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64bfdcedb605c6803b5472cc | 10.26434/chemrxiv-2023-8xvnr-v2 | Selective C–H Activation of Unprotected Allylamines by Control of Catalyst Speciation | An outstanding challenge in the Pd-catalyzed functionalization of allylamines is the control of stereochemistry. Terminal alkenes preferentially undergo Heck-type reactions, while internal alkenes may undergo a mixture of Heck and C–H activation reactions that give mixtures of stereochemical products. In the case of unprotected allylamines, the challenge in achieving C–H activation is that facile in situ formation of Pd nanoparticles leads to preferential formation of trans rather than cis-substituted products. In this study we have demonstrated the feasibility of using mono-protected amino acid (MPAA) ligands as metal protecting groups to prevent aggregation and reduction, allowing the selective synthesis of free cis-arylated allylamines. This method compliments Heck-selective methods, allowing complete stereochemical control over the synthesis of cinnamylamines, an important class of amine that can serve as therapeutics directly or as advanced intermediates. To highlight the utility of the methodology, we have demonstrated rapid access to mu opioid receptor ligands. | Vinod Landge; Ankita Mishra; Waruna Thotamune; Audrey Bonds; Indunil Alahakoon; Ajith Karunarathne; Michael Young | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bfdcedb605c6803b5472cc/original/selective-c-h-activation-of-unprotected-allylamines-by-control-of-catalyst-speciation.pdf |
66168bc3418a5379b08a49fc | 10.26434/chemrxiv-2024-rrsgn | Acridine Photocatalysis Enables Tricomponent Direct Decarboxylative Amine Construction | Amines are centrally important motifs in medicinal chemistry and biochemistry, and indispensable intermediates and linchpins in organic synthesis. Despite their cross-disciplinary prominence, synthetic access to amine continues to rely on two-electron approaches based on reductions and additions of organometallic reagents, limiting their accessible chemical space and necessitating stepwise preassembly of synthetic precursors. We report herein a homogeneous photocatalytic tricomponent decarboxylative radical-mediated amine construction that enables modular access to α-branched secondary amines directly from the broad and structurally diverse chemical space of carboxylic acids in a tricomponent reaction with aldehydes and aromatic amines. Our studies reveal the key role of acridine photocatalysis acting in concert with copper and Brønsted acid catalytic processes in facilitating the previously inaccessible homogeneous photocatalytic reaction and provide a streamlined segue to a wide range of amines and nonproteinogenic α-amino acids. | Xianwei Sui; Hang Dang; Arka Porey; Ramon Trevino; Arko Das; Seth Fremin; William Hughes; Wiliiam Thompson; Shree Krishna Dhakal; Hadi Arman; Oleg Larionov | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66168bc3418a5379b08a49fc/original/acridine-photocatalysis-enables-tricomponent-direct-decarboxylative-amine-construction.pdf |
653bcf44c573f893f13d79f5 | 10.26434/chemrxiv-2023-fwdzw | Demagnetizing Ferromagnetic Catalysts to the Sabatier Op-timal of Haber-Bosch Process | Achieving the Sabatier optimal of a chemical reaction has been the central topic in heterogenous catalysis for a century. However, this ultimate goal is greatly hindered by the extrinsic modifications in previous catalyst design strategies. Accord-ing to the magneto-catalytic effect (MCE), the performance of ferromagnetic catalysts can be promoted without changing its chemical structure. Herein, we use time-dependent density functional perturbation theory (TDDFPT) calculations to elucidate that a partially demagnetized ferromagnet could be a Sabatier optimal catalyst. Using ammonia synthesis as the model reac-tion, we determined the activity of Cobalt at each demagnetized state by including the magnetically thermal excitations via magnon analysis, making the 55% demagnetized Co to the genuine Sabatier optimal. As an essential but under-excavated phenomenon in heterogeneous catalysis, the MCE will open a new avenue to design high-performance catalysts. | Gaomou Xu; Licheng Sun; Tao Wang | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653bcf44c573f893f13d79f5/original/demagnetizing-ferromagnetic-catalysts-to-the-sabatier-op-timal-of-haber-bosch-process.pdf |
60c73dd8842e65da42db1840 | 10.26434/chemrxiv.6211115.v1 | Challenges of Connecting Chemistry to Pharmacology: Perspectives from Curating the IUPHAR/BPS Guide to PHARMACOLOGY | Connecting chemistry
to pharmacology (c2p) has been an objective of GtoPdb and its precursor
IUPHAR-DB since 2003. This has been achieved by populating our database with
expert-curated relationships between documents, assays, quantitative results,
chemical structures, their locations within the documents and the protein
targets in the assays (D-A-R-C-P). A
wide range of challenges associated with this are described in this perspective,
using illustrative examples from GtoPdb entries. Our selection process begins with judgements
of pharmacological relevance and scientific quality. Even though we have a stringent focus for our
small-data extraction we note that assessing the quality of papers has become
more difficult over the last 15 years. We discuss ambiguity issues with the
resolution of authors’ descriptions of A-R-C-P entities to standardised
identifiers. We also describe developments that have made this somewhat easier
over the same period both in the publication ecosystem as well as enhancements
of our internal processes over recent years.
This perspective concludes with a look at challenges for the future
including the wider capture of mechanistic nuances and possible impacts of text
mining on automated entity extraction | Christopher Southan; Joanna L Sharman; Elena Faccenda; Adam J Pawson; Simon D Harding; Jamie A Davies | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd8842e65da42db1840/original/challenges-of-connecting-chemistry-to-pharmacology-perspectives-from-curating-the-iuphar-bps-guide-to-pharmacology.pdf |
6398cbc77b7c9161f0f03909 | 10.26434/chemrxiv-2022-w4g7b-v2 | Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI | Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models, which require an empirical parametrization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF) / vibrational configuration interaction (L-VCI) approach previous established for (linear) anharmonic theoretical vibrational spectroscopy [Panek and Jacob, ChemPhysChem 15, 3365–3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and of dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parametrization of vibrational exciton model for predicting 2D IR spectra. | Julia Brüggemann; Mario Wolter; Christoph Jacob | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6398cbc77b7c9161f0f03909/original/quantum-chemical-calculation-of-two-dimensional-infrared-spectra-using-localized-mode-vscf-vci.pdf |
621f89adc3e9da6d617d9360 | 10.26434/chemrxiv-2022-cqf2x | Monothia [22]pentaphyrin(2.0.1.1.0): A core modified isomer of Sapphyrin | A novel 22π-aromatic sapphyrin isomer endowed with acene moiety is designed and realized for the first time as its core-modified mono-thia analogue. This macrocycle exhibits absorption and emission in the near infrared region. It was diprotonated under strong acidic condition, then it binds anion like sapphyrin. It shows unusual coordination chemistry by acting as a neutral ligand to undergo large out-of-plane deformation to bind Pd (II) ion. | Sipra Sucharita Sahoo; Pradeepta Panda | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621f89adc3e9da6d617d9360/original/monothia-22-pentaphyrin-2-0-1-1-0-a-core-modified-isomer-of-sapphyrin.pdf |
60c743734c89199be8ad2645 | 10.26434/chemrxiv.9185948.v1 | Phenazine–Based Covalent Organic Framework Cathode Materials with High Energy and Power Densities | Redox-active covalent organic frameworks (COFs) are promising materials for energy storage devices because of their high density of redox sites, permanent and controlled porosity, high surface areas, and tunable structures. However, the low electrochemical accessibility of their redox-active sites has limited COF-based devices either to thin films (<250 nm) grown on conductive substrates, or to thicker films (1 µm) when a conductive polymer is introduced into the COF pores. Electrical energy storage devices constructed from bulk microcrystalline COF powders, eliminating the need for both thin-film formation and conductive polymer guests, would offer both improved capacity and potentially scalable fabrication processes. Here we report on the synthesis and electrochemical evaluation of a new phenazine-based 2D COF (DAPH-TFP COF), as well as its composite with poly(3,4-ethylenedioxythiophene) (PEDOT). Both the COF and its PEDOT composite were evaluated as powders that were solution-cast onto bulk electrodes serving as current collectors. The unmodified DAPH-TFP COF exhibited excellent electrical access to its redox sites, even without PEDOT functionalization, and outperformed the PEDOT composite of a previously reported anthraquinone-based system. Devices containing DAPH-TFP COF were able to deliver both high energy (250 Wh/kg) and power densities (2950 W/kg), validating the promise of unmodified redox-active COFs that are easily incorporated into electrical energy storage devices. | Edon Vitaku; Cara Gannett; Keith Carpenter; Luxi Shen; Hector Abruna; William Dichtel | Organic Polymers; Electrochemical Analysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743734c89199be8ad2645/original/phenazine-based-covalent-organic-framework-cathode-materials-with-high-energy-and-power-densities.pdf |
651e00d1bda59ceb9ae29bcd | 10.26434/chemrxiv-2023-f1lfz | Self-assembled Tetrahedral Iron(III) Cage for MRI Guided Delivery of a Gold Drug | A T1 MRI probe based on a self-assembled tetrahedral iron(III) cage acts as a host for a gold(I) anticancer drug, which is added as Au(PEt3)Cl. 1H NMR characterization of the gold complex within the Ga(III) analog of the tetrahedral cage is consistent with loss of chloride to give a mixture of Au(PEt3)(OH2) and Au(PEt3)(OH) within the cage. This aqua species may be converted to encapsulated Au(PEt3)CN by treatment with KCN. The binding constant of the gold aqua complex is estimated as ≈ 103 M-1 by displacement experiments with various ammonium cations. Studies show that the iron cage with encapsulated gold complex binds tightly to serum albumin and that there is little dissociation of iron or gold complexes over 24 hours. The iron-gold host-guest complex shows enhanced contrast of the vasculature, consistent with strong binding of the cage to serum proteins. Uptake of the iron cage into C26 tumors as shown by MRI corresponds to the deposition of gold as measured by ICP-MS. These data suggest that the tetrahedral iron cage may serve as a host and carrier for gold drugs towards applications as theragnostic agents. | Priya Sahoo; Steven Turowski; Joseph Spernyak; Janet Morrow | Biological and Medicinal Chemistry; Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651e00d1bda59ceb9ae29bcd/original/self-assembled-tetrahedral-iron-iii-cage-for-mri-guided-delivery-of-a-gold-drug.pdf |
65c38eb69138d231619d5fcd | 10.26434/chemrxiv-2024-37cnx | Elucidating Nonradiative Decay in Deep Near-Infrared Lumiphores: Leveraging New Design Principles to Develop a Telecom Band Organic Dye Laser | Near-infrared (NIR) lumiphores have been targeted for biological and technological applications; however, these dyes suffer from exponentially decreasing quantum yields as their energy gaps decrease. The accepted model of this phenomenon invokes excited-state coupling to C–H modes. Reduction of these modes has been a popular design strategy to design bright NIR lumiphores, but definitive experimental validation of this strategy is lacking. Here we
systematically evaluate the role of C–H modes in
nonradiative relaxation through isotopic labeling of a NIR-emitting complex. Perdeuteration of the emissive molecule indicates that C–H modes do not contribute significantly to nonradiative relaxation, in direct contrast with accepted models. Our results instead suggest that skeletal modes may play a larger role. This suggests that minimizing
scaffold size is a more promising route for bright NIR lumiphores. We demonstrate the promise of such strategies through the development of the reddest organic-based laser dye yet reported. | Lauren McNamara; Christopher Melnychuk; Jan-Niklas Boyn; Sophie Anferov; David Mazziotti; Richard Schaller; John Anderson | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Spectroscopy (Inorg.); Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c38eb69138d231619d5fcd/original/elucidating-nonradiative-decay-in-deep-near-infrared-lumiphores-leveraging-new-design-principles-to-develop-a-telecom-band-organic-dye-laser.pdf |
60c73e55842e651c5bdb18c7 | 10.26434/chemrxiv.6815672.v1 | Ferrozine Assay for Simple and Cheap Iron Analysis of Silica-Coated Iron Oxide Nanoparticles | The Ferrozinen assay is applied as an accurate and rapid method to quantify the iron content of iron oxide nanoparticles (IONPs) and can be used in biological matrices. The addition of ascorbic aqcid accelerates the digestion process and can penetrate an IONP core within a mesoporous and solid silica shell. This new digestion protocol avoids the need for hydrofluoric acid to digest the surrounding silica shell and provides and accessible alternative to inductively coupled plasma methods. With the updated digestion protocol, the quantitative range of the Ferrozine assay is 1 - 14 ppm. <br /> | Hattie Ring; Zhe Gao; Nathan D. Klein; Michael Garwood; John
C. Bischof; Christy L. Haynes | Coating Materials; Nanostructured Materials - Materials; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e55842e651c5bdb18c7/original/ferrozine-assay-for-simple-and-cheap-iron-analysis-of-silica-coated-iron-oxide-nanoparticles.pdf |
67c9c1f5fa469535b935711c | 10.26434/chemrxiv-2025-fgmbq | Bridging the Gap Between Osmotic and Crystalline Swelling in Smectites Clays Minerals | The swelling behavior of smectite clay minerals has been extensively investigated due to their critical role in construction stability. Two distinct swelling regimes have long been recognized: crystalline swelling, involving the incorporation of a few water sheets between clay layers, and osmotic swelling, characterized by the complete delamination of individual clay layers. Crystalline swelling mechanisms have been well established through hydration techniques applied to dry clay in a humid environment, while osmotic swelling has been observed through the gradual concentration of a diluted clay suspension into a more compact, glassy state. Although a linear transition between these two regimes has been proposed, it has yet to be experimentally demonstrated. In this study, we investigate the complete dehydration process of a levitated smectite suspension droplet using in-situ Small Angle X-ray Scattering (SAXS). The results reveal a gradual shift from osmotic swelling to crystalline swelling, marked by a transition from a pure nematic glass to a coexistence zone where the nematic phase contracts and a saturated crystalline phase emerges, ultimately progressing to an unsaturated crystalline state. This transition occurs through a continuous process in which the interlayer space decreases from four water layers to zero water layers, forming stratified interlayers along the way. | Claire Hotton; Thomas Bizien; Cyrille Hamon; Eric Ferrage; Erwan Paineau | Physical Chemistry; Nanoscience; Earth, Space, and Environmental Chemistry; Environmental Science; Nanostructured Materials - Nanoscience; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c9c1f5fa469535b935711c/original/bridging-the-gap-between-osmotic-and-crystalline-swelling-in-smectites-clays-minerals.pdf |
60c7549e4c891986dbad4569 | 10.26434/chemrxiv.13697464.v1 | Data-Driven Discovery and Synthesis of High Entropy Alloy Hydrides with Targeted Thermodynamic Stability | Solid-state hydrogen storage materials that are optimized for specific use cases could be a crucial facilitator of the hydrogen economy transition. Yet the discovery of novel hydriding materials has historically been a manual process driven by chemical intuition or experimental trial-and-error. Data-driven materials' discovery paradigms provide an alternative to traditional approaches, whereby machine/statistical learning (ML) models are used to efficiently screen materials for desired properties and significantly narrow the scope of expensive/time-consuming first-principles modeling and experimental validation. Here we specifically focus on a relatively new class of hydrogen storage materials, high entropy alloy (HEA) hydrides, whose vast combinatorial composition space and local structural disorder necessitates a data-driven approach that does not rely on exact crystal structures in order to make property predictions. Our ML model quickly screens hydride stability within a large HEA space and permits down selection for laboratory validation based not only on targeted thermodynamic properties, but also secondary criteria such as alloy phase stability and density. To experimentally verify our predictions, we performed targeted synthesis and characterization of several novel hydrides that demonstrate significant destabilization (70x increase in equilibrium pressure, 20 kJ/molH<sub>2</sub> decrease in desorption enthalpy) relative to the benchmark HEA hydride, TiVZrNbHfH<sub>x</sub>. Ultimately, by providing a large composition space in which hydride thermodynamics can be continuously tuned over a wide range, this work will enable efficient materials selection for various applications, especially in areas such as metal hydride based hydrogen compressors, actuators, and heat pumps. | Matthew Witman; Gustav Ek; Sanliang Ling; Jeffery Chames; Sapan Agarwal; Justin Chuan-Chi Wong; Mark Allendorf; Martin Sahlberg; Vitalie Stavila | Energy Storage; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7549e4c891986dbad4569/original/data-driven-discovery-and-synthesis-of-high-entropy-alloy-hydrides-with-targeted-thermodynamic-stability.pdf |
65bff30466c1381729f62ef1 | 10.26434/chemrxiv-2024-tsjsm | Synthesis of Benzenes from Pyridines via N to C switch | The transformation of pyridines into benzene derivatives is described, using a one-pot ANRORC process with soft nucleophiles such as malonate. Triflic anhydride activates the pyridine to ANRORC synthesis of a carbocyclic β-aminoester intermediate, which aromatizes on heating. The reaction has been exemplified with a room temperature protocol, along with direct syntheses of biologi-cally active, tertiary-alkylated and isotopically-labelled benzoates. | Aífe Conboy; Michael Greaney | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bff30466c1381729f62ef1/original/synthesis-of-benzenes-from-pyridines-via-n-to-c-switch.pdf |
645ef7fda32ceeff2d8cf32a | 10.26434/chemrxiv-2023-6gl3t | Coordination and Activation of N2 at Low-Valent Magnesium using a Cooperative Heterobimetallic Approach: Synthesis and Reactivity of a Masked Dimagnesium Diradical | The activation of dinitrogen (N2) by transition metals is central to the highly energy intensive, heterogenous Haber-Bosch process. Considerable progress has been made towards more sustainable homogeneous activations of N2 with d- and f-block metals, though little success has been had with main group metals. Here we report that the reduction of a bulky magnesium(II) amide [(TCHPNON)Mg] (TCHPNON = 4,5-bis(2,4,6-tricyclohexylanilido)-2,7-diethyl-9,9-dimethyl-xanthene) with 5% w/w K/KI yields the magnesium-N2 complex [{K(TCHPNON)Mg}2(-N2)]. DFT calculations and experimental data show that the dinitrogen unit in the complex has been reduced to the N22- dianion, via a transient anionic magnesium(I) radical. The compound readily reductively activates CO, H2 and C2H4, in reactions in which it acts as a masked dimagnesium(I) diradical. | Rahul Mondal; Matthew J Evans; Thayalan Rajeshkumar; Laurent Maron; Cameron Jones | Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Inorg.); Small Molecule Activation (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645ef7fda32ceeff2d8cf32a/original/coordination-and-activation-of-n2-at-low-valent-magnesium-using-a-cooperative-heterobimetallic-approach-synthesis-and-reactivity-of-a-masked-dimagnesium-diradical.pdf |
60c74940469df40626f43b8e | 10.26434/chemrxiv.12033702.v1 | Cytotoxicity of Mn-Based photoCORMs of Ethynyl-α-Diimine Ligands Against Different Cancer Cell Lines: The Key Role of CO-Depleted Metal Fragments | A series of fac-[Mn(CO)3]+ complexes bearing 4-ethynyl-2,2'-bipyridine and 5-ethynyl-1,10-phenanthroline α-diimine ligands were synthetized, characterized and conjugated to vitamin B12, previously used as a vector for drug delivery, to take advantage of its water solubility and specificity toward cancer cells. The compounds act as photoactivatable carbon monoxide-releasing molecules (photoCORMs) rapidly liberating on average ca. 2.3 equivalents of CO upon photo-irradiation. Complexes and conjugates were tested for their anticancer effects, both in the dark and following photo-activation, against breast cancer MCF-7, lung carcinoma A549 and colon adenocarcinoma HT29 cell lines as well as immortalized human bronchial epithelial cells 16HBE14o- as the non-carcinogenic control. Our results indicate that the light-induced cytotoxicity these photoCORMs can be attributed to both their released CO and to their CO-depleted metal fragments (i-photoCORMs) including liberated ligands.<br /> | Jeremie Rossier; Joachim Delasoie; Laetitia Haeni; Daniel Hauser; Barbara Rothen-Rutishauser; Fabio Zobi | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74940469df40626f43b8e/original/cytotoxicity-of-mn-based-photo-cor-ms-of-ethynyl-diimine-ligands-against-different-cancer-cell-lines-the-key-role-of-co-depleted-metal-fragments.pdf |
64e7139d3fdae147fab468ae | 10.26434/chemrxiv-2023-h541x | Enhancing Robustness of Adhesive Hydrogels Through PEG-NHS Incorporation | Tissue wounds are a significant challenge for healthcare system, affecting millions globally. Current methods like suturing and stapling have limitations such as inadequate wound coverage, fail to prevent fluid leakage, and increasing the risk of infection. Effective solutions for diverse wound conditions are still lacking. Adhesive hydrogels, on the other hand, can be a potential alternative for the wound care. They offer benefits such as firm sealing without leakage, easy and rapid application, and the provision of mechanical support and flexibility. However, their in vivo durability is often compromised by excessive swelling and unforeseen degradation, which presents a challenge for widespread use. In this study, we addressed the durability issues of the adhesive hydrogels by incorporating Acrylamide Polyethylene glycol N-hydroxysuccinimide (PEG-NHS) moieties (max 2 wt%) into hydrogels based on hydroxy ethyl acrylamide (HEAam). The results showed that the addition of PEG-NHS significantly enhanced the adhesion performance, achieving up to 2-fold improvement on various soft tissues including skin, trachea, heart, lung, liver, and kidney. We further observed that the addition of PEG-NHS into adhesive hydrogel network improved their intrinsic mechanical properties. The tensile modulus of these hydrogels increased up to 5-fold, while the swelling ratio decreased up to 2-fold in various media. These hydrogels also exhibited improved durability under the enzymatic and oxidative biodegradation induced conditions without causing any toxicity to the cells.
