X-ray powder diffraction, was used to study in detail the
microstructures of the prepared specimens. These results highlighted the strong
intertwining between the TiO<sub>2</sub> nanoparticles and the Cu-based nanoparticles,
which present a metallic core with a CuO rich surface. In addition, we showed that
CuO, joint to TiO<sub>2</sub>, has smaller size compared to pure CuO, which entails
larger surface area available for the glucose electro-oxidation, which consequently
enhanced the electrochemical features. The influence of Cu loading over the sensing
performance of TiO<sub>2</sub> was examined in detail carrying out
electrochemical sensing tests under dark, laboratory and halogen
lamp irradiation. Results demonstrated that, under halogen lamp irradiation, modified CuO–TiO<sub>2</sub> electrodes showed a higher specific response
signal than that of pure CuO. Those increased photo-electrochemical properties in
CuO–TiO<sub>2</sub> heterojunctions are likely due to a synergistic effect between
the microstructural characteristics and effective separation of photo-generated
exciton created at the heterojunction interface. Results of this study offer applicable
guidelines for designing photo-electrochemical screen-printed electrodes based
on nano-sized CuO on titania for an efficient detection of glucose.</p> | David Maria Tobaldi; Claudia Espro; salvarore gianluca leonardi; Luc Lajaunie; Maria Paula Seabra; José Calvino; Silvia Marini; Joao Antonio Labrincha; giovanni neri | Composites; Nanostructured Materials - Materials; Nanodevices; Bioengineering and Biotechnology; Electrochemistry - Mechanisms, Theory & Study; Photochemistry (Physical Chem.); Surface; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74981469df424b6f43be6/original/photo-electrochemical-properties-of-cu-o-ti-o2-heterojunctions-for-glucose-sensing.pdf |
60c749494c89196ab4ad3065 | 10.26434/chemrxiv.12046629.v1 | Stabilization of Bilirubin Oxidase in a Biogel Matrix for High-performance Gas Diffusion Electrodes | Enzyme immobilization on solid conducting surfaces faces some challenges for practical applications in technologies such as biosensors and biofuel cells. Short-term stability, poor electrochemical performance, and enzyme inhibition are some issues that remain unsolved. Here, we propose a simple methodology for bilirubin oxidase (BOD) immobilization on carbon-based gas-diffusion electrodes for a four-electron electrochemical oxygen reduction reaction (ORR). The enzyme is incorporated into a Nafion® polymeric matrix and cross-linked with glutaraldehyde by a one-pot reaction in a buffered solution, producing a stable BOD-based biogel. The biogel prevents the formation of enzyme aggregates, producing a homogeneous bioelectrode surface, and allows access to the direct electron-transfer mechanism of multicopper centers buried in the enzyme. A biocatalytic reduction current of -1.52 ± 0.24 mA cm<sup>-2</sup> at 0.19 ± 0.06 V was observed under gas-diffusion conditions. Additionally, the bioelectrode showed an unprecedented long-term stability under continuous operation combined with satisfactory catalytic current without redox mediator, demonstrating that the BOD-based biogel provides a suitable microenvironment for long-term enzymatic activity involving a bio-three-phase interfacial reaction. Therefore, the present study contributes new insights into enzyme immobilization to overcome the critical short-term stability issue of enzyme-based electrochemical devices for practical applications. | Graziela Sedenho; Ayaz Hassan; Lucyano Macedo; Frank Crespilho | Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749494c89196ab4ad3065/original/stabilization-of-bilirubin-oxidase-in-a-biogel-matrix-for-high-performance-gas-diffusion-electrodes.pdf |
673bbb6b5a82cea2fa95f3c1 | 10.26434/chemrxiv-2024-jr89d | Ferritin Protein Nanocages for Selective Separation and Recovery of Critical Metals | Recycling critical metals from waste streams is increasingly important to meet the rising demand for clean energy technologies and reduce the environmental impact of ore mining. A key step in this process is the selective separation and recovery of high-grade metals from waste leachates containing complex metal mixtures; however, current strategies are limited by high chemical, energy, and resource consumption, substantial financial costs, and production of hazardous byproducts. Herein, we report the pioneering use of ferritin – self-assembling protein nanocages with porous, hollow structures and supercharged inner surfaces – as a high-efficiency biosorbent for eco-friendly, selective metal recovery from mixtures. Ferritin nanocages adsorbed cobalt (Co2+), nickel (Ni2+), and lithium (Li+) primarily through electrostatic interactions, localizing the adsorbed metal cations within their cavities. Adsorption isotherms indicated significantly more effective adsorption of Co2+ and Ni2+ compared to Li+, enabling efficient Co2+/Ni2+ separation from Li+. Leveraging ferritin's ability to concentrate adsorbed metal cations within cavities enabled selective recovery of Co2+ as nearly 95% pure solid carbonate salts from Co2+-Li+ mixtures through single-step precipitation under mild conditions, while Li+ remained in solution. This research opens new avenues for using ferritin nanocages in selective metal separation and recovery from waste streams via simple, environmentally benign adsorption-precipitation processes. | Zhiqian Han; Yifei Ma; Meng Wang | Biological and Medicinal Chemistry; Nanoscience; Earth, Space, and Environmental Chemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673bbb6b5a82cea2fa95f3c1/original/ferritin-protein-nanocages-for-selective-separation-and-recovery-of-critical-metals.pdf |
