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669e180a01103d79c51c3ba7 | 10.26434/chemrxiv-2024-hfc9r | Experimental and Computational Analysis of Slurry-Based Manufacturing of Solid-State Battery Composite Cathode | The rheological properties of the electrode slurry significantly influence the manufacturing process of solid-state batteries (SSBs), affecting coating quality and the resulting cathode microstructure. The correlation between slurry attributes and final electrode characteristics is analyzed using particle size and solid content as key metrics. The performed coarse-grained molecular dynamics simulations closely fit experimental viscosity, indicating the model's suitability for predicting slurry behavior. Then the microstructural properties of the dry and calendered electrodes are calibrated with the experiments. The simulation workflow is fitted completely using only two sets of force fields, one for the slurry and the other for the dry state of the electrode. The effective electronic conductivities are contingent on the particle size, without showing significant limitation on cathode rate capabilities. This comprehensive study highlights the intricate interplay between slurry solid content, microstructure design, and manufacturing processes in optimizing SSB performance. Consistent slurry characteristics are crucial for uniform electrode coating while optimizing particle size and solid content improves electrode porosity. The findings provide valuable insights for enhancing SSB design and manufacturing processes for the adaptation of already established scaling up technologies. | Mohammed Alabdali; Franco Zanotto; Benoit Notredame; Virginie Viallet; Vincent Seznec; Alejandro A. Franco | Theoretical and Computational Chemistry; Materials Science; Energy; Composites; Computational Chemistry and Modeling; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e180a01103d79c51c3ba7/original/experimental-and-computational-analysis-of-slurry-based-manufacturing-of-solid-state-battery-composite-cathode.pdf |
66eb9fd312ff75c3a1c68085 | 10.26434/chemrxiv-2024-l71cj | Photoswitching molecules functionalized with optical cycling centers provide a novel platform for studying chemical transformations in ultracold molecules | A novel molecular structure that merges the fields of molecular optical cycling with molecular photoswitching is presented. It is based on a photoswitching molecule azobenzene functionalized with one and two CaO- groups, which can act as optical cycling centers (OCCs). This paper characterizes the electronic structure of the resulting model systems, focusing on three questions: (1) how the electronic states of the photoswitch are impacted by a functionalization with an OCC; (2) how the states of the OCC are impacted by the scaffold of the photoswitch; (3) whether the OCC can serve as spectroscopic probe of isomerization. The experimental feasibility of the proposed design and the advantages that organic synthesis can offer in fur- ther functionalization of the molecular scaffold are also discussed. This work brings into the field of molecular optical cycling a new dimension of chemical complexity, intrinsic only to polyatomic molecules. | Paweł Wójcik; Taras Khvorost; Guanming Lao; Guozhu Zhu; Antonio Macias Jr; Justin Caram; Wesley Campbell; Miguel García-Garibay; Eric Hudson; Anastassia Alexandrova; Anna Krylov | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66eb9fd312ff75c3a1c68085/original/photoswitching-molecules-functionalized-with-optical-cycling-centers-provide-a-novel-platform-for-studying-chemical-transformations-in-ultracold-molecules.pdf |
6759646e7be152b1d09ae90e | 10.26434/chemrxiv-2024-m5xps | Distal C(sp3)-H Amidation via Ind*RhIII Catalysed Nitrene Transfer using 1,4,2-Dioxazol-5-ones | Building on our discovery that Ind*Rh(III) catalysts accelerated C(sp2)–H amidation, the Ind*Rh(III) catalysed amidation of C(sp3)–H sites was explored harnessing amides as weakly-coordinating directing groups. The combined use of an indenyl-derived catalyst and 2-pyridone additive proved critical in providing the enhanced catalytic activity required to achieve the amidation of both primary and secondary C(sp3)–H sites, affording a diversity of valuable structures. The late-stage amidation and peptide conjugation of pharmaceutical derivatives using the Ind*RhIII/2-pyridone catalytic system was also demonstrated. | Hannah Ross; Yihui Yu; Liselle Atkin; Daniel Priebbenow | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6759646e7be152b1d09ae90e/original/distal-c-sp3-h-amidation-via-ind-rh-iii-catalysed-nitrene-transfer-using-1-4-2-dioxazol-5-ones.pdf |
6454abe707c3f029373dee60 | 10.26434/chemrxiv-2023-gdmxs | Optically enhanced solid-state 1H NMR spectroscopy | Low sensitivity is the primary limitation to extending nuclear magnetic resonance (NMR) techniques to more advanced chemical and structural studies. Photochemically induced dynamic nuclear polarization (photo-CIDNP) is an NMR hyperpolarization technique where light is used to excite a suitable donor–acceptor system, creating a spin-correlated radical pair whose evolution drives nuclear hy-perpolarization. Systems that exhibit photo-CIDNP in solids are not common and this effect has, up to now, only been observed for 13C and 15N nuclei. However, the low gyromagnetic ratio and natural abundance of these nuclei trap the local hyperpolarization in the vicinity of the chromophore and limit the utility for bulk hyperpolarization. Here we report the first example of optically enhanced solid-state 1H NMR spectroscopy in the high-field regime. This is achieved via photo-CIDNP of a donor–chromophore–acceptor molecule in a frozen solution at 0.3 T and 85 K, where spontaneous spin diffusion among the abundant strongly coupled 1H nuclei relays polarization through the whole sample, yielding a 16-fold bulk 1H signal enhancement under continuous laser irradiation at 450 nm. These findings enable a new strategy for hyperpolarized NMR beyond the current limits of conventional microwave-driven DNP. | Federico De Biasi; Michael Hope; Claudia Avalos; Ganesan Karthikeyan; Gilles Casano; Aditya Mishra; Saumya Badoni; Gabriele Stevanato; Dominik Kubicki; Jonas Milani; Jean-Philippe Ansermet; Aaron Rossini; Moreno Lelli; Olivier Ouari; Lyndon Emsley | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6454abe707c3f029373dee60/original/optically-enhanced-solid-state-1h-nmr-spectroscopy.pdf |
60c73fdebdbb8956fca380af | 10.26434/chemrxiv.7528370.v1 | Electrochemical Dearomative 2,3-Difunctionalization of Indoles | We report the use of electrochemistry to perform
a direct oxidative dearomatization of indoles leading to 2,3-dialkoxy or
2,3-diazido indolines under undivided conditions at a constant current. This
operationally simple electro-oxidative procedure avoids the use of an external
oxidant and displays an excellent functional group compatibility. The formation
of the two C-O or C-N bonds is believed to arise from the oxidation of the
indoles into radical cation intermediates. | Ju Wu; Yingchao Dou; Régis Guillot; Cyrille Kouklovsky; Guillaume Vincent | Organic Synthesis and Reactions; Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdebdbb8956fca380af/original/electrochemical-dearomative-2-3-difunctionalization-of-indoles.pdf |
60c743f4bb8c1a1f7d3da3f9 | 10.26434/chemrxiv.7940594.v3 | Analyzing Learned Molecular Representations for Property Prediction | Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows. | Kevin Yang; Kyle Swanson; Wengong Jin; Connor Coley; philipp eiden; Hua Gao; Angel Guzman-Perez; Timothy Hopper; Brian
P. Kelley; miriam mathea; Andrew Palmer; Volker Settels; Tommi S Jaakkola; Klavs F. Jensen; Regina Barzilay | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f4bb8c1a1f7d3da3f9/original/analyzing-learned-molecular-representations-for-property-prediction.pdf |
653fee89a8b423585a974537 | 10.26434/chemrxiv-2023-k2wpt | Relative Cooperativity in Neutral and Charged Molecular Clusters Using QM/MM Calculations | QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct electronic structure calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body interactions involving three or more particles. In contrast, polarizable force fields account partially for many-body effects through polarization, but still handle van der Waals and permanent electrostatic interactions pairwise. We showed that despite those limitations, polarizable and non-polarizable force fields, can reproduce relative cooperativity achieved using Density Functional Theory, due to error compensation mechanisms. In this contribution, we assess the performance of QM/MM methods in reproducing these phenomena. Our study highlights the significance of QM region size and force field choice in QM/MM simulations, emphasizing the importance of parameter validation to obtain accurate interaction energy predictions. | Jorge Nochebuena; Shubin Liu; G. Andrés Cisneros | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653fee89a8b423585a974537/original/relative-cooperativity-in-neutral-and-charged-molecular-clusters-using-qm-mm-calculations.pdf |
66e10886cec5d6c142b9674f | 10.26434/chemrxiv-2024-sdzs1 | Molecular Processes that Control Adiponitrile Electrosynthesis in Near-Electrode Microenvironments | Electrosynthesis at an industrial scale offers an opportunity to use renewable electricity in chemical manufacturing, accelerating the decarbonization of large-scale chemical processes. Organic electrosynthesis can improve product selectivity, reduce reaction steps, and minimize waste byproducts. Electrochemical synthesis of adiponitrile (ADN) via hydrodimerization of acrylonitrile (AN) is a prominent example of industrial organic electrochemical processes. It circumvents the drawbacks of thermochemical synthesis by reducing toxicity and leveraging clean electricity as an energy source. Despite its industrial importance, mechanistic understanding and experimental insights on the near-electrode molecular processes of AN electrohydrodimerization remain insufficient. Here we show, using in-situ ATR-FTIR spectroscopy, that tetraalkylammonium ions populate the electrical double layer (EDL), creating a microenvironment that favors interactions with organic molecules and enhances AN concentration while expelling water molecules. Our results provide experimental evidence supporting long-standing mechanistic hypotheses. Kinetic isotope effect studies reveal that propionitrile (PN) formation is rate-limited by proton transfer, while ADN formation likely is not. Electron paramagnetic resonance spectroscopy confirms the presence of free radicals during AN electroreduction, suggesting that coupling of PN radicals occurs primarily in the electrolyte. These insights highlight the importance of carefully controlling the EDL composition for selective organic electrosynthesis and provide fundamental engineering guidance for designing high-performing electro-organic reactions. We anticipate these findings will guide the optimization of electrolyte formulations and electrode interfaces for ADN synthesis and other emerging electro-organic processes. | Ricardo Mathison; Rasha Atwi; Hannah B. McConnell; Emilio Ochoa; Elina Rani; Toshihiro Akashige; Jason A. Röhr; André D. Taylor; Claudia E. Avalos; Eray S. Aydil; Nav Nidhi Rajput; Miguel A. Modestino | Organic Chemistry; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e10886cec5d6c142b9674f/original/molecular-processes-that-control-adiponitrile-electrosynthesis-in-near-electrode-microenvironments.pdf |
611e6702fa49ace6e8562214 | 10.26434/chemrxiv-2021-t1b6t | Design of semiconducting electrides via electron-metal hybridization: the case of Sc2C | Electrides are exotic materials that have electrons present in well-defined lattice sites. The existence of Y2C and Gd2C as 2D electrides inspired us to examine other trivalent metal carbides, including Sc2C and Al2C. It has been proposed that design rules for electride materials include the need for an electropositive cation adjacent to the electride site, but the effect of cation electronegativity on electronic structure in electride materials is not yet known. Here, we examine trivalent metal carbides with varying degrees of electronegativity and experimentally synthesize a 2D electride, Sc2C, containing the most electronegative metal yet found neighboring the electride site. Further, we find that higher electronegativity of the cation drives greater hybridization between metal and electride orbitals. Our calculations predict that Sc2C is a small band gap semiconductor with a band gap of 0.305 eV, with an experimental conductivity of 1.62 S/cm at room temperature. This is the first 2D electride material to exhibit semiconducting behavior, and we propose that electronegativity of the cation drives the change in band structure. | Lauren McRae; Rebecca Radomsky; Jacob Pawlik; Daniel Druffel; Jack Sundberg; Matthew Lanetti; Carrie Donley; Kelly White; Scott Warren | Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611e6702fa49ace6e8562214/original/design-of-semiconducting-electrides-via-electron-metal-hybridization-the-case-of-sc2c.pdf |
67632d42fa469535b902d5d4 | 10.26434/chemrxiv-2024-hn0fn | Synthesis and Coordination Chemistry of an Integrated Binucleating Ligand Based on Bidentate NacNac and NCN Pincer Frameworks | A new binucleating “Janus” ligand based on the betadiketiminato (“NacNac”) donor combined with an NCN pincer ligand framework has been designed and synthesized. By incorporating pyridyl donors on the imino carbons of the NacNac ligand, two binding sites for metals are introduced. The ligand’s binucleating capabilities are demonstrated by ligating BF2 in the NacNac pocket and NiBr into the NCN pincer bay. The resulting binuclear boron-nickel complexes chemistry was explored by substitution of the bromide ligand on nickel and one fluoride ion on boron with the weakly coordinating triflimide anion [N(SO2CF3)2]- (NTf2). The bromide is replaced preferentially with AgNTf2 and further treatment with Me3SiNTf2 produces a borenium ion by abstracting F- from the BF2 unit. Semiquantitative assessment of the Lewis acidity at the nickel center using the Gutmann-Beckett method shows a substantial increase in Lewis acidity upon conversion of the BF2 to the [BF]+ borenium moiety. | Chia Yun Chang; Michael Sgro; Warren Piers; Wen Zhou | Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67632d42fa469535b902d5d4/original/synthesis-and-coordination-chemistry-of-an-integrated-binucleating-ligand-based-on-bidentate-nac-nac-and-ncn-pincer-frameworks.pdf |
60c751244c89191fb8ad3ecf | 10.26434/chemrxiv.13127240.v1 | Structure-Based Bioactive Phytochemical Design from Ayurvedic Formulations Towards Spike and Mpro Druggable Targets of SARS-CoV-2 | <p>The present COVID-19 global crisis
invoked different disciplines of the biomedical research community to address the
contagious human to human viral transmission and infection severity.
