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63596c4fecdad56930ee292b | 10.26434/chemrxiv-2022-tc7pm | pH-responsive i-motif-conjugated nanoparticles for MRI analysis | Gadolinium (Gd)-based contrast agents (CA) are widely used to enhance anatomical details in magnetic resonance imaging (MRI). Significant research has expanded the field of CAs into bioresponsive CAs by modulating the signal to image and monitor biochemical processes, such as pH. In this work, we introduce the modular, dynamic actuation mechanism of DNA-based nanostructures as a new way to modulate the MRI signal based on rotational correlation time, τR. We combined a pH-responsive oligonucleotide (i-motif) and a clinical standard CA (Gd-DOTA), to develop a pH-responsive MRI CA. The i-motif folds into a quadruplex in acidic conditions and was incorporated onto gold nanoparticles (iM-GNP) to achieve increased relaxivity, r1, compared to unbound i-motif. In vitro, iM-GNP resulted in a significant increase in r1 over a decreasing pH range (7.5 - 4.5) with a calculated pKa = 5.88 ± 0.01 and a 16.7% change per 0.1 pH unit. In comparison, the control CA with a non-responsive DNA strand (T33-GNP) did not show a significant change in r1 over the same pH range. To demonstrate the potential for performance in tissue, CAs were evaluated in an ex vivo rat brain model. When compared to pre-contrast signal intensity (1/T1), the response to a simulated acidic microenvironment was over 5 times higher than the signal measured in a physiological pH. This approach paves a path for novel programmable, dynamic DNA-based complexes for τR-modulated bioresponsive MRI CAs. | Kristine Y. Ma; Mireia Perera Gonzalez; Nicole I. Langlois; Isen Andrew C. Calderon; Heather A. Clark; Chris A. Flask | Analytical Chemistry; Nanoscience; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63596c4fecdad56930ee292b/original/p-h-responsive-i-motif-conjugated-nanoparticles-for-mri-analysis.pdf |
660b4d3666c1381729702ceb | 10.26434/chemrxiv-2024-mt2fp | Improved hydrophobic subtraction model of reversed-phase liquid chromatography selectivity based on a large dataset with a focus on isomer selectivity | Reversed-phase (RP) liquid chromatography is an important tool for the characterization of materials and products in the pharmaceutical industry. Method development is still challenging in this application space, particularly when dealing with closely-related compounds. Models of chromatographic selectivity are useful for predicting which columns out of the hundreds that are available are likely to have very similar, or different, selectivity for the application at hand. The hydrophobic subtraction model (HSM1) has been widely employed for this purpose; the column database for this model currently stands at 750 columns. In previous work we explored a refinement of the original HSM1 (HSM2) and found that increasing the size of the dataset used to train the model dramatically reduced the number of gross errors in predictions of selectivity made using the model. In this paper we describe further work in this direction (HSM3), this time based on a much larger dataset (43,329 total measurements) containing selectivities for compounds covering a broader range of physicochemical properties compared to HSM1. This includes multiple compounds that are actual active pharmaceutical ingredients and related synthetic intermediates and impurities, as well as multiple pairs of closely related structures (e.g., geometric and cis-/trans- isomers). The HSM3 model is based on retention measurements for 75 compounds using 13 RP stationary phases and a mobile phase of 40/60 acetonitrile/25 mM ammonium formate buffer at pH 3.2. This data-driven model produced predictions of ln(alpha) (chromatographic selectivity using ethylbenzene as the reference compound) with average absolute errors of approximately 0.033, which corresponds to errors in alpha of about 3 %. In some cases, the prediction of the trans-/cis- selectivities for positional and geometric isomers was relatively accurate, and the driving forces for the observed selectivity could be inferred by examination of the relative magnitudes of the terms in the HSM3 model. For some geometric isomer pairs the interactions mainly responsible for the observed selectivities could not be rationalized due to large uncertainties for particular terms in the model. This suggests that more work is needed in the future to explore other HSM-type models and continue expanding the training dataset in order to continue improving the predictive accuracy of these models. | Sarah Rutan; Trevor Kempen; Tina Dahlseid; Zachary Kruger; Bob Pirok; Jonathan Shackman; Yiyang Zhou; Qinggang Wang; Dwight Stoll | Analytical Chemistry; Separation Science | CC BY NC 4.0 | CHEMRXIV | 2024-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660b4d3666c1381729702ceb/original/improved-hydrophobic-subtraction-model-of-reversed-phase-liquid-chromatography-selectivity-based-on-a-large-dataset-with-a-focus-on-isomer-selectivity.pdf |
6760c2c581d2151a02fac95b | 10.26434/chemrxiv-2024-rrqrh | Electronic Structure and Adsorption Stability of Ferrocene on Au (111) and Ag (111) Surfaces
| The adsorption behavior and electronic structure of ferrocene (Fc) on Au(111) and Ag(111) surfaces were investigated using density functional theory (DFT). Two Fc conformers, eclipsed (E-Fc) and staggered (S-Fc), were studied in vertical (⏊) and parallel (||) orientations at three adsorption sites—top (T), hollow (H), and bridge (B). Fc preferentially adsorbs in a vertical configuration through the lower Cp ring on hollow sites, with adsorption energies of -0.87 eV (E-Fc) and -0.88 eV (S-Fc) on Au(111) and -0.79 eV for both conformers on Ag(111). These results confirm that Fc adsorptions are more stable on Au(111) than Ag(111), with negligible stability differences between the two conformers in vertical configurations. Parallel configurations are generally less stable; S-Fc cannot stably adsorb parallel on either surface, and E-Fc(||) exhibits significantly weaker adsorption energies (-0.82 eV on Au(111) and -0.62 eV on Ag(111)) than vertical configurations. Electronic structure analysis reveals that Fc acts predominantly as an electron donor on both metal surfaces. A distinctive region-specific charge transfer is observed in vertical configurations, where electrons flow from top-layer Au atoms to the Cp ring of Fc, forming an electron circuit that enhances adsorption strength. This feature is absent in parallel configurations, where charge transfer occurs uniformly from Fc to the surface, resulting in weaker adsorption.
These findings underscore the impact of adsorption geometry and surface type on Fc’s stability and electronic interactions, offering valuable insights into its behavior on metallic surfaces. While results for Fc/Ag(111) are included in supplementary materials, the primary focus is on Fc/Au(111). This study provides a basis for exploring Fc-surface interactions in applications such as corrosion inhibition and catalysis.
| Shuhao Li; Chunqing Li; Feng Wang | Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6760c2c581d2151a02fac95b/original/electronic-structure-and-adsorption-stability-of-ferrocene-on-au-111-and-ag-111-surfaces.pdf |
657313f95bc9fcb5c95c67e0 | 10.26434/chemrxiv-2023-2dzv9 | Fluorotelomer ethoxylates cause developmental toxicity in mice | Poly- and perfluoroalkyl substances are a ubiquitous class of compounds which are considered persistent organic pollutants. Many of these compounds are unregulated and understudied but are still widely used. One group of these compounds are fluorotelomer ethoxylates, which recently emerged as compounds of interest following their recent detection in the environment. To determine the health impacts of these persistent compounds, healthy pregnant CD-1 mice were exposed to 0 ng/L (n=8), 5 ng/L (n=8), or 100 ng/L (n=7) fluorotelomer ethoxylates in drinking water throughout gestation. At gestational day 17.5 (term is 18.5 days), high-frequency ultrasound was performed to investigate the placental and fetal hemodynamic responses following exposure. Maternal exposure to fluorotelomer ethoxylates showed evidence of placental insufficiency, with a significant increase in placental weights (p<0.05), a decrease in the umbilical artery blood flow (p<0.01) and vasodilation of the cerebral circulation (p<0.01), consistent with brain sparing to preserve oxygen delivery to the brain. These results demonstrate that fluorotelomer ethoxylates cause developmental toxicity and motivate further work to evaluate the risk to human pregnancies and other vulnerable populations. | Katherine Steeves; Jenna Hanrahan; Nikita Harvey; Karl Jobst; Lindsay Cahill | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Environmental Analysis; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657313f95bc9fcb5c95c67e0/original/fluorotelomer-ethoxylates-cause-developmental-toxicity-in-mice.pdf |
632c1d84f764e6c2e4fec810 | 10.26434/chemrxiv-2022-d8w78 | An Efficient Multilayer Approach to Model DNA-Based Nano-Biosensors | In this work we present a full computational protocol to successfully obtain the one-electron reduction potential of nano-biosensors based on a self-assembled monolayer of DNA nucleobases linked to a gold substrate. The model is able to account for conformational sampling and environmental effects at a quantum mechanical (QM) level efficiently, by combining classical molecular dynamics (MM) and multilayer QM/MM/continuum calculations within the framework of Marcus theory. The theoretical model shows that a guanine-based biosensor is more prone to be oxidized than the isolated nucleobase in water due to the electrostatic interactions between the assembled guanine molecules. In addition, the redox properties of the biosensor can be tuned by modifying the nature of the linker that anchor the nucleobases to the metal support. | Jesús Lucia-Tamudo; Juan Jose Nogueira; Sergio Díaz-Tendero | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632c1d84f764e6c2e4fec810/original/an-efficient-multilayer-approach-to-model-dna-based-nano-biosensors.pdf |
60c74eba469df445a3f44520 | 10.26434/chemrxiv.12788390.v1 | Multifaceted Substrate–Ligand Interactions Promote the Copper-Catalyzed Hydroboration of Benzylidenecyclobutanes and Related Compounds | A unified synthetic strategy to access tertiary four-membered carbo/heterocyclic boronic esters is reported. Use of a Cu(I) catalyst in combination with a modified dppbz ligand enables regioselective hydroboration of various substituted benzylidenecyclobutanes and carbo/heterocyclic analogs. The reaction conditions are mild, and the method tolerates a wide range of medicinally relevant heteroarenes. The protocol can be conveniently conducted on gram-scale, and the tertiary boronic ester products undergo facile diversification into valuable targets. Reaction kinetics and computational studies indicate that the migratory insertion step is turnover-limiting and accelerated by electron-withdrawing groups on the dppbz ligand. Energy decomposition analysis (EDA) calculations reveal that electron-deficient <i>P</i>-aryl groups on the dppbz ligand enhance the T-shaped π/π interactions with the substrate and stabilize the migratory insertion transition state. | Taeho Kang; Tuğçe Erbay; Kane Xu; Gary Gallego; Alexander Burtea; Sajiv Nair; Ryan Patman; Ru Zhou; Scott Sutton; Indrawan McAlpine; Peng Liu; Keary Engle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling; Homogeneous Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eba469df445a3f44520/original/multifaceted-substrate-ligand-interactions-promote-the-copper-catalyzed-hydroboration-of-benzylidenecyclobutanes-and-related-compounds.pdf |
60c7482e4c8919dccfad2e91 | 10.26434/chemrxiv.11860104.v1 | Autonomous Intelligent Agents for Accelerated Materials Discovery | We present an end-to-end computational system for autonomous materials discovery. The system aims for cost-effective optimization in large, high-dimensional search spaces of materials by adopting a sequential, agent-based approach to deciding which experiments to carry out. In choosing next experiments, agents can make use of past knowledge, surrogate models, logic, thermodynamic or other physical constructs, heuristic rules, and different exploration-exploitation strategies. We show a series of examples for (i) how the discovery campaigns for finding materials satisfying a relative stability objective can be simulated to design new agents, and (ii) how those agents can be deployed in real discovery campaigns to control experiments run externally, such as the cloud-based density functional theory simulations in this work. In a sample set of 16 campaigns covering a range of binary and ternary chemistries including metal oxides, phosphides, sulfides and alloys, this autonomous platform found 383 new stable or nearly stable materials with no intervention by the researchers. | Joseph H. Montoya; Kirsten Winther; Raul A. Flores; Thomas Bligaard; Jens Strabo Hummelshøj; Muratahan Aykol | Alloys; Ceramics; Solid State Chemistry; Theory - Inorganic; Machine Learning; Artificial Intelligence; Structure; Thermodynamics (Physical Chem.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7482e4c8919dccfad2e91/original/autonomous-intelligent-agents-for-accelerated-materials-discovery.pdf |
66c9810d20ac769e5face135 | 10.26434/chemrxiv-2024-ddlz7 | Towards Designer Photocatalysts: Structure-Property Relationships in 2,6-Diaryl-pyryliums | Fully organic photocatalyst systems are highly attractive, not merely because they are transition-metal free, but more importantly due to their unique and often potent reactivity. A detailed understanding of the various redox states, both ground and excited state, and specifically what structural parameters control them is therefore crucial for harnessing the full potential of these system in organic synthesis. However, unlike their organometallic counterparts, detailed structure-property relationships for organic photocatalysts are largely absent from the literature. In this study, we demonstrate linear free-energy relationships across a range of key photophysical and electrochemical properties of 2,6-diarylpyryliums. Electronic absorption and emission maxima can be carefully tuned over the ranges of 83 nm and 102 nm respectively. Intramolecular charge transfer (ICT) interactions were revealed in cases of substitution with polarizable heavy-atoms. A strong linear dependence of ground state reduction potentials on substituent electronics was observed. Notably, the excited state reduction potential, E*red, could be controlled over a range of nearly 1000 mV. Systematic errors in computational modeling of ground and excited state redox potentials were identified and corrected. We believe the quantitative structure-property relationships identified here provide foundational tools for rational and predictive organic photocatalyst design. | Jenna Konzal; McKenna Murley; Alaina Wolter; Lazlo Camou; Alex Oberbroeckling; Madilyn Dekker; Gillianne Wagner; Kate Jennejohn; Natalie Hayes; Cory Franklin; Sydney Tobin; Elizabeth Collier; Ian MacKenzie | Physical Chemistry; Organic Chemistry; Catalysis; Photochemistry (Org.); Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c9810d20ac769e5face135/original/towards-designer-photocatalysts-structure-property-relationships-in-2-6-diaryl-pyryliums.pdf |
60c74663bdbb894671a38be6 | 10.26434/chemrxiv.11310860.v1 | Mechanism of the HF Pulse in the Thermal Atomic Layer Etch of HfO2 and ZrO2: A First Principles Study | <div>HfO2 and ZrO2 are two high-k materials that are important in the down-scaling of semiconductor devices. Atomic level control of material processing is required for fabrication of thin films of these materials at nanoscale device sizes. Thermal Atomic Layer Etch (ALE) of metal oxides, in which up to one monolayer of the material can be removed, can be achieved by sequential self-limiting fluorination and ligand-exchange reactions at elevated temperatures. However, to date a detailed atomistic understanding of the mechanism of thermal ALE of these technologically important oxides is lacking. In this paper, we investigate the hydrogen fluoride pulse in the first step in the thermal ALE process of HfO2 and ZrO2 using first principles simulations. We introduce Natarajan-Elliott analysis, a thermodynamic methodology, to compare reaction models representing the self-limiting (SL) and continuous spontaneous etch (SE) processes taking place during an ALE pulse. Applying this method to the first HF pulse on HfO2 and ZrO2 we found that thermodynamic barriers impeding continuous etch are present at ALE relevant temperatures. We performed explicit HF adsorption calculations on the oxide surfaces to understand the mechanistic details of the HF pulse. A HF molecule adsorbs dissociatively on both oxides by forming metal-F and O-H bonds. HF coverages ranging from 1.0 0.3 to 17.0 0.3 HF/nm2 are investigated and a mixture of molecularly and dissociatively adsorbed HF molecules is present at higher coverages. Theoretical etch rates of -0.61 0.02 Å /cycle for HfO2 and -0.57 0.02 Å /cycle ZrO2 were calculated using maximum coverages of 7.0 0.3 and 6.5 0.3 M-F bonds/nm2 respectively (M = Hf, Zr).</div> | Rita Mullins; Suresh Natarajan; Simon D. Elliott; Michael Nolan | Materials Processing; Thin Films; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74663bdbb894671a38be6/original/mechanism-of-the-hf-pulse-in-the-thermal-atomic-layer-etch-of-hf-o2-and-zr-o2-a-first-principles-study.pdf |
6286cbd1d555504c5fa060fd | 10.26434/chemrxiv-2022-mwrsk | Incorporating Lindblad Decay Dynamics into Mixed Quantum-Classical Simulations | We derive the L-MFE method to incorporate Lindblad jump operator dynamics into the mean-field Ehrenfest (MFE) approach. We map the density matrix evolution of Lindblad dynamics onto pure state coefficients using trajectory averages. We use simple assumptions to construct the L-MFE method that satisfies this exact mapping. This establishes a method that exactly reproduces Lindblad decay dynamics using a wavefunction description, with deterministic changes of the magnitudes of the quantum expansion coefficients, while only adding on a stochastic phase. We further demonstrate that when including nuclei in the Ehrenfest dynamics, the L-MFE method gives semi-quantitatively accurate results, with the accuracy limited by the accuracy of the approximations present in the semiclassical MFE approach. This work provides a general framework to incorporate Lindblad dynamics into semiclassical or mixed quantum-classical simulations. | Eric Koessler; Arkajit Mandal; Pengfei Huo | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2022-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6286cbd1d555504c5fa060fd/original/incorporating-lindblad-decay-dynamics-into-mixed-quantum-classical-simulations.pdf |
60c73d51ee301c881bc78547 | 10.26434/chemrxiv.5743176.v1 | Fabrication of Fe nanowires using anodic alumina template | In this paper, we considered fabrication of Fe nanowires by AAO template, magnetic property, and influences (fabrication voltage of template, temperature, deposition time, and deposition voltage) on them. <br /> | yongson hong | Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51ee301c881bc78547/original/fabrication-of-fe-nanowires-using-anodic-alumina-template.pdf |
