id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
60c774160f50dba93a398825 | 10.26434/chemrxiv.13221851.v2 | Predicting Low Toxicity and Scalable Solvent Systems for High Speed Roll-to-Roll Perovskite Manufacturing | This manuscript introduces solvent toxicity in solar perovskite ink chemistries as a major technoeconomic limitation for the growth of the technology. More specifically, the capital and operational cost of handling such toxic chemicals to maintain a safe working environment can lead to significant added costs. As all record power conversion efficiency devices to date have been solution processed, this represents a major challenge for the perovskite optoelectronic field and of printed electronics as a whole. Knowing this limitation, we propose that solvent selections for ink chemistries should be more quantitative and focus on lowering toxicity. To this end, we show that a Hansen solubility model is effective in predicting ink systems using lower toxicity solvents. We also show that inks formed from this method are applicable for high-speed slot-die coating, limiting the need for long anneal times. These methods and results demonstrate a useful framework for quantitatively engineering solvent systems with reduced toxicity while simultaneously maintaining and surpassing performance. It therefore provides a pathway and major step forward towards the commercialization of solution coated perovskite technologies. | Richard Swartwout; Rahul Patidar; Emma Belliveau; Benjia Dou; David Beynon; Peter Greenwood; Nicole Moody; Dane W. deQuilettes; Moungi Bawendi; Trystan M. Watson; Vladimir Bulovic | Coating Materials; Materials Processing; Optical Materials; Thin Films; Fluid Mechanics; Coordination Chemistry (Organomet.); Photovoltaics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c774160f50dba93a398825/original/predicting-low-toxicity-and-scalable-solvent-systems-for-high-speed-roll-to-roll-perovskite-manufacturing.pdf |
678581a2fa469535b9dc139b | 10.26434/chemrxiv-2025-1szzf | Comprehensive Study on Solvent Dynamics in Gel Polymer Electrolytes for Lithium-Sulfur Battery | Li-Sulfur (Li-S) batteries stand promising as the next-generation energy storage technology but are hindered by sluggish sulfur redox reaction kinetics and sulfur shuttling effect. Many studies tried to address these issues by adopting polycaprolactone (PCL) based gel polymer electrolytes (GPEs), but often overlooked solvent properties, including dielectric constant (ϵ), donor and acceptor numbers (DN and AN), impact performance and prevent the full implementation of GPE-based Li-S batteries. This work compares three distinct electrolytes paired with PCL, namely, dimethoxyethane (DME), dimethyl sulfoxide (DMSO), and tetraethylene glycol dimethyl ether (TEGDME), due to their varied solvent properties, to evaluate their effects on the physical properties of the GPE, Li⁺ transport and solvation, and polysulfide's confinement. The DME-based GPE, with an intermediate DN, exhibited the lowest crystallinity (2.31%), highest ionic conductivity (7.49 mS/cm), and high Li⁺ transference number (0.77), achieving a specific capacity of 795 mAh/g sulfur and an average coulombic efficiency of 97.5% after 120 cycles at C/5, outperforming its competitors. Moreover, operando Raman and UV-Vis spectroscopy confirmed that PCL effectively confines long-chain polysulfides within its network, mitigating the shuttle effect and facilitating reversible polysulfide conversion. These findings highlight that GPEs with moderate DN values and balanced ϵ enhance stability, extend cycle life, and improve rate performance for Li-S batteries, providing unique insights for designing advanced electrolyte systems for practical applications. | Luisa Gomes; Huidong Dai; Daniel Chambers; Victor Ribeiro Sanctis; Kevin Yang; Ruizhi Dong; Anhtu Do; Tongtai Ji; Sanjeev Mukerjee | Materials Science; Nanoscience; Energy; Fuels - Materials; Energy Storage; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678581a2fa469535b9dc139b/original/comprehensive-study-on-solvent-dynamics-in-gel-polymer-electrolytes-for-lithium-sulfur-battery.pdf |
60c73ee2702a9b4639189e67 | 10.26434/chemrxiv.7182215.v1 | Lateral Adsorbate Interactions Inhibit HCOO- While Promoting CO Selectivity for CO2 Electrocatalysis on Ag | <p>The analysis presented in this manuscript helps bridge an important fundamental discrepancy between the existing theoretical and experimental knowledge regarding the performance of Ag catalysts for CO<sub>2</sub> electrochemical reduction (CO<sub>2</sub>ER). The results demonstrate how the intermediate species *OCHO is formed readily en-route the HCOO<sup>– </sup>pathway and plays a decisive role in determining selectivity of a predominantly CO producing catalyst such as Ag. Our theoretical and experimental approach develops a better understanding of the nature of competition as well as the complex interactions between the reaction intermediates leading to CO, HCOO<sup>–</sup> and H<sub>2</sub> during CO<sub>2</sub>ER.</p><p><br /></p><p>Details of computational and experimental methods are present in the Supporting Information provided. </p><p><br /></p><p><br /></p> | Divya Bohra; Isis Ledezma-Yanez; Guanna Li; Wiebren De Jong; Evgeny A. Pidko; Wilson A. Smith | Computational Chemistry and Modeling; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2018-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ee2702a9b4639189e67/original/lateral-adsorbate-interactions-inhibit-hcoo-while-promoting-co-selectivity-for-co2-electrocatalysis-on-ag.pdf |
643698c473c6563f14b690f2 | 10.26434/chemrxiv-2023-b7f0j-v2 | The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry | In this article the recent developments of the open-source OpenMolcas chemistry software environment, since spring 2020, are described, with the main focus on novel functionalities that are accessible in the stable branch of the package and/or via interfaces with other packages. These community developments span a wide range of topics in computational chemistry, and are presented in thematic sections associated with electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report represents a useful summary of these developments, and it offers a solid overview of the chemical phenomena and processes that OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations. | Giovanni Li Manni; Ignacio Fernández Galván; Ali Alavi; Flavia Aleotti; Francesco Aquilante; Jochen Autschbach; Davide Avagliano; Alberto Baiardi; Jie J. Bao; Stefano Battaglia; Letitia Birnoschi; Alejandro Blanco-González; Sergey I. Bokarev; Ria Broer; Roberto Cacciari; Paul B. Calio; Rebecca K. Carlson; Rafael Carvalho Couto; Luis Cerdán; Liviu F. Chibotaru; Nicolas F. Chilton; Jonathan Richard Church; Irene Conti; Sonia Coriani; Juliana Cuéllar-Zuquin; Razan E. Daoud; Nike Dattani; Piero Decleva; Coen de Graaf; Mickaël G. Delcey; Luca De Vico; Werner Dobrautz; Sijia S. Dong; Rulin Feng; Nicolas Ferré; Michael Filatov(Gulak); Laura Gagliardi; Marco Garavelli; Leticia González; Yafu Guan; Meiyuan Guo; Matthew R. Hennefarth; Matthew R. Hermes; Chad E. Hoyer; Miquel Huix-Rotllant; Vishal Kumar Jaiswal; Andy Kaiser; Danil S. Kaliakin; Marjan Khamesian; Daniel S. King; Vladislav Kochetov; Marek Krośnicki; Arpit Arun Kumaar; Ernst D. Larsson; Susi Lehtola; Marie-Bernadette Lepetit; Hans Lischka; Pablo López Ríos; Marcus Lundberg; Dongxia Ma; Sebastian Mai; Philipp Marquetand; Isabella C. D. Merritt; Francesco Montorsi; Maximilian Mörchen; Artur Nenov; Vu Ha Anh Nguyen; Yoshio Nishimoto; Meagan S. Oakley; Massimo Olivucci; Markus Oppel; Daniele Padula; Riddhish Pandharkar; Quan Manh Phung; Felix Plasser; Gerardo Raggi; Elisa Rebolini; Markus Reiher; Ivan Rivalta; Daniel Roca-Sanjuán; Thies Romig; Arta Anushirwan Safari; Aitor Sánchez-Mansilla; Andrew M. Sand; Igor Schapiro; Thais R. Scott; Javier Segarra-Martí; Francesco Segatta; Dumitru-Claudiu Sergentu; Prachi Sharma; Ron Shepard; Yinan Shu; Jakob K. Staab; Tjerk P. Straatsma; Lasse Kragh Sørensen; Bruno Nunes Cabral Tenorio; Donald G. Truhlar; Liviu Ungur; Morgane Vacher; Valera Veryazov; Torben Arne Voß; Oskar Weser; Dihua Wu; Xuchun Yang; David Yarkony; Chen Zhou; J. Patrick Zobel; Roland Lindh | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643698c473c6563f14b690f2/original/the-open-molcas-web-a-community-driven-approach-to-advancing-computational-chemistry.pdf |
63cf07096bc5cae6351832b9 | 10.26434/chemrxiv-2023-2n5dp | Direct π-Activation vs. O-Activation in Halogen Bonding Catalysis | Halogen bond donors had an increasing impact on catalysis in recent years, and their development is highly active. In particular, numerous iodine-based halogen bond donors have been developed and used to promote various reactions through coordinating carbonyl groups, a ubiquitous mode of activation in catalysis. We now report computational data which strongly suggests that an alternative activation mode, through direct π-complexation, is operative for unsaturated carbonyl substrates. Calculations also suggest that solvent polarity could have a clear impact on the preference of the mode of activation, raising the possibility of a mechanistic manifold switch through solvent variation. These findings could profoundly impact the development of the next generation of such halogen-bond donor catalysts. | Raphaël Robidas; Claude Legault | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Computational Chemistry and Modeling; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cf07096bc5cae6351832b9/original/direct-activation-vs-o-activation-in-halogen-bonding-catalysis.pdf |
60c74998bdbb896c37a391d6 | 10.26434/chemrxiv.12085062.v1 | Anions Enhance Rare Earth Adsorption at Negatively Charged Surfaces | Anions are expected to be repelled from negatively charged surfaces. At aqueous interfaces, however, ion-specific effects can dominate over direct electrostatic interactions. Using multiple <i>in situ</i> surface sensitive experimental techniques, we show that surface affinity of SCN<sup>-</sup> ions are so strong that they can adsorb at a negatively charged floating monolayer at the air/aqueous interface. This extreme example of ion-specific effects may be very important for understanding complex processes at aqueous interfaces, such as chemical separations of rare earth metals. Adsorbed SCN<sup>-</sup> ions at the floating monolayer increase the overall negative charge density, leading to enhanced trivalent rare earth adsorption. Surface sensitive X-ray fluorescence measurements show that the surface coverage of Lu<sup>3+</sup> ions can be triple of the apparent surface charge of the floating monolayer in the presence of SCN<sup>-</sup>. Comparison to NO<sub>3</sub><sup>-</sup> samples show that the effects are strongly dependent to the character of the anion, providing further evidence to ion-specific effects dominating over electrostatics. | Srikanth Nayak; Kaitlin Lovering; Wei Bu; Ahmet Uysal | Separation Science; Interfaces; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74998bdbb896c37a391d6/original/anions-enhance-rare-earth-adsorption-at-negatively-charged-surfaces.pdf |
658dc2aee9ebbb4db9eeae00 | 10.26434/chemrxiv-2023-pzrc4 | Competition between C–H‧‧‧S and S–H‧‧‧Cl H-bonds in CHCl3-H2S complex: A matrix isolation IR spectroscopic study | H-bonded complexes between CHCl3 and H2S have been studied in cold and inert argon matrix using IR spectroscopy. Both molecules were found to act as both H-bond donor and acceptor, resulting in two types of, namely C–H‧‧‧S and S–H‧‧‧Cl H-bonds. The H-bonded complex formation has been confirmed by monitoring the spectral changes in ν_(C-H) and ν_(S-H) fundamental vibrations. C–H‧‧‧S H-bonded dimer have been found to be more stable compared to S–H‧‧‧Cl H-bonded dimer. Besides the binary complex, CHCl3-(H2S)2 and (CHCl3)2-H2S complex has also been identified. The quantum chemical results were found to corroborate the experimental findings. | Binod Oram; Monu Morwal; Biman Bandyopadhyay | Physical Chemistry; Clusters; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658dc2aee9ebbb4db9eeae00/original/competition-between-c-h-s-and-s-h-cl-h-bonds-in-ch-cl3-h2s-complex-a-matrix-isolation-ir-spectroscopic-study.pdf |
650d598eed7d0eccc301cd03 | 10.26434/chemrxiv-2023-85hbd | A multimodal view at cancerous liver tissue by chemical bioimaging and image segmentation strategies | Six complementary biomedical imaging modalities are combined providing substantial correlation capabilities between optical, elemental and molecular tissue characteristics. Diseased rat liver tissue with hepatocellular carcinoma (HCC) was investigated, as liver cancer is a leading cause of tumor-related mortality. Bright field microscopy, autofluorescence microscopy and histological examination of hematoxylin-eosin-stained tissue displayed comprehensive optical tissue characteristics. Elemental imaging by non-destructive micro x-ray fluorescence (µXRF) and quantitative laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) revealed lower content for nine elements in HCC and lesions compared to the liver. Non-destructive quantum cascade laser (QCL)-based infrared microspectroscopy visualized higher lipid, protein, and nucleic acid content in the liver compared to HCC, and glycogen accumulations in lesions. Matrix-assisted laser desorption/ionization-trapped ion mobility spectrometry-mass spectrometry (MALDI-TIMS-MS) unveiled individual lipid distributions to characterize HCC, connective and adjacent liver tissue. Detailed image segmentation was facilitated by (bisecting) k-means clustering and interactive clustering using uniform manifold approximation and projection (UMAP) embeddings. | Katharina Kronenberg; Julia Werner; Marten Seeba; Hennes Rave; Lars Linsen; Katja Steiger; Astrid Jeibmann; Peter Bohrer; Philipp Marius Paprottka; Rickmer Früdd Braren; Fabian Karl Lohöfer; Uwe Karst | Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Mass Spectrometry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650d598eed7d0eccc301cd03/original/a-multimodal-view-at-cancerous-liver-tissue-by-chemical-bioimaging-and-image-segmentation-strategies.pdf |
60c743734c89193205ad2646 | 10.26434/chemrxiv.9179255.v1 | Heterogeneous Interactions Promote Crystallization and Spontaneous Resolution of Chiral Molecules | Predicting the crystallization behavior of solutions of chiral molecules is a major challenge in the chemical sciences. In this paper, we use molecular dynamics computer simulations to study the crystallization of a family of coarse-grained models of chiral molecules with a broad range of molecular shapes and interactions. Our simulations reproduce the experimental crystallization behavior of real chiral molecules, including racemic and enantiopure crystals, as well as amorphous solids. Using efficient algorithms for the packing of shapes, we enumerate millions of low energy crystal structures for each model and analyze the thermodynamic landscape of polymorphs. In agreement with recent conjectures, our analysis shows that the ease of crystallization is largely determined by the number of competing polymorphs with low free energy. We find that this number, and hence crystallization outcomes, depend on molecular interactions in a simple way: Strongly heterogeneous interactions across molecules promote crystallization and favor the spontaneous resolution of racemic mixtures. | John Carpenter; Michael Gruenwald | Physical Organic Chemistry; Computational Chemistry and Modeling; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743734c89193205ad2646/original/heterogeneous-interactions-promote-crystallization-and-spontaneous-resolution-of-chiral-molecules.pdf |
6472db674f8b1884b7646ad9 | 10.26434/chemrxiv-2023-pjl0w-v2 | Deep generative model of constructing chemical latent space for large molecular structures with 3D complexity | The structural diversity of chemical libraries, which are systematic collections of compounds that have potential to bind to biomolecules, can be represented by chemical latent space. A chemical latent space is a projection of a compound structure into a mathematical space based on several molecular features, and it can express structural diversity within a compound library in order to explore a broader chemical space and generate novel compound structures for drug candidates. Many of the natural compounds produced by living organisms have complicated structures and are highly biologically active. However, no deep learning models exist that can effectively construct chemical latent spaces to handle large and complex compound structures, such as those found in natural compounds, and furthermore manage chirality, which is an essential factor in the 3D complexity of compounds. In this study, we developed a new deep-learning method, called NP-VAE, based on variational autoencoder for handling natural compounds, and constructed a chemical latent space that projected large and complex compound structures including chirality. NP-VAE was successful in construction of the chemical latent space that showed higher accuracy with respect to reconstruction and generalization than the state-of-the-art deep learning methods. Furthermore, by exploring the acquired latent space, we succeeded in comprehensively analyzing a compound library containing natural compounds and generating novel compound structures with optimized functions. | Toshiki Ochiai; Tensei Inukai; Manato Akiyama; Kairi Furui; Masahito Ohue; Nobuaki Matsumori; Shinsuke Inuki; Motonari Uesugi; Toshiaki Sunazuka; Kazuya Kikuchi; Hideaki Kakeya; Yasubumi Sakakibara | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6472db674f8b1884b7646ad9/original/deep-generative-model-of-constructing-chemical-latent-space-for-large-molecular-structures-with-3d-complexity.pdf |
6404b53d9789de3dd9f6770c | 10.26434/chemrxiv-2023-bvj4f-v2 | The Chemical Bond in H2: An Orbital Exchange Calculation | This paper extends the orbital exchange method calculation of H2 to include the possibility of a [HH, H+H-] resonance. The impact of the resonance on the orbitals overlaps and on the kinetic energy is described. The bond energy for H2 is found by varying the parameters associated with the compression (orbital reduction) and polarization of the 1s bonding orbitals of H and H-, and the extent of resonance, to obtain the maximum bond energy with the bonding overlap less than or equal to 1.0. The solution finds a binding energy, De, of 4.725 e.v. at a bond length of 0.737 with resonance fraction of 0.3628. This is to be compared with the accepted value for De of 4.75 e.v. at 0.741. The success of this calculation strongly supports the hypothesis that overlapping bonding orbitals are not completely distinguishable and the efficacy of the orbital exchange method. | Paul Merrithew | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6404b53d9789de3dd9f6770c/original/the-chemical-bond-in-h2-an-orbital-exchange-calculation.pdf |
661d1fce21291e5d1de10f3e | 10.26434/chemrxiv-2024-g3l5t-v2 | Lewis Acid Catalyzed (4π+2σ) Annulation of Bicyclobutanes with Dienol Ethers for the Synthesis of Bicyclo[4.1.1]octanes | Bicyclic carbocycles containing a high fraction of Csp3 have become highly attractive synthetic targets because of the multiple applications they have found in medicinal chemistry. The formal cycloaddition of bicyclobutanes (BCB) with two- or three- atom partners has recently been extensively explored for the construction of bicyclohexanes and bicycloheptanes, but applications to the synthesis of medium-sized bridged carbocycles remained more limited. We report herein the formal (4π+2σ) cycloaddition of BCB ketones with silyl dienol ethers. The reaction occurred in the presence of 5 mol% aluminium triflate as a Lewis acid catalyst. Upon acidic hydrolysis of the enol ether intermediates, rigid bicyclo[4.1.1]octanes (BCOs) diketones could be accessed in up to quantitative yields. This procedure tolerated a range of both aromatic and aliphatic substituents on both the BCB substrates and the dienes. The obtained BCO products could be functionalized through reduction and cross-coupling reactions. | Stefano Nicolai; Jerome Waser | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d1fce21291e5d1de10f3e/original/lewis-acid-catalyzed-4-2-annulation-of-bicyclobutanes-with-dienol-ethers-for-the-synthesis-of-bicyclo-4-1-1-octanes.pdf |
67c7b0e2fa469535b9f9e321 | 10.26434/chemrxiv-2025-41644 | Mo-Catalyzed Asymmetric Allylic Alkylation Enabling the Con-struction of Highly Enantioenriched 1,4-Dicarbonyl Scaffolds | ABSTRACT: Herein, we report a Mo-catalyzed allylic alkylation that couples malonate nucleophiles with linear, tri-substituted allylic electrophiles, followed by a rapid ozonolysis. The process delivers 1,4-dicarbonyl compounds con-taining an -quaternary aldehyde motif with excellent enantioselectivity. This constitutes the first example of a Mo-catalyzed asymmetric allylic alkylation to form an electrophile-derived all-carbon quaternary stereocenter. The reac-tivity and stereoselectivity of the process was enabled by the invention of ShabyDACH, a novel C1-symmetric diamino-cyclohexane (DACH) pyridyl ligand. The utility of this transformation was demonstrated through a series of diverse synthetic transformations. | Farbod A. Moghadam ; Chloe S. Cerione ; Brian M. Stoltz | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c7b0e2fa469535b9f9e321/original/mo-catalyzed-asymmetric-allylic-alkylation-enabling-the-con-struction-of-highly-enantioenriched-1-4-dicarbonyl-scaffolds.pdf |