For a clinical point of view, we found that PEG-NHS-based hydrogels effectively addressed tracheomalacia, a condition characterized by inadequate mechanical support of the airway due to weak/malacic cartilage rings. Ex vivo study confirmed that the addition of PEG-NHS to a hydrogel network prevented approximately 90% of airway collapse compared to the case without PEG-NHS. Overall, this study offers a promising approach to enhance the durability of adhesive hydrogels by the addition of PEG-NHS, thereby improving their overall performances for various biomedical applications.
| Ece Uslu; Vijay Rana; Yanheng Guo; Theofanis Stampoultzis; François Gorostidi; Kishore Sandu; Dominique Pioletti | Biological and Medicinal Chemistry; Materials Science; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e7139d3fdae147fab468ae/original/enhancing-robustness-of-adhesive-hydrogels-through-peg-nhs-incorporation.pdf |
6193f65e2bf8a90634ded48c | 10.26434/chemrxiv-2021-6v4n0 | Replacing Chemical Intuition by Machine Learning: a Mixed Design of Experiments - Reinforcement Learning Approach to the Construction of Training Sets for Model Hamiltonians | Model Hamiltonians based on the so-called cluster expansion (CE), which consist of a linear fit of parameters corresponding to geometric patterns, provide an efficient and rigorous means to quickly evaluate the energy of diverse arrangements of adsorbate mixtures on reactive surfaces as typically relevant for heterogeneous catalysis. However, establishing the model Hamiltonian is a tedious task, requiring the construction and optimization of many geometries. Today, most of these geometries are constructed by hand, based on chemical intuition or random choices. Hence, the quality of the training set is unlikely to be optimal and its construction is not reproducible. Herein, we propose a reformulation of the construction of the training set as a strategy-based game, aiming at an efficient exploration of the relevant patterns constituting the model Hamiltonian. Based on this reformulation, we exploit a typical active learning solution for machine-learning such a strategy game: an upper confidence tree (UCT) based framework. However, in contrast to standard games, evaluating the true score is computationally expensive, as it requires a costly geometry optimization. Hence, we augment the UCT with a pre-exploration step inspired by the variance-based Design of Experiments (DoE) methods.
This novel mixed UCT+DoE framework allows to automatically construct a well adapted training set, minimizing computational cost and user-intervention. As a proof of principle, we apply our UCT+DoE approach on the CO oxidation reaction on Pd(111), for which a relevant model Hamiltonian has been established previously. The results demonstrate the effectiveness of the custom built UCT and its significant benefits on a DoE-based approach. | Ruben Staub; Stephan Steinmann | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6193f65e2bf8a90634ded48c/original/replacing-chemical-intuition-by-machine-learning-a-mixed-design-of-experiments-reinforcement-learning-approach-to-the-construction-of-training-sets-for-model-hamiltonians.pdf |
6477d58ebe16ad5c574071bd | 10.26434/chemrxiv-2023-r8jlg | A Quest for Platinum(0) Adducts of the Macrocyclic Dibridgehead Diphosphine P((CH2)14)3P | The reaction of trans-Pt(Cl)2(P((CH2)14)3P) and C8K in C6D6 or diethyl ether cleanly gives a species provisionally formulated as trans-Pt(P((CH2)14)3P) (trans-5) based upon NMR data (31P{1H} chemical shift and JPPt values similar to other trans-Pt(PR3)2 species; seven 13C NMR signals, three exhibiting JCP). Consistent with a platinum(0) formulation, addition of CH3I gives the known complex trans-Pt(I)(Me)(P((CH2)14)3P) (trans-10, 83% isolated), and H2 gives the dihydride complex trans-Pt(H)2(P((CH2)14)3P) (trans-11), as evidenced by 31P{1H} and 1H NMR. Additions of ethylene and diphenylacetylene give the corresponding 1:1 π adducts, be¬lieved to have trigonal geometries based upon literature precedent. Alternative formulations or trans-5 are discussed; the 1H NMR spectrum of one sample showed a weak upfield triplet integrat¬ing to < 0.25 H, (–2.43 ppm, JHP = 18.6 Hz), suggesting a Pt-H unit. | Yun Zhu; Tobias Fiedler; John A. Gladysz | Organometallic Chemistry; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6477d58ebe16ad5c574071bd/original/a-quest-for-platinum-0-adducts-of-the-macrocyclic-dibridgehead-diphosphine-p-ch2-14-3p.pdf |
60c73ed94c89198433ad1e78 | 10.26434/chemrxiv.7038428.v2 | `Diet GMKTN55' Offers Accelerated Benchmarking Through a Representative Subset Approach | The GMTKN55 benchmarking protocol introduced by [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184] allows comprehensive analysis and ranking of density functional approximations with diverse chemical behaviours. But this comprehensiveness comes at a cost: GMTKN55's 1500 benchmarking values require energies for around 2500 systems to be calculated, making it a costly exercise. This manuscript introduces three subsets of GMTKN55, consisting of 30, 100 and 150 systems, as `diet' substitutes for the full database. The subsets are chosen via a stochastic genetic approach, and consequently can reproduce key results of the full GMTKN55 database, including ranking of approximations. | Tim Gould | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed94c89198433ad1e78/original/diet-gmktn55-offers-accelerated-benchmarking-through-a-representative-subset-approach.pdf |
60c746bc702a9b71e118ac70 | 10.26434/chemrxiv.11372217.v1 | A 3D-printed Microfluidic System for Automated and Near Real-time Quantitation of Biofilm-induced indole | We developed a novel microfluidic system that enables automated and near real-time quantitation of indole release kinetics from biofilms.<div><br /></div><div>Now published at https://www.sciencedirect.com/science/article/pii/S0924424720311031</div> | Giraso Kabandana; Curtis G. Jones; Sahra Khan Sharifi; Chengpeng Chen | Analytical Apparatus; Biochemical Analysis; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746bc702a9b71e118ac70/original/a-3d-printed-microfluidic-system-for-automated-and-near-real-time-quantitation-of-biofilm-induced-indole.pdf |
616d2d0b0ad1ff90f29966db | 10.26434/chemrxiv-2021-bblhc | Transition metal migration and O2 formation underpin voltage hysteresis in oxygen-redox disordered rocksalt cathodes | Lithium-rich disordered rocksalt cathodes display high capacities arising from redox chemistry on both transition-metal and oxygen ions and are potential candidates for next-generation lithium-ion batteries. The atomic-scale mechanisms governing this O-redox behaviour, however, are not fully understood. In particular, it is not clear to what extent transition metal migration is required for O-redox and what role this may play in explaining voltage hysteresis in these materials. Here, we reveal an O-redox mechanism linking transition metal migration and O2 formation in the disordered rocksalt Li2MnO2F. At high states of charge, O-ions dimerise to form molecular O2 trapped in the bulk structure, leaving vacant O sites surrounding neighbouring Mn ions. This undercoordination drives Mn movement into new fully-coordinated octahedral sites. Mn displacement can occur irreversibly, which results in voltage hysteresis, with a lower voltage upon discharge as observed experimentally. Alternatively, Mn displacement may take place into interstitial octahedral sites, which permits a reversible return of the Mn ion to its original site upon discharge, recovering the original Li2MnO2F structure and resulting in reversible O-redox without voltage loss. These new findings suggest that reversible transition metal ion migration provides a possible design route to retain the high energy density of O-redox disordered rocksalt cathodes on cycling. | Kit McColl; Robert A. House; Gregory J. Rees; Alexander G. Squires; Samuel W. Coles; Peter G. Bruce; Benjamin J. Morgan; M. Saiful Islam | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616d2d0b0ad1ff90f29966db/original/transition-metal-migration-and-o2-formation-underpin-voltage-hysteresis-in-oxygen-redox-disordered-rocksalt-cathodes.pdf |
619e7438c481c358cef761e7 | 10.26434/chemrxiv-2021-4r63w | Enantioselective Au(I)-Catalyzed Multicomponent Annulation via Tethered Counterion-Directed Catalysis | Gold(I) complexes of a new chiral phosphoric acid functionalized phosphine of the CPA-Phos series enable the enantioselective multicomponent reactions between aldehydes, hydroxylamines and cyclic yne-enones, leading to 3,4-dihydro-1H-furo[3,4-d][1,2]oxazines. This represents the first example of highly enantioselective multicomponent reaction in gold(I) catalysis. The reactions proceed at low catalyst loading, provide high yields, total diastereoselectivity and enantiomeric excesses up to 99%. Silver-free conditions can be applied. The method has a very broad scope, as it applies to both aliphatic and aromatic aldehydes and hydroxylamines, to a variety of cyclic yne-enones, as well as to yne-enone derived oximes. DFT calculations are reported that enlighten the enantiocontrol pathway. | Zhenhao Zhang; Nazarii Sabat; Gilles Frison; Angela Marinetti; Xavier GUINCHARD | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619e7438c481c358cef761e7/original/enantioselective-au-i-catalyzed-multicomponent-annulation-via-tethered-counterion-directed-catalysis.pdf |
673481475a82cea2faf9f80c | 10.26434/chemrxiv-2024-9k6z7 | Robust Protein-Ligand Interaction Modeling Integrating Physical Laws and Geometric Knowledge for Absolute Binding Free Energy Calculation | Accurate estimation of protein-ligand (PL) binding free energies is a crucial task in medicinal chemistry and a critical measure of PL interaction modeling effectiveness. However, traditional computational methods are often computationally expensive and prone to errors. Recently, deep learning (DL)-based approaches for predicting PL interactions have gained enormous attention, but their accuracy and generalizability are hindered by data scarcity. In this study, we propose LumiNet, a versatile PL interaction modeling framework that bridges the gap between physics-based models and black-box algorithms. LumiNet utilizes subgraph transformer to extract multiscale information from molecular graphs and employs geometric neural networks to integrate PL information, mapping atomic pair structures into key physical parameters of non-bonded interactions in classical force fields, thereby enhancing accurate absolute binding free energy (ABFE) calculations. LumiNet is designed to be highly interpretable, offering detailed insights into atomic interactions within protein-ligand complexes, pinpointing relatively important atom pairs or groups. Our semi-supervised learning strategy enables LumiNet to adapt to new targets with fewer data points than other data-driven methods, making it more relevant for real-world drug discovery. Benchmarks show that LumiNet outperforms the current state-of-the-art model by 18.5% on the PDE10A dataset, and rivals the FEP+ method in some tests with a speed improvement of several orders of magnitude. We applied LumiNet in the scaffold hopping process, which accurately guided the discovery of the optimal ligands. furthermore, we provide a web service for the research community to test LumiNet. The visualization of predicted inter-molecular energy contributions is expected to provide practical values in drug discovery projects. | Qun Su; Jike Wang; Qiaolin Gou; Renling Hu; Hui Zhang; Linlong Jiang; Tianyue Wang; Yifei Liu; Chao Shen; Yu Kang; Chang-Yu Hsieh; Tingjun Hou | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673481475a82cea2faf9f80c/original/robust-protein-ligand-interaction-modeling-integrating-physical-laws-and-geometric-knowledge-for-absolute-binding-free-energy-calculation.pdf |
660bf5d766c13817297af37a | 10.26434/chemrxiv-2023-s9l13-v2 | Development of a Novel Solid State Organic Fluorophore: Excited-State Aromatization-Induced Structural Planarization | Solid-state emission is pivotal for the functionality of organic compounds in opto-electronic applications. Yet, tailoring the emission characteristics of existing solid-state emissive organic frameworks is a challenging task, primarily due to their intricate structure-activity interplay. In this study, we introduce an innovative family of solid-state luminogens, centered around the dibenzosuberenylidene core. These luminogens are characterized by a remarkable excited-state aromatization-induced structural planarization (ESAISP) behaviour. This unique feature allows for the modulation of their fluorescence properties, including color and intensity, through simple structural alterations, opening new avenues in the development of organic advanced functional materials. | Domenic Pace; Reece Crocker; William Kendrick; Bolong Zhang; Wallace Wong; Binh Khanh Mai; Timothy Schmidt; Thanh Vinh Nguyen | Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Photochemistry (Physical Chem.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660bf5d766c13817297af37a/original/development-of-a-novel-solid-state-organic-fluorophore-excited-state-aromatization-induced-structural-planarization.pdf |
60c748479abda29592f8ca5e | 10.26434/chemrxiv.11877834.v1 | Permeability Through Bacterial Porins Dictates Whole Cell Compound Accumulation | The lack of new drugs for Gram-negative pathogens is a global threat to modern medicine. The complexity of their cell envelope, with an additional outer membrane, hinders internal accumulation and thus, the access of molecules to targets. Our limited understanding of the molecular basis for compound influx and efflux from these pathogens is a major bottleneck for the discovery of effective antibacterial compounds. Here we analyse the correlation between the whole-cell compound accumulation of ~200 molecules and their predicted porin permeability coefficient (influx), using a recently developed scoring function. We found a strong linear relationship (75%) between the two, confirming porins key role in compound penetration. Further, the remarkable prediction ability of the scoring function demonstrates its potentiality to guide the optimization of hits to leads as well as the possibility of screening ultra-large virtual libraries. Eventually, the analysis of false positives, molecules with high-predicted influx but low accumulation, provides new hints on the molecular properties behind efflux.<br /> | Silvia Acosta Gutiérrez; Igor Bodrenko; Matteo Ceccarelli | Drug Discovery and Drug Delivery Systems; Microbiology; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748479abda29592f8ca5e/original/permeability-through-bacterial-porins-dictates-whole-cell-compound-accumulation.pdf |
638f7f4b836cebcb9a760a2a | 10.26434/chemrxiv-2022-ljwdt | Boron-Based Chromophores As Effective Moieties In Optoelectronic Devices | Thermally activated delayed fluorescence (TADF) materials have shown great potential in the design of organic metal-free optoelectronic devices and materials and, therefore, are the subject of intense investigations. This contribution presents the effects of various parameters on the photophysical properties of a series of Boron-based TADF emitters. These include torsion angle, electronic density reorganization, energy gap between the first excited singlet (S1) and the first excited triplet states (T1), oscillator strength (f) and spin – orbit coupling (SOC). Through a comprehensive structural analysis, we firstly show the most favourable arrangement of the ground state of popularly used donor (D) and acceptor (A) moieties in TADF emitters. Further on, the properties of the excited states manifold are obtained with Tamm-Dancoff Approximation (TDA), thus rationalizing their optical and photophysical properties. Globally, our results settle the basis for the rationalization of the effects of different parameters on reverse intersystem crossing (RISC) probabilities, which is the rate-limiting step for TADF, thus favouring the rational design of novel highly efficient TADF materials with strong triplet exciton harvesting. | Pelin Ulukan; Antonio Monari; Saron Catak | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638f7f4b836cebcb9a760a2a/original/boron-based-chromophores-as-effective-moieties-in-optoelectronic-devices.pdf |
67291c7af9980725cf169ef7 | 10.26434/chemrxiv-2024-xpd9p | Redox-Enabled Pathway Complexity in Supramolecular Hydrogels | Pathway complexity in supramolecular assemblies presents a unique opportunity for a single, relatively simple system to exhibit a wide range of properties, allowing for multifunctionality. In this study, we report redox-enabled pathway complexity in amino acid-functionalized perylene diimides (PDIs) and its consequence for the macroscopic hydrogel network. We show that chemical reduction and subsequent oxidation enable a kinetically trapped state of the micellar network, which transforms into different network morphologies in response to heat and time. Our finding that pathway complexity in supramolecular systems can alter bulk material properties suggests the potential for future development of dynamic materials that achieve multiple macroscopic functions with a single building block. | Aleksander Bartnik; Lilian Zeinalvand; Dylan Kodira; Pushp Raj Prasad; Joseph Patterson; Seunghyun Sim | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67291c7af9980725cf169ef7/original/redox-enabled-pathway-complexity-in-supramolecular-hydrogels.pdf |
60c7532dee301cefd3c7ad7e | 10.26434/chemrxiv.13416452.v1 | Molecular Design of a “Two-in-One” Orthosteric-Allosteric Chimeric Mutant Selective EGFR Inhibitor | Inhibitors developed to target the epidermal growth factor receptor (EGFR) are an effective therapy for patients with non-small cell lung cancer harbouring drug-sensitive activating mutations in the EGFR kinase domain. Drug resistance due to treatment-acquired mutations within the receptor itself has motivated development of successive generations of inhibitors that bind in the ATP-site, and third-generation agent osimertinib is now a first-line treatment for this disease. More recently, allosteric inhibitors have been developed to overcome the C797S mutation that confers resistance to osimertinib. In this study, we present the rational structure-guided design and synthesis of a mutant-selective EGFR inhibitor that spans the ATPand allosteric sites. The lead compound consists of a pyridinyl imidazole scaffold that binds irreversibly in the orthosteric site fused with a benzylisoindolinedione occupying the allosteric site. The compound potently inhibits enzymatic activity in L858R/T790M/C797S mutant EGFR (4.9 nM), with relative sparing of wild-type EGFR (47 nM). Additionally, this compound achieves cetuximab-independent, mutant-selective cellular efficacy on the L858R and L858R/T790M variants | Florian Wittlinger; David E. Heppner; Ciric To; Marcel Guenther; Bo Hee Shin; Jaimin K. Rana; Anna M. Schmoker; Tyler S. Beyett; Pasi A. Jänne; Michael J. Eck; Stefan Laufer | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7532dee301cefd3c7ad7e/original/molecular-design-of-a-two-in-one-orthosteric-allosteric-chimeric-mutant-selective-egfr-inhibitor.pdf |