60c74af3ee301c000cc79d3b | 10.26434/chemrxiv.12245549.v1 | Influence of Packaging Material on Polyphenol Content and Antioxidant Activity in Some Commercial Beers | <div><div><div><div><p>Using two methods (ferric reducing antioxidant power and radical scavenging activity), the total polyphenol content (Folin–Ciocalteu reagent) and polyphenol patterns (HPLC) in 10 commercial lager beer brands produced in Romania was determined. Samples bottled in glass, plastic and aluminium packages were analysed for each brand when available. Results have indicated considerable variations in the total and individual phenolic contents as well as antioxidant activity across beer brands. A statistical analysis was performed to assess the influence of packaging type on the antioxidant activity and phenolic content of the beers. Statistical differences were found between the DPPH and FRAP methods in glass, aluminium and plastic material. Moreover, the antioxidant activity based on the DPPH method is influenced by the type of packaging material, while in the case of FRAP method, no statistical difference was reported. Furthermore, the same analysis has shown that the polyphenol concentration is invariant to the type of material.</p></div></div></div></div> | Mihaela Mirela Bratu; Semaghiul Birghila; Antoanela Popescu; Bogdan Stefan Negreanu- Pirjol; Marius Radu | Food | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74af3ee301c000cc79d3b/original/influence-of-packaging-material-on-polyphenol-content-and-antioxidant-activity-in-some-commercial-beers.pdf |
667cdd43c9c6a5c07a7cc36f | 10.26434/chemrxiv-2024-3qzqx | Imaging Dissolution Dynamics of Individual NaCl Nanoparticles during Deliquescence with In Situ Transmission Electron Microscopy | Water vapor condensation on hygroscopic aerosol particles plays an important role in cloud formation, climate change, secondary aerosol formation, and aerosol aging. Conventional understanding considers deliquescence of nanosized hygroscopic aerosol particles a nearly instantaneous solid to liquid phase transition. However, the nanoscale dynamics of water condensation and aerosol particle dissolution prior to and during deliquescence remain obscure due to a lack of high spatial and temporal resolution single particle measurements. Here we use real time in situ transmission electron microscopy (TEM) imaging of individual sodium chloride (NaCl) nanoparticles to demonstrate that water adsorption and aerosol particle dissolution prior to and during deliquescence is a multistep dynamic process. Water condensation and aerosol particle dissolution was investigated for lab generated NaCl aerosols and found to occur in three distinct stages as a function of increasing RH. First, a < 100 nm water layer adsorbed on the NaCl cubes and caused sharp corners to dissolve and truncate. The water layer grew to several hundred nanometers with increasing RH and was rapidly saturated with solute, as evidenced by halting of particle dissolution. Adjacent cube corners displayed second-scale curvature fluctuations with no net particle dissolution or water layer thickness change. We propose that droplet solute concentration fluctuations drove NaCl transport from regions of high local curvature to regions of low curvature. Finally, we observed coexistence of a liquid water droplet and aerosol particle immediately prior to deliquescence. Particles dissolved discretely along single crystallographic directions, separating by few second lag times with no dissolution. This work demonstrates that deliquescence of simple pure salt particles with sizes in the range of 100 nm to several microns is not an instantaneous phase transition and instead involves a range of complex dissolution and water condensation dynamics. | Yuhang Wang; Dewansh Rastogi; Kotiba Malek; Jiayue Sun; Martin Ahn; Akua Asa-Awuku; Taylor Woehl | Analytical Chemistry; Nanoscience; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Imaging | CC BY 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667cdd43c9c6a5c07a7cc36f/original/imaging-dissolution-dynamics-of-individual-na-cl-nanoparticles-during-deliquescence-with-in-situ-transmission-electron-microscopy.pdf |
60c74ee2f96a007e28287b6c | 10.26434/chemrxiv.12816599.v1 | TDPBP Derivative Aiding Liquid-Phase Synthesis Strategy and ACE Inhibitory Structure-activity Relationship of Anti-SARS Octapeptide | The tri(4'-diphenylphosphonyloxylbenzoyl phenyl) phosphate (TDPBP)
derivatives were designed and developed as C-terminal supports to aid the greener and highefficient liquid-phase peptide synthesis (LPPS) without the need of unrecyclable resin and
chromatographic separation, whereby the anti-SARS octapeptide (2) (AVLQSGFR) was
synthesized with TDPBP-OH support via Fmoc chemistry and support-aided precipitation
(SAP) technology. Furthermore, the ACE inhibition and the inhibitory structure-activity
relationship (SAR) between the synthetic C-terminal amidated derivate (1), anti-SARS
octapeptide (2) and its alanine-scanning sequence analogues (3) to (9) were systematically
studied by HPLC analysis and 3D-QSAR via molecular docking.<br /> | Haidi Li; Jin Ren; Zixin Zhang; Junyou Li; Ninghui Chang; Chuanguang Qin | Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ee2f96a007e28287b6c/original/tdpbp-derivative-aiding-liquid-phase-synthesis-strategy-and-ace-inhibitory-structure-activity-relationship-of-anti-sars-octapeptide.pdf |
6687847a01103d79c514444d | 10.26434/chemrxiv-2024-9shgl | Chemoenzymatic Skeletal Editing: P450-Controlled Site-Selective Ring Expansion of Natural Product Scaffolds at Aliphatic C—H Sites | Methods for introducing subtle modifications at the level of single atoms/bonds (‘skeletal editing’) are highly desirable in organic and medicinal chemistry, owing to their potential for fine-tuning the structure and biological activity of organic molecules. While contemporary methods for skeletal editing of organic molecules largely rely on modification of pre-existing functional groups, opportunities for executing these transformations at ubiquitous yet unreactive aliphatic C(sp3)—H sites are currently unavailable. Here, we report a chemoenzymatic strategy for enabling skeletal editing via ring expansion with high site-selectivity at the level of one or more aliphatic C—H sites in complex molecules. By combining cytochrome P450-catalyzed C—H oxidation with chemical oxidation and subsequent Baeyer-Villiger rearrangement or ketone homologation, a panel of structurally and functionally diverse natural products were edited by inserting a lactone or carbonylmethylene moiety into aliphatic regions of their carbocyclic skeletons. Using engineered P450 catalysts with divergent regioselectivity, a set of different ring-expanded products could be readily obtained from a single parent molecule, highlighting the potential of this approach for skeletal edit scanning and/or library generation. By enabling the targeting of aliphatic C—H sites with tunable site-selectivity, this strategy provides a powerful tool to rapidly access skeletally edited derivatives of natural products and other bioactive molecules that would be hard to attain by purely chemical means. We envision this approach can also enable the device of non-traditional retrosynthetic disconnections for the synthesis of complex molecules. | Rudi Fasan; John Bennett; Andrew Bortz | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry; Natural Products; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687847a01103d79c514444d/original/chemoenzymatic-skeletal-editing-p450-controlled-site-selective-ring-expansion-of-natural-product-scaffolds-at-aliphatic-c-h-sites.pdf |
635ebf0f55a0817516cb89cd | 10.26434/chemrxiv-2022-5x13g-v2 | On the trail of molecular hydrophilicity and hydrophobicity at aqueous interfaces | Uncovering microscopic hydrophilicity and hydrophobicity at heterogeneous aqueous interfaces is essential as it dictates physical and chemical properties such as wetting, electrical double layer, reactivity. Here, we combine density functional theory-based MD simulations (DFT-MD) and both theoretical and experimental SFG spectroscopy to explore how the interfacial water responds in contact with self-assembled monolayers (SAM) of tunable hydrophilicity. We introduce a microscopic metric to track the transition from hydrophobic to hydrophilic interfaces, which combines a structural descriptor based on the preferential orientation within the water network in the topmost binding interfacial layer (BIL) and spectroscopic fingerprints of H-bonded and dangling OH groups of water pointing towards the surface carried by BIL-resolved SFG spectra. This metric builds a bridge between molecular descriptors of hydrophilicity/hydrophobicity and spectroscopically measured quantities, and provides a recipe to quantitatively or qualitatively interpret experimental SFG signals. | Wanlin Chen; Stephanie E. Sanders; Burak Ozdamar; Dorian Louaas; Flavio Siro Brigiano; Simone Pezzotti; Poul B. Petersen; Marie-Pierre Gaigeot | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635ebf0f55a0817516cb89cd/original/on-the-trail-of-molecular-hydrophilicity-and-hydrophobicity-at-aqueous-interfaces.pdf |
6737a8d37be152b1d03289de | 10.26434/chemrxiv-2024-9454q | Catalytic Photothermal Hydrogenation of Carbon Dioxide to Liquid Fuels using Pt/GaN prepared via SOMC | Renewable liquid fuels are expected to play a crucial role in transitioning to a more sustainable future. Their synthesis via the hydrogenation of CO2 using solar energy emerges as a promising technology, that combines both the use of a renewable primary energy source and the (re)utilization of a major greenhouse gas. In this context, GaN has attracted a lot of attention in harnessing solar energy to drive chemical transformations. In this work we study GaN by 1H solid-state NMR spectroscopy, revealing the presence of terminal Ga-OH, bridging Ga–NH–Ga as well as Ga–OH–Ga surface functional groups and combinations thereof. With this knowledge in hand, we make use of surface organometallic chemistry (SOMC) to prepare a Pt/GaN catalyst with highly dispersed Pt nanoparticles on GaN. Under photothermal conditions using visible light (>320 nm), the synthesized Pt/GaN promotes the hydrogenation of CO2 to C2+ products such as acetone, EtOH, iPrOH, and acetic acid in a batch reactor at 60 °C and 1 bar of pressure, while the pristine GaN counterpart only produces minor amounts of MeOH and acetone. Furthermore, a recycling test was performed to showcase the stability of the catalyst over multiple batch reaction cycles. | Hyotaik Kang; Enzo Brack; Domenico Gioffrè; Alexander Yakimov; Christophe Copéret; Chao-Jun Li | Inorganic Chemistry; Catalysis; Spectroscopy (Inorg.); Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6737a8d37be152b1d03289de/original/catalytic-photothermal-hydrogenation-of-carbon-dioxide-to-liquid-fuels-using-pt-ga-n-prepared-via-somc.pdf |
6322c191173b5de4cdfe38e4 | 10.26434/chemrxiv-2022-jwf5x-v2 | Noise Reduction of Low Count STEM-EDX Data by Low-rank Regularized Spectral Smoothing | Statistically weighted principal component analysis (wPCA) is widely used to reduce the noise of scanning transmission electron microscopy-energy-dispersive X-ray (STEM-EDX) spectroscopy data. It is beneficial to retain the spatial resolution of observation in each step of the analysis, but the direct application of wPCA without preprocessing, such as spatial averaging, often fails against low count STEM-EDX data. To enhance the applicability of wPCA while retaining spatial resolution, a step-by-step noise reduction method is considered in this study. Specifically, a numerical optimization is developed to simultaneously characterize the smoothness of EDX spectra and the low-rankness of the data. In the presented approach, a low count data is first spectrally smoothed by solving this optimization problem, and then further denoised by using wPCA to project onto a subspace rigorously spanned by a small number of components. A challenging example is provided, and the improved noise reduction performance is demonstrated and compared to using existing spectral smoothing techniques. | Keisuke Ozawa | Materials Science; Analytical Chemistry; Microscopy; Spectroscopy (Anal. Chem.) | CC BY 4.0 | CHEMRXIV | 2022-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322c191173b5de4cdfe38e4/original/noise-reduction-of-low-count-stem-edx-data-by-low-rank-regularized-spectral-smoothing.pdf |
67caf89281d2151a0280bfca | 10.26434/chemrxiv-2025-59zn3 | An Equilibrium Rotator Glass for Long-Ranged Repulsive Colloidal Rods | Glasses, amorphous solid phases nearly always
out of equilibrium, remain poorly understood despite recent progress. Here we show by quantitative real-space experiments and computer simulations the existence of a new equilibrium solid phase which forms due to a subtle interplay between the rotational and translational degrees of freedom in a system of charged colloidal rods. In this rotational glass, the positional coordinates are glassy, while the rotations remain liquid-like. This phase can be reversibly switched into a crystalline solid through a first-order phase transition with minimal particle rearrangements by an external electric field. We speculate that this rotator glass forms due to the anisotropic particle interactions at higher volume fractions, destabilizing the crystal. Finding an equilibrium rotator glass will lead to new insights on how translations and rotations affect phase behavior, including
glass formation and, additionally, allow new theoretical approaches to be used to study this amorphous solid. | Thijs Herman Besseling; Berend Van der Meer; Bing Liu; Laura Filion; Arnout Imhof; Alfons van Blaaderen | Physical Chemistry; Materials Science; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67caf89281d2151a0280bfca/original/an-equilibrium-rotator-glass-for-long-ranged-repulsive-colloidal-rods.pdf |
649d79016e1c4c986b8a0b4e | 10.26434/chemrxiv-2023-6pnk9 | Raman Diffusion-Ordered Spectroscopy | The Stokes-Einstein relation, which relates the diffusion coefficient of a molecule to its hydrodynamic radius, is commonly used to determine molecular sizes in chemical analysis methods. Here, we combine the size-sensitivity of such diffusion-based methods with the structure-sensitivity of Raman spectroscopy by performing Raman diffusion-ordered spectroscopy (Raman-DOSY). The core of the Raman-DOSY setup is a flow cell with a Y-shaped channel containing two inlets, one for the sample solution and one for the pure solvent. The two liquids are injected at the same flow rate, giving rise to two parallel laminar flows in the channel. After the flow stops, the solute molecules diffuse from the solution-filled half of the channel into the solvent-filled half, at a rate determined by their hydrodynamic radius. The arrival of the solute molecules in the solvent-filled half of the channel is recorded in a spectrally resolved manner by Raman micro-spectroscopy. From the time series of Raman spectra, a two-dimensional Raman-DOSY spectrum is obtained, which has Raman frequency on one axis and diffusion coefficient (or equivalently, hydrodynamic radius) on the other. In this way, Raman-DOSY spectrally resolves overlapping Raman peaks arising from molecules with different sizes. We demonstrate Raman-DOSY on samples containing up to three compounds and derive the diffusion coefficients of small molecules, proteins, and supramolecules (micelles), illustrating the versatility of Raman-DOSY. Raman-DOSY is label-free and does not require deuterated solvents, and can thus be applied to samples and matrices that might be difficult to investigate with other diffusion-based spectroscopy methods. | Robert W. Schmidt; Giulia Giubertoni; Federico Caporaletti; Paul Kolpakov; Noushine Shahidzadeh; Freek Ariese; Sander Woutersen | Physical Chemistry; Analytical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649d79016e1c4c986b8a0b4e/original/raman-diffusion-ordered-spectroscopy.pdf |
67ae2e4581d2151a0251552f | 10.26434/chemrxiv-2025-r4t5c | A quantitative figure of merit for battery SEI films and their use as functional solid-state electrolytes | As a key passivation film that governs battery operation, the solid electrolyte interphase (SEI) has long been credited for enabling high-performance batteries or blamed for their eventual death. However, qualitative descriptions of the SEI often found in the literature (e.g., “conductive”, “passivating”) highlight our incomplete understanding of this layer, where even the most basic properties foundational to SEI function remain difficult to measure. Here, we quantify SEI conductivities and SEI transference numbers using a separator-free Cu|SEI|Li architecture that treats the SEI as a functional solid-state electrolyte (SSE). We discover that while any SEI property alone (e.g., electronic conductivity) is weakly correlated (R2<0.71) with battery performance (e.g., Coulombic efficiency), a strong correlation (R2>0.99) can be achieved by defining the “SEI cT number” as a product between the SEI transference number (T) and the ratio of SEI conductivities (c). Analogous to the thermoelectric figure of merit (i.e., zT), SEI cT quantitatively benchmarks the holistic impact of SEI properties on battery performance and underscores the pitfalls of citing such properties in isolation. Perhaps most strikingly, we demonstrate that Li metal deposition and stripping at room temperature is possible in our separator-free Cu|SEI|Li cell, confirming that the SEI can function precisely as an SSE. Together, these results enrich our understanding of the SEI, not just as a passivation layer but as a functional structure that can potentially have important implications for solid-state batteries. | Bo Liu; Dingyi Zhao; Katelyn Lyle; Xintong Yuan; Po-Hung Chen; Xinyue Zhang; Jin Koo Kim; Tian-Yu Wang; Haoyang Wu; Chongzhen Wang; Jiayi Yu; Keyue Liang; Jung Tae Kim; Kaiyan Liang; Yuzhang Li | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae2e4581d2151a0251552f/original/a-quantitative-figure-of-merit-for-battery-sei-films-and-their-use-as-functional-solid-state-electrolytes.pdf |
64b26635b053dad33a496a4c | 10.26434/chemrxiv-2023-nrhjf | Chemisorption model for atoms and molecules on doped
semiconducting oxides | Fundamental understanding of the interaction between atoms and molecules with the surfaces
of oxides including semiconducting oxides is crucial for the development of several thermo-,
photo-, and electro-, catalytic reactions as well as any application where surfaces are exposed to
an environment beyond vacuum. While previous studies have postulated material features (descriptors)
that to some extent suggest the adsorption energy trends on semiconducting oxides,
a physics based model to describe the interaction of atoms and molecules with the surfaces of
these materials is still lacking. In this study, we perform a series of controlled in-silico experiments
involving doping of quintessential semiconducting oxides (SrTiO3, SrZrO3, and TiO2)
to identify the perturbation by the dopant to the electronic structure of the host oxide and its
resultant effect on the adsorption energies of simple atoms and molecules. We identify that a
combination of three surface features: unique surface resonance states of the host-metal and
lattice oxygen atoms of the terminating surface oxide layer as well as the gap states dominated
by the introduced dopants contribute to the adsorption energy in a concerted fashion.