62d97ea681efd07320b60f40 | 10.26434/chemrxiv-2022-xp6w9 | Mechanochemistry of Spiropyran Under Internal Stresses of a Glassy Polymer | Mechanophores are powerful molecular tools used in polymers to track bond rupture and characterize mechanical damage. The majority of mechanophores are known to respond to external stresses and in this study we report the first precedent of a mechanochemical response to internal, residual stresses that accumulate during polymer vitrification. While internal stress is intrinsic to polymers that can form solids, we demonstrate that it can dramatically affect the mechanochemistry of spyropyran probes and alter their intramolecular isomerization barriers by up to 70 kJ·mol-1. This new behavior of spiropyrans enables their application for analysis of internal stresses and their mechanochemical characterization on the molecular level. Spectroscopy and imaging based on spiropyran mechanochemistry showed high topological sensitivity and allowed to discern different levels of internal stress in various locations along the polymer chain. The nature of the developed technique allows for wide field imaging of stress heterogeneities in polymer samples of irregular shapes and dimensions, making it feasible to directly observe molecular level manifestations of mechanical stresses that accompany the formation of a vast number of solid polymer. | Richard Janissen; Georgy Filonenko | Organic Chemistry; Polymer Science; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d97ea681efd07320b60f40/original/mechanochemistry-of-spiropyran-under-internal-stresses-of-a-glassy-polymer.pdf |
60c752b6567dfecf3aec5d04 | 10.26434/chemrxiv.13338905.v1 | Crystal and Electronic Facet Analysis of Ultrafine Ni2P Particles by Solid-State NMR Nanocrystallography | Structural and morphological control of crystalline nanoparticles is crucial in the field of heterogeneous catalysis and the development of “reaction specific” catalysts. To achieve this, colloidal chemistry methods are combined with ab initio calculations in order to define the reaction parameters, which drive chemical reactions to the desired crystal nucleation and growth path. Key in this procedure is the experimental verification of the predicted crystal facet and its corresponding electronic structure, which in case of nanostructured materials becomes extremely difficult. Here, by employing <sup>31</sup>P solid-state nuclear magnetic resonance (ssNMR) aided by advanced density functional theory (DFT) calculations to obtain and assign the Knight shifts, we succeeded in determining the crystal and electronic structure of the terminating surfaces of ultrafine Ni<sub>2</sub>P nanoparticles at atomic scale resolution. Our work highlights the potential of ssNMR nanocrystallography as a unique tool in the emerging field of facet-engineered nanocatalysts. | Wassilios Papawassiliou; José P. Carvalho; Nikolaos Panopoulos; Yasser Alwahedi; Vijay
Kumar Shankarayya Wadi; Xinnan Lu; Kyriaki Polychronopoulou; Jin Bae Lee; Sanggil Lee; Chang Yeon Kim; Hae Jin Kim; Marios Katsiotis; Vasileios Tzitzios; Marina Karagianni; Michael Fardis; Georgios Papavassiliou; Andrew Pell | Catalysts; Nanocatalysis - Catalysts & Materials; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752b6567dfecf3aec5d04/original/crystal-and-electronic-facet-analysis-of-ultrafine-ni2p-particles-by-solid-state-nmr-nanocrystallography.pdf |
61c309af203b4073b995ded2 | 10.26434/chemrxiv-2021-bwqxn | Multiformity of Photoelectron Storages in Functionalized Carbon Nitrides Enabling Reversible and Adaptable Colorimetric Sensing | Colorimetric sensing has been widely used for centuries across diverse fields, thanks to easy operation with no electricity and uncompromised high sensitivity. However, the limited number of chromogenic systems hampers its broader applications. Here, we reported that carbon nitride (CN), the raw materials-abundant and cheap semiconductors with photoelectron storage capability, can be developed as a new chromogenic platform for colorimetric sensing. Beyond most photoelectron storage materials that only demonstrated blue color in the excited state, CN could also exhibit brown color by terminal group functionalization. The experiments and DFT theoretical calculation revealed the origin of the unusual two types of color switches. Cyano and carbonyl terminal groups in CN elongated the centroids distance of electron/hole and stabilized the excited states through a physical and electrochemical pathway, respectively; meanwhile, the counter cations strengthened these processes. As a result, the CN-derived colorimetric O2 sensors demonstrated excellent reversibility in recycling hundreds of times for detection, and exhibited adaptable limit of detection and linear detection range, which was superior to commercial O2 sensors, especially for complex systems with broad variable concentrations. | Dan Han; Hong Yang; Zhixin Zhou; Kaiqing Wu; Jin Ma; Yanfeng Fang; Qing Hong; Guangcheng Xi; Songqin Liu; Yanfei Shen; Yuanjian Zhang | Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Photochemistry (Physical Chem.); Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c309af203b4073b995ded2/original/multiformity-of-photoelectron-storages-in-functionalized-carbon-nitrides-enabling-reversible-and-adaptable-colorimetric-sensing.pdf |
60c73d51469df47746f426c7 | 10.26434/chemrxiv.5717950.v1 | Theoretical and experimental studies of palladium-catalyzed site-selective C(sp3)−H bond functionalization enabled by transient ligands | Transition
metal-catalyzed selective C–H bond functionalization enabled by transient
ligands has become an extremely attractive topic due to its economical and
greener characteristics. However, catalytic pathways of this reaction process
on unactivated sp<sup>3</sup> carbons of reactants have not been well studied
yet. Herein, detailed mechanistic investigation on Pd-catalyzed C(sp<sup>3</sup>)–H
bond activation with amino acids as transient ligands has been systematically
conducted. The theoretical calculations showed
that
higher angle
distortion of C(sp2)-H
bond
over C(sp3)-H
bond
and stronger
nucleophilicity of benzylic anion over its aromatic counterpart, leading to
higher reactivity of corresponding C(sp<sup>3</sup>)–H bonds; the angle strain
of the directing rings of key intermediates determines the site-selectivity of
aliphatic ketone substrates; replacement of glycine with β-alanine as the
transient ligand can decrease the angle tension of the directing rings. Synthetic experiments have confirmed that
β-alanine is indeed a more efficient transient ligand for arylation of
β-secondary carbons of linear aliphatic ketones than its glycine counterpart.<br /><br /> | Haibo Ge; Lei Pan; Piaoping Tang; Ke Yang; Mian Wang; Jianyi Wang; Guigen Li | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51469df47746f426c7/original/theoretical-and-experimental-studies-of-palladium-catalyzed-site-selective-c-sp3-h-bond-functionalization-enabled-by-transient-ligands.pdf |
60c741ee4c89195122ad23b7 | 10.26434/chemrxiv.8194223.v1 | Novel Hydrothermal Synthesis of Pure and Doped Ammonium and Potassium Titanyl Phosphates using a Green Heterogeneous Reaction | <div>Vital inroganic materials are often inefficienty prepared in terms of time, reagents, and manpower. Hydrothermal methods in particular often take many days or even weeks to prepare the desired materials. In this communication, we demonstrate a novel heterogeneous, green synthesis route and the crystal lattice parameters of several pure and intermediate ammonium and potassium titanyl phosphates, representing a significant improvement over existing syntheses in reaction time and precursors used. <br /></div> | Alistair Holdsworth; Monika Gamza; Runjie Mao; Harry Eccles; Gary Bond | Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry; Main Group Chemistry (Inorg.); Minerals; Reaction (Inorg.); Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ee4c89195122ad23b7/original/novel-hydrothermal-synthesis-of-pure-and-doped-ammonium-and-potassium-titanyl-phosphates-using-a-green-heterogeneous-reaction.pdf |
60c740c3337d6c012ce2676d | 10.26434/chemrxiv.7830029.v1 | Apolar Behavior of Hydrated Calcite (10{-1}4) Surface Assists in Naphthenic Acid Adsorption | Water molecules bind strongly to the polar calcite surface and form a surface adsorbed layer that has properties akin to an apolar surface. This has important implications for understanding the thermodynamic driving forces underlying the adsorption of acid groups from crude oil, in particular naphthenic acid, onto calcite. Free energy calculations show that naphthenic acid binds favorably to the water mono-layer adsorbed on the calcite surface. But to bond directly to the calcite, a free energy barrier has to be overcome to expel the intervening layer of water. Further, naphthenic acids with longer alkyl chains bind with lower free energy to the calcite surface than those with shorter alkyl chains, and, for the same chain length, branching also enhances adsorption. To better understand this behavior, for a specified alkyl chain length we study adsorption at different temperatures. Consistent with experiments, we find that adsorption is enhanced at higher temperatures. Examining the enthalpic and entropic contributions to adsorption shows that adsorption of naphthenic acid is entropically favored.<br /> | Arjun Valiya Parambathu; Le Wang; Dilip Asthagiri; Walter Chapman | Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740c3337d6c012ce2676d/original/apolar-behavior-of-hydrated-calcite-10-1-4-surface-assists-in-naphthenic-acid-adsorption.pdf |
60c741a0bdbb89d284a38384 | 10.26434/chemrxiv.8067527.v1 | Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC | We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD and GROMACS programs as QM and MM engines, respectively. The scalability is demonstrated through large-scale benchmark simulations of realistic biomolecular systems employing GGA and hybrid exchange-correlation functionals. We show that the loose-coupling strategy adopted in MiMiC, with its inherent high flexibility, does not carry any significant computational overhead compared to a tight-coupling scheme. Furthermore, we demonstrate that the adopted parallelization strategy enables scaling of up to 13,000 CPU cores with efficiency above 70%, thus making DFT-based QM/MM MD simulations using hybrid functionals at the nanosecond scale accessible. | Viacheslav Bolnykh; Jógvan Magnus Haugaard Olsen; Simone Meloni; Martin P. Bircher; Emiliano Ippoliti; Paolo Carloni; Ursula Rothlisberger | Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a0bdbb89d284a38384/original/extreme-scalability-of-dft-based-qm-mm-md-simulations-using-mi-mi-c.pdf |
60c748ceee301c9ce4c7996a | 10.26434/chemrxiv.11977899.v1 | Field Programmable Gate Arrays (FPGAs) for Enhancing the Speed and Energy Efficiency of Quantum Dynamics Simulations | We present the first application of field programmable gate arrays (FPGAs) as new, <i>customizable</i> hardware architectures that can be harnessed for the fast and energy-efficient calculation of quantum dynamics simulations of large chemical/material systems. Instead of tailoring the software to fixed hardware (which is the typical case for writing quantum chemistry code for CPUs/GPUs), FPGAs allow us to <i>directly customize the underlying hardware</i> - even at the level of specific electrical signals in the circuit - to give a truly optimized computational performance for complex quantum dynamics calculations. By offloading the most intensive and repetitive calculations onto an FPGA, we show that the computational performance of our hardware implementation for real-time electron dynamics calculations can even exceed that of optimized commercial mathematical libraries running on high-performance GPUs. In addition to this impressive computational speedup, we show that FPGAs are immensely energy-efficient and consume 4 times less energy than modern GPU or CPU architectures. These energy savings are a practical and important metric for supercomputing centers (several of which exceed over $1 million in power costs alone), as exascale computing capabilities become more widespread and commonplace. Taken together, the implementation techniques and performance metrics of our study demonstrate that FPGAs could play a promising role in upcoming quantum chemistry and materials science applications, particularly for the acceleration and energy-efficient execution of quantum dynamics calculations. | Jose Rodriguez-Borbon; Amin Kalantar; Sharma Yamijala; M. Belen Oviedo; Wallid Najar; Bryan Wong | Computational Chemistry and Modeling; Theory - Computational; Power; Quantum Mechanics; Quasiparticles and Excitations | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748ceee301c9ce4c7996a/original/field-programmable-gate-arrays-fpg-as-for-enhancing-the-speed-and-energy-efficiency-of-quantum-dynamics-simulations.pdf |
60c74f99bb8c1a76473db960 | 10.26434/chemrxiv.12924005.v1 | Chromium–Salen Complex / Nitroxyl Radical Cooperative Catalysis:A New Combination for Aerobic Intramolecular Dearomative Coupling of Phenols | Herein we describe an aerobic intramolecular dearomative coupling reaction of phenols using a catalytic system with the combination of a chromium–salen (Cr–salen) complex and a nitroxyl radical. This novel catalytic system enables the construction of a spirocyclic dienone product, which is a potentially useful intermediate for the synthesis of various
natural products such as alkaloids and phenylpropanoids from bisphenol in good yield under mild reaction conditions (under O2 and ambient temperature). A preliminary mechanistic study suggests that this reaction system is promoted by a cooperative electron transfer between the Cr(III)–salen complex, nitroxyl radical and bisphenol substrate. | Shota Nagasawa; Shogo Fujiki; Yusuke Sasano; Yoshiharu Iwabuchi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f99bb8c1a76473db960/original/chromium-salen-complex-nitroxyl-radical-cooperative-catalysis-a-new-combination-for-aerobic-intramolecular-dearomative-coupling-of-phenols.pdf |
60c75812567dfe3711ec67b9 | 10.26434/chemrxiv.14496111.v1 | Perchlorinated Triarylmethyl Radical 99% Enriched 13C at the Central Carbon as EPR Spin Probe Highly Sensitive to Molecular Tumbling | <p>Soluble stable radicals are used as spin probes and spin
labels for <i>in vitro</i> and <i>in vivo</i> Electron Paramagnetic Resonance
(EPR) spectroscopy and imaging applications. We report the synthesis and
characterization of a perchlorinated triarylmethyl radical enriched 99% at the
central carbon, <b><sup>13</sup>C<sub>1</sub>-PTMTC</b>.
The anisotropy of the hyperfine splitting with the <sup>13</sup>C<sub>1</sub>
(A<sub>x</sub>=26, A<sub>y</sub>=25, A<sub>z</sub>=199.5 MHz) and the g (g<sub>x</sub>=2.0015,
g<sub>y</sub>=2.0015, g<sub>z</sub>=2.0040) are responsible for a strong effect
of the radical tumbling rate on the EPR spectrum. The rotational correlation
time can be determine by spectral simulation or via the linewidth after
calibration. As spin probe <b><sup>13</sup>C<sub>1</sub>-PTMTC
</b>can be used to measure media microviscosity with high sensitivity. Bound to
a macromolecule as spin label, <b><sup>13</sup>C<sub>1</sub>-PTMTC
</b>could be used to study local mobility and molecular interactions.</p> | Martin Poncelet; Justin L. Huffman; Gareth R. Eaton; Whylder Moore; Sandra Eaton; Benoit Driesschaert | Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75812567dfe3711ec67b9/original/perchlorinated-triarylmethyl-radical-99-enriched-13c-at-the-central-carbon-as-epr-spin-probe-highly-sensitive-to-molecular-tumbling.pdf |
64a9885d9ea64cc167a9755f | 10.26434/chemrxiv-2023-6tsq4 | Unraveling propylene oxide formation in alkali metal batteries | The increasing need for electrochemical energy storage drives the development of post-lithium battery systems. Among the most promising new battery types are sodium-based battery systems. However, like its lithium predecessor, sodium batteries suffer from various issues like parasitic side reactions, which lead to a loss of active sodium inventory, thus reducing the capacity over time. Some problems in sodium batteries arise from an unstable solid electrolyte interphase (SEI) reducing its protective power e.g., due to increased solubility of SEI components in sodium battery systems. While it is known that the electrolyte affects the SEI structure, the exact formation mechanism of the SEI is not yet fully understood. In this study, we follow the initial SEI formation on a piece of sodium metal submerged in propylene carbonate with and without the electrolyte salt sodium perchlorate. We combine X-ray photoelectron spectroscopy, gas chromatography, and density functional theory to unravel the sudden emergence of propylene oxide after adding sodium perchlorate to the electrolyte solvent. We identify the formation of a sodium chloride layer as a crucial step in forming propylene oxide by enabling precursors formed from propylene carbonate on the sodium metal surface to undergo a ring-closing reaction. Based on our combined theoretical and experimental approach, we identify changes in the electrolyte decomposition process, propose a reaction mechanism to form propylene oxide and discuss alternatives based on known synthesis routes. | Daniel Stottmeister; Leonie Wildersinn; Julia Maibach; Andreas Hofmann; Fabian Jeschull; Axel Gross | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Surface | CC BY 4.0 | CHEMRXIV | 2023-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a9885d9ea64cc167a9755f/original/unraveling-propylene-oxide-formation-in-alkali-metal-batteries.pdf |
64d484074a3f7d0c0dec1fb0 | 10.26434/chemrxiv-2023-g79wm | Lossless photon recording of two-color fluorescence correlation spectroscopy for protein dynamics investigations from nanoseconds to milliseconds | Nanosecond-resolved fluorescence correlation spectroscopy (ns-FCS) based on two-color fluorescence detection is a powerful strategy for the investigation of fast dynamics of biological macromolecules labeled with donor and acceptor fluorophores. The standard methods of ns-FCS utilize two single-photon avalanche diodes (SPADs) for the detection of single-color signals (four SPADs for two-color signals) to eliminate the afterpulse artifacts of SPAD at the expense of the efficiency of counting fluorescence photons. In this study, we demonstrated that hybrid photodetectors (HPDs) enable the lossless recording of all the fluorescence photons in ns-FCS based on the minimal system using only two HPDs for the detection of two-color signals. Unexpectedly, HPD was found to show afterpulses at the yield (<10-4) much lower than that of SPADs (~10-2), which could still hamper the correlation measurements. We demonstrated that the simple subtraction procedure could cancel the afterpulse artifacts clearly. The developed system showed the better signal to noise ratio compared to the conventional method for the correlation measurements in the time domain longer than a few nanoseconds. The fast chain dynamics of the B domain of protein A in the unfolded state was observed by the new method. | Yutaka Sano; Yuji Itoh; Supawich Kamonprasetsuk; Leo Suzuki; Atsuhito Fukasawa; Hiroyuki Oikawa; Satoshi Takahashi | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d484074a3f7d0c0dec1fb0/original/lossless-photon-recording-of-two-color-fluorescence-correlation-spectroscopy-for-protein-dynamics-investigations-from-nanoseconds-to-milliseconds.pdf |
60c743b9567dfe0003ec4182 | 10.26434/chemrxiv.9633407.v1 | Generalized Heterodyne Configurations for Photo-induced Force Microscopy | <div>Infrared chemical microscopy through mechanical probing of light-matter interactions by atomic force microscopy (AFM) bypasses the diffraction limit. One increasingly popular technique is photo-induced force microscopy (PiFM), which utilizes the mechanical heterodyne signal detection between cantilever mechanical resonant oscillations and the photo induced force from light-matter interaction. So far, photo induced force microscopy has been operated in only one heterodyne configuration. In this article, we generalize heterodyne configurations of photoinduced force microscopy by introducing two new schemes: harmonic heterodyne detection and sequential heterodyne detection. In harmonic heterodyne detection, the laser repetition rate matches integer fractions of the difference between the two mechanical resonant modes of the AFM cantilever. The high harmonic of the beating from the photothermal expansion mixes with the AFM cantilever oscillation to provide PiFM signal. In sequential heterodyne detection, the combination of the repetition rate of laser pulses and polarization modulation frequency matches the difference between two AFM mechanical modes, leading to detectable PiFM signals. These two generalized heterodyne configurations for photo induced force microscopy deliver new avenues for chemical imaging and broadband spectroscopy at ~10 nm spatial resolution. They are suitable for a wide range of heterogeneous materials across various disciplines: from structured polymer film, polaritonic boron nitride materials, to isolated bacterial peptidoglycan cell walls. The generalized heterodyne configurations introduce flexibility for the implementation of PiFM and related tapping mode AFM-IR, and provide possibilities for additional modulation channel in PiFM for targeted signal extraction with nanoscale spatial resolution.</div> | Le Wang; Devon Jakob; Haomin Wang; Alexis Apostolos; Marcos M. Pires; Xiaoji Xu | Imaging; Microscopy; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b9567dfe0003ec4182/original/generalized-heterodyne-configurations-for-photo-induced-force-microscopy.pdf |
60c74a989abda2469cf8cea8 | 10.26434/chemrxiv.12228992.v1 | Predicting the Effect of Dopants on CO2 Adsorption on Transition Metal Carbides: Case Study on TiC (001) | Previous work has shown that doping the TiC(001)
surface with early transition metals significantly affects CO<sub>2</sub>
adsorption and activation which opens a possible way to control this
interesting chemistry. In this work we explore other possibilities which
include non-transition metals elements (Mg, Ca, Sr, Al, Ga, In, Si, Sn) as well
as late transition metals (Pd, Pt, Rh, Ir) and lanthanides (La, Ce) often used
in catalysis. Using periodic slab models with large supercells and
state-of-the-art density functional theory (DFT) based calculations, we show that,
in all the studied cases, CO<sub>2</sub> appears as bent and, hence, activated.
