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60c744b5337d6c9cdbe26e53 | 10.26434/chemrxiv.8307572.v2 | Mechanistic Study of Nucleation Enhancement in Atomic Layer Deposition by Pre-Treatment with Small Organometallic Molecules | <p>Thermal atomic layer deposition
(ALD) of metals on metal oxide surfaces typically suffers from nucleation delays
that result in poor-quality films. The poor nucleation may be caused by a
lack of suitable chemisorption sites on the oxide surface which are needed for metal
nucleation to occur. In this work, we demonstrate that pre-functionalizing the
surface with a sub-monolayer of small organometallic molecules from the vapor
phase can lead to a significant increase in surface coverage of the metal
deposited by ALD. This process is demonstrated for Pt ALD from (methylcyclopentadienyl)trimethylplatinum
(MeCpPtMe<sub>3</sub>) and O<sub>2</sub>, with nucleation enhanced almost
three-fold at 100 ALD cycles after the pre-treatment, and even more
significantly at lower ALD cycle numbers. We hypothesize that the high coverage
of the organometallic molecule provides an alternative chemisorption mechanism for
the platinum precursor and thus leads to an increase in nucleation sites. The
growth of the platinum deposits was investigated in depth though scanning
electron microscopy (SEM) and grazing incidence small angle x-ray scattering (GISAXS).
These studies show that the pre-treatment results in the growth of larger and
more highly ordered Pt nanoparticles at early cycle numbers, which subsequently
coalesce into continuous and pinhole free films. Surface pretreatment by
organometallic molecules therefore introduces a potential route to achieve
improved nucleation and growth of ultrathin films.</p> | Camila de Paula; Nathaniel Richey; Li Zeng; Stacey Bent | Thin Films; Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.); Ligands (Inorg.); Organometallic Compounds; Coordination Chemistry (Organomet.); Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b5337d6c9cdbe26e53/original/mechanistic-study-of-nucleation-enhancement-in-atomic-layer-deposition-by-pre-treatment-with-small-organometallic-molecules.pdf |
6331738d114b7e36db1df469 | 10.26434/chemrxiv-2022-k6fg5 | Role of Mn ions in altering the morphology and defects in NiO for photocatalytic and energy Storage Applications | Nickel Oxide having many technological applications was doped with Manganese. The ability of Mn to exist in many oxidation states when incorporated in lower concentration further enhanced the properties of NiO as observed through XRD, UV and PL studies. The generation of vacancies, excitons and lattice vibrations got altered effecting the band gap. Evidence of changes in particle shape was also found. The mechanism behind these phenomena which have technological importance in terms of photocatalysis and energy storage devices discussed. | Ritambhara Dash; Arnab Bhattacharyya | Materials Science; Composites; Materials Processing; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6331738d114b7e36db1df469/original/role-of-mn-ions-in-altering-the-morphology-and-defects-in-ni-o-for-photocatalytic-and-energy-storage-applications.pdf |
61849149f4bd357fc4aa764a | 10.26434/chemrxiv-2021-bh4vn | Metasurfaces as energy valves for sustainable energy management | Control of light absorption and transmission by metal-insulator-metal (MIM) metasurfaces are important for applications in optical windows. In this study we show realization of photo-thermal energy conversion for the radiative cooling.
By controlling absorption and transparency of MIM metasurfaces with thin metal substrate and Indium-Tin-Oxide (ITO) substrates, a high transparency at visible wavelengths and high absorption at mid-infrared wavelengths was realized for a prospective application in efficient cooling or heating of the room. | Yoshiaki Nishijima; Shunya Kimura; Yu Takeshima; Saulius Jodkazis | Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61849149f4bd357fc4aa764a/original/metasurfaces-as-energy-valves-for-sustainable-energy-management.pdf |
621083f3a6fb4d1dc55b1e72 | 10.26434/chemrxiv-2022-8zzh0 | Managing Conflicting Economic and Environmental Metrics in Livestock Manure Management | airy farming is a multi-billion {USD} industry that provides essential food products. At the same time, the millions of animals that this industry oversees generate a massive environmental footprint (affecting air, land, and water quality). Specifically, livestock manure is a carbon- and nutrient-rich waste stream that is routinely used as fertilizer. This practice enables nutrient recycling but also leads to emissions of greenhouse gases and to nutrient pollution of soils and waterbodies. Mitigating these environmental impacts requires investment in manure processing technologies; identifying and prioritizing investment strategies requires understanding inherent conflicts (trade-offs) and synergies that exist between economic and environmental impacts. In this work, we present a conflict analysis and resolution framework that integrates techno-economic analysis (TEA), life cycle assessment (LCA), and supply chain (SC) optimization. We use this framework to investigate deployment scenarios of manure processing pathways in the Upper Yahara watershed region of Wisconsin; here, we evaluate LCA metrics (GHG emissions, ammonia emissions, fossil energy use, and nutrient pollution) and TEA metrics (cost and revenue) for different pathways that include manure collection, storage, application, and processing steps. The LCA and TEA metrics are embedded within a SC optimization model that makes decisions on technology selection and geographical placement and on product transport in the study area. A conflict resolution procedure is used to explore trade-offs associated with these decisions and to identify optimal compromise solutions that best balance trade-offs. Our results reveal that there exist non-obvious conflicts and synergies between the explored metrics that can be exploited to mitigate multiple impacts simultaneously. We also find that the deployment of a diverse set of technologies is needed to fully resolve conflicts. The impact of emerging technologies (ultrafiltration and reverse osmosis) and government incentives is also discussed.
| Yicheng Hu; Horacio Aguirre-Villegas; Rebecca Larson; Victor Zavala | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621083f3a6fb4d1dc55b1e72/original/managing-conflicting-economic-and-environmental-metrics-in-livestock-manure-management.pdf |
67828e0081d2151a02b4fd09 | 10.26434/chemrxiv-2025-7js76-v2 | Simplified tuning of long-range corrected time-dependent density functional theory | Range-separated hybrid functionals have dramatically improved the description of charge-transfer excitations in time-dependent density functional theory (TD-DFT), especially when the range-separation parameter is adjusted in order to satisfy the ionization energy (IE) criterion, eHOMO = –IE. However, this "optimal tuning" procedure is molecule-specific, inconvenient, expensive for large systems, and problematic in extended or periodic systems. Here, we consider an alternative procedure known as global density-dependent (GDD) tuning, which sets the range-separation parameter in an automated way based on properties of the exchange hole. In small molecules, we find that both IE- and GDD-tuned functionals afford remarkably similar TD-DFT excitation energies, for both valence and charge-transfer excitations. However, GDD tuning is more efficient and is well-behaved even for large systems, providing a black-box solution to the optimal-tuning problem that can replace IE tuning for many applications of TD-DFT. | Aniket Mandal; John Herbert | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67828e0081d2151a02b4fd09/original/simplified-tuning-of-long-range-corrected-time-dependent-density-functional-theory.pdf |
60d6715de211336c59e0d20e | 10.26434/chemrxiv-2021-t45sg | Intermolecular 2+2 Imine-Olefin Photocycloadditions Enabled by Cu(I)-Alkene MLCT | 2+2 Photocycloadditions are idealized, convergent approaches to the construction of 4-membered heterocyclic rings, including azetidines. However, methods of direct excitation are limited by the unfavorable photophysical properties of imines and electronically unbiased alkenes. Here, we report copper-catalyzed photocycloadditions of non-conjugated imines and alkenes to produce a variety of substituted azetidines. Ligand design allows this base metal-catalyzed method to achieve 2+2 imine-olefin photocycloaddition via selective alkene activation through a coordination-MLCT pathway. | Daniel Flores; Michael Neville; Valerie Schmidt | Organic Chemistry; Catalysis; Organometallic Chemistry; Photocatalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d6715de211336c59e0d20e/original/intermolecular-2-2-imine-olefin-photocycloadditions-enabled-by-cu-i-alkene-mlct.pdf |
646fbb51e64f843f41c46490 | 10.26434/chemrxiv-2023-np05q-v2 | The Role of Emissions Size Distribution on the Efficacy of New Technologies to Reduce Methane Emissions from the Oil and Gas Sector | Methane emissions from oil and gas operations exhibit skewed distributions. New technologies such as aerial-based leak detection surveys promise cost-effective detection of large emitters. Recent policies such as the proposed US Environmental Protection Agency methane rule that allows the use of new technologies as part of conventional leak detection and repair (LDAR) require demonstration of equivalence with existing optical gas imaging (OGI)-based LDAR programs. In this work, we illustrate the impact of emission size distribution on the equivalency between OGI-based LDAR programs and that of alternative LDAR programs that use site-wide surveys. We find that emission size distribution compiled from aerial measurements across four oil and gas basins include significantly more emitters in the 1 – 10 kg/h and an order of magnitude lower average emission rate for large emitters compared to the emissions distribution in the EPA methane rule. As a result, equivalence between OGI-based surveys and site-wide screening may be achieved at lower site-wide survey frequencies when using technologies with detection threshold below 10 kg/h, compared to the EPA methane rule. However, equivalency cannot be achieved for site-wide screening with a detection threshold of 30 kg/h at any survey frequency because most emitters across most US oil and gas basins exhibit emission rates below 30 kg/h. We find that equivalence is a complex trade-off between the choice of technologies, design of hybrid LDAR programs, and survey frequency that can have more than one unique solution set. | Haojun Xia; Alan Strayer; Arvind Ravikumar | Energy; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646fbb51e64f843f41c46490/original/the-role-of-emissions-size-distribution-on-the-efficacy-of-new-technologies-to-reduce-methane-emissions-from-the-oil-and-gas-sector.pdf |
612bcbc4b817b44b6a0dbab1 | 10.26434/chemrxiv-2021-899lq | meso-Antracenyl-BODIPY dyad as a new photocatalyst in ATRA reac-tions | We demonstrate that because of the efficient generation of triplet excited state under UV or visible-light irradiation, meso-antracenyl-BODIPY donor-acceptor dyad can catalyze ATRA reactions between bromomalonate and alkenes. This finding paves the way for the design and application of the new type of heavy atom-free organic chromophores for photocatalysis. | Sara Abuhadba; Miu Tsuji; TOMOYASU MANI; Tatiana Esipova | Physical Chemistry; Organic Chemistry; Catalysis; Organocatalysis; Photocatalysis; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612bcbc4b817b44b6a0dbab1/original/meso-antracenyl-bodipy-dyad-as-a-new-photocatalyst-in-atra-reac-tions.pdf |
60c7499c337d6c0c88e27749 | 10.26434/chemrxiv.11879805.v2 | Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics | The speciation of calcium carbonate in water is important to the geochemistry of the world’s oceans and has ignited significant debate regarding the mechanism by which nucleation occurs. Here it is vital to be able to quantify the thermodynamics of ion pairing versus higher order association processes in order to distinguish between possible pathways. Given that it is experimentally challenging to quantify such species, here we determine the thermodynamics for ion pairing and multiple binding of calcium carbonate species using bias-enhanced molecular dynamics. In order to examine the uncertainties underlying these results, we have derived a new polarizable force field for both calcium carbonate and bicarbonate in water based on the AMOEBA model to compare against our earlier rigid-ion model, both of which are further benchmarked against ab initio molecular dynamics for the ion pair. Both force fields consistently indicate that the association of calcium carbonate ion pairs is stable, though with an equilibrium constant that is lower than for ion pairing itself. | Paolo Raiteri; Alicia Schuitemaker; Julian Gale | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7499c337d6c0c88e27749/original/ion-pairing-and-multiple-ion-binding-in-calcium-carbonate-solutions-based-on-a-polarizable-amoeba-force-field-and-ab-initio-molecular-dynamics.pdf |
671bd8a21fb27ce124989280 | 10.26434/chemrxiv-2024-n6bzp-v2 | Integration of gold nanoparticles into BiVO4/WO3 photoanodes via electrochromic activation of WO3 for enhanced photoelectrochemical water splitting | The development of highly efficient photoanodes is crucial for enhancing energy conversion efficiency in photoelectrochemical (PEC) water splitting. Herein, we report a facile approach to fabricating an Au/BiVO4/WO3 ternary junction that leverages the unique benefits of WO3 for efficient electron transport, BiVO4 for broadband light absorption, and Au nanoparticles (NPs) for surface plasmon effects. The BiVO4/WO3 binary junction was constructed by depositing a BiVO4 layer onto the surface of WO3 nanobricks via consecutive drop-casting. Au NPs were subsequently integrated into the BiVO4/WO3 structure through the electrochromic activation of WO3. The optimal BiVO4 loading for the highest-performing BiVO4/WO3 heterostructure and the light intensity dependence of photocurrent efficiency were also determined. Flatband potential measurements confirmed an appropriate band alignment that facilitates electron transfer from BiVO4 to WO3, while work function measurements corroborated the formation of a Schottky barrier between the incorporated Au NPs and BiVO4/WO3, improving charge separation. The best-performing Au NP-sensitized BiVO4/WO3 photoanode thin films exhibited a photocurrent density of 0.578 mA cm–2 at 1.23 V vs. RHE under AM 1.5G (1 sun) illumination and a maximum applied-bias photoconversion efficiency (ABPE) of 0.036% at 1.09 V vs. RHE, representing an enhancement factor of 12 and 2.3 compared to pristine BiVO4 and WO3 photoanodes, respectively. This study presents a promising and scalable route for fabricating noble metal-sensitized, metal oxide-based nanocomposite photoanodes for solar water splitting. | Ali Can Güler; Milan Masař; Michal Urbánek; Michal Machovský; Mohamed M. Elnagar; Radim Beranek; Ivo Kuřitka | Physical Chemistry; Nanoscience; Interfaces; Photochemistry (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671bd8a21fb27ce124989280/original/integration-of-gold-nanoparticles-into-bi-vo4-wo3-photoanodes-via-electrochromic-activation-of-wo3-for-enhanced-photoelectrochemical-water-splitting.pdf |
60c758e24c89196085ad4c98 | 10.26434/chemrxiv.14605392.v1 | Reverse Regioselectivity in Reductive Ring Opening of Epoxide Enabled by Zirconocene and Photoredox Catalysis | A ring opening of epoxide with zirconocene and photoredox catalysis has been developed. Compared to the ring opening methods with titanocene, the present protocol exhibited reverse regioselectivity to afford more-substituted alcohols via putative less-stable radicals. DFT calculations indicated that the observed regioselectivity could be explained by shifting the transition states to more reactant-like structures by changing the metal center of the metallocene catalyst. | Junichiro Yamaguchi; Eisuke Ota; Marina Hirao; Kazuhiro Aida; Aiko Funabashi; Natsuhiko Sugimura | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758e24c89196085ad4c98/original/reverse-regioselectivity-in-reductive-ring-opening-of-epoxide-enabled-by-zirconocene-and-photoredox-catalysis.pdf |
62fdb3de60751b5b1b086bd5 | 10.26434/chemrxiv-2022-m9fr1 | Revealing the thermal decomposition mechanism of RDX crystal by a neural network potential | A neural network potential (NNP) is developed to investigate the complex reaction dynamics of RDX thermal decomposition. Our NNP model is proven to possess good computational efficiency and retain the ab initio accuracy, which allows the investigation of the entire decomposition process of bulk RDX crystal from an atomic perspective. A series of molecular dynamics (MD) simulations are performed on the NNP to calculate the physical and chemical properties of the RDX crystal. The results show that the NNP can accurately describe the physical properties of RDX crystal, like cell parameters and equation of state. The simulations of RDX thermal decomposition reveal that the NNP could capture the evolution of species at the ab initio accuracy. The complex reaction network was established, and a reaction mechanism of RDX decomposition was provided. The N-N homolysis is the dominant channel, which cannot be observed in previous DFT studies of gas RDX. In addition, the H abstraction reaction by NO2 is found to be the critical pathway for NO and H2O formation, while the HONO elimination is relatively weak. The NNP gives an atomic insight into the complex reaction dynamics of RDX and can be extended to investigate the reaction mechanism of novel energetic materials. | Qingzhao Chu; Xiaoya Chang; Kang Ma; Xiaolong Fu; Dongping Chen | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Chemical Kinetics; Physical and Chemical Processes; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fdb3de60751b5b1b086bd5/original/revealing-the-thermal-decomposition-mechanism-of-rdx-crystal-by-a-neural-network-potential.pdf |
64363cf8a41dec1a56e860d4 | 10.26434/chemrxiv-2023-2w41l | Development of a Natural Product Optimization Strategy for inhibitors against the cell wall synthesis enzyme MraY, a promising antibacterial target | Optimization of natural products is often required to improve their drug-like properties for therapeutic use. However, chemical modifications of natural products are painstaking tasks due to complex synthetic processes, which is a bottleneck in advancing natural products to clinic. Here, we developed a strategy for a comprehensive in situ evaluation of the build-up library, which enables us to streamline the preparation of the analogue library and directly assess its biological activities. We applied this approach to a series of natural product inhibitors for MraY, an important target for the antibacterial development. Through construction and evaluation of the 686-compound library, we identified promising analogues that exhibit potent and broad-spectrum antibacterial activity against highly drug-resistant strains in vitro as well as in vivo in an acute thigh infection model Structures of the MraY-analogue complexes reveal distinct interaction patterns, suggesting that these analogues represent new types of MraY inhibitors with unique pharmacological profiles. | Kazuki Yamamoto; Toyotaka Sato; Aili Hao; Kenta Asao; Rintaro Kaguchi; Shintaro Kusaka; Ruddarraju Radhakrishnam Raju; Daichi Kazamori; Kiki Seo; Satoshi Takahashi; Motohiro Horiuchi; Shin-ichi Yokota; Seok-Yong Lee; Satochi Ichikawa | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Combinatorial Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64363cf8a41dec1a56e860d4/original/development-of-a-natural-product-optimization-strategy-for-inhibitors-against-the-cell-wall-synthesis-enzyme-mra-y-a-promising-antibacterial-target.pdf |
6694037fc9c6a5c07a481bee | 10.26434/chemrxiv-2024-smh4c | A multidimensional network-based approach to elucidate the molecular mechanism underlying tuberculosis and HIV coinfection | Tuberculosis (TB) and human immunodeficiency virus (HIV) coinfection is a severe global health challenge with high morbidity and mortality rates. In this study, we employed a novel bioinformatics approach to gain a comprehensive understanding of the state of TB/HIV coinfection. Using a multidimensional graph-based clustering methodology, we identified several key pathways associated with infectious and autoimmune diseases, immune and inflammatory responses, cardiovascular dysfunctions, and metabolic processes. We identified therapeutic biomarkers regulated by established therapeutic chemicals and developed robust machine learning-based quantitative structure-activity relationship (ML-QSAR) models to identify effective drug candidates. Our models successfully identified S5105 proanthocyanidin as a promising modulator of the key inflammatory biomarkers TNF, IL1B, and IFNG. Furthermore, we analyzed the influence of environmental factors, such as arsenic, air pollutants, and carbon monoxide, on the progression and occurrence of TB/HIV coinfection. Our findings revealed that these toxicants can trigger a cascade of inflammatory responses, leading to lung fibrosis and a cytokine storm that exacerbates immune dysregulation in coinfected individuals. Additionally, the impact of air pollutants on cardiovascular health and neurological complications, such as AIDS-Dementia Complex, adds to the complexity of managing TB/HIV coinfection. Again, with the findings of multidimensional graphs, we tried to elucidate the correlation between the air quality indices and the occurrence of TB/HIV coinfection. The models highlighted particulate matter (PM)10 and PM2.5 concentrations as critical predictors, indicating that poor air quality is positively correlated with higher rates of HIV testing among TB patients and an increased percentage of HIV-positive TB patients on antiretroviral therapy (ART). This suggests regions with worse air quality may have more comprehensive health monitoring. By identifying these associations, we can better understand how arsenic and air pollutants might contribute to immune deterioration and disease progression in TB and HIV patients. Thus, a multidimensional methodology can significantly enhance drug discovery and environmental toxicological efforts by integrating diverse data sources and analytical techniques to uncover complex interactions, identify potential therapeutic targets, and assess the impact of environmental toxins on health with greater precision. | Ashok Aspatwar; Ratul Bhowmik; Sagar Singh Shyamal; Rajarshi Ray; Fabrizio Carta; Claudiu T. Supuran; Seppo Parkkila | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6694037fc9c6a5c07a481bee/original/a-multidimensional-network-based-approach-to-elucidate-the-molecular-mechanism-underlying-tuberculosis-and-hiv-coinfection.pdf |