Traditional or de novo drug discovery approach is a very time consuming process
and will conflict with the urgency to discover new anti-viral drugs for combating
the present global pandemic. Modern anti-viral drugs are not very effective and
show resistance with serious adverse effects. Thus, identifying bioactive
natural ingredients (phytochemical) from different medicinal plants or Ayurvedic
formulations provides an effective alternative therapy for SARS-CoV-2 viral
infections. We performed structure-based phytochemical design studies involving
bioactive phytochemicals from medicinal plants towards two key druggable targets,
spike glycoprotein and main protease (M<sup>pro</sup>) of SARS-CoV-2. Phyllaemblicin class of phytocompounds showed
better binding affinity towards both these SARS-CoV-2 targets and its binding mode revealed
interactions with critical amino acid residues at its active sites. Also, we
have successfully shown that the SARS-CoV-2 spike glycoprotein interaction towards human ACE2 receptor as its port
of human cellular entry was blocked due to conformational variations in ACE2
receptor recognition by the binding of the phytocompound, Phyllaemblicin C at the
ACE2 binding domain of spike protein. Our study shows that the Phyllaemblicin
class of phytochemicals can be a potential dual inhibitor of spike and M<sup>pro</sup> proteins of SARS-CoV-2 and could be
promising for the treatment of COVID-19. </p> | Anju Choorakottayil Pushkaran; Prajeesh Nath EN; Shantikumar V Nair; Rammanohar P; C Gopi Mohan | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751244c89191fb8ad3ecf/original/structure-based-bioactive-phytochemical-design-from-ayurvedic-formulations-towards-spike-and-mpro-druggable-targets-of-sars-co-v-2.pdf |
60c74d680f50db4f6139702f | 10.26434/chemrxiv.12290282.v2 | Ab initio calculations of free energy of activation at multiple electronic structure levels made affordable: An effective combination of perturbation theory and machine learning | <div>While free energies are fundamental thermodynamic quantities to characterize chemical reactions, their calculation based on ab initio theory is usually limited by the high computational cost. This is particularly true if multiple levels of theory have to be tested to establish their relative accuracy, if highly expensive quantum mechanical approximations are of interest, and also if several different temperatures have to be considered. We present an ab initio approach that effectively couples perturbation theory and machine learning to make ab initio free energy calculations more affordable. Starting from results based on a certain production ab initio theory, perturbation theory is applied to obtain free energies. The large number of single point calculations required by a brute force application of this approach are here significantly decreased by applying machine learning techniques. Importantly, the training of the machine learning model requires only a small amount of data and does not need to be performed again when the temperature is decreased. The accuracy and efficiency of this method is demonstrated by computing the free energy of activation of the proton exchange reaction in the zeolite chabazite. Starting from an ab initio calculation based on a semilocal approximation of density functional theory, free energies based on significantly more expensive non-local van der Waals and hybrid functionals are obtained with only a few tens of additional single point calculations. In this way this work paves the route to quick free energy calculations using different levels of theory or approximations that would be too computationally expensive to be directly employed in molecular dynamics or Monte Carlo simulations.</div> | Tomas Bucko; Monika Gešvandtnerová; Dario Rocca | Computational Chemistry and Modeling; Machine Learning; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d680f50db4f6139702f/original/ab-initio-calculations-of-free-energy-of-activation-at-multiple-electronic-structure-levels-made-affordable-an-effective-combination-of-perturbation-theory-and-machine-learning.pdf |
67727e08fa469535b93d7015 | 10.26434/chemrxiv-2024-x0dzz | Understanding thermal transport in polymer semiconductors via two-channel mechanism | The vibrational thermal conductivity of polymer semiconductors is crucial for the performance of organic electronic devices, yet its underlying mechanisms remain elusive. This work presents a novel two-channel model to elucidate the vibrational heat transport in semiconducting polymers with extended side chains. We reveal a striking splitting of vibrational modes along the polymer chain, which is driven by the significant difference in force constants between the covalent bonds of the backbone and the van der Waals forces between the side chains. This leads to the emergence of two distinct longitudinal acoustic-like branches: a dominant backbone branch, featuring phonon-like propagons that predominantly dictate thermal conductivity, and a side chain branch, primarily composed of non-propagating diffusons, contributing minimally to heat transport. The reduced thermal conductivity of these polymer semiconductors relative to their side chain-free counterparts is attributed to phonon scattering with the low-frequency optical modes of the side chains, as validated by both first-principles calculations and inelastic neutron scattering experiments. Our findings highlight that the strategic modification of side chains offers a potent approach for fine-tuning thermal conductivity, as demonstrated by substituting side chain atoms with heavier elements. This finding opens new pathways for improving the thermoelectric performance of polymer semiconductors. | Chunlin Xu; Dongyang Wang; Zhaodong Zhu; Svemir Rudić; Sihai Yang; Chong-an Di; Dong Wang | Theoretical and Computational Chemistry; Materials Science; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67727e08fa469535b93d7015/original/understanding-thermal-transport-in-polymer-semiconductors-via-two-channel-mechanism.pdf |
6273c30587d01fdaa1d96723 | 10.26434/chemrxiv-2022-lm0f7 | Force-based method to determine the potential dependence in electrochemical barriers | Determining ab-initio potential dependent energetics are critical to investigating mechanisms for electrochemical reactions. While methodology for evaluating reaction thermodynamics is established, simulation techniques for the corresponding kinetics is still a major challenge owing to a lack of potential control, finite cell size effects or computational expense. In this work, we develop a model which allows for computing electrochemical activation energies from just a handful of Density Functional Theory (DFT) calculations. The sole input into the model are the atom centered forces obtained from DFT calculations performed on a homogeneous grid composed of varying field-strengths. We show that the activation energies as a function of the potential obtained from our model are consistent for different super-cell sizes and proton concentrations for a range of electrochemical reactions. | Sudarshan Vijay; Georg Kastlunger; Joseph A Gauthier; Anjli Patel; Karen Chan | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study; Surface | CC BY 4.0 | CHEMRXIV | 2022-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6273c30587d01fdaa1d96723/original/force-based-method-to-determine-the-potential-dependence-in-electrochemical-barriers.pdf |
6630ce2b418a5379b0173692 | 10.26434/chemrxiv-2024-zkgvx | A photocatalytic active Titanium-Metal-organic framework-inorganic glass composite | Metal-organic framework (MOF) composites are proposed as solutions to the mechanical instability of pure MOF materials. Here we present a new compositional series of the recently discovered MOF-crystalline inorganic glass composites. In this case, formed by the combination of a photocatalytic titanium MOF (MIL-125-NH2) and a phosphate-based glass (20%Na2O-10%Na2SO4-70%P2O5). This new family of composites has been synthesised and characterised using powder X-ray diffraction, thermal gravimetric analysis, differential scanning calorimetry, scanning electron microscopy and X-ray total scattering. Through the analysis of the pair distribution function extracted from X-ray total scattering data, the atom-atom interactions at the MOF-glass interface are described. Nitrogen and carbon dioxide isotherms demonstrate good surface area values, despite the pelletisation and mixing of the MOF with a dense inorganic glass. The catalytic activity of these materials was investigated in the photooxidation of amines to imines, showing retention of the photocatalytic effectiveness of the parent pristine MOF. | Celia Castillo-Blas; Montaña García; Ashleigh Chester; Matjaz Mazaj; Georgina Robertson; Ayano Kono; James Steele; Luis León-Alcaide; Bruno Poletto-Rodrigues; Phillip Chater; Silvia Cabrera; Andraž Krajnc; Lothar Wondraczek; David A. Keen; José Alemán; Thomas Bennett | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630ce2b418a5379b0173692/original/a-photocatalytic-active-titanium-metal-organic-framework-inorganic-glass-composite.pdf |
65a9329866c1381729be2f66 | 10.26434/chemrxiv-2024-36b1n | Approaching the Complete Basis Set Limit for Transition Metal Spin–State Energetics | Convergence to the complete basis set (CBS) limit is analyzed for the problem of transition metal (TM) spin-state energetics by taking under scrutiny a benchmark set of 18 energy differences between spin states for 13 chemically diverse TM complexes. The performance of conventional CCSD(T) and explicitly correlated CCSD(T)-F12a/b calculations in approaching the CCSD(T)/CBS limits is systematically studied. An economic computational protocol is developed based on the CCSD-F12a approximation and (here proposed) modified scaling of the perturbative triples term, (T#). This computational protocol recovers relative spin–state energetics of the benchmark set in excellent agreement with the reference CCSD(T)/CBS limits (mean absolute deviation 0.4, mean signed deviation 0.2, and maximum deviation 0.8 kcal/mol) and enables performing canonical CCSD(T) calculations for mononuclear TM complexes sized up to ca. 50 atoms, which is illustrated by application to heme-related metalloporphyrins. Furthermore, a good transferability of the basis set incompleteness error (BSIE) is demonstrated for spin–state energetics calculated using CCSD(T) and other wave-function methods (MP2, CASPT2, CASPT2/CC, NEVPT2, MRCI+Q), which justifies efficient focal-point approximations and simplifies construction of multi-method benchmark studies. | Gabriela Drabik; Mariusz Radoń | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a9329866c1381729be2f66/original/approaching-the-complete-basis-set-limit-for-transition-metal-spin-state-energetics.pdf |
638391091234cbdb2924e47b | 10.26434/chemrxiv-2022-g18jf | Fouling Resistance and Release Properties of Poly(sulfobetaine) Brushes with Varying Alkyl Chain Spacer Length and Molecular Weight | We examined the effects of alkyl carbon spacer length (CSL) and molecular weight on fouling resistance and release properties of zwitterionic poly(sulfobetaine methacrylate) brushes. Using surface-initiated atom transfer radical polymerization, we synthesized two series of brushes with CSL = 3 and 4 and molecular weight from 19 - 1500 kg mol-1, corresponding to dry brush thickness from around 6 - 180 nm. The brush with CSL = 3 was nearly completely wet with water (independent of molecular weight), whereas the brush with CSL = 4 exhibited a strong increase in water contact angle with molecular weight. Though the two brush series had distinct wetting properties, both series of brushes exhibited similarly great resistance against fouling by Staphylococcus epidermidis bacteria and Aspergillus niger fungi spores when submerged in water, indicating that neither molecular weight nor carbon spacer length strongly affected the antifouling behavior. We also compared the efficacy of brushes against fouling by fungi and silicon oil in air. Brushes grafted to filter paper were strongly fouled by fungi and silicon oil in air. Grafting the polymers to the filter paper, however, greatly enhanced removal of the foulant upon rinsing. The removal of fungi and silicon oil when rinsed with a salt solution was enhanced by 219 and 175%, respectively, as compared to a blank filter paper control. Thus, our results indicate that these zwitterionic brushes can promote foulant removal for dry applications in addition to their well-known fouling-resistance in submerged conditions. | Fahimeh Khakzad; Narendra Dewangan; Tzu-Han Li; Farshad Safi Samghabadi; Ronard Herrera Monegro; Megan Robertson; Jacinta Conrad | Materials Science; Polymer Science; Polyelectrolytes - Materials; Polymer brushes | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638391091234cbdb2924e47b/original/fouling-resistance-and-release-properties-of-poly-sulfobetaine-brushes-with-varying-alkyl-chain-spacer-length-and-molecular-weight.pdf |
6355bddfac45c744ed9541fe | 10.26434/chemrxiv-2022-qm9wx-v2 | Redox Inversion: A Radical Analog of Umpolung Reactivity for Base and Metal-Free Catalytic C(sp3)–C(sp3) Coupling | The construction of alkyl–alkyl bonds is a powerful tool in organic synthesis. Redox inversion–defined as the radical analog of polarity inversion–is used as a strategy for C(sp3)–C(sp3) coupling. Herein is reported a base and metal-free photocatalytic coupling of carboxylic acids to form biologically relevant bibenzyls through a radical-radical coupling. Mechanistic insight is gained through control reactions that implicate this new redox inversion strategy. In this work, the previously unexplored redox-opposite relationship between a carboxylic acid and its in situ activated redox active ester is implemented in catalysis. | Chris Seong; Annabel Ansel; Courtney Roberts | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6355bddfac45c744ed9541fe/original/redox-inversion-a-radical-analog-of-umpolung-reactivity-for-base-and-metal-free-catalytic-c-sp3-c-sp3-coupling.pdf |
63d97931d8f55fd0aa989c8c | 10.26434/chemrxiv-2023-90s5n | Quantum chemical and microkinetic study of H2 dissociation on Cu4 cluster in the gas phase | Here we study the H2 dissociation mechanism on cationic and neutral Cu4 clusters using master equation based microkinetic modelling. Cationic cluster hinders the H2 dissociation compared to the neutral one. This can be explained by the electron donation to the H2 LUMO. The H2 dissocation is greatly influenced by the temperature, but Cu4 dissociate H2 already at mild conditions | Tibor Höltzl; Máté Szalay | Physical Chemistry; Chemical Kinetics; Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d97931d8f55fd0aa989c8c/original/quantum-chemical-and-microkinetic-study-of-h2-dissociation-on-cu4-cluster-in-the-gas-phase.pdf |
60c73d3a337d6ccb6ee26103 | 10.26434/chemrxiv.5518798.v1 | Distributed Representation of Chemical Fragments | <p>1.
Approximately
3.7 million (3,700,103) PubChem compounds were used in training the fragment
vectors. Five million compounds (from CID 1 to 5,000,000) were downloaded in
SMILES format from PubChem Download Service<sup>1</sup> for this purpose. Inorganic
part of salts, charges on certain atoms were neutralized, components of mixtures
were split and only one chemical from sets of duplicates were kept. Approximately 100,000 chemicals were held out
for future needs.</p>
<p>2.
Hansen<sup>2</sup>
and Bursi<sup>3</sup> Ames mutagenicity benchmark datasets were used. The data
was preprocessed in the same way as the PubChem chemicals, except in the case
of duplicates, the compound with the highest mutagenicity value was retained, leaving
6771 compounds (3639 mutagenic and 3132 non-mutagenic).</p>
<p>3.
A
dataset of 575 compounds was taken from the publication of Ghose <i>et al</i><sup>4</sup> to compute molar
refractivity of the fragments. </p>
An in-house dataset<sup>5</sup> of 7000 chemicals (Zhu Hao et al) with
their experimentally observed LogP was also used to help in computing LogP
contribution of the fragments.<div><br /></div><div>
<p>1.
PubChem
Download Service, URL: https://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch.cgi.</p>
<p>2.
Hansen,
K., Mika, S., Schroeter, T., Sutter, A., Laak, A. T., Steger-Hartmann, T.,
Heinrich, N. and Müller, K. R. (2009) Benchmark Data Set for in Silico
Prediction of Ames Mutagenicity. J. Chem. Inf. Model. 49, 2077-2081.</p>
<p>3.
Kazius,
J., McGuire, R., Bursi, R. (2005) Derivation and validation of toxicophores for
mutagenicity prediction. J. Med. Chem. 48, 312-320.</p>
<p>4.
Ghose,
A. K., Crippen, G. M. (1987) Atomic physicochemical parameters for
three-dimensional-structure-directed quantitative structure-activity
relationships. 2. Modeling dispersive and hydrophobic interactions. J. Chem.
Inf. Comput. Sci. 27(1), 21-35.</p>
Zhu, H., Sedykh, A., Chakravarti, S. K., Klopman, G.