However, the effect is especially pronounced for dopants with large ionic crystal radii. These can
increase desorption temperature by up to 230K, almost twice the value predicted
when early transition metals are used as dopants. However, a detailed analysis
of the results shows that the main effect does not come from electronic
structure perturbations but from the distortion that the dopant generates into
the surface atomic structure. A simple descriptor is proposed that would allow
predicting the effect of the dopant on the CO<sub>2</sub> adsorption energy in
transition metal carbide surfaces without requiring DFT calculations. | Marti Lopez; Francesc Vines; Michael Nolan; Frances Illas | Catalysts; Thin Films; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a989abda2469cf8cea8/original/predicting-the-effect-of-dopants-on-co2-adsorption-on-transition-metal-carbides-case-study-on-ti-c-001.pdf |
6445fda8df78ec50154a63bb | 10.26434/chemrxiv-2023-v55b5 | Coordinatively Unsaturated Metallates of Cobalt(II), Nickel(II), and Zinc(II) Gated by a Rigid and Narrow Void | Both natural enzymatic systems and synthetic porous material catalysts utilize well-defined and uniform channels to dictate reaction selectivities on the basis of size or shape. Mimicry of this design element in homogeneous systems is generally difficult owing to the flexibility inherent to most small molecular species. Herein, we report the synthesis of a tripodal ligand scaffold which orients a narrow and rigid cavity atop accessible metal coordination space. The permanent void is formed through a macrocyclization reaction whereby the 3,5-dihydroxyphenyl arms are covalently linked through methylene bridges. Deprotonative metallation leads to anionic and coordinatively unsaturated complexes of divalent cobalt, nickel, and zinc. An analogous series of trigonal monopyramidal complexes bearing a non-macrocyclized variant of the tripodal ligand are also reported. Physical characterization of the coordination complexes has been carried out using multiple spectroscopic techniques (NMR, EPR, UV-Vis), cyclic voltammetry, and X-ray diffraction. Complexes of the macrocyclized [LOCH2O]3– ligand retain a rigid cavity upon metallation, with this cavity gating entrance to the open axial coordination site. Through a combination of spectroscopic and computational studies, it is shown that acetonitrile entry into the void is sterically precluded, disrupting anticipated coordination at the intracavity site. | Christopher Hastings; Lucy Huffman; Chandan Tiwari; Jolaine Galindo Betancourth; William Brennessel; Brandon Barnett | Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6445fda8df78ec50154a63bb/original/coordinatively-unsaturated-metallates-of-cobalt-ii-nickel-ii-and-zinc-ii-gated-by-a-rigid-and-narrow-void.pdf |
666c5cae5101a2ffa89706cd | 10.26434/chemrxiv-2024-kl45n | Enhancing Resource Recovery through Electro-Assisted Regeneration of an Ammonia-Selective Cation Exchange Resin | Ammonia-selective adsorbents can manage reactive nitrogen in the environment and promote a circular nutrient economy. Weak acid cation exchangers loaded with zinc exhibit high ammonia selectivity but face two implementation barriers: the stability of the zinc-carboxylate bond in complex wastewaters and energy- and logistics-intensive adsorbent regeneration with acidic solutions. In this study, we examined the stability of the zinc-carboxylate bond in varying solutions (pure ammonium solution, synthetic urine, and real urine) and during electro-assisted regeneration. For electrochemical regeneration, both electrolyte concentration and current density influenced the tradeoff between ammonia regeneration and zinc elution. Using 10 mM K2SO4 anolyte at 0.08 mA/cm2 current density, we achieved 4% zinc elution and 61% ammonia regeneration. In contrast, using 100 mM K2SO4 at 4.96 mA/cm2 improved regeneration efficiency to 97% but eluted 60% of zinc. We found that the electrolyte concentration was the key factor influencing the regeneration efficiency of NH3-selective adsorbents. Due to prevalent zinc elution, we designed an in-situ procedure for reforming the zinc-carboxylate bond and achieved similar adsorption densities between pre- and post-regenerated resin, thus enabling multiple cycle resin use. Ultimately, this study advances the understanding of ammonia-selective resins that can facilitate high-purity, selective, and durable nutrient recovery from waste streams. | Edward Apraku; Chloe Marie Laguna; Robert Matthew Wood; Neha Sharma; Hang Dong; William Tarpeh | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666c5cae5101a2ffa89706cd/original/enhancing-resource-recovery-through-electro-assisted-regeneration-of-an-ammonia-selective-cation-exchange-resin.pdf |
66eab37fcec5d6c1426ce7a6 | 10.26434/chemrxiv-2024-1xd84 | Integrated methods for gold leaching and recovery from ore and electronic waste | Acutely toxic substances such as cyanide salts and mercury metal are commonly used in gold mining. Mercury amalgamation in artisanal gold mining is especially problematic and the largest source of mercury pollution on Earth. New strategies are needed that do not rely on cyanide and mercury for gold recovery. To address this problem, trichloroisocyanuric acid, activated by a halide catalyst, was used to oxidatively dissolve gold metal. A polysulfide polymer sorbent was then used to selectively bind the gold, even in complex mixtures. The gold can be recovered in high purity by pyrolyzing the sorbent. Alternatively, a recyclable polysulfide sorbent was made that can be depolymerized in its separation from gold. This material was synthesized using a novel photochemical ring-opening polymerization of a cyclic trisulfide. These integrated extraction and recovery methods were validated on ore, electronic waste, and other mixed-metal waste streams. Prospects for uptake are discussed. | Maximilian Mann; Thomas Nicholls; Harshal Patel; Lynn Lisboa; Jasmine Pople; Le Nhan Pham; Max Worthington; Matthew Smith; Yanting Yin; Gunther Andersson; Christopher Gibson; Louisa Esdaile; Claire Lenehan; Michelle Coote; Zhongfan Jia; Justin Chalker | Inorganic Chemistry; Polymer Science; Organic Polymers; Polymerization (Polymers); Minerals | CC BY 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66eab37fcec5d6c1426ce7a6/original/integrated-methods-for-gold-leaching-and-recovery-from-ore-and-electronic-waste.pdf |
64a3cec8ba3e99daef7c5c33 | 10.26434/chemrxiv-2023-6vnvt-v2 | Computational Medicinal Chemistry applications to cure Asian-prevalent strain of Hepatitis C Virus | Hepatitis C Virus (HCV), affecting millions of people worldwide, is the leading cause of the liver disorder, cirrhosis, and hepatocellular carcinoma. HCV is genetically diverse having eight gen-otypes and several subtypes predominant in different regions of the globe. The HCV NS3/4A protease is a primary therapeutic target for HCV with various FDA-approved antivirals and several clinical developments. However, available protease inhibitors (PIs) have lower potency against HCV genotype 3 (GT3), prevalent in South Asia. In this study, the incumbent computational tools were utilized to understand and explore interactions of the HCV GT3 receptor with the potential inhibitors after the virtual screening of one million compounds retrieved from the ZINC database. The molecular dynamics, pharmacological studies, and experimental studies uncovered the potential PIs as ZINC000224449889, ZINC000224374291, and ZINC000224374456 and derivative of ZINC000224374456 from the ZINC library. The study revealed that these top hit compounds exhibited good binding and better pharmacokinetics properties that might be considered the most promising compound against HCV GT3 protease. Viability test, on primary healthy Human Gingival Fibroblasts (HGFs) and cancerous AGS cell line were also performed to assess their safety profile after administration. In addition, Surface Plasmon Resonance (SPR) was also performed for determination of affinity and kinetics of synthesized compounds with target proteins. | rashid hussain; Zulkarnain Haider; Hira Khalid; M.Qaiser Fatmi; Simone Carradori; Amelia Cataldi; Susi Zara | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a3cec8ba3e99daef7c5c33/original/computational-medicinal-chemistry-applications-to-cure-asian-prevalent-strain-of-hepatitis-c-virus.pdf |
60c743f1567dfe4f8aec41ce | 10.26434/chemrxiv.9700214.v1 | Implications of the Fractional Charge of Hydroxide at the Electrochemical Interface | <div>
<div>
<div>
<p>Rational design of materials that efficiently convert electrical energy into chemical
bonds will ultimately depend on a thorough understanding of the electrochemical inter-
face at the atomic level. Towards this goal, the use of density functional theory (DFT)
at the generalized gradient approximation (GGA) level has been applied widely in the
past 15 years. In the calculation of electrochemical reaction energetics using GGA-DFT,
it is frequently implicitly assumed that ions in the Helmholtz plane have unit charge.
However, the ion charge is observed to be fractional near the interface through both
a capacitor model and through Bader charge partitioning. In this work, we show that
this spurious charge transfer can be effectively mitigated by continuum charging of the
electrolyte. We then show that, similar to hydronium, the observed fractional charge
of hydroxide is not due to a GGA level self-interaction error, as the partial charge is
observed even when using hybrid level exchange-correlation functionals.
</p>
</div>
</div>
</div> | Joseph Gauthier; Leanne D. Chen; Michal Bajdich; Karen Chan | Electrocatalysis; Heterogeneous Catalysis; Energy Storage; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f1567dfe4f8aec41ce/original/implications-of-the-fractional-charge-of-hydroxide-at-the-electrochemical-interface.pdf |
6643e3aa418a5379b04dbc0b | 10.26434/chemrxiv-2024-51nj8 | Selective Sensing of Catechol Aldehydes Levels in Living Systems using FLIM-FRET | Endogenous catechol aldehydes (CAs), namely 3,4-dihydroxyphenylacetaldehyde (DOPAL) and 3,4-dihydroxyphenylglycolaldehyde (DOPEGAL), play pivotal roles in neurobehavioral, cardiovascular, and metabolic processes. Dysregulation of CA levels contributes to neurological disorders and heart diseases. Thus, detecting imbalances in CAs levels is crucial for diagnosing early stages of CA-associated diseases. Here, we present innovative fluorescent sensors designed for rapid and selective detection of CAs within cells and tissue, overcoming the limitations of conventional diagnostic methods that necessitate cell destruction. The sensor operates by a dual-reaction trigger, leveraging the exceptional selectivity of o-phenylenediamine for aldehyde and phenylboronic acid for catechol, resulting in the production of a FRET signal exclusively for CAs in the presence of other aldehydes and catechols within cells. To circumvent issues such as spectral cross-talk, excitation intensity fluctuations, inner filtering, photobleaching, and detector sensitivity, we employed Fluorescence Lifetime Imaging Microscopy (FLIM) combined with FRET (FLIM-FRET) to accurately measure CAs levels at a nanosecond scale. This makes FLIM-FRET highly proficient for live cell and tissue imaging. Remarkably, we utilized this dual-reaction trigger FLIM-FRET system to detect endogenous CAs levels within cells in response to enzyme activators and inhibitors and within diseased-model mice tissue. These probes have the potential to serve as early warning systems for neurological diseases linked to CAs within living systems, laying the foundation for further investigations. | John Talbott; Rachel Wills; Rajendra Pratap Shirke; Leslie Hassanein; David Weinshenker; Monika Raj | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Biochemical Analysis; Imaging; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6643e3aa418a5379b04dbc0b/original/selective-sensing-of-catechol-aldehydes-levels-in-living-systems-using-flim-fret.pdf |
66c49442a4e53c4876f068d3 | 10.26434/chemrxiv-2024-5lbjg | Broadband CARS hyperspectral classification of single leukemia cells | Broadband CARS is a coherent Raman scattering technique that provides access to the full biological vibrational spectrum within milliseconds, facilitating the recording of widefield hyperspectral Raman images. In this work, BCARS hyperspectral images of two different unstained leukemic blood cells were recorded and analysed using multivariate statistical algorithms in order to determine the spectral differences between the species. A classifier was trained, which could distinguish the known cells with a 97 % out-of-bag accuracy. The classifier was then applied to unlabelled samples containing a mixture of the two cell types on the same coverslip. This work demonstrates the effective label-free high-throughput single-cell analysis of blood using BCARS. A key feature of this work is the use of an image-based deep-learning cell segmentation algorithm that enables the spectra recorded within a given cell boundary to be integrated producing a high quality single cell spectrum for classification. | Ryan Muddiman; Sarah Harkin; Marion Butler; Bryan Hennelly | Analytical Chemistry; Microscopy; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c49442a4e53c4876f068d3/original/broadband-cars-hyperspectral-classification-of-single-leukemia-cells.pdf |
60c749084c89192b03ad300b | 10.26434/chemrxiv.12016389.v1 | Structural and Spectroscopic Characterization of Photoactive Yellow Protein and Photoswitchable Fluorescent Protein Constructs Containing Heavy Atoms | Photo-induced structural rearrangements of chromophore-containing proteins are essential for various light-dependent signaling pathways and optogenetic applications. Ultrafast structural and spectroscopic methods have offered insights into these structural rearrangements across many timescales. However, questions still remain about exact mechanistic details, especially regarding photoisomerization of the chromophore within these proteins femtoseconds to picoseconds after photoexcitation. Instrumentation advancements for time-resolved crystallography and ultrafast electron diffraction provide a promising opportunity to study these reactions, but achieving enough signal-to-noise is a constant challenge. Here we present four new photoactive yellow protein constructs and one new fluorescent protein construct that contain heavy atoms either within or around the chromophore and can be expressed with high yields. Structural characterization of these constructs, most at atomic resolution, show minimal perturbation caused by the heavy atoms compared to wild-type structures. Spectroscopic studies report the effects of the heavy atom identity and location on the chromophore’s photophysical properties. None of the substitutions prevent photoisomerization, although certain rates within the photocycle may be affected. Overall, these new proteins containing heavy atoms are ideal samples for state-of-the-art time-resolved crystallography and electron diffraction experiments to elucidate crucial mechanistic information of photoisomerization. | Matthew Romei; Chi-Yun Lin; Steven Boxer | Dyes and Chromophores; Biophysical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749084c89192b03ad300b/original/structural-and-spectroscopic-characterization-of-photoactive-yellow-protein-and-photoswitchable-fluorescent-protein-constructs-containing-heavy-atoms.pdf |
60c74e070f50db086639713b | 10.26434/chemrxiv.12616151.v2 | Attacking COVID-19 Progression using Multi-Drug Therapy for Synergetic Target Engagement | We are presenting our on going studies with inhibitory research on Tmprss2, S-protein:Ace2, and 3CLpro using compound screening coupled with X-ray crystallography, molecular modeling, live virus screening using host human cells (BSL3 facility at UC Center for Infectious Disease and Vector Research, and organ-on-a-chip at Harvard Medical School for safety profiling before proceeding to animal models with InVivo BioSystems for ADMET.<br /><div>We have derived a useful chemical toolkit of 350 compounds for the community to study with biochemical assays and other biophysical-chemical studies that will prove useful in searching for optimal inhibitors of these targets to find suitable pharmacophores for blocking each of these enzyme's activities -- that would be beneficial for human health. Our past successes with these methodologies have resulted in over 28 patents, 11 technologies and two startup companies. </div> | Mathew Coban; Juliet Morrison; William Freeman; Evette S. Radisky; Karine Le Roch; Thomas Caulfield | Biochemistry; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e070f50db086639713b/original/attacking-covid-19-progression-using-multi-drug-therapy-for-synergetic-target-engagement.pdf |
622700285f1d9a40aeb4944d | 10.26434/chemrxiv-2022-7bsz1 | Discovery and heterologous expression of microginins from Microcystis aeruginosa LEGE 91341 | Microginins are a large family of cyanobacterial lipopeptide protease inhibitors. A hybrid polyketide synthase (PKS)/non-ribosomoal peptide synthetase (NRPS) biosynthetic gene cluster (BGC) found in several microginin-producing strains – mic – was proposed to encode the production of microginins, based on bioinformatic analysis. Here, we explored a cyanobacte-rium, Microcystis aeruginosa LEGE 91341, which contains a mic BGC, to discover twelve new microginin variants. The new compounds contain uncommon amino acids, namely homophenylalanine (Hphe), homotyrosine (Htyr) or methylproline, as well as a 3-aminodecanoic acid (Ada) residue, which in some variants was chlorinated at its terminal methyl group. We have used Direct Pathway Cloning (DiPaC) to heterologously express the mic BGC from M. aeruginosa LEGE 91341 in E. coli, which led to the production of several microginins. This proved that the mic BGC is, in fact, responsible for the biosynthesis of microginins and paves the way to accessing new variants from (meta)genome data or through pathway engineering. | Nádia Eusébio; Raquel Castelo-Branco; Diana Sousa; Marco Preto; Paul D'Agostino; Tobias Gulder; Pedro Leão | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622700285f1d9a40aeb4944d/original/discovery-and-heterologous-expression-of-microginins-from-microcystis-aeruginosa-lege-91341.pdf |