60c74ff1469df45dc1f44793 | 10.26434/chemrxiv.12964574.v1 | A Bridging Carbonyl of Unlikely Geometry: On the True Nature of the Technetium Complex [Tc2(μ-CO)2(CO)6(NC5H5)2] | The title compound was reported a decade ago by Zuhayra et al as the main product of the reaction of [Tc2(CO)10] with pyridine at room temperature. Chemical information, coupled to density functional theory calculations, have now been used to show that the "bridging carbonyls" then proposed from the crystallographic data most likely correspond to bridging hydroperoxide groups. <br /> | Miguel Ruiz; Daniel García-Vivó | Organometallic Compounds; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ff1469df45dc1f44793/original/a-bridging-carbonyl-of-unlikely-geometry-on-the-true-nature-of-the-technetium-complex-tc2-co-2-co-6-nc5h5-2.pdf |
60fb65db171fc75265b854c5 | 10.26434/chemrxiv-2021-h6ls0 | Electrically fueled active supramolecular materials | Fuel-driven dissipative supramolecular assemblies in biology, such as actin filaments and microtubules contribute to the formation of complex, dynamic structures in living organisms and give rise to emergent functions such as motility, homeostasis, self-healing, and camouflage. Several synthetic dissipative supramolecular materials have been created using chemicals or light as fuel, with the goal of furthering our understanding of biological systems and creating synthetic materials that have life-like dynamic properties. However, electrical energy, one of the most common energy sources, has remained mostly unexplored for such purposes. Here we demonstrate the use of electrically fueled dissipative assembly as a new platform for creating active supramolecular materials. Through an electrochemical redox reaction network operating in mild aqueous buffers, a transient and highly active supramolecular assembly based on a redox-sensitive cysteine derivative is achieved by applying an electric potential. The dissipative self-assembly as well as its emergent properties can be spatiotemporally controlled by modulation of electrical signals on patterned microelectrodes. Using electrical energy as a readily available and clean fuel, we are able to create dissipative supramolecular materials rapidly (in seconds to minutes) and repetitively under mild conditions with directional and spatiotemporal control. As electronic signals are the default information carriers in modern technology, the described approach offers a promising opportunity to integrate active materials into electronic devices for bioelectronics applications. | Zhibin Guan; Serxho Selmani; Eric Schwartz; Justin Mulvey; Hong Wei; Adam Grosvirt-Dramen; Wyeth Gibson; Allon Hochbaum; Joseph Patterson; Regina Ragan | Materials Science; Aggregates and Assemblies; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fb65db171fc75265b854c5/original/electrically-fueled-active-supramolecular-materials.pdf |
66fc8a1751558a15efc1a501 | 10.26434/chemrxiv-2024-h37x4-v2 | Discrete and mixed-variable experimental design with surrogate-based approach | Experimental design plays an important role in efficiently acquiring informative data for system characterization and deriving robust conclusions under resource limitations. Recent advancements in high-throughput experimentation coupled with machine learning have notably improved experimental procedures. While Bayesian optimization (BO) has undeniably revolutionized the landscape of optimization in experimental design, especially in the chemical domain, it is important to recognize the role of other surrogate-based approaches in conventional chemistry optimization problems. This is particularly relevant for chemical problems involving mixed-variable design space with mixed-variable physical constraints, where conventional BO approaches struggle to obtain feasible samples during the acquisition step while maintaining exploration capability. In this paper, we demonstrate that integrating mixed-integer optimization strategies is one way to address these challenges effectively. Specifically, we propose the utilization of mixed-integer surrogates and acquisition functions—methods that offer inherent compatibility with problems with discrete and mixed-variable design space. This work focuses on Piecewise Affine Surrogate-based optimization (PWAS), a surrogate model capable of handling medium-sized mixed-variable problems (up to around 100 variables after encoding) subject to known linear constraints. We demonstrate the effectiveness of this approach in optimizing experimental planning through three case studies. By benchmarking PWAS against state-of-the-art optimization algorithms, including genetic algorithms and BO variants, we offer insights into the practical applicability of mixed-integer surrogates, with emphasis on problems subject to known discrete/mixed-variable linear constraints. | Mengjia Zhu; Austin Mroz; Lingfeng Gui; Kim Jelfs; Alberto Bemporad; Ehecatl Antonio del Río Chanona; Ye Seol Lee | Biological and Medicinal Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc8a1751558a15efc1a501/original/discrete-and-mixed-variable-experimental-design-with-surrogate-based-approach.pdf |
60c75738702a9b6ae818ca2c | 10.26434/chemrxiv.14376899.v1 | Quantifying the Impact of Parametric Uncertainty on Automatic Mechanism Generation for CO2 Hydrogenation on Ni(111) | Automatic mechanism generation is used to determine mechanisms for the CO2
hydrogenation on Ni(111) in a two-stage process, while considering the uncertainty
in energetic parameters systematically. In a coarse stage, all the possible chemistry is
explored with gas-phase products down to the ppb level, while a refined stage discovers
the core methanation submechanism. 5,000 unique mechanisms were generated, which
contain minor perturbations in all parameters. Global uncertainty assessment, global
sensitivity analysis, and degree of rate control analysis are performed to study the effect
1
of this parametric uncertainty on the microkinetic model predictions. Comparison of
the model predictions with experimental data on a Ni/SiO2
catalyst find a feasible set
of microkinetic mechanisms that are in quantitative agreement with the measured data,
without relying on explicit parameter optimization. Global uncertainty and sensitivity
analyses provide tools to determine the pathways and key factors that control the
methanation activity within the parameter space. Together, these methods reveal that
the degree of rate control approach can be misleading if parametric uncertainty is not
considered. The procedure of considering uncertainties in the automated mechanism
generation is not unique to CO2 methanation and can be easily extended to other
challenging heterogeneously catalyzed reactions<br /> | Bjarne Kreitz; C. Franklin Goldsmith; Richard West; Emily Mazeau; Katrin Blondal; Gregor Wehinger; Thomas Turek; Khachik Sargsyan | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75738702a9b6ae818ca2c/original/quantifying-the-impact-of-parametric-uncertainty-on-automatic-mechanism-generation-for-co2-hydrogenation-on-ni-111.pdf |
60c73ed8469df4d964f42931 | 10.26434/chemrxiv.7122089.v1 | Benchmarking Computational Alchemy for Carbide, Nitride, and Oxide Catalysts | <p>Kohn-Sham density functional theory (DFT)-based searches for hypothetical catalysts are too computationally demanding for wide searches through diverse materials space. Our group has been critically evaluating the performance of an alternative computational method called computational alchemy. An advantage with this method is that it effectively brings no computational cost once a single DFT reference calculation is made. Extending from our 2017 publication in <i>J. Phys. Chem. Lett </i>(DOI: 10.1021/acs.jpclett.7b01974) that tested computational alchemy for transition metal alloys, we now assess the accuracy of computational alchemy schemes on carbides, nitrides, and oxides. </p> | Charles D. Griego; Karthikeyan Saravanan; John Keith | Catalysts; High-throughput Screening; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed8469df4d964f42931/original/benchmarking-computational-alchemy-for-carbide-nitride-and-oxide-catalysts.pdf |
60c74706702a9b2c8d18ad0d | 10.26434/chemrxiv.11481834.v1 | Cupin Variants as Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes | Cupin superfamily proteins (TM1459) work as a macromolecular ligand framework with a double-stranded beta-barrel structure ligating to a Cu ion through histidine side chains. Variegating the first coordination sphere of TM1459 revealed that H52A and H54A/H58A mutants effectively catalyzed the diastereo- and enantio-selective Michael addition reaction of nitroalkanes to an α,β-unsaturated ketone. Moreover, in silico substrate docking signified C106N and F104W single-point mutations, which inverted the diastereoselectivity of H52A and further improved the stereoselectivity of H54A/H58A, respectively. | Nobutaka Fujieda; Miho Yuasa; Yosuke Nishikawa; Genji Kurisu; Shinobu Itoh; Haruna Ichihashi | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74706702a9b2c8d18ad0d/original/cupin-variants-as-macromolecular-ligand-library-for-stereoselective-michael-addition-of-nitroalkanes.pdf |
66f46e8412ff75c3a1770f63 | 10.26434/chemrxiv-2024-z7nw5 | Effect of Confinement on the Translational Diffusivity of Small Dye Molecules in Thin Polystyrene Films and Its Connection to Tg-Confinement and Fragility-Confinement Effects
| Using fluorescence, we study the impact of nanoscale confinement on the translational diffusivity (D) of trace levels of a small-molecule dye, 9,10-bis(phenylethynyl)anthracene (BPEA), in supported polystyrene (PS) films via Förster resonance energy transfer (FRET). Reductions in BPEA diffusivity are observed in films thinner than ~200 nm, with D decreasing by 80–90% in 100-nm-thick films compared to bulk. The activation energy of BPEA diffusivity increases from ~210 kJ/mol in bulk films to ~370 kJ/mol in 130-nm-thick films. BPEA exhibits a greater diffusivity-confinement effect than a larger dye, decacyclene, in terms of both the length scale at which confinement effects become evident and the percentage reduction in diffusivity. For both BPEA and decacyclene, the diffusivity-confinement effect in PS films occurs at a length scale much larger than that for the glass transition temperature (Tg)-confinement effect and somewhat larger than that for the fragility-confinement effect. This difference in confinement-effect length scales can be rationalized as follows: small-molecule dye diffusivity relates predominantly to short times in the α-relaxation distribution, whereas Tg relates to long times in the α-relaxation distribution, and fragility reflects the overall breadth of this relaxation time distribution. If confinement results in a narrower relaxation time distribution in PS with the short-time relaxations being shifted to higher times and the longest-time relaxation regimes being shifted to lower times, then Tg, diffusivity, and fragility all decrease at sufficient levels of confinement. If the narrowing with confinement begins with the shortest relaxation time regimes, then fragility and small-molecule dye diffusivity are influenced by confinement at larger length scales than Tg. | Tian Lan; Logan Fenimore; John Torkelson | Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Coating Materials; Dyes and Chromophores; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f46e8412ff75c3a1770f63/original/effect-of-confinement-on-the-translational-diffusivity-of-small-dye-molecules-in-thin-polystyrene-films-and-its-connection-to-tg-confinement-and-fragility-confinement-effects.pdf |
659c3233e9ebbb4db9b4c9be | 10.26434/chemrxiv-2024-slhjp | Activation of alkyl hydroperoxides by manganese com
plexes of tmtacn for initiation of radical polymerisation
of alkenes | The activation of alkyl hydroperoxides to generate radicals is a key step in the initiation of radical polymerisations in many industrial applications, not least protective coatings. Cobalt soaps are highly effective catalysts under ambient conditions but viable alternatives based on less scarce catalysts are desirable, with especially iron and manganese catalysts showing potential. Manganese complexes of the ligand N,N',N"-trimethyl-1,4,7-triazacyclononane (tmtacn) are long established as catalysts for organic oxidations with H2O2, however their reactivity with alkyl hydroperoxides is less studied especially in low- or apolar solvents. Here we show that this family of complexes can be employed as catalysts for the decomposition of alkyl hydroperoxides in apolar solvents such as styrene/methyl methacrylate mixtures and resins based on styrene/bisphenol-A based diglycidyl ether bismethacrylate (BADGE-MA). The progress of alkene polymerisation in crosslinking resins is followed by Raman spectroscopy to establish its dependence on the oxidation state of the manganese catalyst used, as gelation time and onset of autoacceleration are of particular interest for many applications. We show, through reaction progress monitoring with UV/vis absorption and Raman spectroscopy, that the stability of the manganese complexes in the resin mixtures has a substantial effect on curing progress and that the oxidation state of the resting state of the catalyst is most likely Mn(II), in contrast to reactions with H2O2 as oxidant in which the oxidation state of the resting state of catalyst is Mn(III). Manganese complexes of tmtacn are shown to be capable initiators of alkene radical polymerisations, and their rich coordination and redox chemistry means that resin curing kinetics can potentially be tuned more readily than with cobalt soaps. | Linda E. Eijsink; Andy S. Sardjan; Esther G. Sinnema; Hugo den Besten; Yanrong Zhang; Ronald Hage; Keimpe van den Berg; Jitte Flapper; Ben Feringa; Wesley Browne | Inorganic Chemistry; Polymer Science; Organic Polymers; Kinetics and Mechanism - Inorganic Reactions; Spectroscopy (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659c3233e9ebbb4db9b4c9be/original/activation-of-alkyl-hydroperoxides-by-manganese-com-plexes-of-tmtacn-for-initiation-of-radical-polymerisation-of-alkenes.pdf |
60c73d4f0f50db0ccf39544f | 10.26434/chemrxiv.5579716.v1 | Atomic Level Mechanism of the White Phosphorous Demolition by Di-iodine | A detailed mechanism of the I2-induced transformation of white phosphorus into PI3 emerges from a DFT analysis. The multi-step process implies at any stage one P P and two I I bond cleavages, associated to the formation of two P I bonds plus an in situ generated brand new I2 molecule. Significant electron transfer between atoms is observed at any step, but the reactions better define as concerted rather than redox. Along the steepest descent to the product, no significant barrier is encountered except for the very first P4 activation, which costs +14.6 kcal mol-1. At the atomic level, one first I2 molecule, a typical mild oxidant, is first involved in a linear halogen bonding interaction (XB) with one P donor, while its terminal I atom is engaged in an additional XB adduct with a second I2. Significant electron transfer through the combined diatomics allows the external I atom of the dangling I3 grouping to convey electrons into the * level of one P P bond with its consequent cleavage. This implies at some point the appearance of a six-membered ring, which alternative switches its bonding and no-bonding interactions. The final transformation of the P2I4 diphosphine into two PI3 phosphines is enlightening also for the specific role of the I substituents. In fact, it is proved that an organo-diphosphine analogue hardly undergoes the separation of two phosphines, as reported in literature. This is attributable to the particularly high donor power of the carbo-substituted P atoms, which prevents the concertedness of the reaction but favors charge separation in an unreactive ion pair. <br /> | Carlo Mealli; Andrea Ienco; Maurizio Peruzzini; Gabriele Manca | Bonding; Main Group Chemistry (Inorg.); Reaction (Inorg.); Small Molecule Activation (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2017-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4f0f50db0ccf39544f/original/atomic-level-mechanism-of-the-white-phosphorous-demolition-by-di-iodine.pdf |
60e49b01b9b601309721e6fd | 10.26434/chemrxiv-2021-sg66n | Direct and indirect photodegradation of atrazine and S-metolachlor in agriculturally impacted surface water and associated C and N isotope fractionation | Knowledge of direct and indirect photodegradation of pesticides and associated isotope fractionation can help to assess pesticide degradation in surface waters. Here, we investigated carbon (C) and nitrogen (N) isotope fractionation during direct and indirect photodegradation of the herbicides atrazine and S-metolachlor in synthetic water, mimicking agriculturally impacted surface waters containing nitrates (20 mg L–1) and dissolved organic matter (DOM, 5.4 mgC L–1). Atrazine and S-metolachlor were quickly photodegraded by both direct and indirect pathways (half-lives <5 and <7 days, respectively). DOM slowed down photodegradation while nitrates increased degradation rates. The analysis of transformation products showed that oxidation mediated by hydroxyl radicals (HO•) predominates during indirect photodegradation. UV light (254 nm) caused significant C and N isotope fractionation, yielding isotope enrichment factors ε_C = 2.7 ± 0.3 and 0.8 ± 0.1‰, and ε_N = 2.4 ± 0.3 and –2.6 ± 0.7‰ for atrazine and S-metolachlor, respectively. In contrast, photodegradation under simulated sunlight led to negligible C and slight N isotope fractionation, indicating the influence of the radiation wavelength on the direct photodegradation-induced isotope fractionation. Altogether, this study highlights the relevance of using simulated sunlight to evaluate photodegradation pathways in the environment and the potential of CSIA to distinghuish photodegradation from other dissipation pathways in surface waters. | Guillaume Drouin; Boris Droz; Frank Leresche; Sylvain Payraudeau; Jeremy Masbou; Gwenaël Imfeld | Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e49b01b9b601309721e6fd/original/direct-and-indirect-photodegradation-of-atrazine-and-s-metolachlor-in-agriculturally-impacted-surface-water-and-associated-c-and-n-isotope-fractionation.pdf |
60c758fe4c89198326ad4cc7 | 10.26434/chemrxiv.14622915.v1 | Role of Lewis Acids in Preventing the Degradation of Dithioester-Dormant Species in the RAFT Polymerization of Acrylamides in Methanol to Enable the Successful Dual Control of Molecular Weight and Tacticity | Reversible
addition-fragmentation chain transfer (RAFT) polymerization of acrylamide in
methanol using dithioester RAFT chain-transfer agents was unsuccessful
due to degradation of the end group. However, this degradation was completely
suppressed by the addition of rare-earth metal triflates (RMTs). As RMTs are
effective for the stereoselective polymerization of acrylamides, RAFT
polymerization in the presence of RMTs afforded the corresponding
poly(acrylamide)s with controlled molecular weight and tacticity. The conditions allowed the synthesis of high-molecular-weight
polyacrylamides with molecular weights up to 168,000, low
dispersity (<1.5) and high tacticity (90% <i>meso</i> diad selectivity). The
degradation mechanism initiated by nucleophilic attack of acrylamide on the
dithioester group was experimentally clarified for the first time. As RMT is a
Lewis acid, its coordination to the amide group of acrylamide reduces its
nucleophilicity. | Yuji Imamura; Shigeru Yamago | Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758fe4c89198326ad4cc7/original/role-of-lewis-acids-in-preventing-the-degradation-of-dithioester-dormant-species-in-the-raft-polymerization-of-acrylamides-in-methanol-to-enable-the-successful-dual-control-of-molecular-weight-and-tacticity.pdf |
632250f8173b5de837fdbe00 | 10.26434/chemrxiv-2022-x694w | Roadmap to Pharmaceutically Relevant Reactivity Models Leveraging High-Throughput Experimentation | The merger of High-Throughput Experimentation (HTE) and data science presents an opportunity to both accelerate and inspire innovations in synthetic chemistry. Similarly, developments in machine learning (ML) have enabled the distillation of large and complex data sets into predictive models capable of generalizing patterns in the data. However, efforts to merge HTE with ML remain constrained by a few reported datasets with limited structural diversity and corresponding trained models that do not extrapolate well to substrates beyond the training set. Herein, we detail the first ML models for Pd-catalyzed C–N couplings using pharmaceutically relevant structurally diverse large data sets (~ 5000 unique products) generated using nanomole scale compatible chemistry. Careful consideration is given to both the diversity of the data set and accurate model predictions for substrates bearing features beyond those present in the training set. The structural diversity in the data set is enabled by leveraging the Merck & Co., Inc Building Block Collection with an initial focus on C–N coupling using secondary amines. The large dataset enables the systematic evaluation of model performance using five different data-splitting strategies. These five splits are carefully designed to evaluate the model’s ability to extrapolate beyond the substrates in the training set. The accuracy of classification models built with a lens toward application to medicinal chemistry campaigns exceeded the baseline precision-recall by 25-67% depending on the splitting strategy. These results would manifest as significant enrichment of successful C–N couplings using the hits recommended by the models. In addition, the accuracy of the best models for each of the five splits ranges between 70-87% suggesting excellent overall predictivity of the models even for completely unseen substrates. | Jessica Xu; Dipannita Kalyani; Thomas Struble; Spencer Dreher; Shane Krska; Stephen L. Buchwald; Klavs F. Jensen | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Machine Learning; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632250f8173b5de837fdbe00/original/roadmap-to-pharmaceutically-relevant-reactivity-models-leveraging-high-throughput-experimentation.pdf |
62d915037aab5823e9c9725c | 10.26434/chemrxiv-2022-vkr3w | The Impact of COVID-19 Outbreak on the Digital Teaching and Learning Process in Indian Higher Education Institutions | The year 2020 was tagged by transformation, adaptation, and evolvement in Higher Education Institutions (HEIs). The rapid shift to online learning during the pandemic has greatly enhanced the e-learning experience for both teachers and students. For students to remain involved and active in classroom instruction, custom-made tools/learning management systems are useful. The pandemic has shown teachers, students how to use various interactive learning technologies. In new normal situations, teachers and students should be encouraged to continue on-line tools to develop teaching and learning process.