60c748df9abda206a8f8cb21 | 10.26434/chemrxiv.11323571.v2 | Mapping Solvation Heterogeneity in Live Cells by Hyperspectral Stimulated Raman Scattering Microscopy | <p>Water provides a dynamic matrix in which all biochemical processes occur in living organisms. The structure and dynamics of intracellular water constitute the cornerstone for understanding all aspects of cellular function. Fundamentally, direct visualization of subcellular solvation heterogeneity is essential but remains challenging with commonly used NMR methods due to poor spatial resolution. To explore this question, we demonstrate a vibrational-shift imaging approach by combining the spectral-focusing hyperspectral stimulated Raman scattering (hsSRS) technique with an environmentally-sensitive nitrile probe. The sensing ability of a near-infrared nitrile-containing molecule is validated in the solution phase, microscopic droplets and cellular environments. Finally, we quantitatively measure the subcellular solvation variance between the cytoplasm (29.5%, S.E. 1.8%) and the nucleus (57.3%, S.E. 1.0%), which is in good agreement with previous studies. This work sheds light on heterogenous solvation in live systems using coherent Raman microscopy and opens up new avenues to explore environmental variance in complex systems with high spatiotemporal resolution.</p> | Xiaoqi Lang; Kevin Welsher | Biophysical Chemistry; Optics; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748df9abda206a8f8cb21/original/mapping-solvation-heterogeneity-in-live-cells-by-hyperspectral-stimulated-raman-scattering-microscopy.pdf |
61f40497e4d9b84b73fad632 | 10.26434/chemrxiv-2022-b3087 | Single Molecule Magnetism in Linear Fe(I) Complexes with Aufbau and non-Aufbau ground-state | With the ongoing efforts on synthesizing mono-nuclear single-ion magnets (SIMs) with promising applications in high-density data storage and spintronics devices, the linear Fe(I) complexes emerge as the enticing candidates possessing large unquenched angular momentum. Herein, we have studied five experimentally synthesized linear Fe(I) complexes to uncover the origin of single-molecule magnetic behavior of these complexes. To begin with, we benchmarked our methodology on the experimentally
and theoretically well-studied complex, [Fe{C(SiMe3)}3]−1] (1) (SiMe3 = trimethylsilyl) which is characterized with large spin-reversal barrier of 226 cm−1 [Nat. Chem. 2013, 5, 577–581]. Further, the two Fe(I) complexes, i.e., [Fe(cyIDep)2]+1 (2) ((cyIDep= 1,3-bis(20,60-diethylphenyl)-4,5-(CH2)4-imidazol-2-ylidene) and [Fe(sIDep)2]+1] (3) (sIDep = 1,3-bis(20,60-diethylphenyl)-imidazolin-2-ylidene) are studied that do not possess SIM behavior under ac or dc magnetic fields, however, they are reported to exhibit large opposite axial zero field splitting (-62.4 and +34.0 cm−1 respectively) from ab initio calculations. Employing state-of-the-art ab initio calculations, we have unwrapped the origin of this contrasting observation between experiment and theory by probing their magnetic relaxation pathways and the pattern of d-orbitals splitting. Additionally, the two experimentally synthesized Fe(I) complexes, i.e., [(η6-C6H6)FeAr*-3,5-Pri 2] (4) (Ar*-3,5-Pri 2 = C6H-2,6-(C6H2-2,4,6-Pri 3)2-3,5-Pri 2) and [(CAAC)2Fe]+1 (5) (CAAC = cyclic (alkyl)(amino)carbene) are investigated for SIM behavior, since there is no report
on their magnetic properties. To this end, complex 4 presents itself as the potential candidate for SIM. | Rishu Khurana; Md. Ehesan Ali | Theoretical and Computational Chemistry; Inorganic Chemistry; Magnetism; Transition Metal Complexes (Inorg.); Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f40497e4d9b84b73fad632/original/single-molecule-magnetism-in-linear-fe-i-complexes-with-aufbau-and-non-aufbau-ground-state.pdf |
66bef373a4e53c4876893d9f | 10.26434/chemrxiv-2024-n2vzq | Towards a Generalizable Machine-Learned
Potential for Metal-Organic Frameworks | Machine-learned Potentials (MLPs) have transformed the field of molecular simulations by scaling `quantum-accurate' potentials to linear time complexity. Yet, while they provide a more accurate reproduction of structural properties as compared to empirical force fields, it is still computationally costly to generate their training dataset from \textit{ab initio} calculations. However, in the current literature, one MLP model is always specifically developed and employed for a specific system, and it is unexplored if one `general' MLP can be developed for a wide variety of structures. Herein, by leveraging upon data-efficient equivariant MLPs, we demonstrate the possibility of developing a general MLP for nearly 3,000 Zn-based Metal-Organic Frameworks (MOFs). After generating a training dataset comprising augmented structures generated from DFT-optimized ones, we validated the trained MLP's reliability in predicting accurate forces and energies when evaluated on the test set that comprises chemically distinct MOF structures. Despite incurring slightly higher errors on structures containing rare chemical moieties, the general MLP can still reliably reproduce thermal and bulk properties for a large sample of Zn-based MOFs. Crucially, by developing one MLP for many structures, the computational cost of developing MLP(s) for high-throughput screening is potentially reduced by a few orders of magnitude. This enables us to predict `quantum-accurate' properties for notable Zn-MOFs that were previously un-investigated via expensive theoretical calculations. More broadly, our contribution facilitates the development of general MLPs to accelerate chemical discoveries among other systems of interest at a fraction of the computational cost. | Yifei Yue; Mohamed Saad Aldin; N. Duane Loh; Jianwen Jiang | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bef373a4e53c4876893d9f/original/towards-a-generalizable-machine-learned-potential-for-metal-organic-frameworks.pdf |
60c7426c469df4fa6bf42fb2 | 10.26434/chemrxiv.8281787.v1 | NMR-Enhanced Crystallography Aids Open Metal-Organic Framework Discovery Using Solvent-Free Accelerated Aging | NMR-enhanced crystallography enables the characterization of a novel cadmium-based, open metal-organic framework (MOF) from a solvent-free "accelerated aging" process. Whereas accelerated aging was devised as a clean, mild route for making MOFs, these results highlight how it application in materials discovery and characterization is aided by a combination of X-ray diffraction and solid-state NMR spectroscopy.<br /> | Christopher A. O’Keefe; Cristina Mottillo; László Fábián; Tomislav Friscic; Robert W. Schurko | Hybrid Organic-Inorganic Materials; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426c469df4fa6bf42fb2/original/nmr-enhanced-crystallography-aids-open-metal-organic-framework-discovery-using-solvent-free-accelerated-aging.pdf |
60c73e16567dfe1307ec3783 | 10.26434/chemrxiv.6450545.v1 | Insights into the Structural Dynamics of PLGA at Terahertz Frequencies | The mechanical properties of an amorphous copolymer are directly related to the dynamic processes occurring at the molecular level. Poly lactic-co-glycolic acid (PLGA) is a biodegradable co-polymer, and in this work we investigate the dynamics of PLGA and its glass transition behaviour by performing variable temperature terahertz time-domain spectroscopy (THz-TDS) experiments. We correlate PLGA dynamics, as measured at terahertz frequencies, their temperature dependence, molecular weight (MW), lactide to glycolide ratio, and free volume. The THz-TDS data can be used to detect two distinct glass transition processes, T<sub>g,α</sub> and T<sub>g,β</sub>. To complement our analysis, we use dynamic mechanical analysis (DMA) to probe the β- and α-relaxation processes in PLGA, and compare the results obtained from the DMA experiments with those obtained using THz-TDS. We attribute T<sub>g,β</sub> to the change in dipole moments associated with the β-relaxation process, originating from the local rotation of C-O macromolecular chain segments, and T<sub>g,α</sub> to the change in dipole moments due to large segmental motion of the copolymer backbone associated with the α-relaxation process. We connect our experimental results to the free volume theory proposed by Fox and Flory, and demonstrate our results are consistent with the relationship between the experimentally determined T<sub>g,β</sub> and T<sub>g,α</sub> and free volume and PLGA dynamics. | Talia A. Shmool; J. Axel Zeitler | Physical Organic Chemistry; Organic Polymers; Polymers; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2018-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e16567dfe1307ec3783/original/insights-into-the-structural-dynamics-of-plga-at-terahertz-frequencies.pdf |
62606aceed4d8899c812de59 | 10.26434/chemrxiv-2022-qvrl4 | S,O-Ligand Promoted meta-C–H Arylation of Anisole Derivatives via Palladium/Norbornene Catalysis | Reversing the conventional site-selectivity of C−H activation processes provides new retrosynthetic disconnections to otherwise unreactive bonds. Here, we report the realization of non-conventional site-selectivity through Pd/Norbornene cooperative-catalysis. Specifically, we report a new catalytic system based on Pd/norbornene with an S,O-ligand for the meta-C−H arylation of aryl ethers. Furthermore, we demonstrate the unique ability of this system to employ alkoxyarene substrates bearing both electron donating and withdrawing substituents. Additionally, ortho-substituted aryl ethers are well tolerated, with the ortho constraint overcome through the use of a novel norbornene mediator. Remarkably, the monoarylation of alkoxyarenes is achieved efficiently enabling the subsequent introduction of a second, different aryl coupling partner to rapidly furnish unsymmetrical terphenyls. | Verena Sukowski; Manuela van Borselen; Simon Mathew ; M. Ángeles Fernández-Ibáñez | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation | CC BY NC 4.0 | CHEMRXIV | 2022-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62606aceed4d8899c812de59/original/s-o-ligand-promoted-meta-c-h-arylation-of-anisole-derivatives-via-palladium-norbornene-catalysis.pdf |
62baa45b1672a2354b50b55c | 10.26434/chemrxiv-2022-x0fj6 | The Principal Component Analysis of the Ring Deformation in the Nonadiabatic Surface Hopping Dynamics | The analysis of the leading active molecular motions in the on-the-fly trajectory surface hopping stimulation provides the essential information to understand the geometrical evolution in nonadiabatic dynamics. When the ring deformation is involved, the identification of the key active coordinates becomes challenging. A "hierarchical" protocol based on the dimensionality reduction method and clustering approaches is proposed for the automatic analysis of the ring deformation in the nonadiabatic molecular dynamics. The representative system keto isocytosine is taken as the prototype to illustrate this protocol. The results indicate that the current hierarchical analysis protocol is a powerful way to clearly clarify both of the major and minor active molecular motions of the ring distortion in nonadiabatic dynamics. | Yifei Zhu; Jiawei Peng; Xu Kang; Chao Xu; Zhenggang Lan | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62baa45b1672a2354b50b55c/original/the-principal-component-analysis-of-the-ring-deformation-in-the-nonadiabatic-surface-hopping-dynamics.pdf |
616134adb564b660c3717447 | 10.26434/chemrxiv-2021-r8zv6 | Unified Template Strategy for Editing Multiple Remote C–H Bonds | Through consecutive selective C–H functionalization at multiple sites, the direct molecular editing of heteroarene carbon-hydrogen (C–H) bonds has the potential to grant rapid access into diverse molecular space; a valuable but often challenging venture to achieve in medicinal chemistry. Contrasting with electronically-biased heterocyclic C–H bonds, remote benzocyclic C–H bonds on bicyclic aza-arenes are especially difficult to differentiate due to lack of intrinsic steric/electronic biases. Through careful consideration of distance and geometric parameters, we herein report a unified catalytic directing template strategy that enables the modular functionalization of chemically-similar and adjacent remote positions on bicyclic aza-arene scaffolds. Differentiated by using two structurally distinct catalytic directing templates, this method enables direct C–H olefination, alkynylation, and allylation at previously inaccessible C6 and C7 positions of quinolines, and is amenable to the iterative, modular, and late-stage C–H editing of quinoline-containing pharmacophores and pharmaceuticals. This report, in combination with our previous C5-selective template and other complementary methods, now fully establishes a unified ‘molecular editing’ strategy to directly modify aza-arene heterocycles at any given site. | Zhoulong Fan; Xiangyang Chen ; Keita Tanaka; Han Seul Park; Nelson Y. S. Lam; Jonathan J. Wong; K. N. Houk; Jin-Quan Yu | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616134adb564b660c3717447/original/unified-template-strategy-for-editing-multiple-remote-c-h-bonds.pdf |
6215d6f0ce899b696d9fed7b | 10.26434/chemrxiv-2022-gjzh3 | Biodegradable Peptide Polymers as Alternatives to Antibiotics Used in Aquaculture | The pressure of antimicrobial resistance has forced many countries to reduce or even prohibit the use of antibiotics in feed. Therefore, it is in urgent need to develop alternatives to antibiotics to control infectious diseases in feed and aquaculture. To address this long-lasting challenge, we prepared peptide polymers that display potent and broad-spectrum activity against common pathogenic bacteria in aquaculture, low hemolysis and low cytotoxicity, and doesn’t induce bacteria to develop resistance or cross resistance to antibiotics. The optimal peptide polymer demonstrates strong in vivo therapeutic potential in an adult zebrafish infection model. Moreover, the optimal peptide polymer is biodegradable by enzyme into single amino acids and dipeptides to totally lose antibacterial activity and, therefore, will not cause antimicrobial selective pressure. Our study suggests that peptide polymers are promising alternatives to antibiotics in aquaculture and open new avenues to address the global challenge of antimicrobial resistance. | Pengcheng Ma; Yueming Wu; Weinan Jiang; Ning Shao; Min Zhou; Yuan Chen; Jiayang Xie; Zhongqian Qiao; Runhui Liu | Polymer Science; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6215d6f0ce899b696d9fed7b/original/biodegradable-peptide-polymers-as-alternatives-to-antibiotics-used-in-aquaculture.pdf |
60c73d0e469df4264ef42676 | 10.26434/chemrxiv.5410777.v1 | Mean bond-length variations in crystals for ions bonded to oxygen | Variations in mean bond-length are examined in oxide and oxysalt crystals for 55 cation configurations bonded to oxygen. The assignment of a coordination-based radius to oxygen is found not to be supported by experimental data. | Olivier Charles Gagné; Frank Christopher Hawthorne | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2017-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e469df4264ef42676/original/mean-bond-length-variations-in-crystals-for-ions-bonded-to-oxygen.pdf |
6707921651558a15efadb100 | 10.26434/chemrxiv-2024-s4gbh | Electrochemical Single-Carbon Insertion: Unlocking para-Insertion via Distonic Radical Cation Intermediates | The synthesis of polysubstituted (hetero)aromatic compounds is essential in various fields, including pharmaceuticals, where such compounds are fundamental to many approved drugs. In this study, we present a novel electrochemical method for sin-gle-carbon insertion targeting various (hetero)aromatic compounds, with a particular focus on pyridines. In this process, the electrochemical oxidation of pyrrole derivatives produces a radical cation intermediate, which then undergoes nucleophilic attack by diazo compounds to yield polysubstituted pyridine derivatives. Notably, the insertion position is influenced by the electronic properties of N-protecting groups, allowing for unprecedented para-selective insertion through the introduction of electron-withdrawing groups. This approach is applicable to various substrates such as indole, imidazole, indene, and cyclo-pentadiene, resulting in the desired carbon-inserted products. Insights from in-situ spectroscopy and theoretical calculations suggest the involvement of distonic radical cation intermediates, facilitating carbon-atom migration on the aromatic ring and enabling insertion at different positions. This study expands the chemical toolkit for synthesizing polysubstituted (het-ero)aromatic compounds and introduces a new concept for single-carbon insertion chemistry. | Tatsuya Morimoto; Yoshio Nishimoto; Taku Suzuki-Osborne; Su-Gi Chong; Kazuhiro Okamoto; Azusa Kikuchi; Daisuke Yokogawa; Mahito Atobe; Naoki Shida | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707921651558a15efadb100/original/electrochemical-single-carbon-insertion-unlocking-para-insertion-via-distonic-radical-cation-intermediates.pdf |
61b8a7b5a53f1bf79e9abd65 | 10.26434/chemrxiv-2021-6jftj-v2 | Explore High Thermal Conductivity Amorphous Polymers using Reinforcement Learning | Developing amorphous polymers with desirable thermal conductivity has significant implications, as they are ubiquitous in applications where thermal transport is critical. Conventional Edisonian approaches are slow and without guarantee of success in material development. In this work, using a reinforcement learning scheme, we design polymers with thermal conductivity above 0.4 W/m- K. We leverage a machine learning model trained against 469 thermal conductivity data calculated from high-throughput molecular dynamics (MD) simulations as the surrogate for thermal conductivity prediction, and we use a recurrent neural network trained with around one million virtual polymer structures as a polymer generator. For all newly generated polymers with thermal conductivity > 0.400 W/m-K, we have evaluated their synthesizability by calculating the synthesis accessibility score and validated the thermal conductivity of selected polymers using MD simulations. The best thermally conductive polymer designed has a MD-calculated thermal conductivity of 0.693 W/m-K, which is also estimated to be easily synthesizable. Our demonstrated inverse design scheme based on reinforcement learning may advance polymer development with target properties, and the scheme can also be generalized to other materials development tasks for different applications. | RUIMIN MA; Hanfeng Zhang; Tengfei Luo | Polymer Science; Conducting polymers | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b8a7b5a53f1bf79e9abd65/original/explore-high-thermal-conductivity-amorphous-polymers-using-reinforcement-learning.pdf |