63ac4e3c04902a23ce12798e | 10.26434/chemrxiv-2022-skdq1-v2 | Mild Photocatalysis Removes Microbial Inhibition and Enables Effective Biological Treatment of Naphthenic Acids | Bitumen extraction from the Athabasca oil sands involves large volumes of water known as oil sands process affected water (OSPW). OSPW contains naphthenic acids (NAs), a class of aliphatic and cyclic carboxylic acids that can be toxic and are recalcitrant to natural attenuation. A passive advanced oxidation process (P-AOP), such as solar photocatalysis (PC) with buoyant photocatalysts (BPCs, TiO2-coated buoyant microspheres), is promising for NA treatment, through conversion to more hydrophilic forms (partial oxidation) or to CO2 (complete mineralization), depending on the solar dose. Although BPCs exhibit strong reactivity, full NA mineralization can require impractical hydraulic retention times. Biodegradation is another promising passive approach, but biodegradation rates are ultimately inhibited by the toxicity and structural complexity of NAs. We hypothesized that biological NA removal kinetics could be enhanced through BPC pre-treatment, since partial oxidation can lower NA toxicity and improve their biodegradability. Different PC exposure durations were used to pre-treat simulated OSPW prior to a biological treatment stage (with natural microbial culture from OSPW), to understand their impacts on NA chemical speciation and biodegradation kinetics. PC pre-treatment (2 d) enabled full mineralization (to <3 mg/L COD) and >99.9% removal of acid-extractable organics (AEO) in secondary biological treatment (21 d). Mineralization was achieved earlier in the combined PC+bio treatment than by photocatalysis alone (33 d vs. >42.2 d), and microbial growth rate was accelerated 23-fold compared to the non-pre-treated water. Overall, BPCs can improve NA biodegradability to achieve mineralization through a fully passive combined treatment process, without chemical or energy inputs. | Cassandra Chidiac; Timothy Michael Carter Leshuk; Frank Gu | Biological and Medicinal Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Environmental biology; Water Purification; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ac4e3c04902a23ce12798e/original/mild-photocatalysis-removes-microbial-inhibition-and-enables-effective-biological-treatment-of-naphthenic-acids.pdf |
61c0cfdcf52bc4205ac7bea0 | 10.26434/chemrxiv-2021-1nj64-v4 | A mechanism of abiogenesis based on complex reaction networks organized by seed-dependent autocatalytic systems | The core of the origin-of-life problem is to explain how a complex dissipative system could emerge spontaneously from a simple environment, perpetuate itself, and complexify over time. This would only be possible, we argue, if prebiotic chemical reaction networks had autocatalytic features organized in a way that permitted the accretion of complexity even in the absence of genetic control. To evaluate this claim, we developed tools to analyze the autocatalytic organization of food-driven reaction networks and applied these tools to both abiotic and biotic networks. Both networks contained seed-dependent autocatalytic systems (SDASs), which are subnetworks that can use a flux of food chemicals to self-propagate if, and only if, they are first seeded by some non-food chemicals. Moreover, SDASs were organized such that the activation of a lower-tier SDAS could render new higher-tier SDASs accessible. The organization of SDASs is, thus, similar to trophic levels (producer, primary consumer, etc.) in a biological ecosystem. Furthermore, similar to ecological succession, we found that higher-tier SDASs may produce chemicals that enhance the ability of the entire chemical ecosystem to utilize food more efficiently. The SDAS concept explains how driven abiotic environments, namely ones receiving an ongoing flux of food chemicals, can incrementally complexify even without genetic polymers. This framework predicts that it ought to be possible to detect the spontaneous emergence of life-like features, such as self-propagation and adaptability, in driven chemical systems in the laboratory. Additionally, SDAS theory may be useful for exploring general properties of other complex systems. | Zhen Peng; Jeff Linderoth; David Baum | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c0cfdcf52bc4205ac7bea0/original/a-mechanism-of-abiogenesis-based-on-complex-reaction-networks-organized-by-seed-dependent-autocatalytic-systems.pdf |
61e564206afbef27ef67a643 | 10.26434/chemrxiv-2022-q8n0b | Metal–Free Ring–Opening Metathesis Polymerization
with Hydrazonium Initiators
| A new strategy for the ring–opening metathesis polymerization (ROMP) of cycloalkenes using hydrazonium initiators is described. The initiators, which are formed by the condensation of 2,3-diazabicyclo[2.2.2]octane and an aldehyde, polymerize cyclopropene monomers by a sequence of [3+2] cycloaddition and cycloreversion reactions. This process generates short chain polyolefins (Mn ≤ 9.4 kg/mol) with relatively low dispersities (Đ ≤ 1.4). The optimized conditions showed efficiency comparable to that achieved with Grubbs’ catalyst. A positive correlation between monomer to initiator ratio and degree of polymerization was revealed through NMR spectroscopy. | Phong Quach; Jesse Hsu; Ivan Keresztes; Brett Fors; Tristan Lambert | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Organic Polymers; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e564206afbef27ef67a643/original/metal-free-ring-opening-metathesis-polymerization-with-hydrazonium-initiators.pdf |
610bf2ecd800ad406b402fe2 | 10.26434/chemrxiv-2021-spjw4 | Spreadability of Metal Powders for Laser-Powder Bed Fusion via Simple Image Processing Steps | This paper investigates the spreadability of the spherical CoCrWMo powder for Laser- Powder Bed Fusion (PBF-LB) by using image processing algorithms coded in MATLAB. Besides, it also aims to examine the spreadability correlation with the other characteristics such as flow rate, apparent density, angle of repose. Powder blends in four different particle size distributions are prepared, characterized, and spreadability tests are performed with the PBF-LB. The results demonstrate that an increase in fine particle ratio by volume (below 10 µm) enhances the agglomeration and decreases the flowability, causing poor spreadability. These irregularities on the spread layers are quantified with simple illumination invariant analysis. | Cekdar Vakifahmetoglu; Beyza Hasdemir | Materials Science; Materials Processing | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610bf2ecd800ad406b402fe2/original/spreadability-of-metal-powders-for-laser-powder-bed-fusion-via-simple-image-processing-steps.pdf |
6310848c58843b2d95a54224 | 10.26434/chemrxiv-2022-7642g | Molecular Framework Analysis of the Generated Database GDB-13s | The generated databases (GDBs) list billions of possible molecules from systematic enumeration following simple rules of chemical stability and synthetic feasibility. To assess the originality of GDB molecules, we compared their Bemis and Murcko molecular frameworks (MFs) with those in public databases. MFs result from molecules by converting all atoms to carbons, all bonds to single bonds, and removing terminal atoms iteratively until none remain. We compared GDB-13s (99,394,177 molecules up to 13 atoms containing simplified functional groups, 22,130 MFs) with ZINC (885,905,524 screening compounds, 1,016,597 MFs), PubChem50 (100,852,694 molecules up to 50 atoms, 1,530,189 MFs) and COCONUT (401,624 natural products, 42,734 MFs). While MFs in public databases mostly contained linker bonds and 6-membered rings, GDB-13s MFs had diverse ring sizes and ring systems without linker bonds. Most GDB-13s MFs were exclusive to this database, and many were relatively simple, representing attractive targets for synthetic chemistry aiming at innovative molecules. | Ye Buehler; Jean-Louis Reymond | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6310848c58843b2d95a54224/original/molecular-framework-analysis-of-the-generated-database-gdb-13s.pdf |
641d6a4b91074bccd0354396 | 10.26434/chemrxiv-2023-hzk8c | Photo-SABRE: hyperpolarization of cis-trans photoswitchable molecules by parahydrogen | Over the past decade, azobenzene-based molecular photoswitches have emerged as promising control devices in a range of fields, including chemistry, biology, materials science, physics, energy storage and pharmacology. Previous studies revealed that cis isomer of azobenzene gains strong nonequilibrium polarization (called hyperpolarization) of 15N nuclear spins through interaction with parahydrogen molecules (i.e., a dihydrogen isomer with protons having zero total spin, pH2) in the reversible exchange with Ir-complex. This technique, known as SABRE (Signal Amplification by Reversible Exchange), enhances inherently weak NMR signals by several orders of magnitude at relatively low operational cost. We demonstrate that performing SABRE in the presence of light irradiation allows to hyperpolarize trans-azobenzene, which direct coordination with the SABRE Ir-complex is sterically hindered. The proposed approach, which we called photo-SABRE, is robust and efficient, as well as non-destructive and reproducible. It combines coherent polarization transfer from pH2 to cis-azobenzene with the reversible cis-trans-photoisomerization. Moreover, using photo-SABRE, it is possible to hyperpolarize the long-lived spin order of 15N spin pair in trans-azobenzene, with a lifetime of about 25 minutes, which greatly exceeds the ordinary relaxation times T1 of its 15N nuclei at high (around 10 s) and low (around 200 s) magnetic fields. Photo-SABRE amplification of the NMR signals of cis-trans photoswitchable compounds has a potential to become a valuable tool in the ascending field of photopharmacology and novel light-controlled materials. | Alexey Kiryutin; Vitaly Kozinenko; Alexandra Yurkovskaya | Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641d6a4b91074bccd0354396/original/photo-sabre-hyperpolarization-of-cis-trans-photoswitchable-molecules-by-parahydrogen.pdf |
60c743d54c89195463ad26e7 | 10.26434/chemrxiv.9638879.v1 | Semi-Analytic Evaluation of 1, 2 and 3-Electron Coulomb Integrals with Gaussian Expansion of Distance Operators W= RC1-nRD1-M, RC1-Nr12-M, R12-Nr13-M | The equations derived help to evaluate semi-analytically (mostly for k=1,2 or 3) the important Coulomb integrals Int rho(r1)…rho(rk) W(r1,…,rk) dr1…drk, where the one-electron density, rho(r1), is a linear combination (LC) of Gaussian functions of position vector variable r1. It is capable to describe the electron clouds in molecules, solids or any media/ensemble of materials, weight W is the distance operator indicated in the title. R stands for nucleus-electron and r for electron-electron distances. The n=m=0 case is trivial, the (n,m)=(1,0) and (0,1) cases, for which analytical expressions are well known, are widely used in the practice of computation chemistry (CC) or physics, and analytical expressions are also known for the cases n,m=0,1,2. The rest of the cases – mainly with any real (integer, non-integer, positive or negative) n and m - needs evaluation. We base this on the Gaussian expansion of |r|^-u, of which only the u=1 is the physical Coulomb potential, but the u≠1 cases are useful for (certain series based) correction for (the different) approximate solutions of Schrödinger equation, for example, in its wave-function corrections or correlation calculations. Solving the related linear equation system (LES), the expansion |r|^-u about equal SUM(k=0toL)SUM(i=1toM) Cik r^2k exp(-Aik r^2) is analyzed for |r| = r12 or RC1 with least square fit (LSF) and modified Taylor expansion. These evaluated analytic expressions for Coulomb integrals (up to Gaussian function integrand and the Gaussian expansion of |r|^-u) are useful for the manipulation with higher moments of inter-electronic distances via W, even for approximating Hamiltonian. | Sandor Kristyan | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743d54c89195463ad26e7/original/semi-analytic-evaluation-of-1-2-and-3-electron-coulomb-integrals-with-gaussian-expansion-of-distance-operators-w-rc1-n-rd1-m-rc1-nr12-m-r12-nr13-m.pdf |
657da682e9ebbb4db907ef69 | 10.26434/chemrxiv-2023-tb1z1 | Orientation of a model PAS-domain protein at a polyelectrolyte surface via chiral vibrational spectroscopy and molecular dynamics simulations | PAS domains mediate protein-protein interactions, which give them key functions ranging from sensing and signaling to dimerization and localization. PYP is one of the PAS-domain model proteins that regulates negative phototactic signal response, and its photoreaction is well characterized. In turn, a protein dimer is usually required to maintain its function as a PAS family domain. However, no partner protein for the signaling pathway of PYP has been identified yet. Here, we investigated the intermolecular interaction of PYP with a charged homopolypeptide, poly-L-lysine, in situ by combining chiral vibrational sum-frequency generation (VSFG) spectroscopy with molecular dynamics simulations and VSFG spectral calculations. Our combined experimental and theoretical approach enabled us to study the structure and orientation of proteins at interfaces based on probing the chiral N-H stretching and amide I and II vibrational modes. We found that PYP has a preferred orientation at the PLL interface, mainly due to dipole-dipole interaction, despite its water-soluble, i.e., cytoplasmic nature. Interestingly, the interaction surface and the orientation of PYP resulted in our model being nearly identical to a homodimer of PYP and a heterodimer in CNBh domains consisting of a PAS member. Our methodology provides a promising route for revealing orientational preferences of molecular groups during in situ protein-protein interactions and may ultimately help identify target proteins in PAS-domain signaling pathways. | Bogar Ferenc; Horvath Janos; Zoltan Nasztor; Mark Mero; Szilvia Krekic; Andras Der; Zsuzsanna Heiner | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657da682e9ebbb4db907ef69/original/orientation-of-a-model-pas-domain-protein-at-a-polyelectrolyte-surface-via-chiral-vibrational-spectroscopy-and-molecular-dynamics-simulations.pdf |
60c74712567dfe6856ec4757 | 10.26434/chemrxiv.10303703.v2 | The Performance of Dunning, Jensen and Karlsruhe Basis Sets on Computing Relative Energies and Geometries | <div>In an effort to assist researchers in choosing basis sets for quantum mechanical modeling of molecules (i.e. balancing calculation cost versus desired accuracy), we present a systematic study on the accuracy of computed conformational relative energies and their geometries in comparison to MP2/CBS and MP2/AV5Z data, respectively. In order to do so, we introduce a new nomenclature to unambiguously indicate how a CBS extrapolation was computed. Nineteen minima and transition states of buta-1,3-diene, propan-2-ol and the water dimer were optimized using forty-five different basis sets. Specifically, this includes one Pople (i.e. 6-31G(d)), eight Dunning (i.e. VXZ and AVXZ, X=2-5), twenty-five Jensen (i.e. pc-n, pcseg-n, aug-pcseg-n, pcSseg-n and aug-pcSseg-n, n=0-4) and nine Karlsruhe (e.g. def2-SV(P), def2-QZVPPD) basis sets. The molecules were chosen to represent both common and electronically diverse molecular systems. In comparison to MP2/CBS relative energies computed using the largest Jensen basis sets (i.e. n=2,3,4), the use of smaller sizes (n=0,1,2 and n=1,2,3) provides results that are within 0.11--0.24 and 0.09-0.16 kcal/mol. To practically guide researchers in their basis set choice, an equation is introduced that ranks basis sets based on a user-defined balance between their accuracy and calculation cost. Furthermore, we explain why the aug-pcseg-2, def2-TZVPPD and def2-TZVP basis sets are very suitable choices to balance speed and accuracy.</div> | Karl Kirschner; Dirk Reith; Wolfgang Heiden | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74712567dfe6856ec4757/original/the-performance-of-dunning-jensen-and-karlsruhe-basis-sets-on-computing-relative-energies-and-geometries.pdf |
642589a191074bccd08850f0 | 10.26434/chemrxiv-2023-253pv | Redox-Neutral Synthesis of Sulfilimines through the S-Alkylation of Sulfenamides | Sulfilimines are a class of bioisosteres with immense potential in medicinal chemistry, characterized by the presence of a tetravalent sulfur atom bearing one nitrogen and two distinct carbon substitutes. The conventional methods for synthesizing sulfilimines, relying on metal-catalyzed oxidative thioesters, suffer from a poor atomic economy and wastage of resources. To this end, we present a metal-free and redox-neutral approach for the first selective S-alkylation of sulfenamides under basic conditions to obtain sulfilimines. Our sustainable and efficient strategy involves sulfur-selective alkylation of easily accessible sulfenamides and commercially available halogenated hydrocarbons, leading to the successful synthesis of 60 sulfimides with high yields (36–99%) in a short reaction time. This novel approach not only offers a promising alternative to traditional methods but also expands the synthetic toolbox for the preparation of sulfilimines in medicinal chemistry. | Xunbo Lu; Guoling Huang; Kaiyuan Yang; Xinyu Xu | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642589a191074bccd08850f0/original/redox-neutral-synthesis-of-sulfilimines-through-the-s-alkylation-of-sulfenamides.pdf |
60c74ed1702a9b898a18ba70 | 10.26434/chemrxiv.12805367.v1 | Impacts of the 2020 COVID-19 Shutdown Measures on Ozone Production in the Los Angeles Basin | In March and April 2020, the South Coast Air Basin of California (USA) experienced noticeable declines in on-road activity and primary traffic-related pollutant emissions. However, secondary ozone concentration trends were not consistent across the basin. This research letter explores the impact of meteorology and emissions during this time period. The study elucidates the potential impacts on ozone nonattainment status for the region. | Cesunica Ivey; Ziqi Gao; Khanh Do; Arash Kashfi Yeganeh; Armistead Russell; Charles L. Blanchard; Sang-Mi Lee | Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ed1702a9b898a18ba70/original/impacts-of-the-2020-covid-19-shutdown-measures-on-ozone-production-in-the-los-angeles-basin.pdf |
60c7580a469df46e1af4557a | 10.26434/chemrxiv.14494362.v1 | Efficient Hydro- and Organogelation by Minimalistic Diketopiperazines Containing a Highly Insoluble Aggregation Induced Emission Luminophore | In this manuscript we describe a 2,5-diketopiperazine (DKP) which is further functionalized with a carbazol-luminophore. Gelation properties as well as optical properties of produced organo- and hydrogels based on this small molecule are described.<br /> | Martin Molkenthin; Werner M. Nau; Boris Nachtsheim | Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry; Aggregates and Assemblies; Biocompatible Materials; Biodegradable Materials; Dyes and Chromophores; Elastic Materials; Nanostructured Materials - Materials; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7580a469df46e1af4557a/original/efficient-hydro-and-organogelation-by-minimalistic-diketopiperazines-containing-a-highly-insoluble-aggregation-induced-emission-luminophore.pdf |