(2005) A new group contribution approach to the calculation of LogP. Current
Computer-Aided Drug Design 1, 3-9. <br /></div> | Suman Chakravarti | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d3a337d6ccb6ee26103/original/distributed-representation-of-chemical-fragments.pdf |
63f38c751d2d184063d1b8bd | 10.26434/chemrxiv-2023-fm3q1 | DFT studies of perylenetetracarboxylic dianhydride and perylene diimide derivatives | Perylenetetracarboxylic dianhydride (PTCDA) and perylene diimide (PDI) have been widely used as photosensitizers in many applications. Photophysical properties are key factors for efficient application of these materials. Furthermore, many functionalization of these materials come from the motivation of tuning their solubility, which may affect the photophysical properties of the resulting materials. As such, it is imperative to study the electronic and photophysical properties of PTCDA and PDI derivatives. In this work, we report DFT studies of 36 molecules consisting 18 PTCDA molecules and 18 PDI derivatives with the same set of functionalization at the bay positions. DFT results show that the impact of functionalization is similar in HOMO and LUMO energies to both PTCDA and PDI derivatives. Analysis of electronic results indicates extension of electron delocalization along the bay positions 1 and 7 is important in altering absorption wavelengths or HOMO-LUMO gaps | Junpeng Zhuang; Lichang Wang | Physical Chemistry; Materials Science; Energy; Dyes and Chromophores; Optical Materials; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f38c751d2d184063d1b8bd/original/dft-studies-of-perylenetetracarboxylic-dianhydride-and-perylene-diimide-derivatives.pdf |
63641d8dac45c741a9a44074 | 10.26434/chemrxiv-2022-lq2j3 | Advances in understanding the phosphate binding in
soil: A Computational Chemistry perspective | Phosphorus (P) is an indispensable element to all forms of life and its efficient use in fertilizers is one of the conditions for food security. The efficiency of P fertilizers is affected by P mobilization and P fixation, both depending on the P binding strength to soil constituents. This review provides an overview of the P binding to soil constituents, especially to P-fixing mineral surfaces and its investigation using state-of-the-art Computational Chemistry (CC). Specifically, a brief overview will be given on experimental efforts related to the P adsorption at mineral surfaces and the factors affecting this process. Moreover, a brief introduction into common CC methods, techniques, and applications is presented. The main part of this review is focused on a possible strategy to cope with the soil heterogeneity by breaking down the complexity of P behavior in soil into well-defined models that can be discussed in terms of particular key factors. Hence, different molecular model systems and molecular simulations are introduced to reveal the P binding to soil organic matter (SOM), metal ions, and mineral surfaces. Simulation results provided an in-depth understanding of the P binding problem and explained at a molecular level the effects of surface plane, binding motif, kind and valency of metal ions, SOM composition, water, pH, and redox potential on the P binding in soil. On this basis, an overall molecular picture of P binding in soil can be then obtained by combining results for the different models. Eventually, challenges and further modifications of the existing molecular modeling approaches are discussed, such as steps necessary to bridge the molecular with the mesoscale. | Ashour A. Ahmed; Peter Leinweber; Oliver Kühn | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Computational Chemistry and Modeling; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63641d8dac45c741a9a44074/original/advances-in-understanding-the-phosphate-binding-in-soil-a-computational-chemistry-perspective.pdf |
63d3c1176bc5cac1bc1cd996 | 10.26434/chemrxiv-2022-v9z6n-v2 | Space charge governs the kinetics of metal exsolution | Nanostructured composite electrode materials play a major role in the field of catalysis and electrochemistry. Self‐assembly of metallic nanoparticles on oxide supports via metal exsolution relies on the transport of reducible dopants towards the perovskite surface to provide accessible catalytic centers at the solid/gas interface. However, it is unclear if exsolution can be driven from the oxide bulk or if the process is limited to surfaces and interfaces, where strong electrostatic gradients and space charges typically control the properties of oxides. Here we reveal that the nature of the surface‐dopant interaction is the main determining factor for the exsolution kinetics of nickel in SrTi0.9Nb0.05Ni0.05O3‐ẟ and that the exsolution depth is strongly limited to the near‐surface region of the perovskite oxide. Electrostatic interaction of dopants with surface space charge regions forming upon thermal annealing result in strong surface passivation i.e. a retarded exsolution response. We furthermore demonstrate the controllability of the exsolution response via engineering of the perovskite surface chemistry. Our findings indicate that tailoring the electrostatic gradients at the perovskite surface is an essential step to improve exsolution type materials in catalytic converters. | Moritz Lukas Weber; Břetislav Šmíd; Uwe Breuer; Marc-André Rose; Norbert H. Menzler; Regina Dittmann; Rainer Waser; Olivier Guillon; Felix Gunkel; Christian Lenser | Materials Science; Catalysis; Nanoscience; Catalysts; Composites; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d3c1176bc5cac1bc1cd996/original/space-charge-governs-the-kinetics-of-metal-exsolution.pdf |
60c73d0eee301c9248c784d9 | 10.26434/chemrxiv.5388046.v1 | Inhibition of NGLY1 inactivates the transcription factor Nrf1 and potentiates proteasome inhibitor cytotoxicity | We discovered that the proteostasis modulating transcription factor Nrf1 requires cytosolic de-N-glycosylation by the N-glycanase NGly1 as part of its activation mechanism. Through a covalent small molecule library screen, we discovered an inhibitor of NGly1 that blocks Nrf1 activation in cells and potentiates the activity of proteasome inhibitor cancer drugs. The requirement of NGly1 for Nrf1 activity likely underlies several pathologies associated with a rare hereditary deficiency in NGly1. | Carolyn Bertozzi; Fred Tomlin; Ulla Gerling-Driessen; Yi-Chang Liu; Ryan Flynn; Janakiram Vangala; Christian Lentz; Sandra Clauder-Muenster; Petra Jakob; William F. Mueller; Diana Ordoñez-Rueda; Malte Paulsen; Naoko Matsui; Deirdre Foley; Agnes Rafalko; Tadashi Suzuki; Matthew Bogyo; Lars M. Steinmetz; Senthil K. Radhakrishnan | Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2017-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0eee301c9248c784d9/original/inhibition-of-ngly1-inactivates-the-transcription-factor-nrf1-and-potentiates-proteasome-inhibitor-cytotoxicity.pdf |
67ceb1b56dde43c90840cdbe | 10.26434/chemrxiv-2025-m7t9g | Hard-wired Solid-state Micropore Bioelectronic Metal-Protein-Metal Devices | We report the design, fabrication, and application of robust ultrathin (~20 nm) metal-protein-metal junctions. These junctions are formed by sandwiching protein layers between a roughness-controlled bottom Au substrate/electrode and an evaporated Pd top contact within a micropore device (MpD) configuration. Our bottom-up fabrication approach incorporates extensive control and optimization strategies to ensure device reproducibility. A specialized protocol was developed to maintain the nanoscale roughness of the bottom electrode also within the micropore region, facilitating uniform protein layer integration. Multi-layered protein films composed of a globular or a membrane protein, human serum albumin, and reconstituted bacteriorhodopsin, respectively, were used to test device feasibility. For reliable top electrode deposition, a refined E-beam evaporation process was designed to mitigate void-induced short-circuiting of the junctions. Palladium (Pd) was selected for its preferred two-dimensional growth to decrease the chance of metal penetration between proteins. Impedance phase response analysis at high frequencies identified ~60% of the junctions as transport-active, highlighting the efficacy of the fabrication approach. These protein-based MpD junctions offer a firm platform for electron transport studies of a variety of soft materials esp. biomaterials such as proteins. | Sudipta Bera; Eran Mishuk; Sigal Keshet; Sharon Garusi; Leonid Tunik; Israel Pecht; Ayelet Vilan; Mordechai Sheves; David Cahen | Physical Chemistry; Materials Science; Nanoscience | CC BY 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ceb1b56dde43c90840cdbe/original/hard-wired-solid-state-micropore-bioelectronic-metal-protein-metal-devices.pdf |
65a56215e9ebbb4db9399eb6 | 10.26434/chemrxiv-2024-b3d86 | Evaluation of Ketoclomazone and its Analogues as Inhibitors of Thiamine Diphosphate (ThDP)-dependent Enzymes | Most pathogenic bacteria, apicomplexan parasites and plants rely on the methylerythritol phosphate (MEP) pathway to obtain precursors of isoprenoids. 1-Deoxy-D-xylulose 5-phosphate synthase (DXPS), a thiamine diphosphate (ThDP)-dependent enzyme, catalyses the first and rate-limiting step of the MEP pathway. Due to its absence in humans, DXPS is considered as an attractive target for the development of anti-infectious agents and herbicides. However, major challenges in designing therapeutic agents that target DXPS include: a) discovering drug-like inhibitors to occupy a highly polar active site; and b) selectively targeting DXPS over other ThDP-dependent enzymes. Ketoclomazone is one of the earliest reported inhibitors of DXPS and antibacterial and herbicidal activities have been documented. This study aimed to investigate the activity of ketoclomazone on DXPS from various species, as well as the broader ThDP-dependent enzyme family. To gain further insights into the inhibition, we have prepared analogues of ketoclomazone and evaluated their activity in biochemical and computational studies. Our findings support the potential of ketoclomazone as a selective antibacterial agent. | Alex H. Y. Chan; Terence C. S. Ho; Imam Fathoni; Rawia Hamid; Anna K. H. Hirsch; Kevin J. Saliba; Finian James Leeper | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a56215e9ebbb4db9399eb6/original/evaluation-of-ketoclomazone-and-its-analogues-as-inhibitors-of-thiamine-diphosphate-th-dp-dependent-enzymes.pdf |
60c73e60bb8c1a66933d98ff | 10.26434/chemrxiv.6972785.v1 | Integrated Synthesis of Nucleotide and Nucleosides Directed by Amino Acids | <p><b>Research
on the origin of nucleic acids and proteins has been approached by either
multi-step synthesis or simple one-pot reactions, but exploration of their
prebiotic chemistry is normally done separately. However, if nucleotides and
amino acids co-existed on early Earth, their mutual interactions and reactivity
should be considered in exploring the emergence of complex chemical systems
that can ultimately evolve. To explore this idea, we set out to investigate
nucleotide/nucleoside formation by a simple dehydration reaction of the constituent
building blocks (sugar, phosphate, and nucleobase) in the presence of amino
acids (<i>i.e.</i> glycine,</b> <b>arginine, glutamic acid, threonine,
methionine, phenylalanine and tryptophan). Herein, we report the first example
of simultaneous formation of glycosidic bonds between ribose, purines, and
pyrimidines under mild conditions without a catalyst or activated reagents, as
well as nucleobase exchange. We observed not only the simultaneous formation of
nucleotide and nucleoside isomers from several nucleobases, but also the
selection of distribution of glycosylation products when glycine was present.
This work shows how reaction networks of nucleotides and amino acids should be
considered when exploring the emergence of catalytic networks in the context of
molecular evolution. </b></p> | Irene Suárez-Marina; Rebecca Turk-MacLeod; Yousef Abul-Haija; Piotr S. Gromski; Geoffrey Cooper; Leroy Cronin | Bioorganic Chemistry; Biochemical Analysis; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e60bb8c1a66933d98ff/original/integrated-synthesis-of-nucleotide-and-nucleosides-directed-by-amino-acids.pdf |
66ab82065101a2ffa8ca289d | 10.26434/chemrxiv-2024-54w68-v2 | Theoretical study on the correlation between open-shell electronic structures and third-order nonlinear optical properties in one-dimensional chains of π-radicals | This paper theoretically investigated the correlation between open-shell electronic structure and third-order nonlinear optical (NLO) properties of one-dimensional (1D) stacked chains of π-radicals. By employing the finite N-mer models consisting of methyl or phenalenyl radicals with different stacking distances, we evaluated the average and standard deviation of diradical characters yi for N-mer models of π-radicals (yav and ySD). Then, we estimated these diradical characters at the limit N → ∞. These y-based indices were helpful in discussing the correlation between the open-shell electronic structures and the second hyperpolarizability per dimer at the limit N → ∞, γ∞, for the 1D chains with stacking distance alternation (SDA). The calculated γ∞ values and the polymer/dimer ratio γ∞/γ(N = 2) were enhanced significantly when both the stacking distance and the SDA are small. We also found that the spin-unrestricted long-range corrected (LC-)UBLYP method with the range-separating parameter μ = 0.47 bohr-1 reproduced well the trend of γ∞ of this type of 1D chains estimated at the spin-unrestricted coupled-cluster levels. The present study is expected to contribute to establishing the design guidelines for future high-performance open-shell molecular NLO materials. | Jinki Shoda; Masako Yokoyama; Wataru Yoshida; Hiroshi Matsui; Ryota Sugimori; Ryohei Kishi; Yasutaka Kitagawa | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ab82065101a2ffa8ca289d/original/theoretical-study-on-the-correlation-between-open-shell-electronic-structures-and-third-order-nonlinear-optical-properties-in-one-dimensional-chains-of-radicals.pdf |
6698c9b401103d79c5508b76 | 10.26434/chemrxiv-2024-xl3kt | A Multi-Reflection Time-of-Flight Analyzer with a Long Focus Lens | Multi-reflection time-of-flight (MR-ToF) analyzers must control the transversal ion dispersion, orthogonal to the axis of reflection, conventionally via periodic refocusing, or more recently the shaped electrode structure adopted by the Astral analyzer. In principle, the complexity of the dispersion control on every oscillation may be avoided at a cost of a smaller number of oscillations, during which the dispersion doesn't exceed the limit of unrecoverable overlap. A method of dispersion control has been demonstrated experimentally and in simulation, whereby the ion beam is configured by a long focus trans-axial lens made of a pair of quasi-elliptical plates mounted above and below the ion beam, in order to optimize the spatial spread of the ions at a distant detector. The collimation concept was shown to effectively control beam expansion. For experimental confirmation, a prototype Astral ana-lyzer was modified, and resolving power above 70k demonstrated. | Hamish Stewart; Dmitry Grinfeld; Aivaras Venckus; Amelia Peterson; Bernd Hagedorn; Robert Ostermann; Eduard Denisov; Matthew Garland; Alexander Wagner; Alexander Makarov; Christian Hock | Analytical Chemistry; Analytical Apparatus; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6698c9b401103d79c5508b76/original/a-multi-reflection-time-of-flight-analyzer-with-a-long-focus-lens.pdf |
60c74b29469df471e3f43e7b | 10.26434/chemrxiv.11910735.v2 | Reduction of carbon impurities in aluminium nitride from time-resolved chemical vapour deposition using trimethylaluminum | <p>Aluminium
nitride (AlN) is a semiconductor with a wide range of applications from light
emitting diodes to high frequency transistors. Electronic grade AlN is
routinely deposited at 1000 °C by chemical vapour deposition (CVD) using trimethylaluminium
(TMA) and NH<sub>3</sub> while low temperature CVD routes to high quality AlN
are scarce and suffer from high levels of carbon impurities in the film. We
report on an ALD-like CVD approach with time-resolved precursor supply where thermally
induced desorption of methyl groups from the AlN surface is enhanced by the
addition of an extra pulse, H<sub>2</sub>, N<sub>2</sub> or Ar between the TMA