66c252daa4e53c4876c98475 | 10.26434/chemrxiv-2024-08t4n | Design and synthesis of pillared metal-organic frameworks featuring olefinic fragments | While metal-organic frameworks (MOFs) are known primarily for their well-defined crystalline porous structures that make them desirable in myriads of applications, they also distinguish themselves with their chemical tunability. One strategy for chemical tailoring of MOF structures is post-synthetic modification (PSM) targeting moieties present in their organic building blocks (linkers). In that context, alkene (olefinic) fragments are underrepresented in the realm of MOFs despite their extremely well-established and versatile chemistry. With the majority of reported olefinic MOFs falling into the microporous regime, the PSM opportunities involving bulkier reagents are severely limited. Herein, we report a family of UofT (University of Toronto) pillared MOFs constructed around olefinic 1,4-bis(2-(pyridin-4-yl)vinyl)benzene (BPVB) and tetrakis(4-carboxyphenyl)porphyrin (TCPP) linkers. By utilizing a variety of M(II) [M = Zn, Ni, Co] precursors, three structurally distinct frameworks were synthesized and characterized. Most notably, the nickel-based framework represents the first reported example of stable mesoporous olefinic pillared MOF. In addition to de novo formation of stable pillared MOF, Ni(II) is also used in a cation exchange process to structurally reinforce zinc-based framework. | Rachel Mander; Ashley Schmidt; Michael Ruf; Maciej Korzyński | Inorganic Chemistry; Coordination Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c252daa4e53c4876c98475/original/design-and-synthesis-of-pillared-metal-organic-frameworks-featuring-olefinic-fragments.pdf |
62437a5d3b5f992fdec94709 | 10.26434/chemrxiv-2022-9gw50 | Post-synthetic modification of a porous hydrocarbon cage to give a discrete Co24 organometallic complex | A new alkyne-based hydrocarbon cage was synthesized in high overall yield using alkyne–alkyne coupling in the cage forming step. The cage is porous and displays a moderately high BET surface area (546 m2 g–1). The cage loses crystallinity on activation and thus is porous in its amorphous form, while very similar cages have been either non-porous, or retained crystallinity on activation. Reaction of the cage with Co2(CO)8 results in exhaustive metalation of its 12 alkyne groups to give the Co24(CO)72 adduct of the cage in good yield. | Chriso Thomas; Weibin Liang; Dan Preston; Christian Doonan; Nicholas White | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62437a5d3b5f992fdec94709/original/post-synthetic-modification-of-a-porous-hydrocarbon-cage-to-give-a-discrete-co24-organometallic-complex.pdf |
671ab13098c8527d9e4279c2 | 10.26434/chemrxiv-2024-gqwk5 | Conjugated molecular wires on indium-tin oxide: investigation of the electron transfer mechanism and application in tin perovskite solar cells | Electron transfer through ‘molecular wires’ underpins numerous research fields, ranging from single molecule electronics to fundamental biological processes and their application in (bio)electrocatalysis. Here, we report a series of 1-3 nm long conjugated molecular wires, anchored to indium tin oxide (ITO) electrodes, that exhibit a hopping electron transfer (ET) mechanism (with a β value of 0.043 Å⁻¹) previously unknown over these relatively short distances. We show that the nature of the electrode induces a change in the ET mechanism from tunneling to hopping, by reducing the energy gap between the electron donor and acceptor. The applicability of these anchored molecular wires was demonstrated in a tin perovskite solar cell as hole-selective contacts, leading to solar to electrical power conversion efficiency approaching 10% with improved stability under ambient environmental conditions. This work not only opens new avenues for mechanistic investigations of electron transfer using molecular wires, but also showcases their potential impact in applications e.g. in a solar cell. | Fang Fang; Ang Li; Blaise Geoghegan; Yunfei Dang ; Troy Bennett ; Amanz Azaden; Francesco Vanin; Adam Sills; Nicholas Long; Saif Haque; Maxie Roessler | Materials Science; Analytical Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671ab13098c8527d9e4279c2/original/conjugated-molecular-wires-on-indium-tin-oxide-investigation-of-the-electron-transfer-mechanism-and-application-in-tin-perovskite-solar-cells.pdf |
65a11333e9ebbb4db9feeb4c | 10.26434/chemrxiv-2024-tsqzh | Inorganic Metal Thiocyanates | Metal thiocyanates are some of the earliest reported molecular framework materials and adopta diverse range of structures. This review describes the structures, properties and syntheses ofthe known binary and ternary thiocyanates. It provides a categorization of their diverse structures,and connects them to the structures of atomic inorganic materials. In addition to this description ofcharacterized binary and ternary thiocyanates, the review summarizes the state of knowledge forall other binary metal thiocyanates. The review concludes by highlighting opportunities for futurematerials development. | Matthew Cliffe | Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a11333e9ebbb4db9feeb4c/original/inorganic-metal-thiocyanates.pdf |
6560ae7ecf8b3c3cd70637f4 | 10.26434/chemrxiv-2023-kk2hn | Solvent suppression in pure shift NMR | Intense solvent signals in 1H solution state NMR experiments typically cause severe distortion of spectra and mask nearby solute signals. It is often infeasible or undesirable to replace a solvent with its perdeuteriated form, for example when analysing formulations in situ, when exchangeable protons are present, or for practical reasons. Solvent signal suppression techniques are therefore required. WATERGATE methods are well known to provide good solvent suppression while enabling retention of signals undergoing chemical exchange with the solvent signal. Spectra of mixtures, such as pharmaceutical formulations, are often complicated by signal overlap, high dynamic range, the narrow spectral width of 1H NMR, and signal multiplicity. Here, we show that, by combining WATERGATE solvent suppression with pure shift NMR, ultra-high resolution 1H NMR spectra can be acquired while suppressing intense solvent signals and retaining exchangeable 1H signals. The new method is demonstrated in the analysis of cyanocobalamin, a vitamin B12 supplement, and an eye-drop formulation of atropine. | Emma Gates; Jonathan P. Bradley; Daniel B. G. Berry; Mathias Nilsson; Gareth A. Morris; Ralph W. Adams; Laura Castañar | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6560ae7ecf8b3c3cd70637f4/original/solvent-suppression-in-pure-shift-nmr.pdf |
642b31d616782ec9e64bdfec | 10.26434/chemrxiv-2023-9v4s5 | Untangling the Fundamental Electronic Origins of Non-Local Electron-Phonon Coupling in Organic Semiconductors | Organic semiconductors with distinct molecular properties and large carrier mobilities are constantly developed in attempt to produce highly-efficient electronic materials. Recently, designer molecules with unique structural modifications have been expressly developed to suppress molecular motions in the solid state that arise from low-energy phonon modes, which uniquely limit carrier mobilities through electron-phonon coupling. However, such low-frequency vibrational dynamics often involve complex molecular dynamics, making comprehension of the underlying electronic origins of electron-phonon coupling difficult. In this work, we first generate a mode-resolved picture of electron-phonon coupling in a series of materials that were specifically designed to suppress detrimental vibrational effects. From this foundation, we develop a method based on the crystalline orbital Hamiltonian population analyses to resolve the origins -- down to the single atomic-orbital scale -- of surprisingly large electron-phonon coupling constants of particular vibrations, explicitly detailing the manner in which the intermolecular wavefunction overlap is perturbed. Overall, this approach provides a comprehensive explanation into the unexpected effects of less-commonly studied molecular vibrations, revealing new aspects of molecular design that should be considered for creating improved organic semiconducting materials. | Peter Banks; Gabriele D'Avino ; Guillaume Schweicher; Jeff Armstrong; Chrisitian Ruzie; Jong Won Chung; Chizuru Sawabe; Jeong-Il Park; Toshihiro Okamoto; Jun Takeya; Henning Sirringhaus ; Michael Ruggiero | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642b31d616782ec9e64bdfec/original/untangling-the-fundamental-electronic-origins-of-non-local-electron-phonon-coupling-in-organic-semiconductors.pdf |
6661cdb5418a5379b0380bca | 10.26434/chemrxiv-2024-xpzd0 | Rapid flipping between electrolyte and metallic states in ammonia solutions of alkali metals | Insulator-to-metal transitions are among the most fascinating phenomena in material science, associated with strong correlations, large fluctuations, and related features relevant to applications in electronics, spintronics, and optics. Dissolving alkali metals in liquid ammonia results in the formation of solvated electrons, which are localised in dilute solutions but exhibit metallic behaviour at higher concentrations, forming a disordered liquid metal. The electrolyte-to-metal transition in these systems appears to be gradual, but its microscopic origins remain poorly understood. Here, we provide a molecular-level time-resolved picture of the electrolyte- to-metal transition in solutions of lithium in liquid ammonia, employing ab initio molecular dynamics and many-body perturbation theory, which are validated against photoelectron spectroscopy experiments. We find a rapid flipping with a ∼40 fs timescale between metallic and electrolyte states within a broad range of concentrations. These flips are characterised by abrupt opening and closing of the band gap, which is connected with minute changes in the solution structure and the associated electron density distribution. | Marco Vitek; Igor Rončević; Ondrej Marsalek; H. Christian Schewe; Pavel Jungwirth | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6661cdb5418a5379b0380bca/original/rapid-flipping-between-electrolyte-and-metallic-states-in-ammonia-solutions-of-alkali-metals.pdf |
657fa8a166c1381729718408 | 10.26434/chemrxiv-2023-msgw0 | Nickel-catalyzed Difluoromethylation of Alkene using Difluoroacetic Anhydride | Herein, we describe a nickel-catalyzed reductive difluoromethylation reaction of alkene using inexpensive and easy-to-handle DFAA/pyridine N-oxide reagent system. A variety of C(sp3)-CF2H containing compounds were prepared through a hydrodifluoromethylation process with good efficiency under mild conditions. In addition, various gem-difluoroalkenes bearing CF2H or 1o, 2o, 3o alkyl group were synthesized from trifluoromethyl alkenes via a defluorination process using this new established approach. | Zhenkang Ai; Hui Chen; Xuebin Liao | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657fa8a166c1381729718408/original/nickel-catalyzed-difluoromethylation-of-alkene-using-difluoroacetic-anhydride.pdf |
63952c5f7b7c913c8cec685d | 10.26434/chemrxiv-2022-vzpv2 | Facile Synthesis and Chiral Resolution of Expanded Helicenes with up to 35 cata-Fused Benzene Rings | Expanded helicenes are expected to show enhanced chiroptical properties as compared to the classical helicenes but the synthesis is very challenging. Herein, we report the facile synthesis of a series of expanded helicenes Hn (n=1-4) containing 11, 19, 27 and 35 cata-fused benzene rings through Suzuki coupling-based oligomerization followed by Bi(OTf)3-mediated regioselective cyclization of vinyl ethers. Their structures were determined by X-ray crystallographic analysis. Enantiopure H2, H3, and H4 can be isolated by chiral HPLC and they all exhibit strong chiroptical responses with high absorption dissymmetry factor (|gabs|) values (0.020 for H2, 0.021 for H3, and 0.021-0.024 for H4). | Gui-Fei Huo; Toshiya M. Fukunaga; Xudong Hou; Yi Han; Wei Fan; Shaofei Wu; Hiroyuki Isobe; Jishan Wu | Organic Chemistry; Materials Science | CC BY 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63952c5f7b7c913c8cec685d/original/facile-synthesis-and-chiral-resolution-of-expanded-helicenes-with-up-to-35-cata-fused-benzene-rings.pdf |
6407b4840e6a36fabae76b43 | 10.26434/chemrxiv-2023-lql3r | Copper(I) as reducing agent for the synthesis of bimetallic PtCu catalytic nanoparticles | Catalysis plays a significant role in modern science and technology and is considered a central pillar in green chemistry to preserve our environment. With the increases in pollutants, contamination leads to global climate change and an urgent need to find new, fast, and greener chemical processes and methodologies is needed. In the present work, we have explored the possibility of use Cu(I) to reduce the platinum salt K2PtCl4 to produce stable nanoparticles. The nanoparticles present copper in the final structure, making it one easy and accessible methodology to produce bimetallic nanostructures. The catalytic applications of the new nanomaterials have been exploited as artificial metalloenzymes and in dye degradation. | Adrian Fernandez-Lodeiro; Javier Fernández-Lodeiro; Noelia Losada-Garcia; Silvia Nuti; José Luis Capelo-Martinez; Jose M Palomo; Carlos Lodeiro | Nanoscience; Nanocatalysis - Catalysts & Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6407b4840e6a36fabae76b43/original/copper-i-as-reducing-agent-for-the-synthesis-of-bimetallic-pt-cu-catalytic-nanoparticles.pdf |
66cc088aa4e53c4876a311e3 | 10.26434/chemrxiv-2024-jppwm | Anharmonicity and Vibrational Stark Fields in Phosphinic Acid Dimers | Phosphinic acid is unique among oxyacids of phosphorus with the ability to form cyclic dimers via intermolecular hydrogen bonding, analogous to carboxylic acid dimers with exceptional stability and higher dimerization enthalpies due to stronger hydrogen bonding interactions. The strength of the hydrogen bond with different combinations of substituents on the monomeric units can be effectively studied by evaluation of electric fields along the hydrogen-bonded OH donor groups. The correlation between OH stretch vibrational frequency and electric field was linear with average stark tuning rates of 45.6 and 11.8 cm-1(MV cm-1)-1 respectively for the primary and secondary substitution effects, which by comparison is more than double relative to carboxylic acid dimers. Further, the Stark tuning rate for the anharmonic O–D frequency shifts on average was about 40-50% higher compared to the corresponding harmonic O–D frequency shifts, which suggests the presence of strong anharmonicity of O–H/O–D oscillators in phosphinic acid dimers. | Manjusha Boda; G Naresh Patwari | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cc088aa4e53c4876a311e3/original/anharmonicity-and-vibrational-stark-fields-in-phosphinic-acid-dimers.pdf |
6438a39d08c86922fff06f49 | 10.26434/chemrxiv-2023-vl26d | Assessing the Performance of Docking, FEP, and MM/GBSA Methods on a Series of KLK6 Inhibitors | Kallikrein 6 (KLK6) is an attractive drug target for the treatment of neurological diseases and for various cancers. Herein, we explore the accuracy and efficiency of different computational methods and protocols to predict the free energy of binding (ΔGbind) of a series of KLK6 inhibitors. We found that the performance of the methods varied strongly with the tested system. For only one of the three KLK6 datasets, the docking scores were in good agreement (R2 ≥ 0.5) with experimental values of ΔGbind. A similar result was obtained with MM/GBSA calculations based on single minimized structures. Improved binding affinity predictions were obtained with the free energy perturbation (FEP) method, with an overall MUE and RMSE of 0.53 and 0.68 kcal/mol, respectively. This result indicates that FEP can be a promising tool for the structure-based optimization of KLK6 inhibitors. | Wemenes José Lima Silva; Renato Ferreira de Freitas | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6438a39d08c86922fff06f49/original/assessing-the-performance-of-docking-fep-and-mm-gbsa-methods-on-a-series-of-klk6-inhibitors.pdf |
64ef3b44dd1a73847fd3b395 | 10.26434/chemrxiv-2023-88l2m | Passive permeability controls synthesis for the allelochemical sorgoleone in sorghum root exudate | Competition for soil nutrients and water with other plants foster competition within the biosphere for access to these limited resources. The roots for the common grain sorghum produce multiple small molecules that are released via root exudates into the soil to compete with other plants. Sorgoleone is one such compound, which suppresses weed growth near sorghum by acting as a quinone analog and interferes with photosynthesis. Since sorghum also grows photosynthetically, and may be susceptible to sorgoleone action if present in tissues above ground, it is essential for sorgoleone to be excreted efficiently. However, since the P450 enzymes that synthesize sorgoleone are intracellular, the release mechanism for sorgoleone remain unclear. In this study, we conducted an in silico assessment for sorgoleone and its precursors to passively permeate biological membranes. To facilitate accurate simulation, CHARMM parameters were newly optimized for sorgoleone and its precursors. These parameters were used to conduct one microsecond of unbiased molecular dynamics simulations to compare the permeability of sorgoleone with its precursors molecules. We find that interleaflet transfer is maximized for sorgoleone, suggesting that the precursor molecules may remain in the same leaflet for access by biosynthetic P450 enzymes. Since no sorgoleone was extracted during unbiased simulations, we compute a permeability coefficient using the inhomogeneous solubility diffusion model. The requisite free energy and diffusivity profiles for sorgleone through a sorghum plasma membrane model were determined through Replica Exchange Umbrella Sampling (REUS) simulations. The REUS calculations highlight that any soluble sorgleone would quickly insert into a lipid bilayer, and would readily transit. When sorgleone forms aggregates in root exudate as indicated by our equilibrium simulations, aggregate formation would lower the effective concentration in aqueous solution, creating a concentration gradient that would facilitate passive transport. This suggests that sorgoleone synthesis occurs within sorghum root cells and that sorgoleone is exuded by permeating through the cell membrane without the need for a transport protein. | Saad Raza; Troy Sievertsen; Sakiko Okumoto; Josh Vermaas | Theoretical and Computational Chemistry; Agriculture and Food Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ef3b44dd1a73847fd3b395/original/passive-permeability-controls-synthesis-for-the-allelochemical-sorgoleone-in-sorghum-root-exudate.pdf |
62c30f1b08a0f92de55b6ee7 | 10.26434/chemrxiv-2022-ssh16 | A quality by design approach for the synthesis of palmitoyl carnitine loaded nanoemulsions as drug delivery systems | Nanoemulsions (NE) are lipid nanocarriers that can efficiently load hydrophobic active compounds, like palmitoyl-L-carnitine (pC), used here as model molecule. The use of design of experiments (DoE) approach is a useful tool to develop NE with optimized properties, requiring less experiments compared to trial-and-error approach. The optimized formulation was studied for its stability, scalability, pC entrapment, loading capacity, and biodistribution in mice. NE were prepared by the solvent injection technique. DoE was implemented for designing pC-loaded NE, using a two-level fractional factorial design as model. NE were fully characterized by a combination of techniques, and biodistribution was studied ex-vivo after injection of fluorescent NE in healthy mice.