66045642e9ebbb4db9b2b927 | 10.26434/chemrxiv-2024-5b3qt-v3 | High Voltage Symmetric Supercapacitors Employing Porous DyFeO3 Electrodes and Aqueous-Based Electrolytes | Aqueous supercapacitors (SCs) encounter limitations in operational voltage and energy density due to the low decomposition voltage of water. Here, we fabricate aqueous symmetric supercapacitors (ASSCs) employing DyFeO3 as an electrode material. This hybrid SC in a 0.5 M Na2SO4 aqueous electrolyte exhibits a significantly high working voltage of 2.5 V, with an energy density of 41.81 W h kg-1 at a power density of 1250 W kg-1, maintaining 94% capacitance retention after 5000 cycles. By incorporating 20% volume of acetonitrile with water in the electrolyte, we extend the potential window to 3.1 V, with an energy density of 84.43 W h kg-1 at a power density of 1550 W kg-1. The as-fabricated ASSC shows promising stability during a 300-hour float voltage test with almost intact capacitance retention and Coulombic efficiency. For the first time, our study unveils the potential of porous DyFeO3 as an electrode material for advancing ASSCs, featuring an unprecedented ultra-wide voltage window, along with significantly large energy and power densities. | Mohasin Tarek; Ferdous Yasmeen; M.A. Basith | Materials Science; Nanoscience; Energy; Nanostructured Materials - Materials; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66045642e9ebbb4db9b2b927/original/high-voltage-symmetric-supercapacitors-employing-porous-dy-fe-o3-electrodes-and-aqueous-based-electrolytes.pdf |
64512fca07c3f0293718ceaa | 10.26434/chemrxiv-2023-cfjw4 | cis-Selective Acyclic Diene Metathesis Polymerization using Bulky Cyclometalated Ruthenium Carbene Catalysts | The regulation of cis-trans configuration is important for investigating the structure-property relationship and fine-tuning the properties of olefin-containing polymers. While classic metathesis polymerization typically yields trans-enriched polymer backbones, the selective construction of all-cis-configured polyalkenamers was previously restricted to the use of strained cyclic olefins or methyl/ethyl-capped acyclic cis-dienes as monomers. Here, we reported an efficient and diverse-oriented cis-selective ADMET using readily available terminal acyclic dienes, which achieves a high cis-percentage of up to 99% and satisfactory molar mass by a bulky cyclometalated ruthenium-carbene catalyst. This method is further compatible with trans-olefin embedded triene monomers, providing a convenient tool for constructing alternative cis-trans configurations in polyalkenamers. A cis-ADMET-prepared and G2-degradable polymer was also explored. This work expands the possibilities for precision polymer synthesis and may offer new avenues for material design. | Yisong Wang; Zepeng Zhang; Yan Xu | Catalysis; Polymer Science | CC BY 4.0 | CHEMRXIV | 2023-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64512fca07c3f0293718ceaa/original/cis-selective-acyclic-diene-metathesis-polymerization-using-bulky-cyclometalated-ruthenium-carbene-catalysts.pdf |
60c743ab842e655d31db22dc | 10.26434/chemrxiv.9396266.v1 | Beta-Amino Phosphine Mn Catalysts for 1,4-Transfer Hydrogenation of Chalcones and Allylic Alcohol Isomerization | <p>Beta-amino phosphines derived from amino-acids are excellent supporting ligands for Mn(I) transfer hydrogenation catalysts. Namely, a variety of ketones and chalcones are efficiently reduced under mild conditions (2-propanol, 3 h, 60 °C). Moreover, chalcones are selectively reduced to the saturated ketone in 2-propanol and allylic alcohols are quantitatively converted into the same product in toluene.</p> | Vipulan Vigneswaran; David Lacy | Organic Synthesis and Reactions; Coordination Chemistry (Inorg.); Ligands (Inorg.); Organometallic Compounds; Homogeneous Catalysis; Catalysis; Coordination Chemistry (Organomet.); Ligands (Organomet.); Reaction (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ab842e655d31db22dc/original/beta-amino-phosphine-mn-catalysts-for-1-4-transfer-hydrogenation-of-chalcones-and-allylic-alcohol-isomerization.pdf |
657cec6be9ebbb4db9fd26e5 | 10.26434/chemrxiv-2023-hgvj4 | Structure of poly(ionic liquid)s in solutions: a small angle scattering study | We investigate the phase behaviour and scattering properties of a polymerised ionic liquid (poly(1-butyl- 3-vinylimidazolium bis(trifluoromethanesulfonyl)imide)) in 24 solvents of varying dielectric constants and solubility parameters. The polymer is found to be soluble in polar aprotic solvents and insoluble in non- polar or highly protic solvents. Three types of behaviour can be observed: in high permittivity solvents, the correlation length is inversely proportional to the square root of the polymer concentration c, and the proportionality constant decreases with solvent dielectric constant if the Bjerrum length is larger than ≃ 1 nm. For solvents with modest dielectric constants (ε ≃ 18 − 30), the correlation length scales as ξ ∝ c−1/3, suggesting a pearl-necklace conformation. Finally, in THF, the scattering pattern follows the Ornstein- Zernike behaviour. The scaling of the correlation length and zero-angle scattering intensity are similar to those of neutral polymers in good solvents. The solvophobic polyelectrolytes. | Carlos G. Lopez; Atsushi Matsumoto; Anish Gulati; Can Hou; Yuna Mizutani; Hiroto Osada; Yume Tao; Kakeru Fujii; Walter Richtering; Takaichi Watanabe | Physical Chemistry; Polymer Science; Polyelectrolytes - Polymers; Polymer chains | CC BY NC 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657cec6be9ebbb4db9fd26e5/original/structure-of-poly-ionic-liquid-s-in-solutions-a-small-angle-scattering-study.pdf |
633d2dfa084700d948950c01 | 10.26434/chemrxiv-2022-3gvmg | Isocyanide Chemistry Enabled by Continuous Flow Technology | Isocyanides are valuable compounds for organic synthesis. However, the poor stability and distressing odour have often limited their widespread applications in common laboratory practice and industrial setting. Herein, a continuous flow approach to enable the synthesis, purification and in-line multicomponent reaction of isocyanides, is presented. | Bruno Cerra; Cecile Blondeau; Rolando Cannalire; Mariateresa Giustignano; Shiva Shandiz; Antimo Gioiello | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633d2dfa084700d948950c01/original/isocyanide-chemistry-enabled-by-continuous-flow-technology.pdf |
65a5aeff9138d23161007b99 | 10.26434/chemrxiv-2024-c9n3w | Sampling Chemical Space: Activity Cliffs, Extended Similarity, and ML Performance | The presence of Activity Cliffs (ACs) has been known to represent a challenge for QSAR modeling. With its data high dependency, Machine Learning QSAR models will be highly influenced by the activity landscape of the data. We propose several extended similarity and extended SALI methods to study the implications of ACs distribution on the training and test sets on the model’s errors. Non-uniform ACs and chemical space distribution tends to lead to worse models than the proposed uniform methods. ML modeling on AC-rich sets needs to be analyzed case-by-case. Proposed methods can be used as a tool to study the dataset, with random and uniform splitting being the better overall data splitting alternatives. | Kenneth Lopez-Perez; Ramon Miranda-Quintana | Theoretical and Computational Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a5aeff9138d23161007b99/original/sampling-chemical-space-activity-cliffs-extended-similarity-and-ml-performance.pdf |
60c751fe4c8919102cad4060 | 10.26434/chemrxiv.13239422.v1 | Computational Methods for Training Set Selection and Error Assessment Applied to Catalyst Design: Guidelines for Deciding Which Reactions to Run First and Which to Run Next | The application of machine learning (ML) to problems in homogeneous catalysis has
emerged as a promising avenue for catalyst optimization. An important aspect of such optimization
campaigns is determining which reactions to run at the outset of experimentation and which future
predictions are the most reliable. Herein, we explore methods for these two tasks in the context of
our previously developed chemoinformatics workflow. First, different methods for training set
selection are compared, including algorithmic selection and selection informed by unsupervised
learning methods. Next, an array of different metrics for assessment of prediction confidence are
examined in multiple catalyst manifolds. These approaches will inform future computer-guided
studies to accelerate catalyst selection and reaction optimization. Finally, this work demonstrates
the generality of the Average Steric Occupancy (ASO) and Average Electronic Indicator Field
(AEIF) descriptors in their application to transition metal catalysts for the first time. <br /> | Scott Denmark; Andrew Zahrt; William Darrow; Brennan Rose; Jeremy Henle | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751fe4c8919102cad4060/original/computational-methods-for-training-set-selection-and-error-assessment-applied-to-catalyst-design-guidelines-for-deciding-which-reactions-to-run-first-and-which-to-run-next.pdf |
628c60215d9485a206cc8ecc | 10.26434/chemrxiv-2022-c8jm3 | VSFlow: an open-source ligand-based virtual screening tool | Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to identify similar structures. Here we report an open-source command line tool which includes a substructure-, fingerprint- and shape-based virtual screening. Most of the implemented features fully rely on the RDKit cheminformatics framework. VSFlow accepts a wide range of input file formats and is highly customizable. Additionally, a quick visualization of the screening results as pdf and/or pymol file is supported. | Sascha Jung; Helge Vatheuer; Paul Czodrowski | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628c60215d9485a206cc8ecc/original/vs-flow-an-open-source-ligand-based-virtual-screening-tool.pdf |
60c74fb7337d6ce5dce281aa | 10.26434/chemrxiv.12934817.v1 | Heterocyclic Group Transfer Reactions with I(III) N-HVI Reagents: Access to N-Alkyl (Heteroaryl)onium Salts via Olefin Aminolactonization | <p>Pyridinium and related N-alkyl (heteroaryl)onium salts are versatile synthetic intermediates in organic chemistry, with applications ranging from ring functionalizations to provide diverse piperidine scaffolds to their recent emergence as radical precursors in deaminative cross couplings. Despite their ever-expanding applications, methods for their synthesis have seen little innovation, continuing to rely on a limited set of decades old transforms. Herein, we leverage (bis)cationic nitrogen-ligated I(III) hypervalent iodine reagents, or <i>N</i>-HVIs, as “heterocyclic group transfer reagents” to provide access to a broad scope of (heteroaryl)onium salts via the aminolactonization of alkenoic acids. The reactions proceed in excellent yields, under mild conditions, and are capable of incorporating a broad scope of sterically and electronically diverse aromatic heterocycles. The <i>N</i>-HVI reagents can be generated <i>in situ</i>, the products isolated via simple trituration, and subsequent derivatizations demonstrate the power of this platform for diversity-oriented synthesis of 6-membered nitrogen heterocycles. Mechanistic studies indicate the reaction proceeds via initial olefin activation followed by lactonization and subsequent intermolecular nucleophilic displacement of an (alkyl)(aryl)iodonium salt hypernucleofuge.</p> | Anthony F. Tierno; Jennifer C. Walters; Andres Vazquez-Lopez; Xiao Xiao; Sarah Wengryniuk | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fb7337d6ce5dce281aa/original/heterocyclic-group-transfer-reactions-with-i-iii-n-hvi-reagents-access-to-n-alkyl-heteroaryl-onium-salts-via-olefin-aminolactonization.pdf |
63eba2bffcfb27a31fc75905 | 10.26434/chemrxiv-2023-5g6gp | Machine learning determination of new Hammett's constants for meta- and para-substituted benzoic acid derivatives employing quantum chemical atomic charge methods | Hammett's constants quantify the electron or electron acceptor power of a chemical group bonded to an aromatic ring. Their experimental values have been successfully used in a large variety of applications, but some of them may have inconsistent values or were not measured. For this reason, developing an accurate and consistent set of Hammett's values is paramount. In this work, we employed the machine learning (ML) regression algorithms Decision Tree Regressor, the neural network Multilayer Perceptron Regressor, and Lasso Lars IC in a cross-validation (CV) approach combined with quantum chemical calculations of atomic charges to estimate theoretically the new Hammett's constants for 90 chemical donor or acceptor groups by employing different types of quantum chemical atomic charges of the groups as input properties. New 219 sigma values, including previously unknown ones, are proposed for 90 chemical donor or acceptor groups by employing different types of quantum chemical atomic charges of the groups as input properties. The different substituent groups were bonded to benzene and meta- and para-substituted benzoic acid derivatives. Among the investigated atomic charge methods (Mulliken, Lwdin, Hirshfeld, and ChelpG), Hirshfeld's method showed the best regressions for most of the different kinds of sigma values. For each type of Hammett constant, linear expressions depending only on the atomic charges of the group were obtained. Correlation coefficients as high as 0.945, mean squared errors (MSE) as low as 0.004, and root mean square errors (RMSE) as low 0.062, were found. The ML approach, in most cases, showed very close predictions to the original experimental values, with the values from meta- and para-substituted benzoic acid derivatives showing the most accurate values. A new consistent set of Hammetts constants is presented, as well as simple equations for predicting new values for groups not included in the original set of 90. | Gabriel Monteiro-de-Castro; Julio Cesar Duarte; Itamar Borges Jr. | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eba2bffcfb27a31fc75905/original/machine-learning-determination-of-new-hammett-s-constants-for-meta-and-para-substituted-benzoic-acid-derivatives-employing-quantum-chemical-atomic-charge-methods.pdf |
60c74a1cbdbb896603a392f0 | 10.26434/chemrxiv.12155394.v1 | Synthesis of Tertiary Amines by Direct Brønsted Acid Catalyzed Reductive Amination | Tertiary amines are ubiquitous and valuable compounds in synthetic chemistry, with a wide range of applications in organocatalysis, organometallic complexes, biological processes and pharmaceutical chemistry. One of the most frequently used pathways to synthesize tertiary amines is the reductive amination reaction of carbonyl compounds. Despite developments of numerous new reductive amination methods in the past decades, this reaction generally requires non-atom-economic processes with harsh conditions and toxic transition-metal catalysts. Herein we report simple yet practical protocols using triflic acid as catalyst to efficiently promote direct reductive amination reactions of carbonyl compounds on a broad ranges of substrates. Applications of this new method to generate valuable heterocyclic frameworks and polyamines are also included.<br /> | Thanh Vinh Nguyen; Mohanad A. Hussein; An Huy Dinh; Vien Huynh | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a1cbdbb896603a392f0/original/synthesis-of-tertiary-amines-by-direct-br-nsted-acid-catalyzed-reductive-amination.pdf |
6483f9fabe16ad5c57b93f74 | 10.26434/chemrxiv-2023-7r8cb | Ultrafast Photo-Controlled Rotation in Molecular Motor Investigated by Machine Learning-Based Nonadiabatic Dynamics Simulations | The thermal helix inversion (THI) of the overcrowded-alkene-based molecular motors determines the speed of the unidirectional rotation due to the high reaction barrier in the ground state, in comparison with the ultrafast photo-reaction process. Recently, a phosphine-based motor has achieved all-photochemical rotation experimentally, promising to be controlled without thermal step. However, the mechanism of this photochemical reaction has not been fully revealed. The comprehensive computational studies on photoisomerization still resort to nonadiabatic molecular dynamics (NAMD) simulations based on electronic structure calculations, which remains a high computational cost for large systems like molecular motors. Machine learning (ML) has become an accelerating tool in NAMD simulations recently, where excited-state potential energy surfaces are constructed analytically with high accuracy, providing an efficient approach for simulations in photochemistry. Herein the reaction pathway is explored by a spinflip time-dependent density functional theory (SF-TDDFT) approach in combination with ML-based NAMD simulations. According to our computational simulations, we notice one of the key factors of fulfilling all-photochemical rotation in the phosphinebased motor is that the excitation energies of four isomers are similar. Additionally, a shortcut photo-induced transformation between unstable isomers replaces the THI step, which shares the conical intersection (CI) with photoisomerization. In this study, we provide a practical approach to speed up the NAMD simulations in photochemical reactions for a large system, which could be extended to other complex systems. | Haoyang Xu; Boyuan Zhang; Yuanda Tao; Weijia Xu; Bo Hu; Feng Yan; Jin Wen | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Machine Learning; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6483f9fabe16ad5c57b93f74/original/ultrafast-photo-controlled-rotation-in-molecular-motor-investigated-by-machine-learning-based-nonadiabatic-dynamics-simulations.pdf |
63a51b0aa53ea67f2254ae4c | 10.26434/chemrxiv-2022-q0w1l | Minimizing non-radiative decay in molecular aggregates through optimal control of excitonic coupling | The widely known ``Energy Gap Law'' (EGL) predicts a monotonically exponential increase in the non-radiative decay rate (knr) as the energy gap narrows, which hinders the development of near-infrared (NIR) emissive molecular materials. Recently, several experiments proposed that the exciton delocalization in molecular aggregates could counteract EGL to facilitate NIR emission.
In this work, the nearly exact time-dependent density matrix renormalization group (TD-DMRG) method is developed to evaluate the non-radiative decay rate for exciton-phonon coupled molecular aggregates.
Systematical numerical simulations show, by increasing the excitonic coupling, knr will first decrease, then reach a minimum, and finally start to increase to follow the EGL, which is an overall result of two opposite effects of a smaller energy gap and a smaller effective electron-phonon coupling.
This anomalous non-monotonic behavior is found robust in a number of models, including dimer, one-dimensional chain, and two-dimensional square lattice.