We find that this intricate interplay between on the one hand host-metal and on the other
hand oxygen surface resonance states with the adsorbate, respectively, results in a deviation
from the well-established adsorbate scaling relations seen for NHx(x=0-2) and CHx(x=0-3) but
not OHx and SHx. Through this lens, we develop a physics based adsorption model hitherto
referred as the Generalized Concerted Coupling model (GCC-model). The introduced model
provides a physical understanding with an associated electronic structure descriptor rooted in
the unique surface resonances that accurately captures the adsorption energy trends on doped
semiconducting oxides. This paves the way for the atomistic design of doped semiconducting
oxides for different catalytic applications, including sustainable energy applications such as
electrochemical water-splitting. | Abhinav S. Raman; Colin Lehman-Chong; Aleksandra Vojvodic | Theoretical and Computational Chemistry; Materials Science; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b26635b053dad33a496a4c/original/chemisorption-model-for-atoms-and-molecules-on-doped-semiconducting-oxides.pdf |
62751af043d1f073ea21e600 | 10.26434/chemrxiv-2022-j603q-v2 | Mechanochemical synthesis of inverse vulcanized polymers | Inverse vulcanization, a sustainable platform, can transform an industrial by-product, sulfur, into polymers with broad green applications such as heavy metal capture and recyclable materials. However, the process usually requires high temperatures (≥159 °C), and the crosslinkers needed to stabilise the sulfur are therefore limited to high-boiling-point monomers only. Here, we report an alternative route for inverse vulcanization — mechanochemical synthesis, with advantages of mild conditions (room temperature), short reaction time (3 h), high atom economy, less H2S, and broader monomer range. Successful generation of polymers using crosslinkers ranging from aromatic, aliphatic to volatile, including renewable monomers, demonstrates this method is powerful and versatile. Compared with thermal synthesis, the mechanochemically synthesized products show enhanced mercury capture. The resulting polymers show thermal and light induced recycling. The speed, ease, versatility, safety, and green nature of this process offers a more sustainable future for inverse vulcanisation, and enables further unexpected discoveries. | Peiyao Yan; Wei Zhao; Fiona McBride; Diana Cai; Joseph Dale; Veronica Hanna; Tom Hasell | Materials Science; Polymer Science; Materials Processing; Polymerization (Polymers); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62751af043d1f073ea21e600/original/mechanochemical-synthesis-of-inverse-vulcanized-polymers.pdf |
664f7950418a5379b01bf1cf | 10.26434/chemrxiv-2024-fk05l | Observed declines in upper ocean phosphate-to-nitrate availability | Climate warming is increasing ocean stratification, which in turn should decrease the flux of nutrients to the upper ocean. This may slow marine primary productivity, causing cascading effects throughout food webs. However, observing changes in nutrient concentrations at the ocean surface is challenging because they are often below detection limits. The nutricline depth, where nutrient concentrations reach well-detected levels, is related with productivity and indicates upper ocean nutrient availability. Here, we quantified nutricline depths from a global database of observed vertical nitrate and phosphate profiles (1972 - 2022) to assess contemporary trends in global nutrient availability. We found strong evidence that the P-nutricline (phosphacline) is mostly deepening, especially throughout the southern hemisphere, but the N-nutricline (nitracline) remains mostly stable. Earth System Model simulations support the hypothesis that reduced iron stress and increased nitrogen fixation buffer the nitracline, but not phosphacline, against increasing stratification. These contemporary trends are expected to continue in the coming decades, leading to increasing phosphorus but not nitrogen stress for marine phytoplankton, with important ramifications for ocean biogeochemistry and food web dynamics. | Skylar Gerace; Jun Yu; J. Keith Moore; Adam Martiny | Earth, Space, and Environmental Chemistry; Environmental Science; Geochemistry | CC BY 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664f7950418a5379b01bf1cf/original/observed-declines-in-upper-ocean-phosphate-to-nitrate-availability.pdf |
661a3ae891aefa6ce177b701 | 10.26434/chemrxiv-2024-814pv | Insights into Serotonin-Receptor Binding and Stability via Molecular Dynamics Simulations: Key Residues for Electrostatic Interactions and Signal Transduction | Serotonin-receptor binding plays a key role in several neurological and biological processes, including mood, sleep, hunger, cognition, learning, and memory. In this article, we performed molecular dynamics simulation to examine the key residues that play an essential role in the binding of serotonin to the G-protein-coupled 5-HT$_{1B}$ receptor (5HT$_{1B}$R) via electrostatic interactions. Key residues for electrostatic interactions were identified via bond distance analysis and frustration analysis method. An end-point free energy calculation method determines the stability of the 5-HT$_{1B}$R due to serotonin binding. The single-point mutation of the polar/charged amino acid residues (Asp129, Thr134) on the binding sites and the calculation of binding free energy validates the quantitative contribution of these residues in the stability of the serotonin-receptor complex. The principal component analysis reflects that the serotonin-bound 5-HT$_{1B}$R is more stabilized than the apo-receptor regarding dynamical changes. The difference dynamic cross-correlations map shows the correlation between the transmembranes and mini-G$_{o}$, which indicates that the signal transduction happens between mini-G$_{o}$ and the receptor. Allosteric pathway analysis reveals the key nodes for signal transduction in 5-HT$_{1B}$R. These results provide useful insights into the study of signal transduction pathways and mutagenesis to regulate the functionality of the complex. The developed protocols can be applied to study local non-covalent interactions and long-range allosteric communications in any protein-ligand system for computer-aided drug design. | Arunima Verma; padmabati mondal | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661a3ae891aefa6ce177b701/original/insights-into-serotonin-receptor-binding-and-stability-via-molecular-dynamics-simulations-key-residues-for-electrostatic-interactions-and-signal-transduction.pdf |
64da1fa2dfabaf06ff42804b | 10.26434/chemrxiv-2023-4m96k | An Artificial Intelligence Platform for Automated PFAS Subgroup Classification: A Discovery Tool for PFAS Screening | Since structural analyses and toxicity assessments have not been able to keep up with the discovery of unknown per- and polyfluoroalkyl substances (PFAS), there is an urgent need for effective categorization and grouping of PFAS. In this study, we presented PFAS Atlas, an artificial intelligence-based platform containing a rule-based automatic classification system and a machine learning-based grouping model. Compared with previously developed classification software, the platform’s classification system follows the latest Organization for Economic Co-operation and Development (OECD) definition of PFAS and reduces the number of uncategorized PFAS. In addition, the platform incorporates deep unsupervised learning models to visualize the chemical space of PFAS by clustering similar structures and linking related classes. Through real-world use cases, we demonstrate that PFAS Atlas can rapidly screen for relationships between chemical structure and persistence, bioaccumulation, or toxicity data for PFAS. The platform can also guide the planning of the PFAS testing strategy by showing which PFAS classes urgently require further attention. Ultimately, the release of PFAS Atlas will benefit both the PFAS research and regulation communities. | An Su; Yingying Cheng; Chengwei Zhang; Yun-Fang Yang; Yuan-Bin She; Krishna Rajan | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64da1fa2dfabaf06ff42804b/original/an-artificial-intelligence-platform-for-automated-pfas-subgroup-classification-a-discovery-tool-for-pfas-screening.pdf |
657cb7af66c138172945efbc | 10.26434/chemrxiv-2023-4bhpv | A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the Dynamic Behavior of the Catalytic Site of the Tryptophan Synthase | L-tryptophan (L-Trp), a vital amino acid for the survival of various organisms, is synthesized by the enzyme tryptophan synthase (TS) in organisms such as eubacteria, archaebacteria, protista, fungi, and plantae. TS, a pyridoxal 5′-phosphate (PLP)- dependent enzyme, comprises α and β subunits that typically form an α2β2 tetramer. The enzyme’s activity is regulated by the conformational switching of its α and β subunits between the open (T state) and closed (R state) conformations. Many microorganisms rely on TS for growth and replication, making the enzyme and the L-Trp biosynthetic pathway potential drug targets. For instance, Mycobacterium tuberculosis, Chlamydiae bacteria, Streptococcus pneumoniae, Francisella tularensis, Salmonella bacteria, and Cryptosporidium parasitic protozoa depend on L-Trp synthesis. Antibiotic- resistant salmonella strains have emerged, underscoring the need for novel drugs targeting the L-Trp biosynthetic pathway, especially for salmonella-related infections. A single amino acid mutation can significantly impact enzyme function, affecting stability, conformational dynamics, and active or allosteric sites. These changes influence interactions, catalytic activity, and protein-ligand/protein-protein interactions. This study focuses on the impact of mutating the βGln114 residue on the catalytic and allosteric sites of TS. Extensive MD simulations were conducted on E(PLP), E(AEX1), E(A-A), and E(C3) forms of TS using the WT, βQ114A, and βQ114N versions. The results show that both the βQ114A and βQ114N mutations increase protein backbone RMSD fluctuations, destabilizing all TS forms. Conformational and hydrogen bond analyses suggest the significance of βGln114 drifting away from cofactor/intermediates and forming hydrogen bonds with water molecules necessary for L-Trp biosynthesis. The βQ114A mutation creates a gap between βAla114 and cofactor/intermediates, hindering hydrogen bond formation due to short sidechains, disrupting β-sites. Conversely, the βQ114N mutation positions βAsn114 closer to cofactor/intermediates, forming hydrogen bonds with O3 of cofactors/intermediates and nearby water molecules, potentially disrupting the L-Trp biosynthetic mechanism. | Anupom Roy; Mikko Karttunen | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657cb7af66c138172945efbc/original/a-molecular-dynamics-simulation-study-of-the-effects-of-gln114-mutation-on-the-dynamic-behavior-of-the-catalytic-site-of-the-tryptophan-synthase.pdf |
641aabbedab08ad68f830283 | 10.26434/chemrxiv-2023-dg43t | Biocompatible, sustainable coatings based on photo-crosslinkable cellulose derivatives | Materials derived from renewable resources have great potential to replace fossil-based plastics in biomedical applications. In this study, the synthesis of cellulose-based photoresists by esterification with methacrylic acid anhydride and sorbic acid was investigated. These resists polymerize under UV irradiation in the range λ=254 nm to 365 nm, with or even without the use of an additional photoinitiator concerning the sorbic acid derivative. Usability for biomedical applications was demonstrated by investigating the adhesion and viability of a fibrosarcoma cell line (HT-1080). Compared to polystyrene, the material widely used for cell culture dishes, cell adhesion to the biomaterials tested was even stronger, as assessed by a centrifugation assay. This is all the more remarkable since chemical surface modification of cellulose with methacrylate and sorbic acid allows direct attachment of HT-1080 cells without the addition of protein modifiers or ligands. Furthermore, cells on both biomaterials show similar cell viability, not significantly different from polystyrene, indicating no significant impairment or enhancement. This will allow the future use of these cellulose derivatives as support structures for scaffolds or as self-supporting coatings also for cell culture, based solely on renewable and sustainable resources. | Maximilian Rothammer; Philipp Strobel; Cordt Zollfrank; Corinna Urmann | Biological and Medicinal Chemistry; Cell and Molecular Biology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641aabbedab08ad68f830283/original/biocompatible-sustainable-coatings-based-on-photo-crosslinkable-cellulose-derivatives.pdf |
61573330b19c7e7e0de683dd | 10.26434/chemrxiv-2021-3p2sx | Excited States of Crystalline Point Defects with Multireference Density Matrix Embedding Theory | Accurate and affordable methods to characterize the electronic structure of solids are important for targeted materials design. Embedding-based methods provide an appealing balance in the trade-off between cost and accuracy - particularly when studying localized phenomena. Here, we use the density matrix embedding theory (DMET) algorithm to study the electronic excitations in solid-state defects with a restricted open-shell Hartree--Fock (ROHF) bath and multireference impurity solvers, specifically, complete active space self-consistent field (CASSCF) and n-electron valence state second-order perturbation theory (NEVPT2). We apply the method to investigate an oxygen vacancy (OV) on a MgO(100) surface and find absolute deviations within 0.05 eV between DMET using the CASSCF/NEVPT2 solver, denoted as CAS-DMET/NEVPT2-DMET, and the non-embedded CASSCF/NEVPT2 approach. Next, we establish the practicality of DMET by extending it to larger supercells for the OV defect and a neutral silicon-vacancy in diamond where the use of non-embedded CASSCF/NEVPT2 is extremely expensive. | Abhishek Mitra; Hung Pham; Riddhish Pandharkar; Matthew Hermes; Laura Gagliardi | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Processes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61573330b19c7e7e0de683dd/original/excited-states-of-crystalline-point-defects-with-multireference-density-matrix-embedding-theory.pdf |
67cae81afa469535b95da695 | 10.26434/chemrxiv-2025-xxd9x | Electrochemical CO2 capture, release and reduction by a benzothiadiazole molecule with multiple redox states | Using small organic molecular redox carriers to reversibly capture CO2 and catalyze its conversion to carbon-based chemicals is a promising approach to mitigate the ongoing climate crisis. 2,1,3-benzothiadiazole (BT) is an interesting unit due to its proven interaction with CO2 upon reduction and the ease of tuning its structure. In this work, by introducing two CN in BT, the molecule 2,1,3-benzothiadiazole-4,7-dicarbonitrile (BTDN) has multiple reduced states as compared to BT and is found to interact with CO2 at multiple reduced states. The work is carried out with a combination of (spectro-)electrochemical and computational studies. Cyclic voltammetry experiments in the presence of CO2 show a clear interaction between BTDN and CO2 upon the second reduction of BTDN and a large cur-rent increase at the third reduction. DFT calculations show a large variety of possible CO2-bound spe-cies that can potentially match the experimental data. The binding of CO2 on BTDN is shown to be re-versible upon the oxidation of the species, especially with low concentrations of CO2. From gas chro-matography, NMR and IR experiments, certain amount of oxalate was detected after bulk electrolysis. | Martin Axelsson; Carlos Enrique Torres-Mendez; Mun Hon Cheah; Haining Tian | Physical Chemistry; Organic Chemistry; Catalysis; Electrocatalysis; Organocatalysis; Redox Catalysis | CC BY 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cae81afa469535b95da695/original/electrochemical-co2-capture-release-and-reduction-by-a-benzothiadiazole-molecule-with-multiple-redox-states.pdf |
630057d40c5277d5cebb8768 | 10.26434/chemrxiv-2022-dqprx | Origin of Magnetic Anisotropy in Nickelocene Molecular Magnet and Resilience of its Magnetic Behavior | Robustness of nickelocene’s (NiCp<sup>2</sup>, Cp = cyclopentadienyl) magnetic anisotropy and addressability of its spin states make this molecular magnet attractive as a spin sensor. However, microscopic understanding of its magnetic anisotropy is still lacking, especially when NiCp<sup>2</sup> is deposited on a surface to make quantum sensing devices. Quantum chemical calculations of such molecule/solid-state systems are limited to density functional theory (DFT) or DFT+U (Hubbard correction to DFT). We investigate the magnetic behavior of NiCp<sup>2</sup> using the equation-of-motion coupled-cluster (EOM-CC) framework. Our first-principle calculations agree well with experimentally derived magnetic anisotropy and susceptibility values. The calculations show that magnetic anisotropy in NiCp<sup>2</sup> originates from a large spin-orbit coupling (SOC) between the triplet ground state and the third singlet state, whereas the coupling with lower singlet excited states is negligible. We also considered a set of six ring-substituted NiCp<sup>2</sup> derivatives and a model system of the NiCp<sup>2</sup>/MgO(001) adsorption complex. To gain insight into the electronic structure of these systems, we analyze spinless transition density matrices and their natural transition orbitals (NTOs). The NTO analysis of SOCs explains how spin states and magnetic properties are retained upon modification of the NiCp<sup>2</sup> coordination environment and upon its adsorption on a surface. Such resilience of the NiCp<sup>2</sup> magnetic behavior supports using NiCp<sup>2</sup> as a spin-probe molecule by functionalization of the tip of a scanning tunneling microscope. | Maristella Alessio; Saikiran Kotaru; Goran Giudetti; Anna I. Krylov | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630057d40c5277d5cebb8768/original/origin-of-magnetic-anisotropy-in-nickelocene-molecular-magnet-and-resilience-of-its-magnetic-behavior.pdf |
60c75681bb8c1ab6e23dc62d | 10.26434/chemrxiv.14257274.v1 | An Analysis of Recent BLYP and PBE-Based Range-Separated Double-Hybrid Density Functional Approximations for Main-Group Thermochemistry, Kinetics and Noncovalent Interactions | <div>
<div>
<div>
<p>We investigate the effects of range separation of the exchange energy on electronic ground-state properties for recently published double-hybrid density functionals (DHDFs) with the extensive GMTKN55 database for general main-group thermochemistry, kinetics and noncovalent interactions. We include the semi-empirical range-separated DHDFs ωB2PLYP and ωB2GP-PLYP developed by our group for excitation energies, together with their ground-state-parametrized variants, which we denote
herein as ωB2PLYP18 and ωB2GP-PLYP18. We also include the non-empirical range-separated DHDFs RSX-0DH and RSX-QIDH. For all six DHDFs, damping parameters
for the DFT-D3 dispersion correction (and for its DFT-D4 variant) are presented. We
comment on when the range-separated functionals can be more beneficial than their
global counterparts, and conclude that range separation alone is no guarantee for overall
improved results. We observe that the BLYP-based functionals generally outperform the PBE-based functionals. We finally note that the best-performing double-hybrid
density functionals for GMTKN55 are still the semi-empirical range-separated double
hybrids ωDSD3-PBEP86-D4 and ωDSD72-PBEP86-D4, the former of which includes a
third-order perturbative correlation term in addition to the more conventional second-
order perturbation that DHDFs are based upon.</p>
</div>
</div>
</div> | Asim Najibi; Marcos Casanova Paez; Lars Goerigk | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75681bb8c1ab6e23dc62d/original/an-analysis-of-recent-blyp-and-pbe-based-range-separated-double-hybrid-density-functional-approximations-for-main-group-thermochemistry-kinetics-and-noncovalent-interactions.pdf |
65cf95a79138d23161474af1 | 10.26434/chemrxiv-2024-l7lhp | Direct C-H Electrophilic Borylation with (C6F5)2B-NTf2 to Generate B-N Dibenzo[a,h]pyrenes | The borylation of aryl substituted pyridines is an effective way of preparing B-N doped conjugated organic frameworks. Trihaloborane Lewis acids are often employed for this protocol, and may require further functionalization to replace the remaining halides on boron. We report a new, fully characterized, electrophilic borylating agent, (C6F5)2B(2-NTf2), that smoothly incorporates a -B(C6F5)2 unit into the model substrate 2-phenylpyridine. To demonstrate its utility in preparing more complex B-N doped structures, we use it to prepare seven examples of the 6a,13a-diaza-7,14-dibora-dibenzo[a,h]pyrene framework, with substituents of varying donor properties. The structural, redox and photophysical properties of this new family of B-N doped polycyclic hydrocarbon compounds were probed experimentally and computationally. | Tony Nguyen; Jason Dutton; Chia Yun Chang; Wen Zhou; Warren Piers | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Main Group Chemistry (Organomet.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cf95a79138d23161474af1/original/direct-c-h-electrophilic-borylation-with-c6f5-2b-n-tf2-to-generate-b-n-dibenzo-a-h-pyrenes.pdf |
62a087bea784d128ce774718 | 10.26434/chemrxiv-2022-flnh4-v2 | Dissipative self-assembly of metal-organic complexes | Implementing dissipative processes in networks of dynamic molecules holds great promise for developing new functional behaviours. Here we report the use of trichloroacetic acid as a chemical fuel to temporarily push networks of dynamic imine-based metal complexes far from thermodynamic equilibrium, forcing them to express high free-energy complexes otherwise unfavourable under equilibrium conditions. Basic design principles were determined for the creation of such networks. Where a complex distribution of products was obtained at equilibrium, the fuel-induced rearrangement temporarily yielded a simplified output, forcing a more structured high-energy distribution of products. Where a single complex was obtained at equilibrium, the fuel-induced rearrangement temporarily modified the properties of this complex. By doing so, the mechanical properties of an helical macrocyclic complex could be temporarily altered by rearranging it into a [2]catenane. | Jean-François Ayme; Bernd Bruchmann; Lydia Karmazin; Nathalie Kyritsakas | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a087bea784d128ce774718/original/dissipative-self-assembly-of-metal-organic-complexes.pdf |
60c74d1d567dfe014cec52c9 | 10.26434/chemrxiv.12462080.v2 | Docking Adenosine Receptor Ligands to SARS-CoV2 mRNA Cap 2’-O-Methyltransferase | This is a computational study using a high resolution crystallographic structure for the SARS-CoV2 mRNA cap 2'-O-methyltransferase (nsp16) and ligands obtained from the ZINC database. Using iGEMDOCK for docking and Desmond/Schrodinger for energy minimization, we identify adenosine receptor binders that potentially bind a previously identified adenosine binding site in SARS-CoV2 nsp16 better than adenosine does, some of which may induce conformational changes in nsp16. | David Snyder; Shweta Mehta | Bioinformatics and Computational Biology; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d1d567dfe014cec52c9/original/docking-adenosine-receptor-ligands-to-sars-co-v2-m-rna-cap-2-o-methyltransferase.pdf |
6130588cb817b47cb510e922 | 10.26434/chemrxiv-2021-578vg | Electric field orientations in solution and enzyme active site revealed by a two-directional vibrational probe | The catalytic power of an electric field depends on its magnitude and orientation with respect to the reactive chemical species. Understanding and designing new catalysts for electrostatic catalysis thus requires methods to measure the electric field orientation and magnitude at the molecular scale. We demonstrate that electric field orientations can be extracted using a two-directional vibrational probe by exploiting the vibrational Stark effect of both the C=O and C-D stretches of a deuterated aldehyde. Combining spectroscopy with molecular dynamics and electronic structure partitioning methods, we demonstrate that despite distinct polarities, solvents act similarly in their preference for electrostatically stabilizing large bond dipoles at the expense of destabilizing small ones. In contrast, we find that for an active site aldehyde inhibitor of liver alcohol dehydrogenase, the electric field orientation deviates markedly from that found in solvents, providing direct evidence for the fundamental difference between the electrostatic environments of solvents and a preorganized enzyme active site. | Chu Zheng; Yuezhi Mao; Jacek Kozuch; Austin Atsango; Zhe Ji; Thomas Markland; Steven Boxer | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Theory - Computational; Biocatalysis; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6130588cb817b47cb510e922/original/electric-field-orientations-in-solution-and-enzyme-active-site-revealed-by-a-two-directional-vibrational-probe.pdf |
62f18841d62bc0d1613ec424 | 10.26434/chemrxiv-2022-zhd87 | Artificial Neural Network to Predict Structure-based Protein-protein Free Energy of Binding from Rosetta-calculated Properties | The prediction of the free energy (ΔG) of binding for protein-protein complexes is of general scientific interest that allows a variety of applications in the fields of molecular and chemical biology, material sciences, and biotechnology. Despite its centrality in understanding protein association phenomena and protein engineering, the ΔG of binding is a daunting quantity to be obtained theoretically. In this work, we devise a novel Artificial Neural Network model to predict the ΔG of binding for a given three-dimensional structure of a protein-protein complex with Rosetta-calculated properties. Our model presents a root-mean-square error of 1.667 kcal/mol outperforming available state-of-art tools. Validation of the model for a variety of protein-protein complexes is showcased.