and NH<sub>3</sub> pulses. The enhanced desorption allowed deposition of AlN films
with carbon content of 1 at. % at 480 °C. Kinetic-
and quantum chemical modelling suggest that the extra pulse between TMA and NH<sub>3</sub>
prevents re-adsorption of desorbing methyl groups terminating the AlN surface after
the TMA pulse. </p> | Polla Rouf; Pitsiri Sukkaew; Lars Ojamäe; Henrik Pedersen | Coating Materials; Materials Processing; Optical Materials; Thin Films; Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Organometallic Compounds; Reaction (Inorg.); Interfaces; Surface | CC BY 4.0 | CHEMRXIV | 2020-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b29469df471e3f43e7b/original/reduction-of-carbon-impurities-in-aluminium-nitride-from-time-resolved-chemical-vapour-deposition-using-trimethylaluminum.pdf |
672069ae1fb27ce124e63953 | 10.26434/chemrxiv-2024-3mw8k | Towards Hypervalent Iodine Macrocycle based Supramolecular Cages | Supramolecular cages, featuring well-defined molecular cavities, have gained interest in material chemistry owing to their adjustable shapes and sizes, selective host-guest chemistry, and dynamic bonding behavior. This study explored our attempts to synthesize supramolecular cages based on dynamic secondary bonding in hypervalent iodine systems. Hypervalent iodine-based cage precursors consisting of two iodine centers were linked together by di-yne pillars were successfully synthesized in multiple steps. Unfortunately, preliminary attempts to convert the cage precursor into a desired cage material have resulted in insoluble materials that are difficult to characterize. As an attempt to address solubility issues, an alternative alkoxy derived cage precursor was synthesized successfully in multiple steps. Upon attempted formation of the cage compound, these soluble chain-containing materials also suffered from low solubilities. The general design strategy and synthesis of the precursor materials is provided. | Krishna Pandey; Ain Uddin; Kyle Plunkett | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672069ae1fb27ce124e63953/original/towards-hypervalent-iodine-macrocycle-based-supramolecular-cages.pdf |
66d9b574cec5d6c1423643e4 | 10.26434/chemrxiv-2024-wjqsq | Konnektor: A framework for using graph theory to plan networks for free energy calculations | Alchemical free energy campaigns can be planned using graph theory by building up networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce Konnektor, an open-source Python package, for systematically planning, modifying, and analyzing free energy calculation networks. Konnektor is designed to aid in the drug discovery process by enabling users to easily setup free energy campaigns using complex graph manipulation methods. The package contains functions for network operations including concatenation of networks, deletion of transformations, and clustering of molecules, along with a framework for combining these tools with existing network generation algorithms to enable the development of more complex methods for network generation. A comparison of the various network layout features offered is carried out using toy datasets. Additionally, Konnektor contains visualization and analysis tools, making the investigation of network features much simpler. Besides the content of the package, the paper also offers application examples, demonstrating how Konnektor can be used and how the different networks perform from a graph theory perspective. Konnektor is freely available via GitHub at https://github.com/OpenFreeEnergy/konnektor under the permissive MIT License. | Benjamin Ries; Richard J Gowers; James RB Eastwood; Irfan Alibay; Hannah M Baumann; David WH Swenson; Michael M Henry; David Mobley | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d9b574cec5d6c1423643e4/original/konnektor-a-framework-for-using-graph-theory-to-plan-networks-for-free-energy-calculations.pdf |
65168f9e00659409121a74b4 | 10.26434/chemrxiv-2023-90n1q | Inhibitory Potential of Furanocoumarins Against Cyclin Dependent Kinase 4 Using Integrated Docking, MD and ONIOM Methods | Cyclin Dependent Kinase 4 (CDK4) is vital in the process of cell-cycle and serves as a G1 phase checkpoint in cell division. Selective antagonists of CDK4 which are in use as clinical chemotherapeutics cause various side-effects in patients. Furanocoumarins induce anti-cancerous effects in a range of human tumours. Therefore, targeting these compounds against CDK4 is anticipated to enhance therapeutic effectiveness. This work intended to explore CDK4 inhibitory potential of 50 furanocoumarin molecules, using a comprehensive approach that integrates the processes of docking, drug likeness, pharmacokinetic analysis, molecular dynamics simulations and ONIOM (Our own N-layered Integrated molecular Orbital and Molecular mechanics) methods. The top five best docked compounds obtained from docking studies were screened for subsequent analysis. The molecules displayed good pharmacokinetic properties and no toxicity. Epoxybergamottin, dihydroxybergamottin and notoperol were found to inhabit the ATP-binding zone of CDK4 with substantial stability and negative binding free energy forming hydrogen bonds with key catalytic residues of the protein. Notopterol exhibiting the highest binding energy was subjected to ONIOM calculations wherein the hydrogen bonding interactions were retained with significant negative interaction energy. Hence, through these series of computerised methods, notopterol was screened as a potent CDK4 inhibitor, and can act as a starting point in successive processes of drug design. | Srutishree Sarma; Dikshita Dowerah; Moumita Basumatary; Ambalika Phonglo; Ramesh Chandra Deka | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65168f9e00659409121a74b4/original/inhibitory-potential-of-furanocoumarins-against-cyclin-dependent-kinase-4-using-integrated-docking-md-and-oniom-methods.pdf |
66bb961520ac769e5f7c42fb | 10.26434/chemrxiv-2024-b583m | DNA Nanotechnology in Oligonucleotide Drug Delivery Systems: Prospects for Bio-nanorobots in Cancer Treatment | DNA-based nanomaterials have shown great potential in numerous applications, thanks to their unique properties including DNA's various molecular interactions, programmability, and versatility with biological modules. Meanwhile, the DNA origami platforms have shown promise in the creation of drug carriers. This technique has paved the way for the production of nanomachines with outstanding performance. Moreover, DNA’s encoding capability and its massive parallelism help us to manipulate it for DNA computation. The DNA nanotechnology method holds potential, particularly for oligonucleotide therapeutics that enable precision medicine for cancers.
Here, we explore the potential of DNA nanotechnology in this context, focusing on the DNA origami method and our efforts to streamline its production process. We then delve into studies demonstrating the application of DNA nanotechnology in delivering oligonucleotide drugs for tumor targeting. Following this, we examine DNA-based dynamic nanodevices that can be activated through molecular binding, environmental stimuli, and external field manipulation. Subsequently, we investigate the role of DNA computation in the production of logic gates, DNA circuits, data storage, and machine learning. Finally, we envision the future development of 'bio-nanorobots' based on DNA, enabled by advancements in DNA computation. We propose that combining DNA computation with DNA nanomachines could facilitate the realization of this vision, distinguishing it from conventional drug delivery systems.
| HANIYEH ABDOLLAHZADEH; Tonya Peeples; Mohammad Shahcheraghi | Biological and Medicinal Chemistry; Nanoscience; Chemical Engineering and Industrial Chemistry; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bb961520ac769e5f7c42fb/original/dna-nanotechnology-in-oligonucleotide-drug-delivery-systems-prospects-for-bio-nanorobots-in-cancer-treatment.pdf |
60c74fb60f50db7e51397450 | 10.26434/chemrxiv.12058026.v3 | REINVENT 2.0 – an AI Tool for De Novo Drug Design | With this application note we aim to offer the community a production-ready tool for de novo design. It can be effectively applied on drug discovery projects that are striving to resolve either exploration or exploitation problems while navigating the chemical space. By releasing the code we are aiming to facilitate the research on using generative methods on drug discovery problems and to promote the collaborative efforts in this area so that it can be used as an interaction point for future scientific collaborations. | Thomas Blaschke; Josep Arús-Pous; Hongming Chen; Christian Margreitter; Christian Tyrchan; Ola Engkvist; Kostas Papadopoulos; Atanas Patronov | Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fb60f50db7e51397450/original/reinvent-2-0-an-ai-tool-for-de-novo-drug-design.pdf |
65fb20d1e9ebbb4db9200312 | 10.26434/chemrxiv-2024-tm9x7-v2 | Unveiling the Multifaceted Nature of 4-(4-MethylphenylThio)benzophenone: A Combined DFT, NBO, and Spectroscopic Investigation of its Electronic Structure and Excited States | Benzophenone and its derivatives play a crucial role as UV (ultra-violet) lters and UV-ink photoinitiators. The photoinitiating properties of benzophenones are primarily linked to the degree of -conjugation and the extent of delocalization within the molecule. Understanding the intricate interplay of conjugation, delocalization, and substituent effects allows for the precise customization of benzophenone derivatives to meet speci c application requirements. Quantum mechanical calculations, employing the B3LYP/6-311++G(d, p) density functional theory (DFT), are utilized to compute chemical reactivity, stability, and photoinitiating properties for 4-4 (methylphenylthio) benzophenone. Various parameters such as proton af nity, ionization energy, electron af nity, reactivity, and spectroscopic properties are determined. The DFT-computed infrared spectra align well with available experimental results. The UV/Visible spectra obtained using TD-DFT reveal absorption toward higher wavelengths, attributed to the extended delocalization of -electrons. In an aqueous medium, the absorption spectra of 4-4 (methylphenylthio) benzophenone exhibit a high- intensity peak with a longer wavelength shift in the visible region compared to gas-phase spectra. This knowledge provides the foundation for designing novel initiators with tailored light absorption, excited state lifetimes, and reaction selectivities. Consequently, these advancements open doors to bene ts in UV-curing, photopolymerization, and other light-driven processes. | MANJEET BHATIA | Theoretical and Computational Chemistry; Polymer Science; Polymerization (Polymers); Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fb20d1e9ebbb4db9200312/original/unveiling-the-multifaceted-nature-of-4-4-methylphenyl-thio-benzophenone-a-combined-dft-nbo-and-spectroscopic-investigation-of-its-electronic-structure-and-excited-states.pdf |
645d03f1fb40f6b3ee6b04a7 | 10.26434/chemrxiv-2023-8k7pf | Interfacial behavior and partitioning of partially neutralized naphthenic acids: experiments versus HLD-NAC predictions. | Recent studies have shown that naphthenic acids (NAs) and sodium naphthenates dominate the interfacial activity of bitumen and the formation of bitumen emulsions. NAs are naturally occurring mixtures of carboxylic acids in bitumen, where their concentration can reach 4 wt%. Unlike other fatty acid-containing oils, alkaline neutralization of NAs in bitumen does not lead to ultralow interfacial tensions (IFT<0.1 mN/m). Ultralow IFTs are beneficial towards separating emulsions and could be beneficial in the separation of bitumen emulsions. Two possible reasons for the lack of ultralow IFTs with neutralized NAs were explored. One involved insufficient adsorption and neutralization of NA, and the other was the partition of naphthenic species in different phases. Dynamic IFT and pH studies suggest that adsorption and neutralization of NA proceed as predicted by the stoichiometry of the reaction. On the other hand, it was determined that a large fraction of the sodium naphthenates (NaNs) formed at the interface partitioned back into the oil. By forcing the participation of NaNs at the interface via their introduction through the aqueous phase, it is possible to create transient ultralow IFTs. The conditions (NA and NaN concentration and the salinity of the system) that led to ultralow IFTs were predicted by an HLD-NAC model previously validated for the neutralization of oleic acid. | Rafael Perez; Sujit Bhattacharya; Edgar Acosta | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Interfaces | CC BY NC 4.0 | CHEMRXIV | 2023-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645d03f1fb40f6b3ee6b04a7/original/interfacial-behavior-and-partitioning-of-partially-neutralized-naphthenic-acids-experiments-versus-hld-nac-predictions.pdf |
637f7c8d0146ef68cd044bfc | 10.26434/chemrxiv-2022-clnbj | Modular chemical construction of IgG-like mono- and bispecific synthetic antibodies (SynAbs) | In recent years there has been rising interest in the field of protein–protein conjugation, especially related to bispecific antibodies (bsAbs) and their therapeutic applications. These constructs contain two paratopes capable of binding two distinct epitopes on target molecules and are thus able to perform complex biological functions (mechanisms of action) not available to monospecific mAbs. Traditionally these bsAbs have been constructed through protein engineering, but recently chemical methods for their construction have started to (re-)emerge. While these have been shown to offer increased modularity, speed and for some methods, even the inherent capacity for further functionalization (e.g., with small molecule cargo), most of these approaches lacked the ability to include a fragment crystallizable (Fc) modality. The Fc component of IgG antibodies offers effector function and increased half-life. Here we report a first-in-class disulfide re-bridging and click-chemistry-based method for the generation of Fc-containing, IgG-like mono- and bispecific antibodies. These are in the FcZ (FabX)-FabY format, i.e., two distinct Fabs and an Fc, potentially all from different antibodies, attached in a homogeneous and covalent manner. We have dubbed these molecules synthetic antibodies (SynAbs). We have constructed a bispecific T cell-engager (BiTE) SynAb, FcCD20-(FabHER2)-FabCD3, and have confirmed that it exhibits the expected biological functions, including the ability to kill HER2+ target cells in a co-culture assay with T cells. | Fabien Thoreau; Peter A. Szijj; Michelle K. Greene; Léa N. C. Rochet; Ioanna A. Thanasi; Jaine K. Blayney; Antoine Maruani; James R. Baker; Christopher J. Scott; Vijay Chudasama | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2022-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637f7c8d0146ef68cd044bfc/original/modular-chemical-construction-of-ig-g-like-mono-and-bispecific-synthetic-antibodies-syn-abs.pdf |
65cbfaa4e9ebbb4db94cce18 | 10.26434/chemrxiv-2024-7vfzk | Encapsulation of functional solvents for improved thermal stability in CO2 capture applications | Herein we address the efficiency of CO2 sorption of ionic liquids (IL) with hydrogen bond donors (e.g., glycols) added as viscosity modifiers and the impact of encapsulating them to limit sorbent evaporation. Ethylene glycol, propylene glycol, 1,3-propanediol, and diethylene glycol were added to three different ILs: 1-ethyl-3-methylimidazolium 2-cyanopyrrolide ([EMIM][2-CNpyr]), 1-ethyl-3-methylimidazolium tetrafluoroborate ([EMIM][BF4]), and 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]). Incorporation of the glycols decreased viscosity on average 51% compared to bulk IL. After encapsulation of the liquid mixtures using a soft template approach, thermogravimetric analysis revealed reductions in volatility of 36 and 40 % on average compared to the unencapsulated liquid mixtures, based on isotherms at 25 and 55 °C, respectively. The encapsulated mixtures of [EMIM][2-CNpyr]:1,3-propanediol and [EMIM][2-CNpyr]:diethylene glycol exhibited the lowest volatility (0.0019 and 0.0002 mmol/h at 25 °C, respectively) and were further evaluated as CO2 absorption/desorption materials. Based on capacity determined from breakthrough measurements, [EMIM][2-CNpyr]:1,3-propanediol had lower transport limited absorption rate for CO2 sorption compared to [EMIM][2-CNpyr]:diethylene glycol with 0.08 and 0.03 mol CO2/kg sorbent, respectively; however, [EMIM][2-CNpyr]:diethylene glycol capsules exhibited higher absorptions capacity at ~500 ppm CO2 (0.66 compared to 0.47 mol CO2/kg sorbent for [EMIM][2-CNpyr]:1,3-propanediol). These results show that multiple glycols can be used to reduce IL viscosity while increasing physisorption sites for CO2 sorption and encapsulation can be utilized to mitigate evaporation of volatile viscosity modifiers. | Cameron Taylor; Aidan Klemm; Luma Al-Mohbobi; Braden Bradford; Burcu Gurkan; Emily Pentzer | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cbfaa4e9ebbb4db94cce18/original/encapsulation-of-functional-solvents-for-improved-thermal-stability-in-co2-capture-applications.pdf |