The optimal excitonic coupling strength that gives the minimum knr is about half of the monomer reorganization energy and is also influenced by temperature, system size, and dimensionality. | Yuanheng Wang; Jiajun Ren; Zhigang Shuai | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a51b0aa53ea67f2254ae4c/original/minimizing-non-radiative-decay-in-molecular-aggregates-through-optimal-control-of-excitonic-coupling.pdf |
665e5b51418a5379b0067102 | 10.26434/chemrxiv-2024-ml4cx | HF trimer: A new full-dimensional potential energy surface and rigorous 12D quantum calculations of vibrational states | HF trimer, as the lightest cyclic hydrogen-bonded (HB) trimer, has long been a favorite prototype system for spectroscopic and theoretical investigations of the structure, energetics, and dynamics of hydrogen-bond networks, and the role that nonadditive, three-body interactions play in shaping these properties. Recently, rigorous quantum 12D calculations of the coupled intra- and intermolecular vibrations of this fundamental HB trimer [P.M. Felker and Z. Bačić, J. Chem. Phys. 2023, 158, 234109] were performed, employing an older ab initio-based many-body potential energy surface (PES). While the theoretical results were found to be in reasonably good agreement with the available spectroscopic data, it was also evident that it is highly desirable to develop a more accurate 12D PES of HF trimer. Motivated by this, here we report a new 12D PES of this paradigmatic system. Approximately 42,540 geometries were sampled and calculated at the level of CCSD(T)-F12a/AVTZ. The permutationally invariant polynomial-neural network based Δ-machine learning approach [Y. Liu and J. Li, J. Phys. Chem. Lett. 2022, 13, 4729] was employed to perform cost-efficient calculations
of the basis-set-superposition error (BSSE) correction. By strategically selecting data points, this approach facilitated the construction of a high-precision PES with BSSE correction, while requiring only a minimal number of BSSE value computations. The fitting error of the final PES is only 0.035 kcal/mol. To assess its performance, the 12D fully coupled quantum calculations of excited intra- and intermolecular vibrational states of HF trimer are carried out using the rigorous methodology developed by us earlier. The results are found to be in a significantly better agreement with the available spectroscopic data than those obtained with the previously existing 12D PES. | Jia Li; Patricia Vindel Zandbergen; Jun Li; Peter Felker; Zlatko Bacic | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665e5b51418a5379b0067102/original/hf-trimer-a-new-full-dimensional-potential-energy-surface-and-rigorous-12d-quantum-calculations-of-vibrational-states.pdf |
61562d4fcea2e9710803cfb7 | 10.26434/chemrxiv-2021-0jbhj | Anisotropic strength behavior of single-crystal TATB | High-rate strength behavior plays an important role in the shock initiation of high explosives, with plastic deformation serving to localize heat into hot spots and as a mechanochemical means to enhance reactivity. Recent simulations predict that detonation-like shocks produce highly reactive nanoscale shear bands in the layered crystalline explosive TATB (1,3,5-triamino-2,4,6-trinitrobenzene), but the thresholds leading to this response are poorly understood. We utilize molecular dynamics (MD) to simulate the high-rate compressive stress-strain response of TATB, with a focus on understanding flow behavior. The dependence of strength on pressure and loading axis (crystal orientation) is explored. The deformation mechanisms fall broadly into two categories, with compression along crystal layers activating a buckling/twinning mode and compression normal to the layers producing nanoscale shear bands. Despite the complexity of the underlying mechanisms, the crystal exhibits relatively straightforward stress-strain curves. Most of the crystal orientations studied show rapid strain softening following the onset of yielding, which settles to a steady flow state. Trajectories are analyzed using five metrics for local states and structural order, but most of these metrics yield similar distributions for these deformation mechanisms. On the other hand, a recently proposed measure of intramolecular strain energy is found to most cleanly distinguish between these mechanisms, while also providing a plausible connection with mechanochemically accelerated decomposition kinetics. Localization of intramolecular strain energy is found to depend strongly on crystal orientation and pressure. | Matthew Kroonblawd; Brad Steele; Matthew Nelms; Laurence Fried; Ryan Austin | Materials Science; Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61562d4fcea2e9710803cfb7/original/anisotropic-strength-behavior-of-single-crystal-tatb.pdf |
673ddf917be152b1d0db3eef | 10.26434/chemrxiv-2024-jzqcz | Hydrogenation of nitrile to primary amine with carbon-coated Ni/NiO@C catalyst under mild conditions | Reusable catalysts based on non-noble metals with broad applicability used in nitrile catalytic hydrogenation synthesis are a key to a more sustainable production of primary amine. Herein, a simple and efficient carbon-coated non-noble metal nickel-based catalyst (Ni/NiO@C-600-200-1-H2O) was prepared for the hydrogenation of aromatic substituted nitrile to aromatic substituted amine under mild conditions (120 °C, 10 bar H2, 4 h). The carbon-coated catalyst has excellent anti-agglomeration ability due to its special carbon-coated metal structure, which can enhance the cyclic stability of the catalyst. Several aromatic substituted nitriles containing diffident functional groups such as halogen, methyl, methoxy, etc. are well tolerated in the Ni-based catalytic hydrogenation and can be converted to the corresponding amine with high activities (conversion rate over 99%, product selectivity reached 98.25%). Moreover, the catalyst can be easily recovered and reused due to its magnetic nature. In addition, we also applied the catalyst to the continuous flow reactor to catalyze benzylamine hydrogenation of benzonitrile under optimized conditions, the conversion rate and selectivity of the reaction were > 99%, and the continuous operation time was up to 31 h. | Weidong Liu; Jianguo Liu | Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ddf917be152b1d0db3eef/original/hydrogenation-of-nitrile-to-primary-amine-with-carbon-coated-ni-ni-o-c-catalyst-under-mild-conditions.pdf |
61ce2129d1f662d46a4ad0dd | 10.26434/chemrxiv-2022-5hb5r | The Synergetic and Multifaceted Nature of Carbon-Carbon Rotation Reveals the Origin of Stability for Bulky Alkane Dimers | Designing compounds with as long carbon-carbon bond distances as possible to challenge conventional chemical wisdom is of current interest in the literature. These compounds with exceedingly long bond lengths are commonly believed to be stabilized by dispersion interactions. In this work, we build nine dimeric models with varying sizes of alkyl groups, let the carbon-carbon bond flexibly rotate, and then analyze rotation barriers with energy decomposition and information-theoretic approaches in density functional theory. Our results show that these rotations lead to extraordinarily elongated carbon-carbon bond distances and rotation barriers are synergetic and multifaceted in nature. The dominant factor contributing to the stability of the dimers with bulky alkane groups is not the dispersion force but the electrostatic interaction with steric and exchange-correlation effects playing minor yet indispensable roles. | Shubin Liu; Xinjie Wan; Xin He; Meng Li; Bin Wang; Chunying Rong | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ce2129d1f662d46a4ad0dd/original/the-synergetic-and-multifaceted-nature-of-carbon-carbon-rotation-reveals-the-origin-of-stability-for-bulky-alkane-dimers.pdf |
666605c2409abc034506b047 | 10.26434/chemrxiv-2024-d4qs8 | Biomimetic total synthesis and paired omics identify an intermolecular Diels-Alder reaction as the key step in lugdunomycin biosynthesis | Microbial natural products are the basis of the majority of the clinical drugs, such as antibiotics, anticancer agents, antifungals and immunosuppressants. The sharp rise in antimicrobial resistance (AMR) requires new ways to replenish the drug-discovery pipelines, whereby the discovery of truly novel structural scaffolds is a major challenge. Lugdunomycin is a highly rearranged angucycline polyketide produced by Streptomyces sp. QL37, but the later stages of its biosynthesis so far remained elusive. Here, using combined biomimetic chemical synthesis, computational methods, genomics and mutational analysis, we shed important new light on the biosynthesis of a molecule with highly complex chemical scaffold. We show that lugdunomycin is formed by a rare intermolecular Diels-Alder reaction, with elmonin as a masked diene and iso-maleimycin as dienophile. The biosynthesis of the two substrates is encoded by distinct biosynthetic gene clusters (BGCs), whereby elmonin is specified by an angucycline BGC, while the biosynthesis of iso-maleimycin is encoded by a BGC for a β-lactone-like compound. Biomimetic total synthesis of lugdunomycin showed that the Diels-Alder reaction leads to the production of a diastereomer of lugdunomycin as the main product in vitro. The diastereomeric ratio of the in vitro Diels-Alder reaction shifted towards lugdunomycin in the presence of proteinaceous material, suggesting that the in vivo Diels-Alder reaction is templated. The requirement of distinct biosynthetic pathways and complex chemical reactions indicate the challenges we face in discovering new chemical space. | Michiel T. Uiterweerd; Isabel Nunez Santiago; Remco Havenith; Chao Du; Le Zhang; Helga van der Heul; Somayah Elsayed; Adri Minnaard; Gilles van Wezel | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666605c2409abc034506b047/original/biomimetic-total-synthesis-and-paired-omics-identify-an-intermolecular-diels-alder-reaction-as-the-key-step-in-lugdunomycin-biosynthesis.pdf |
644a98880d87b493e35ebc7a | 10.26434/chemrxiv-2023-xmmw4 | Rapid and effective method of laser metallization of dielectric materials using deep eutectic solvents with copper acetate | In this paper, we proposed rapid laser-induced synthesis of copper micropatterns on the surface of oxide glass from deep eutectic solvents (DESs) consisting of choline chloride, citric or tartaric acid and copper acetate as copper plating solutions. It was shown that upon irradiation with continuous-wave 532-nm laser radiation, it is possible to increase the deposition rate of copper and create micropatterns with a resistance close to the value of pure metal together with high adhesion to the substrate surface. This metallization method is favorable for the practical use of copper patterns, including in production of new printable microelectronic devices. Thus, we demonstrated the possibility of copper deposition on arbitrary three-dimensional surfaces. Moreover, the resulting copper micropatterns were tested as working electrodes for non-enzymatic glucose. Finally, the proposed technology can be successfully used for design and development of sensor platforms for the electrochemical analysis and microelectronic devices | Evgeniia Khairullina; Andrey Shishov; Dmitry Gordeychuk; Lev Logunov; Aleksandra Levshakova; Vladimir Sosnovsky; Aleksandra Koroleva; Vladimir Mikhailovsky; Evgeny Gurevich; Ivan Chernyshov; Maxim Panov; Ilya Tumkin | Physical Chemistry; Materials Science; Coating Materials; Thin Films; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644a98880d87b493e35ebc7a/original/rapid-and-effective-method-of-laser-metallization-of-dielectric-materials-using-deep-eutectic-solvents-with-copper-acetate.pdf |
64cf100b4a3f7d0c0dadac98 | 10.26434/chemrxiv-2023-vkgq7 | Temperature-Programmed Desorption Approach to Understanding the Development of Semiconductors and Catalysts | This comprehensive article review delves into the extensive utility of temperature-programmed desorption (TPD) as a valuable technique for understanding the intricate development of semiconductors and catalysts. TPD serves as a powerful tool that provides profound insights into the surface chemistry of materials, enabling researchers to gain a comprehensive understanding of various crucial aspects. The article covers a wide range of TPD aspects, including the analysis of surface functional groups, system temperature control, the impact of oxidation and surface treatment, the significance of heat treatment, the dynamics of adsorption and desorption processes, the thermodynamics underlying TPD measurements, surface group characterization techniques, accurate analysis, and measurements considerations, and the importance of sequential surface treatment. By comprehending these multifaceted aspects, researchers can effectively optimize the performance of semiconductors and catalysts, as well as develop novel materials with enhanced properties. Ultimately, the article emphasizes the remarkable versatility and power of TPD in the dynamic realm of semiconductor and catalyst development. | Asishana Onivefu | Catalysis; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cf100b4a3f7d0c0dadac98/original/temperature-programmed-desorption-approach-to-understanding-the-development-of-semiconductors-and-catalysts.pdf |
67de515b6dde43c908d056fd | 10.26434/chemrxiv-2025-vj1mc | Forming chemisorbed single-molecule junctions through loss of stable carbocations | Recent studies have found that “chemically inert” gold surfaces may drive S-C(sp3) bond cleavage reactions in thioether (-SR) linker groups, providing access to single-molecule junctions with chemisorbed Au-S contacts following the elimination of R+. Here we demonstrate that such transformations occur more readily at elevated temperatures, and perhaps surprisingly, in non-polar solvents. We further show that a greater proportion of chemisorbed bonds are formed when R = -CPh3 or -C7H7 than when R = -tBu, consistent with the relative stability of [tBu]+ < [CPh3]+ ~ [C7H7]+ carbocations. Our contact chemistry assignments are supported by first principles transmission calculations, and we apply potential energy calculations to expose the relatively small influence of applied external electric fields on this bond breaking process. Together, this work provides a deeper understanding of reactivity at metal surfaces, of broad relevance to heterogenous catalysis and critical to the stability and function of molecular junctions and monolayers. | Jazmine Prana; Luana Zagami; Kelly Yan; Daniel Hernangómez-Pérez; María Camarasa-Gómez; Michael Inkpen | Physical Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Interfaces; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67de515b6dde43c908d056fd/original/forming-chemisorbed-single-molecule-junctions-through-loss-of-stable-carbocations.pdf |
671cc6d998c8527d9e701112 | 10.26434/chemrxiv-2024-k04rf | PHASE RELATIONS BETWEEN THERMALLY INDUCED STRAIN–HYSTERESIS AND BENDING DEFORMATIONS IN ELASTIC CRYSTALS OF CAFFEINE COCRYSTAL SOLVATE | More than a decade ago, the discovery of elastic bending in single crystals of caffeine cocrystal solvates opened up a new area of research in mechanical properties of molecular crystals. Here we report its structural transition at T > 320 K that is accompanied by negative area expansion of the planes normal to the bending axis; and non-linear increase of intermolecular distances within π···π stacks and the unit cell volume. Upon applying heating–cooling cycles from 360 K ≤ T ≤ 380 K to T = 100 K, three structurally irreversible states are discovered associated with hysteresis of the area of the planes and intermolecular distances. During these various thermal processes, the acid-base dimers rotate as well as move apart. The ratio between variation in rotations and distances (η) reveals that its order in the high T phase as well as those of irreversible structural states are similar to those known for mechanical bending at T = 100 K. | Somnath Dey; Hans Gildenast; Shibabrata Nandi; B. Villiam Hakala; Hend Shahed; Andrzej Grzechnik; Sitaram Ramakrishnan; Sander van Smaalen; Carsten Paulmann; Martin Tolkiehn; Georg Roth; Lars Peters | Physical Chemistry; Materials Science; Elastic Materials; Structure; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671cc6d998c8527d9e701112/original/phase-relations-between-thermally-induced-strain-hysteresis-and-bending-deformations-in-elastic-crystals-of-caffeine-cocrystal-solvate.pdf |
6596bd53e9ebbb4db96c5520 | 10.26434/chemrxiv-2024-gfk84 | A facile strategy to determine photon flux and effective optical path length in intensified continuous-flow photoreactors | Photocatalysis for small molecule activation has seen significant advancements over the past decade, yet its scale-up remains a challenge due to photon attenuation effects. A promising solution lies in harnessing high photonic intensities paired with continuous-flow reactor technology. However, a deep grasp of photon transport is essential, typically demanding resource-intensive experiments. To address this, we introduce an innovative approach to photochemical reactor setup characterization, starting with radiometric light source analysis and progressing to a 3D reactor simulation for photon flux determination. Contrary to conventional techniques that prioritize complete photon absorption, our technique operates optimally when the reaction mixture is unsaturated. This strategy decouples photon flux and path length determination, substantially curtailing the experimental process. The workflow proves versatile across various reactor systems, simplifying intricate light interactions into a single one-dimensional parameter, i.e., the effective optical path length. Combined with the photon flux, this parameter effectively characterizes photochemical setups, irrespective of scale, geometry, light intensity, or photocatalyst concentration. Employing radiometry further offers insights into light source positioning and reactor design, and obviates the need for repeated chemical actinometry measurements due to light source degradation. Additionally, the proposed workflow facilitates experiments at lower concentrations, ensuring optimal reactor operation. In essence, our approach provides a thorough, efficient, and consistent framework for reactor irradiation characterization. | Stefan Zondag; Jasper Schuurmans; Arnab Chaudhuri; Robin Visser; Cintia Soares; Natan Padoin; Koen Kuijpers; Matthieu Dorbec; John Van der Schaaf; Timothy Noel | Chemical Engineering and Industrial Chemistry; Pharmaceutical Industry | CC BY 4.0 | CHEMRXIV | 2024-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6596bd53e9ebbb4db96c5520/original/a-facile-strategy-to-determine-photon-flux-and-effective-optical-path-length-in-intensified-continuous-flow-photoreactors.pdf |
627c036444bdd52106600b4c | 10.26434/chemrxiv-2022-wtb5r | Efficient electrospray deposition of surfaces smaller than the spray plume | Electrospray deposition (ESD) uses charged droplets at the micro- and nano-scale to create a wide variety of particles and coatings. In ESD, an electrostatic force is applied to a solution, which then disperses charged droplets loaded with the materials to be deposited on a grounded target. Because the droplets carry charge, repulsive effects due to accumulation of charge in a coating (self-limiting electrospray) or “crowding” of the spray droplets can reduce the efficiency of the approach. This is especially the case when the targets are smaller than the characteristic size of the spray plume. For this reason, while many studies have presumed high efficiency in ESD, the actual measured efficiencies for small targets are much lower. Here, it is shown how architecting the local “charge landscape” can lead to ESD coatings approaching 100% deposition efficiency on both flat and microneedle array targets composed of multiple model materials, including biocompatible polymers, proteins, and bioactive small molecules. In this way, ESD can be considered a viable alternative to other conformal approaches, such as dip or inkjet coating. | Sarah Park; Lin Lei; Darrel D'Souza; Alex Liu; Emran Lallow; Robert Zipkin; Emily DiMartini; Jerry Shan; Jeffrey Zahn; David Shreiber; Hao Lin; Joel Maslow; Jonathan Singer | Materials Science; Biocompatible Materials; Materials Processing; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627c036444bdd52106600b4c/original/efficient-electrospray-deposition-of-surfaces-smaller-than-the-spray-plume.pdf |
66a11acbc9c6a5c07ac62653 | 10.26434/chemrxiv-2024-t0t94 | Synthesis of Aryl-fused Bicyclo[3.1.1]heptanes (BCHeps) and Validation as Naphthyl Bioisosteres | While naphthalene rings are often encountered in drugs, candidates and lead molecules, they can be susceptible to cy-tochrome P450-mediated metabolism in biological systems and exhibit flat, sp2-rich structures, limiting their utility in drug-like candidates. Herein, we report the first library of derivatisable aryl-fused Bicyclo[3.1.1]heptanes (BCHeps) as bioisosteric replacements for (β-)naphthalene and other fused bicyclic aromatics. We incorporate the BCHep-based naphthyl isosteres into the AhR antagonist ezutromid and observe geometrically similar exit vectors while reducing Fsp2, and retainment of biological activity while improving metabolic stability towards CYP metabolism, validating these motifs as ‘true’ bioisosteric replacements for meta-substituted arenes and 2-naphthalenes. | Aidan Kerckhoffs; Maud Tregear; Pol Hernandez-Llado; Massimiliano Runfola; Holly Shearsmith; Nils Frank; Sarah Squire; Lee Moir; Kirsten Christensen; Fernanda Duarte; Kay Davies; Angela Russell | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a11acbc9c6a5c07ac62653/original/synthesis-of-aryl-fused-bicyclo-3-1-1-heptanes-bc-heps-and-validation-as-naphthyl-bioisosteres.pdf |
636c055081f22378429308d1 | 10.26434/chemrxiv-2021-zjcs8-v2 | Electrolytic Synthesis of White Phosphorus is Promoted in Oxide-Deficient Molten Salts | Elemental white phosphorus (P4) is a key feedstock for the entire phosphorus-derived chemicals industry, spanning everything from herbi-cides to food additives. The electrochemical reduction of phosphate salts could enable the sustainable production of P4; however, such electrosynthesis requires the cleavage of strong, inert P—O bonds. By analogy to the promotion of bond activation in aqueous electrolytes with high proton activity (Brønsted-Lowry acidity), we show that low oxide anion activity (Lux-Flood acidity) enhances P—O bond activa-tion in molten salt electrolytes. We develop electroanalytical tools to quantify the oxide dependence of phosphate reduction, and find that Lux acidic phosphoryl anhydride linkages enable selective, high-efficiency electrosynthesis of P4 at a yield of 95% faradaic efficiency. These fundamental studies provide a foundation that may enable the development of low-carbon alternatives to legacy carbothermal synthesis of P4. | Jonathan Melville; Andrew Licini; Yogesh Surendranath | Inorganic Chemistry; Electrochemistry; Main Group Chemistry (Inorg.); Reaction (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636c055081f22378429308d1/original/electrolytic-synthesis-of-white-phosphorus-is-promoted-in-oxide-deficient-molten-salts.pdf |
60c73d0e702a9b4a4f189ae3 | 10.26434/chemrxiv.5383627.v1 | Affinity of Metal Ions Incorporated Bentonite for Enantiomeric Interactions with Alanine | <div>
<table>
<tr>
<td>
<p>To find the prebiotic route of
homochirality present in amino acids, considering the abiotic evolution of
life, surface interaction of L-alanine (L-ala) and D-alanine (D-ala) on
Bentonite (BNT) and its divalent metal ion (M=Ca<sup>2+</sup>, Mg<sup>2+</sup>, Ni<sup>2+</sup>, Cu<sup>2+</sup> and
Zn<sup>2+</sup>) incorporated BNT has been carried out.Further, absolute value of metal
ion affinities with ala (ala—M<sup>2+</sup>) and hydration effect
on the relative stability and geometry of the individual species of ala— M<sup>2+</sup>×(H<sub>2</sub>O)n,
(n =2 and 4) has also been evaluated using DFT calculation.