We selected the optimal formulation of NE, named pC-NEU, after DoE analysis of four variables. pC-NEU incorporated pC in a very efficient manner, with high entrapment efficiency and loading capacity. pC-NEU did not change its initial colloidal properties stored at 4ºC in water during 120 days, nor in buffers with different pH values (5.3 and 7.4) during 30 days. The scalability process did not affect NE stability properties. Biodistribution study showed that pC-NEU formulation was predominantly concentrated in the liver, with minimal accumulation in spleen, stomach and kidneys.
| Eva María Arroyo Urea; María Muñoz Hernando; Marta Leo Barriga; Fernando Herranz; Ana Gonzalez Paredes | Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c30f1b08a0f92de55b6ee7/original/a-quality-by-design-approach-for-the-synthesis-of-palmitoyl-carnitine-loaded-nanoemulsions-as-drug-delivery-systems.pdf |
64c90b95658ec5f7e58f09e3 | 10.26434/chemrxiv-2023-gn9z7-v2 | Zinc-reinforced ZSM-5 subject to a rare-earth magnet and the presence of a legume yields substantial copper extraction | Adsorption, using chemically modified zeolites, is a common conventional method of mitigating heavy metal pollution. However, the physical modification of zeolites with reducing agents subject to static magnets and biological trappers is yet to be explored. In this laboratory-based work, we partly gel-coated raw ZSM-5 pellets with zinc coarse powder and tested their performance in copper extraction from a polluted medium with copper sulfate. We also examined the performance subject to the presence of a neodymium magnet, with and without faba bean, Vicia faba, as a copper bio-trap. Additionally, on a limited scale, we plasma-sputtered ZSM-5 pellets with zinc and tested their copper extraction under the magnet effect. Inductively coupled plasma mass spectrometry (ICP) revealed that the reinforced zeolite led to the fastest copper extraction, outperforming the raw zeolite and the bio-trap, especially as time advanced. Accompanying the reinforced zeolite with the bio-trap was the most effective over time, followed by having both the magnet and the bio-trap to accompany the reinforced zeolite. However, interestingly, having the magnet as a sole companion of the reinforced zeolite was always better than using raw zeolite, but slightly of a lesser yield than having the reinforced companionless. The bio-trap was a better companion than the magnet, but after 20min having both companions was more beneficial than having the magnet alone and less yielding than having the bio-trap solo in the long term, indicating a synergistic effect between the reinforced zeolite and the bio-trap. Brunauer, Emmett and Teller (BET), Energy-Dispersive X-ray Spectroscopy (EDAX), and X-ray diffraction analyses, provided supportive information that underscored the stability yet the differential performance of ZSM-5. Although the extraction efficacy deteriorated sharply over time, the zinc-sputtered zeolite showed promising early results, exceeding those of the raw and the reinforced zeolites when the magnet was absent and almost identical to the outcome when the magnet accompanied the reinforced zeolite. Our amalgamative approach provides user-friendly novel methods of notable copper extraction, with high applicability potential for the extraction of other heavy metals from aquatic media.
| Mouhammad Shadi Khudr; Cristian Baleca; Nasser Alqahtani ; Hassan Alhassawi ; Arthur Garforth ; Gordon Tiddy; Abdullatif Alfutimie | Chemical Engineering and Industrial Chemistry; Water Purification | CC BY 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c90b95658ec5f7e58f09e3/original/zinc-reinforced-zsm-5-subject-to-a-rare-earth-magnet-and-the-presence-of-a-legume-yields-substantial-copper-extraction.pdf |
60c75857702a9b08c718cce4 | 10.26434/chemrxiv.14540742.v1 | Solving the Wigner Equation with Signed Particles Monte Carlo for Chemically Relevant Potentials | This paper presents the Signed Particles Monte Carlo algorithm for the solution of the transient Wigner equation for potentials relevant in chemical physics. Benchmarks include the harmonic and the double well potentials. | Yu Wang; Lena Simine | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75857702a9b08c718cce4/original/solving-the-wigner-equation-with-signed-particles-monte-carlo-for-chemically-relevant-potentials.pdf |
669f627ac9c6a5c07a9a6d86 | 10.26434/chemrxiv-2023-gp81w-v3 | Single-Point Grand Potential and Nuclear Derivatives of Finite-Temperature Kohn-Sham Density-Functional Theory | We present a new implementation of single-point grand potential, nuclear gradient and nuclear hessian for finite-temperature Kohn-Sham density-functional theory (FT-DFT) in the grand canonical ensemble. It is shown that evaluation of single-point grand potential and nuclear gradient of FT-DFT can be formulated in a way similar to that of single-point energy and nuclear gradient of zero-temperature DFT, with no need for nested-loop optimization or approximation present in prevalent methods. In the current formulation, the nuclear hessian is divided into two parts, the fixed-occupation-number component and the variable-occupation-number one, as a result of fractional occupation of molecular orbitals. We have developed two techniques, namely the non-idempotent CPSCF and the occupation-gradient CPSCF for those two components, respectively. The convergence of single-point grand potential is discussed, while the analytical nuclear derivatives are verified via comparison with numerical results. | Yichi ZHANG; Ka Lok Chan; Fu Kit Sheong | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669f627ac9c6a5c07a9a6d86/original/single-point-grand-potential-and-nuclear-derivatives-of-finite-temperature-kohn-sham-density-functional-theory.pdf |
670c74f151558a15effb22cf | 10.26434/chemrxiv-2023-bvvdb-v7 | Powerful and Reliable Prediction using Latent Variables of Experimentally Unobservable Reactions in Organic Synthesis | In this study, a novel machine learning algorithm was designed to assist in the development of organic reactions. This algorithm addresses the complexities inherent in batch- type organic reactions, including the necessity for numerous experiments and the effects of intricate characteristics of reaction pathways. By integrating molecular relationships and actual yields from observable reactions, the algorithm is used to estimate untested yields via extrapolation. An approach based on Bayesian optimization and dual annealing optimization is employed to compute expected values and evaluate plausibility. The algorithm’s dual-loop 2 structure, incorporating latent variables and experimental values, maximizes the coefficient of determination. Physicochemical aspects of the algorithm are validated using natural bond orbital charges, and its utility in synthesizing perfluoroiodinated naphthalenes is demonstrated. The algorithm exhibits potential for application in predicting experimentally unobservable reactions, thereby advancing the field of synthetic organic chemistry. | Kazuhiro TAKEDA; Naoya OHTSUKA; Toshiyasu SUZUKI; Norie MOMIYAMA | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670c74f151558a15effb22cf/original/powerful-and-reliable-prediction-using-latent-variables-of-experimentally-unobservable-reactions-in-organic-synthesis.pdf |
6132bd95d5f0801af9ba34fe | 10.26434/chemrxiv-2021-rssv5 | Efficient Infrared Emission of Colloidal PbSe Nanoplatelets by Lateral Size Control | Colloidal two-dimensional (2D) lead chalcogenide nanoplatelets (NPLs) represent highly interesting materials for near- and short wave-infrared applications including innovative glass fiber optics exhibiting negligible attenuation. In this work, we demonstrate a direct synthesis route for 2D PbSe NPLs with cubic rock salt crystal structure at low reaction temperatures of 0 °C and room temperature. A lateral size tuning of the PbSe NPLs by controlling the temper-ature and by adding small amounts of octylamine to the reaction leads to excitonic absorption features in the range of 800 – 1000 nm (1.6 – 1.3 eV) and narrow photoluminescence (PL) seamlessly covering the broadband infrared spec-tral window of 900 – 1450 nm (1.4 – 0.9 eV). The PL quantum yield of the as-synthesized PbSe NPLs is more than doubled by a postsynthetic treatment with CdCl2 (e.g. from 14.7 % to 37.4 % for NPLs emitting at 980 nm with a FWHM of 214 meV). An analysis of the slightly asymmetric PL line shape of the PbSe NPLs and their characterization by ultrafast transient absorption and time-resolved PL spectroscopy reveal a surface trap related PL contribution which is successfully reduced by the CdCl2 treatment from 40 % to 15 %. Our results open up new pathways for a direct synthesis and straightforward incorporation of colloidal PbSe NPLs as efficient infrared emitters at technologi-cally relevant telecommunication wavelengths. | Lars F. Klepzig; Leon Biesterfeld; Michel Romain; André Niebur; Anja Schlosser; Jens Hübner; Jannika Lauth | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Solution Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6132bd95d5f0801af9ba34fe/original/efficient-infrared-emission-of-colloidal-pb-se-nanoplatelets-by-lateral-size-control.pdf |
673aefc07be152b1d0745242 | 10.26434/chemrxiv-2024-1t4vt | Unveiling CO2 reactivity with data-driven methods | Carbon dioxide is a versatile C1 building block in organic synthesis. Understanding its reactivity is crucial for predicting reaction outcomes and identifying suitable substrates for the creation of value-added chemicals and drugs. A recent study [Li et al., J. Am. Chem. Soc., 2020, 142, 8383] estimated the reactivity of CO2 in the form of Mayr's electrophilicity parameter E on the basis of a single carboxylation reaction. The disagreement between experiment (E = –16.3) and computation (E = –11.4) corresponds to a deviation of up to ten orders of magnitude in bimolecular rate constants of carboxylation reactions. Here, we introduce a data-driven approach incorporating supervised learning, quantum chemistry, and uncertainty quantification to resolve this discrepancy. The dataset used for reducing the uncertainty in E(CO2) represents 15 carboxylation reactions in DMSO. However, experimental data is only available for one of these reactions. To ensure reliable predictions, we selected a training set composed of this and 19 additional reactions comprising heteroallenes other than CO2 for which experimental data is available. With the new data-driven protocol, we can narrow down the electrophilicity of carbon dioxide to E = –14.6(5) with 95 % confidence. | Maike Eckhoff; Kerstin L. Bublitz; Jonny Proppe | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673aefc07be152b1d0745242/original/unveiling-co2-reactivity-with-data-driven-methods.pdf |
654eb3f7dbd7c8b54b099054 | 10.26434/chemrxiv-2023-90fpz-v2 | The Colloidal Stability and Solubility of Metal-Organic Framework Particles
| Chemical separation membranes, drug delivery agents, and other nascent applications of metal-organic frameworks (MOFs) benefit from preparing MOFs as nanoparticles (nanoMOFs) and by controlling their particle surfaces. Despite the lack of deliberately added surface ligands, common examples of nanoMOFs exhibit multi-week colloidal stability in a range of polar solvents, in stark contrast with most conventional nanoparticles that require surface functionalization with bulky ligands. And yet, the origin of this stability remains unknown. Although nanoMOF zeta potentials exceed |±20 mV|, electrostatics alone cannot explain colloidal stability. Here, we demonstrate that nanoMOFs suspend only in solvents that dissolve the constituent MOF linkers. Moreover, the maximum “solubility” of nanoMOFs, i.e., the concentration of saturated particle suspensions, correlates with the solubility of the linkers in the same solvent. Calorimetry measurements indicate that nanoMOF immersion enthalpies resemble the solvation enthalpies of the linkers, suggesting solvent-linker interactions dictate nanoMOF colloidal stability. As a proof-of-concept, whereas nanoMOFs generally suspend only in polar solvents, we achieve toluene nanoMOF suspensions by identifying linkers soluble in toluene. Furthermore, atomistic molecular dynamics simulations reveal that solvents best at dissolving nanoMOFs are those that pack densely into the pores and interact with the MOF linkers. These results provide a predictive tool for achieving nanoMOF colloidal stability and highlight the uniqueness of defining a MOF “surface”, where solvents access both interior and exterior surfaces. | Michael LeRoy; Anton Perera; Shasanka Lamichhane; Ashley Mapile; Faiqa Khaliq; Kentaro Kadota; Xianghui Zhang; Su Ha; Racheal Fisher; Di Wu; Chad Risko; Carl Brozek | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654eb3f7dbd7c8b54b099054/original/the-colloidal-stability-and-solubility-of-metal-organic-framework-particles.pdf |
60c7468abdbb8923d8a38c1e | 10.26434/chemrxiv.11347055.v1 | Simultaneous Concentration of Dissolved Solids and Recovery of Clean Water from Acid Mine Drainage Employing Membrane Distillation | This study explored the techno-economic feasibility of using membrane distillation to recover clean water from acid mine drainage employing both renewable and nonrenewable energy sources. A microporous hydrophobic polypropylene membrane displaying 0.45 um pores exhibited the highest water flux during long-term testing under steady state continuous process conditions. Currently, natural gas and electricity are the most economical energy sources for the proposed membrane separation process to treat acid mine drainage. However, by 2030 renewable sources, and PV in particular, will become competitive with nonrenewable energy sources. | Jungshik Kang; Vadim Guliants; Joo-Youp Lee | Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7468abdbb8923d8a38c1e/original/simultaneous-concentration-of-dissolved-solids-and-recovery-of-clean-water-from-acid-mine-drainage-employing-membrane-distillation.pdf |
623dcf32658bc04b47b7d705 | 10.26434/chemrxiv-2022-dwmsv | Molecular interpretation of single-molecule force spectroscopy experiments with computational approaches | Single molecule force-spectroscopy techniques have granted access to unprecedented molecular-scale details about biochemical and biological mechanisms. However, the interpretation of the experimental data is often challenging and it benefits from the perspective brought by computational approaches. In many cases, these simulations (all-atom steered MD simulations in particular) are key to provide molecular details about the associated mechanisms, to help test different hypotheses and to predict experimental results. We will review here some of our recent efforts directed towards the molecular interpretation of single-molecule force spectroscopy experiments on proteins and protein-related systems, often in close collaboration with experimental groups. These results will be discussed in the broader contexts of the field, highlighting the recent achievements and the ongoing challenges for computational biophysicists and biochemists. In particular, we will focus on the input gained from molecular simulations approaches to rationalize the origins for the unfolded protein elasticity and the protein conformational behavior under force, to understand how force denaturation differs from chemical, thermal or shear unfolding, and to unravel the molecular details of unfolding events for a variety of systems. We will also discuss the use of models based on Langevin dynamics on a 1-D free-energy surface to understand the effect of protein segmentation on the work exerted by a force, or, at the other end of the spectrum of computational techniques, how quantum calculations can help to understand the reactivity of disulfide bridges exposed under force. | STIRNEMANN Guillaume | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Theory - Computational; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623dcf32658bc04b47b7d705/original/molecular-interpretation-of-single-molecule-force-spectroscopy-experiments-with-computational-approaches.pdf |
63285b24f764e637b0fadd07 | 10.26434/chemrxiv-2022-7f475 | Recyclable and Convenient-to-Handle Pt/Ethylene Glycol Catalytic System – an Approach to Sustainable Hydrosilylation | This study presents a highly efficient and simple recyclable catalytic system for heterophase hydrosilylation. This catalytic system consisting of a commercially available platinum precatalyst, namely K2PtCl4, and a cheap green solvent, namely ethylene glycol (EG), is easily prepared by dissolving K2PtCl4 in EG without employing ligands, additives, or an inert atmosphere, at r.t. The suggested method allows up to 45 recycles with quantitative conversion under air at r.t. to be performed. The high reaction rate (from 2 to 20 min per cycle) and low catalyst load (0.001 – 0.1 mol%) allow high values of TON (up to ~ 104 – 105) and TOF (up to ~ 103 – 106) to be reached. This approach is applicable to a wide range of unsaturated compounds, such as functional and nonfunctional terminal or internal alkenes, alkynes, and alkyl-, phenyl-, and siloxy-containing hydride silanes. Moreover, the heterophase catalytic system is suitable for the synthesis of linear and cross-linked polyorganosiloxanes. In most cases, the reaction provides high yields (up to 95-99%) and selectivity. It gives mostly anti-Markovnikov products which can be isolated from the catalytic system by simple decantation. The process is scalable to gram quantities. | Irina Goncharova; Irina Beletskaya; Ashot Arzumanyan | Organometallic Chemistry; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63285b24f764e637b0fadd07/original/recyclable-and-convenient-to-handle-pt-ethylene-glycol-catalytic-system-an-approach-to-sustainable-hydrosilylation.pdf |