| Matheus Ferraz; José Neto; Roberto Lins; Erico Teixeira | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f18841d62bc0d1613ec424/original/artificial-neural-network-to-predict-structure-based-protein-protein-free-energy-of-binding-from-rosetta-calculated-properties.pdf |
62ab981aeb1f0c64bd8b9294 | 10.26434/chemrxiv-2022-tlkgq | Copper-based 2D Conductive Metal Organic Framework Thin Films for Ultrasensitive Detection of Perfluoroalkyls in Drinking Water | Perfluoroalkyls (PFAS) continue to emerge as a global health threat making their effective detection and capture extremely important. Though metal organic frameworks (MOF) have stood out as a promising class of porous materials for sensing PFAS, detection limits remain insufficient and fundamental understanding of detection mechanisms warrant further investigation. Here we show the use of a 2D conductive MOF film based on copper hexahydroxy triphenylene (Cu-HHTP) to fabricate a chemiresistive sensing device for detecting PFAS in drinking water. We further show ultrasensitive detection using electrochemical impedance spectroscopy. Owing to excellent electrostatic attractions and electrochemical interactions between the copper-based MOF and PFAS, the MOF-based sensor reported herein exhibits unprecedented affinity and sensitivity towards perfluorinated acids at concentrations as low as of 0.002 ng/L. | Aristide Gumyusenge; Tyler Quill; Gan Chen; Huaxin Gong; Zhenan Bao; Alberto Salleo | Materials Science; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ab981aeb1f0c64bd8b9294/original/copper-based-2d-conductive-metal-organic-framework-thin-films-for-ultrasensitive-detection-of-perfluoroalkyls-in-drinking-water.pdf |
650956e8ed7d0eccc3cd60f5 | 10.26434/chemrxiv-2023-ddxlh | Enhancing Molecular Energy Predictions with Physically Constrained Modifications to the Neural Network Potential | Exclusively prioritizing the precision of energy prediction frequently proves inadequate in satisfying multifaceted requirements. A heightened focus is warranted on assessing the rationality of potential energy curves predicted by machine learning-based force fields (MLFF), alongside evaluating the pragmatic utility of these MLFF. This study introduces SWANI, an optimized Neural Network Potential (NNP) stemming from the ANI framework. Through the incorporation of supplementary physical constraints, SWANI aligns more cohesively with chemical expectations, yielding rational potential energy profiles. It also exhibits superior predictive precision compared to the ANI model. Additionally, a comprehensive comparison is conducted between SWANI and a prominent Graph Neural Network (GNN)-based model. The findings indicate that SWANI outperforms the latter, particularly for molecules exceeding the dimensions of the training set. This outcome underscores SWANI's exceptional capacity for generalization and its proficiency in handling larger molecular systems. | Weiqiang Fu; Yujie Mo; Yi Xiao; Chang Liu; Feng Zhou; Yang Wang; Jielong Zhou; Yingsheng Zhang | Theoretical and Computational Chemistry; Nanoscience; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650956e8ed7d0eccc3cd60f5/original/enhancing-molecular-energy-predictions-with-physically-constrained-modifications-to-the-neural-network-potential.pdf |
6703fbffcec5d6c14273d4ce | 10.26434/chemrxiv-2024-wrvr4 | AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction | Accurate prediction of molecular geometries is crucial for drug discovery and materials science. Existing fast conformer prediction algorithms often rely on approximate empirical energy functions, resulting in low accuracy. More accurate methods like ab initio molecular dynamics and Markov chain Monte Carlo can be computationally expensive due to the need for evaluating quantum mechanical energy functions. To address this, we introduce AGDIFF, a novel machine learning framework that utilizes diffusion models for efficient and accurate molecular structure prediction. AGDIFF extends previous models (such as GeoDiff) by enhancing the global, local, and edge encoders with attention mechanisms, an improved SchNet architecture, batch normalization, and feature expansion techniques. AGDIFF outperforms GeoDiff on both the GEOM-QM9 and GEOM-Drugs datasets. For GEOM-QM9, with a threshold (δ) of 0.5 Å, AGDIFF achieves a mean COV-R of 93.08% and a mean MAT-R of 0.1965 Å. On the more complex GEOM-Drugs dataset, using δ = 1.25 Å, AGDIFF attains a median COV-R of 100.00% and a mean MAT-R of 0.8237 Å. These findings demonstrate AGDIFF's potential to advance molecular modeling techniques, enabling more efficient and accurate prediction of molecular geometries, thus contributing to computational chemistry, drug discovery, and materials design. \url{https://github.com/ADicksonLab/AGDIFF} | André Brasil Vieira Wyzykowski; Fatemeh Fathi Niazi; Alex Dickson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6703fbffcec5d6c14273d4ce/original/agdiff-attention-enhanced-diffusion-for-molecular-geometry-prediction.pdf |
60c758f3f96a00d7da288f11 | 10.26434/chemrxiv.14607963.v1 | Naturally Derived Organic Dyes for LED Lightings of High Color Rendering and Fidelity Index | <p>Light-emitting diodes (LEDs) are a lighting technology with a
huge and ascending market. Typically, LED backlights are often paired with inorganic
phosphors made from rare-earth elements (REEs) to tune the emission lineshapes for
different applications. However, REE production is a resource-intensive process
with many negative environmental impacts. Herein we develop organic hybrid LEDs
using organic dyes synthesized from an abundant and non-toxic natural product
(theobromine) to replace REE phosphors. The resulting hybrid LED generates
continuous emission from 400 – 740 nm, resulting in high color rendering index
(the current industry standard) of 90 and color fidelity index (the most
advanced and comprehensive standard) of 92, challenging commercial LEDs based
on REE phosphors. In addition, the light-converting composite is made from 99
wt% SBS, an inexpensive industrial polymer, and 1wt% theobromine dyes, reducing
the cost of the light converter to ¢1.30 for a 1 W LED, compared to
approximately ¢ 19.2 of commercial products. The light converting efficiency of
the dye-SBS composite is 82%. Excited state kinetics experiments were also conducted
to provide guidance to further increase the light-converting efficiency of the
theobromine dyes while maintaining excellent color rendering and fidelity. </p> | Yunping Huang; Theodore A. Cohen; Christine K. Luscombe | Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758f3f96a00d7da288f11/original/naturally-derived-organic-dyes-for-led-lightings-of-high-color-rendering-and-fidelity-index.pdf |
649da65dba3e99daef3fb7fd | 10.26434/chemrxiv-2023-6hwpx | Design, Molecular Docking and Synthesis of Pyrazole-Oxadiazole in search of
potent insecticidal agents
|
A series of sixteen substituted pyrazole oxadiazole derivatives are designed, synthesised and characterized by 1H NMR, 13C NMR and mass spectrometry. The ligands have been docked with Acetylcholine receptor to understand the binding efficiency and amino acids interactions, indicative of all of the sixteen molecules bind efficiently better than Fipronil and Pyrafluprole. These compounds will provide a lead for designing new compounds with improved insecticidal activity.
| Amar Patil ; Rahul Jadhav ; Nachiket More; Hemant Raundal ; Ashok Desai ; Sonali Deore ; Vivek Bobade | Organic Chemistry; Agriculture and Food Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649da65dba3e99daef3fb7fd/original/design-molecular-docking-and-synthesis-of-pyrazole-oxadiazole-in-search-of-potent-insecticidal-agents.pdf |
61b7fc256927e37ead05b21a | 10.26434/chemrxiv-2021-hf714 | Growth Kinetics of Single Polymer Particles in Solution via Active-Feedback 3D Tracking | The ability to directly observe chemical reactions at the single-molecule and single-particle level has enabled the discovery of behaviors otherwise obscured by the ensemble averaging in bulk measurements. However powerful, a common restriction of these studies to date has been the absolute requirement to surface tether or otherwise immobilize the chemical reagent/reaction of interest. This constraint arose from a fundamental limitation of conventional microscopy techniques, which could not track molecules or particles rapidly diffusing in three dimensions, as occurs in solution. However, much chemistry occurs in the solution phase, leaving single-particle/-molecule analysis of this critical area of science beyond the scope of available technology. Here we report the first solution-phase studies and measurements of any chemical reaction at single-particle/-molecule level in freely diffusing solution. During chemical reaction, freely diffusing polymer particles (D ~ 10-12 m2/s) yielded single-particle 3D trajectories and real-time volumetric images that were analyzed to extract the growth rates of individual particles. These volumetric images show that the average growth rate is a poor representation of the true underlying variability in polymer-particle growth behavior. These data revealed statistically significant populations of faster- and slower-growing particles at different depths in the sample, showing emergent heterogeneity while particles are still in the solution phase. These results go against the prevailing premise that chemical processes freely diffusing in solution will exhibit uniform kinetics. These new understandings of mechanisms behind polymer growth variations bring about an exciting opportunity to control particle-size and plausibly molecular weight polydispersity by the rational design of conditions to dictate spatial growth gradients. We anticipate that these studies will launch a new field of solution-phase, nonensemble-averaged measurements of chemical reactions. | Donggeng Yu; Antonio Garcia IV; Suzanne A. Blum; Kevin D. Welsher | Catalysis; Analytical Chemistry; Polymer Science; Polymerization kinetics; Microscopy; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b7fc256927e37ead05b21a/original/growth-kinetics-of-single-polymer-particles-in-solution-via-active-feedback-3d-tracking.pdf |
67d3503881d2151a0249886c | 10.26434/chemrxiv-2025-l6bhl | Blockage effects in the chemotaxis of diffusiophoretic particles | Transport mechanisms at the micro- and nano-scale play an essential role in regulating intracellular organization. Recent work indicates that directed motion of constituents inside cells can emerge through diffusiophoretic transport, in which colloidal particles move under the influence of chemical gradients. Here, we examine how blockers—passive or actively consuming—reshape those gradients and thereby influence the motion of diffusiophoretic particles. By combining analytical solutions with finite element simulations, we first show that a single blocker can distort a background gradient enough to create or eliminate stagnation points, significantly modifying particle transport. We then introduce a second, explicitly sized blocker at one of these stagnation points and measure how its finite radius alters the diffusiophoretic velocity field for a test particle. Even moderate changes in the second blocker’s size can cause noticeable shifts in the substrate distribution, highlighting the importance of accounting for explicit particle radii under crowded or consumption-driven conditions. Our findings underscore that subtle geometric variations—such as the radii and positions of two or more blockers—can profoundly affect diffusiophoretic motion, providing a more complete picture of how blocking and crowding phenomena shape intracellular transport. | Zehao Song; Matthew Farnese; Ahis Shrestha; Monica Olvera de la Cruz | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Chemical Kinetics | CC BY 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d3503881d2151a0249886c/original/blockage-effects-in-the-chemotaxis-of-diffusiophoretic-particles.pdf |
6252da796c989c79f6b367cd | 10.26434/chemrxiv-2022-sbg4h | Suppressing H2O2 formation in oxygen reduction reaction using Co-Cu composite electrodes | Transition metal oxides form the basis of promising oxygen reduction electrocatalysts due to their low cost, high activity, and abundance on the planet. A new class of Cu[Co]Ox/Au catalyst was found to exhibit high activity and selectivity for the complete reduction of oxygen to water. The Cu-rich composite Cu0.8Co0.2Ox/Au electrodes exhibited nearly 97.5 % selectivity for water compared to either CuOx/Au (80 %) or CoOx/Au (70 %). Cu0.8Co0.2Ox/Au exhibited higher activity, stability, and better selectivity over a wide potential range when compared to well-known ORR catalysts such as Pt. In situ Raman spectroscopy revealed that the introduction of Co into CuOx resulted in the formation of under-coordinated Co centers within CuOx frameworks. These under-coordinated Co centers act as active sites for the scission of O-O bonds resulting in preferential formation of 4e reduction products. The composite electrode also demonstrated a superior hydrogen peroxide reduction ability. | Sekhar Biswal; Chinmoy Ranjan | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Fuel Cells; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6252da796c989c79f6b367cd/original/suppressing-h2o2-formation-in-oxygen-reduction-reaction-using-co-cu-composite-electrodes.pdf |
6144f18478257bea7a2042f5 | 10.26434/chemrxiv-2021-z8kf5-v2 | Plasmon Character Index: An Accurate and Efficient Metric for Identifying and Quantifying Plasmons in Molecules | Plasmons, which are collective and coherent oscillations of charge carriers driven by an external field, play an important role in applications such as solar energy harvesting, sensing, and catalysis. Plasmons can be found in bulk and nanomaterials, and in recent years, plasmons have also been identified in molecules and these molecules have been utilized to build plasmonic devices. As molecular plasmons can no longer be described by classical electrodynamics, a description using quantum mechanics is necessary. Many methods have been developed to identify and quantify molecular plasmons based on the properties of plasmonic excitations. However, there is not currently a method that is widely accepted, connects to collectivity and coherence, and is computationally practical. Here we develop a metric to accurately and efficiently identify and quantify plasmons in molecules. A number, which we call plasmon character index (PCI), can be calculated for each electronic excited state and describes the plasmonicity of the excitation. PCI is developed from the collective and coherent excitation picture in orbitals and shows excellent agreement with the predictions from scaled time-dependent density functional theory but is vastly more computationally efficient. Therefore, PCI can be a useful tool in identifying and quantifying plasmons and will inform the rational design of plasmonic molecules and small nanomaterials. | James Langford; Xi Xu; Yang Yang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6144f18478257bea7a2042f5/original/plasmon-character-index-an-accurate-and-efficient-metric-for-identifying-and-quantifying-plasmons-in-molecules.pdf |
61ddb7d75015ebc674b70323 | 10.26434/chemrxiv-2022-0m443 | Synthesis and Characterization of Novel PEPPSI type Pd–BICAAC Complexes | A series of bicyclic alkylamino carbenes (BICAAC) (where N-aryl = dipp, mes, 2,6-dimethyl-4-(dimethylamino)phenyl, 5a-d) and their novel air- and moisture-resistant pyridine (pyridine, 4 dimethylaminopyridine) containing palladium PEPPSI-type Pd(II) complexes (6a-e) were synthetized and characterized. The new palladium complexes have shown high activity in Mizoroki–Heck coupling reaction even at as low as 100 ppm loading (TON up to 10000). Kinetic studies revealed that reactions carried out in the presence of elemental mercury resulted in decrease in activity. It indicates that the coupling reaction may have both molecular and Pd(0)-mediated catalytic paths. | Márton Nagyházi; Balázs Almási; Ádám Lukács; Attila Bényei; Tibor Nagy; Sándor Kéki; Róbert Tuba | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2022-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ddb7d75015ebc674b70323/original/synthesis-and-characterization-of-novel-peppsi-type-pd-bicaac-complexes.pdf |
6353d5bcecdad507a3e817b7 | 10.26434/chemrxiv-2022-hp2f0 | Orientation-dependent real-time single-molecule
photobleaching inside uniform electrodynamic
interfaces of nanofluidic confinement | The functioning of single molecules in nanofluidic confinement is a typical process in cell biology. The orientation of molecules is a critical parameter for this. We discern the orientation of a single molecule in a nanofluidic environment while it's functioning in an engineered solid-state device. Molecular properties depend on the electrodynamic interface. Our manufacturing ability of uniform electrodynamic interfaces at nanometric lengthscale opens the avenue of imitating biological abilities to handle single molecules with single-charge precision. We present a step-wise single-molecule fluorescence photobleaching study in a nanoconfined space of 25 nm to 45 nm. The uniform electrodynamics interfaces of silica-silica let us study the artefact-free dependence of molecular interface and its effect on step-wise photobleaching with a controlled environment of oxygen at room temperature. | Chinmaya KV; Moumita Ghosh; Siddharth Ghosh | Physical Chemistry; Analytical Chemistry; Nanoscience; High-throughput Screening; Nanofluidics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6353d5bcecdad507a3e817b7/original/orientation-dependent-real-time-single-molecule-photobleaching-inside-uniform-electrodynamic-interfaces-of-nanofluidic-confinement.pdf |
60c741a7337d6c2c57e26903 | 10.26434/chemrxiv.8079890.v1 | Converting SMILES to Stacking Interaction Energies | <p>Predicting
the strength of stacking interactions involving heterocycles is vital for several
fields, including structure-based drug design.