Interestingly Mg<sup>2+ </sup>exchanged BNT have shown the
selective adsorption of L-ala in comparison to the D-ala at pH 4.0±0.1. These
results can help us to understand chemical evolution of life and design our
future experiments for the in-depth evaluation of origin of life in
Earth and possibility of bio-markers in other planets like Mars.</p>
</td>
</tr>
</table>
</div> | Pramod Pandey; Preeti Bhatt; Jia Yan; Le Peng; Mohan Singh Mehata; Chandra Kala Pant | Geochemistry; Space Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e702a9b4a4f189ae3/original/affinity-of-metal-ions-incorporated-bentonite-for-enantiomeric-interactions-with-alanine.pdf |
6241c756d6d3ed389aa269ba | 10.26434/chemrxiv-2022-vnf6p | Identification of histone peptide binding specificity and small molecule ligands for the bromodomains of TRIM33α and TRIM33β | TRIM33 is a member of the tripartite motif (TRIM) family of proteins, some of which possess E3 ligase activity and are involved in the ubiquitin-dependent degradation of proteins. Four of the TRIM family proteins, TRIM24 (TIF1α), TRIM28 (TIF1β), TRIM33 (TIF1γ) and TRIM66, contain C-terminal plant homeodomain (PHD) and bromodomain (BRD) modules, which bind to methylated lysine (KMen) and acetylated lysine (KAc), respectively. Here we investigate the differences between the two isoforms of TRIM33, TRIM33α and TRIM33β using structural and biophysical approaches. We show that the N1039 residue, which is equivalent to N140 in BRD4(1) and which is conserved in most BRDs, has a different orientation in each isoform. In TRIM33β this residue coordinates KAc, but this is not the case in TRIM33α. Despite these differences, both isoforms show similar affinities for H31-27K18Ac, and bind preferentially to H31-27K9Me3K18Ac. We used this information to develop an AlphaScreen assay, with which we have identified four new ligands for the TRIM33 PHD-BRD cassette. These findings provide fundamental new information regarding which histone marks are recognized by both isoforms of TRIM33, and suggest starting points for the development of chemical probes to investigate the cellular function of TRIM33. | Angelina Sekirnik; Jessica Reynolds; Larissa See; Joseph Bluck; Amy Scorah; Cynthia Tallant; Bernadette Lee; Katarzyna Leszczynska; Rachel Grimley; Ian Storer; Marta Malattia; Sara Crespillo; Sofia Caria; Stephanie Duclos; Ester Hammond; Stefan Knapp; Garrett Morris; Fernanda Duarte; Philip Biggin; Stuart Conway | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6241c756d6d3ed389aa269ba/original/identification-of-histone-peptide-binding-specificity-and-small-molecule-ligands-for-the-bromodomains-of-trim33-and-trim33.pdf |
67175c0d12ff75c3a12bc020 | 10.26434/chemrxiv-2024-wh7zw-v2 | Modern hit-finding with structure-guided de novo design: identification of novel nanomolar adenosine A2A receptor ligands using reinforcement learning | Generative chemical language models have demonstrated success in learning language-based molecular representations for de novo drug design. Here, we integrate structure-based drug design (SBDD) principles with chemical language models to present a modern hit-finding workflow to go from protein structure to novel small-molecule ligands, without a priori knowledge of ligand chemistry. Using Augmented Hill-Climb we successfully optimised multiple objectives within a practical timeframe, including protein-ligand complementarity. Generated de novo molecules contained both known and promising adenosine A2A receptor ligand chemistry that is not available in commercial vendor libraries, accessing commercially novel areas of chemical space. Experimental validation identified three nanomolar ligands with confirmed functional activity, two of which contain novel chemotypes. Overall, demonstrating a binding hit rate of 88% with 50% of the binders demonstrating confirmed functional activity emphasising the complex relationships in translating binding to downstream pharmacology. Lastly, the two strongest binders were co-crystallised with the A2A receptor revealing their binding mechanisms that can be used to inform future iterations of structure-guided de novo design, closing the AI SBDD loop. | Morgan Thomas; Pierre G. Matricon; Robert J. Gillespie; Maja Napiórkowska; Hannah Neale; Jonathan S. Mason; Jason Brown; Charlotte Fieldhouse; Nigel A. Swain; Tian Geng; Noel M. O'Boyle; Francesca Deflorian; Andreas Bender; Chris de Graaf | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67175c0d12ff75c3a12bc020/original/modern-hit-finding-with-structure-guided-de-novo-design-identification-of-novel-nanomolar-adenosine-a2a-receptor-ligands-using-reinforcement-learning.pdf |
628e4a6a44bdd5811e701428 | 10.26434/chemrxiv-2022-dsf0r | CytroCell micronized cellulose enhances the structural and thermal properties of IntegroPectin cross-linked films | Added to grapefruit IntegroPectin in solution the micronized cellulose CytroCell, co-product of the IntegroPectin extraction via hydrodynamic cavitation, enhances the structural and thermal properties of the resulting cross-linked composite films. The films become strong but remain highly flexible as no transition glass temperature is observed, whereas the thermal properties are substantially improved. No organic solvent, acid or base is used from the extraction of the new pectin and cellulose biopolymers through filming their nanocomposites, thereby establishing a completely green route to a new class of biobased 2D films (and 3D scaffolds) with numerous potential application in regenerative medicine, tissue engineering and in the treatment of infections. | Antonino Scurria; Mario Pagliaro; Giuseppe Pantaleo; Francesco Giordano; Francesco Meneguzzo; Rosaria Ciriminna | Biological and Medicinal Chemistry; Bioengineering and Biotechnology | CC BY NC 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e4a6a44bdd5811e701428/original/cytro-cell-micronized-cellulose-enhances-the-structural-and-thermal-properties-of-integro-pectin-cross-linked-films.pdf |
6222178ec3e9da990e7fe55f | 10.26434/chemrxiv-2022-lzwc5-v2 | A Deep Insight into the Application of Linear Free Energy Relationships (LFER) to Five Membered Heterocyclic Ring Systems: A Review | Hammett and Taft equations are applied to the acid dissociation equilibriums of 4 and 5-substituted furan, pyrrole, thiophene, tellurophen, isoxazole, pyrazole carboxylic acids, to solvolysis data of 4 and 5-substituted-2-furylmethylcarbinyl p-nitrobenzoates and to the permanganate ion oxidation of 5-substituted-2-furfurals. Excellent correlations were observed in these studies except in the case of 1-Me-4/5-X-3-pyrazole-COOH. In the case of 5-X-2-furoic, pyrrole, thiophene carboxylic acids only the substituent -COOH deviated from these correlations for which possible explanation is given in terms of intramolecular hydrogen bonding between the -COOH and the ring heteroatom and two types of intramolecular hydrogen bonding between -COOH and ring nitrogen atom and -COOH and H of NH of pyrrole. In the case of 3,5-X-4-isoxazole carboxylic acids the -NH2 group at 5 position deviated for which the explanation in terms of H-bonding between -NH2 and -COOH is given. Even the possibility of the formation of zwitterion is not ruled out. 5-X-1, 2, 3-triazole-4-carboxylic acids did not follow any LFER. The solvolysis rate constants of both 4 and 5-substituted-2-furylmethylcarbinyl p-nitrobenzoates correlated well with para substituent constants. Further the correlation with Brown’s + values is still better. It is noteworthy that MnO4- oxidation of 5-X-2-furfural correlated well with all the para, meta and ortho substituent constants. An attempt is made for the first time from our laboratory to apply the LFER to 5 membered ring systems with one heteroatom viz. pyrroles, two heteroatoms viz. pyrazoles, imidazoles, isoxazoles, three heteroatoms viz. the triazoles and four heteroatoms viz. tetrazoles. For the first time we have shown that the pKa values of N(1)H-acidities of 3-X-pyrroles, 3-X-pyrazoles, 4-X-pyrazoles, 4-X-imidazoles, 3-X-1,2,4-triazole, 4-X-1,2,3-triazole and 5-X-1,2,3,4-tetrazoles correlated well with Hammett values. | Sanjeev Rachuru; jagannadham vandanapu | Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6222178ec3e9da990e7fe55f/original/a-deep-insight-into-the-application-of-linear-free-energy-relationships-lfer-to-five-membered-heterocyclic-ring-systems-a-review.pdf |
6723b19d7be152b1d097d10a | 10.26434/chemrxiv-2024-6gsnd | Transformation of TiN to TiNO films via In-situ Temperature-dependent Oxygen Diffusion Process and their Electrochemical Behavior | Titanium oxynitride (TiNO) thin films have attracted a lot of attention as a material system that is beneficial for a wide range of applications including, energy storage devices, solar cells, sensors, durable protective coatings, and electrocatalysis. This study reports the synthesis of TiNO thin films with controlled variation of the oxygen levels followed by a detailed structural investigation using X-ray diffraction (XRD), X-ray reflectivity (XRR), X-ray photon spectroscopy (XPS), X-ray absorption spectroscopy (XAS), and Non-Rutherford backscattering spectrometry (N-RBS). These characterization methods allowed detailed analysis that identified phase, composition, and crystallinity of the films. Structural control was established through temperature dependent oxygen in-diffusion and nitrogen out-diffusion processes and adatom mobility associated nucleation growth processes. Our XPS analysis made it clear that the TiNO films are heterogeneous mixtures of TiN, TiNO, and TiO2 phases. We were able to examine correlations between the structure and electrochemical behavior of the films. Through these observations we noticed that the TiNO films with relatively higher N/O ratio, meaning less oxidized, were more electrochemically active than the films with lower N/O ratio (i.e. TiN films with more oxidized phase). The more oxidized films exhibited an increase in crystallinity and improved stability during electrochemical polarization. These findings underscore the significance of substrate temperature control in tailoring the properties of TiNO film, which is a fundamental part of designing and optimizing an efficient electrode material. | Sheilah Cherono; Ikenna Chris-Okoro; Mengxin Liu; R. Soyoung Kim; Swapnil Nalawade; Wisdom Akande; Diana Maria Mihai; Johannes Mahl; Christopher Hale; Junko Yano; Shyam Aravamudhan; Ethan Crumlin; Valentin Craciun; Dhananjay Kumar | Materials Science; Catalysis; Energy; Catalysts; Thin Films; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6723b19d7be152b1d097d10a/original/transformation-of-ti-n-to-ti-no-films-via-in-situ-temperature-dependent-oxygen-diffusion-process-and-their-electrochemical-behavior.pdf |
6220b6c157a9d2ffa8717bd0 | 10.26434/chemrxiv-2022-wt95d | Gram-scale asymmetric synthesis of fluorinated amino acids using a chiral nickel(II) complex | Fluorinated amino acids play an important role in the field of peptide and protein engineering. Although several different syntheses have been published in recent decades, obtaining fluorinated amino acids on a gram-scale still poses a challenge. Furthermore, the described pathways to obtain fluorinated amino acids are based on different synthetic strategies, making a uniform approach from similar starting materials highly interesting. Chiral Ni(II) complexes were introduced as powerful tools in the synthesis of non-canonical amino acids. In this work, we present a strategy for the synthesis of a diverse range of fluorinated amino acids from the corresponding Ni(II) complex on a gram-scale from which the products can be obtained in enantiopure form (>94%ee). In addition, we describe syntheses for alkyl iodide building blocks which are required for the alkylation reactions with the corresponding Ni(II) complex. Finally, we characterized the synthesized fluorinated amino acids with regard to their hydrophobicity and α-helix propensity. | Thomas Hohmann; Michael Dyrks; Suvrat Chowdhary; Manuela Weber; Duy Nguyen; Johann Moschner; Beate Koksch | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6220b6c157a9d2ffa8717bd0/original/gram-scale-asymmetric-synthesis-of-fluorinated-amino-acids-using-a-chiral-nickel-ii-complex.pdf |
60c753edbb8c1a86993dc143 | 10.26434/chemrxiv.13578320.v1 | Crystal Structure and Electrical/thermal Transport Properties of Li1-xSn2+xP2 and Its Performance as a Li-Ion Battery Anode Material | A new ternary layered pnictide, Li<sub>1-x</sub>Sn<sub>2+x</sub>P<sub>2</sub>, was synthesized by a solid-state reaction and its properties were examined to explore its potential as a multifunctional material. The compound crystallizes in a layered structure in the R-3m space group with buckled honeycomb Sn-P layers separated by mixed-occupation Li/Sn layers. Crystal structure analysis using synchrotron X-ray diffraction showed that the substitution degree of Li by Sn (x) is approximately 0.3. Local ordering of Li/Sn occupation was demonstrated using <sup>31</sup>P nuclear magnetic resonance analysis. The lattice thermal conductivity of Li<sub>1-x</sub>Sn<sub>2+x</sub>P<sub>2</sub> was found to be relatively low (1.2 Wm<sup>−1</sup>K<sup>−1</sup> at 525 K). The room-temperature electrical resistivity of Li<sub>1-x</sub>Sn<sub>2+x</sub>P<sub>2</sub> was found to be 0.3-0.4 mohm cm and metallic conductivity was observed down to 0.5 K. First-principles calculations demonstrated that the electronic structure and Fermi energy of Li<sub>1-x</sub>Sn<sub>2+x</sub>P<sub>2</sub> are significantly dependent upon x. Electrochemical measurements using a single-particle technique demonstrated the activity of Li<sub>1-x</sub>Sn<sub>2+x</sub>P<sub>2</sub> as an anode material for rechargeable Li-ion batteries. <br /> | Yosuke Goto; Shota Nakanishi; Yusuke Nakai; Takeshi Mito; akira miura; Chikako Moriyoshi; Yoshihiro Kuroiwa; Hidetomo Usui; Tatsuma D. Matsuda; Yuji Aoki; Yoshifumi Nakacho; Yuto Yamada; Kiyoshi Kanamura; Yoshikazu Mizuguchi | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753edbb8c1a86993dc143/original/crystal-structure-and-electrical-thermal-transport-properties-of-li1-x-sn2-x-p2-and-its-performance-as-a-li-ion-battery-anode-material.pdf |
60c74898567dfeb7f0ec4a26 | 10.26434/chemrxiv.11938065.v1 | Computational Analysis of Electron Transfer Kinetics for CO2 Reduction with Organic Photoredox Catalysts | <div>
<div>
<div>
<p>We present a fundamental description of the electron transfer (ET) step from substituted oligo(p-phenylene) (OPP) radical anions to CO2, with the larger goal of assessing
the viability of underexplored, organic photoredox routes for utilization of anthropogenic CO2. This work varies the electrophilicity of para-substituents to OPP and
probes the dependence of rate coefficients and interfragment interactions on the substituent Hammett parameter, σp, using constrained density functional theory (CDFT)
and energy decomposition analysis (EDA). Large electronic coupling elements across substituents indicate an adiabatic electron transfer process for reactants at contact.
As one might intuitively expect, free energy changes dominate trends in ET rate coefficients in most cases, and rates increase with substituent electron-donating ability.
However, we observe an unexpected dip in rate coefficients for the most electron-
donating groups, due to the combined impact of flattening free energies and a steep
increase in reorganization energies. Our analysis shows that flattening OPP LUMO
levels lower the marginal increase in free energy with decreasing σp. Reorganization
energies do not exhibit a direct dependence on σp. They are higher for substituents
containing lone pairs of electrons since substituent orientation varies with OPP charge.
EDA reveals that interfragment orbital relaxation, or charge transfer interaction, plays
a critical role in stabilizing the vertically excited charge transfer state. Subsequent relaxation to the final state geometry lowers charge transfer stabilization. A concurrent
increase in long-range electrostatic interactions is observed, which are more favorable
for electron-withdrawing substituents. Our study therefore suggests that while a wide
range of ET rates are observed, there is an upper limit to rate enhancements achievable
by tuning substituent electrophilicity.</p></div></div></div> | Kareesa Kron; Samantha Gomez; Robert Cave; Shaama Mallikarjun Sharada | Organocatalysis; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74898567dfeb7f0ec4a26/original/computational-analysis-of-electron-transfer-kinetics-for-co2-reduction-with-organic-photoredox-catalysts.pdf |
6578f32bfd283d7904dd7ac6 | 10.26434/chemrxiv-2023-8bjsk | From the Kitchen to the Lab: Discovery and Application of Food Catalysts to Promote the Coupling of Quinone with Amines | Biocatalysts are used to catalyze specific reactions in various industries, and they often provide environmentally friendly and sustainable alternatives to chemical catalysts. Enzymes are well-known examples of biocatalysts; however, their cata-lytic activities are lost upon denaturation. We report the discovery of novel protein-based biocatalysts from processed foods, including skimmed milk, soy milk, cheese, and tofu (dried). Considering the reaction of the physiologically interest-ing pyrroloquinoline quinone (PQQ) dehydrogenase coenzyme with amino acids, it was found that the reaction with gly-cine to form imidazolopyrroquinoline (IPQ) did not proceed when PQQ was present at very low concentrations. In con-trast, in the presence of protein-based foods, this reaction was accelerated, and it even proceeded at significantly lower PQQ concentrations (i.e., 600-times lower). It was also deduced that milk can accelerate the reaction between PQQ and various amino acids, primary amines, and secondary amines. Investigations into the reaction rate revealed that food ca-talysis is a non-enzymatic reaction. Furthermore, nuclear magnetic resonance spectroscopy was used to demonstrate that the components of milk interacted with the amino substrates owing to the ability of amines to react with quinones on colloidal surfaces. Finally, the application of skimmed milk enhanced the PQQ detection limit during HPLC following IPQ derivatization. Such food catalysts therefore show promise in the fields of biocatalysis and food technology. | Kazuto Ikemoto; Satoko Imaruoka; Nur Syafiqah Mohamad Ishak | Analytical Chemistry; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6578f32bfd283d7904dd7ac6/original/from-the-kitchen-to-the-lab-discovery-and-application-of-food-catalysts-to-promote-the-coupling-of-quinone-with-amines.pdf |
63ea5d4b9da0bc6b33dd0fde | 10.26434/chemrxiv-2023-zgdq8 | Taming non-classical carbocations to control small ring reactivity | The positional selectivity of ring opening of small, strained organic rings is often considered to be governed by the maximal release of ring strain. However, reactions under cationic conditions can lead to multiple products due to the intermediacy of non-classical carbocations (carbonium ions cations featuring a formally pentavalent carbon atom). A famous example is the solvolysis of cyclobutyl or cyclopropylmethyl derivatives, which proceed via two equilibrating non-classical carbocations the cyclopropylcarbinyl ion (CC), and the bicyclobutonium ion (BB) generating up to three products on nucleophilic capture. The utility of such reactions is therefore often limited, despite the value of the small ring products. Using bicyclo[1.1.0]butanes (BCBs) as a template, we show that the regiochemical outcome of small ring opening can be controlled by subtle changes to the structure of non-classical carbocation intermediates, in turn enabling the rational prediction of regioselectivity. We find that the regio- and stereochemistry of ring opening depends not only on the degree of substitution, but also the nature of the substituents, of the BCB ring system and its resulting cationic intermediate. We show that these outcomes can be rationalised by computational models, where bond lengths in the non-classical carbocation inform on the site of reaction. As BCBs are finding increasing use as tools in chemical synthesis and bioconjugation, understanding the factors that control their ring opening offers new opportunities for applications of these molecules. These findings also have consequences for the design of other chemical transformations that proceed through such non-classical intermediates. | Ryan McNamee; Nils Frank; Kirsten Christensen; Fernanda Duarte; Edward Anderson | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea5d4b9da0bc6b33dd0fde/original/taming-non-classical-carbocations-to-control-small-ring-reactivity.pdf |
62309589202c06be28d49ea5 | 10.26434/chemrxiv-2022-0835v | Bioisostere Effects on the EPSA of Common Permeability-Limiting Groups | Polar molecular surface area provides a valuable metric when optimizing properties as varied as membrane permeability and efflux susceptibility. The EPSA method to measure this quantity has had a substantial impact in medicinal chemistry, providing insight into the conformational and stereoelectronic features that govern the polarity of small molecules, targeted protein degraders, and macrocyclic peptides. Recognizing the value of bioisosteres in replacing permeation-limiting polar groups, we determined the effects of common amide, carboxylic acid, and phenol bioisosteres on EPSA, using matched molecular pairs within the Merck compound collection. Our findings highlight bioisosteres within each class that are particularly effective in lowering EPSA and others which, despite widespread use, offer little to no such benefit. Our method for matched-pair identification is generalizable across large compound collections and thus may constitute a flexible platform to study the effects of bioisosterism both in EPSA and other in vitro assays. | Andrew Ecker; Dorothy Levorse; Daniel Victor; Matthew Mitcheltree | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62309589202c06be28d49ea5/original/bioisostere-effects-on-the-epsa-of-common-permeability-limiting-groups.pdf |
661f1c1e91aefa6ce1b662c4 | 10.26434/chemrxiv-2024-jfd46 | Methylthio-D-ribose-1-Phosphate Isomerase Uses a Novel Mechanism for Aldose–Ketose Isomerization | The enzyme-catalyzed interconversion of aldoses and ketoses historically involves one of two mechanisms, both of which require an aldehyde form of the substrate. Methylthio-D-ribose-1-phosphate (MTR1P) isomerase (MtnA), which functions in the methionine-salvage pathway, poses a challenge to this canon because its substrate cannot readily access such a form. In converting MTR1P to its ketose isomer, methylthio-D-ribulose 1-phosphate, MtnA must catalyze opening of the ribofuranose ring and hydrogen transfer between C-2 and C-1. Primary 2H and 13C kinetic isotope effects measured at these positions in MTR1P and ribose 1-phosphate indicate that these two events occur in a common and rate-limiting step with respect to kcat/KM. An inverse kinetic solvent viscosity effect and inverse solvent kinetic isotope effect were measured for this constant, implicating an open–closed protein conformational change after substrate binding and the participation of Cys160 as the catalytic base responsible for shuttling the proton between C-1 and C-2. An E2 elimination–tautomerization sequence is most consistent with these findings and represents a third mechanism for enzymatic aldose–ketose isomerization. | Andrew Murkin; Subashi Ubayawardhana | Biological and Medicinal Chemistry; Catalysis; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f1c1e91aefa6ce1b662c4/original/methylthio-d-ribose-1-phosphate-isomerase-uses-a-novel-mechanism-for-aldose-ketose-isomerization.pdf |
66432b28418a5379b0380af1 | 10.26434/chemrxiv-2024-m3mln | Modeling Realistic Structures of Trimetallic Nanoalloy Catalysts Using Chemically Meaningful Descriptors | The computational design of alloy catalysts is hindered by the uncertainty in their structure and arrangement of constituent elements within the lattice of catalyst particles, i.e., their chemical ordering. Moreover, chemical ordering in alloy nanoparticles (nanoalloys) can be affected by the reaction temperature due to thermal disorder. In this study, we develop a method for realistic simulations of trimetallic alloy nanocrystallites with the lowest energy chemical ordering or chemical ordering taking into account thermal disorder in the nanoalloy. This method is based on Monte Carlo simulations using topological lattice Hamiltonian, whose parameters are fitted to the results of density functional (DFT) simulations of thoughtfully designed archetypal nanoalloy structures. The implementation of this method in Python code is freely available online. Using this method, we characterized chemical orderings in nanoparticles composed of 79 and 338 atoms of metals with known catalytic activity in CO2 hydrogenation, namely, Pd-Pt-Cu, Ni-Pd-Cu, and Co-Rh-Cu. Our simulations show that the thermal disorder in these alloys significantly affects the composition of surface sites. Such structural changes are demonstrated to affect the average binding energies of reaction intermediates to the catalyst surface by up to 1.1 eV, implying their critical effect on the alloy’s catalytic properties. Moreover, we demonstrate how the developed code can be used for brute-force evaluation of entropic contributions to mixing free energies in alloy nanoparticles. The demonstrated abilities of the proposed method to generate realistic models of trimetallic nanoalloys in a computationally efficient manner enable reliable simulations of catalytic properties of trimetallic catalysts for their in-depth understanding and computational design. | Arravind Subramanian; Mikhail Polynski; Mathan K. Eswaran; Sergey Kozlov | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66432b28418a5379b0380af1/original/modeling-realistic-structures-of-trimetallic-nanoalloy-catalysts-using-chemically-meaningful-descriptors.pdf |
67dac432fa469535b9cc7701 | 10.26434/chemrxiv-2025-cvb1v-v2 | Exploring Chemistry and Catalysis by Biasing Skewed Distributions via Deep Learning | The automated discovery of chemical and catalytic reactions remains a major challenge in computational
chemistry, particularly in complex systems where conventional methods struggle to identify optimal searching
directions. Here, we propose Loxodynamics, a machine-learning-driven approach for reaction exploration
via biased molecular dynamics. By leveraging the skewness of local probability distributions, Loxodynamics
dynamically determines low-energy barrier directions, efficiently guiding the system toward metastable states.