679b8b076dde43c908f9d290 | 10.26434/chemrxiv-2025-187x2-v2 | In Silico Analysis of 6-Gingerol for Antifungal Efficacy Against Candida albicans | Candida albicans, a major fungal pathogen, poses significant challenges due to antifungal resistance, particularly in immunocompromised individuals. Natural compounds, such as 6-gingerol, derived from Zingiber officinale (ginger), have gained attention for their therapeutic potential. This study investigates the antifungal activity of 6-gingerol against C. albicans using in silico approaches, including molecular docking, ADMET profiling, and interaction analysis. Molecular docking results demonstrated that 6-gingerol exhibits potential inhibitory interactions with key fungal targets N-myristoyltransferase and Sterol 14-alpha demethylase, facilitated by hydrogen bonding and hydrophobic forces. ADMET analysis revealed favorable pharmacokinetic and safety profiles, including low toxicity, supporting its potential as a natural antifungal agent. These findings suggest that 6-gingerol, a bioactive compound from ginger, holds promise for further exploration in antifungal drug development. Experimental assessment using in vitro and in vivo experiments is advised to verify its effectiveness and suitability for clinical applications. | TANZIM AHMED | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679b8b076dde43c908f9d290/original/in-silico-analysis-of-6-gingerol-for-antifungal-efficacy-against-candida-albicans.pdf |
669157bb01103d79c5d4e251 | 10.26434/chemrxiv-2024-18mqh | Discovery of VEGFR-2 Inhibitors employing Junction
Tree Variational Encoder with Local Latent Space
Bayesian Optimization and Gradient Ascent Exploration | (VEGFR-2), which belongs to the protein tyrosine kinase family, emerges as one of the most significant
targets of interest. The ongoing Food and Drug Administration (FDA) approval of novel
therapeutic medicines towards VEGFR-2 emphasizes the urgent need to discover sophisticated molecular
structures that are capable of reliably limiting VEGFR-2 activity. Recognizing the huge potential
of deep learning-based molecular model advancements, we focused our study on exploring the chemical
space to find small molecules potentially inhibiting VEGFR-2. To achieve this goal, we utilized
the Junction Tree Variational Autoencoder in combination with two optimization approaches on the
latent space: the local Bayesian optimization on the initial dataset and the gradient ascent on nine
FDA-approved drugs targeting VEGFR-2. The optimization results yielded a set of 493 uncharted
small molecules. Quantitative structure-activity relationship (QSAR) models and molecular docking
were used to assess the generated molecules for their inhibitory potential using their predicted
pIC50 and binding affinity. The QSAR model constructed on RDK7 fingerprints using the CatBoost
algorithm achieved remarkable coefficients of determination (R2) of 0.792 ± 0.075 and 0.859 with
respect to internal and external validation. Molecular docking was implemented using the 4ASD complex
with optimistic retrospective control results (the ROC-AUC value being 0.710 and the binding
activity threshold being -7.90 kcal/mol). Newly generated molecules possessing acceptable results
corresponding to both assessments were shortlisted and checked for interactions with the protein at
the binding site on important residues, including Cys919, Asp1046, and Glu885 | Gia-Bao Truong; Thanh-An Pham; Van-Thinh To; Hoang-Son Lai Le; Phuoc-Chung Van Nguyen; The-Chuong Trinh; Tieu-Long Phan; Tuyen Ngoc Truong | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669157bb01103d79c5d4e251/original/discovery-of-vegfr-2-inhibitors-employing-junction-tree-variational-encoder-with-local-latent-space-bayesian-optimization-and-gradient-ascent-exploration.pdf |
60c7592c337d6c9301e29353 | 10.26434/chemrxiv.14664789.v1 | The Role of Water Loading and Germanium Content in Germanosilicate Hydrolysis | New zeolitic frameworks can be prepared through the Assembly-Disassembly-Organisation-Reassembly (ADOR) process by exploiting the lability of Ge-O bonds in germanosilicate zeolites to control their hydrolysis. In the disassembly step, two key factors are water and germanium content, but their exact roles remain unknown. Nevertheless, we combined experimental water-vapor adsorption with first principles simulations to identify the mechanism of germanosilicate zeolite disassembly. The results showed that water vapor adsorption on <b>UTL</b> germanosilicate proceeds in reversible (at low partial pressures) and irreversible (at higher partial pressures) modes. Based on our ab initio molecular dynamics simulations, we related these two modes to weak physisorption at low water loading and to reactive transformations at high water loading, via collective mechanisms requiring high local water concentrations. This bimodal behavior also depends on the germanium content as high Ge-content further decreases <b>UTL</b> hydrolytic stability by opening up yet another low-energy disassembly pathway at high water loading. Overall, we discovered, verified and explained the mechanisms of <b>UTL</b> disassembly and its factors. These findings will likely be generalized to other ADORable germanosilicate zeolites and help to find the optimal protocol for the synthesis of new zeolites. | Mengting Jin; Ondřej Veselý; Christopher Heard; Martin Kubů; Petr Nachtigal; Jiří Čejka; Lukas Grajciar | Catalysts; Computational Chemistry and Modeling; Heterogeneous Catalysis; Chemical Kinetics; Interfaces; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7592c337d6c9301e29353/original/the-role-of-water-loading-and-germanium-content-in-germanosilicate-hydrolysis.pdf |
60c745c1337d6ce997e27036 | 10.26434/chemrxiv.10248764.v1 | Bacterial Peptidoglycan Stapling with Functionalized D-Amino Acids | Transpeptidation reinforces the structure of cell wall peptidoglycan, an extracellular heteropolymer that protects bacteria from osmotic lysis. The clinical success of transpeptidase-inhibiting β-lactam antibiotics illustrates the essentiality of these cross-linkages for cell wall integrity, but the presence of multiple, seemingly redundant transpeptidases in many bacterial species makes it challenging to determine cross-link function precisely. Here we present a technique to covalently link peptide strands by chemical rather than enzymatic reaction. We employ bio-compatible click chemistry to induce triazole formation between azido- and alkynyl-D-alanine residues that are metabolically installed in the cell walls of Gram-positive and Gram-negative bacteria. Synthetic triazole cross-links can be visualized by substituting azido-D-alanine with azidocoumarin-D-alanine, an amino acid derivative that undergoes fluorescent enhancement upon reaction with terminal alkynes. Cell wall stapling protects the model bacterium Escherichia coli from β-lactam treatment. Chemical control of cell wall structure in live bacteria can provide functional insights that are orthogonal to those obtained by genetics.<br /> | Sylvia L. Rivera; Akbar Espaillat; Arjun K. Aditham; Peyton Shieh; Chris Muriel-Mundo; Justin Kim; Felipe Cava; M. Sloan Siegrist | Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c1337d6ce997e27036/original/bacterial-peptidoglycan-stapling-with-functionalized-d-amino-acids.pdf |
623f2bd32c501065da89626e | 10.26434/chemrxiv-2022-zb1kd | Photocatalyzed dehydrogenation of aliphatic N- heterocycles releasing dihydrogen | We report the iridium-nickel dual photocatalytic acceptorless and redox neutral dehydrogenation of aliphatic heterocycles yielding cyclic alkenes without overoxidation at room temperature. Excitation of the iridium photocatalyst initiates the formation of a nickel hydride intermediate that yields alkenes and H2 via β-hydrogen elimination. The reaction proceeds regioselective and the scope was demonstrated by the synthesis of ten biologically relevant molecules and drugs. In addition, commercially and easily available N-heterocyclic alkane starting materials were converted by the method into functionalized alkenes of high synthetic and commercial value. | Ritu; Saikat Das; Ya Ming Tian; Tobias Karl; Nidhi Jain; Burkhard Koenig | Organic Chemistry; Catalysis; Homogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623f2bd32c501065da89626e/original/photocatalyzed-dehydrogenation-of-aliphatic-n-heterocycles-releasing-dihydrogen.pdf |
66f1238fcec5d6c142ec63e3 | 10.26434/chemrxiv-2024-x7qx6 | 27Al NMR chemical shifts in zeolite MFI via machine learning acceleration of structure sampling and shift prediction | Zeolites, such as MFI, are versatile microporous aluminosilicate materials that are widely used in catalysis and adsorption processes. The location of the aluminium within the zeolite framework is one of the important determinants of performance in industrial applications, and is typically probed by 27Al NMR spectroscopy. However, interpretation of 27Al NMR spectra is challenging, while first-principles computational modelling struggles to achieve the timescales and model complexity needed to provide reliable assignments. In this study, we deploy advanced machine learning-based methods to predict 27Al chemical shifts, complemented by molecular dynamics simulations with neural network potentials to achieve significant speed-up compared to traditional density functional theory (DFT) approaches, while maintaining high accuracy. This allows us to comprehensively explore various conditions relevant to catalysis, including water loading, temperature, and the relative positions of aluminium (pairs). We demonstrate that both water content and temperature significantly affect the chemical shift and do so in a non-trivial way that is highly T-site dependent, highlighting a need for adoption of realistic, case-specific models. Notably, we are able, based on quantitative agreement with relevant experimental data, to assign experimental NMR peaks to specific T-sites, even in such a complex zeolite as MFI. These findings provide a testament to the capabilities of machine learning approaches in providing reliable predictions of important spectroscopic observables for complex industrially relevant materials under realistic conditions. | Daniel Willimetz; Andreas Erlebach; Christopher J. Heard; Lukáš Grajciar | Theoretical and Computational Chemistry; Materials Science; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f1238fcec5d6c142ec63e3/original/27al-nmr-chemical-shifts-in-zeolite-mfi-via-machine-learning-acceleration-of-structure-sampling-and-shift-prediction.pdf |
60c73dd59abda2ef96f8b7c3 | 10.26434/chemrxiv.6185339.v1 | Identification of Key Proteins Associated with Myocardial Infarction using Bioinformatics and Systems Biology | <p>Myocardial
infarction, more commonly known as heart attack, is a huge health problem
around the world. It is a result of inadequate blood supply to certain parts of
the heart and death of heart muscle cells in that region. Although it has been
around for a long time, newer and newer ways of probing myocardial infarction
is being followed. Bioinformatics and Systems Biology are relatively recent fields
to try to give new insights into myocardial infarction. Following the footsteps
of others, this <i>in silico</i> study has
tried to chime in on the investigation into myocardial infarction. The study
began with the gene expression omnibus dataset uploaded to the NCBI from a whole-genome
gene expression analysis carried out at Mayo Clinic in Rochester, Minnesota.
From the dataset, differentially expressed genes following first-time
myocardial infarction were identified and classified into up-regulated and down-regulated
ones. Gene Set Enrichment Analysis (GSEA) was carried out on the up-regulated
genes which were statistically significant and corresponded with the NCBI
generated annotations. Protein-Protein Interaction Network for these genes was
constructed. GSEA revealed 5 transcription factors, 5 microRNAs and 3 pathways
significantly associated with them. From the Protein-Protein Interaction
Network, 6 key proteins (hub nodes) have been identified. These 6 proteins may
open a new window of opportunity for the discovery/design of new drugs for mitigating
the damage caused by myocardial infarction.</p> | Ishtiaque Ahammad | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd59abda2ef96f8b7c3/original/identification-of-key-proteins-associated-with-myocardial-infarction-using-bioinformatics-and-systems-biology.pdf |
67c370ac6dde43c9080ef0bb | 10.26434/chemrxiv-2025-9rg6z | The Unintentional Confusion Surrounding the Reference Scale in Electrochemistry | Electrochemical techniques have been extensively employed across various fields of research due to their pivotal role in advancing the clean energy transition. This interdisciplinary integration, however, requires special attention to the fundamental aspects of electrochemistry. As the number of researchers adopting these techniques continues to grow — whether they are trained electrochemists or not — the need for standardize parameters and terminology has become increasingly evident in recent years. Moreover, the rise of artificial intelligence applied to science emphasizes even more the importance of such normalizations. This text demonstrates the divergent practices in the representation of reference scales in electrochemical results and initiates a discussion on the need for their standardization. | Nicolas A. Ishiki | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c370ac6dde43c9080ef0bb/original/the-unintentional-confusion-surrounding-the-reference-scale-in-electrochemistry.pdf |
650dffacb927619fe7a2df62 | 10.26434/chemrxiv-2023-ft1l8-v3 | Indoor Air Quality Implications of Germicidal 222 nm Light | One strategy for mitigating the indoor transmission of airborne pathogens, including the SARS-CoV-2 virus, is irradiation by germicidal UV light (GUV). A particularly promising approach is 222 nm light from KrCl excimer lamps (GUV222); this inactivates airborne pathogens and is thought to be relatively safe for human skin and eye exposure. However, the impact of GUV222 on the composition of indoor air has received little experimental study. Here, we conduct laboratory experiments in a 150 L Teflon chamber to examine the formation of secondary species by GUV222. We show that GUV222 generates ozone (O3) and hydroxyl radicals (OH), both of which can react with volatile organic compounds to form oxidized volatile organic compounds and secondary organic aerosol particles. Results are consistent with a box model based on known photochemistry. We use this model to simulate GUV222 irradiation under more realistic indoor air scenarios, and demonstrate that under some conditions, GUV222 irradiation can lead to levels of O3, OH, and secondary organic products that are substantially elevated relative to normal indoor conditions. The results suggest that GUV222 should be used at low intensities and in concert with ventilation, decreasing levels of airborne pathogens while mitigating the formation of air pollutants. | Victoria Barber; Matthew Goss; Lesly Franco Deloya; Lexy LeMar; Yaowei Li; Erik Helstrom; Manjula Canagaratna; Frank Keutsch; Jesse Kroll | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650dffacb927619fe7a2df62/original/indoor-air-quality-implications-of-germicidal-222-nm-light.pdf |
60c74bdbbdbb89ba90a39681 | 10.26434/chemrxiv.12378140.v1 | Connecting Experimental Synthetic Variables with the Microstructure and Electronic Properties of Doped Ferroelectric Oxides Using High-Throughput Frameworks | <div>
<div>
<div>
<p>Doping remains as the most used technique to photosensitize ferroelectric oxides for solar cell
applications. However, optimizing these materials is still a challenge. First, many variables should
be considered, for instance dopant nature and concentration, synthesis method or temperature.
Second, all these variables should be connected with the microstructure of the solid solution and
its optoelectronic properties. Here, a computational high-throughput framework that combines
Boltzmann statistics with DFT calculations is presented as a solution to accelerate the optimization
of theses materials for solar cells applications. This approach has two main advantages: i) the
automatic and systematic exploration of the configurational space and ii) the connection between
the changes in the microstructure of the material and its electronic properties. One of the most
studied doped-ferroelectric systems, [KNbO3]1−x[BaNi1/2Nb1/2O3−δ]x, is used as a study case. Our
results not only agree with previous theoretical and experimental reports, but also explain the effect
of some of the variables to consider when this material is synthesized.