Keywords: COVID Outbreak, online education, teaching learning process, higher education institutes, e-learning, blended learning. | Kiran Patil; Varsha Patil | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d915037aab5823e9c9725c/original/the-impact-of-covid-19-outbreak-on-the-digital-teaching-and-learning-process-in-indian-higher-education-institutions.pdf |
642ab01e16782ec9e64707c5 | 10.26434/chemrxiv-2023-kld71 | Early stage growth process of dinaphtho[2, 3-b:2', 3'-f]thieno[3, 2-b]thiophene (DNTT) thin film | Early stage growth process of Dinaphtho[2, 3-b:2', 3'-f]thieno[3, 2-b]thiophenes (DNTTs) thin film was investigated using grazing incidence X-ray diffraction (GIXD) and surface morphology analysis using atomic force microscopy (AFM). The thin film growth conditions were controlled by the slow deposition method. The vertical orientation of DNTT was confirmed from the first layer growth by GIXD. The morphologies of first layer grains were universal in the growth rate range of 0.155 ML/min - 0.017 ML/min. In addition, the dependence of the nuclei density on the deposition flow rate indicates that the number of molecules required for nucleation is 2 molecules (dimers). This result indicates that fewer molecules are sufficient for nucleation in the case of DNTT compared to the pentacene thin film growth on SiO2. | Nobuya HIROSHIBA; Yuta Kawano; Richard Ongko; Ryosuke Matsubara; Atsushi Kubono; Hirotaka Kojima; Kazuto Koike | Physical Chemistry; Materials Science; Thin Films; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642ab01e16782ec9e64707c5/original/early-stage-growth-process-of-dinaphtho-2-3-b-2-3-f-thieno-3-2-b-thiophene-dntt-thin-film.pdf |
60c7592dbb8c1a05f33dcb81 | 10.26434/chemrxiv.14639778.v1 | Directed Markovnikov Hydroarylation and Hydroalkenylation of Alkenes Under Nickel Catalysis | We report a full account of our research on nickel-catalyzed Markovnikov-selective hydroarylation and hydroalkenylation of non-conjugated alkenes, which has yielded a toolkit of methods that proceed under mild conditions with alkenyl sulfonamide, ketone, and amide substrates. Regioselectivity is controlled through catalyst coordination to the native Lewis basic functional groups contained within these substrates. To maximize product yield, reaction conditions were fine-tuned for each substrate class, reflecting the different coordination properties of the directing functionality. Detailed kinetic and computational studies shed light on the mechanism of this family of transformations, pointing to transmetalation as the turnover-limiting step. | Zi-Qi Li; Omar Apolinar; Ruohan Deng; Keary Engle | Organic Synthesis and Reactions; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7592dbb8c1a05f33dcb81/original/directed-markovnikov-hydroarylation-and-hydroalkenylation-of-alkenes-under-nickel-catalysis.pdf |
66b8ac96c9c6a5c07ae597d2 | 10.26434/chemrxiv-2024-j0r6p | QM/MM simulations distinguish insulin-regulated aminopeptidase substrate (oxytocin) and inhibitor (angiotensin IV) and reveal determinants of activity and inhibition | Insulin-regulated aminopeptidase (IRAP) is a zinc-dependent metalloenzyme involved in the regulation of glucose metabolism and insulin sensitivity identified as a novel target for combating diabetes-induced diseases. IRAP’s catalytic domain catalyzes the N-terminal peptide bond hydrolysis of the natural substrate oxytocin, a neuroactive pep-tide linked to improved cognition and other elemental brain functions. Angiotensin IV and similar peptides are recognized as cognitive enhancers due to their ability to competitively inhibit proteolytic activity of IRAP, reducing the degradation of natural neuropeptides. Despite a very similar binding complex between the substrate and the inhibitor with IRAP, especially around the scissile bond, it is unclear why the enzyme metabolizes oxytocin but does not efficiently degrade angiotensin IV. We employed enhanced sampling QM/MM molecular dynamics simulations to explore free energy landscapes for reaction of these two peptides in IRAP. A significantly higher energy barrier for the formation of the oxyanion tetrahedral intermediate (TI) and higher overall barrier for the peptide cleavage was observed for the reaction of angiotensin IV. Electronic structure analysis (NBO and NCI) revealed the reasons for different reactivity, including stabilization of the on the sigma hole of the N-terminus disulfide in oxytocin by the hybridizing lone pair of the scissile peptide nitrogen. The interplay between weak non-covalent spodium bond and strong bi-dentate coordination of the catalytic Zn2+ by angiotensin IV caused larger deviation of valine C-Cα-Cβ angle from the ideal tetrahedral, which destabilizes the TI. The results emphasise the importance of analysing dynamics, interactions and electronic properties of reaction intermediates and transition states in enzymes, and have implications for the de-sign and development of IRAP inhibitors for the treatment of memory disorders, neurodegenerative diseases, and diabetes. | Marko Hanzevacki; Rebecca M. Twidale; Eric J. M. Lang; Will Gerrard; David W. Wright; Vid Stojevic; Adrian J. Mulholland | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Chemical Biology; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b8ac96c9c6a5c07ae597d2/original/qm-mm-simulations-distinguish-insulin-regulated-aminopeptidase-substrate-oxytocin-and-inhibitor-angiotensin-iv-and-reveal-determinants-of-activity-and-inhibition.pdf |
622639bac3e9da2aaf83806b | 10.26434/chemrxiv-2022-l76sc | Development of a chiral SFC-MS/MS and reversed-phase LC-MS/MS platform for the quantitative metabolic profiling of octadecanoid oxylipins | Octadecanoids are broadly defined as oxylipins (i.e., lipid mediators) derived from 18-carbon fatty acids. In contrast to the well-studied eicosanoids, there is a lack of analytical methods for octadecanoids, hampering further investigations in the field. We developed an integrated workflow combining chiral separation by supercritical fluid chromatography (SFC) and reversed-phase liquid chromatography (LC) coupled to tandem-MS detection for quantification of a broad panel of octadecanoids. The platform included 70 custom-synthesized analytical and internal standards to extend the coverage of the octadecanoid synthetic pathways. A total of 103 octadecanoids could be separated by chiral SFC and complex enantioseparations could be performed in <13 minutes, while the achiral LC method separated 67 species in 13.5 minutes. The LC method provided a robust complementary approach with greater sensitivity relative to the SFC method. Both methods were validated in solvent and surrogate matrix in terms of linearity, lower limits of quantification (LLOQ), recovery, accuracy, precision, and matrix effects. Instrumental linearity was good for both methods (R2>0.995) and LLOQ ranged from 0.03-6.00 ng/mL for SFC and 0.01-1.25 ng/mL for LC. The average accuracy in solvent and surrogate matrix ranged from 89-109% in SFC and from 106-220% in LC, whereas coefficients of variation (CV) were <14% (at medium and high concentration) and 26% (at low concentration). Validation in surrogate matrix showed negligible matrix effects (<16% for all analytes) and average recoveries ranged from 71-83%. The combined methods provide a platform to investigate the biological activity of octadecanoids and expand our understanding of these little studied compounds. | Alessandro Quaranta; Benedikt Zöhrer; Johanna Revol-Cavalier; Kurt Benkestock; Laurence Balas; Camille Oger; Gregory S. Keyes; Åsa M. Wheelock; Thierry Durand; Jean-Marie Galano; Christopher E. Ramsden; Mats Hamberg; Craig E. Wheelock | Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622639bac3e9da2aaf83806b/original/development-of-a-chiral-sfc-ms-ms-and-reversed-phase-lc-ms-ms-platform-for-the-quantitative-metabolic-profiling-of-octadecanoid-oxylipins.pdf |
64f9624b79853bbd784381c4 | 10.26434/chemrxiv-2023-b8pxv | Comparison of nanozymatic behavior of protein-protected gold and SiO2@gold nanoparticles | Herein, the nanozymatic behavior of protein-protected gold and SiO2@gold nanoparticles were evaluated and their results compared with each other. The results showed that both protein-protected gold and SiO2@gold nanoparticles reveal intrinsic peroxidase-like activity. Hence, to precise comparison of nanozymatic behavior of these nanozymes, the kinetic studies were performed using the Michaelis–Menten steady-state kinetics model and the velocity and affinity factors were calculated for both nanozyme and then utilized as a reliable way for comparison of nanozymatic behavior of these nanozymes. The results showed that the Vmax of protein-protected gold nanoparticles was 12.0-fold higher than that of SiO2@gold nanoparticles, revealing that the catalytic efficiency of protein-protected gold nanoparticles is 12.0-fold higher than SiO2@AuNPs nanocomposite. Besides, the Km value of SiO2@gold nanoparticles was 2-order higher than that of protein-protected gold nanoparticles, indicating that the substrate affinity toward protein-protected gold nanoparticles is 2.0-order higher than the SiO2@gold nanoparticles. Based on the results of this work it can be concluded that protein-protected gold nanoparticles are more efficient nanozymes than SiO2@gold nanoparticles. | Saeed Reza Hormozi Jangi | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f9624b79853bbd784381c4/original/comparison-of-nanozymatic-behavior-of-protein-protected-gold-and-si-o2-gold-nanoparticles.pdf |
60c743ed0f50db6394395fdc | 10.26434/chemrxiv.9695978.v1 | Structural Characterisation of Amorphous Solid Dispersions via Metropolis Matrix Factorisation of Pair Distribution Function Data | We measure the X-ray pair distribution functions (PDFs) of a series of felodipine:copovidone amorphous solid dispersions. Using a newly-developed Metropolis Matrix Factorisation (MMF) algorithm we extract from these data the PDF of the amorphous felodipine component in isolation. Our MMF analysis allows quantification of the degree of drug crystallinity in each sample, and structural characterisation of the amorphous drug <i>via</i>its PDF. Comparison with atomistic simulations reveals that the (in)accessibility of conformational rotamers distinguishes amorphous and crystalline felodipine, in turn suggesting design routes for stabilising the amorphous form. We discuss the conceptual importance of our results in the context of characterising not only amorphous pharmaceuticals, but complex mixtures in general. | Harry Geddes; Helen Blade; James McCabe; Leslie
P. Hughes; Andrew Goodwin | Structure; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ed0f50db6394395fdc/original/structural-characterisation-of-amorphous-solid-dispersions-via-metropolis-matrix-factorisation-of-pair-distribution-function-data.pdf |
60cb26d1afe54fb617a39ed7 | 10.26434/chemrxiv-2021-4x2n8 | Revisiting the structure of calcined and hydrated AlPO-11 with DFT-based molecular dynamics simulations
| Published crystal structures of the AEL-type aluminophosphate AlPO-11 in its calcined form (space group Ima2) show some peculiar features, such as unusually short Al−O and P−O bonds and near-linear Al−O−P angles. Although experimental evidence for the presence of dynamic disorder was presented, the nature of the associated distortions remained unresolved. In this study, ab initio molecular dynamics (AIMD) calculations in the framework of density functional theory (DFT) were employed to study the dynamic behaviour of this zeotype. At 100 K, static local distortions that break the Ima2 symmetry are present in the time-averaged structures computed from the AIMD trajectories. At 300 and 500 K, the time-averaged structures approach Ima2 symmetry. Although shortened Al−O and P−O bonds and near-linear Al−O−P angles were found in the average structures, an analysis of radial and angular distribution functions confirmed their absence in the instantaneous structures. This deviation is due to a precession-like motion of some oxygen atoms around the Al−P connection line, which moves their time-averaged positions closer to the connection line. In hydrated AlPO-11, some of the water molecules are coordinated to framework Al atoms, leading to an octahedral coordination of 1/5 of the Al sites. DFT optimisations and AIMD simulations on partially hydrated models delivered evidence for an adsorption at the Al1 site. No dynamic disorder was observed for the hydrated form. | Michael Fischer | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Structure; Materials Chemistry; Crystallography | CC BY NC 4.0 | CHEMRXIV | 2021-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cb26d1afe54fb617a39ed7/original/revisiting-the-structure-of-calcined-and-hydrated-al-po-11-with-dft-based-molecular-dynamics-simulations.pdf |
60c755e19abda2372ef8e458 | 10.26434/chemrxiv.14176718.v1 | Synthesis, Characterization and Thermal Study of Divalent Germanium, Tin and Lead Triazenides for Atomic Layer Deposition | <p>The number of M–N bonded divalent group 14 precursors suitable for
atomic layer deposition is limited, in particular for Ge and Pb. A majority of
the reported precursors are dicoordinated, with the only tetracoordinated example
being the Sn(II) amidinate. No such Ge(II) and Pb(II) compounds have been
demonstrated. Herein, we present tetracoordinated Ge(II), Sn(II) and Pb(II) complexes
bearing two sets of the bidentate 1,3-di-<i>tert</i>-butyl triazenide ligands. These
compounds are highly volatile and show ideal behavior by thermogravimetric
analysis. However, they have unusual thermal properties and exhibit instability
during sublimation. Interestingly, the instability is not only temperature
dependent but also facilitated by reduced pressure. Using quantum-chemical
density functional theory, a gas-phase decomposition pathway was mapped out.