While quantum chemical computations can provide accurate stacking
interaction energies, these come at a steep computational cost. To address this challenge, we recently developed
quantitative predictive models of stacking interactions between drug-like heterocycles
and the aromatic amino acids Phe, Tyr, and Trp (DOI: 10.26434/chemrxiv.7628939.v4). These models depend on heterocycle
descriptors derived from electrostatic potentials (ESPs) computed using density
functional theory and provide accurate stacking interactions without the need
for expensive computations on stacked dimers. Herein, we show that these ESP-based
descriptors can be reliably evaluated directly from the atom connectivity of
the heterocycle, providing a means of predicting both the descriptors and the potential
for a given heterocycle to engage in stacking interactions without resorting to
any quantum chemical computations. This
enables the conversion of simple molecular representations (<i>e.g</i>. SMILES) directly into accurate<i> </i>stacking interaction energies using a
freely-available online tool, thereby providing a way to rapidly rank the
stacking abilities of large sets of heterocycles.</p>
<p> </p> | Andrea
N. Bootsma; Steven Wheeler | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a7337d6c2c57e26903/original/converting-smiles-to-stacking-interaction-energies.pdf |
671a848283f22e42140c14b9 | 10.26434/chemrxiv-2024-rpgkj | Antibody–Bottlebrush Conjugates Unlock Diverse Payloads for Targeted Cancer Therapy | Antibody drug conjugates (ADCs), which feature a monoclonal antibody (mAb) for cell targeting linked to a cytotoxic payload for cell killing, are a remarkably effective class of targeted therapeutics. Despite their success, however, ADCs typically rely on highly potent payloads, precluding the use of less potent payloads and a broader range of payload mechanisms of action (MoA).1-4 Moreover, the emerging perspective that passive targeting mechanisms play roles in ADC function in vivo suggests opportunities to engineer new ADCs based on stable prodrug scaffolds with tunable release mechanisms.5,6 Here, inspired by the physics, shape, and chemical versatility of molecular bottlebrush polymers,7-11 we introduce “Antibody–Bottlebrush prodrug Conjugates” (ABCs) as a next-generation targeted cancer therapy platform designed to enable the modular and predictable use of a broad range of payloads with varied potencies and MoAs. ABCs feature an IgG1 mAb covalently conjugated to the terminus of a compact bivalent bottlebrush prodrug (BPD) with payloads bound via cleavable linkers and hydrophilic poly(ethylene glycol) (PEG) branches on each repeat unit. This design enables the synthesis of ABCs with tunable drug-to-antibody ratios (DARs) up to two orders-of-magnitude greater than traditional ADCs without negatively impacting the physical properties of the mAb. The efficiency of ABC manufacturing is highlighted by the synthesis of >10 different variants for distinct targets (HER2 and MUC1) and with payload potencies spanning several orders-of-magnitude, imaging agents for direct ABC visualization, and photocatalysts for proximity-based labeling of the ABC interactome. ABCs display excellent target engagement, cell uptake, and efficacy in antigen expressing tumor-bearing mouse models, suggesting that they may be promising for future clinical translation. | Bin Liu; Hung Nguyen; Yivan Jiang; Aiden Wang; Valerie Lensch; Zehao Sun; Zane Boyer; Philip Raftopoulos; Yutong Dai; Piper MacNicol; Yuyan Wang; Nidhi Jyotsana; Wencong Wang; Sachin Bhagchandani; Sanjana Hemdev; Peyton Shieh; Samantha Kristufek; Magalie Boucher; Michael Downes; Ronald Evans; David MacMillan; Jeremiah Johnson | Biological and Medicinal Chemistry; Organic Chemistry; Polymer Science; Drug delivery systems; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a848283f22e42140c14b9/original/antibody-bottlebrush-conjugates-unlock-diverse-payloads-for-targeted-cancer-therapy.pdf |
62b0b0c40bba5d82606d2cae | 10.26434/chemrxiv-2022-q2kl6 | Periodic Density Matrix Embedding for CO Adsorption on the MgO(001)Surface | The adsorption of simple gas molecules to metal oxide surfaces is a primary step in many heterogeneous catalysis applications. Quantum chemical modeling of these reactions is a challenge both in terms of cost and accuracy, and quantum-embedding methods are promising, especially for localized chemical phenomena. In this work, we employ density matrix embedding theory (DMET) for periodic systems to calculate the adsorption energy of CO to the MgO(001) surface. Using coupled-cluster theory with single and double excitations and second-order Møller-Plesset perturbation theory as quantum chemical solvers, we perform calculations with embedding clusters up to 266 electrons in 306 orbitals; the largest embedding models agreeing to within 1.2 kcal/mol of the non-embedding references. Due to the need of large impurity clusters for surface chemistry, we present a memory-efficient procedure of storing and manipulating electron repulsion integrals in the embedding space within the framework of periodic DMET. | Abhishek Mitra; Matthew Hermes; Minsik Cho; Valay Agarwal; Laura Gagliardi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b0b0c40bba5d82606d2cae/original/periodic-density-matrix-embedding-for-co-adsorption-on-the-mg-o-001-surface.pdf |
6516c4f8a69febde9eeb8ad2 | 10.26434/chemrxiv-2023-hrbpx-v2 | First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex | Abstract The dynamics of delocalized excitons in light-harvesting complexes (LHCs) can be investigated using different experimental techniques, and transient absorption spectroscopy (TA) is one of the most valuable methods for this purpose. A careful interpretation of TA spectra is essential for the clarification of excitation energy transfer (EET) processes occurring during light-harvesting. However, even in the simplest LHCs, a physical model is needed to interpret transient spectra, as the number of EET processes occurring at the same time is too large to be disentangled from measurements alone. Physical EET models are commonly built by fittings of the microscopic exciton Hamiltonians and exciton-vibrational parameters, an approach that can lead to biases. Here we present a first-principles strategy to simulate EET and transient absorption spectra in LHCs, combining molecular dynamics and accurate multiscale quantum chemical calculations to obtain an independent estimate of the excitonic structure of the complex. The microscopic parameters thus obtained are then used in EET simulations to obtain the population dynamics and the related spectroscopic signature. We apply this approach to the CP29 minor antenna complex of plants, for which we follow the EET dynamics and transient spectra after excitation in the chlorophyll b region. Our calculations reproduce all the main features observed in the transient absorption spectra and provide independent insight on the excited-state dynamics of CP29. The approach presented here lays the groundwork for the accurate simulation of EET and unbiased interpretation of transient spectra in multichromophoric systems. | Piermarco Saraceno; Vladislav Sláma; Lorenzo Cupellini | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516c4f8a69febde9eeb8ad2/original/first-principles-simulation-of-excitation-energy-transfer-and-transient-absorption-spectroscopy-in-the-cp29-light-harvesting-complex.pdf |
60c75526842e65206edb42b5 | 10.26434/chemrxiv.14045915.v1 | Rational Engineering of a Carboxylesterase for the Synthesis of Polyesters for Biomedical Applications | <div>Reengineered variants of a hyperthermophilic carboxylesterase with improved product yield in the synthesis of poly(ε-caprolactone) and triblock poly(ε-caprolactone)-co-poly(ethylene glycol)<br /></div>Methods: Quantum Mechanics/Molecular Mechanics Molecular Dynamics simulations, enzyme expression, enzymatic assays and characterization of the products. | Beatriz Almeida; Pedro Figueiredo; Daniel F.A.R. Dourado; Stephanie Paul; Derek J. Quinn; Thomas S. Moody; Andreia F. Sousa; Armando J.D. Silvestre; Alexandra Carvalho | Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75526842e65206edb42b5/original/rational-engineering-of-a-carboxylesterase-for-the-synthesis-of-polyesters-for-biomedical-applications.pdf |
65d33090e9ebbb4db9af8171 | 10.26434/chemrxiv-2024-7sdx8-v2 | High Molar Mass Polycarbonates as Closed-Loop Recyclable Thermoplastics | Using carbon dioxide (CO2) to make recyclable thermoplastics could reduce greenhouse gas emissions associated with polymer manufacturing. CO2/cyclic epoxide ring-opening copolymerization (ROCOP) allows for >30 wt% of the polycarbonate to derive from CO2; so far, the field has largely focused on oligocarbonates. In contrast, efficient catalysts for high molar mass polycarbonates are under-investigated and the resulting thermoplastic structure-property relationships, processing and recycling need to be elucidated. This work describes a new organometallic Mg(II)Co(II) catalyst that combines high productivity, low loading tolerance, the highest polymerization control and yields polycarbonates with Mn values from 4-130 kg mol-1, with narrow, monomodal distributions. It is used in the ROCOP of CO2 with bicyclic epoxides to produce a series of samples, each with Mn>100 kg mol-1, of poly(cyclohexene carbonate) (PCHC), poly(vinyl-cyclohexene carbonate) (PvCHC), poly(ethyl-cyclohexene carbonate) (PeCHC, by hydrogenation of PvCHC) and poly(cyclopentene carbonate) (PCPC). All these materials are amorphous thermoplastics, with high glass transition temperatures (85 < Tg < 126 °C, by DSC) and high thermal stability (Td > 260 °C). The cyclic ring substituents mediate the materials’ chain entanglements, viscosity, and glass transition temperatures. Specifically, PCPC was found to have 10x lower entanglement Mn and 100x lower zero-shear viscosity compared to PCHC, showing potential as a future thermoplastic. All these high molecular weight polymers are fully recyclable, either by re-processing or by using the Mg(II)Co(II) catalyst for highly selective depolymerizations to epoxides and CO2. PCPC shows the fastest depolymerization rates, achieving an activity of 2500 h-1 and >99% selectivity for cyclopentene oxide and CO2. | Gloria Rosetto; Fernando Vidal; Thomas M. McGuire; Ryan W. F. Kerr; Charlotte K. Williams | Organometallic Chemistry; Polymer Science; Organic Polymers; Polymerization (Polymers); Polymerization catalysts; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d33090e9ebbb4db9af8171/original/high-molar-mass-polycarbonates-as-closed-loop-recyclable-thermoplastics.pdf |
65095a55ed7d0eccc3cdea5a | 10.26434/chemrxiv-2023-12jjk | Dynamics of Electron–Hole Coulomb Attractive Energy and Dipole Moment of Hot Excitons in Donor–Acceptor Polymers | Understanding charge separation processes after photo-excitation in organic photovoltaics is of great importance for optimizing device performance. Many studies have associated a polaron-pair or intrachain charge transfer state in organic polymers with increased charge separation efficiency. It is then natural to ask how the chemical structure influences charge separation, enabling a more targeted materials design. Here, we report on non-adiabatic ab-initio molecular dynamics simulations of the hot exciton dynamics following photo-excitation for a series of donor-acceptor polymers. We provide detailed insights into Coulomb attractive energy and dynamical evolution of dipole moments in the excited states. The former is correlated with polaron-pair recombination thus preventing charge separation, the latter is a potential enabler of charge separation. We calculate the ultrafast dynamics of these relatively simple charge-separation-efficiency quantifiers, correlate them with the underlying chemical structure, and relate them to their static counterparts in statistical ensembles. The insights obtained here can be extended to more complex molecular compound scenarios and will inform future optimization of materials and device performance. | Fabian Bauch; Chuan-Ding Dong; Stefan Schumacher | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65095a55ed7d0eccc3cdea5a/original/dynamics-of-electron-hole-coulomb-attractive-energy-and-dipole-moment-of-hot-excitons-in-donor-acceptor-polymers.pdf |
60c7424ef96a0071d52865ad | 10.26434/chemrxiv.8247179.v1 | Assemblies of D-peptides for Targeting Cell Nucleolus | <p>Selectively targeting
cell nucleolus remains a challenge. Here we report the first case that
D-peptides form membraneless molecular condensates with RNA for targeting cell
nucleolus. A D-peptide derivative, enriched with lysine and hydrophobic
residues, self-assembles to form nanoparticles, which enter cells through
clathrin dependent endocytosis and mainly accumulate at cell nucleolus.
Structural analogue of the D-peptide reveals that particle morphology of the
assemblies, which depends on the side chain modification, favors the cellular
uptake. Contrasting to those of the D-peptide, the assemblies of the
corresponding L-enantiomer largely localize in cell lysosomes. Preliminary
mechanism study suggests that the D-peptide nanoparticles interact with RNA to
form membraneless condensates in the nucleolus, which further induces DNA
damage and results in cell death. This work illustrates a new strategy for
rationally designing supramolecular assemblies of D-peptides for targeting
subcellular organelles.</p> | Huaimin Wang; Zhaoqianqi Feng; Weiyi Tan; Bing Xu | Nanostructured Materials - Materials; Cell and Molecular Biology; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7424ef96a0071d52865ad/original/assemblies-of-d-peptides-for-targeting-cell-nucleolus.pdf |
66288c4991aefa6ce143c0c9 | 10.26434/chemrxiv-2024-9crwq-v2 | An efficient state-specific frozen natural orbital based equation of motion coupled cluster method for core-ionization energies: theory, implementation and benchmark | We have implemented a reduced-cost partial triples correction scheme to the equation of motion coupled cluster method for core-ionization energy based on state-specific natural orbitals. The second-order Algebraic Diagrammatic Construction (ADC) method is used to generate the state-specific natural orbital, which provides quicker convergence of the core IP value with respect to the size of the virtual space than that observed in standard MP2-based natural orbitals. The error due to the truncation of the virtual orbital can be reduced by using a perturbative correction. The accuracy of the method can be controlled by a single threshold and is a black box to use. The inclusion of the partial triples correction in the natural orbital based EOM-CCSD method greatly improves the agreement of the results with the experiment. The efficiency of the present implementation is demonstrated by calculating the core-ionization energy of a molecule containing 60 atoms and more than two thousand basis functions. | Amrita Manna; Bhavnesh Jangid; Rakesh Pant; Achintya Kumar Dutta | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66288c4991aefa6ce143c0c9/original/an-efficient-state-specific-frozen-natural-orbital-based-equation-of-motion-coupled-cluster-method-for-core-ionization-energies-theory-implementation-and-benchmark.pdf |
67c1e201fa469535b953d7b8 | 10.26434/chemrxiv-2025-2rjd0 | Accurate and non-invasive monitoring of biofilms in drinking water distribution systems through the analysis of quorum sensing-related mRNA in the effluent | Biofilm growth and dispersion in drinking water distribution systems (DWDS) pose risks to water quality and public health. Although monitoring biofilm formation in DWDS is essential for mitigating the risk of waterborne disease infections, current approaches that analyze the properties of the effluent cannot differentiate between planktonic and biofilm-associated bacteria. Quorum sensing (QS) systems are microbial communication mechanisms that regulate gene expression based on population density and are known to be more active in biofilm-associated bacteria than in planktonic bacteria. We hypothesize that bacteria dispersed from biofilms in DWDS influence QS-related mRNA levels detected in tap water effluent. Using Pseudomonas aeruginosa PAO1, a common bacterium found in DWDS, as a model organism, we examined the expression of the lasI gene, a key component of the las QS system, responsible for synthesizing QS signaling molecules. Specifically, the transcriptional activity of the lasI gene (i.e., RNA/DNA levels) in P. aeruginosa was systematically analyzed under various growth conditions. Our experiments confirmed that P. aeruginosa exhibits significantly higher lasI mRNA levels in biofilms compared to planktonic states. Additionally, we cultivated P. aeruginosa biofilms in flow channels and demonstrated that lasI mRNA levels in the effluent correlate with biofilm growth conditions within the flow channels. These findings indicate that biofilm growth in DWDS can be investigated non-invasively and accurately by analyzing lasI mRNA in the effluent. This rapid, non-invasive, and accurate biofilm monitoring approach has the potential to enable large-scale inspections and routine monitoring of biofilm growth within DWDS, ultimately improving public health. | Khuong Trinh; Shota Konno; Sangdo Yook; Hyun-Suk Oh; Chamteut Oh | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1e201fa469535b953d7b8/original/accurate-and-non-invasive-monitoring-of-biofilms-in-drinking-water-distribution-systems-through-the-analysis-of-quorum-sensing-related-m-rna-in-the-effluent.pdf |
60c7420ebb8c1ab8193da05e | 10.26434/chemrxiv.8206721.v1 | A Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases | Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group C-H···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (< 2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multi-scale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the S<sub>N</sub>2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein the majority of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity). | Zhongyue Yang; Fang Liu; Adam H. Steeves; Heather Kulik | Biochemistry; Biophysics; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7420ebb8c1ab8193da05e/original/a-quantum-mechanical-description-of-electrostatics-provides-a-unified-picture-of-catalytic-action-across-methyltransferases.pdf |
60c740a39abda2dd11f8bd1b | 10.26434/chemrxiv.7785446.v1 | The Mechanisms App: Development of a New Learning Tool for Active Learning in Organic Chemistry | This paper details the development of the Mechanisms app for organic chemistry, from inception to prototype and commercial release and expansion. The early research with students and instructors is described. | Julia Winter; Sarah E. Wegwerth; Brittland K. DeKorver; Layne A. Morsch; Dane DeSutter; Lawrence M. Goldman; Lauren Reutenauer | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a39abda2dd11f8bd1b/original/the-mechanisms-app-development-of-a-new-learning-tool-for-active-learning-in-organic-chemistry.pdf |
60c73e99ee301c3212c7876c | 10.26434/chemrxiv.7052027.v1 | Controlling Nanoemulsion Surface Chemistry with Poly(2-Oxazoline) Amphiphiles | Emulsions are dynamic materials that have been extensively employed within pharmaceutical, food and cosmetics industries. However, their use beyond conventional applications has been hindered by difficulties in surface functionalization, and an inability to selectively control physicochemical properties. Here, we employ custom poly(2-oxazoline) block copolymers to overcome these limitations. We demonstrate that poly(2-oxazoline) copolymers can effectively stabilize nanoscale droplets of hydrocarbon and perfluorocarbon in water. The living polymerization allows for the incorporation of chemical handles into the surfactants such that covalent modification of the emulsion surfaces can be performed. Through post-emulsion modification, we are able to access nanoemulsions with modified surface chemistries, yet consistent sizes. By decoupling size and surface charge, we explore structure-activity relationships involving the cellular uptake of nanoemulsions. | Daniel A. Estabrook; Amanda F. Ennis; Rachael Day; Ellen Sletten | Nanostructured Materials - Materials; Drug delivery systems; Organic Polymers; Cell and Molecular Biology; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e99ee301c3212c7876c/original/controlling-nanoemulsion-surface-chemistry-with-poly-2-oxazoline-amphiphiles.pdf |
6170b8f0913a745f3b61a6fa | 10.26434/chemrxiv-2021-7r9s4 | Superatomic Au25(SC2H5)18 Nanocluster under Pressure | The last decade has witnessed significant advances in the synthesis and structure determination of atomically precise metal nanoclusters. However, little is known about the condensed matter properties of these nanosized metal nanoclusters packed in a crystal lattice under high pressure. Here using density function theory calculations, we simulate the crystal of a representative superatomic gold cluster, [Au25(SR)18]0 (R = C2H5), under various pressures. At ambient conditions, [Au25(SC2H5)18]0 clusters are packed in a crystal via dispersion interactions; being a 7e superatom, each cluster carries a magnetic moment of 1μB or one unpaired electron. Upon increasing compression (from 10 to 110 GPa), we observe the formation of inter-cluster Au-Au, Au-S, and S-S covalent bonds between staple motifs, thereby linking the clusters into a network. The pressure-induced structural change is accompanied by the vanishment of the magnetic moment and the semiconductor-to-metal transition. Our work shows that subjecting crystals of atomically precise metal nanoclusters to high pressures could lead to new crystalline states and physical properties. | Qing Tang; Fuhua Li; De-en Jiang | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6170b8f0913a745f3b61a6fa/original/superatomic-au25-sc2h5-18-nanocluster-under-pressure.pdf |