6758aaa57be152b1d08e015d | 10.26434/chemrxiv-2024-ms8x6-v2 | PAH101: A GW +BSE Dataset of 101 Polycyclic Aromatic Hydrocarbon (PAH) Molecular Crystals | The excited-state properties of molecular crystals are important for applications in organic electronic devices. The GW approximation and Bethe-Salpeter equation (GW +BSE) is the state-of-the-art method for calculating the excited-state properties of crystalline solids with periodic boundary conditions. We present the PAH101 dataset of GW +BSE calculations for 101 molecular crystals of polycyclic aromatic hydrocarbons (PAHs) with up to ∼500 atoms in the unit cell. The data records include the GW quasiparticle band structure, the fundamental band gap, the static dielectric constant, the first singlet exciton energy (optical gap), the first triplet exciton energy, the dielectric function, and optical absorption spectra for light polarized along the three lattice vectors. In addition, the dataset includes the density functional theory (DFT) single-molecule and crystal features used in Liu et al. [npj Computational Materials, 8, 70 (2022)]. We envision the dataset being used to (i) identify correlations between DFT and GW +BSE quantities, (ii) discover materials with desired electronic/ optical properties in the dataset itself, and (iii) train machine-learned models to help in materials discovery efforts. We provide examples to illustrate these three use cases. | Siyu Gao; Xingyu Liu; Yiqun Luo; Xiaopeng Wang; Kaiji Zhao; Vincent Chang; Bohdan Schatschneider; Noa Marom | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6758aaa57be152b1d08e015d/original/pah101-a-gw-bse-dataset-of-101-polycyclic-aromatic-hydrocarbon-pah-molecular-crystals.pdf |
60c750734c89192e00ad3da2 | 10.26434/chemrxiv.13041884.v1 | Influence of Sub-angstrom Change in Interstitial Ion Size on Clay Swelling | <div>Clay minerals in contact with aqueous bulk reservoir undergo a geological transformation of swelling or shrinking by exchanging interstitial cations. For geological applications, it is crucial to understand the stability of these layered materials. Here, we demonstrate that a sub-angstrom change in the interstitial cation size with similar hydration characteristics is enough to destabilize the optimum spacing of layered materials. We used molecular simulations to investigate the stability of water layers in the K-, Rb-, and Cs-mica pores. We find that ±0.1 Å, change in the size of interstitial cation - from Rb<sup>+</sup> to K<sup>+</sup> or Cs<sup>+</sup> ion - leads to -15 to 5 % change in equilibrium loading of adsorbed water and 2 to 35 % change in interlayer spacing. Our thermodynamic analysis reveals an intricate interplay between enthalpic and entropic contributions caused by the structural change of water in the pores due to the hydration of interstitial cations. The understanding from this work has direct implications in designing clay swelling inhibitors in the oil/gas recovery using fracking and sealing materials for radioactive waste. </div> | Sai Adapa; Ateeque Malani | Multilayers; Geochemistry; Computational Chemistry and Modeling; Interfaces; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750734c89192e00ad3da2/original/influence-of-sub-angstrom-change-in-interstitial-ion-size-on-clay-swelling.pdf |
60c75593f96a005ffc2888c9 | 10.26434/chemrxiv.14129996.v1 | Pseudo-Tetrahedral vs Pseudo-Octahedral ErIII Single Molecule Magnets and the 'Disruptive' Role of Coordinated TEMPO Radicals | Erbium(III) complexes are the most interesting candidates for high-performance single molecule magnets (SMMs) just after dysprosium(III). Herein, we thoroughly explore the underrepresented class of neutral pseudo-tetrahedral erbium(III) SMMs and demonstrate their exceptional slow magnetization dynamics controlled by the Raman relaxation mechanism and the molecular magnetic memory effect in the form of a waist-restricted magnetic hysteresis loop. The influence of the coordinated TEMPO radical on the slow magnetization relaxation performance is also demonstrated and discussed.<br /> | Maria Brzozowska; Gabriela Handzlik; Katarzyna Kurpiewska; Mikołaj Zychowicz; Dawid Pinkowicz | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Ligands (Inorg.); Magnetism; Supramolecular Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75593f96a005ffc2888c9/original/pseudo-tetrahedral-vs-pseudo-octahedral-er-iii-single-molecule-magnets-and-the-disruptive-role-of-coordinated-tempo-radicals.pdf |
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