The core of our framework is Skewencoder, an autoencoder augmented with a skewness-based loss function that
extracts reaction coordinates from minimal sampling data. Through iterative sample-and-search cycles, the
system adaptively maps the free energy surface, capturing finite-temperature effects critical to complex reactive
environments. We validate our method across model potentials, gas-phase reactions (S_N 2 and Diels-Alder), and
catalytic ethanol dehydration in acidic chabazite under operando conditions. Loxodynamics offers a systematic
and data-driven strategy for reaction discovery, overcoming the limitations of conventional techniques. | Zhikun Zhang; GiovanniMaria Piccini | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dac432fa469535b9cc7701/original/exploring-chemistry-and-catalysis-by-biasing-skewed-distributions-via-deep-learning.pdf |
60c74d35567dfec0f9ec52fc | 10.26434/chemrxiv.12330737.v4 | Hydrothermal Synthesis and Solid-State Laser Refrigeration of Ytterbium-Doped Potassium Lutetium Fluoride (KLF) Microcrystals | Fluoride crystals, due to their low phonon energies, are attractive hosts of trivalent lanthanide ions for applications in upconverting phosphors, quantum information science, and solid-state laser refrigeration. In this article, we report the rapid, low-cost hydrothermal synthesis of potassium lutetium fluoride (KLF) microcrystals for applications in solid-state laser refrigeration. Four crystalline phases were synthesized, namely orthorhombic K<sub>2</sub>LuF<sub>5</sub> (Pnma), trigonal KLuF<sub>4</sub> (P3<sub>1</sub>21), orthorhombic KLu<sub>2</sub>F<sub>7</sub> (Pna2<sub>1</sub>), and cubic KLu<sub>3</sub>F<sub>10</sub> (Fm3m), with each phase exhibiting unique microcrystalline morphologies. Luminescence spectra and emission lifetimes of the four crystalline phases were characterized based on the point-group symmetry of trivalent cations. Laser refrigeration was measured by observing both the optomechanical eigenfrequencies of microcrystals on cantilevers in vacuum, and also the Brownian dynamics of optically trapped microcrystals in water. Among all four crystalline phases, the most significant cooling was observed for 10%Yb:KLuF<sub>4</sub> with cooling of 8.6 $\pm$ 2.1 K below room temperature. Reduced heating was observed with 10%Yb:K<sub>2</sub>LuF<sub>5</sub> | Xiaojing Xia; Anupum Pant; Xuezhe Zhou; Elena Dobretsova; Alex Bard; Matthew Lim; Joo Yeon Roh; Daniel R. Gamelin; Peter Pauzauskie | Nanostructured Materials - Materials; Optical Materials; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d35567dfec0f9ec52fc/original/hydrothermal-synthesis-and-solid-state-laser-refrigeration-of-ytterbium-doped-potassium-lutetium-fluoride-klf-microcrystals.pdf |
644280cb83fa35f8f602c5e2 | 10.26434/chemrxiv-2023-4p00l-v2 | Efficient automatic construction of atom-economical QM regions with point-charge variation analysis | The setup of QM/MM calculations is not trivial since many decisions have to be made by the simulation scientist to achieve reasonable and consistent results. The main challenge to be tackled is the construction of the QM region to make sure to take into account all important parts of the adjacent environment and exclude less important ones. In our previous work [J. Chem. Theory Comput. 65, 18, 2584–2596 (2022)], we introduced the point charge variation analysis (PCVA) as a simple and reliable tool to systematically construct QM regions based on the sensitivity of the reaction energy with respect to variations of the MM point charges. Here, we assess several simplified variants of this PCVA approach for the example of catechol O-methyltransferase and apply PCVA for another system, the triosephosphate isomerase. Furthermore, we extend its scope by applying it to a DNA system. Our results indicate that PCVA offers an efficient and versatile approach of the automatic construction of atom-economical QM regions, but also identify possible pitfalls and limitations. | Felix Brandt; Christoph Jacob | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644280cb83fa35f8f602c5e2/original/efficient-automatic-construction-of-atom-economical-qm-regions-with-point-charge-variation-analysis.pdf |
64759687e64f843f4101dd4a | 10.26434/chemrxiv-2023-6kdlb | Rose Bengal Promoted Catalytic Amyloid-β Oxygenation via Sono-Activation | Catalytic photo-oxygenation of amyloid-β is a leading therapeutic strategy for the treatment of Alzheimer disease. However, the limited tissue-permeability of light hampers its clinical application. We here report an alternative catalytic sono-oxygenation strategy to circumvent this problem. Amyloid-β aggregates were oxygenated using rose bengal as a sonosensitizer under ultrasound irradiation. Structure-activity relationships revealed that xanthene-derived catalysts containing halogen atoms furnished superior amyloid oxygenation activity. | Wataru Atsumi; Keiichi Kawabata; Mina Yamane; Miku Oi; Harunobu Mitsunuma; Youhei Sohma; Yukiko Hori; Taisuke Tomita; Motomu Kanai | Biological and Medicinal Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64759687e64f843f4101dd4a/original/rose-bengal-promoted-catalytic-amyloid-oxygenation-via-sono-activation.pdf |
60c75900bdbb895f75a3ae90 | 10.26434/chemrxiv.14618622.v1 | Open-shell Donors and Closed-shell Acceptors in Organic Solar Cells | The active materials of organic solar cells are widely recognized to show closed-shell singlet ground state and their electron spin resonance signals are attributed to the defects and impurities. Herein, we disclose the inherent open-shell singlet ground state of donors and the closed-shell structure of acceptors via the combination of variable temperature NMR, electron spin resonance, superconducting quantum interference device and theoretical calculation, providing a new perspective to understand the intrinsic molecular structure in organic solar cells. | Zhongxin Chen; Yuan Li; Wenqiang Li; Weiya Zhu; Miao Zeng; Jingwen Wang; Xiaojin Zhang; Xiaobin Peng; Tian Du; Yunfeng Deng; Ren Zhang; Gongqiang Li; Jianhui Hou; fei huang; LI YUAN | Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75900bdbb895f75a3ae90/original/open-shell-donors-and-closed-shell-acceptors-in-organic-solar-cells.pdf |
62b9ff868c5523423024c74a | 10.26434/chemrxiv-2022-4x1rr | An Organic Chemistry Honors Option Focus on 13C Chemical Shift Studies for Substituted Benzenes and 4-Substitued Pyridines: A Historical and Retrospective View of the Data | The results of a first-year organic chemistry study of 1H and 13C chemical shifts for substituted benzenes and 4-substiuted pyridines is given from a historical perspective. The study examines data from the early days of NMR spectroscopy when tetramethylsilane (TMS) was not the standard by which chemical shifts were measured for all nuclei, and samples from a sequence of compounds were often run in different solvents. In the 1960s some studies involved the NMR spectra for compounds in the same series being run in different solvents, when it was already known that solvent affected chemical shifts. The trend in chemical shifts at the C1 carbon in monosubstituted benzenes has been shown to be in concert with the C4 carbon in a like-substituted set of 4-substituted pyridines. However, further review of the correlations indicates a marked improvement when data is used where all the samples are run in CDCl3 as solvent and referenced using TMS, which is the norm for most NMR spectral acquisitions today. Advances in spectral acquisition also allow for investigating the 15N chemical shift variations with substituents in the substituted pyridines. The revisited correlations have been utilized to predict the 13C and 15N chemical shifts for the less favored tautomer of 4-pyridinone; 4-hydroxypyridine. | Madeline Malfara; Annie Jansen; John Tierney | Theoretical and Computational Chemistry; Organic Chemistry; Chemical Education; Organic Compounds and Functional Groups; Physical Organic Chemistry; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b9ff868c5523423024c74a/original/an-organic-chemistry-honors-option-focus-on-13c-chemical-shift-studies-for-substituted-benzenes-and-4-substitued-pyridines-a-historical-and-retrospective-view-of-the-data.pdf |
64147c5d2bfb3dc251ed32c0 | 10.26434/chemrxiv-2023-1r41c | Flue-to-Fuel: Biomediated carbon capture and utilization of dilute CO2 gas streams to biomethane | Capturing anthropogenic carbon dioxide (CO2) and utilizing it as a feedstock for chemical production has been identified as an essential step towards mitigating climate change. The most dominant CO2 emissions originate from flue gases that contain diluted concentrations of CO2 emitted from combustion and industrial processes. Conventional capture technologies such as amine scrubbing are impeded by their high energy demand due to the thermodynamically low driving force for desorbing CO2. A new concept is here presented that exploits the robustness of microbial catalysts to simultaneously desorb the CO2 from an amine-based absorbent and convert the captured CO2 to biomethane (CH4) in a single step by the use of renewable hydrogen. The concept combines carbon capture with that of power-to-methane, to hereby abate CO2 emissions and use the captured CO2 as a resource. Experimental results of the conceptual design in batch reactors demonstrated high microbial biocompatibility with amine methyl diethanolamine (MDEA). The biocompatibility was examined in the range of 0 – 500 mM MDEA, and the system demonstrated almost full bioavailability of the absorbed CO2 until 120 mM of MDEA. Within this range, the CH4 productivity ranged from 40.7 - 63.6 NmLCH4 L-1culture h-1 from synthetically absorbed CO2 with a maximum conversion 1.77 times higher than traditional biomethanation with gaseous CO2. Conversion of raw flue gas from a biogas engine resulted in only a slight decrease in conversion efficiency compared to that of pure gasses, which demonstrated that the concept has high robustness to the impurities and oxygen present in raw flue gas. | Mads Ujarak Sieborg; Lars Ditlev Mørck Ottosen; Michael Vedel Wegener Kofoed | Biological and Medicinal Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Bioengineering and Biotechnology; Energy Storage; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64147c5d2bfb3dc251ed32c0/original/flue-to-fuel-biomediated-carbon-capture-and-utilization-of-dilute-co2-gas-streams-to-biomethane.pdf |
66c8c3a120ac769e5f9959e4 | 10.26434/chemrxiv-2024-gzx7t | Oxoammonium-Catalyzed Ether Oxidation via Hydride Abstraction: Methodology Development and Mechanistic Investigation using Paramagnetic Relaxation Enhancement NMR | Hydride abstraction represents a promising yet underexplored approach in the functionalization of C–H bonds. In this work, we report the oxidation of α-C–H bonds of ethers via oxoammonium catalysis using 3-chloroperbenzoic acid (mCPBA) as the terminal chemical oxidant or by means of electrochemistry. Mechanistic studies revealed intricate equilibria and interconversion events between various catalytic intermediates in the presence of mCPBA, which alone however was incompetent to drive catalytic turnover. The addition of a small amount of strong acid HNTf2 or weakly coordinating salt NaSbF6 turned on catalytic turnover and promoted ether oxidation with excellent efficiency. NMR experiments leveraging paramagnetic relaxation enhancement effect allowed for quantification of open-shell catalytic intermediates in real time during the reaction course, which aided the identification of catalyst resting states and elucidation of reaction mechanisms. | Yukun Cheng; Jonas Rein; Nguyen Le; Song Lin | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c8c3a120ac769e5f9959e4/original/oxoammonium-catalyzed-ether-oxidation-via-hydride-abstraction-methodology-development-and-mechanistic-investigation-using-paramagnetic-relaxation-enhancement-nmr.pdf |
621d3fd9ce899bcf73a7ba0a | 10.26434/chemrxiv-2022-nr55r | Spike selection in SARS-CoV-2 variants across different geographical regions reveals unique signature patterns and differential stability with drug interaction | The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus since its emergence in 2019 has yielded several new viral variants with varied infectivity, disease severity, and antigenicity. Although most mutations are expected to be relatively neutral, mutations at the Spike region of the genome has shown to have a major impact on the viral transmission and infection in humans. Therefore, it is crucial to survey the structures of spike protein across the global virus population to contextualize the rate of therapeutic success against these variants. In this study, high-frequency mutational variants from different geographic regions were pooled in order to study the structural evolution of the spike protein through drug docking and MD simulations. We investigated the mutational burden in the spike sub regions and have observed that the different variants harbour unique signature patterns in the spike sub regions, with certain domains being highly prone to mutations. Further, the MD simulations and docking study revealed that different variants show differential stability when docked for the same set of drug targets. This work sheds light on the mutational burden and the stability landscape of the spike protein across the variants from different geographical regions. | Devang Haresh Liya; Nithishwer Mouroug Anand; Ashwin Kumar Jainarayanan; Mirudula Elanchezhian; Madhumati Seetharaman; Dhanuush Balakannan; Arpit Kumar Pradhan | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621d3fd9ce899bcf73a7ba0a/original/spike-selection-in-sars-co-v-2-variants-across-different-geographical-regions-reveals-unique-signature-patterns-and-differential-stability-with-drug-interaction.pdf |
66a176bac9c6a5c07ad12b81 | 10.26434/chemrxiv-2024-v9kl5 | Synthesis of Pyrrolidine-2-ylidenes from Isoxazolines and Allenes | An addition and rearrangement reaction has been developed for the synthesis of pyrrolidine-2-ylidenes from NH-isoxazolines and electron-deficient allenes. This method generates pyrrolidine-2-ylidenes with a gem-dione at the 4-position via the rearrangement of a proposed N-alkenylisoxazoline intermediate. Reaction optimization and substrate scope are described, in addition to studies comparing the reactivity of the gem-dione and enaminone groups of the products. This method overcomes functional group tolerance limitations of alternative approaches and expands the scope of accessible pyrrolidine-2-ylidenes. | Dylan Keane; Guanqun Zhang; Abdullah Alshreimi; Donald Wink; Laura Anderson | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a176bac9c6a5c07ad12b81/original/synthesis-of-pyrrolidine-2-ylidenes-from-isoxazolines-and-allenes.pdf |
675053d77be152b1d0eaaa07 | 10.26434/chemrxiv-2024-xsgmm | Effect of tertiary amine selection on CO2 to formic acid hydrogenation with Au-np catalyst | The influence of the tertiary amine on CO2 conversion and product selectivity for the direct hydrogenation of CO2 towards formic acid is experimentally studied in batch and packed bed reactors using a Au/TiO2 catalyst. A wide range of tertiary amines were selected, based on their boiling point, kinetic diameter, pKa and solubility with alcohol-based solvents and formic acid. Following these criteria, 15 amines were selected having a wide range of pKa values and molecule sizes. To allow for an initial screening of kinetic rates, formic acid decomposition reactions were performed in batch reactors using an Au/TiO2 catalyst. Following the selection of the most promising amines in terms of CO2 conversion rates, high pressure fixed bed experiments were executed.
Steric hindrance and the pKa of the tertiary amine were identified as key parameters influencing both the observed kinetic rates as well as the CO2 conversion. The usage of solventless polar amines such as diethylethanolamine allowed for FA productivity up to 5x that of the benchmark triethylamine system. Catalyst deactivation of the Au/TiO2 catalyst was observed for all amines studied within this work, and the deactivation mechanism was shown to be sintering of the Au nanoparticles with no significant leaching, morphological changes or oxidation of the Au species observed.
| Anouk W.N. de Leeuw den Bouter; Luca M.P. Meijer ; Larissa Brito ; Adeline Miquelot; Pierre Olivier ; John van der Schaaf | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675053d77be152b1d0eaaa07/original/effect-of-tertiary-amine-selection-on-co2-to-formic-acid-hydrogenation-with-au-np-catalyst.pdf |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.