62eb1fe9adfd357091262a22 | 10.26434/chemrxiv-2022-tcm9v-v3 | Assessment of the generalization abilities of machine-learning scoring functions for structure-based virtual screening | In structure-based virtual screening (SBVS), it is critical that scoring functions capture protein-ligand atomic interactions. By focusing on the local domains of ligand binding pockets, a standardized pocket Pfam-based clustering (Pfam-cluster) approach was developed to assess the cross-target generalization ability of machine-learning scoring functions (MLSFs). Subsequently, 11 typical MLSFs were evaluated using random cross-validation (Random-CV), protein sequence similarity-based cross-validation (Seq-CV), and pocket Pfam-based cross-validation (Pfam-CV) methods. Surprisingly, all of the tested models showed decreased performances from Random-CV to Seq-CV to Pfam-CV experiments, not showing satisfactory generalization capacity. Our interpretable analysis suggested that the predictions on novel targets by MLSFs were dependent on buried solvent-accessible surface area (SASA)-related features of complex structures, with larger predicted binding affinities on complexes owning larger protein-ligand interfaces. By combining buried SASA-related features with target-specific patterns that were only shared among structurally similar compounds in the same cluster, random forest (RF)-Score attained a good performance in Random-CV test. Based on these findings, we strongly advise to assess the generalization ability of MLSFs with Pfam-cluster approach and to be cautious with the features learned by MLSFs. | Hui Zhu; Jincai Yang; Niu Huang | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eb1fe9adfd357091262a22/original/assessment-of-the-generalization-abilities-of-machine-learning-scoring-functions-for-structure-based-virtual-screening.pdf |
639b970481e4ba5ef54ef0d0 | 10.26434/chemrxiv-2022-r66h5 | Tuning Material Properties of Alkaline Anion Exchange Membranes Through Crosslinking: A Review of Synthetic Strategies and Property Relationships | Alkaline anion exchange membranes (AAEMs) are an enabling component for next generation electrochemical applications, including alkaline fuel cells, alkaline water electrolyzers, CO2 electrochemical reduction, and flow batteries. While commercial systems, notably fuel cells, have traditionally relied on proton-exchange membranes (PEMs), hydroxide-ion conducting AAEMs hold promise as a way to reduce cost-per-device by enabling the use of less expensive non-platinum group electrodes and cheaper cell components. AAEMs have undergone significant material development over the past two decades resulting in substantial improvements in hydroxide conductivity, alkaline stability, and dimensional stability. Despite these advances, challenges still remain in the areas of durability, water management, high temperature performance, and selectivity. In this review we discuss crosslinking as a synthesis tool for tuning various AAEM material properties, such as water uptake, conductivity, alkaline stability, and selectivity, and we describe synthetic strategies for incorporating crosslinks during membrane fabrication. | Auston L. Clemens; Buddhinie S. Jayathilake; John J. Karnes; Johanna J. Schwartz; Sarah E. Baker; Eric B. Duoss; James S. Oakdale | Materials Science; Polymer Science; Energy; Polyelectrolytes - Polymers; Energy Storage; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b970481e4ba5ef54ef0d0/original/tuning-material-properties-of-alkaline-anion-exchange-membranes-through-crosslinking-a-review-of-synthetic-strategies-and-property-relationships.pdf |
61debad0a1605092849e6ea1 | 10.26434/chemrxiv-2022-kb1s1 | Investigating educators’ perspectives towards systems thinking in chemistry education from international contexts | Systems thinking in chemistry education (STICE) has been proposed as an approach that could better equip students with abilities to connect their chemistry knowledge with other disciplines, with the skills needed to tackle complex global issues. However, educational change in chemistry is a complex effort that involves many interconnected factors that enable or hinder chemistry educators’ adoption of new pedagogical approaches. Using an adapted version of the Teacher-Centered Systemic Reform (TCSR) model, we investigated factors that connect with chemistry educators’ willingness and ability to implement a STICE approach in their courses. We surveyed a group of 56 secondary and post-secondary chemistry educators from ten different countries, to capture chemistry educators’ perspectives towards a STICE approach. Through thematic analysis of responses, we found that educators’ willingness and ability to implement STICE is influenced by their knowledge, beliefs, experiences, contextual and personal factors. We discuss specific aspects of the reform model that experts and administrators can address to reduce barriers to implement and engage with STICE. We also highlight future chemistry education research that is needed to explore specific aspects of educators’ perspectives and STICE more broadly. | Alisha R. Szozda; Kathryn Bruyere; Hayley Lee; Peter G. Mahaffy; Alison B. Flynn | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61debad0a1605092849e6ea1/original/investigating-educators-perspectives-towards-systems-thinking-in-chemistry-education-from-international-contexts.pdf |
6512166cb927619fe7d1023c | 10.26434/chemrxiv-2023-8n737 | Leveraging Multitask Learning to Improve the Transferability of Machine Learned Force Fields | Transferable neural network potentials have shown great promise as an avenue to increase the accuracy and applicability of existing atomistic force fields for organic molecules and inorganic materials. Training sets used to develop transferable potentials are very large, typically millions of examples, and as such, are restricted to relatively inexpensive levels of ab initio theory, such as density functional theory in a double- or triple-zeta quality basis set, which are subject to significant errors. It has been previously demonstrated using transfer learning that a model trained on a large dataset of such inexpensive calculations can be re-trained to reproduce energies of a higher level of theory using a much smaller dataset. Here, we show that more generally, one can use hard parameter sharing to successfully train to multiple levels of theory simultaneously. We demonstrate that simultaneously training to two levels of theory is an alternative to freezing layers in a neural network and re-training. Further, we show that training multiple levels of theory can improve the overall performance of all predictions and that one can transfer knowledge about a chemical domain present in only one of the datasets to all predicted levels of theory. This methodology is one way in which multiple, incompatible datasets can be combined to train a transferable model, increasing the accuracy and domain of applicability of machine learning force fields. | Leif Jacobson; James Stevenson; Farhad Ramezanghorbani; Steven Dajnowicz; Karl Leswing | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2023-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6512166cb927619fe7d1023c/original/leveraging-multitask-learning-to-improve-the-transferability-of-machine-learned-force-fields.pdf |
66d200c4f3f4b05290a57edb | 10.26434/chemrxiv-2024-vrv83 | External Photosensitizer Free Function-Integrated Cu(II)-Complex Catalyzed Photo Driven CO2 Reduction | Developing a function-integrated catalyst from earth-abundant elements, capable of efficient light harvesting and electron transfer, is crucial for enhancing the efficacy of CO2 transformation, a critical step in environmental cleanup and advancing clean energy prospects. Traditional approaches relying on external photosensitizers, comprising of 4d/5d metal complexes, often face challenges in intermolecular electron transfer, and attachment of photosensitizing arms to the catalyst increases dependency on intramolecular electron transfer kinetics, underscoring the need for a more integrated solution. We report a new Cu(II) complex, K[CuNDPA] (1[K(18-crown-6)]), bearing a dipyrrin amide-based trianionic tetradentate ligand, NDPA (H3L), which is capable of harnessing light energy, despite having a paramagnetic Cu(II) center, without any external photosensitizer and photocatalytically reducing CO2 to CO in acetonitrile: water (19:1 v/v) with a TON as high as 1132, a TOF of 566 h-1 and a selectivity of 99%. This complex also shows hemilability in the presence of water, which not only plays a role in a proton relay mechanism but also helps stabilize a crucial Cu(I)-NDPA intermediate. The hemilability was justified by the formation of N3O (2) and N2O2 (3) coordinated congeners of the N4 bound complex 1. The overall mechanism was further investigated via spectroscopic techniques like EPR, UV-vis, and Spectroelectrochemistry, culminating in the justification of a single electron-reduced Cu(I)NDPA species as a proposed intermediate. In the next step, the binding of CO2 to Cu(I) complex and subsequent electron transfer to form Cu(II)-CO2•‾ was indirectly probed by a radical trapping experiment via the addition of p-methoxy-2,6-ditertbutylphenol that led to the formation of a phenoxyl radical. This work opens new strategies for designing earth-abundant robust molecular catalysts that can function as photocatalysts without the aid of any external photosensitizers. | Soumadip Das; Aritra Roy; Navonil Chakrabarti; Narottam Mukhopadhyay; Aniruddha Sarkar; Sayam Sen Gupta | Inorganic Chemistry; Catalysis; Energy; Coordination Chemistry (Inorg.); Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d200c4f3f4b05290a57edb/original/external-photosensitizer-free-function-integrated-cu-ii-complex-catalyzed-photo-driven-co2-reduction.pdf |
60c74294bdbb896970a384fe | 10.26434/chemrxiv.8312450.v1 | Irᴵᴵᴵ as a Strategy for Preorganization in H-Bonded Motifs | Here we present the synthesis and characterisation of four hydrogen bonded systems based on thiourea derivatives. These motifs are considered to be stable and desirable for supramolecular hydrogen-bonded functional materials. Interpretation of the structural design of thiourea based ligand and its incorporation into metal complexes can contribute to the understanding of preorganised self-assembly and open new pathways in design of novel soft materials. This work contributes to the unexplored library of hydrogen bonded metal complexes based on iridium. Further we examined the photoluminescence of the system of general formula [Ir(C^N)<sub>2</sub>(N^S)] and the effect of hydrogen bonding on the emission properties when combined with different <i>n</i>-heteroacenes. | Barbora Balonova; Helena J. Shepherd; Christopher Serpell; Barry Blight | Bonding; Ligands (Inorg.); Supramolecular Chemistry (Inorg.); Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74294bdbb896970a384fe/original/ir-iii-as-a-strategy-for-preorganization-in-h-bonded-motifs.pdf |
659bbb7be9ebbb4db9ada167 | 10.26434/chemrxiv-2024-qdtpf | Direct Laser-Printing of Molecularly-Dispersed Strongly-Anchored Sulfur-Graphene Layers as High-Performance Cathodes for Polysulfide Shuttle Effect-Inhibited Lithium-Sulfur Batteries | Sulfur has recently emerged as a promising cathode material for lithium-ion batteries, offering high theoretical capacity and low cost. Its abundant availability and environmentally friendly nature make it an attractive alternative to conventional cathode materials. However, challenges such as sulfur's intrinsically low electrical conductivity and rapid degradation during cycling still need to be overcome for its widespread adoption in commercial batteries. This study presents an innovative, scalable and straightforward strategy to overcome these challenges of sulfur cathodes in lithium battery applications. Here, we present a novel method, using low-power laser irradiation to fabricate three-dimensional highly micro-porous molecularly dispersed and strongly anchored sulfur-graphene composite electrodes. By subjecting sulfur-embedded carbon precursors to laser irradiation, a well-structured graphene composite is formed, while molecularly-entrapping the sulfur moieties within its framework. This 3D porous architecture provides high surface area for improved electrolyte wetting, efficient ion transport, and effectively accommodates volume changes during cycling while strongly entrapping the active sulfur moieties and remarkably inhibiting the occurrence of the detrimental polysulfide shuttle effect. The resulting sulfur-graphene cathodes exhibit exceptional electrochemical properties. They demonstrate remarkable cyclic stability, sustaining over 1500 cycles with impressive capacity retention of >70% at fast cycling rates, and registering over 1000 mAh g-1 at lower rates with >70% retention over 400 cycles. Furthermore, high sulfur loading ratios, compatible to real world battery applications, are readily attainable. The simplicity and versatility of this laser-based writing single-step approach open various new avenues for the scalable and cost-effective production of high-performance lithium-ion batteries. This development brings us closer to realizing efficient energy storage solutions for various applications, from portable electronics to electric vehicles and grid storage systems. | Avinash Kothuru; Adam Cohen; Gil Daffan; Fernando Patolsky | Nanoscience; Energy; Nanostructured Materials - Nanoscience; Energy Storage; Power; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659bbb7be9ebbb4db9ada167/original/direct-laser-printing-of-molecularly-dispersed-strongly-anchored-sulfur-graphene-layers-as-high-performance-cathodes-for-polysulfide-shuttle-effect-inhibited-lithium-sulfur-batteries.pdf |
64c9f6e19ed5166e93e4db80 | 10.26434/chemrxiv-2023-rgtbw-v2 | Solid polymer electrolytes under nanoscale confinement: a molecular dynamics simulation | Solid polymer electrolytes (SPEs), though widely regarded as materials that can enable next-generation lithium metal battery with improved safety, extended stability, and high capacity, suffer from problems of low ionic conductivity. Myriads of strategies have been proposed to improve the performance of polymer electrolytes, but with little success, and the state-of-the-art polymer electrolytes are still based on LiTFSI dissolved in PEO, which have been proposed for more than 40 years. New design concepts are indispensable to improving the performance of SPEs. Using molecular dynamics simulation, we examine SPEs under nanoscale confinement, which has been demonstrated to accelerate the diffusion of neutral molecules such as water. While ion diffusion indeed shows an acceleration by more than two orders when the channel diameter decreases from 15~nm to 2~nm, the ionic conductivity does not show a paralleling increase. Instead, as the nanochannel diameter decreases, ionic conductivity shows a non-monotonic variation, with an optimal value above yet on the same order as its bulk counterparts. The reason for this trend is due to enhanced ion association with decreasing channel size, which leaves a smaller amount of effective charge carriers. This effect competes with accelerated ion diffusion, leading to the non-monotonicity in ion conductivity. We further show that this trend also appears in two-dimensional nanoslit pores. These findings not only manifest the intricacies of ionic transport behavior but also provide new concepts and necessary implications for designing composite SPEs. | Xiupeng Chen; Xian Kong | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Materials; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c9f6e19ed5166e93e4db80/original/solid-polymer-electrolytes-under-nanoscale-confinement-a-molecular-dynamics-simulation.pdf |