The pathway account for the unusual thermal behavior of the compounds and is
supported by electron impact mass spectrometry data.</p> | Rouzbeh Samii; David Zanders; Anton Fransson; Goran Bačić; Sean Barry; Lars Ojamäe; Vadim Kessler; Henrik Pedersen; Nathan O'Brien | Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry; Ligands (Inorg.); Main Group Chemistry (Inorg.); Organometallic Compounds; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e19abda2372ef8e458/original/synthesis-characterization-and-thermal-study-of-divalent-germanium-tin-and-lead-triazenides-for-atomic-layer-deposition.pdf |
61678ab08b620d56ee4ec257 | 10.26434/chemrxiv-2021-8f5ws | An Expedited Phenotypic Approach Towards Organic Reaction Generality | Reaction generality is crucial in determining the overall impact and usefulness of organic synthetic methods. In contrast, contemporary generalization processes seem unable to meet the growing demand for robust methodology. We sought to develop an accelerated approach towards achieving generality, inspired by phenotypic screening, that rapidly expands the scope and utility of synthetic methods. This approach was validated by example of the metallaphotoredox decarboxylative arylation, resulting in the discovery of a novel additive that overcomes many lingering limitations of this method and has significant mechanistic implications for nickel-catalyzed cross couplings in general. | Cesar N. Prieto Kullmer; Jacob A. Kautzky; Shane W. Krska; Timothy Nowak; Spencer D. Dreher; David W. C. MacMillan | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61678ab08b620d56ee4ec257/original/an-expedited-phenotypic-approach-towards-organic-reaction-generality.pdf |
65bc6c3c9138d2316140c111 | 10.26434/chemrxiv-2024-trwx9 | Rapid Production of Native and Mirror-Image Tumor Necrosis Factor-α through the Synergy of Automated Flow Peptide Synthesis and Native Chemical Ligation | Tumor necrosis factor-alpha (TNF-α) plays a central role in immune response regulation. Due to the correlation between elevated TNF-α production and a range of diseases, inhibiting the interaction of this protein with its native receptors as a therapeutic avenue has been thoroughly explored. Despite advancements in the development of lead TNF-α inhibitors, concerns remain regarding immunogenicity and loss of activity in vivo. To facilitate the discovery of stable and less immunogenic therapeutic modalities, we describe a rapid synthesis protocol that capitalizes on the synergy between automated fast-flow peptide synthesis (AFPS) technology, native chemical ligation (NCL), and high-throughput screening of folding conditions to arrive at functional synthetic proteins, native and mirror-image TNF-α. Specifically, an NCL reaction using only two fragments that were readily produced by AFPS afforded synthetic L- and D-TNF-α in milligram quantities (up to 5.5 mg, ~28% yield). Subsequent oxidation and dialysis led to folded TNF-α homotrimers, exhibiting analogous characteristics to the recombinant TNF-α. Overall, this innovative approach can serve as a general protocol for accessing proteins that are intractable by modern protein synthesis methods, therefore enabling the development of novel and stable therapeutics. | Ahmet Yesilcimen; Alex J. Callahan; Tara L. Travaline; Satish Gandhesiri; Olena S. Tokareva; Andrei Loas; John H. McGee; Bradley L. Pentelute | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bc6c3c9138d2316140c111/original/rapid-production-of-native-and-mirror-image-tumor-necrosis-factor-through-the-synergy-of-automated-flow-peptide-synthesis-and-native-chemical-ligation.pdf |
60c7415fbb8c1a5f5f3d9f08 | 10.26434/chemrxiv.8009720.v1 | Hydrogen Atom Transfer Reaction Free Energy as a Predictor of Abiotic Nitroaromatic Reduction Rate Constants: A Comprehensive Analysis | <div>A linear free energy model is presented that predicts the second order rate constant for the abiotic reduction of nitroaromatic compounds (NACs). For this situation previously presented models use the one electron reduction potential of the NAC reaction. If such value is not available, it has been has been proposed that it could be computed directly or estimated from the electron affinity (EA). The model proposed herein uses the Gibbs free energy of the hydrogen atom transfer (HAT) as the parameter in the linear free energy model. Both models employ quantum chemical computations for the required thermodynamic parameters. The available and proposed models are compared using second order rate constants obtained from five investigations reported in the literature in which a variety of NACs were exposed to a variety of reductants. A comprehensive analysis utilizing all the NACs and reductants demonstrate that the computed hydrogen atom transfer model and the experimental one electron reduction potential model have similar root mean square errors and residual error probability distributions. In contrast, the model using the computed electron affinity has a more variable residual error distribution with a significant number of outliers. The results suggest that a linear free energy model utilizing computed hydrogen transfer reaction free energy produces a more reliable prediction of the NAC abiotic reduction second order rate constant than previously available methods. The advantages of the proposed hydrogen atom transfer model and its mechanistic implications are discussed as well.</div> | Dominic Di Toro; Kevin P. Hickey; Herbert E. Allen; Richard F. Carbonaro; Pei C. Chiu | Environmental Science; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7415fbb8c1a5f5f3d9f08/original/hydrogen-atom-transfer-reaction-free-energy-as-a-predictor-of-abiotic-nitroaromatic-reduction-rate-constants-a-comprehensive-analysis.pdf |
673cd39b7be152b1d0afdc25 | 10.26434/chemrxiv-2024-g4q8t-v2 | Dynamic formation of Au-C anchors in molecular junctions | Terminal anchor groups play a key role in controlling the stability and electronic properties of molecular junctions. Single molecule junctions typically consist of two terminal anchors linking organic molecules to metal electrodes. Here, we show that p-terphenyl derivatives containing only a single terminal anchor exhibit conductance features similar to junctions with two terminal anchors, which arises due to dynamic Au-C bond formation due to a single electron oxidation event at the electrode. A set of p-terphenyl derivatives with one terminal anchor was prepared and characterized using automated chemical synthesis, single molecule electronics experiments, molecular dynamics (MD) simulations, and non-equilibrium Green’s function-density functional theory (NEGF-DFT) calculations. Our results show that 4-amino-p-terphenyl (PPP) exhibits a distinct and well-defined high conductance state that is greatly diminished or absent in other p-terphenyl derivatives with single terminal anchors, whereas a low conductance state is observed in all amino-p-terphenyl derivatives due to non-covalent dimeric interactions. The electronic properties of PPP are characterized using a combination of cyclic voltammetry, electrolysis, and electron spin resonance, revealing that the high conductance state in PPP arises due to robust Au-C bond formation facilitated by a single electron oxidation event and stabilized by a rigid resonance structure under an electric field. A series of control experiments with different anchor groups reveals the role of primary amines in forming dynamic linkages in molecular junctions. Overall, these results suggest that Au-C bond formation gives rise to high conductance pathways in organic molecules containing only one terminal anchor. Insights from this work can be leveraged in the design of molecular electronic devices, particularly in understanding the mechanisms of molecular binding and junction formation. | Rajarshi Samajdar; Hao Yang ; Seungjoo Yi ; Chun-I Wang; Michael A. Pence ; Moeen Meigooni; Seth Putnam; Xiaolin Liu; Jitong Ren; Jeffrey S. Moore ; Emad Tajkhorshid; Joaquín Rodríguez-López; Nicholas E. Jackson; Charles M. Schroeder | Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Electrochemical Analysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673cd39b7be152b1d0afdc25/original/dynamic-formation-of-au-c-anchors-in-molecular-junctions.pdf |
65e7769a66c1381729441856 | 10.26434/chemrxiv-2024-z6966 | Oxygen-assisted supercapacitive swing adsorption of carbon dioxide | We report enhanced supercapacitive swing adsorption (SSA) of carbon dioxide in the presence of oxygen using activated carbon electrodes, and deliquescent, aqueous electrolytes. The presence of O2 in the gas mixture results in up to 11 times increased CO2 adsorption capacity with 3M MgBr2 and up to 4-5 times increased adsorption capacity with 3M MgCl2. Varying the oxygen concentration (5-20% O2) does not affect the energetics and adsorptive performance. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) of the electrodes demonstrate that the specific capacitance increases while the diffusion resistance decreases in the presence of oxygen, indicating enhanced pore wettability, and the reversible formation of oxygen functionalities on the pore surfaces, which enhance the adsorption. The electrodes show good performance for more than 100 hours of operation. | Muhammad Bilal; Jiajie Li; Neelesh Kumar; Bar Mosevitzky; Israel Wachs; Kai Landskron | Energy; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e7769a66c1381729441856/original/oxygen-assisted-supercapacitive-swing-adsorption-of-carbon-dioxide.pdf |
66683e70409abc034526a886 | 10.26434/chemrxiv-2024-12c67 | Exciton-Polaron in a quasi-one-dimensional chain of hexyl-diammonium-BiI5 octahedra | Lower dimensional hybrid perovskite exhibits intriguing similarities to traditional quantum confined inorganic semiconductors with comparable exciton binding energies. The presence of flexible organic cations acting as spacers and stabilizers enhances electron-phonon couplings, further amplifying the potential for modular light-matter interactions in these materials. One-dimensional analogs of perovskite remain largely unexplored in the literature, representing a promising frontier for optoelectronic investigations. Herein we unravel the nature of excitons in a class of quasi-1D chain of corner-sharing Bismuth Iodide octahedral that mimics the low-dimensional hybrid organic-inorganic perovskite materials. Using broadband femtosecond impulsive Raman spectroscopy and detailed electronic structure calculations, we quantify the exciton lifetime and electron-phonon coupling constants to fully describe the excitation as an exciton-polaron. Our findings shed light on the immense potential of one-dimensional analogs of perovskites in developing novel materials with enhanced optoelectronic properties amenable to light conversion technologies. | Jyotishman Dasgupta; Dipin Tomar; Swapnil Deshpande; Shubam Gupta; Pabitra Nayak; Sudip Chakrabarty | Physical Chemistry; Energy; Photovoltaics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66683e70409abc034526a886/original/exciton-polaron-in-a-quasi-one-dimensional-chain-of-hexyl-diammonium-bi-i5-octahedra.pdf |
676abc40fa469535b9a57d6e | 10.26434/chemrxiv-2024-t7z5d | Gold(I)-catalyzed hydration reactions of diynes to access tetrasubstituted cyclohexenones | Tetrasubstituted 2-carboalkoxy-3-substituted-cyclohexenones are powerful building blocks for the synthesis of a variety of bioactive target molecules. Their preparations requires multi-steps sequence involving the use of stoichiometric quantities of various reagents, while the catalytic approaches are limitited to trisubstituted cyclohexenones. We describe here an efficient catalytic approach based on gold(I)-catalysis starting from unsymmetrical diynyl mono-ester or symmetrical diynyl di-ester substrates. The carbon chain linking the two alkyne functions can bear two or one substituent, or even be unsubstituted. Regardless of the nature of the substrates and independently of its substitution, the cyclohexenone derivatives are cleanly produced. | JEAN-FRANCOIS BETZER; Théo MASSARD; Guillaume ARCILE; Géraldine LE GOFF; Elsa VAN ELSLANDE | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676abc40fa469535b9a57d6e/original/gold-i-catalyzed-hydration-reactions-of-diynes-to-access-tetrasubstituted-cyclohexenones.pdf |
615b128abe10741baa9187c7 | 10.26434/chemrxiv-2021-xtlzj-v2 | Hydration dynamics gives the distinctive brown color in the "brown ring" nitrate test | The chemistry of the brown-ring test has been investigated for nearly a century. Though recent studies have focused on solid state structure determination and the measurement of spectra, mechanistic details and kinetics, the aspects of solution structure and dynamics remain unknown. From ab initio molecular dynamics simulations of the brown-ring complex in aqueous solution, we have identified that the classically established pseudo-octahedral [Fe(H2O)5(NO)]2+ complex is in equilibrium with a square-pyramidal [Fe(H2O)4(NO)]2+ complex through the exchange of one of the coordinated H2O molecules. We also find, using ab-initio multi-reference methods, that the mixture of these two complexes is what gives the distinctive brown coloration to the brown-ring test. We show that its UV-vis spectrum can be theoretically reproduced only by accounting these two species and not the [Fe(H2O)5(NO)]2+ complex alone. The energetics of the two complexes are also investigated with multi-reference methods. | Ambar Banerjee; Michael R. Coates; Michael Odelius | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Theory - Inorganic; Transition Metal Complexes (Inorg.); Theory - Organometallic | CC BY NC 4.0 | CHEMRXIV | 2021-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615b128abe10741baa9187c7/original/hydration-dynamics-gives-the-distinctive-brown-color-in-the-brown-ring-nitrate-test.pdf |
67350c807be152b1d0fc98bc | 10.26434/chemrxiv-2024-lgkjh-v3 | Pairing a Global Optimization Algorithm with EXAFS to Accelerate Prediction of Lanthanide Structures in Solution | Ensemble-average sampling of structures sampled from ab initio molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple non-rigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures. As case studies, we examine two systems: Eu(NO3)3 dissolved in acetonitrile with a terpyridine ligand (terpyNO2), and Nd(NO3)3 dissolved in acetonitrile. The theoretical spectra for structures identified by NWPEsSe were compared to both experimental and AIMD-derived EXAFS spectra. The NWPEsSe algorithm successfully identified the proper solvation structure for both Eu(NO3)3(terpyNO2) and Nd(NO3)(acetonitrile)3, with the calculated EXAFS signals closely matching the experimental spectra for the Eu-ligand complex and showing good similarity for the Nd salt; the better agreement with the ligand-containing structure is attributed to a less dynamic coordination environment due to the rigid ligand. The key advantage of the global optimization algorithm lies in its ability to sample the coordination environment across the potential energy surface. The structure identification process can be done with a variety of methods and generally has reduced the time required from a month to within a week. | Thomas Summers; Difan Zhang; Josiane Sobrinho; Ana de Bettencourt-Dias; Roger Rousseau; Vassiliki-Alexandra Glezakou; David Cantu | Theoretical and Computational Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67350c807be152b1d0fc98bc/original/pairing-a-global-optimization-algorithm-with-exafs-to-accelerate-prediction-of-lanthanide-structures-in-solution.pdf |
675a8aa6085116a1332391ed | 10.26434/chemrxiv-2024-78w36-v2 | Enhancing Activation Energy Predictions under Data Constraints Using Graph Neural Networks | Accurately predicting activation energies is crucial for understanding chemical reactions and modeling complex reaction systems. However, the high computational cost of quantum chemistry methods often limits the feasibility of large-scale studies, leading to a scarcity of high-quality activation energy data. In this work, we explore and compare three innovative approaches—transfer learning, delta learning, and feature engineering—to enhance the accuracy of activation energy predictions using graph neural networks, specifically focusing on methods that incorporate low-cost, low-level computational data. Using the Chemprop model, we systematically evaluated how these methods leverage data from semiempirical quantum mechanical (SQM) calculations to improve predictions. Delta learning, which adjusts low-level SQM activation energies to align with high-level CCSD(T)-F12a targets, emerged as the most effective method, achieving high accuracy with substantially reduced high-level data requirements. Notably, delta learning trained with just 20%–30% of high-level data matched or exceeded the performance of other methods trained with full datasets, making it advantageous in data-scarce scenarios. However, its reliance on transition state searches imposes significant computational demands during model application. Transfer learning, which pretrains models on large datasets of low-level data, provided mixed results, particularly when there was a mismatch in the reaction distributions between the training and target datasets. Feature engineering, which involves adding computed molecular properties as input features, showed modest gains, particularly when incorporating thermodynamic properties. Our study highlights the trade-offs between accuracy and computational demand in selecting the best approach for enhancing activation energy predictions. These insights provide valuable guidelines for researchers aiming to apply machine learning in chemical reaction engineering, helping to balance accuracy with resource constraints. | Han-Chung Chang; Ming-Hsuan Tsai; Yi-Pei Li | Theoretical and Computational Chemistry; Machine Learning; Quantum Computing; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675a8aa6085116a1332391ed/original/enhancing-activation-energy-predictions-under-data-constraints-using-graph-neural-networks.pdf |
6726033df9980725cfdb7843 | 10.26434/chemrxiv-2024-76drx | Odor Classification: Exploring Feature Performance and Imbalanced Data Learning Techniques | This research delves into olfaction, a sensory modality that remains complex and inadequately understood. We aim to fill in two gaps in recent studies that attempted to use machine learning and deep learning approaches to predict human smell perception. The first one is that molecules are usually represented with molecular fingerprints, mass spectra, and vibrational spectra; however, the influence of the selected representation method on predictive performance is inadequately documented in direct comparative studies. To fill this gap, we assembled a large novel dataset of 2606 molecules with three kinds of features: mass spectra (MS), vibrational spectra (VS) and molecular fingerprint features (FP). We evaluated their performance using four different multi-label classification models. The second objective is to address an inherent challenge in odor classification multi-label datasets (MLD)—the issue of class imbalance by random resampling techniques and an explainable, cost-sensitive multilayer perceptron model (CSMLP). Experimental results suggest significantly better performance of the molecular fingerprint-based features compared with mass and vibrational spectra with the micro-averaged F1 evaluation metric. The proposed resampling techniques and cost-sensitive model outperform the results of previous studies. We also report the predictive performance of multimodal features obtained by fusing the three mentioned features. This comprehensive and systematic study compares the predictive performance for odor classification of different features and utilises a multifaceted approach to deal with data imbalance. Our explainable model sheds further light on features and odour relations. The results hold the potential to guide the development of the electric nose and our dataset will be made publicly available. | Durgesh Ameta; Laxmidhar Behera; Aniruddha Chakraborty; Tushar Sandhan; Surendra Kumar; Rishav Mishra | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6726033df9980725cfdb7843/original/odor-classification-exploring-feature-performance-and-imbalanced-data-learning-techniques.pdf |
6392c29844ccbc22c7143ce7 | 10.26434/chemrxiv-2022-7bmzv-v2 | Using physical property surrogate models to perform multi-fidelity global optimization of force field parameters | Dispersion-repulsion interactions, commonly represented in atomistic force fields by the Lennard-Jones (LJ) potential, play an important role in the accuracy of molecular simulations. Training the force field parameters used in the LJ potential is challenging, generally requiring adjustment based on simulations of macroscopic physical properties. The computational expense of these simulations limits the size of training data set and number of optimization steps that can be taken, often requiring modelers to perform optimizations within a local parameter region.