63eb09e0fcfb27a31fbfe60b | 10.26434/chemrxiv-2022-xv8bk-v2 | Photoinduced Crystal Melting with Luminescence Evolution Based on Conformational Isomerisation | The phenomenon of crystal melting by light irradiation, known as photoinduced crystal-melt transition (PCMT), can dramatically change material properties with high spatiotemporal resolution. However, the diversity of compounds exhibiting PCMT is severely limited, which hampers further functionalisation of PCMT-active materials and the fundamental understandings of PCMT. Here, we report on heteroaromatic 1,2-diketones as the new class of PCMT-active compounds, whose PCMT is based on conformational isomerisation. In particular, one of the diketones demonstrates luminescence evolution prior to crystal melting. Thus, the diketone crystal exhibits dynamic multistep changes in the luminescence colour and intensity during continuous ultraviolet irradiation. This luminescence evolution can be ascribed to the sequential PCMT processes of crystal loosening and conformational isomerisation before macroscopic melting. Single-crystal X-ray structural analysis, thermal analysis, and theoretical calculations of two PCMT-active and one inactive diketones revealed weaker intermolecular interactions for the PCMT-active crystals. In particular, we observed a characteristic packing motif for the PCMT-active crystals, consisting of an ordered layer of diketone core and a disordered layer of triisopropylsilyl moieties. Our results demonstrate the integration of photofunction with PCMT, provide fundamental insights into the melting process of molecular crystals, and will diversify the molecular design of PCMT-active materials beyond classical photochromic scaffolds such as azobenzenes. | Mao Komura; Hikaru Sotome; Hiroshi Miyasaka; Takuji Ogawa; Yosuke Tani | Organic Chemistry; Materials Science; Physical Organic Chemistry; Aggregates and Assemblies; Dyes and Chromophores; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eb09e0fcfb27a31fbfe60b/original/photoinduced-crystal-melting-with-luminescence-evolution-based-on-conformational-isomerisation.pdf |
6171b5d58acf7ece28c6e7e5 | 10.26434/chemrxiv-2021-xcbvc | Improved syntheses of halogenated benzene-1,2,3,4-tetracarboxylic diimides | The preparation of halogenated benzene-1,2,3,4-tetracarboxylic diimide derivatives is challenging because of the possibility of competitive incorrect cyclizations and SNAr reactivity. Here, we demonstrate that the direct reaction of benzene-1,2,3,4-tetracarboxylic acids with primary amines in acetic acid solvent successfully provides a range of desirable ortho-diimide products in good yields. Furthermore, we demonstrate that sterically challenging N-derivatizations can be readily achieved under microwave reactor conditions, and that SNAr reactivity is only observed when excess amine is used. The halogenated diimides described here are attractive building blocks for organic materials chemistry. | Brian Zou; Kellie A. Stellmach; Stella M. Luo; Feven L. Gebresilassie; Cathy K. Zhang; Adam D. Bass; Daron E. Janzen; Dennis D. Cao | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6171b5d58acf7ece28c6e7e5/original/improved-syntheses-of-halogenated-benzene-1-2-3-4-tetracarboxylic-diimides.pdf |
666cec53c9c6a5c07a8212e7 | 10.26434/chemrxiv-2024-86g6r | Pristine and Aged Microplastics Can Nucleate Ice Through Immersion Freezing | Microplastics (MP) are ubiquitous in the environment; their atmospheric relevance is increasingly recognized. Because of their atmospheric concentrations, a question exists as to whether MP can act as ice nucleating particles in the atmosphere. This study investigates the immersion freezing activity of lab-prepared MP of four different compositions—low density polyethylene (LDPE), polypropylene (PP), poly(vinyl chloride) (PVC), and polyethylene terephthalate (PET)—using droplet freezing assays. The MP are also exposed to ultraviolet light, ozone, sulfuric acid, and ammonium sulfate to mimic environmental aging of the plastics to elucidate the role that these processes play in the ice nucleating activity of MP. Results show that all studied MP act as immersion nuclei and aging processes can modify this ice nucleating activity, leading, primarily, to decreases in ice nucleating activity for LDPE, PP, and PET. The ice nucleating activity of PVC generally increased following aging which we attribute to a cleaning of chemical defects present on the surface of the stock material. Chemical changes were monitored with infrared spectroscopy (ATR-FTIR) and the growth of a peak at 1650-1800 cm-1 was associated with a decrease in ice nucleating activity while loss of an existing peak in that region was associated with an increase in ice nucleating activity. The studied MP have ice nucleating activities sufficient to be a non-negligible source of ice nucleating particles in the atmosphere if present in sufficiently high concentrations. | Heidi Busse; Devaka Ariyasena; Jessica Orris; Miriam Freedman | Physical Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Analysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666cec53c9c6a5c07a8212e7/original/pristine-and-aged-microplastics-can-nucleate-ice-through-immersion-freezing.pdf |
67b35da981d2151a02d99dae | 10.26434/chemrxiv-2025-08vpx | Leveraging complementary ion activation methods with proton transfer charge reduction reactions for comprehensive characterization of monoclonal antibody heavy chain subunits | Characterization of large proteins by top-down mass spectrometry is challenged by low S/N of fragment ions and spectral congestion. Proton transfer charge reduction (PTCR) is one strategy that has shown great potential for addressing spectral congestion and enhancing sequence coverage of large proteins, but low S/N remains an obstacle, requiring extensive spectral averaging. Here we advance the characterization of large proteins, including an antibody (mAb) and an antibody drug conjugate (ADC), on a liquid chromatography timescale by implementing a hybrid strategy that combines ultraviolet photodissociation (UVPD), electron transfer higher collision energy dissociation (EThcD), PTCR, and gas-phase fractionation. By leveraging purposeful chromatographic peak broadening, fractionation + PTCR strategies, and the complementary nature of multiple activation methods, sequence coverages as a high as 83% and 79% were achieved for 50 kDa heavy chain (Hc) subunits of an mAb and ADC, respectively. Furthermore, unambiguous differentiation of two payload positional isomers of the ADC Hc was achieved. | Sean Dunham; Kyle Juetten; Jessica Hellinger; Mohamed Gadallah; Olivia Dioli; Jennifer Brodbelt | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b35da981d2151a02d99dae/original/leveraging-complementary-ion-activation-methods-with-proton-transfer-charge-reduction-reactions-for-comprehensive-characterization-of-monoclonal-antibody-heavy-chain-subunits.pdf |
64adb8caba3e99daefebe0d0 | 10.26434/chemrxiv-2023-0mq0h | Revealing the complex structure of molten FLiBe (2LiF−BeF2) by experimental x-ray scattering, neutron scattering, and deep neural network-based molecular dynamics | The use of molten salts as coolants, fuels, and tritium breeding blankets in the next generation of fission and fusion nuclear reactors benefits from furthering the characterization of the molecular structure of molten halide salts, paving the way to predictive capability of chemical and thermo-physical properties of molten salts. Due to its neutronic, chemical, and thermo-chemical properties, 2LiF−BeF2 is a candidate molten salt for several fusion and fission reactor designs. We perform neutron and X-ray total scattering measurements to determine the atomic structure of 2LiF−BeF2. We also perform ab-initio and neural network molecular dynamics simulations to predict the structure obtained by neutron and X-ray diffraction experiments. The use of machine learning provides improvements to the efficiency in predicting the structure at a longer length scales than is achievable with ab-initio simulations at significantly lower computational expense while retaining near ab-initio accuracy. The comparison among experimental and modeling results at a higher resolution and efficiency than previous measurements provides the opportunity to explore the structural determination of 2LiF−BeF2 beyond the first-nearest neighbor analysis that had been previously achieved with X-ray diffraction measurements of a FLiBe melt. This work may serve as a reference for future studies of salt structure and macroscopic properties with and without the addition of solutes. | Sean Fayfar; Rajni Chahal; Haley Williams; D. Nathanael Gardner; Guiqiu Zheng; David Sprouster; Joerg Neuefeind; Dan Olds; Andrea Hwang; Joanna Mcfarlane; Ryan C. Gallagher; Mark Asta; Stephen Lam; Raluca O. Scarlat; Boris Khaykovich | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Theory - Computational; Machine Learning; Structure | CC BY 4.0 | CHEMRXIV | 2023-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64adb8caba3e99daefebe0d0/original/revealing-the-complex-structure-of-molten-f-li-be-2li-f-be-f2-by-experimental-x-ray-scattering-neutron-scattering-and-deep-neural-network-based-molecular-dynamics.pdf |
636d7f3cbef5d43cdc50868a | 10.26434/chemrxiv-2022-zsx7m | Effects of Metal Amendments on the Reductive Dechlorination of Carbon Tetrachloride by Green Rust | The reductive dechlorination of carbon tetrachloride (CT) was examined in aqueous suspensions of sulfate green rust (GRSO4) amended with either Co(II), Cr(VI), Hg(II), Mn(II), Mo(VI), Ni(II), Pb(II), V(III), or Zn(II). The rate of CT reduction in the Hg(II)-amended GRSO4 suspension was ~1000 times faster than in unamended GRSO4. CT reduction was moderately enhanced in the Cr(III) , Mn(II)-, Mo(VI)-, Pb(II)-, and V(III)-amended systems. No increase in the rate of CT reduction was observed in the Co(II)-, Ni(II)-, or Zn(II)-amended systems. Chloroform (CF) was the major product of CT reduction, with minor amounts of methane and traces of ethene, and ethane; dichloromethane and chloromethane were not observed. A reaction pathway scheme is proposed in which CT is reduced primarily to chloroform (CF) and minor non-chlorinated end products, largely through a series of one-electron reductions forming radicals and carbenes/carbenoids. | Edward J. O'Loughlin; Maxim I. Boyanov; Kenneth M. Kemner; David R. Burris | Earth, Space, and Environmental Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d7f3cbef5d43cdc50868a/original/effects-of-metal-amendments-on-the-reductive-dechlorination-of-carbon-tetrachloride-by-green-rust.pdf |
65c0b54ae9ebbb4db9b4e168 | 10.26434/chemrxiv-2024-jcvkh | Electronic vector potential from the exact factorization of a complex wavefunction | We generalize the definitions of local scalar potentials named vkin and vN−1, which are relevant to properly describe phenomena such as molecular dissociation with density-functional theory, to the case in which the electronic wavefunction corresponds to a complex current-carrying state. In such a case, an extra term in the form of a vector potential appears which cannot be gauged away. Both scalar and vector potentials are introduced via the exact factorization formalism which allows to expand the given Schrödinger equation in two coupled equations, one for the marginal and one for the conditional amplitude. The electronic vector potential is directly related to the paramagnetic current density carried by the total wavefunction and to the diamagnetic current density in the equation for the marginal amplitude. An explicit example of this vector potential in a triplet state of two non-interacting electrons is showcased together with its associated circulation, giving rise to a non-vanishing geometric phase. Some connections with the exact factorization for the full molecular wavefunction beyond the Born-Oppenheimer approximation are also discussed. | Sara Giarrusso; Paola Gori-Giorgi; Federica Agostini | Theoretical and Computational Chemistry; Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c0b54ae9ebbb4db9b4e168/original/electronic-vector-potential-from-the-exact-factorization-of-a-complex-wavefunction.pdf |
65fba7f79138d23161e8e373 | 10.26434/chemrxiv-2024-kgf9g | Synergistic metabolism intervention and immune activation for antitumor therapy by biomineralized lactate oxidase | Depleting tumoral lactate is a promising strategy to enhance the immune response and thereby suppressing tumorigenesis. However, the direct use of lactate oxidase (LOx), the most straightforward lactate-eliminating agent, faces several issues including low stability, no targeting capacity. To solve these problems, a “carrier-free” nanodrug LOx@manganese sulfide (LOx@MnS) was facilely prepared via biomineralization. This way, all the constituents integrated in the nanodrug, including LOx, Mn2+, and hydrogen sulfide (H2S), could be readily delivered into tumor cells and exert their effects. LOx combined with Mn2+ to convert lactate to cytotoxic reactive oxygen species (ROS) through the cascade reaction, meanwhile the crosstalk between H2S and ROS induced metabolism suppression to further augment the therapeutic efficacy. Consequently, the multi-mode therapeutic modalities led to effective immune activation and tumor suppression, suggesting the great potential for tumor treatment. We believe this strategy opens a new avenue to construct functional materials from frangible biomolecules and expand their applications. | Yuxuan Ge; Zixin Wang; Yujia Lu; Fan Rong; Bin Hao; Zhao Li; Junsheng Chen; Yin Wang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fba7f79138d23161e8e373/original/synergistic-metabolism-intervention-and-immune-activation-for-antitumor-therapy-by-biomineralized-lactate-oxidase.pdf |
61677becaa918db6bf2a31cb | 10.26434/chemrxiv-2021-vr43g | Self-Supervised Learning for Molecular Property Prediction | Predicting molecular properties remains a challenging task with numerous potential applications, notably in drug discovery. Recently, the development of deep learning, combined with rising amounts of data, has provided powerful tools to build predictive models. Since molecules can be encoded as graphs, Graph Neural Networks (GNNs) have emerged as a popular choice of architecture to tackle this task. Training GNNs to predict molecular properties however faces the challenge of collecting annotated data which is a costly and time consuming process. On the other hand, it is easy to access large databases of molecules without annotations. In this setting, self-supervised learning can efficiently leverage large amounts of non-annotated data to compensate for the lack of annotated ones. In this work, we introduce a self-supervised framework for GNNs tailored specifically for molecular property prediction. Our framework uses multiple pretext tasks focusing on different scales of molecules (atoms, fragments and entire molecules). We evaluate our method on a representative set of GNN architectures and datasets and also consider the impact of the choice of input features. Our results show that our framework can successfully improve performance compared to training from scratch, especially in low data regimes. The improvement varies depending on the dataset, model architecture and, importantly, on the choice of input feature representation. | Laurent Dillard | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61677becaa918db6bf2a31cb/original/self-supervised-learning-for-molecular-property-prediction.pdf |
65cfc5d8e9ebbb4db9867dc2 | 10.26434/chemrxiv-2024-n471d | The Lewis Structure explorer: Accessible by Design | Successfully learning principles from drawing Lewis Structures sets the foundation for understanding more complex representations of chemical concepts. As these visual-based concepts are core competencies in chemical pedagogies, it is incumbent and required for educational institutions and faculty to provide usable accommodations for all students, including those with blindness and low-vision (BLV). The shift to visually based interactive digital media increases the technical challenge for addressing accessibility for BLV students and makes creating these accommodations by faculty even more difficult. This technology report presents research and development for providing a digital learning system for Lewis Structures designed to be directly accessible by BLV students and other screen reader users. This Lewis Structure explorer can be used by all students and includes a form-driven keyboard accessible control panel. The alternative (alt) text for the structural representations is generated dynamically with user input. The results from two usability studies, one with over 300 sighted college students and the other with four BLV adults who depend on alt text for non-text information, are presented. | Sarah E. Wegwerth; Alexa Urrea; Debra R. Nischik; Julia E. Winter | Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cfc5d8e9ebbb4db9867dc2/original/the-lewis-structure-explorer-accessible-by-design.pdf |
662058fb91aefa6ce1c71155 | 10.26434/chemrxiv-2024-1zd0b | In-insect synthesis of oxygen-doped molecular nanocarbons | Many functional molecules and materials have been produced using flask chemical reactions. Meanwhile, individual organisms, such as insects, have the potential to serve as natural, high-density cultivation equipment with multiple enzymes capable of complex reactions. However, research in this area has focused on the composition and reactivity of enzymes involved in biological reactions. Here, we report a unique "in-insect" unnatural product synthesis. Biotransformation using insect xenobiotic metabolism can selectively transform belt- and ring-shaped molecular nanocarbons into other difficult-to-prepare functional oxygen-doped derivatives. Cytochrome P450 variants are most likely the enzymes responsible for this reaction. Molecular dynamics simulations and quantum chemical calculations indicated a possible mode of substrate incorporation into the enzyme and an unconventional mechanism of direct oxygen insertion into carbon-carbon bonds. | Atsushi Usami; Hideya Kono; Vic Austen; Quan Manh Phung; Hiroki Shudo; Tomoki Kato; Hayato Yamada; Akiko Yagi; Kazuma Amaike; Kazuhiro Fujimoto; Takeshi Yanai; Kenichiro Itami | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662058fb91aefa6ce1c71155/original/in-insect-synthesis-of-oxygen-doped-molecular-nanocarbons.pdf |
65ea9e5566c138172986af66 | 10.26434/chemrxiv-2024-n4cj7-v2 | Purinyl N-Directed Aroylation of 6-Arylpurine Ribo- and 2’-Deoxyribonucleosides, and Mechanistic Insights | The purinyl ring contains four embedded nitrogen atoms of varying basicities. Selective utilization of these ring nitrogen atoms can lead to relatively facile remote functionalization, yielding modified purinyl motifs that are otherwise not easily obtained. Herein, we report previously undescribed N-directed aroylation of 6-arylpurine ribo and the more labile 2’-deoxyribonucleosides. Kinetic isotope analysis as well as reaction with a well-defined dimeric, palladated 9-benzyl 6-arylpurine provided evidence for N-directed cyclometallation as a key step, with a plausible rate-limiting C–H bond cleavage. Radical inhibition experiments indicate the likely intermediacy of aroyl radicals. The chemistry surmounts difficulties often posed in the functionalization of polynitrogenated and polyoxygenated nucleosidic structures that possess complex reactivities and a labile glycosidic bond that is more sensitive in the 2’-deoxy substrates. | Mahesh Lakshman; Casina Malinchak; Nathaniel Shank; Michelle Neary; Lothar Stahl | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ea9e5566c138172986af66/original/purinyl-n-directed-aroylation-of-6-arylpurine-ribo-and-2-deoxyribonucleosides-and-mechanistic-insights.pdf |