65f18fcae9ebbb4db99e37a3 | 10.26434/chemrxiv-2024-pt1ln | C-Terminal Peptide Modification: Merging the Passerini Reaction with Chemo-Enzymatic Synthesis | Over the past few decades, peptide/protein synthesis and bio-conjugation has gained increasing interest in the research community owing to the high demand for strategies that provide modified protein adducts in a site-selective fashion. Herein, we report a novel approach that combines the Passerini multicomponent reaction and chemo-enzymatic peptide synthesis (CEPS) for the selective bio-conjugation of peptide C-termini. The Passerini utilizes aqueous acidic buffer conditions to establish chemoselectivity for the carboxylic acids, while the subsequent enzymatic ligation selectively targets the formed C-terminal substrates. We functionalized a diverse set of pentapeptides utilizing numerous isocyanide and car-bonyl compounds and successfully performed subsequent ligations. This combined multicomponent chemoenzymatic method therefore represents a valuable novel technology for future research into site-selective C-terminal modification of peptides/proteins. | Jay Hanssens; Sam van Dun; Tessa H.G. Lokate; Vincent R.A.M. Reinartz; Leendert J. van den Bos; Romano V.A. Orrù; Jordy M. Saya | Organic Chemistry; Catalysis; Bioorganic Chemistry; Organic Synthesis and Reactions; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f18fcae9ebbb4db99e37a3/original/c-terminal-peptide-modification-merging-the-passerini-reaction-with-chemo-enzymatic-synthesis.pdf |
60c744fbbb8c1aba7f3da5e7 | 10.26434/chemrxiv.9938939.v1 | Modelling the Hydrolysis of Iron-Sulfur Clusters | <div>Iron-sulfur (FeS) clusters are essential metal cofactors involved in a wide variety of biological functions. Their catalytic efficiency, biosynthesis and regulation depend on FeS stability in aqueous solution. Here, molecular modelling is used to investigate the hydrolysis of an oxidized (ferric) mononuclear FeS cluster by bare dissociation and water substitution mechanisms in neutral and acidic solution. First, approximate electronic structure descriptions of FeS reactions by density functional theory are validated against high-level wave-function CCSD(T) calculations. Solvation contributions are evaluated by an all-atom model with hybrid quantum chemical/molecular mechanical (QM/MM) potentials and enhanced sampling molecular dynamics simulations. The free energy profile obtained for FeS cluster hydrolysis indicates the hybrid functional M06 together with an implicit solvent correction capture the most important aspects of FeS cluster reactivity in aqueous solution. Then, 20 reaction channels leading to two consecutive Fe--S bond ruptures were explored with this calibrated model. For all protonation states, nucleophilic substitution with concerted bond breaking and forming to iron is the preferred mechanism, both kinetic and thermodynamically. In neutral solution, proton transfer from water to the sulfur leaving group is also concerted. Dissociative reactions show higher barriers and will not be relevant for FeS reactivity when exposed to solvent. These hydrolysis mechanisms may help to explain the stability and catalytic mechanisms of FeS clusters of multiple sizes and proteins</div><div><br /></div> | Murilo H. Teixeira; Felipe Curtolo; Sofia R. G. Camilo; Martin J. Field; Peng Zheng; Hongbin Li; Guilherme M. Arantes | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fbbb8c1aba7f3da5e7/original/modelling-the-hydrolysis-of-iron-sulfur-clusters.pdf |
669f6492c9c6a5c07a9a938b | 10.26434/chemrxiv-2024-94zjd | Chiral N-Hydroxyalkyl Pyrid-2-ylidenes: a new class of ligand for Copper-Catalyzed Asymmetric Allylic Alkylation | A new class of chiral N-Heterocyclic Carbenes derived from pyridine, namely N-hydroxyalkyl pyrid-2-ylidenes, was developed. Capitalizing the exceptional steric and electronic features of pyrid-2-ylidene core with the presence of the chiral hydroxyalkyl-chelating arm on the nitrogen-atom, these ligands demonstrated high performances in copper-catalyzed asymmetric allylic alkylation of dialkylzincs to various allylic or dienic phosphates with excellent gamma-selectivity (>98%) and enantioselectivity (up to 95% ee). Importantly, the catalyst loading can be decreased below to 0.5 mol% without any loss of catalyst efficiency, thus outperforming N-hydroxyalkyl imidazoline-2-ylidene congeners. Moreover, thanks to the versatile post-transformation of resulting enantioenriched skipped 1,4-dienes, various relevant building blocks were synthesized, notably a key intermediate in the total synthesis of (+) Phorbasin C. Furthermore, by involving a transient oxazolidine, which acts as a masked carbene before the insertion of the metal center, a well-defined but air-sensitive N-hydroxyalkyl pyrid-2-ylidene copper(I) chloride complex was isolated. Deuteration experiments and computational studies provided valuable insights about the formation of the oxazolidine and the corresponding copper complex. | Dylan Bouëtard; Ziyun Zhang; Thomas Vives; Marie Cordier; Luigi Cavallo; Lucie Jarrige; Laura Falivene; Marc MAUDUIT | Organic Chemistry; Catalysis; Organometallic Chemistry; Stereochemistry; Homogeneous Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669f6492c9c6a5c07a9a938b/original/chiral-n-hydroxyalkyl-pyrid-2-ylidenes-a-new-class-of-ligand-for-copper-catalyzed-asymmetric-allylic-alkylation.pdf |
60c74fa0ee301c5675c7a720 | 10.26434/chemrxiv.12673100.v2 | Spin-Resolved Charge Displacement Analysis as Intuitive Tool for the Evaluation of cPCET and HAT Scenarios | We introduce here the spin-resolved version of the charge displacement function, which is applied to two competing pathways of proton-coupled electron transfer in oxidation catalysis (hydrogen-atom transfer, concerted proton-coupled electron transfer). The difference in charge displacement between the two mechanisms is directly observable and can be translated to electron flow using this new analysis tool. | Lorenzo D'Amore; Leonardo Belpassi; Johannes
E. M. N. Klein; Marcel Swart | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fa0ee301c5675c7a720/original/spin-resolved-charge-displacement-analysis-as-intuitive-tool-for-the-evaluation-of-c-pcet-and-hat-scenarios.pdf |
64787ba7e64f843f41234ada | 10.26434/chemrxiv-2023-14c0t | Effects of Surfactant Adsorption on the Wettability and Friction of Biomimetic Surfaces | The properties of solid-liquid interfaces can be markedly altered by surfactant adsorption. Here, we use molecular dynamics simulations to study the adsorption of ionic surfactants at the interface between water and heterogeneous solid surfaces with randomly arranged hydrophilic and hydrophobic regions, which mimic the surface properties of human hair. We use the coarse-grained MARTINI model to describe both the hair surfaces and surfactant solutions. We consider negatively-charged virgin and bleached hair surface models with different grafting densities of neutral octadecyl and anionic sulfonate groups. The adsorption of cationic cetrimonium bromide (CTAB) and anionic sodium dodecyl sulfate (SDS) surfactants from water are studied above the critical micelle concentration. The simulated adsorption isotherms suggest that cationic surfactants adsorb to the surfaces via a two-stage process, initially forming monolayers and then bilayers at high concentrations, which is consistent with previous experiments. Anionic surfactants weakly adsorb via hydrophobic interactions, forming only monolayers on both virgin and medium bleached hair surfaces. We also conduct non-equilibrium molecular dynamics simulations, which show that applying cationic surfactant solutions to bleached hair successfully restores the low friction seen with virgin hair. Friction is controlled by the combined surface coverage of the grafted lipids and the adsorbed CTAB molecules. Treated surfaces containing monolayers and bilayers both show similar friction, since the latter are easily removed by compression and shear. Further wetting MD simulations show that bleached hair treated with CTAB increases the hydrophobicity to similar levels seen for virgin hair. Treated surfaces containing CTAB monolayers with the tailgroups pointing predominantly away from the surface are more hyrophobic than bilayers due to the electrostatic interactions between water molecules and the exposed cationic headgroups. | Erik Weiand; Francisco Rodriguez-Ropero; Yuri Roiter; Peter H. König; Stefano Angioletti-Uberti; Daniele Dini; James P. Ewen | Physical Chemistry; Materials Science; Fibers; Surfactants; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64787ba7e64f843f41234ada/original/effects-of-surfactant-adsorption-on-the-wettability-and-friction-of-biomimetic-surfaces.pdf |
6505e21eb338ec988a96fc96 | 10.26434/chemrxiv-2023-qcjkh | Calculating Pairwise Similarity of Polymer Ensembles via Earth Mover’s Distance | Synthetic polymers, in contrast to small molecules and deterministic biomacromolecules, are typically ensembles comprised of polymer chains with varying numbers, lengths, sequences, chemistry, and topologies. While numerous approaches exist for measuring pairwise similarity among small molecules and sequence-defined biomacromolecules, accurately determining the pairwise similarity between two polymer ensembles remains challenging. This work proposes the earth mover’s distance (EMD) metric to calculate the pairwise similarity score between two polymer ensembles. EMD offers a greater resolution of chemical differences between polymer ensembles than the averaging method and provides a quantitative numeric value representing the pairwise similarity between polymer ensembles in alignment with chemical intuition. The EMD approach for assessing polymer similarity enhances the development of accurate chemical search algorithms within polymer databases and can improve machine learning techniques for polymer design, optimization, and property prediction. | Jiale Shi; Dylan Walsh; Weizhong Zou; Nathan Rebello; Michael Deagen; Katharina Fransen; Xian Gao; Bradley Olsen; Debra Audus | Theoretical and Computational Chemistry; Polymer Science; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6505e21eb338ec988a96fc96/original/calculating-pairwise-similarity-of-polymer-ensembles-via-earth-mover-s-distance.pdf |
62b08ef01278ae56efe853dc | 10.26434/chemrxiv-2022-2qzzj | Orthogonal enzyme-driven timers for DNA strand displacement reactions | Here we demonstrate a strategy to rationally program a delayed onset of toehold-mediated DNA strand-displacement reactions. The approach is based on blocker strands that efficiently inhibit the strand displacement by binding to the toehold domain of the target DNA. Specific enzymatic degradation of the blocker strand subsequently enables the strand displacement reaction. The kinetics of the blocker enzymatic degradation thus controls the time at which the strand displacement reaction starts. By varying the concentration of the blocker strand and the concentration of the enzyme we show that we can finely tune and modulate the delayed onset of the strand displacement reaction. Additionally, we show that the strategy is versatile and can be orthogonally controlled by different enzymes each specifically targeting a different blocker strand. We designed and established three different delayed strand displacement reactions using RNase H and the two DNA repair enzymes Fpg and UDG and corresponding blockers. The achieved temporal delay can be programmed with high flexibility without undesired leak and can be conveniently predicted using kinetic modeling. Finally, we show that the delayed strand displacement reactions can be coupled to downstream processes and used to control the onset of ligand release from a DNA nanodevice as well as protein inhibition by a DNA aptamer. | Juliette Bucci; Patrick Irmisch; Erica Del Grosso; Ralf Seidel; Francesco Ricci | Physical Chemistry; Analytical Chemistry; Nanoscience; Nanodevices; Self-Assembly; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b08ef01278ae56efe853dc/original/orthogonal-enzyme-driven-timers-for-dna-strand-displacement-reactions.pdf |
66daac6251558a15ef35021e | 10.26434/chemrxiv-2024-p94mm-v2 | Fluorescent Antimicrobial Peptides Based on Nile Red: Effect of Conjugation Site and Chemistry on Wash-free Staining of Bacteria | Fluorescent probes for bacterial detection can be obtained by conjugating antimicrobial peptides with fluorescent dyes. However, little is known about the effect of the conjugation site and linker chemistry on staining efficiency. We synthesized three conjugates of the antimicrobial peptide ubiquicidin with the environmentally sensitive fluorophore Nile Red that differed by the attachment site and the chemical composition of the linker. We showed that incorporating fluorophore as a minimalistic non-natural amino acid resulted in a superior probe compared with the typically used bioconjugation approaches. The new peptide-based probe named UNR-1 displayed red fluorescence and enabled robust wash-free staining of Gram-positive and Gram-negative bacteria. The probe exhibited selectivity over mammalian cells and enabled rapid fluorescence detection of bacteria by fluorescence microscopy and flow cytometry in an add-and-read format. Our results may foster the development of next-generation fluorescent AMPs for clinical laboratory diagnostics and medical imaging. | Lucille Weiss; Antoine Mirloup; Léa Blondé; Hanna Manko; Jean Peluso; Dominique Bonnet; Dmytro Dziuba; Julie Karpenko | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66daac6251558a15ef35021e/original/fluorescent-antimicrobial-peptides-based-on-nile-red-effect-of-conjugation-site-and-chemistry-on-wash-free-staining-of-bacteria.pdf |
61c6f8e1f52bc4a3c2cd00ec | 10.26434/chemrxiv-2021-pz7kj | Benzene and NOx photocatalytic assisted removal using indoor lighting conditions | Modern life-style is creating an indoor generation: human beings spend approximately 90% of their time indoors, almost 70% of which is at home – this trend is now exacerbated by the lockdowns/restrictions imposed due to the COVID-19 pandemic. That large amount of time spent indoors may have negative consequences on health and well-being. Indeed, poor indoor air quality is linked to a condition known as sick building syndrome. Therefore, breathing the freshest air possible it is of outmost importance. Still, due to reduced ventilation rates, indoor air quality can be considerably worse than outdoor. HVAC, air filtration systems and a well-ventilated space are a partial answer. However, these approaches involve only a physical removal. Photocatalytic mineralisation of pollutants into non-hazardous, or at least less dangerous compounds, is a more viable solution for their removal. Titanium dioxide, the archetype photocatalytic material, needs UVA light to be “activated”. However, modern household light emitting diode lamps irradiate only in the visible region of the solar spectrum. In this short-communication, we show that the surface of titanium dioxide nanoparticles modified with copper oxide(s) and graphene shows promise as a viable way to remove gaseous pollutants (benzene and NOx) by using a common light emitting diode bulb, mimicking real indoor lighting conditions. Titanium dioxide, modified with 1 mol% CuxO and 1 wt% graphene, proved to have a stable photocatalytic degradation rate, three times higher than that of unmodified titania. Materials produced in this research work are thus strong candidates for offering a safer indoor environment. | David Maria Tobaldi; Dana Dvoranová; Luc Lajaunie; Kristina Czikhardtová; Bruno Figueiredo; Maria Paula Seabra; José Juan Calvino; João António Labrincha | Materials Science; Catalysis; Energy; Carbon-based Materials; Photocatalysis; Energy Storage | CC BY 4.0 | CHEMRXIV | 2021-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c6f8e1f52bc4a3c2cd00ec/original/benzene-and-n-ox-photocatalytic-assisted-removal-using-indoor-lighting-conditions.pdf |