To allow for global LJ parameter optimization against large training sets, we introduce a multi-fidelity optimization technique which uses Gaussian process surrogate modeling to build inexpensive models of physical properties as a function of LJ parameters. This allows for fast evaluation of objective functions, greatly accelerating searches over parameter space. We use an iterative framework which performs global optimization at the surrogate level, followed by validation at the simulation level and surrogate refinement. Using this technique on two previously studied training sets, containing up to 195 physical property targets, we refit a subset of the LJ parameters for the OpenFF 1.0.0 ``Parsley'' force field. We demonstrate that this multi-fidelity technique can find improved parameter sets compared to a purely simulation-based optimization by searching more broadly and escaping local minima. In most cases, these parameter sets are transferable to other similar molecules in a test set. This multi-fidelity technique provides a platform for fast optimization against physical properties that can be refined and applied in multiple ways to the development of molecular models. | Owen Madin; Michael Shirts | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6392c29844ccbc22c7143ce7/original/using-physical-property-surrogate-models-to-perform-multi-fidelity-global-optimization-of-force-field-parameters.pdf |
60c749c9567dfe61eaec4c52 | 10.26434/chemrxiv.12033804.v2 | London Dispersion Governs the Interaction Mechanism of Small Polar and Non-Polar Molecules in Metal-Organic Frameworks | <div>In this work we investigate the adsorption of chlorinated methanes (CH<sub>x</sub>Cl<sub>4-x</sub>, x=0-4) in a representative layer-pillar Metal-Organic Framework (MOF), the flexible MOF Ni<sub>2</sub>(ndc)<sub>2</sub>(dabco) (ndc = 2,6-naphthalene-dicarboxylate, dabco = 1,4-diazabicyclo-[2.2.2]-octane), also known as DUT-8(Ni). The guest molecules show a systematic increase of polarizability with increasing number of chlorine atoms, while the dipole moment exceeds 2 Debye for x = 2 and 3. Our ligand field molecular mechanics (LFMM) simulations show that, counter-intuitively, the host-guest interactions are mainly characterized by London dispersion, despite the molecular dipole moments reaching magnitudes as large as water. This highlights the importance of London dispersion interactions in the description of host-guest interactions.<br /></div> | Patrick Melix; Thomas Heine | Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749c9567dfe61eaec4c52/original/london-dispersion-governs-the-interaction-mechanism-of-small-polar-and-non-polar-molecules-in-metal-organic-frameworks.pdf |
63f32ccb1d2d184063ce96b5 | 10.26434/chemrxiv-2023-gxjr8-v2 | A Single-domain Protein Catenane of Dihydrofolate Reductase | A single-domain protein catenane refers to two mechanically interlocked polypeptide rings that fold synergistically into a compact and integrated structure, which is extremely rare in nature. Herein, we report a single-domain protein catenane of dihydrofolate reductase (cat-DHFR). The design was achieved by rewiring the connectivity between secondary motifs to introduce artificial entanglement and the synthesis was readily accomplished by a series of programmed streamlined post-translational processing events in cells without any additional in vitro reactions. The target molecule contains few exogenous motifs and has been thoroughly characterized by combined techniques of LC-MS, SDS-PAGE, protease cleavage experiment, and ion mobility mass spectrometry. Compared to the linear control, cat-DHFR retains the catalytic capability and exhibits enhanced stability against thermal or chemical denaturation due to conformational restriction. The results suggest that linear proteins may be converted into concatenated single-domain counterparts with almost identical chemical composition, well-preserved function, and elevated stability, which represents an entirely new horizon in protein science. | Jing Fang; Tianzuo Li; Jiyeon Lee; Dahye Lim; Lianjie Xu; Yajie Liu; Jongcheol Seo; Wen-Bin Zhang | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f32ccb1d2d184063ce96b5/original/a-single-domain-protein-catenane-of-dihydrofolate-reductase.pdf |
62bb72eaf5193979b5777a60 | 10.26434/chemrxiv-2022-pbbr5-v2 | Synthesis Enabled Investigations into the Acidity and Stability of Atmospherically-relevant Isoprene-derived Organosulfates | Atmospheric organosulfates are a class of compounds present in secondary organic aerosols that are thought to serve as a marker of anthropogenic pollution. Organosulfates derived from isoprene epoxydiol (IEPOX) have been shown to be the most abundant and ubiquitous class of these compounds, but a lack of authentic standards that account for regiochemical and stereochemical derivatives has made the study of these compounds challenging. Herein we present a synthetic protocol to access the suite of the eight IEPOX-derived organosulfates that utilizes prenol as a common starting material and affords each compound as an ammonium salt. Our method generates either syn or anti stereochemical isomers with complete control over sulfate-ester regiochemistry. We present an evaluation of the inherent acidities of each compound by measuring aqueous pH of organosulfate solutions. The syn and anti tertiary organosulfate isomers demonstrated the lowest acidity (2.45 and 2.33, respectively) compared to the primary and secondary regioisomers of the suite. We also present preliminary stability data for each organosulfate compound utilizing aqueous time-point NMR spectroscopy. Primary and secondary organosulfates demonstrated no spectral change under both neutral and acidic conditions. The syn and anti tertiary organosulfates showed decomposition in approximately 30 days under aqueous conditions, and 10 and 12 days respectively under acidic conditions. The results presented provide new insights into the physical properties and atmospheric fate of IEPOX-derived organosulfates that should be valuable for climate modeling and future atmospheric studies. | Jonathan Varelas; Marvin Vega; Mary Alice Upshur; Franz Geiger; Regan Thomson | Organic Chemistry; Earth, Space, and Environmental Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Atmospheric Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bb72eaf5193979b5777a60/original/synthesis-enabled-investigations-into-the-acidity-and-stability-of-atmospherically-relevant-isoprene-derived-organosulfates.pdf |
674e19505a82cea2fac148ce | 10.26434/chemrxiv-2024-6150s | A new Constructed Wetland design for enhanced nitrogen recovery, footprint reduction and process intensification | Nutrient recovery is a way to reduce water scarcity. Constructed Wetlands (CW) could be of interest to manage and recover nitrogen from high-load composting leachates. However, they require large treatment area which limits their spread to industries lacking available surfaces. In this study, a Verticalized SubSurface Flow constructed Wetland (VSSFW) offering 2.7 m² of treatment surface on 0.9 m² footprint was designed and compared to a 0.75 m² footprint Vertical Flow Constructed Wetland (VFCW) of same packing-bed volume using a test solution simulating diluted composting leachates. The VSSFW showed higher performances for reducing NH4-N and P concentrations (RE (%) = 98.3 and 95.3 % respectively), and converting NH4-N to NO3-N (conversion rate of 1 : 0.56) than the VFCW (RE (%) = 59.2 and 46.3 % respectively, conversion rate of 1 : 0.14). The nitrate-concentrated solution obtained after treatment held 2.95 / 110 / 19.5 mg .L-1 NH4-N / NO3-N / P concentrations and could have interest for uses as fertilizer and hydroponic feeding solution. Intensification techniques in the form of microbubbles aeration and addition of external carbon (CaCO3) were afterward applied on the VSSFW. The intensified VSSFW showed higher performances (RENH4-N (%) = 97.5 % in 24h only, conversion rate 1 : 0.91), and a quicker production of final nitrate-concentrated solutions. The intensified VSSFW performed 16.5 times higher than the average CW. | Rémi Soret; Paul-Etienne Fontaine | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Natural Resource Recovery; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674e19505a82cea2fac148ce/original/a-new-constructed-wetland-design-for-enhanced-nitrogen-recovery-footprint-reduction-and-process-intensification.pdf |
6555f1782c3c11ed7182228b | 10.26434/chemrxiv-2023-x8f25 | A safer and more sustainable by design perspective in biocatalytic amide-bond coupling of in silico controlled chemical space | Amide bond synthesis is ranked as the second most important challenge in key green chemistry research areas identified by the ACS Green Chemistry Institute. Generating amides by chemical synthesis typically relies on toxic chemicals, the use of organic solvents, and stoichiometric amounts of coupling reagents, which is associated with generation of considerable amounts of waste. While developing more sustainable amide-bond forming reactions has been in focus, significantly less attention has been given to toxicity, sustainability and environmental aspects of the underlying amine and acid substrates and their corresponding coupled products. Here, we explore biocatalytic amide bond formation from a Safer and more Sustainable by Design perspective, for which a controlled chemical space was navigated based on potential human and environmental toxicity of the substrates and related products. In silico filtering of 15374 amines and 25994 acids generated 188 amine and 54 acid building blocks that could be classified as safe by the threshold we established, referred to herein as “safechems”. Based on the match of the known substrate scope of the marinacarboline amide bond synthetase McbA from Marinactinospora thermotolerans SCSIO 00652 with the structures of safechems, we generated a panel of robust and promiscuous ancestral ATP-dependent amide bond synthetases (ABS) using McbA as template. Ancestral ABS enzymes exhibited an increased thermostability of up to 20 °C and generated complementary biocatalysts to the extant enzyme with respect to amine and acid specificities in the coupling of a representative safechem subset of 17 amines and 16 acids (responding to 272 possible amides). Out of the 272 possible amides considered experimentally from the subset of safechems that were tested in biocatalytic coupling, 38 amides were detected by UPLC-MS out of which 32 were novel structures. Finally, the pool of safechems and their corresponding amides were evaluated by USEtox (the UNEP-SETAC toxicity model), analyzing not only the intrinsic properties of the compounds but also performing a risk assessment based on fate and exposure. The amides were in general predicted as more toxic compared to the starting acids and amines, emphasizing the importance of starting from low-toxicity building blocks. Even when restricting the pool of amines and acids based on their predicted toxicity, it did not prevent the discovery of new amides with potentially potent applications as exemplified here by substructures that are part of drug candidates for e.g. cancer treatment. Safer and more sustainable by design is capable of generating an array of novel products within a controlled chemical space. | Elisabeth Söderberg; Kerstin Felicitas von Borries; Ulf Norinder; Mark Petchey; Swapnil Chavan; Hanna Holmquist; Magnus Johansson; Ian Cotgreave; Martin Hayes; Peter Fantke; Per-Olof Syrén | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6555f1782c3c11ed7182228b/original/a-safer-and-more-sustainable-by-design-perspective-in-biocatalytic-amide-bond-coupling-of-in-silico-controlled-chemical-space.pdf |
60c75644567dfe7e68ec642d | 10.26434/chemrxiv.14173538.v2 | Unlocking the Potential of High-Throughput Experimentation for Electrochemistry with a Standardized Microscale Reactor | Organic
electrochemistry has emerged as an enabling and sustainable technology in
modern organic synthesis. Despite the recent renaissance of electrosynthesis,
the broad adoption of electrochemistry in the synthetic community and,
especially in industrial settings, has been hindered by the dearth of general,
standardized platforms for high-throughput experimentation (HTE). Herein, we
disclose the design of the HT<i>e<sup>-</sup></i>Chem,
a high-throughput microscale electrochemical reactor that is compatible with
existing HTE infrastructure, and enables rapid evaluation of a broad array of electrochemical
reaction parameters. Utilizing the HT<i>e<sup>-</sup></i>Chem
to accelerate reaction optimization, reaction discovery, and chemical library
synthesis is illustrated using a suite of oxidative and reductive transformations
under constant current, constant voltage, and electrophotochemical conditions. | Jonas Rein; James R. Annand; Michael K. Wismer; Jiantao Fu; Juno C. Siu; Artis Klapars; Neil A. Strotman; Dipannita Kalyani; Dan Lehnherr; Song Lin | Combinatorial Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Process Chemistry; Industrial Manufacturing; Pharmaceutical Industry; Process Control; Reaction Engineering; Electrocatalysis; Heterogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75644567dfe7e68ec642d/original/unlocking-the-potential-of-high-throughput-experimentation-for-electrochemistry-with-a-standardized-microscale-reactor.pdf |
6734877df9980725cf0b4f98 | 10.26434/chemrxiv-2024-5b4dn | Instruction set and language for chemical nomenclature | Processing of chemical information by computational intelligence methods faces the challenge of the structural complexity of molecular graphs. These graphs are not amenable to being represented in a suitable way for such methods. The most popular representation is the SMILES notation standard. However, it comes with some limitations such as the abundance of non-valid strings and the fact that similar strings often represent very different molecules.
In this work, a completely different approach to chemical nomenclature is presented. A reduced instruction set is defined, and the language of all strings that are sequences of such instructions is considered. All strings of this language are valid, i.e., each string represents a molecule. Moreover, slight changes in a string usually correspond to small modifications in the represented molecule. Therefore, this approach is appropriate for its use if state-of-the-art computational intelligence systems for chemical information processing, including deep learning models. | Ezequiel López-Rubio | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6734877df9980725cf0b4f98/original/instruction-set-and-language-for-chemical-nomenclature.pdf |
619bf6a947f47dfeffad7e55 | 10.26434/chemrxiv-2021-0hjxl | Electrochemical Studies of Chlorine Containing Silanes | The reduction potentials of a series of mono-, di- and trichloro alkyl and aryl substituted silanes was investigated by cyclic voltammetry. It was shown that chlorosilanes can be reduced in two one electron steps at potentials more positive than -1V vs SCE. The solvent type (THF, MeCN), silane type and polymerization and electrolyte concentration were varied and found to greatly impact the reduction potential. | Mark Hoddenbagh; Daniel Foucher; Dennis Worsfold | Inorganic Chemistry; Polymer Science; Inorganic Polymers; Electrochemistry; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619bf6a947f47dfeffad7e55/original/electrochemical-studies-of-chlorine-containing-silanes.pdf |
650cacedb927619fe7949487 | 10.26434/chemrxiv-2023-kbd4t | Electrochemical Performance of Mixed Redox-Active Organic Molecules in Redox Flow Batteries | Designing electrolytes based on mixture of different organic redox active molecules brings the opportunity of enhancing the volumetric energy density of flow batteries and removes the requirement of high solubility for individual organic species in the mixture. In the present work, we conduct computational and experimental analysis to investigate the electrochemical performance of mixed redox-active organic molecules. A zero-dimensional transient model is employed to investigate the changes in the half-cell potential and the concentrations and partial currents of individual redox reactions in a mixture of organic molecules over time. The model demonstrates the effects of individual properties of species such as kinetic rate constants, mass transfer coefficients, concentration ratios and standard redox potentials and reports the effect of energy-losing homogenous chemical redox reaction on the voltage efficiency and concentration ratios of the mixed species. Pairs of anthraquinone negolyte species were selected for an experimental case study. A mixture of 2,6-N-TSAQ and 2,6-DHAQ showed 40% increase in the volumetric energy density compared to the performance of 2,6-DHAQ alone. Based on the results of the experimental and computational analysis, we propose guidelines for the design of suitable mixed redox-active organic species. | Kiana Amini; Yan Jing; Jinxu Gao; Jordan Sosa; Roy Gordon; Michael Aziz | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650cacedb927619fe7949487/original/electrochemical-performance-of-mixed-redox-active-organic-molecules-in-redox-flow-batteries.pdf |
6299b97b6057b1707f8fba40 | 10.26434/chemrxiv-2021-cxxt1-v3 | Mass difference matching unfolds hidden molecular structures of dissolved organic matter | Ultrahigh-resolution Fourier transform mass spectrometry (FTMS) has revealed unprecedented detail of natural complex mixtures such as dissolved organic matter (DOM) on a molecular formula level, but we lack approaches to access the underlying structural complexity. We here explore the hypothesis that every DOM precursor ion is potentially linked with all emerging product ions in FTMS2 experiments. The resulting mass difference (Δm) matrix is deconvoluted to isolate individual precursor ion Δm profiles and matched with structural information, which was derived from 42 Δm features from 14 in-house reference compounds and a global set of 11477 Δm features with assigned structure specificities, using a dataset of ~18000 unique structures. We show that Δm matching is highly sensitive in predicting potential precursor ion identities in terms of molecular and structural composition. Additionally, the approach identified unresolved precursor ions and missing elements in molecular formula annotation (P, Cl, F). Our study provides first results how Δm matching refines structural annotations in Van Krevelen space, but simultaneously demonstrates the wide overlap between potential structural classes. We show that this effect is likely driven by chemodiversity and offers an explanation for the observed ubiquitous presence of molecules in the center of the Van Krevelen space. Our promising first results suggest that Δm matching can both unfold the structural information encrypted in DOM and assess the quality of FTMS-derived molecular formulas of complex mixtures in general. | Carsten Simon; Kai Dührkop; Daniel Petras; Vanessa-Nina Roth; Sebastian Böcker; Pieter Dorrestein; Gerd Gleixner | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6299b97b6057b1707f8fba40/original/mass-difference-matching-unfolds-hidden-molecular-structures-of-dissolved-organic-matter.pdf |
636d14d0924538458087befa | 10.26434/chemrxiv-2022-bszdt | Role of Counterions in the Structural Stabilisation of Redox-Active Metal-Organic Frameworks | The crystal structures of metal-organic frameworks (MOFs) are typically determined by the strong chemical bonds formed between the organic and inorganic building units. However, the latest generation of redox-active frameworks often rely on counterions in the pores to access specific charge states of the components. Here, we model the crystal structures of three layered MOFs based on the redox-active ligand 2,5-dihyroxybenzoquinone (dhbq): Ti$_2$(Cl$_2$dhbq)$_3$, V$_2$(Cl$_2$dhbq)$_3$ and Fe$_2$(Cl$_2$dhbq)$_3$ with implicit and explicit counterions. Our full-potential first-principles calculations indicate that while the reported hexagonal structure is readily obtained for Ti and V, the Fe framework is stabilised only by the presence of explicit counterions. For high counterion concentrations, we observe the formation of an electride-like pocket in the pore center. An outlook is provided on the implications of solvent and counterion control for engineering the structures and properties of porous solids. | Matthias Golomb; Kasper Tolborg; Joaquín Calbo; Aron Walsh | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d14d0924538458087befa/original/role-of-counterions-in-the-structural-stabilisation-of-redox-active-metal-organic-frameworks.pdf |
669420bf5101a2ffa8637c33 | 10.26434/chemrxiv-2024-21hd2 | Exploring the applications of formulation-based drug development strategies in neurological disorders using artificial intelligence and machine learning approaches | The study of artificial intelligence (AI), a multidimensional field, empowers machines with the ability to understand, reason, learn, and perform tasks autonomously. As a pivotal branch of computer science, AI excels in analyzing complex medical data and uncovering significant relationships for diverse diagnostic purposes. In neurology, innovative AI techniques have revolutionized diagnostics, management, and outcome prediction, opening new avenues for tackling neurological disorders. AI encompasses two key subsets: machine learning (ML) and deep learning (DL), which have gained immense popularity for predicting bioactivity, toxicology, physical and chemical properties, formulation quality, and drug-target interactions. The complexity of neurological diseases (ND) presents unique challenges in developing treatments for the central nervous system (CNS), given obstacles like the blood-brain barrier and high medication attrition rates. However, AI algorithms, leveraging vast datasets, efficiently analyze, interpret, and predict unknown facts, significantly accelerating CNS drug discovery. Deep learning architectures have furthered our understanding of AI's potential to address complex CNS disease issues, transforming the drug development landscape. This review delves into AI, ML, and their applications in advancing CNS drug and formulation development. It provides comprehensive, up-to-date insights on AI/ML advancements in neurology, emphasizing nanoparticle-based drug delivery systems. Additionally, the review covers ML algorithms' roles in de novo drug design, structure-based drug design, ligand-based drug design, absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction, and drug repurposing. Despite notable progress, significant challenges remain in enhancing AI's practical application in neurology. Overcoming these hurdles requires compiling extensive data and developing interpretable AI systems, paving the way for groundbreaking advancements in CNS drug development. | Ashok Aspatwar; Ranajit Nath; Ratul Bhowmik; Rajesh Jesudasan | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669420bf5101a2ffa8637c33/original/exploring-the-applications-of-formulation-based-drug-development-strategies-in-neurological-disorders-using-artificial-intelligence-and-machine-learning-approaches.pdf |
6235900021e2d04615a90636 | 10.26434/chemrxiv-2022-w8h26 | Atroposelective arene-forming alkene metathesis | Alkene metathesis catalysed by enantiopure metal alkylidene complexes enables versatile strategies to products with configurationally-defined stereocentres. Desymmetrisation processes thereby provide particularly reliable stereoselective routes to aliphatic structures, while the differentiation of aromatic stereogenic units remained an outstanding challenge. Herein, we describe the feasibility of alkene metathesis to catalytically control stereogenic axes by traceless arene formation. Stereodynamic trienes are selectively converted into corresponding binaphthalene atropisomers upon exposure to a chiral molybdenum catalyst. Remarkably, stereoselective arene-forming metathesis allows high yields and enantioselectivities of up to 98:2 e.r. As the disconnection of each bond of aromatic products is retrosynthetically conceivable, it is anticipated that forging arenes by means of stereoselective metathesis will enable versatile approaches for the synthesis of a broad range of molecular topologies with precisely defined configuration.