64a2d7e2ba3e99daef72c27f | 10.26434/chemrxiv-2023-dlzrb | The Influence of Nitrogen Doping of the Acceptor in Orange–Red Thermally Activated Delayed Fluorescence Emitters and OLEDs | Nitrogen-containing polycyclic aromatic hydrocarbons (N-PAH) have been widely used as deep lowest unoccupied molecular orbital (LUMO) acceptors in donor-acceptor (D-A) red thermally activated delayed fluorescent (TADF) emitters and their use in organic light-emitting diodes. However, most of the studies have focused disparately on donor/acceptor combinations to yield efficient emitters, while it is rare that there is a methodological study to investigate the influence of the nitrogen (N) doping ratios on the ground and excited states of PAH acceptors. Here, we report a family of four different N-PAH acceptors containing different numbers of nitrogen atoms within the N-PAH and their use in D-A TADF emitters, DMACBP, DMACPyBP, DMACBPN and DMACPyBPN, when coupled to the same donor, 9,9-dimethyl-9,10-dihydroacridine (DMAC). As the nitrogen content in the acceptor increases the LUMO becomes progressively more stabilized while the singlet-triplet energy gap (ΔEST) decreases and the rate constant for reverse intersystem crossing (kRISC) increases. In particular, introducing nitrogen at the 10-position of the dibenzo[a,c]phenazine (BP) leads to a more than ten-fold enhancement in kRISC in DMACPyBP and DMACPyBPN compared to DMACBP and DMACBPN. Among the OLEDs with all four emitters that with DMACBPN demonstrates the highest EQEmax of 19.4% at an emission peak of 588 nm. while the deepest red emitting device employed DMACPyBPN (EL = 640 nm) with an EQEmax of 5.4%. | Changfeng Si; Yan-Nan Hou; Dianming Sun; Kai Wang; Xiao-hong Zhang; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a2d7e2ba3e99daef72c27f/original/the-influence-of-nitrogen-doping-of-the-acceptor-in-orange-red-thermally-activated-delayed-fluorescence-emitters-and-ole-ds.pdf |
674d7ae45a82cea2fab1d973 | 10.26434/chemrxiv-2024-2gsrn-v2 | High-Throughput Solid Phase Extraction for Targeted and Non-Targeted Exposomics | Characterizing the chemical exposome relies on advanced instrumentation including tandem mass spectrometry coupled to liquid chromatography (LC-MS/MS), and non-targeted analysis (NTA) using high-resolution MS. However, proper sample pretreatment, balancing broad analyte coverage, method robustness, and throughput remain a major bottleneck in exposomics. Here, we developed a robust and scalable solid-phase extraction (SPE) protocol in 96-well format for human urine and plasma and optimized it for a panel of 94 highly diverse environmental and food-related contaminants (LogP -0.7 ~ 6.8). Extraction recoveries (RE) and signal suppression and enhancement (SSE) were determined using targeted LC-MS/MS. Acceptable REs (60% - 140%) were achieved for >70% of all analytes, and acceptable SSE values (60% -140%) for 86% and 90% in urine and plasma, respectively. Subsequently, the method was transferred to 96-well format, significantly improving throughput to meet the capacity requirements needed for exposome-wide association studies (ExWAS). The established workflow is approximately 10× faster than routinely used metabolomics-based protein precipitation approaches when comparing the estimated total analysis time for 1000 samples. The method’s applicability for NTA and suspect screening was tested and compared to a generic protein precipitation protocol using NIST standard reference materials for urine (SRM 3672) and plasma (SRM 1950). Better performance was shown for the protein precipitation workflow while the SPE protocol demonstrated promising results. Therefore, the developed workflow is not only superior for future high-throughput targeted exposomics but also offers an option for NTA applications. The presented well-balanced approach is likely applicable to research in pharmacology, food safety, or systems toxicology. | Yunyun Gu; Max Lennart Feuerstein; Benedikt Warth | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674d7ae45a82cea2fab1d973/original/high-throughput-solid-phase-extraction-for-targeted-and-non-targeted-exposomics.pdf |
60c754b44c89191e2ead458e | 10.26434/chemrxiv.13710046.v1 | Cyclotetrabenzoin Acetate: A Macrocyclic Porous Molecular Crystal for CO2 Separations by Pressure Swing Adsorption | A porous molecular crystal (PMC) assembled by close-packing of macrocyclic cyclotetrabenzoin acetate is an efficient adsorbent for selective CO<sub>2</sub> capture. The 7.1´7.1 Å square pore of PMC and its ester C=O group play important roles in improving its affinity for CO<sub>2</sub> molecules. Thermodynamically, the benzene walls of macrocycle strongly promote CO<sub>2</sub> adsorption via [p···p] interactions at low pressure. In addition, the polar carbonyl groups pointing inward the square channels reduce the size of aperture to a 5.0´5.0 Å square, which offers kinetic selectivity for CO<sub>2</sub> capture. The PMC features water tolerance and high structural stability under vacuum and various gas adsorption conditions, which are rare among intrinsically porous organic molecules. In mixed-gas breakthrough experiments, it exhibits efficient CO<sub>2</sub>/N<sub>2</sub> and CO<sub>2</sub>/CH<sub>4</sub> separations under kinetic flow conditions. Most importantly, the moderate adsorbate–adsorbent interaction allows the PMC to be readily regenerated, and therefore applied to pressure swing adsorption (PSA) processes. The eluted N<sub>2</sub> and CH<sub>4</sub> are obtained with over 99.9% and 99.8% purity, respectively, and the separation performance is stable for 30 cycles. Coupled with its easy synthesis, these properties make cyclotetrabenzoin acetate a promising adsorbent for CO<sub>2</sub> separations from flue and natural gases. | Yao-Ting Wang; Corie M. McHale; Xiqu Wang; Chung-Kai Chang; Yu-Chun Chuang; Watchareeya Kaveevivitchai; Ognjen Miljanic; Teng-Hao Chen | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754b44c89191e2ead458e/original/cyclotetrabenzoin-acetate-a-macrocyclic-porous-molecular-crystal-for-co2-separations-by-pressure-swing-adsorption.pdf |
66f5774451558a15ef34ff1f | 10.26434/chemrxiv-2024-hn2m6 | Catalytic Serine Labeling in Nonaqueous, Acidic Media | Chemoselective modification of alkylalcohols (e.g., serine residues) on proteins has been a daunting challenge especially in aqueous media. Herein, we report chemical modifications of alkylalcohols in protein and cell lysate samples using carboxylic acid-based bioconjugation media. The acidic medium is not only useful to suppress reactivity of other nucleophiles in proteins, but the medium also serves as a potentially biomolecule-compatible solvent. The acidic labeling strategy has a unique selectivity paradigm compared to the common active-serine-targeted method and would act as a new strategy for studying biological roles of serine residues. | Seiya Ishizawa; Chiamaka Uzoewulu; Yume Iwakura; Anuja Koirala; Shinichi Sato; Jun Ohata | Organic Chemistry; Bioorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f5774451558a15ef34ff1f/original/catalytic-serine-labeling-in-nonaqueous-acidic-media.pdf |
6509b003ed7d0eccc3d2f70f | 10.26434/chemrxiv-2023-wqp0d | Delocalized, Asynchronous, Closed-Loop Discovery of Organic Laser Emitters | Contemporary materials discovery requires intricate sequences of synthesis, formulation and characterization that often span multiple locations with specialized expertise or instrumentation. To accelerate these workflows, we present a cloud-based strategy that enables delocalized and asynchronous design–make–test–analyze cycles. We showcase this approach through the exploration of molecular gain materials for organic solid-state lasers as a frontier application in molecular optoelectronics. Distributed robotic synthesis and in-line property characterization, orchestrated by a cloud-based AI experiment planner, resulted in the discovery of 21 new state-of-the-art materials. Automated gram-scale synthesis ultimately allowed for the verification of best-in-class stimulated emission in a thin-film device. Demonstrating the asynchronous integration of five laboratories across the globe, this workflow provides a blueprint for delocalizing – and democratizing – scientific discovery. | Felix Strieth-Kalthoff; Han Hao; Vandana Rathore; Joshua Derasp; Théophile Gaudin; Nicholas H. Angello; Martin Seifrid; Ekaterina Trushina; Mason Guy; Junliang Liu; Xun Tang; Masashi Mamada; Wesley Wang; Tuul Tsagaantsooj; Cyrille Lavigne; Robert Pollice; Tony C. Wu; Kazuhiro Hotta; Leticia Bodo; Shangyu Li; Mohammad Haddadnia; Agnieszka Wolos; Rafal Roszak; Cher-Tian Ser; Carlota Bozal-Ginesta; Riley J. Hickman; Jenya Vestfrid; Andrés Aguilar-Gránda; Elena L. Klimareva; Ralph C. Sigerson; Wenduan Hou; Daniel Gahler; Slawomir Lach; Adrian Warzybok; Oleg Borodin; Simon Rohrbach; Benjamin Sanchez-Lengeling; Chihaya Adachi; Bartosz A. Grzybowski; Leroy Cronin; Jason E. Hein; Martin D. Burke; Alán Aspuru-Guzik | Theoretical and Computational Chemistry; Organic Chemistry; Photochemistry (Org.); Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509b003ed7d0eccc3d2f70f/original/delocalized-asynchronous-closed-loop-discovery-of-organic-laser-emitters.pdf |
639307cf14d92d1978a774e2 | 10.26434/chemrxiv-2022-2qnp0 | Tightly-Twisted One-Handed Helical Tubular Ladder Polymers with π-Electron-Rich Cylindrical Helical Cavities for Chromatographic Enantioseparation | Defect-free one-handed contracted helical tubular ladder polymers with a π-electron-rich cylindrical helical cavity were synthesized by alkyne benzannulations of the random-coil precursor polymers containing 6,6´-linked-1,1´-spirobiindane-7,7´-diol-based chiral monomer units. The resulting tightly-twisted helical tubular ladder polymers showed remarkably high enantioseparation abilities toward a variety of chiral hydrophobic aromatics with point, axial, and planar chiralities. The random-coil precursor polymer and analogous rigid-rod extended helical ribbon-like ladder polymer with no internal helical cavity exhibited no resolution abilities. The molecular dynamics simulations suggested that the π-electron-rich cylindrical helical cavity formed in the tightly-twisted tubular helical ladder structures is of key importance for producing the highly-enantioseparation ability, by which chiral aromatics can be enantioselectively encapsulated by specific π–π and/or hydrophobic interactions. | Wei Zheng; Kosuke Oki; Ranajit Saha; Yuh Hijikata; Eiji Yashima; Tomoyuki Ikai | Polymer Science; Conducting polymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639307cf14d92d1978a774e2/original/tightly-twisted-one-handed-helical-tubular-ladder-polymers-with-electron-rich-cylindrical-helical-cavities-for-chromatographic-enantioseparation.pdf |
67b500cf81d2151a02092d59 | 10.26434/chemrxiv-2025-zbc8x | Fragment to Framework: Bottom-Up Engineering of Band Gaps in Covalent Organic Frameworks | Understanding structure-property relationships in ordered functional materials is essential for their rational design and optimisation. Fragment-based approaches relating materials’ properties to those of their building blocks (fragments) are intuitive to chemistry and have been successfully applied in the design of metal-organic frameworks (MOFs). However, covalent organic frameworks (COFs) are resistant to such in silico fragmentation due to their covalent bonds and ambiguous definitions of nodes and linkers. Here we introduce a new algorithm, deCOFpose, designed to systematically fragment COFs into building blocks according to chemically intuitive rules, enabling fragment-based structure-property analysis, and exemplify the latter for COFs band gaps. Our results reveal that the electronic features (e.g., energies of the frontier molecular orbitals) of the building blocks alone are insufficient to fully represent these materials, and the inclusion of their topological characteristics is required to engineer bespoke COFs with desired band structures. | Michelle Ernst; Rostislav Fedorov; Alessandro Calzolari; Fabian F. Grieser; Sophia Ber; Ganna Gryn'ova | Theoretical and Computational Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b500cf81d2151a02092d59/original/fragment-to-framework-bottom-up-engineering-of-band-gaps-in-covalent-organic-frameworks.pdf |
66343ead418a5379b04d79b1 | 10.26434/chemrxiv-2024-dpbq3 | Rigid and planar π-conjugated molecules leading to long-lived intramolecular charge-transfer states exhibiting thermally activated delayed fluorescence | Intramolecular charge transfer (ICT) is a fundamental chemical process whereby excitation moves charge from an electron donor to an electron acceptor within the same molecule. Thermally activated delayed fluorescence (TADF) exploits the ICT property to harvest triplet excited states, leading to extensive optoelectronic applications, including OLEDs. However, the highly twisted conformation of TADF molecules results in limited device lifetimes. Rigid molecules offer increased stability, yet their typical planarity and π-conjugated structures impede ICT. Herein, we introduce a new paradigm for achieving dispersion-free triplet harvesting in ICT molecules. Using fused indolocarbazole-phthalimide molecules, we demonstrate remarkably stable co-planar ICT states, yielding blue/green-TADF with good photoluminescence quantum yield and a small singlet-triplet energy gap (∆EST) <50 meV. The formation of ICT is dictated by the bonding connectivity between the donor and acceptor fragments, leading to excited-state conjugation breaking stabilising the planar ICT excited state, revealing a new criteria for designing efficient TADF materials. | Suman Kuila; Hector Miranda-Salinas; Julien Eng; Chunyong Li; Martin R. Bryce; Thomas J. Penfold; Andrew P. Monkman | Physical Chemistry; Organic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66343ead418a5379b04d79b1/original/rigid-and-planar-conjugated-molecules-leading-to-long-lived-intramolecular-charge-transfer-states-exhibiting-thermally-activated-delayed-fluorescence.pdf |
66c3162d20ac769e5f0fb6da | 10.26434/chemrxiv-2024-ctxkm | Kinetically Induced Memory Effect in Li-ion Batteries | Effective optimization and control of lithium-ion batteries cannot neglect the relation between fundamental physicochemical phenomena and performance. In this work, we apply a multi-step charging protocol to commercially relevant electrodes, such as LiNi0.8Mn0.1Co0.1O2 (NMC811), LiFePO4 (LFP), LiMn1.5Ni0.5O4 (LMNO), LiMn0.4Fe0.6PO4 (LMFP), Li4Ti5O12 (LTO) and Na3V2(PO4)3 (NVP), to investigate how the initial rate affects their kinetic response. Remarkably, electrodes undergoing phase separation exhibit a pronounced counter-intuitive memory effect under high-rate operating conditions. Using operando micro-beam X-ray diffraction, the origin is demonstrated to be embedded in the rate-dependent multi-electrode particle dynamics. Developed phase-field electrochemical models capture the ensemble behavior of electrode particles underlying the kinetically induced memory effect, establishing how the thermodynamics of the nanoscale (particle) level affects macroscopic battery behavior under realistic conditions. These results challenge established battery management strategies, opening the doors for improved characterization and optimization of fast-charging protocols, crucial in minimizing aging and heat production while enhancing energy efficiency and benefitting a wide range of battery-powered applications. | Pierfrancesco Ombrini; Qidi Wang; Alexandros Vasileiadis; Fangting Wu; Ziyao Gao; Xia Hu; Martijn van Hulzen; Baohua Li; Chenglong Zhao; Marnix Wagemaker | Physical Chemistry; Materials Science; Energy; Energy Storage; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c3162d20ac769e5f0fb6da/original/kinetically-induced-memory-effect-in-li-ion-batteries.pdf |
62669a3088636c68381eadc8 | 10.26434/chemrxiv-2022-zxtfw | Renewed «Isoxazoline Route» for the Synthesis of Densely Functionalized
Ketones | In this work, the «isoxazoline route» to aldols involving the [3+2]-cycloaddition of nitrile oxide to alkenes and hydrogenolysis of oxime group was revisited. To avoid regioselectivity issues, [4+1]-annulation of nitroalkenes with sulfonium ylides was used to construct the isoxazoline ring bearing an N-oxide moiety. Subsequent deoxygenative C-H functionalization using Boekelheide rearrangement and hydrogenolysis of the isoxazoline ring afforded α’-acyloxy-substituted aldols, which are difficult to access both by classical aldol reaction and the «isoxazoline route». The products are formed in good to high overall yields and as single diastereomers in most cases. The synthetic use of these aldols was showcased by their smooth transformation into diastereomerically pure triols and a 2,3-diaryl-4-hydroxy-substituted tetrahydrofurane derivative, which is structurally related to Cinncassin B. | Pavel Ushakov; Sema Ioffe; Alexey Sukhorukov | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62669a3088636c68381eadc8/original/renewed-isoxazoline-route-for-the-synthesis-of-densely-functionalized-ketones.pdf |
642c6ad0db1a20696e843c2b | 10.26434/chemrxiv-2023-0vs6r | Mass Transport Modifies the Interfacial Electrolyte to Influence Electrochemical Nitrate Reduction | The electrochemical nitrate reduction reaction (NO3RR) can facilitate remediation of nitrate-polluted wastewater and sustainable production of ammonia. As an important component of the reaction microenvironment, the interfacial electrolyte substantially influences NO3RR but remains underexplored. Mass transport modifies the interfacial electrolyte properties (e.g., pH, solute concentrations) and thus regulates NO3RR activity and selectivity. In a representative flow-cell configuration with a titanium NO3RR electrode, we systematically controlled mass transport conditions and demonstrated their impacts on NO3RR performance. With continuum model simulation and in situ infrared absorption spectroscopy, we characterized the interfacial electrolyte environment under varied mass transport conditions. Furthermore, we strategically tuned the interfacial electrolyte properties and experimentally deconvoluted their impacts on NO3RR activity and selectivity. We found that diffusion layer thickness and background electrolyte concentration govern NO3RR activity, while interfacial pH steers NO3RR selectivity. Inspired by these findings, we applied pulsed potential to periodically refresh the interfacial electrolyte environment and lower the local pH, successfully tripling the relative ammonia-to-nitrite selectivity. Distinct from NO3RR studies that focus on reaction kinetics, this study was conducted under commonly observed mass transport limitations to advance mechanistic understanding behind mass transport effects and to help identify engineering opportunities that optimize ammonia production. | Jinyu Guo; Paige Brimley; Matthew Liu; Elizabeth Corson; Carolina Munoz; Wilson Smith; William Tarpeh | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Water Purification; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642c6ad0db1a20696e843c2b/original/mass-transport-modifies-the-interfacial-electrolyte-to-influence-electrochemical-nitrate-reduction.pdf |
66a990ecc9c6a5c07a8d5708 | 10.26434/chemrxiv-2024-1vkn7-v2 | Modeling homogeneous ice nucleation from drop-freezing experiments: Impact of droplet volume dispersion and cooling rates | Homogeneous nucleation is the prominent mechanism of glaciation in cirrus and other high-altitude clouds. Ice nucleation rates can be studied in laboratory assays that gradually lower the temperature of pure water droplets. These experiments can be performed with different cooling rates, different droplet sizes, and often with a distribution of droplet sizes. We combine nucleation theory, survival probability analysis, and published data on the fraction of frozen droplets as a function of temperature to understand how cooling rate, droplet size, and size dispersity influence the nucleation rates. The framework, implemented in the Python code AINTBAD, provides a temperature dependent nucleation rate on a per volume basis, in terms of approximately temperature-independent prefactor (A) and barrier (B) parameters. We find that less than an order of magnitude dispersion in droplet diameters, if not properly included in the analysis, can cause apparent nucleation barriers to be underestimated by 50\%. This result highlights the importance of droplet size-dispersion in efforts to model glaciation in the polydisperse droplets of clouds. We also developed a theoretical framework, implemented in the Python code IPA, to predict the fraction of frozen droplets at each temperature for arbitrary droplet size dispersions and cooling rates. Finally, we present a sensitivity analysis for the effect of temperature uncertainty on the nucleation spectrum. Our framework can improve models for ice nucleation in clouds by explicitly accounting for droplet polydispersity and cooling rates. | Ravi Kumar Reddy Addula; Ingrid de Almeida Ribeiro; Valeria Molinero; Baron Peters | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a990ecc9c6a5c07a8d5708/original/modeling-homogeneous-ice-nucleation-from-drop-freezing-experiments-impact-of-droplet-volume-dispersion-and-cooling-rates.pdf |
628e495ca42e9c15e64d620c | 10.26434/chemrxiv-2022-7w90m | Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo | Water molecules play a key role in biomolecular systems, particularly when bound at protein-ligand interfaces. Simulation studies are hampered by the relatively long timescales on which water exchange between protein and solvent can take place. Grand canonical Monte Carlo (GCMC) is a simulation technique which avoids this issue by attempting the direct insertion and deletion of water molecules. GCMC is, however, hampered by low acceptance probabilities for insertions in congested systems. To address this issue, here, we combine GCMC with nonequilibrium candidate Monte Carlo (NCMC) to yield a new method, grand canonical nonequilibrium candidate Monte Carlo (GCNCMC), in which water insertions and deletions are carried out in a gradual, nonequilibrium fashion. We compare GCNCMC and GCMC simulations of bulk water, and three protein binding sites. We find the efficiency of water sampling is improved by GCNCMC, and that increased sampling of bound ligand conformations is also observed. | Oliver Melling; Marley Samways; Yunhui Ge; David Mobley; Jonathan Essex | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e495ca42e9c15e64d620c/original/enhanced-grand-canonical-sampling-of-occluded-water-sites-using-nonequilibrium-candidate-monte-carlo.pdf |