66346ea091aefa6ce10615ad | 10.26434/chemrxiv-2024-8w0sg | Efficient Energy Conversion using Tri-nuclear M-Ru(II)-M[M= Pt(II), Re(I)] Catalysts | The tri-nuclear Pt(II)-Ru(II)-Pt(II)(RuPt2) and Re(I)-Ru(II)-Re(II)(RuRe2) complexes, synthesized from mononuclear Ru(II) complex were explored for efficient energy conversion through water splitting and CO2 reduction. The catalysts show excellent activity, serving as promising platforms for sustainable energy applications. The study focuses on designing, stepwise synthesis of the catalysts with insights into the multiple components’ contribution to enhanced catalytic performance. Photophysical and electrochemical analyses highlight the role of the complexes as photocatalysts, where the Ru(II)-polypyridyl unit acts as photosensitizer and the Pt(II)/ Re(I)-polypyridyl units as catalytic sites. Synergistic effects among the components lead to stability, improved performance and emphasizes the significance of multi-nuclear M-Ru(II)-M[M= Pt(II), Re(I)] catalysts in promoting cleaner and more sustainable energy sources. | Shrabani Khan; Sanwayee Biswas; Bishnu Das; Sakira Tabassum Borah; Deep Lahan; Parna Gupta | Inorganic Chemistry; Catalysis; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66346ea091aefa6ce10615ad/original/efficient-energy-conversion-using-tri-nuclear-m-ru-ii-m-m-pt-ii-re-i-catalysts.pdf |
627eb37459f0d6fc588fbc2a | 10.26434/chemrxiv-2022-3f333 | Direct Photochemical Route for Amine- and Catalyst-Free Synthesis of Azoxybenzene and Functional Azoxy Derivatives via Accessible Nitroarene Homocoupling under Ambient Conditions | We report on a direct photochemical method for the one-pot, catalyst- and additive-free synthesis of azoxybenzene and substituted azoxy derivatives from nitrobenzene building blocks. This reaction is conducted at room temperature and under air, and can be applied to substrates with a wide range of substituents. Yields of products derived from para- and meta-substituted nitrobenzenes are typically good, while sterically encumbered ortho-substituted substrates are not as fruitful. Photochemical Wallach rearrangement of generated azoxybenzenes to ortho-hydroxyazoxybenzenes was observed in some cases, most markedly in selected ortho-halogenated nitrobenzenes. Overall, this method provides an efficient, green pathway to highly value-added azoxybenzene products. | Ali Yaghoubian; Gregory Hodgson; Marc Adler; Stefania Impellizzeri | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627eb37459f0d6fc588fbc2a/original/direct-photochemical-route-for-amine-and-catalyst-free-synthesis-of-azoxybenzene-and-functional-azoxy-derivatives-via-accessible-nitroarene-homocoupling-under-ambient-conditions.pdf |
66ec1d3d12ff75c3a1d29e52 | 10.26434/chemrxiv-2024-qbjg2-v3 | Optimization of Cosolvent Enhanced Lignocellulosic Fractionation for Isolating Switchgrass Lignin with Distinct Structural Features Using Response Surface Methodology | Pretreatment and fractionation technologies have been used to separate and isolate biomass polymers for conversion into fuels, chemicals, and other products. A great deal of work has focused on dialing in reaction conditions (e.g., time, temperature, acid concentration, etc.) that are amenable to isolating an uncondensed lignin product that could be converted into high value aromatic platform molecules. Pretreatment severity emerged as a term that combines time, temperature, and acid concentration into a single value that can be used to compare various pretreatment technologies. However, combining the effects of these conditions into a single term, while convenient, confounds the effects that these conditions have on lignin quality, both individually and when combined with each other. Moreover, pretreatment and fractionation reactors do not have a severity “knob,” and several different sets of conditions could mathematically achieve the same severity but have different effects on the resulting lignin product slate. In this study, we set out to model the effects of time (10-30 min), temperature (140-180 °C), and acid concentration (0.025-0.1 M H2SO4) on lignin yield (up to quantitative), molecular weight (Mw = 700-2000 g/mol), and hydroxyl group content (3.55-6.06 mmol OH/g) using the co-solvent enhanced lignocellulosic fractionation (CELF) process on switchgrass. Our results show that lignin yield is most sensitive to acid concentration, with an additional 4.96% yield per 10 mM of acid. In addition, molecular weight is sensitive to acid concentration and temperature, with a decrease of 77.9 g/mol per 10 mM of acid and a decrease of 19.3 g/mol per °C. Moreover, total hydroxyl group content decreases at a rate of 89 μmol total OH per g lignin per min at short time (t = 12 min, T = 160 °C) and is increases at a rate of 125 μmol total OH per g lignin per min at long time (t = 28 min, T = 160 °C). Finally, our results demonstrate that residence time does not have a statistically significant effect on yield or molecular weight within the studied ranges, which could have implications for continuous and flow-through processes, where short residence times could lead to substantial cost savings. Overall, these results demonstrate that practitioners can design a process that maximizes one or more of industrially relevant lignin properties by exerting careful control of fractionation conditions, which could ultimately lead to greater utilization of lignin for fuels, chemicals, and other products. | James Godwin; Hojae Yi; Kendhl Seabright; David Harper; Stephen Chmely | Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ec1d3d12ff75c3a1d29e52/original/optimization-of-cosolvent-enhanced-lignocellulosic-fractionation-for-isolating-switchgrass-lignin-with-distinct-structural-features-using-response-surface-methodology.pdf |
649bfca39ea64cc1671b7ba9 | 10.26434/chemrxiv-2023-rjcz6 | Critical Step in the HCl Oxidation Reaction over Single-Crystalline CeO₂₋ₓ(111): Peroxo-Induced Site Change of Strongly Adsorbed Surface Chlorine | The catalytic oxidation of HCl by molecular oxygen (Deacon process) over ceria allows the recovery of molecular chlorine from omnipresent HCl waste produced in various industrial processes. Previous density functional theory (DFT) model-calculations1 proposed, that the most critical reaction step in this process is the displacement of tightly bound chlorine at a vacant oxygen position on the CeO₂(111) surface Cl(vac) towards a less strongly bound cerium on-top Cl(top) position. This step is highly endothermic by more than 2 eV. On the basis of a dedicated model study, namely the re-oxidation of a chlorinated single crystalline Cl(vac)-CeO₂₋ₓ(111)-(√3 × √3)R30° surface structure, we provide unique spectroscopic data (high resolution core level spectroscopy (HRCLS) and X-ray adsorption near edge structure (XANES)) for this oxygen-induced de-chlorination process. Combined with theoretical evidence from DFT calculations, the Cl(vac) → Cl(top) displacement reaction is predicted to be induced by a surface-adsorbed peroxo species (O₂²⁻), making the displacement step concerted and exothermic by 0.6 eV with an activation barrier of only 1.04 eV. The peroxo species is shown to be important for the re-oxidation of Clvac-CeO₂₋ₓ(111) and is considered essential for understanding the function of ceria in oxidation catalysis. | Volkmar Koller; Pablo Lustemberg; Alexander Spriewald-Luciano; Sabrina M. Gericke; Alfred Larsson; Christian Sack; Alexei Preobrajenski; Edvin Lundgren; M. Veronica Ganduglia-Pirovano; Herbert Over | Physical Chemistry; Materials Science; Catalysis; Thin Films; Heterogeneous Catalysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649bfca39ea64cc1671b7ba9/original/critical-step-in-the-h-cl-oxidation-reaction-over-single-crystalline-ce-o2-x-111-peroxo-induced-site-change-of-strongly-adsorbed-surface-chlorine.pdf |
65b1beb2e9ebbb4db9e966d0 | 10.26434/chemrxiv-2024-6nqnq | Strain-Based Design, Direct Macrocyclization, and Metal Complexation of Thiazole-Containing Calix[3]pyrrole Analogues | Coordination chemistry of ring-contracted porphyrins, such as subporphyrin and calix[3]pyrrole, has been largely unexplored due to the synthetic difficulty of their free-base analogues. Here, we report strain-based molecular design and high yield synthesis of thiazole-containing calix[3]pyrrole analogues for metal complexation. The AFIR method and StrainViz analysis were used to perform a conformational search and evaluate/visualize ring strain, respectively. The results indicated that thiazole-containing analogues are less strained than the parent calix[3]pyrrole, while incorporation of imidazole or oxazole unexpectedly leads to an increase in total strain. In fact, calix[1]furan[2]thiazole was obtained in 60% yield by direct macrocyclization between α-bromoketone and bis(thioamide), whereas meso-N(sp2)-bridged analogue, which was calculated to be more strained by 5.1 kcal/mol, was obtained only in a 2% yield. Calix[1]furan[2]thiazole was converted to calix[1]pyrrole[2]thiazole for investigation of metal complexation. Through reaction with Et2Zn, calix[1]pyrrole[2]thiazole bound a Zn(II) ion in a tridentate fashion adopting a cone conformation, furnishing water/air stable organozinc complex that catalyzes polymerization of lactide. Whereas, Ag(I) and Pd(II) ions were chelated by partial cone conformation of calix[1]pyrrole[2]thiazole in a bidentate fashion. Strain-based molecular design has expanded the synthetic access to contracted porphyrinoids and opened up the opportunity of their rich coordination chemistry. | Keita Watanabe; Kotaro Shibata; Tomoya Ichino; Yuki Ide; Tomoki Yoneda; Satoshi Maeda; Yasuhide Inokuma | Theoretical and Computational Chemistry; Organic Chemistry; Organometallic Chemistry; Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b1beb2e9ebbb4db9e966d0/original/strain-based-design-direct-macrocyclization-and-metal-complexation-of-thiazole-containing-calix-3-pyrrole-analogues.pdf |
6227b837c3e9daf51d855f2c | 10.26434/chemrxiv-2022-3pfpl | Optimization of pressure-vacuum swing adsorption processes for nitrogen rejection from natural gas streams using a nitrogen selective metal organic framework | A vanadium(II/III) metal-organic organic framework (MOF), V2Cl2.8(btdd), that is selective to CH4 over N2 was recently discovered. Process optimizations were performed to determine the performance of this MOF to reach the pipeline transport purity of 96 mol% CH4. Two cycles were considered: the basic 3-step cycle and the Skarstrom cycle. First, the 3-step cycle was considered with a wide range of operating conditions. Three inlet compositions (55/45, 80/20 and 92/8 mol% CH4/N}), three process temperatures (30, 40 and 50C) and a range of adsorption pressures (100 to 500 kPa) were considered. A detailed process model in tandem with machine learning-aided optimization was employed to determine the optimal set of operating conditions. The 3-step cycle was unable to meet the 96 mol% CH4 purity requirement in most cases studied. However, the Skarstrom cycle was able to meet the 96 mol% CH4 purity requirement in all cases studied. The maximum recovery, at a purity of 96 mol%, was at 84.2% for the Skarstrom cycle with a methane feed composition of 80 mol% at 50C and an adsorption pressure of 100 kPa. For the Skarstrom cycle, at a feed temperature of 50C, an adsorption pressure of 100 kPa and a feed methane composition of 92 mol%, the productivity could be as high as 21.18 tonnes per day CH4 m-3 at a recovery of 73%. The achievable recovery-productivity values were comparable to a carbon molecular sieve process reported in the literature at similar operating conditions. | Nicholas Wilkins; Kasturi Nagesh Pai; Arvind Rajendran | Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6227b837c3e9daf51d855f2c/original/optimization-of-pressure-vacuum-swing-adsorption-processes-for-nitrogen-rejection-from-natural-gas-streams-using-a-nitrogen-selective-metal-organic-framework.pdf |
651238aced7d0eccc339179d | 10.26434/chemrxiv-2023-fs2f2 | Insights into Molten Salts Induced Structural Defects in Graphitic Carbon Nitrides for Piezo-Photocatalysis with Multiple H2O2 Production Channels | Recently, the production of hydrogen peroxide (H2O2) from water (H2O) and oxygen (O2) in the presence of graphitic carbon nitrides (g-C3N4) via a piezo-photocatalytic process has considerably ignited global interest in achieving sustainability. To fabricate porous g-C3N4, soft templates are frequently employed, leading to structural modifications originating from heteroatoms. However, many recent reports have ignored the roles of trace quantity of heteroatoms. Hence, to understand the impacts of the mentioned factors, we fabricated g-C3N4 containing oxygen and halogen atoms in the structures for piezo-photosynthesis of H2O2. Based on our analyzed results, oxygen atoms might be inserted into g-C3N4 in-plane structures, while halogen atoms tend to become intercalated between g-C3N4 layers. Furthermore, the presence of ammonium molten salts during the synthesis alters the concentration of mono and cluster vacancies of carbon and nitrogen in the materials. These defective contributions would meaningfully accelerate catalytic performance by providing trapping states. From the mechanistic view, different reduction and oxidation channels would play a pivotal role in generating H2O2. Thus, this study highlights the importance of modulating in-plane and out-of-plane structures of g-C3N4, benefiting catalytic properties under simultaneous irradiation. | Ly Pho Phuong; Duc-Viet Nguyen; Luu Anh Tuyen; Nguyen Quang Hung; Pham Thi Hue; Nguyen Thi Ngoc Hue; Minh-Thuan Pham; Thuy Thi Dieu Ung; Do Danh Bich; Phan Pham Duc Minh; Nguyen Hoai Anh; Huynh Phuoc Toan; Dai-Phat Bui; Seung Hyun Hur; Hoai-Thanh Vuong | Catalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651238aced7d0eccc339179d/original/insights-into-molten-salts-induced-structural-defects-in-graphitic-carbon-nitrides-for-piezo-photocatalysis-with-multiple-h2o2-production-channels.pdf |
6377a59d2079812a572c22cc | 10.26434/chemrxiv-2022-x2dj7-v2 | Insights into Generalization of the Rate-Limiting Steps of the Dehalogenation by LinB and DhaA: A Computational Approach
| LinB and DhaA are well-known haloalkane dehalogenases (HLDs) capable of converting a plethora of halogenated alkanes, also those considered persistent pollutants. The dehalogenation reaction that these two enzymes catalyze has been studied to determine its rate-limiting step (rls) for the last two decades now. As a result, it has been determined that HLDs can show different rate-limiting steps for individual substrates, and at this point we do not have a basis for any generalization in this matter. Therefore, in this work we aimed at gaining insights into the enzymatic dehalogenation of selected dibromo- and bromochloro- ethanes and propanes by LinB and DhaA using computational approach to determine whether defined structural similarities of the substrates result in a unified mechanism and the same rls. By predicting halogen binding isotope effects (BIEs) as well as computing interaction energy for each HLD-ligand complex the nature of the protein-ligand interactions has been characterized. Furthermore, C and Br kinetic isotope effects (KIEs) as well as the minimum free energy paths (MFEPs) were computed to investigate the chemical reaction for the selected systems. Accuracy of the approach and robustness of the computational predictions were validated by measuring KIEs on the selected reactions. Overall results strongly indicate that any generalization with respect to the enzymatic process involving various ligands in the case of DhaA is impossible, even if the considered ligands are structurally similar as those analyzed in the present study. Moreover, even small structural differences such as changing of one of the (non-leaving) halogen substituents may lead to significant changes in the enzymatic process and result in a different rls in the case of LinB. It has also been demonstrated that KIEs themselves cannot be used as rls indicators in the reactions catalyzed by the studied HLDs. | Agata Sowińska; Michał Rostkowski; Agnieszka Krzemińska; Tzofia Englman; Faina Gelman; Agnieszka Dybala-Defratyka | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6377a59d2079812a572c22cc/original/insights-into-generalization-of-the-rate-limiting-steps-of-the-dehalogenation-by-lin-b-and-dha-a-a-computational-approach.pdf |
67132e53cec5d6c142910973 | 10.26434/chemrxiv-2024-sbh10 | Mechanochemical Treatment of Waste Poly (Vinyl Chloride) for Alcohol Halogenation by Ball Milling and Triboelectric Material | Polyvinyl chloride (PVC), one of the most extensively produced polymers, has raised significant environment
and public health concerns due to its persistence in ecosystem, long-term accumulation and associated toxicity.