| Zlatko Jončev ; Christof Sparr | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6235900021e2d04615a90636/original/atroposelective-arene-forming-alkene-metathesis.pdf |
60c73dd60f50dbd680395569 | 10.26434/chemrxiv.5899393.v2 | A New Kinetic Model for Multicomponent Adsorption in Batch Systems | In many of kinetic studies on binary component adsorption, the kinetic models for unary component adsorption were used although binary adsorption process were more complex than unary ones. We proposed a new kinetic model for multicomponent adsorption in batch systems. This model, using the deactivation kinetics model(DKM) for the noncatalytic heterogeneous reaction, is represented by a set of simultaneous ordinary differential equations, the characteristic is to calculate the concentration of adsorbates and the overall deactivation degree of the adsorbent with time together. The multicomponent adsorption kinetic model was solved with ODE function of MATLAB and the kinetic parameters were estimated by the nonlinear least squares fitting. The results of nonlinear fitting to the previous experimental data show that the proposed kinetic model can be useful for kinetics modeling of multicomponent adsorption in batch systems. <br /> | yongson hong; Kye-Ryong Sin; Yong-U Ri; Jong-Su Pak; Yung Jon; Chol-Sik Kim; Chol-Su Jang; Hye-Ryon Ju; Sung-Hwan Ri | Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd60f50dbd680395569/original/a-new-kinetic-model-for-multicomponent-adsorption-in-batch-systems.pdf |
6405d52e6642bf8c8f0efce6 | 10.26434/chemrxiv-2023-qsh4c | Nonaromatic benzocorroles | Introduced here are new hybrid benzocorrole ligands, displaying both the cavity size of corroles and the dianionic character of porphyrins. Nonaromatic and yet sporting deceptively porphyrin-like optical spectra, they are readily accessible via a simple three-step synthetic protocol. | Łukasz Kielesiński; Francesco Summa; Jeanet Conradie; Hilah Honig; Ariel Friedman; Gugliemo Monaco; Lior Elbaz; Abhik Ghosh; Daniel Gryko | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6405d52e6642bf8c8f0efce6/original/nonaromatic-benzocorroles.pdf |
61f8a5d4191637746dfb103e | 10.26434/chemrxiv-2022-235cj-v2 | A simple predictor of interface orientation of fluids of disk-like anisotropic particles and its implications for organic semiconductors | From classical molecular dynamics simulations, we identify a simple and general predictor of molecular orientation at solid and vapour interfaces of isotropic fluids of disk-like anisotropic particles based on their shape and interaction anisotropy. For a wide variety of inter-particle interactions, temperatures, and substrate types within the range of typical organic semiconductors and their processing conditions, we find remarkable universal scaling of the orientation at the interface with the free energy calculated from pair interactions between close-packed nearest neighbours and an empirically derived universal relationship between the entropy and the shape anisotropy and bulk volume fraction of the fluid particles. The face-on orientation of fluid particles at the solid interface is generally predicted to be the equilibrium structure, although the alignment can be controlled by tuning the particle shape and substrate type, while changing the strength of fluid--fluid interactions is likely to play a less effective role. At the vapour interface, only the side-on structure is predicted, and conditions for which the face-on structure may be preferred, such as low temperature, low interaction anisotropy, or low shape anisotropy, are likely to result in little orientation preference (due to the low anisotropy) or be associated with a phase transition to an anisotropic bulk phase for systems with interactions in the range of typical organic semiconductors. Based on these results, we propose a set of guidelines for the rational design and processing of organic semiconductors to achieve a target orientation at a solid or vapour interface. | Belinda Boehm; David Huang | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f8a5d4191637746dfb103e/original/a-simple-predictor-of-interface-orientation-of-fluids-of-disk-like-anisotropic-particles-and-its-implications-for-organic-semiconductors.pdf |
6193cc48b039f2e0aaa6f7b1 | 10.26434/chemrxiv-2021-mw0p5 | Direct Synthesis of Vinylene Carbonates from Aromatic Aldehydes | Substituted vinylene carbonates were directly prepared from aromatic aldehydes following a one-pot Benzoin condensation / transcarbonation sequence under solvent-free conditions. The combination of a N-phenyl substituted triazolium salt NHC precursor and 4-dimethylaminopyridine (DMAP) was found essential to reach high yield and selectivity. The reaction scope was investigated with a range of aromatic aldehydes and the corresponding vinylene carbonates were obtained with 32-86% isolated yields (14 examples). | Killian Onida; Leyli Ibrahimli; Nicolas Duguet | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6193cc48b039f2e0aaa6f7b1/original/direct-synthesis-of-vinylene-carbonates-from-aromatic-aldehydes.pdf |
614757fa6fc3a870f6a4bbe2 | 10.26434/chemrxiv-2021-5c5l1-v2 | Exploring graph traversal algorithms in graph-based molecular generation | Here we explore the impact of different graph traversal algorithms on molecular graph generation. We do this by training a graph-based deep molecular generative model to build structures using a node order determined via either a breadth- or depth-first search algorithm. What we observe is that using a breadth-first traversal leads to better coverage of training data features compared to a depth-first traversal. We have quantified these differences using a variety of metrics on a dataset of natural products. These metrics include: percent validity, molecular coverage, and molecular shape. We also observe that using either a breadth- or depth-first traversal it is possible to over-train the generative models, at which point the results with the graph traversal algorithm are identical | Rocío Mercado; Esben Bjerrum; Ola Engkvist | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614757fa6fc3a870f6a4bbe2/original/exploring-graph-traversal-algorithms-in-graph-based-molecular-generation.pdf |
60c74ef80f50db4f18397300 | 10.26434/chemrxiv.12824921.v1 | Tropolonate Salts as Acyl Transfer Catalysts for Esterification Reactions under Thermal and Photochemical Conditions | Acyl transfer catalysis is a frequently used tool to promote the formation of carboxylic acid derivatives, which are important synthetic precursors and target compounds in organic synthesis. However, there have been only a few structural motifs known to efficiently catalyze the acyl transfer reaction. Herein we introduce a new acyl transfer catalytic paradigm based on the tropolone framework. We show that tropolonate salts, due to their strong nucleophilicity and photochemical activity, can promote the coupling reaction between alcohols and carboxylic acid anhydrides or chlorides to give the products with excellent efficiency under thermal or blue light-photochemical conditions. Kinetic studies and density functional theory (DFT) calculations suggest interesting mechanistic insights for reactions promoted by this new acyl transfer catalytic system. | Demelza Lyons; Claire Empel; Domenic Pace; An Huy Dinh; Binh Khanh Mai; Rene Koenigs; Thanh Vinh Nguyen | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ef80f50db4f18397300/original/tropolonate-salts-as-acyl-transfer-catalysts-for-esterification-reactions-under-thermal-and-photochemical-conditions.pdf |
65693e07cf8b3c3cd784ae51 | 10.26434/chemrxiv-2023-5jsc8-v3 | Understanding the Dielectric Relaxation of Liquid Water Using Neural Network Potential and Classical Pairwise Potential
| Understanding the role of hydrogen bond networks in determining the relaxation dynamics is essential for understanding natural phenomena in liquid water. Classical pairwise additive models have been widely utilized for elaborating the underlying mechanism behind the relaxation phenomena. However, they have shown their limits due to either the absence or inaccurate descriptions of many-body and medium-to-long-range interactions. This work demonstrates that the Deep Potential Molecular Dynamics (DPMD) model trained with SCAN functional help calculate the dielectric constant at the accuracy of the first-principles simulations. The DPMD model outperforms the classical force fields (SPC/Fw and TIP4P/epsilon) in predicting dielectric spectra especially in replicating high-frequency excesses, attributed to its adeptness in simulating intricate hydrogen bond networks. Through a comprehensive analysis of the simulation results, it becomes evident that only the DPMD model effectively accommodates a wide range of hydrogen bond coordination scenarios thereby characterizing the intricate nature of the hydrogen bond network. This adaptability stems from the intricate interplay of many-body interactions and intramolecular dynamics. In addition, orientation defects within the DPMD model play a significant role in shaping the potential energy barrier due to the adaptability. | Jae Hyun Ryu; Ji Woong Yu; Tae Jun Yoon; Won Bo Lee | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65693e07cf8b3c3cd784ae51/original/understanding-the-dielectric-relaxation-of-liquid-water-using-neural-network-potential-and-classical-pairwise-potential.pdf |
60c73e98702a9b7741189dc2 | 10.26434/chemrxiv.6629150.v2 | Exploring Drugbank in Virtual Reality Chemical Space | The
recent general availability of low-cost virtual reality headsets, and
accompanying 3D engine support, presents an opportunity to bring the concept of
chemical space into virtual environments. While virtual reality applications
represent a category of widespread tools in other fields, their use in the
visualization and exploration of abstract data such as chemical spaces has been
experimental. In our previous work we established the concept of interactive 2D
maps of chemical spaces, followed by interactive web-based 3D visualizations,
culminating in the interactive web-based 3D visualization of extremely large
chemical spaces. Virtual reality chemical spaces are a natural extension of
these concepts. As 2D and 3D embeddings, and projections of high-dimensional
chemical fingerprint spaces were shown to be valuable tools in chemical space
visualization and exploration, existing pipelines of data mining and
preparation can be extended to be used in virtual reality applications. Here we
present an application based on the Unity engine and the virtual reality
toolkit (VRTK), allowing for the interactive exploration of chemical space
populated by Drugbank compounds in virtual reality. The source code of the
application as well as the most recent build are available on GitHub. | Daniel Probst; Jean-Louis Reymond | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e98702a9b7741189dc2/original/exploring-drugbank-in-virtual-reality-chemical-space.pdf |
65a2b95ce9ebbb4db9142c20 | 10.26434/chemrxiv-2023-w7b90-v2 | Molecular O2 Dimers and Lattice Instability in a Perovskite Electrocatalyst | Structural degradation of oxide electrodes during electrocatalytic oxygen evolution reaction (OER) is a major challenge in water electrolysis. Although the OER is known to induce changes in the surface layer, little is understood about its effect on the bulk of the electrocatalyst and the overall phase stability. Here, we show that under OER conditions a highly active SrCoO3-x electrocatalyst develops bulk lattice instability, which results in the formation of molecular O2 dimers in the bulk and nanoscale amorphization induced via chemo-mechanical coupling. Using high-resolution resonant inelastic X-ray scattering (RIXS) and first principles calculations, we unveil the potential-dependent evolution of lattice oxygen inside the perovskite and demonstrate that O2 dimers are stable in a densely packed crystal lattice, thus challenging the assumption that O2 dimers require sufficient inter-atomic spacing. We also show that SrCoO3-x develops unusual amorphous bands under intercalation-induced stress that indicates the lattice requires a remarkably low energy to undergo the order-disorder transition. As a result, we propose the amorphization energy as a descriptor of the electrocatalyst stability that can be calculated from the first principles. Our study demonstrates that extreme oxidation of electrocatalysts under OER can intrinsically destabilize the lattice and result in bulk anion redox and disorder, suggesting why some oxide materials are unstable and develop a thick amorphous layer under water electrolysis conditions. | Jan Bosse; Jian Gu; Jaewon Choi; Vladimir Roddatis; Yong-Bin Zhuang; Nagaarjhuna A. Kani; Anna Hartl; Mirian Garcia-Fernandez; Ke-Jin Zhou; Alessandro Nicolaou; Thomas Lippert; Jun Cheng; Andrew Akbashev | Materials Science; Catalysis; Energy; Thin Films; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a2b95ce9ebbb4db9142c20/original/molecular-o2-dimers-and-lattice-instability-in-a-perovskite-electrocatalyst.pdf |
658270269138d231611451b2 | 10.26434/chemrxiv-2023-02jpq | Nominal appearance of inverted singlet and triplet excited state behaviour induced by the presence of a higher lying triplet excited state | In recent years, thermally activated delayed fluorescence (TADF) has attracted intense attention owing to its straightforward application to high-efficiency organic light-emitting diodes. Further, to develop high-performance TADF materials, many researchers have designed novel molecules that have a small energy gap between the lowest excited singlet and triplet states (∆E_ST), and detailed analysis suggest a significant contribution of higher lying excited states for spin flipping processes. In this study, we studied the spin-flipping process of the donor–acceptor TADF molecule with 1,3,6,8-tetramethyl-9H-carbazole as the donor unit and 5,9-dioxa-13b-boranaphtho[3,2,1-de]anthracene as the acceptor unit (TMCz-BO) and observed peculiar thermally activated behaviour similar to that of the negative gap molecule HzTFEX2 (a heptazine derivative). By comprehensive kinetic analysis across various temperatures in various solvents, the peculiar thermal behaviour of TMCz-BO can be explained with a normal four-state configuration without a negative small energy gap between the S1 and T1 states. While the activation energy has previously been treated as being temperature independent, we stress that it should be a dynamic parameter affected by the environmental temperature, especially in the case of a small energy gap of ~10 meV. Insufficient analysed results would cause confusion and inhibit the visualization of the true picture of the TADF mechanism. We anticipate that the comprehensive analysis in this study will provide information for the molecular design of advanced TADF emitters in organic light-emitting diodes. | Youichi Tsuchiya; Keito Mizukoshi; Masaki Saigo; Tomohiro Ryu; Keiko Kusuhara; Kiyoshi Miyata; Ken Onda; Chihaya Adachi | Physical Chemistry; Materials Science; Optical Materials; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658270269138d231611451b2/original/nominal-appearance-of-inverted-singlet-and-triplet-excited-state-behaviour-induced-by-the-presence-of-a-higher-lying-triplet-excited-state.pdf |
60c7511fbb8c1a389e3dbc11 | 10.26434/chemrxiv.13120283.v1 | 1,2-Difunctionalized Bicyclo[1.1.1]pentanes: Long Sought After Bioisosteres for ortho/meta-Substituted Arenes | <p>The development of a versatile platform for the synthesis of 1,2-difunctionalized bicyclo[1.1.1]pentanes to potentially mimic ortho/meta-substituted arenes is described. The synthesis of useful building blocks bearing alcohol, amine, and carboxylic acid functional handles has been achieved from a simple common intermediate. Several ortho and/or meta-substituted benzene analogues as well as simple molecular matched pairs have also been prepared using this platform. In-depth biological and computational studies are currently in progress to validate the ortho and/or meta-character of these new bioisosteres. Results of these investigations will be reported in due course.</p> | Jin-Xin Zhao; Yuxuan Chang; Jeff Elleraas; T. Patrick Montgomery,; Jillian E. Spangler; Sajiv K. Nair; Matthew Del Bel; Gary M. Gallego; James
J. Mousseau; Matthew A. Perry; Michael R. Collins; Julien Vantourout; Phil Baran | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7511fbb8c1a389e3dbc11/original/1-2-difunctionalized-bicyclo-1-1-1-pentanes-long-sought-after-bioisosteres-for-ortho-meta-substituted-arenes.pdf |
66080b07e9ebbb4db9fd8479 | 10.26434/chemrxiv-2024-qhmqn | Myelin surfactant assemblies shaping the electrodeposition of copper dendrites. | Self-organization of inorganic matter enables bottom-up construction of materials with targetted shapes suited to their function. Positioning the building blocks in the growth process involves a well-balanced interplay of reaction and diffusion. Whereas (supra)molecular structures have been used to template such growth processes, we reasoned that molecular assemblies can be employed to actively create concentration gradients which shape the deposition of solid, wire-like structures. The core of our approach comprises the interaction between myelin assemblies that deliver copper(II) ions to the tips of copper dendrites, which in turn grow along the Cu2+-gradient upon electrodeposition. First, we successfully include Cu2+ ions amongst amphiphile bilayers in myelin filaments, which grow from C12E3-based source droplets over air-water interfaces. Second, we characterize the growth of dendritic copper structures upon electrodeposition from a negative electrode at the sub-mM Cu2+ concentrations that are anticipated upon release from the copper loaded myelins. Third, we assess the intricate growth of copper dendrites upon electrodeposition, when combined with copper loaded myelins. The myelins deliver Cu2+ at a negative electrode, feeding copper dendrite growth upon electrodeposition. Intriguingly, the copper dendrites follow the Cu2+ gradient towards the myelins, and grow along them towards the source droplet. We demonstrate the growth of dynamic connections amongst electrodes and surfactant droplets in reconfigurabe setups – featuring a unique interplay between molecular assemblies and inorganic, solid structures. With the growing interest in neuromorphic circuitry, we envision such a self-organizing system opening entirely new pathways for interconnected networks of (semi)conductive wires that are integrated with soft-matter based systems. | José Ferreira; Jeroen Michiels; Marty Herregraven; Peter A. Korevaar | Physical Chemistry; Inorganic Chemistry; Electrochemistry; Interfaces; Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66080b07e9ebbb4db9fd8479/original/myelin-surfactant-assemblies-shaping-the-electrodeposition-of-copper-dendrites.pdf |
63f39b8ffcfb27a31f1dc775 | 10.26434/chemrxiv-2023-g5xh3 | Integrated Capture and Solar-driven Utilization of CO2 from Flue Gas and Air | Integration of carbon capture with utilization technologies can lead the way to a net-zero carbon economy. Nevertheless, direct chemical conversion of captured CO2 products remains challenging due to their thermodynamic stability. Here, we demonstrate CO2 capture from flue gas/air and its direct conversion into syngas under solar irradiation without any externally applied voltage. The system captures CO2 with an amine/hydroxide solution and photoelectrochemically converts it into syngas (CO:H2 1:2 (concentrated CO2), 1:4 (simulated flue gas), and 1:30 (air)) using a perovskite-based photocathode with an immobilized molecular Co-phthalocyanine catalyst. At the anode, plastic-derived ethylene glycol is oxidized into glycolic acid over a Cu26Pd74 alloy catalyst. The overall process uses flue gas/air as carbon source and discarded plastic waste as electron donor, opening avenues for integrated carbon-neutral/negative solar fuel and waste upcycling technologies. | Sayan Kar; Motiar Rahaman; Virgil Andrei; Subhajit Bhattacharjee; Souvik Roy; Erwin Reisner | Catalysis; Energy; Photocatalysis; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f39b8ffcfb27a31f1dc775/original/integrated-capture-and-solar-driven-utilization-of-co2-from-flue-gas-and-air.pdf |