6764944bfa469535b924261d | 10.26434/chemrxiv-2024-8k69t | Design of Enaminitrile Switches with Enhanced Protofluorochromic Properties | Functional switches exhibiting distinct functionalities responding to a specific stimulus are highly desirable for fabricating advanced devices with superior dynamic performances. Herein, we explored a series of enaminitrile switches as protofluorochromic entities by modulation of their structures, assisted by DFT calculations. The switches show high stabilities, and exhibit reversible E/Z isomerization behavior, along with tunable fluorescence intensity in both protic and aprotic media. Switches based on 2-pyridyl- or 2-pyridylmethyl-containing N-components exhibited strong fluorescence in their protonated Z-configurations, compared to their phenyl/benzyl counterparts. This behavior could be attributed to variations in intramolecular charge transfer (ICT) or excited-state intramolecular proton transfer (ESIPT) effects. The Z-isomers were furthermore studied in their aggregated solid/film/dispersion states, resulting in notable aggregration-induced emission (AIE) behavior. | Zhen Yang; Olof Ramstrom | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Supramolecular Chemistry (Org.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6764944bfa469535b924261d/original/design-of-enaminitrile-switches-with-enhanced-protofluorochromic-properties.pdf |
63aa9c5f16e9a8922e364d67 | 10.26434/chemrxiv-2022-whjt7 | Polysubstituted cyclohexane γ-amino acids induce a double α-/β-turn in short non-natural peptides | We describe short non-natural peptides that adopt α- and β-turn folds in solution and in the crystal. The peptides are constituted by a core of trans and cis stereoisomers of polyhydroxylated cyclohexane γ-amino acids, flanked by dimers of L-α-alanine, resulting in hybrid hexapeptides with an ααγγαα backbone. DFT calculations and spectroscopic analysis by NMR, CD and FT-IR in solution are consistent with structural changes upon deprotection of certain hydroxyl groups of the central polyhydroxylated γ-amino acids. X-ray diffraction analysis of a crystalline sample revealed a double α-/β-turn that was also identified by NMR spectroscopy in acetonitrile-d3 solution. | Reza David; Nolis Pau; Sánchez-Pedregal Víctor M.; Kang Young Kee ; Estévez Ramón J.; Estevez Juan C. | Organic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63aa9c5f16e9a8922e364d67/original/polysubstituted-cyclohexane-amino-acids-induce-a-double-turn-in-short-non-natural-peptides.pdf |
62db490c3787f1f26ac2b1e3 | 10.26434/chemrxiv-2022-7hxsc-v2 | Extended Conjugation Refining Carbon Nitride for Non-sacrificial H2O2 Photosynthesis and Hypoxic Tumor Therapy | Artificial photocatalysis offers a clean approach for producing H2O2. However, the poor selectivity and activity of H2O2 production hamper traditional industrial applications and emerging photodynamic therapy (PDT)/chemodynamic therapy (CDT). Here, we report a well-defined C5N2 photocatalyst with a conjugated C=N linkage for highly selective and efficient non-sacrificial H2O2 production both in normoxic and hypoxic systems. The strengthened delocalization of π-electrons by linkers in C5N2 significantly downshifted the band position, which eliminated the side photoreduction reaction of H2 evolution in thermodynamics and promoted water oxidation ability in kinetics. As a result, C5N2 had a competitive overall H2O2 production with solar-to-chemical conversion efficiency of 0.55% and more interestingly, exhibited the highest activity so far in hypoxic condition (698 μM/h). C5N2 was further applied to hypoxic PDT/CDT, exhibiting outstanding performance in conspicuous cancer cell death and synchronous bioimaging. It shed light on unlocking linker functions in electronic structure engineering of carbon nitrides for highly efficient overall photosynthesis of H2O2 and expanded the scope of their prospective application in health care. | Jin Ma; Xiaoxiao Peng; Zhixin Zhou; Hong Yang; Kaiqing Wu; Zhengzou Fang; Dan Han; Yanfeng Fang; Songqin Liu; Yanfei Shen; Yuanjian Zhang | Biological and Medicinal Chemistry; Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62db490c3787f1f26ac2b1e3/original/extended-conjugation-refining-carbon-nitride-for-non-sacrificial-h2o2-photosynthesis-and-hypoxic-tumor-therapy.pdf |
65428e5da8b423585abd31fe | 10.26434/chemrxiv-2023-5tjg0-v2 | Bioinformatic Discovery of a Cambialistic Monooxygenase | Dinuclear monooxygenases mediate challenging C-H bond oxidation reactions throughout Nature. Many of these enzymes are presumed to exclusively utilize diiron cofactors. Herein, we report the bioinformatic discovery of an orphan dinuclear monooxygenase that preferentially utilizes a heterobimetallic manganese-iron (Mn/Fe) cofactor to mediate an O2 dependent C-H bond hydroxylation reaction. Unlike the structurally similar Mn/Fe-dependent monooxygenase AibH2, the diiron form of this enzyme (SfbO) exhibits nascent enzymatic activity. This behavior raises the possibility that many other dinuclear monooxygenases may be endowed with the capacity to harness cofactors with variable metal content. | Chang Liu; Magan Powell; Guodong Rao; R. David Britt; Jonathan Rittle | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65428e5da8b423585abd31fe/original/bioinformatic-discovery-of-a-cambialistic-monooxygenase.pdf |
62c6dd5314201fdc012971a6 | 10.26434/chemrxiv-2022-6btc7 | Electronic Energy Levels and Optical Transitions in Samarium(III) Solvates | Lanthanide luminescence fascinates with complicated electronic structure and ’forbidden’ transitions. By studying the photophysics of lanthanide(III) solvates, a close to ideal average coordination geometry can be used to map both electronic energy levels and transition probabilities. Some lanthanide(III) ions are simpler to study than others, and samarium(III) belongs to the more difficult ones. The 4f5 system has numerous absorption and emission lines in the visible and infrared part of the spectrum, and in this work the energy levels giving rise to these transitions were mapped, the transition probability between them was calculated, and it was shown that the electronic structure of the samarium(III) solvates in DMSO, MeOH and water are different. | Sabina Svava Mortensen ; Malthe Asmus Marciniak Nielsen ; Patrick R Nawrocki; Thomas Just Sørensen | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c6dd5314201fdc012971a6/original/electronic-energy-levels-and-optical-transitions-in-samarium-iii-solvates.pdf |
60c74c50842e65e625db32a7 | 10.26434/chemrxiv.12458252.v1 | Classification of Coffee and Wine with a Microwave Resonator and Deep Learning Machine Technique | In this study, coffee and wine were measured using
an microwave resonator, and a deep learning system was trained using the
acquired data, and then tested to see if the deep leaning system could
distinguish these samples. We tested 6 kinds of wine, 6 kinds of cold brew
coffee and 6 kinds of bottled coffee. The microwave resonance spectra of all
samples were graphically displayed. The graphical images were processed by an
artificial intelligence (AI) technique. By applying deep learning machine technique
instead of the peak assignment for complex compounds in general, it was
possible to facilitate the classification of coffee or wine with high accuracy. | Hyo Bong Hong; Jae-Chan Jeong; Hans Joachim Krause | Computational Chemistry and Modeling; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c50842e65e625db32a7/original/classification-of-coffee-and-wine-with-a-microwave-resonator-and-deep-learning-machine-technique.pdf |
6468820bf2112b41e9db74f7 | 10.26434/chemrxiv-2023-14d8j | MetaGTM: VISUALIZATION AND ANALYSIS OF THE CHEMICAL LIBRARY SPACE | In chemical library analysis, it may be useful to describe libraries as individual items, rather than as collections of compounds. This is particularly true for ultra-large non-cherry pickable compound mixtures, such as DNA-Encoded Libraries (DELs). In this sense, the Chemical Library Space (CLS) is useful for the management of a portfolio of libraries, just like Chemical Space (CS) helps managing a portfolio of molecules. Several possible CLSs were previously defined using vectorial library representations obtained from Generative Topographic Mapping (GTM). Given the steadily growing number of DEL designs, the CLS becomes “crowded”, and requires analysis tools beyond pairwise library comparison. Therefore, herein we investigate the cartography of CLS on meta-(µ)GTMs – “meta” to remind that these are maps of the CLS, itself based on responsibility vectors issued by regular CS GTMs. 2,5K DELs and ChEMBL (reference) were projected on the µGTM, producing landscapes of library-specific properties. These describe both inter-library similarity and intrinsic library characteristics in the same view, herewith facilitating the selection of the best project-specific libraries. | Regina Pikalyova; Yuliana Zabolotna; Dragos Horvath; Gilles Marcou; Alexandre Varnek | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6468820bf2112b41e9db74f7/original/meta-gtm-visualization-and-analysis-of-the-chemical-library-space.pdf |
670df5f451558a15ef19938c | 10.26434/chemrxiv-2024-8772n | Synthesis of 4,5-Disubstituted o-Phenylenediamines: An Enabling Platform for Electrochemical Evaluation of Intramolecular Concerted Proton–Electron Transfer Reactions | Proton-coupled electron transfer (PCET) reactions occur in many reactions of global importance, including H2 evolution, among other applications. Surprisingly, knowledge gaps remain in our fundamental understanding of PCET and CPET reactions. In recent studies graphitic electrode systems that are modified by o-phenylenediamines have been singled out as an ideal platform for studying single-site CPET. Although this CPET experimental platform has been established, synthetic access to 4,5-o- phenylenediamines remains limited. Herein we discuss three distinct synthetic strategies aimed toward developing a modular synthetic route to symmetrical and asymmetrical 4,5-o-phenylenediamines. We demonstrate the utility of 4,5-o-dinitrobenzenes as relatively stable precursors to 4,5-o- phenylenediamines and a modular route to make 4,5-o-phenylenediamines in just 2-4 steps from commercial material. | Dennis Tang; Jasmin Rose; John Gonzalez; Marco Giles; Shane Ardo; Matthew Minus; Yogesh Surendranath | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670df5f451558a15ef19938c/original/synthesis-of-4-5-disubstituted-o-phenylenediamines-an-enabling-platform-for-electrochemical-evaluation-of-intramolecular-concerted-proton-electron-transfer-reactions.pdf |
64f97fc73fdae147faaac6b5 | 10.26434/chemrxiv-2023-34wl2 | Active Sites in Cr(III)-based Ethylene Polymerization Catalysts from Machine Learning-Supported XAS and EPR Spectroscopy | The ethylene polymerization Phillips catalyst has been employed for decades and is central to the polymer industry. While Cr(III) alkyl species are proposed to be the propagating sites, there is so far no direct experimental evidence for such proposal. In this work, by coupling Surface organometallic chemistry (SOMC), EPR spectroscopy, and machine learning-supported XAS studies, we have studied the electronic structure of well-defined silica-supported Cr(III) alkyls, and identified the presence of several surface species from high to low spin Cr(III), associated with different coordination environments. Notably, low-spin Cr(III) sites are shown to participate in ethylene polymerization, indicating that similar Cr(III) alkyl species could be involved in the related Phillips catalyst. | Anton Ashuiev; Anna Giorgia Nobile; David Trummer; Daniel Klose; Sergey Guda; Olga V. Safonova; Christophe Copéret; Alexander Guda; Gunnar Jeschke | Inorganic Chemistry; Polymers; Solid State Chemistry; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f97fc73fdae147faaac6b5/original/active-sites-in-cr-iii-based-ethylene-polymerization-catalysts-from-machine-learning-supported-xas-and-epr-spectroscopy.pdf |
61629491fb861901b2f36d7b | 10.26434/chemrxiv-2021-w1bm5 | Ideal Gas Reference for Association and Dissociation Reactions: I. Basic Concepts | Starting with a distance-based definition of molecules consisting of non-interacting atoms, which is in line with IUPAC terminology, we construct an ideal gas reference for chemical association and dissociation reactions. The corresponding ideal equations for equilibria and kinetics reveal the mathematical structure, known for real systems, in comprehensible clarity. The ideal gas reference corresponds to the limit of an entirely flat potential energy surface of the system where chemical equilibria and kinetics are determined by "unspecific" particle number combinatorics according to the reaction stoichiometry. The ideal equilibrium and rate constants provide a reference for the definition of excess equilibrium and rate constants of real reactions that quantify all "system-specific" contributions resulting from the particular shape of the potential energy surface. The ideal gas reference therefore enables a distinction between unspecific and system-specific aspects in the equilibria and kinetics of chemical association/dissociation reactions. Whereas conventional equilibrium and rate constants suffer from incompatibility between reactions of different stoichiometry, excess equilibrium and rate constants can be consistently compared across different reaction orders. Furthermore, whereas the conventional treatment requires an arbitrary specification of reference concentrations, e.g. at standard conditions, the ideal gas framework introduces an intrinsic concentration scale that is equal to the inverse of a molecular volume. | Tobias Binninger; Adrian Heinritz; Rhiyaad Mohamed | Physical Chemistry; Chemical Kinetics; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61629491fb861901b2f36d7b/original/ideal-gas-reference-for-association-and-dissociation-reactions-i-basic-concepts.pdf |
672914f37be152b1d0f9029c | 10.26434/chemrxiv-2024-hndjp | Equations and Electrochemical Methods for Measuring the Interfacial Charge-Transfer Kinetics of Li-ion Battery Active Materials at High Current Densities | Experimental measurements and quantitative models of the interfacial charge-transfer kinetics of Li-ion battery (LIB) active materials (AM) are essential for accurate predictions of LIB rate performance, safety, and lifetime. The Butler-Volmer (BV) equation is commonly used to describe interfacial kinetics in LIBs as a function of the transfer coefficient (α) and exchange current (I0). It is tacitly assumed that α ≈ 0.5, so experimental measurements of α for LIB AMs have rarely been attempted. In this work, mathematical models are derived to fit the apparent α and I0 values from the electrochemical data at high current densities by reformulating the BV equation to describe the current dependence of charge-transfer resistance (Rct) and differential charge-transfer resistance (R’ct). Pseudo-steady-state extrapolation chronopotentiometry (S3E-CP), large-amplitude galvano EIS (LA-GEIS), and operando galvano EIS (O-GEIS) techniques are developed, and each is shown to be capable of accurately and precisely measuring the values of α and I0 while maintaining the conditions of stability, stationarity, and linearity. Symmetric coin cells are demonstrated as a simple and widely accessible tool for achieving the most accurate kinetic measurements, and preliminary results are reported for LiCoO2 symmetric cells at 50% state-of-charge. S3E-CP and LA-GEIS measurements yield apparent α values of, respectively, 0.420 and 0.431, while O-GEIS measurements show that these data are consistent with a two-step reaction with α1 = 0.5 and α2 = 3. The equations and electrochemical methods developed herein are broadly applicable for empirically measuring and modeling the interfacial charge-transfer kinetics in rechargeable batteries. | Kevin Scanlan; Arumugam Manthiram | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672914f37be152b1d0f9029c/original/equations-and-electrochemical-methods-for-measuring-the-interfacial-charge-transfer-kinetics-of-li-ion-battery-active-materials-at-high-current-densities.pdf |
659c5faf66c138172900a17e | 10.26434/chemrxiv-2024-zf1k8 | Innovative Virtual Screening of PD-L1 Inhibitors: The Synergy of Molecular Similarity, Neural Networks, and GNINA Docking | Immune checkpoint inhibitors have garnered significant attention in oncological research over recent years. A plethora of studies have elucidated that inhibitors targeting the Programmed Death-Ligand 1 (PD-L1) play a pivotal role in circumventing the evasion mechanisms of cancer cells against the immune system. This study aimed to develop an integrated screening model combining an Artificial Neural Network (ANN), Molecular Similarity (MS) assessments, and GNINA 1.0 molecular docking, targeting PD-L1 inhibitors. A database of 2044 substances with known PD-L1 inhibitory activity was compiled from Google Patents and used to enhance molecular similarity evaluations and train the machine learning model. For retrospective validation of the docking procedure, the human PD-L1 protein, with the Protein Data Bank (PDB) ID: 5N2F, was employed as a control. In this phase of the study, 15,235 compounds from the DrugBank database were subjected to a series of screening processes: initially through medicinal chemistry filters, followed by MS assessments, the ANN model, and culminating with molecular docking using GNINA 1.0. The decoy generation yielded promising outcomes, evidenced by an AUC-ROC 1NN value of 0.52 and Doppelganger scores with a mean of 0.24 and a maximum of 0.346, indicating a high resemblance of the decoys to the active set. For MS, the AVALON emerged as the most effective fingerprint for similarity searching, demonstrating an Enrichment Factor (EF) of 1% at 10.96%, an AUC-ROC of 0.963, and an optimal similarity threshold of 0.32. The ANN model demonstrated superior performance in cross-validation, achieving an average precision of 0.863±0.032 and an F1 score of 0.745±0.039, outperforming both the Support Vector Classifier (SVC) and Random Forest (RF) models, albeit not significantly. In external validation, the ANN model maintained its superiority with an average precision of 0.851 and an F1 score of 0.790. GNINA 1.0, employed for molecular docking, was validated through redocking and retrospective control, achieving an AUC of 0.975, with a critical cnn_pose_score threshold of 0.73. From the initial 15,235 compounds, 128 were shortlisted using the MS and ANN models. Further screening through GNINA 1.0 identified 22 potential candidates, among which (3S)-1-(4-acetylphenyl)-5-oxopyrrolidine-3-carboxylic acid emerged as the most promising, with a cnn_pose_score of 0.79, a PD-L1 inhibitory probability of 70.5%, and a Tanimoto coefficient of 0.35.
| Van-Thinh To; Tieu-Long Phan; Bao-Vy Ngoc Doan; Phuoc-Chung Van Nguyen; Dong-Nghi Hoang Nguyen; Quang-Huy Nguyen Le; Hoang-Huy Nguyen; The-Chuong Trinh; Tuyen Ngoc Truong | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659c5faf66c138172900a17e/original/innovative-virtual-screening-of-pd-l1-inhibitors-the-synergy-of-molecular-similarity-neural-networks-and-gnina-docking.pdf |
64945a57853d501c00552305 | 10.26434/chemrxiv-2023-99815 | Timed Pulses in DNA strand displacement reactions | Inspired by naturally occurring regulatory mechanisms that allow complex temporal pulse features with programmable delays in gene expression and biological pathways, we demonstrate here a strategy to achieve temporally programmed pulse output signals in DNA-based Strand Displacement Reactions (SDRs). To achieve this, we rationally designed input strands that, once bound to their target duplex, can be gradually degraded, resulting in a pulse output signal. We also designed blocker strands that suppress strand displacement and determine the time at which the pulse reaction is generated. We show that by controlling the degradation rate of blocker and input strands we can finely control the delayed pulse output over a range of 10 hours. We also prove that it is possible to orthogonally delay two different pulse reactions in the same solution by taking advantage of the specificity of the degradation reactions for input and blocker strands. Finally, we show here two possible applications of such delayed pulse SDRs: the time-programmed pulse decoration of DNA nanostructures and the sequentially-appearing and self-erasing formation of DNA-based patterns. | Juliette Bucci; Patrick Irmisch; Erica Del Grosso; Ralf Seidel; Francesco Ricci | Physical Chemistry; Analytical Chemistry; Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64945a57853d501c00552305/original/timed-pulses-in-dna-strand-displacement-reactions.pdf |
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