</p>
</div>
</div>
</div> | Jose J Plata; Antonio Marquez; Santiago Cuesta-López; Javier
Fdez. Sanz | Nanostructured Materials - Materials; Photovoltaics; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bdbbdbb89ba90a39681/original/connecting-experimental-synthetic-variables-with-the-microstructure-and-electronic-properties-of-doped-ferroelectric-oxides-using-high-throughput-frameworks.pdf |
67ba2fb981d2151a029bce03 | 10.26434/chemrxiv-2025-4prds | Comprehensive Analysis of Crystalline Hydrophobic Alkylated Poly(ethyleneimine)s | Polyethyleneimine (PEI) is a widely used polymer in catalysis, gas separation, water treatment, drug delivery, textile, and paper production. We propose a new method of transforming hydrophobic and hygroscopic PEIs into hydrophobic and crystalline materials via simple alkylation. The crystalline structure of the alkylated PEIs was characterized using powder X-ray diffraction, small-angle X-ray scattering, thermogravimetric analysis, and inelastic neutron scattering. Consequently, the amine-rich alkylated polymer demonstrates CO2 responsiveness for CO2-mediated desalination. | Anand Ayyar; Rodrigo Lima; Adedeji Adelodun; Berit Nagorsen; Jacob Kirkensgaard; Svemir Rudić; Heloisa Bordallo; Jiwoong Lee | Polymer Science; Organic Polymers; Polymer brushes; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ba2fb981d2151a029bce03/original/comprehensive-analysis-of-crystalline-hydrophobic-alkylated-poly-ethyleneimine-s.pdf |
60c74ae1567dfe308aec4e49 | 10.26434/chemrxiv.12268730.v1 | In Search for Effective and Safe Drugs Against SARS-CoV-2: Part III] the Electronic Factors of Remdesivir and the Naturally Extracted Aspirochlorine Drugs | This report is associated with an ongoing coronavirus outbreak. We selected Remdesivir (used in the treatment of Ebola) and Aspirochlorine (a natural product found in <i>Aspergillus oryzae)</i>, and their binding to specific peptide sequences of the coronavirus S-protein: ACE2 interface-drug binding adduct were calculated. The stable intermolecular adducts between the chosen drug molecules with the S protein and ACE2 result in limited host-virus interactions. The electrophilicity and nucleophilicity indices of the drugs showed that both drugs act as electron sinks to shield ACE2 from interacting with the S protein. Aspirochlorine acts as an electron acceptor (electrophile) toward both individual targets, the ACE2, and S proteins (nucleophiles). Aspirochlorine electronically shields ACE2 from the interaction with S protein by sinking the electronic charge of the S protein. The electrophilicity and nucleophilicity parameters of Remdesivir were higher than those of ACE2, and both molecules were bound via hydrogen bonding intermolecular interactions without intermolecular electron transfer. Remdesivir also shields ACE2 from the S protein. The results obtained strongly suggest the beneficial use of both drugs. The results reported indicate that the association of remdesivir with the target proteins was exothermic, while it was endothermic in the case of Aspirochlorine. Both drugs offer protection and/or treatment against the coronavirus S-protein COVID-19. | M. Sabry Abdel-Mottaleb; Yousra Abdel-Mottaleb | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae1567dfe308aec4e49/original/in-search-for-effective-and-safe-drugs-against-sars-co-v-2-part-iii-the-electronic-factors-of-remdesivir-and-the-naturally-extracted-aspirochlorine-drugs.pdf |
60c74a1a702a9b762718b22d | 10.26434/chemrxiv.12152661.v1 | Chemical Space Exploration: How Genetic Algorithms Find the Needle in the Haystack | We attempt to explain why search algorithms can find molecules with particular properties in an enormous
chemical space (ca 10<sup>60</sup> molecules) by considering only a tiny subset (typically 10<sup>3−6</sup> molecules). Using
a very simple example, we show that the number of potential paths that the search algorithms can follow
to the target is equally vast. Thus, the probability of randomly finding a molecule that is on one of these
paths is quite high and from here a search algorithm can follow the path to the target molecule. A path is
defined as a series of molecules that have some non-zero quantifiable similarity (score) with the target
molecule and that are increasingly similar to the target molecule. The minimum path length from any
point in chemical space to the target corresponds is on the order of 100 steps, where a step is the
change of and atom- or bond-type. Thus, a perfect search algorithm should be able to locate a particular
molecule in chemical space by screening on the order of 100s of molecules, provided the score changes
incrementally. We show that the actual number for a genetic search algorithm is between 100 and several
millions, and depending on the target property and its dependence on molecular changes, the molecular
representation, and the number of solutions to the search problem. | Emilie S. Henault; Maria Harris Rasmussen; Jan H. Jensen | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a1a702a9b762718b22d/original/chemical-space-exploration-how-genetic-algorithms-find-the-needle-in-the-haystack.pdf |
60c73ed80f50dbf8d23956da | 10.26434/chemrxiv.7119887.v1 | Catalytic Enantioselective Benzylation Directly from Aryl Acetic Acids | The stability and wide availability of carboxylic acids make them valuable reagents in chemical synthesis. Most transition metal catalyzed processes using carboxylic acid substrates are initiated by a decarboxylation event that generates reactive carbanion or radical intermediates. Developing enantioselective methodologies relying on these principles can be challenging, as highly reactive species tend to react indiscriminately without selectivity. Furthermore, anionic or radical intermediates generated from decarboxylation can be incompatible with protic and electrophilic functionality, or groups that undergo trapping with radicals. We demonstrate that metal-catalyzed enantioselective benzylation reactions of allylic electrophiles can occur directly from aryl acetic acids. The reaction proceeds via a pathway in which decarboxylation is the terminal event, occurring after stereoselective carbon–carbon bond formation. The mechanistic features of the process enable enantioselective benzylation without the generation of a highly basic nucleophile. Thus, the process has broad functional group compatibility that would not be possible employing established protocols.<br /> | Patrick Moon; Zhongyu Wie; Rylan Lundgren | Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed80f50dbf8d23956da/original/catalytic-enantioselective-benzylation-directly-from-aryl-acetic-acids.pdf |
6645b79a418a5379b06c0791 | 10.26434/chemrxiv-2024-bmvt7 | 3’-O-β-Glycosylation of nucleoside analogues using a promiscuous bacterial glycosyltransferase | Nucleoside analogue therapeutics have a proven capability within drug discovery as antimicrobial, antiviral and antineoplastic agents. However, their efficacy can be limited by poor cellular uptake, high off target toxicity and poor bioavailability. Prodrugs of such analogues contribute to an improved pharmacokinetic profile. Herein, we explore biocatalytic glycosylation of nucleoside analogues. The activity of the nucleoside-specific 3’-O-glycosyltransferase AvpGT from Streptomyces sp. AVP053U2 is investigated against a panel of both natural and clinically relevant purine and pyrimidine nucleoside analogues. AvpGT demonstrates broad substrate promiscuity, with 16 of 22 nucleosides tested showing glycosylation by HILIC-MS. Of these, 13 nucleosides were successfully glycosylated on 25 μmol scale in 39-91% yields, including four nucleoside analogue therapeutics. Furthermore, a novel β-glucosidase, AvpGS, was identified from the same Streptomyces sp. strain, heterologously expressed, purified and shown to display high substrate promiscuity in subsequently removing glucose from the glycoconjugates. | Jonathan Dolan; Tessa Keenan; Caecilie Benckendorff; Aisling Ní Cheallaigh; Martin Fascione; Gavin Miller | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6645b79a418a5379b06c0791/original/3-o-glycosylation-of-nucleoside-analogues-using-a-promiscuous-bacterial-glycosyltransferase.pdf |
652f25cbbda59ceb9acc0ed1 | 10.26434/chemrxiv-2023-h0zh1 | Non-idealities in CO2 electroreduction mechanisms revealed by automation-assisted kinetic analysis | In electrocatalysis, mechanistic analysis of reaction rate data often relies on linearization of relatively simple rate equations; this is the basis for typical Tafel and reactant order dependence analyses. However, for more complex reaction phenomena, such as surface coverage effects or mixed control, these common linearization strategies will yield incomplete or uninterpretable results. Cohesive kinetic analysis, which is often used in thermocatalysis and involves quantitative model fitting for data collected over a wide range of reaction conditions, requires more data but also provides a more robust strategy for interrogating reaction mechanisms. In this work, we report a robotic system that improves the experimental workflow for collecting electrochemical rate data by automating sequential testing of up to ten electrochemical cells that can each have a different electrode, electrolyte, gas-phase reactant composition, and applied voltage. We use this system to investigate the mechanism of carbon dioxide electroreduction to carbon monoxide at several immobilized metal tetrapyrroles. Specifically, at cobalt phthalocyanine (CoPc), cobalt tetraphenylporphyrin (CoTPP), and iron phthalocyanine (FePc), we see signatures of complex reaction mechanisms, where observed bicarbonate and CO2 order dependences change with applied potential. We illustrate how phenomena such as electrolyte poisoning and potential-dependent degrees of rate control can explain the observed kinetic behaviors. Our mechanistic analysis suggests that CoPc and CoTPP share a similar reaction mechanism, akin to one that has been previously proposed, whereas the mechanism for FePc likely involves a species later in the catalytic cycle as the most abundant reactive intermediate. Our study illustrates that complex reaction mechanisms which are not amenable to common Tafel and order dependence analyses may be quite prevalent across this class of immobilized metal tetrapyrrole electrocatalysts. | Joy Zeng; Vineet Padia; Joseph Maalouf; Aditya Limaye; Alexander Liu; Michael Yusov; Ian Hunter; Karthish Manthiram | Catalysis; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652f25cbbda59ceb9acc0ed1/original/non-idealities-in-co2-electroreduction-mechanisms-revealed-by-automation-assisted-kinetic-analysis.pdf |
6230b58313d4782e6e8f8fab | 10.26434/chemrxiv-2022-f05w8 | Design of a potent, selective and brain penetrant inhibitor of Wnt-deactivating enzyme Notum by optimization of a crystallographic fragment hit | Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human disease such as colorectal cancer and Alzheimer’s disease supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we describe the discovery and profile of 8l (ARUK3001185) as a potent, selective and brain pentrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identifed 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases and drug targets. | Nicky Willis; William Mahy; James Sipthorp; Yuguang Zhao; Hannah Woodward; Benjamin Atkinson; Elliott Bayle; Fredrik Svensson; Sarah Frew; Fiona Jeganathan; Amy Monaghan; Stefano Benvegnu; Sarah Jolly; Luca Vecchia; Reinis Ruza; Svend Kjaer; Steven Howell; Ambrosius Snidjers; Magda Bictash; Patricia Salinas; Jean-Paul Vincent; Yvonne Jones; Paul Whiting; Paul Fish | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6230b58313d4782e6e8f8fab/original/design-of-a-potent-selective-and-brain-penetrant-inhibitor-of-wnt-deactivating-enzyme-notum-by-optimization-of-a-crystallographic-fragment-hit.pdf |
60c74436bdbb890270a387a1 | 10.26434/chemrxiv.9758423.v1 | The Missing Label Problem: Addressing False Assumptions Improves Ligand-Based Virtual Screening | <div>Ligand-based virtual screening (LBVS) uses machine readable representations of chemicals to learn a mapping function that can predict binding interactions with protein labels. Because it is highly scalable it is increasingly used in drug development in academic and pharmaceutical contexts. We have identified assumptions commonly used in LBVS that are false, which collectively can be described as the missing label problem. Firstly, many of the binding interactions in the bioactivity databases typically used to train LBVS models have never been tested before, but the absence of a label is interpreted by most models as a true negative. Secondly, many proteins have multiple binding sites with unrelated shapes but the associated ligands are grouped together under the one protein label. These assumptions frustrate the ability of the model to learn a correct mapping function. Here we use statistical techniques to predict values for the missing labels and binding sites and show how this improves the ability of LBVS models to rank ligands correctly. In the process we introduce a new technique for removing bias during model evaluation based on data blocking from experimental design theory. All data and code for analysis and generating figures is publicly available on github (https://github.com/ljmartin/Missing_label_problem).<br /></div> | Lewis Martin; Michael Bowen | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74436bdbb890270a387a1/original/the-missing-label-problem-addressing-false-assumptions-improves-ligand-based-virtual-screening.pdf |
66636a51409abc0345e3fec5 | 10.26434/chemrxiv-2023-9ldvr-v2 | Understanding Reactivity and Stability of Rhodium Supported on Different Ceria Facets in Catalytic NO Reduction and CO/Hydrocarbon Oxidation Reactions | Synthesis of robust and hydrothermally stable PGM/ceria materials for NO, CO and hydrocarbon abatement remains a formidable challenge as ceria and PGMs are known to sinter severely >800 °C under hydrothermal conditions, leading to irreversible activity loss. Herein, we tackle this challenge by synthesizing well-defined catalysts with atomically dispersed rhodium supported on ceria with varying abundance of (100), (101) and (111) facets. Evaluation of these catalysts for NO reduction by CO, as well as CO and propylene oxidation under model and industrially relevant conditions reveals pronounced reactivity and stability differences. Different modes of interaction of Rh+3 ions with the ceria facets and their facile reducibility were shown to be the crucial parameters controlling reactivity, resulting in pronounced activity and stability variations. Facet-dependent poisoning of surfaces by nitrites was identified as the main reason for deactivation of the catalysts at low temperature, which is mitigated for (111) ceria facets. (111)-enriched ceria nanoparticles survive extremely harsh hydrothermal aging at 950 °C by maintaining and preserving (111) facets, unlike ceria nanoparticles which sinter into irregularly shaped particles. Thus, putting atomically dispersed PGM sites on (111) ceria facets leads to the catalytic material with the highest activity and stability for all studied reactions, providing the pathway to novel catalysts that can endure extreme hydrothermal aging conditions. | Inhak Song; Libor Kovarik; Mark Engelhard; Janos Szanyi; Yong Wang; Konstantin Khivantsev | Physical Chemistry; Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Interfaces; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66636a51409abc0345e3fec5/original/understanding-reactivity-and-stability-of-rhodium-supported-on-different-ceria-facets-in-catalytic-no-reduction-and-co-hydrocarbon-oxidation-reactions.pdf |
61dc8886636cc9a27346538c | 10.26434/chemrxiv-2021-51rbb-v3 | Carbon Dioxide Capture Chemistry of Amino Acid Functionalized Metal-Organic Frameworks in Humid Flue Gas | Metal-organic framework-808 has been functionalized with 11 amino acids (AA) to produce a series of MOF-808-AA structures. The adsorption of CO2 under flue gas conditions revealed that glycine- and DL-lysine-functionalized MOF-808 (MOF-808-Gly and -DL-Lys) have the highest uptake capacities. Enhanced CO2 capture performance in the presence of water was observed and studied using single-component sorption isotherms, CO2/H2O binary isotherm, and dynamic breakthrough measurements. The key to the favorable performance was uncovered by deciphering the mechanism of CO2 capture in the pores and attributed to the formation of bicarbonate as evidenced by 13C and 15N solid-state nuclear magnetic resonance spectroscopy studies. Based on these results, we examined the performance of MOF-808-Gly in simulated coal flue gas conditions and found that it is possible to capture and release CO2 by vacuum swing adsorption. MOF-808-Gly was cycled at least 80 times with full retention of performance. This study significantly advances our understanding of CO2 chemistry in MOFs by revealing how strongly bound amine moieties to the MOF backbone create the chemistry and environment within the pores, leading to the binding and release of CO2 under mild conditions without application of heat. | Hao Lyu; Oscar Iu-Fan Chen; Nikita Hanikel; Mohammad I. Hossain; Robinson W. Flaig; Xiaokun Pei; Ameer Amin; Mark D. Doherty; Rebekah K. Impastato; T. Grant Glover; David R. Moore; Omar M. Yaghi | Inorganic Chemistry; Energy; Coordination Chemistry (Inorg.); Fuels - Energy Science; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dc8886636cc9a27346538c/original/carbon-dioxide-capture-chemistry-of-amino-acid-functionalized-metal-organic-frameworks-in-humid-flue-gas.pdf |
60c741eb337d6c2a8be269a3 | 10.26434/chemrxiv.8182025.v1 | Machine Learning Accelerates the Discovery of Design Rules and Exceptions in Stable Metal-Oxo Intermediate Formation | <p>Metal-oxo moieties are important catalytic intermediates in the selective partial oxidation of hydrocarbons and in water splitting. Stable metal-oxo species have reactive properties that vary depending on the spin state of the metal, complicating the development of structure-property relationships. To overcome these challenges, we train the first machine learning (ML) models capable of predicting metal-oxo formation energies across a range of first-row metals, oxidation states, and spin states. Using connectivity-only features tailored for inorganic chemistry as inputs to kernel ridge regression or artificial neural network ML models, we achieve good mean absolute errors (4-5 kcal/mol) on set-aside test data across a range of ligand orientations. Analysis of feature importance for oxo formation energy prediction reveals the dominance of non-local, electronic ligand properties in contrast to other transition metal complex properties (e.g., spin-state or ionization potential). We enumerate the theoretical catalyst space with an ANN, revealing both expected trends in oxo formation energetics, such as destabilization of the metal-oxo species with increasing <i>d</i>-filling, as well as exceptions, such as weak correlations with indicators of oxidative stability of the metal in the resting state or unexpected spin-state dependence in reactivity. We carry out uncertainty aware evolutionary optimization using the ANN to explore a > 37,000 candidate catalyst space. New metal and oxidation state combinations are uncovered and validated with density functional theory (DFT), including counter-intuitive oxo-formation energies for oxidatively stable complexes. This approach doubles the density of confirmed DFT leads in originally sparsely populated regions of property space, highlighting the potential of ML-model-driven discovery to uncover catalyst design rules and exceptions.</p> | Aditya Nandy; Jiazhou Zhu; Jon Paul Janet; Chenru Duan; Rachel Getman; Heather Kulik | Theory - Inorganic; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741eb337d6c2a8be269a3/original/machine-learning-accelerates-the-discovery-of-design-rules-and-exceptions-in-stable-metal-oxo-intermediate-formation.pdf |
6289478c5d94855f1eca0cd2 | 10.26434/chemrxiv-2022-jdzlr | Localized Active Space State Interaction: A Multireference Method For Chemical Insight | Multireference electronic structure methods, like the complete active space (CAS) selfconsistent
field model, have long been used to characterize chemically interesting processes.
Important work has been done in recent years to develop modifications having lower computational
cost than CAS, but typically these methods offer no more chemical insight than
that from the CAS solution being approximated. In this paper, we present the localized active
space - state interaction (LASSI) method that can be used not only to lower the intrinsic cost of
the multireference calculation, but also to improve interpretability. The localized active space
(LAS) approach utilizes the local nature of electron-electron correlation to express a composite
wave function as an antisymmetrized product of unentangled wave functions in local
active subspaces. LASSI then uses these LAS states as a basis from which to express complete
molecular wave functions. This not only makes the molecular wave function more compact,
but it also permits flexibility in choosing those states to include in the basis. Such selective
inclusion of states translates to selective inclusion of specific types of interactions, thereby allowing
a quantitative analysis of these interaction. We demonstrate the use of LASSI to study
charge migration and spin-flip excitations in multireference organic molecules. We also compute
the J coupling parameter for a bimetallic compound using various LAS bases to construct
the Hamiltonian to provide insight into the coupling mechanism. | Riddhish Pandharkar; Matthew R. Hermes; Christopher J. Cramer; Laura Gagliardi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6289478c5d94855f1eca0cd2/original/localized-active-space-state-interaction-a-multireference-method-for-chemical-insight.pdf |
60e6c72f882582246da61245 | 10.26434/chemrxiv-2021-p52b9 | A Six-Coordinate High-Spin FeIV=O Species of Cucurbit[5]uril: A Highly Potent Catalyst for C-H Hydroxylation of Methane, If synthesised | DFT and ab initio DLPNO-CCSD(T) calculations predict a stable S =2 six-coordinate FeIV=O species with cucurbit[5]uril (CB[5]) as a ligand ([(CB[5])FeIV=O(H2O)]2+(1)). The aggressive reactivity pattern of 1 far exceeds even metalloenzymes such as sMMOs in activating inert substrates such as methane, setting a stage for new generation biomimic catalysts | Gopalan Rajaraman; Ravi Kumar; Mahesh Sundararajan | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Small Molecule Activation (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e6c72f882582246da61245/original/a-six-coordinate-high-spin-fe-iv-o-species-of-cucurbit-5-uril-a-highly-potent-catalyst-for-c-h-hydroxylation-of-methane-if-synthesised.pdf |
60c75077337d6c40d7e28310 | 10.26434/chemrxiv.12518357.v3 | Area-Selective Deposition of Ruthenium by Area-Dependent Surface Diffusion | <div>
<div>
<p>Area-selective deposition (ASD) enables
the growth of materials on target regions of patterned substrates for
applications in fields ranging from microelectronics to catalysis. Selectivity
is often achieved through surface modifications aimed at suppressing or
promoting the adsorption of precursor molecules. Here we show, instead, that
varying the surface composition can enable ASD by affecting surface diffusion
rather than adsorption. Ru deposition from (carbonyl)- (alkylcyclohexadienyl)Ru
and H<sub>2</sub> produces smooth films on metal nitrides and nanoparticles on
SiO<sub>2</sub>. The latter form by surface diffusion and aggregation of Ru
adspecies. Kinetic modeling shows that changing the surface termination of SiO<sub>2</sub>
from -OH to -CH<sub>3</sub>, and thus its surface energy, leads to larger and
fewer nanoparticles because of a 1000-fold increase in surface diffusion rates.