627dc7497087674fa850ef4f | 10.26434/chemrxiv-2022-z9n00 | Exponential Water Uptake in Ionomer Membranes Results from Polymer Plasticization | Water content is the most influential factor in the performance of ion exchange membranes (IEM), controlling their mechanical rigidity, ionic conductivity, and degradation rates. Membranes absorb water exponentially at high water activity (aw), making that region of the sorption isotherm the most influential on membrane properties. Plasticization of the polymer by water has been proposed to cause this exponential uptake at high aw. However, an integrated microscopic picture of the structure, thermodynamic, and mechanical properties of IEM as a function of aw has remained elusive. Here we use large-scale molecular simulations validated with experimental measurements to compute the sorption isotherms, Young’s modulus, polymer dynamics and structure of IEM. The simulations unveil that the exponential increase in water uptake coincides in all cases with the glass to rubber transition of the membrane, as measured through its Young’s modulus and segmental polymer dynamics. Functionalization of the polymer with alkyl groups further contributes to the plasticization of the polymer, increasing the water uptake at a given ion exchange capacity (IEC) and aw. We conclude that the alkyl chains act synergistically with water to plasti-cize the polymer matrix and allow water penetration in the membrane. The simulations reveal that the width of the water chan-nels depends on the ratio λ of water to ions in the membrane but is independent of its IEC. We conclude that differences in the polymer matrix –not the water channels- are responsible for the distinct uptake response of ion exchange membranes to the thermodynamic driving force of water activity. | Adam Barnett; John Karnes; Jibao Lu; Dale Major; James Oakdale; Kyle Grew; Joshua McClure; Valeria Molinero | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Structure; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627dc7497087674fa850ef4f/original/exponential-water-uptake-in-ionomer-membranes-results-from-polymer-plasticization.pdf |
660331cbe9ebbb4db99c1452 | 10.26434/chemrxiv-2024-0jh8g | Condensing Molecular Docking CNNs via Knowledge Distillation | Knowledge of the bound protein-ligand structure is critical to many drug discovery tasks. One tool for in silico bound structure elucidation is molecular docking, which samples and scores ligand binding conformations. Recent work has demonstrated that convolutional neural networks (CNNs) for protein-ligand pose scoring outperform conventional scoring functions. Scoring performance can be further increased by taking the average of multiple CNN models, termed ensembles. However, ensembles of large parameter models require significant computational resources and therefore are difficult to apply to high-throughput molecular docking for virtual screening. We investigate knowledge distillation as a framework to condense the knowledge of large, powerful CNN model ensembles into a single reduced CNN model for a significant reduction in computational cost. Ensemble KD produces single models that outperform non-KD trained single models. | Andrew McNutt; Yanjing Li; Paul Francoeur; David Koes | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660331cbe9ebbb4db99c1452/original/condensing-molecular-docking-cn-ns-via-knowledge-distillation.pdf |
646b7445b3dd6a65308dedb4 | 10.26434/chemrxiv-2023-z72fg | Characteristic nuclear spin-induced optical rotation in oxygen-containing organic molecules | Nuclear spin-induced optical rotation (NSOR) is a nuclear magneto-optic effect that manifests itself as a rotation of the plane of polarization of linearly polarized light. The effect is induced by ordered nuclear magnetic moments within a molecule. NSOR is sensitive to specific, localized interactions. Hence, the connection between the local chemical environment and the corresponding NSOR signal is crucial to understand. Despite the fact that contributions to better understand the connection have been made, the general systematics still remain unknown. In this paper, NSOR in oxygen compounds is investigated systematically to better understand the impact of oxygen atoms on the NSOR signal. NSOR signals are computed using density-functional theory methods for five different classes of oxygen compounds. The ability of NSOR to distinguish different molecules and individual nuclei in the molecules is studied and the information provided by NSOR is compared to conventional NMR spectroscopy. The results reveal that NSOR is capable of chemical distinction between nuclei and molecules, and by using NMR and NSOR together it is possible to distinguish nuclei near the oxygen atom. | Eelis Kamula; Juha Vaara; Petr Štěpánek | Theoretical and Computational Chemistry; Physical Chemistry; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b7445b3dd6a65308dedb4/original/characteristic-nuclear-spin-induced-optical-rotation-in-oxygen-containing-organic-molecules.pdf |
678a6874fa469535b96764e7 | 10.26434/chemrxiv-2025-mtlpf | Enhanced Pesticide Screening in Wines and Juices by Column-Switching Liquid Chromatography-Tandem Mass Spectrometry Using Multiple Activation Methods | A commercial QqTOF platform (ZenoTOF 7600 system) was modified to enable three fragmentation modes, collision induced dissociation (CID), electron activated dissociation (EAD) and ultraviolet photodissociation (UVPD) at 266 nm. 168 pesticides, which showed fragmentation in CID provides also EAD spectra. In the case of UVPD, 158 compounds fragmented under 266 nm photon irradiation. The performance of the novel platform was evaluated using data independent CID SWATH acquisition for the general screening and schedule multiple product ion acquisition with CID/EAD/UVPD for confirmatory analysis of pesticides in juice, white and red wines samples. A column-switching LC method with online dilution was developed allowing for injection of large volumes (80 μL) into the system. The approach enabled the detection and concentration estimation of approximately thirty pesticides in juices and wines, including insecticides, neonicotinoids and fungicides. Pesticide LODs were found to be in the pg/ml to ng/ml range for MS1 and MS2 acquisitions. | Romain Giraud; J.C. Yves Le Blanc; Mircea Guna; Gérard Hopfgartner | Analytical Chemistry; Environmental Analysis; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a6874fa469535b96764e7/original/enhanced-pesticide-screening-in-wines-and-juices-by-column-switching-liquid-chromatography-tandem-mass-spectrometry-using-multiple-activation-methods.pdf |
649ba9749ea64cc1671678fa | 10.26434/chemrxiv-2023-sjl2p | Resonance Tunability and Ultra-Long Range Enhancement of Plasmon-Coupled Resonance Energy Transfer Facilitated by Silver Nanorods (I): An Overview via Computational Study | Resonance energy transfer (RET) between molecules or quantum dots is an important process in many energy related applications. Different environmental structures have been studied and demonstrated to be able to enhance the RET rate between a nearby donor-acceptor pair. In particular, cylindrical silver nanorods and nanowires have shown extraordinary ability to transfer energy along its longitudinal axis over large distances. However, the mechanism of such transfer and the exact effects on molecular RET process are yet elusive. In this study, we use the recently developed computational tool based on the plasmon-coupled resonance energy transfer (PC-RET) method to systematically study the effects of nanorods with different dimensions on RET rates. We find that highly frequency-dependent coupling factor (CF) spectra, whose amplitudes determine RET rates, can be obtained due to the localized surface plasmon polariton (LSPP) modes of the rods with nanoscale dimensions. Simple phenomenological models can be derived for the wavelengths of CF peaks in relation to the length and width of the nanorods, providing easy tunability for enhancing RET rate in specific wavelength ranges. When coupled to longer rods with mesoscale lengths, exponential decay of the CF over long donor-acceptor distances with a small decay constant is observed, leading to the possibility of long-range RET processes. Furthermore, drumhead resonance modes emerge on the flat ends of the rod when the rod's diameter reaches 300~nm, resulting in extra enhancement to RET rate compared to certain thinner rods. These findings shed new light on the mechanism of plasmonic enhancement with silver nanorods and establish design principles for how to optimally utilize these structures to manipulate RET processes for various applications. | Albert Benjamin Lamonda; David F. Coker; Wendu Ding | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649ba9749ea64cc1671678fa/original/resonance-tunability-and-ultra-long-range-enhancement-of-plasmon-coupled-resonance-energy-transfer-facilitated-by-silver-nanorods-i-an-overview-via-computational-study.pdf |
60c749014c8919180bad2ffa | 10.26434/chemrxiv.12009018.v1 | pH Dependent Differential Binding Behavior of Prtotease Inhibitor Molecular Drugs for SARS-COV-2 | <p>In this research we used the structure of
SARS-CoV-2 main protease (Mpro) for docking with Anti-HIV protease inhibitor drug molecules within pH 4-8. By carrying
out the variance analysis of binding energies at pH 4-8, it was revealed that the
binding energy and mode of interaction of the potential ligands with
SARS-CoV-2 Mpro, was dependent on variation of pH. We found out that two of the
selected protease inhibitors have differential binding characteristics with
changing pH hence their binding energies and mode of interaction depends upon
intracellular pH. This differential
binding behavior can lead to development of pH selective potent drug molecules
for binding with viral protease at lowered intracellular pH of virus infected
cell. </p> | Hamdullah Khadim Sheikh; Tanzila Arshad; Zainab Sher Mohammad; Iqra Arshad; Mohtasheemul Hassan | Biochemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749014c8919180bad2ffa/original/p-h-dependent-differential-binding-behavior-of-prtotease-inhibitor-molecular-drugs-for-sars-cov-2.pdf |
656dc56b29a13c4d47a01b56 | 10.26434/chemrxiv-2023-tbw7q | Watching a Full Photocatalytic Cycle by Electron Paramagnetic Resonance
| Molecular photocatalysis has shown tremendous success in sustainable energy and chemical synthesis. However, visualizing the intricate mechanisms in photocatalysis is a significant and long-standing challenge. By employing our recently developed sensitivity-enhanced time-resolved electron paramagnetic resonance technique, we directly observed all radicals and radical ions involved in the photocatalytic addition of a tertiary amine to tert-butyl acrylate. The full picture of the photocatalytic cycle has been vividly illustrated by the fine structures, chemical kinetics, and dynamic spin polarization of all open-shell intermediates directly observed in this prototypical system. Given the universality of this methodology, we believe it greatly empowers the research paradigm of direct observation in both photocatalysis and radical chemistry. | Jian-Qing Qi; Weiqun Suo; Jing Liu; Songtao Sun; Lei Jiao; Xingwei Guo | Physical Chemistry; Organic Chemistry; Catalysis; Photocatalysis; Chemical Kinetics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656dc56b29a13c4d47a01b56/original/watching-a-full-photocatalytic-cycle-by-electron-paramagnetic-resonance.pdf |
6455032e27fccdb3ea88e0c0 | 10.26434/chemrxiv-2023-kqbhs | Assessing the Performance of Approximate Density Functional Theory on 95 Experimentally Characterized Fe(II) Spin Crossover Complexes | Spin crossover (SCO) complexes, which exhibit changes in spin state in response to external stimuli, have applications in molecular electronics and are challenging materials for computational design. We curate a data set of 95 Fe(II) SCO complexes (SCO-95) from the Cambridge Structural Database that have available low- and high-temperature crystal structures and, in most cases, confirmed experimental spin transition temperatures (T1/2). We study these complexes using density functional theory (DFT) with thirty functionals spanning across multiple rungs of “Jacob’s ladder” to understand the effect of exchange-correlation functional on electronic and Gibbs free energies associated with spin crossover. We specifically assess the effect of varying the Hartree–Fock exchange fraction (aHF) in structures and properties within the B3LYP family of functionals. We identify three best-performing functionals, a modified version of B3LYP (aHF = 0.10), M06-L, and TPSSh, that accurately predict SCO behavior for the majority of the complexes. Contrary to observations from prior studies, double-hybrids with higher aHF values are found to strongly stabilize high-spin states and therefore exhibit poor performance in predicting SCO behavior. Computationally predicted T1/2 values are consistent among the three functionals but show limited correlation to experimentally reported T1/2 values. These failures are attributed to the lack of crystal packing effects and counter-anions in the DFT calculations that would be needed to account for phenomena like hysteresis and two-step SCO behavior. The SCO-95 set thus presents opportunities for method development, both in terms of increasing model complexity and method fidelity. | Vyshnavi Vennelakanti; Michael Taylor; Aditya Nandy; Chenru Duan; Heather Kulik | Theoretical and Computational Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6455032e27fccdb3ea88e0c0/original/assessing-the-performance-of-approximate-density-functional-theory-on-95-experimentally-characterized-fe-ii-spin-crossover-complexes.pdf |
60c747eaee301c1376c797d1 | 10.26434/chemrxiv.11821341.v1 | Nickel-Catalyzed Three-Component Olefin Reductive Dicarbofunctionalization to Access Highly Functionalized Alkylborates | We
report a three-component olefin reductive dicarbofunctionalization for
constructing densely functionalized alkylborates, specifically,
nickel-catalyzed reductive dialkylation and alkylarylation of vinyl boronates
with a variety of alkyl bromides and aryl iodides. This reaction exhibits good
coupling efficiency and excellent functional group compatibility, providing
convenient access to the late-stage modification of complex natural products
and drug molecules. Combined with versatile alkylborate transformations, this
reaction could also find applications in the modular and convergent synthesis
of complex, densely functionalized compounds. | Xiao-Xu Wang; Xi Lu; Shi-Jiang He; Yao Fu | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747eaee301c1376c797d1/original/nickel-catalyzed-three-component-olefin-reductive-dicarbofunctionalization-to-access-highly-functionalized-alkylborates.pdf |
64ca237ddfabaf06ff92e5e3 | 10.26434/chemrxiv-2023-5krqd | Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations | We computationally study Zika NS3 helicase, a biological motor using ATP hydrolysis energy for nucleic acid remodelling. Through classical and QM/MM simulations, we explore the conformational landscape of Motif V, a conserved loop connecting the active sites for ATP hydrolysis and nucleic acid binding. ATP hydrolysis, initiated by a meta-phosphate group formation, involves the nucleophilic attack of a water molecule activated by Glu286 proton abstraction. Motif V hydrogen bonds to this water via Gly415 backbone NH group, assisting hydrolysis. Post-hydrolysis, free energy is released when the inorganic phosphate moves away from the coordination shell of the magnesium ion, inducing a significant shift in the conformational landscape of Motif V to establish a hydrogen bond between Gly415 NH and Glu285. Zika NS3 helicase acts as a ratchet biological motor with Motif V transitions steered by Gly415’s γ-phosphate sensing in the ATPase site. | Adrián García-Martínez; Kirill Zinovjev; J. Javier Ruiz-Pernía; Iñaki Tuñón | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca237ddfabaf06ff92e5e3/original/conformational-changes-and-atp-hydrolysis-in-zika-helicase-the-molecular-basis-of-a-biomolecular-motor-unveiled-by-multiscale-simulations.pdf |
60c74de2bb8c1a44073db663 | 10.26434/chemrxiv.12670691.v1 | Tin Oxynitride-based Ferroelectric Semiconductors for Solar Energy Conversion Applications | Lead-halide perovskites have emerged as a promising class of semiconductors;
however they suffer from issues related to lead-toxicity and instability. We report results of a firstprinciples-based design of heavy-metal-based oxynitrides as alternatives to lead-halide
perovskites. We have used density-functional-theory calculations to search a vast composition
space of ABO2N and ABON2 compounds, where B is a p-block cation, and A is an alkaline, alkaliearth, rare-earth or transition metal cation, and identify 10 new ABO2N oxynitride semiconductors
that we expect to be formable. Specifically, we discover a new family of ferroelectric
semiconductors with A3+SnO2N stoichiometry (A = Y, Eu, La, In, and Sc) in the LuMnO3-type
structure, which combine the strong bonding of metal oxides with the low carrier effective mass
and small, tunable band gaps of the lead-halide perovskites. These tin oxynitrides have predicted
direct band gaps ranging from 1.6 – 3.3 eV, and a sizeable electric polarization up to 17 μC/cm2
,
which is predicted to be switchable by an external electric field through a non-polar phase. With
their unique combination of polarization, low carrier effective mass and band gaps spanning the
entire visible spectrum, we expect ASnO2N ferroelectric semiconductors will find useful
applications as photovoltaics, photocatalysts, and for optoelectronics. | Steven Hartman; Arashdeep Thind; Rohan Mishra | Ceramics; Optical Materials; Theory - Computational; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de2bb8c1a44073db663/original/tin-oxynitride-based-ferroelectric-semiconductors-for-solar-energy-conversion-applications.pdf |
63f6b143937392db3deae0c7 | 10.26434/chemrxiv-2023-zw2cs-v2 | Spectrophotometric Measurement of Lithium in Human Saliva Using the Chromogenic Reagent Thorin | This study explored the feasibility of using the chromogenic dye Thorin to spectrophotometrically measure the lithium concentration in human saliva. The absorbance wavelength maximum of the Li-Thorin complex was determined to be 480 nm. Lithium concentrations were measured spectrophotometrically at 480 nm in human pooled saliva with lithium added to produce calibration standards of 0.00-5.29 mEq/L of lithium, which corresponds to a blood lithium range of 0.00-2.60 mEq/L, assuming a saliva/blood ratio of 2/1. A least-squares fit of the absorbance vs lithium concentration calibration data produced a regression equation y = 0.128x + 1.449 with correlation coefficient = 0.997. This regression equation was then used to predict lithium concentrations from absorbance data in prepared lithium/saliva test solutions and in hospitalized patients being treated with lithium. The results generally agreed well with those determined by atomic absorption spectroscopy. By measuring absorbance of test saliva vs reagent blank containing the same amount of saliva, interfering effects of saliva protein and electrolytes in the test samples were avoided. This study supports the continued exploration of this method as a non-invasive point-of-care testing approach for monitoring saliva lithium during lithium treatment. | Stephen Robert Levitt, MD, PhD* | Biological and Medicinal Chemistry; Inorganic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Ligands (Inorg.); Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f6b143937392db3deae0c7/original/spectrophotometric-measurement-of-lithium-in-human-saliva-using-the-chromogenic-reagent-thorin.pdf |
62f1c4efe78f7008a3348b24 | 10.26434/chemrxiv-2022-b6f3m | Graphite-supported Ptn Cluster Electrocatalysts: Major Change of Active Sites as a Function of the Applied Potential | The oxygen reduction reaction (ORR) plays a key role in renewable energy transformation processes. Unfortunately, it is inherently sluggish, which greatly limits its industrial application. Sub-nano cluster decorated electrode interfaces are promising candidate ORR electrocatalysts. However, understanding the nature of the active sites on these catalysts in electrocatalytic conditions presents a formidable challenge for both experiment and theory, due to their dynamic fluxional character. Here, we combine global optimization with the electronic Grand Canonical DFT, to elucidate the structure and dynamics of sub-nano Ptn clusters deposited on electrified graphite. We show that under electrochemical conditions, these clusters exist as statistical ensembles of multiple states, whose fluxionality is greatly affected by the applied potential, electrolyte, and adsorbate coverage. The results reveal the presence of potential-dependent active sites, and hence, reaction energetics. | Julen Munarriz; Zisheng Zhang; Philippe Sautet; Anastassia N. Alexandrova | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f1c4efe78f7008a3348b24/original/graphite-supported-ptn-cluster-electrocatalysts-major-change-of-active-sites-as-a-function-of-the-applied-potential.pdf |
66c2381920ac769e5f004710 | 10.26434/chemrxiv-2024-34n5h | Harnessing DFT and Machine Learning for Accurate Optical Gap Prediction in Conjugated Polymers | Conjugated polymers (CPs), characterized by alternating σ and π bonds, have attracted significant attention for their diverse structures and adjustable electronic properties.
However, predicting the optical band gap (E_gap^exp) of CPs remains challenging. This study presents a rational model that integrates density functional theory (DFT) calculation with a data-driven machine learning (ML) approach to predict the experimentally measured E_gap^exp of CPs, using 1096 data points. Through alkyl side chain truncation and conjugated backbone extension, the modified oligomers effectively capture the electronic properties of CPs, significantly improving the correlation between the DFT-calculated HOMO-LUMO gap (E_gap^oligomer) and E_gap^exp (R2=0.51) compared to the unmodified side-chain-containing monomers (R2=0.15). Moreover, we trained six ML models with two categories of features as input: E_gap^oligomer to represent the extended backbone and molecular features of unmodified monomers to capture the alkyl-side-chain effect. The best model, XGBoost-2, achieved an R2 of 0.77 and an MAE of 0.065 eV for predicting E_gap^exp, falling within the experimental error margin of ∼0.1 eV. We further validated XGBoost-2 on a dataset of 227 newly synthesized CPs collected from literature without further retraining. Notably, XGBoost-2 exhibits both excellent interpolation for BT-, BTA-, QA-, DPP-, and TPD-based CPs, and exceptional extrapolation for PDI-, NDI-, DTBT-, BBX-, and Y6-based CPs, which are attributed to the integration of DFT methods with rationally designed oligomer structures. For the first time, we demonstrated a novel and effective strategy combining quantum chemistry calculations with ML modeling for accurate and efficient prediction of experimentally measured fundamental properties of CPs. Our study paves the way for the accelerated design and development of high-performance CPs in photoelectronic applications. | Bin Liu; Yunrui Yan; Mingjie Liu | Theoretical and Computational Chemistry; Polymer Science; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c2381920ac769e5f004710/original/harnessing-dft-and-machine-learning-for-accurate-optical-gap-prediction-in-conjugated-polymers.pdf |
646b7d47ccabde9f6e2eeaa4 | 10.26434/chemrxiv-2023-v13tv | Machine learning accelerated photodynamics simulations | Machine learning (ML) continues to revolutionize computational chemistry by accelerating predictions and simulations by training on experimental or accurate but expensive quantum chemical (QC) calculations. Photodynamics simulations require hundreds of trajectories coupled with multiconfigurational QC calculations of energies, forces, and non-adiabatic couplings that contribute to the prohibitive computational cost at long timescales and complex organic molecules. ML accelerates photodynamics simulations by combining nonadiabatic photodynamics simulations with an ML model trained with high-fidelity QC calculations of energies, forces, and non-adiabatic couplings. This approach has provided time-dependent molecular structural information for understanding photochemical reaction mechanisms of organic reactions in vacuum and complex environments (i.e., explicit solvation). This review focuses on the fundamentals of QC calculations and machine learning techniques. We then discuss the strategies to balance adequate training data and the computational cost of generating these training data. Finally, we demonstrate the power of applying these ML-photodynamics simulations to understand the origin of reactivities and selectivities of organic photochemical reactions, such as cis-trans isomerization, [2+2]-cycloaddition, 4π-electrostatic ring-closing, and hydrogen roaming mechanism. | Jingbai Li; Steven Lopez | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b7d47ccabde9f6e2eeaa4/original/machine-learning-accelerated-photodynamics-simulations.pdf |
6564582729a13c4d4716a8f3 | 10.26434/chemrxiv-2023-fllc8 | Strain Stiffening of Flexible Polymer Chains | Both polymer size and chain elasticity depend on long-range bond correlations. These correlations are gradually cut off for higher externally applied force thus increasing chain stiffness. We develop a theory for tension-dependent elasticity and validate it with simulations. Our model explains the higher stiffness measured in single-molecule force spectroscopy experiments compared with scattering experiments of unperturbed chains. | Liel Sapir; Danyang Chen; Michael Rubinstein | Polymer Science; Polymer chains | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6564582729a13c4d4716a8f3/original/strain-stiffening-of-flexible-polymer-chains.pdf |
60c73d8f567dfe1cc4ec3639 | 10.26434/chemrxiv.5851857.v1 | Protein-Ligand Binding Enthalpies from Near-Millisecond Simulations: Analysis of a Preorganization Paradox | Calorimetric studies of protein-ligand binding often yield thermodynamic data that are difficult to explain in physical terms. Today, explicit solvent molecular dynamics simulations are fast enough that we can begin to use them to look for explanations of such thermodynamic puzzles. Additionally, when such simulations generate results that do not agree well with experiment, this may motivate further development of computational methods and force fields. Here, we apply near-millisecond duration simulations to compute and analyze the binding of four peptidic ligands with the Grb2 SH2 domain, focusing on relative binding enthalpies. The ligands fall into matched pairs, which differ only in the presence or absence of a conformationally constraining bond, which preorganizes two of the ligands for binding. Prior experimental work had revealed, unexpectedly, that binding of the constrained ligands is favored enthalpically, rather than entropically, relative to their flexible<br />analogs. However, the present calculations yield the opposite trend. On further analysis, the computed relative binding enthalpies are found to be small balances of much larger underlying differences in the mean energies of structural components, such as the ligand and the binding site residues. As a consequence, the deviations from experiment in the relative binding enthalpies represent small differences between these large numbers. We also computed first order estimates of changes in configurational entropy on binding. These suggest that the more rigid constrained ligands reduce the entropy of binding site residues more than their flexible analogs do. The implications of these calculations for the use of simulations to understand the thermodynamics of molecular recognition, and for the computational analysis of binding thermodynamics, are discussed. | Amanda Li; Michael Gilson | Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2018-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d8f567dfe1cc4ec3639/original/protein-ligand-binding-enthalpies-from-near-millisecond-simulations-analysis-of-a-preorganization-paradox.pdf |
60c74bed469df458fef43fcc | 10.26434/chemrxiv.12401921.v1 | Supramolecular Behaviour and Fluorescence of Rhodamine-Functionalised ROMP Polymer | <p>Inherently fluorescent
polymers are of interest in materials and medicine. We report a ring-opening
metathesis polymerisation (ROMP) platform for creation of amphiphilic block copolymers
in which one block is formed from rhodamine B-containing monomers. The polymers
self-assemble into well-defined micelles which are able to sequester molecular
dyes and further interact with them by energy transfer. Despite incorporating a
cationic dye known to bind DNA, the polymer micelles do not interact with DNA,
indicating that they are potentially safe for use in bioanalytical applications.</p> | Lee Birchall; Sara Shehata; Sean McCarthy; Helena J. Shepherd; Ewan Clark; Christopher Serpell; Stefano Biagini | Biopolymers; Polymer brushes | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bed469df458fef43fcc/original/supramolecular-behaviour-and-fluorescence-of-rhodamine-functionalised-romp-polymer.pdf |
675c61227be152b1d0e0cf1d | 10.26434/chemrxiv-2024-1d7pt-v2 | Compositional flexibility in irreducible antifluorite electrolytes for next-generation battery anodes | Solid state batteries currently receive ample attention due to their potential to outperform lithium ion batteries in terms of energy density when featuring next generation anodes such as lithium metal or silicon. One key remaining challenge is identifying solid electrolytes that combine high ionic conductivity with stability in contact with the highly reducing potentials of next-generation anodes. Fully reduced electrolytes, based on irreducible anions, offer a promising solution by avoiding electrolyte decomposition altogether. In this study, we demonstrate the compositional flexibility of the disordered antifluorite framework accessible by mechanochemical synthesis and leverage it to discover irreducible electrolytes with high ionic conductivities. We show that the recently investigated Li9N2Cl3 and Li5NCl2 phases are part of the same solid solution of Li-deficient antifluorite phases existing on the LiCl-Li3N tie line with a general chemical formula of Li1+2xCl1-xNx (0.33<x<0.5). Using density functional theory calculations, we identify the origin of the 5-order of magnitude conductivity increase of the Li1+2xCl1-xNx phases compared to the structurally related rock salt LiCl phase. Finally, we demonstrate that SCl and BrCl substituted analogues of the Li1+2xCl1-xNx phases may be synthesized, enabling significant conductivity improvements by a factor of 10, reaching 0.2 mS cm-1 for Li2.31S0.41Br0.14N0.45. This investigation demonstrates for the first time that irreducible antifluorite-like phases are compositionally highly modifiable; this finding lays the ground for discovery of new compositions of irreducible antifluorite-like phases with even further increased conductivities, which could help eliminate solid-electrolyte decomposition and decomposition-induced Li losses on the anode side in high-performance next-generation batteries. | Victor Landgraf; Mengfu Tu; Zhu Cheng; Alexandros Vasileiadis; Marnix Wagemaker; Theodosios Famprikis | Physical Chemistry; Inorganic Chemistry; Electrochemistry; Solid State Chemistry; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c61227be152b1d0e0cf1d/original/compositional-flexibility-in-irreducible-antifluorite-electrolytes-for-next-generation-battery-anodes.pdf |
6372335574b7b61d98fcf3a7 | 10.26434/chemrxiv-2022-z9kq4 | Palladium Catalyzed syn-1,2-ArylMethylation of Internal Alkynes | A Pd-catalyzed syn-1,2-arylmethylation of internal alkynes (ynamides/ yne-acetates) is described. The readily available and bench stable coupling partners iodo-arenes, and methyl boronic acid are successfully being used to access the methyl containing tetra substituted olefins; notably, the transformation is regio as well stereoselective. The scope is broad (52 examples), showing excellent functional-group tolerance. Finally, synthetic manifestations of the products were also demonstrated. | Shubham Dutta; Akhila K. Sahoo | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6372335574b7b61d98fcf3a7/original/palladium-catalyzed-syn-1-2-aryl-methylation-of-internal-alkynes.pdf |
6687debc01103d79c519ed12 | 10.26434/chemrxiv-2024-6sp7h | A fully-polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework | In this work, we present the development of a fully-polarizable KS-DFT/AMOEBA embedding scheme for delocalized basis sets such as plane-waves and real-space grids. The augmented problem of electron spill-out inherent to a polarizable QM/MM implementation with plane-wave basis sets is addressed and the periodicity for the MM subsystem is taken into account, as implemented in the Tinker-HP software. We discuss the software design and how computational efficiency is enabled through the interoperable multiscale simulation framework MiMiC. The implementation is validated on QM/MM energies for dimer systems and a quantitative assessment of molecular dipoles of embedded solutes in order to estimate the magnitude of errors related to the damping parameters used in the model. | Sonata Kvedaravičiūtė; Andrej Antalík; Olivier Adjoua; Thomas Plé; Louis Lagardère; Ursula Rothlisberger; Jean-Philip Piquemal; Jógvan Magnus Haugaard Olsen | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687debc01103d79c519ed12/original/a-fully-polarizable-ks-dft-amoeba-embedding-scheme-for-plane-wave-basis-sets-through-the-mi-mi-c-framework.pdf |
63c13331ee6f18d6419f211d | 10.26434/chemrxiv-2023-spndb | Using Native Mass Spectrometry to Analyse Proteins Directly from Food | Globally, food is a multi-trillion-pound industry for which proteomic analysis represents a key tool in ensuring that consumer health and rights are maintained. Here we use native mass spectrometry methodology to analyse a series of natural food products of varying complexity, namely: cow milk (liquid); chicken egg white (viscous liquid) and jack bean meal (solid). Our approach permits rapid detection (~5-30 mins) and unambiguous identification of the majority (>80%) of proteins present within milk and egg white, which are foodstuffs that between them comprise two of the most prominent sources of allergenic proteins within the food industry. Furthermore, we show that this method also enables the retention of bioactive protein complexes directly from natural sources, exemplified by the detection of three multimeric states (monomer, dimer and tetramer) of concanavalin A, naturally found in jack beans (Canavalia ensiformis). As such, we propose that native mass spectrometry methods can augment the current bottom up proteomic toolkit employed within food analyses and may prove useful for fast detection and high accuracy identification of suspected proteinaceous allergens/adulterants within sufficiently noncomplex food substances. | Aidan France; Francesco Bramonti; Sarah Vickers; Jakub Ujma; Jordan Bye; Kathleen Cain; Bruno Bellina; Robin Curtis; Perdita Barran | Analytical Chemistry; Agriculture and Food Chemistry; Mass Spectrometry; Separation Science; Food | CC BY NC 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c13331ee6f18d6419f211d/original/using-native-mass-spectrometry-to-analyse-proteins-directly-from-food.pdf |
60c758b7bdbb897071a3ae01 | 10.26434/chemrxiv.14587401.v1 | DoE Optimization Empowers the Automated Preparation of Enantiomerically Pure [18F]Talazoparib and its In Vivo Evaluation as a PARP Radiotracer. | PARP inhibitors are proven chemotherapeutics and serve as lead structures for the development of PARP-targeted in vivo imaging probes. Given the clinical potential of PARP imaging for the detection and stratification of various cancers, the development of novel PARP imaging probes with improved pharmacologi-cal profiles over established PARP imaging agents is warranted. Here, we present a novel 18F-labeled PARP radiotracer based on the clinically superior PARP inhibitor talazoparib. An automated radiosynthesis of [18F]talazoparib (RCY: 13 ± 3.4 %; n = 4; molar radioactivity 52 – 176 GBq/μmol) was achieved using a “Design of Experiments” (DoE) optimized copper-mediated radiofluorination reaction. The chiral product was isolated from the reaction mixture using 2D reversed-phase/chiral radio-HPLC (>99% ee). (8S, 9R)-[18F]Talazoparib demonstrated PARP binding in HCC1937 cells in vitro and showed an excellent tumor-to-blood ratio in xeno-graft-bearing mice (10.2 ± 1.5). Despite expected uptake into muscle, bone, and abdominal tissue, a favorable pharmacological profile in terms of excretion, blood half-life, and target engagement was observed in the pilot in vivo study. This synthesis of [18F]talazoparib exemplifies how a DoE based tracer development pipeline can enable the radiosyntheses of clinically relevant but synthetically challenging radiolabeled compounds of high interest to the imaging community. | Gregory D. Bowden; Sophie Stotz; Johannes Kinzler; Christian Geibel; Michael Laemmerhofer; Bernd J. Pichler; Andreas Maurer | Organic Synthesis and Reactions; Process Chemistry; Stereochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758b7bdbb897071a3ae01/original/do-e-optimization-empowers-the-automated-preparation-of-enantiomerically-pure-18f-talazoparib-and-its-in-vivo-evaluation-as-a-parp-radiotracer.pdf |
65c10a469138d231617eb830 | 10.26434/chemrxiv-2023-4jm5t-v2 | Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library | Computational exploration of chemical space is crucial in modern cheminformatics research for accelerating the discovery of new biologically active compounds. In this study, we present a detailed analysis of the chemical library of potential glucocorticoid receptor (GR) ligands generated by the molecular generator, Molpher. To generate the targeted GR library and to construct the classification models, structures from the ChEMBL database as well as from the internal IMG library, that was experimentally screened for biological activity in the primary luciferase reporter cell assay, were utilized. The composition of the targeted GR ligand library was compared with a reference library that randomly samples chemical space. A random forest model was used to determine the biological activity of ligands, incorporating its applicability domain using conformal prediction. It was demonstrated that the GR library is significantly enriched with GR ligands compared to the random library. Furthermore, prospective analysis demonstrated that Molpher successfully designed compounds which were subsequently experimentally confirmed to be active on the GR. A collection of 34 potential new GR ligands was also identified. Moreover, an important contribution of this study is the establishment of a comprehensive workflow for the evaluation of computationally generated ligands, particularly those with potential activity against targets that are challenging to dock. | Maria Isabel Agea; Ivan Čmelo; Wim Dehaen; Ya Chen; Johannes Kirchmair; David Sedlák; Petr Bartůněk; Martin Šícho; Daniel Svozil | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c10a469138d231617eb830/original/chemical-space-exploration-with-molpher-generating-and-assessing-a-glucocorticoid-receptor-ligand-library.pdf |
62835ffb3f1e7c0217c0c887 | 10.26434/chemrxiv-2022-zwqd1 | Visualizing On-Surface Decomposition Chemistry at the Nanoscale Using Tip-Enhanced Raman Spectroscopy | Chemical imaging of molecular decomposition processes at solid-liquid interfaces is a long-standing problem in achieving mechanistic understanding. Conventional analytical tools fail to meet this challenge due to the lack of required chemical sensitivity and specificity at the nanometer scale. In this work, we demonstrate that high-resolution hyperspectral tip-enhanced Raman spectroscopy (TERS) imaging can be a powerful analytical tool to study on-surface decomposition chemistry at the nanoscale. Specifically, we present a TERS based hyperspectral approach to visualize the on-surface decomposition process of a pyridine-4-thiol (4-PyS) self-assembled monolayer on atomically flat Au(111) surfaces under ambient conditions. Reactive intermediates involved in the degradation process are spectroscopically detected with 5 nm spatial resolution. With supporting density functional theory simulations, a key species could be assigned to the disulfide reaction intermediate. This work opens a new application area of studying on-surface decomposition chemistry and related dynamics quantitatively at solid-liquid interfaces with nanometer spatial resolution. | Zhen-Feng Cai; Timon Käser; Naresh Kumar; Renato Zenobi | Physical Chemistry; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62835ffb3f1e7c0217c0c887/original/visualizing-on-surface-decomposition-chemistry-at-the-nanoscale-using-tip-enhanced-raman-spectroscopy.pdf |
60c9e3b1059ce2634376bb43 | 10.26434/chemrxiv.14778147.v1 | Uptake, Trapping, and Release of Organometallic Cations in Redox-Active Cationic Hosts | The host-guest chemistry of metal-organic nanocages is
typically driven by thermodynamically favorable interactions with their guests,
such that uptake and release of guests can be controlled by switching affinity
on/off. Herein, we achieve this effect by reducing porphyrin-walled cationic
nanoprisms <b>1a<sup>12+</sup></b> and <b>1b<sup>12+</sup></b> to zwitterionic
states that rapidly uptake organometallic cations Cp*<sub>2</sub>Co<sup>+</sup>
or Cp<sub>2</sub>Co<sup>+</sup>. Cp*<sub>2</sub>Co<sup>+</sup> binds strongly (<i>K</i><sub>a</sub>
= 1.3 x 10<sup>3</sup> M<sup>−1</sup>)
in the neutral state <b>1a<sup>0</sup></b> of host <b>1a<sup>12+</sup></b>,
which has its three porphyrin walls doubly reduced and its six (bipy)Pt<sup>2+</sup>
linkers singly reduced. The less-reduced states of the host <b>1a<sup>3+</sup></b>
and <b>1a<sup>9+</sup></b> also bind Cp*<sub>2</sub>Co<sup>+</sup>, though with
lower affinities. The smaller Cp<sub>2</sub>Co<sup>+</sup> cation binds
strongly (<i>K</i><sub>a</sub> = 1.7 x 10<sup>3</sup> M<sup>-1</sup>) in the 3
e<sup>−</sup> reduced state <b>1b<sup>9+</sup></b>
of (tmeda)Pt<sup>2+</sup> linked host <b>1b<sup>12+</sup></b>. Upon reoxidation
of the hosts with Ag<sup>+</sup>, the guests become trapped to provide
unprecedented metastable cation-in-cation complexes <b>Cp*<sub>2</sub>Co<sup>+</sup>@1a<sup>12+</sup>
</b>and <b>Cp<sub>2</sub>Co<sup>+</sup>@1b<sup>12+</sup></b> that persist for
>1 month. Thus, dramatic kinetic effects reveal a way to confine the guests
in thermodynamically unfavorable environments. Experimental and DFT studies
indicate that PF<sub>6</sub><sup>−</sup>
anions kinetically stabilize <b>Cp*<sub>2</sub>Co<sup>+</sup>@1a<sup>12+</sup> </b>through
electrostatic interactions and by influencing conformational changes of the
host that open and close its apertures. However, when <b>Cp*<sub>2</sub>Co<sup>+</sup>@1a<sup>12+</sup>
</b>was prepared using ferrocenium (Fc<sup>+</sup>) instead of Ag<sup>+</sup>
to reoxidize the host, dissociation was accelerated >200-fold even though neither
Fc<sup>+</sup> nor Fc have any competing affinity for <b>1a<sup>12+</sup></b>.
This finding shows that metastable host-guest complexes can respond to subtler
stimuli than are required to induce guest release from thermodynamically
favorable complexes. | Iram F. Mansoor; Kaitlyn Dutton; Daniel A. Rothschild; Richard C. Remsing; Mark C. Lipke | Supramolecular Chemistry (Org.); Electrochemistry; Organometallic Compounds; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b1059ce2634376bb43/original/uptake-trapping-and-release-of-organometallic-cations-in-redox-active-cationic-hosts.pdf |
64ed66523fdae147fa09c410 | 10.26434/chemrxiv-2023-8dxvc | General rules for the design of molecular photoswitches based on electrocyclization | Molecular photoswitches undergo a structural transformation upon excitation with light to intraconvert between two or more stable forms. In some cases, the structural rearrangement involves a cyclization reaction, that is, the transition between ring-open and ring-closed molecular forms. In this work we develop simple guidelines for the design of organic molecules able to undergo photochemical electrocyclization, using electronic structure calculations on one of the most widely-used family of molecules in the field, dithienylethene (DTE)-based compounds. We conclude that the ability to photocyclize can be predicted from the localization and symmetry of frontier molecular orbitals. These ideas are based on the Woodward- Hoffmann rules, but go beyond them, allowing the behavior of a more general family of chromophores, chemically substituted DTEs, to be understood. Moreover, our rules have been validated by assessment of a large number of molecular photoswitches that have been previously investigated experimentally. We have also explored the relationship between thermal stability of the closed form and aromaticity. We use the DTE scaffold as the workhorse model in our computational study, however, these simple yet powerful guidelines are expected to be generally valid to guide the design of other diarylethenes. | Clàudia Climent; Zhen Xu; Michael O. Wolf; David Casanova | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ed66523fdae147fa09c410/original/general-rules-for-the-design-of-molecular-photoswitches-based-on-electrocyclization.pdf |
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