Kinetic Monte Carlo simulations show that even surface diffusion alone can
enable ASD because adspecies tend to migrate from high- to low-diffusivity
regions. This is corroborated by deposition experiments on 3D TiN-SiO<sub>2</sub>
nanopatterns, which are consistent with Ru migrating from SiO<sub>2</sub> to
TiN. Such insights not only have implications for the interpretation of
experimental results but may also inform new ASD protocols, based on chemical
vapor and atomic layer deposition, that take advantage of surface diffusion.</p></div></div> | Fabio Grillo; Job Soethoudt; Esteban A. Marques; Lilian de Martin; Kaat Van Dongen; J. Ruud van Ommen; Annelies Delabie | Aggregates and Assemblies; Catalysts; Coating Materials; Nanostructured Materials - Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75077337d6c40d7e28310/original/area-selective-deposition-of-ruthenium-by-area-dependent-surface-diffusion.pdf |
670aa269cec5d6c142f3b11a | 10.26434/chemrxiv-2024-rrbhc | Composition and structure analyzer/featurizer for explainable machine-learning models to predict solid state structures | Traditional and non-classical machine learning models for solid-state structure prediction have predominantly relied on compositional features (derived from properties of constituent elements) to predict the existence of structure and its properties. However, the lack of structural information can be a source of suboptimal property mapping and increased predictive uncertainty. To address the challenge, we introduce a strategy that generates and combines both compositional and structural features with minimal programming expertise required. Our approach utilizes open-source, interactive Python programs named Composition Analyzer Featurizer (CAF) and Structure Analyzer Featurizer (SAF). CAF generates numerical compositional features from a list of formulas provided in an Excel file, while SAF extracts numerical structural features from a .cif file by generating a supercell. 133 features from CAF and 94 features from SAF were used either individually or in combination to cluster nine structure types in equiatomic AB intermetallics. The performance was comparable to those with features state-of-the art featurizers in advanced machine learning models. Our SAF+CAF features provided a cost-efficient and reliable solution, even with the PLS-DA method, where a significant fraction of the most contributing features were the same as those identified in the more computationally intensive XGBoost models. | Emil Jaffal; Sangjoon Lee; Danila Shiryaev; Alex Vtorov; Nikhil Barua; Holger Kleinke; Anton Oliynyk | Materials Science; Inorganic Chemistry; Bonding; Coordination Chemistry (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670aa269cec5d6c142f3b11a/original/composition-and-structure-analyzer-featurizer-for-explainable-machine-learning-models-to-predict-solid-state-structures.pdf |
60c74c5ebdbb891ebda39771 | 10.26434/chemrxiv.12458549.v1 | A Voltammetric pH Sensor for Food and Biological Matrices | <div>Measurement of pH is of fundamental importance in a wide range of environmental, biological and industrial applications. Glass electrode and litmus paper are widely used for this, but the former is difficult to miniaturize, prone to drift and fragile, the latter is inaccurate. This paper describes a pH sensor based on an indoaniline-derivative (4-((4-aminophenyl)imino)-2,6-dimethoxycyclohexa-2,5dien-1-one), which exploits alternating current voltammetry to measure pH in the range between 2 and 12 . The synthetized indoaniline-derivative was not genotoxic (A. cepa assay), and the sensor reliably measured pH in milk, tea, orange juice, blood, urine and saliva. Results were comparable with those obtained with a glass electrode calibrated with certified solutions (maximum relative standard deviation of 3 % and accuracy less than 0.2 pH unit). The sensor had negligible hysteresis, an almost Nernstian sensitivity (56 mV/pH) and was fully functional after a two-month storage. Sensor response showed a limited dependence on temperature (0.14 mV per pH unit and °C) and limited sensitivity to possible interferents such as lithium and sodium ions; its response to these was similar to that of a glass electrode, and was absent for ascorbic acid. </div> | Federico Maria Vivaldi; Delio Santalucia; Noemi Poma; Andrea Bonini; Pietro Salvo; Lorenzo Del Noce; Bernardo Melai; Arno Kirchhain; Viliam Kolivoska; Romana Sokolova; Magdaléna Hromadovà; Fabio Di Francesco | Analytical Chemistry - General; Analytical Apparatus; Biochemical Analysis; Electrochemical Analysis; Food; Electrochemistry; Sensors | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c5ebdbb891ebda39771/original/a-voltammetric-p-h-sensor-for-food-and-biological-matrices.pdf |
6396f43b9e687bcd12484682 | 10.26434/chemrxiv-2022-q2413-v2 | Modulating the lifetime of DNA motifs using visible light and small molecules | Here we regulate the formation of dissipative assemblies built from DNA using a merocyanine photoacid that responds to visible light. The operation of our system, and the relative distribution of species within it, are controlled by irradiation time, initial pH value, and the concentration of a small molecule binder that inhibits the reaction cycle. This approach is modular, does not require DNA modification, and can be used for several DNA sequences and lengths. Our system design allows for waste-free control of dissipative DNA nanotechnology, towards the generation of non-equilibrium, life-like nanodevices. | Laura Wimberger; Felix Rizzuto; Jonathon Beves | Physical Chemistry; Organic Chemistry; Nanoscience; Supramolecular Chemistry (Org.); Nanodevices; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6396f43b9e687bcd12484682/original/modulating-the-lifetime-of-dna-motifs-using-visible-light-and-small-molecules.pdf |
60c7451abb8c1a16363da600 | 10.26434/chemrxiv.9962000.v1 | Compression of Spin-Adapted Multi-Configurational Wave Functions in Exchange-Coupled Polynuclear Spin Systems | We present a protocol based on unitary transformations of molecular orbitals to reduce the number of non-vanishing coefficients of spin-adapted configuration interaction expansions. Methods that exploit the sparsity of the Hamiltonian matrix and compactness of its eigensolutions, such as the FCIQMC algorithm in its spin-adapted implementation, are well suited to this protocol. The wave function compression resulting from this approach is particularly attractive for anti-ferromagnetically coupled polynuclear spin systems, such as transition metal cubanes in bio-catalysis and, Mott and charge-transfer insulators in solid state physics. Active space configuration interaction calculations on the stretched N2 and square N4 compounds, the chromium dimer, and a [Fe2S2] model system are presented as a proof-of-concept. For the Cr2 case large and intermediate bond distances are discussed, showing that the approach is effective in cases where static and dynamic correlation are equally important. The [Fe2S2] case shows the general applicability of the method. | Giovanni Li Manni; Werner Dobrautz; Ali Alavi | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7451abb8c1a16363da600/original/compression-of-spin-adapted-multi-configurational-wave-functions-in-exchange-coupled-polynuclear-spin-systems.pdf |
62ebf375adfd35301026e432 | 10.26434/chemrxiv-2022-01g9l | The Role of Ion Solvation in Lithium Mediated Nitrogen Reduction | Since its verification in just 2019, there have been numerous high-profile papers reporting improved efficiency of the lithium-mediated electrochemical nitrogen reduction system to make ammonia. However, the literature lacks a cohesive investigation systematically linking bulk electrolyte properties to electrochemical performance and Solid Electrolyte Interphase (SEI) properties. In this study, we vary electrolyte salt concentration and observe a transition from an unstable working electrode potential to working electrode potential stability and peak in Faradaic efficiency of 7.8 ± 0.5 % at 0.6 M LiClO4. The behaviour is linked to the formation of Solvent Separated Ion Pairs in the electrolyte through Raman spectroscopy. Time of Flight Secondary Ion Mass Spectrometry and X-Ray Photoelectron Spectroscopy reveal a more inorganic, and therefore more stable, SEI layer with increasing salt concentration. A drop in Faradaic efficiency is seen at concentrations higher than 0.6 M LiClO4, which is attributed to a combination of a loss in nitrogen solubility and diffusivity as well as increased SEI conductivity as measured by Electrochemical Impedance Spectroscopy. | Olivia Westhead; Matthew Spry; Alexander Bagger; Zonghao Shen; Hossein Yadegari; Silvia Favero; Romain Tort; Maria-Magdalena Titirici; Mary P. Ryan; Rhodri Jervis; Ainara Aguadero; Anna Regoutz; Alexis Grimaud; Ifan E.L. Stephens | Materials Science; Catalysis; Catalysts; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ebf375adfd35301026e432/original/the-role-of-ion-solvation-in-lithium-mediated-nitrogen-reduction.pdf |
66100d1f91aefa6ce1e04e4b | 10.26434/chemrxiv-2024-6c1pj | Addition, Elimination, and Rearrangement Reactions of Cyclopropyl-Substituted Nitrenium Ions: A Computational and Experimental Investigation | Two cyclopropyl substituted nitrenium ions were generated through photolysis of their corresponding N-aminopyridinium ion photoprecursors. In the case of N-biphenyl-N-cyclopropyl nitrenium ion (5). Stable products are derived from a combination of cyclopropyl ring expansion, forming N-biphenylazetium ion, and ethylene elimination, forming biphenylisonitrilium ion. When present in high concentrations, methanol can add to the cyclopropyl ring forming N-3-methoxypropyl-N-biphenyl iminium ion. In contrast, the only detectable product from N-benzyl-N-cyclopropyl nitrenium ion (6) is benzylisonitrile, resulting from elimination of ethylene. DFT calculations predict the product distributions from the more stable biphenyl system 5 with reasonable accuracy. However product distributions from the less stable benzyl system 6 are forecast with less accuracy. | Donald Hong; Daniel Falvey | Theoretical and Computational Chemistry; Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66100d1f91aefa6ce1e04e4b/original/addition-elimination-and-rearrangement-reactions-of-cyclopropyl-substituted-nitrenium-ions-a-computational-and-experimental-investigation.pdf |
670f810ecec5d6c1424c6893 | 10.26434/chemrxiv-2024-vqktn | ELECTRUM: An Electron Configuration-based Universal Metal Fingerprint for Transition Metal Compounds | Machine learning has experienced a drastic rise in interest and applications in all fields of chemistry, enabling researchers to leverage large chemical datasets to gain novel insights. The success of machine learning-driven projects in chemistry hinges on three key factors: access to robust and comprehensive datasets, a well-defined objective, and effective molecular representations that convert chemical structures into machine-readable formats. Transition metal complexes have lagged behind their organic counterparts on all three of these avenues. The large diversity of structures, coordination numbers and modes have made its translation to a machine-readable format an ongoing challenge. Here we introduce ELECTRUM, an electron configuration-based universal metal fingerprint for transition metal compounds. Its lightweight implementation enables the straightforward conversion of any transition metal complex into a simple fingerprint. Utilising a novel dataset generated from the Cambridge Structural Database (CSD), we demonstrate that ELECTRUM effectively captures the structural diversity of transition metal complexes. By plotting nearest-neighbor relationships in ELECTRUM space, we reveal meaningful clustering in two-dimensional representations. Furthermore, we use the ELECTRUM encoding to train machine learning models on the prediction of metal complex coordination numbers from ligand structures and metal identity alone. We show that on a subset of this data, we can train models to predict the oxidation state of metal complexes. These case studies showcase the potential of ELECTRUM as an easy-to-implement fingerprint for metal complexes. We rely on the community to further test, validate, and improve it. | Angelo Frei; Markus Orsi | Theoretical and Computational Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670f810ecec5d6c1424c6893/original/electrum-an-electron-configuration-based-universal-metal-fingerprint-for-transition-metal-compounds.pdf |
66e1704012ff75c3a104a4dd | 10.26434/chemrxiv-2024-wxt4z | Excited-state structural characterisation of a series of nanosecond-lived [Fe(terpy)2]2+ derivatives using X-ray Solution Scattering | [Fe(terpy)2]2+ (terpy = 2,2':6',2''-terpyridine) is a transition metal complex where the spin state is photoswitchable and where the properties of the metal-centered quintet excited state (5MC) can be tuned by substituting different Electron Withdrawing (EW) or Electron Donating (ED) groups on the 4' position of the terpyridine. To better understand the physics determining the photoswitching performance, a deeper insight into the positions of the relevant potential energy surfaces and the molecular structure of the 5MC state is needed. We present a structural investigation based on Time Resolved X-ray Solution Scattering (TR-XSS) by which we determine the average d(Fe-N) bond-length elongation following population of the 5MC state as well as the lifetime of this state in a series of seven modified [Fe(terpy)2]2+ systems in aqueous solution following photo-excitation. The analysis of the TR-XSS data is supported by Density Functional Theory (DFT) and Molecular Dynamics (MD) calculations. The quintet state lifetime is determined to vary by more than a factor of ten (from 1.5 to 16 nanoseconds) based on the electron withdrawing/donating properties of the substituting group. Both the DFT calculations and the structural analysis of the experimental data show that the main photo-induced change in metal-ligand bond lengths Δd(Fe-N) is ~0.2 Å for all systems. | Bianca L. Hansen; Verena Markmann; Mátyás Pápai; Philipp Lenzen; Morten Lunn Haubro; Antal Mikeházi; Zoltán Németh; Andor Vancza; Matteo Levantino; Serhane Zerdane; Diana Bregenholt Zederkof; Dmitry Khakhulin; Asmus Ougaard Dohn; Martin Meedom Nielsen; Kristoffer Haldrup; György Vankó | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e1704012ff75c3a104a4dd/original/excited-state-structural-characterisation-of-a-series-of-nanosecond-lived-fe-terpy-2-2-derivatives-using-x-ray-solution-scattering.pdf |
67ae62516dde43c908c25528 | 10.26434/chemrxiv-2025-b1jjg | Intelligent machining of CFRP composites via data-driven prediction and optimization: Advances, challenges and future prospects | The global drive towards net-zero has accelerated the adoption of carbon fibre reinforced polymers (CFRP) for lightweight structures in various sectors such as aerospace, automotive, energy and biomedical. Mechanical machining of CFRP is often necessary to meet dimensional or assembly-related requirements. However, significant challenges including surface defects (delamination, burr, surface roughness), rapid tool wear and material transition issues in drilling CFRP/metal stack, underscore the need for effective, automated process prediction / optimization for improved machining performance. Conventional physics-based models often fall short due to their reliance on extensive computational resources and inability to capture CFRP’s complex machining dynamics arising from thermo-mechanical load coupling and process uncertainties. To address these limitations, recent advancements in artificial intelligence (AI) offer promising, data-driven solutions that reduce reliance on domain-specific knowledge while delivering fast, accurate predictions by uncovering patterns within dataset. This provides a promising solution towards intelligent CFRP machining process with improved quality and efficiency. To date, there is a lack of comprehensive, up-to-date review of data-driven methods in CFRP machining process prediction/optimization. This review fills this gap and provides a critical analysis of data-driven methods in four key application settings: (i) machining process characteristics and surface quality/defects prediction; (ii) tool wear prediction; (iii) material transition recognition in CFRP/metal stacks machining; (iv) vision-based surface defects recognition. By presenting a state-of-the-art overview of advances, challenges and future research directions, this review highlights the transformative potential of data-driven methods in advancing intelligent CFRP machining within the manufacturing value chain. | Jia Ge; Jiduo Zhang; Moran Xu; Ming Wu; Zequan Yao; Guoyu Fu; Wenchang Zhang; Brian G. Falzon; Giuseppe Catalanotti; Jinyang Xu; Yan Jin; Dan Sun | Materials Science; Polymer Science; Composites; Fibers | CC BY 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae62516dde43c908c25528/original/intelligent-machining-of-cfrp-composites-via-data-driven-prediction-and-optimization-advances-challenges-and-future-prospects.pdf |
623338b0d756275d891b7c62 | 10.26434/chemrxiv-2022-lsg9d-v2 | Metal-free Catalytic Hydrogenolysis of Silyl Triflates and Halides into Hydrosilanes | The metal-free catalytic hydrogenolysis of silyl triflates and halides (I, Br) to hydrosilanes is unlocked by using arylborane Lewis acids as catalysts. In the presence of a nitrogen base, the catalyst acts as a Frustrated Lewis Pair (FLP) able to split H2 and generate a boron hydride intermediate prone to reduce (pseudo)halosilanes. This metal-free organocatalytic system is competitive with metal-based catalysts and enables the formation of a variety of hydrosilanes at r.t. in high yields (>85 %) under a low pressure of H2 (≤ 10 bar). | Gabriel Durin; Albane Fontaine; Jean-Claude Berthet; Emmanuel Nicolas; Pierre Thuéry; Thibault Cantat | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623338b0d756275d891b7c62/original/metal-free-catalytic-hydrogenolysis-of-silyl-triflates-and-halides-into-hydrosilanes.pdf |
60c74951842e655cfedb2d01 | 10.26434/chemrxiv.10792877.v2 | Molecular Recognition and Band Alignment in 3-D Covalent Organic Frameworks for Co-Crystalline Organic Photovoltaics | Covalent organic frameworks (COFs) have emerged as versatile, functional materials comprised of low-cost molecular building blocks. The permanent porosity, long-range order, and high surface area of 3D-COFs permit co-crystallization with other materials driven by supramolecular interactions. We designed a new subphthalocyanine-based 3-D covalent organic framework (NEUCOF1) capable of forming co-crystals with fullerene (C60) via periodic ball-and-socket binding motifs. The high co-crystalline surface area and long-range order of NEUCOF1 eliminates the typical surface area vs. structural order trade-off in organic photovoltaics (OPVs). We used plane-wave density functional theory (PBE) to minimize NEUCOF1 and NEUCOF1–C60 co-crystals and determine their electronic band structures. Molecular dynamics (MD) simulations showed that NEUCOF1–C60 is likely to be stable up to 350 K. The band structures at 0 and 350 K suggest that charge transfer to the C60 acceptors is favorable and that directional charge transport is possible for these co-crystalline OPVs. | Jordan M Cox; Bradley Mileson; Ananthan Sadagopan; Steven Lopez | Carbon-based Materials; Optical Materials; Computational Chemistry and Modeling; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74951842e655cfedb2d01/original/molecular-recognition-and-band-alignment-in-3-d-covalent-organic-frameworks-for-co-crystalline-organic-photovoltaics.pdf |
627439c76b12b62a21671b79 | 10.26434/chemrxiv-2022-m6ngp | Carbodiimide-induced formation of transient polyether cages | The use of “fuel” compounds to drive chemical systems out of equilibrium is currently of interest because of the potential for temporally controlled, responsive behavior. We have recently shown that transiently formed crown ethers exhibit counterintuitive templation effects when generated in the presence of alkali metal cations: “matched” cations, such as K+ with an 18-crown-6 analogue, suppress the formation of the macrocycles (negative templation). Here we describe two macrocyclic diacids that, on treatment with carbodiimides, give transient macrobicyclic cages analogous to polyether cages first reported by Parsons. Cage formation was followed by NMR spectroscopy. Similar negative templation effects are observed for the smaller cage when generated in the presence of K+ and Na+, but with a weak, but reproducible, positive templation effect in the presence of Li+. The larger cage behaves similarly in the presence of Li+, K+, Rb+, and Cs+, but differently with Na+, which appears to bind to both the cage and the initial macrocycle. | Mohammad Mosharraf Hossain; Isuru M. Jayalath; Renuka Baral; C. Scott Hartley | Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627439c76b12b62a21671b79/original/carbodiimide-induced-formation-of-transient-polyether-cages.pdf |
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