The well-established mechanical recycling approach for treating waste PVC often result in polymer
degradation and release of hazardous by-products, such as corrosive HCl. We envisage that mechanical
recycling in tandem with a halogenation reaction provide a new solution to waste PVC management. Herein,
we demonstrated that PVC plastic could serve as chlorination reagents, in combination with triboelectric
catalyst, to achieve efficient halogenation of alcohols under ball milling condition. The triboelectric catalyst,
TiO2, mediates the single electron transfer process that promotes the dehydrochlorination of PVC, thereby
enabling the in-situ chlorination of alcohols. This strategy was applicable to a variety of aliphatic and benzylic
alcohols, yielding the corresponding organic chlorides in moderate to excellent yields. In particular, the yield
of benzyl chloride reached 95% after 4 h of ball milling. Structural analysis confirmed that polymer formed by
dehydrochlorination of PVC contained olefin, carbonyl and aromatic structures. Additionally, Cl could be
completely removed, and the molecular weight decreased from 65.0 kDa to 4.6 kDa after recycling and
reusing PVC five times. This mechanochemical approach was also successfully applied in real plastics
applications and scale-up experiments. Overall, this method provides inspiration for using PVC as a chlorine
source to initiate chemical reactions through mechanochemical approaches. | Du Chen; Shengming Li; Ziye Ren; Chenyu Wang; Jinxing Chen; zhao wang | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67132e53cec5d6c142910973/original/mechanochemical-treatment-of-waste-poly-vinyl-chloride-for-alcohol-halogenation-by-ball-milling-and-triboelectric-material.pdf |
60c748b0ee301c54bdc7990d | 10.26434/chemrxiv.11890128.v2 | Xanthine-Based Photoaffinity Probes Allow Assessment of Ligand Engagement by TRPC5 Channels | TRPC1/4/5 cation channels are emerging drug targets for the treatment of, amongst others, central nervous system (CNS) disorders, kidney disease, and cardiovascular and metabolic disease. Various small-molecule TRPC1/4/5 modulators have been reported, including highly potent xanthine derivatives that can distinguish between specific TRPC1/4/5 tetramers. However, there is a paucity of information about their binding mode, which limits the ability to develop them further as chemical probes of specific TRPC1/4/5 channels for use in fundamental biological studies and drug discovery programmes. Here, we report the development of a set of potent xanthine-based photoaffinity probes that functionally mimic the xanthines Pico145 and AM237, respectively. Using these probes, we have developed a quantitative photoaffinity labelling protocol for TRPC5 channels. Our results provide the first direct evidence that xanthines modulate TRPC5 channels through a direct binding interaction with TRPC5 protein, and the first quantitative method for the assessment of binding interactions of TRPC5 and small molecules. Our method may allow the study of the mode-of-action of other TRPC1/4/5 modulators, and the identification of small molecule binding sites of TRPC1/4/5 channels. | Claudia Bauer; Aisling Minard; Isabelle Pickles; Matthew Burnham; Nikil Kapur; David Beech; Stephen Muench; Megan Wright; Stuart Warriner; Robin Bon | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748b0ee301c54bdc7990d/original/xanthine-based-photoaffinity-probes-allow-assessment-of-ligand-engagement-by-trpc5-channels.pdf |
6613c4d921291e5d1d6061cf | 10.26434/chemrxiv-2024-dj4dm | Digitally Enabled Generic Analytical Framework Accelerating the Pace of Liquid Chromatography Method Development for Vaccine Adjuvant Formulations | The growing use of adjuvants in the fast-paced formulation of new vaccines has created an unprecedented need for meaningful analytical assays that deliver reliable quantitative data from complex adjuvant and adjuvant-antigen mixtures. Due to their complex chemical and physical properties, method development for the separation of vaccine adjuvants is considered a highly challenging and laborious task. Reversed-phase liquid chromatography (RPLC) is among the most important tests in the (bio)pharmaceutical industry for release and stability indicating measurements including adjuvant content, identity, and purity profile. However, the time constraints of developing “on-demand” robust quantitative methods prior to each change in formulation can easily lead to sample analysis becoming a bottleneck in vaccine development. Herein a simple and efficient generic analytical framework capable of chromatographically resolving the most commonly used non-aluminum based adjuvants across academic and industrial sectors is introduced. This was designed to seek a more proactive approach for fast-paced assay development endeavors that evolved from extensive stationary phase screening in conjunction with multifactorial in silico simulations of adjuvant retention time (RT) as a function of gradient time, temperature, organic modifier blending, and buffer concentration. The multifactorial retention models yield 3D resolution maps with excellent baseline separation of all adjuvants in a single run, which was found to be very accurate, with differences between experimental and simulated retention times of less than 1%. The analytical framework described here also includes the introduction of a more versatile approach to method development by introducing a dynamic RT database for adjuvants covering the entire library of adjuvants with broad mechanisms of action across numerous vaccine formulations with excellent linearity, accuracy, precision, and specificity. The power of this framework was also demonstrated with numerous analytical assays that can be generated rapidly from simulations guiding vaccine processes in the development of new adjuvant formulations. Analytical assay in this work covers content, purity profile by RPLC-UV-CAD, and component identification (RPLC-MS) across complex vaccine formulations, including the use of surfactants (e.g., polysorbates), as well as their separation from adjuvant targets. | Mohamed Hemida; Rodell Barrientos; Caleb Kinsey; Nathan Kuster; Mayank Bhavsar; Armen Beck; Heather Wang; Andrew Singh; Pankaj Aggarwal; Arthur Arcinas; Malini Mukherjee; Emmanuel Appiah-Amponsah; Erik Regalado | Analytical Chemistry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6613c4d921291e5d1d6061cf/original/digitally-enabled-generic-analytical-framework-accelerating-the-pace-of-liquid-chromatography-method-development-for-vaccine-adjuvant-formulations.pdf |
657af59c9138d23161a05879 | 10.26434/chemrxiv-2023-wj8lc | Carboxylate catalyzed silylation of alkynes | A carboxylate-catalyzed, metal-free C-silylation protocol for terminal alkynes is reported using a quaternary ammonium pivalate as the catalyst and commercially available N,O-bis(silyl)acetamides as silylating agents. The reaction proceeds under mild conditions, tolerates a range of functionalities, and enables concomitant O- or N-silylation of acidic OH or NH groups. A Hammett ρ value of +1.4±0.1 obtained for p-substituted 2-arylalkynes is consistent with the proposed catalytic cycle involving turnover-determining deprotonation step. | Anton Bannykh; Petri Pihko | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657af59c9138d23161a05879/original/carboxylate-catalyzed-silylation-of-alkynes.pdf |
66ca0962f3f4b05290020bd4 | 10.26434/chemrxiv-2024-pm2rp | Superposition Rules for Molecular Circuits Embedded in a Single Molecule Bis-Terpyridine Breadboard Junction | Molecular electronics, which is governed by quantum mechanics, urgently requires establishing predictive frameworks and rules to combine molecular components and create miniaturized integrated circuits. To this end, we have recently demonstrated a bis-terpyridine based molecular breadboard with four conductance state formed by the superposition of five 2-5ring circuits. Here, we develop a generic analytical/statistical model to extract the conductance of the five embedded circuits in a bis-terpyridine based molecular breadboard junction. The model can be used to experimentally verify the rules for superposing the conductance of multiple molecular circuits, a key step towards building molecular circuitry. Further, our study provides a general framework to simulate and analyze break-junction conductance histograms of complex molecular junctions with more than two electrode anchoring groups. | Ravinder Kumar; Veerabhadrarao Kaliginedi; Ravindra Venkatramani | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ca0962f3f4b05290020bd4/original/superposition-rules-for-molecular-circuits-embedded-in-a-single-molecule-bis-terpyridine-breadboard-junction.pdf |
65d3d2fae9ebbb4db9b8d254 | 10.26434/chemrxiv-2024-p8xxp | Interception and Synthetic Application of Diradical and Diene Forms of Dual-Nature Azabicyclic o-Quinodimethanes Generated by 6pi-Azaelectrocyclization | We demonstrate that 2-alkenylarylaldimines and ketimines undergo thermal 6pi-azaelectrocyclization to generate a wide range of azabicyclic o-quinodimethanes (o-QDMs). These o-QDMs exist as a hybrid of a diene and a benzylic diradical. The diradical nature was confirmed by their ability to undergo dimerization and react with H-atom donor, TEMPO and O2. In addition, the interception of the diradicaloid o-QDMs by H-atom transfer was used to synthesize five tetrahydroisoquinoline alkaloids and related bioactive molecules. The diene form can undergo [4 + 2] cycloaddition reactions with different dienophiles to generate bridged azabicycles in high endo:exo selectivity. The azabicyclic o-QDMs can be generated for [4 + 2] cycloaddition from a wide range of electronically and sterically varied 2-alkenylarylimines, including mono, di, tri and tetrasubstituted alkenes, and imines derived from arylamine, alkylamine (1°, 2°, 3°), benzylamine, benzylsulfonamide and Boc-amine. | Majji Shankar; Daniel J. Lee; Supuni I. N. Hewa Inaththappulige; Ayush Acharya; Hemant P. Yennawar; Ramesh Giri | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d3d2fae9ebbb4db9b8d254/original/interception-and-synthetic-application-of-diradical-and-diene-forms-of-dual-nature-azabicyclic-o-quinodimethanes-generated-by-6pi-azaelectrocyclization.pdf |
64258d3091074bccd08870a0 | 10.26434/chemrxiv-2023-2frs3 | Transition-Metal-Free and Redox-Neutral Strategy for Sulfilimines Synthesis via S-Arylation of Sulfenamides | In this investigation, an unprecedented transition-metal-free and redox-neutral synthesis of sulfilimines was realized through the S-arylation of readily obtainable sulfenamides employing diaryliodonium salts. The pivotal step encompassed the tautomerization between bivalent nitrogen-centered anions, engendered post-deprotonation of sulfenamides under alkaline conditions, and sulfinimidoyl anions. The experimental outcomes demonstrate that sulfinimidoyl anionic species function as efficacious nucleophilic reagents, affording sulfilimines with notable to exceptional yields and superlative chemoselectivity, all executed within a transition-metal-free protocol and under exceptionally mild conditions. | Guoling Huang; Xunbo Lu; Fangpeng Liang | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64258d3091074bccd08870a0/original/transition-metal-free-and-redox-neutral-strategy-for-sulfilimines-synthesis-via-s-arylation-of-sulfenamides.pdf |
60c74f2c0f50db367a397356 | 10.26434/chemrxiv.12824135.v1 | Electrochemical Aziridination of Internal Alkenes with Primary Amines | Aziridines are useful synthetic building blocks,
widely employed for the preparation of various nitrogen-containing derivatives.
As the current methods require the use of prefunctionalized amines, the
development of a synthetic strategy towards aziridines, that can establishe the
union of alkenes and amines, would be of great synthetic value. Herein, we report an electrochemical
approach, which realizes this concept via an oxidative coupling between alkenes
and primary alkyl amines. The reaction is carried out in an electrochemical
flow reactor, leading to short reaction times (5 min), high yields and broad
scope. At the cathode, hydrogen is generated, which can be used in a second
reactor to reduce the aziridine, yielding the corresponding hydroaminated
product. Mechanistic investigations and DFT calculations revealed that the
alkene is first anodically oxidized and subsequently reacted with the amine
coupling partner. | Maksim Oseka; Gabriele Laudadio; Nicolaas P. van Leest; Marco Dyga; Aloisio de Andrade Bartolomeu; Lukas Goossen; B. de Bruin; Kleber Thiago de Oliveira; Timothy Noel | Organic Compounds and Functional Groups | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f2c0f50db367a397356/original/electrochemical-aziridination-of-internal-alkenes-with-primary-amines.pdf |
61d09b689efae767912e5ac2 | 10.26434/chemrxiv-2021-6n061-v2 | Accurate Prediction of Voltage of Battery Electrode Materials Using Attention Based Graph Neural Networks | Performing first principle calculations to discover electrodes’ properties in the large chemical space is a challenging task. While machine learning (ML) has been applied to effectively accelerate those discoveries, most of the applied methods ignore the materials’ spatial information and only use pre-defined features: based only on chemical compositions. We propose two attention-based graph convolutional neural network techniques to learn the average voltage of electrodes. Our proposed method, which combines both atomic composition and atomic coordinates in 3D-space, improves the accuracy in voltage prediction by 17% when compared to composition based ML models. The first model directly learns the chemical reaction of electrodes and metal-ions to predict their average voltage, whereas the second model combines electrodes’ ML predicted formation energy (Eform) to compute their average voltage. Our models demonstrates improved accuracy in transferability from our subset of learned metal-ions to other metal-ions.
| Steph-Yves Louis; Edirisuriya Siriwardane; Rajendra Joshi; Sadman Omee; Neeraj Kumar; Jianjun Hu | Physical Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d09b689efae767912e5ac2/original/accurate-prediction-of-voltage-of-battery-electrode-materials-using-attention-based-graph-neural-networks.pdf |
6150143118be8575b030ad43 | 10.26434/chemrxiv-2021-2x06r-v3 | On the Use of Real-World Datasets for Reaction Yield Prediction | The lack of publicly available, large, and unbiased datasets is a key bottleneck for the application of machine learning (ML) methods in synthetic chemistry. Data from electronic laboratory notebooks (ELNs) could provide less biased, large datasets, but no such datasets have been made publicly available. The first real-world dataset from the ELNs of a large pharmaceutical company is disclosed and its relationship to high-throughput experimentation (HTE) datasets is described. For chemical yield predictions, a key task in chemical synthesis, an attributed graph neural network (AGNN) performs as good or better than the best previous models on two HTE datasets for the Suzuki and Buchwald-Hartwig reactions. However, training of the AGNN on the ELN dataset does not lead to a predictive model. The implications of using ELN data for training ML-based models are discussed in the context of yield predictions. | Mandana Saebi; Bozhao Nan; John Herr; Jessica Wahlers; Zhichun Guo; Andrzej Zurański; Thierry Kogej; Per-Ola Norrby; Abigail Doyle; Olaf Wiest; Nitesh Chawla | Theoretical and Computational Chemistry; Analytical Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6150143118be8575b030ad43/original/on-the-use-of-real-world-datasets-for-reaction-yield-prediction.pdf |
60c74061469df40a9bf42c29 | 10.26434/chemrxiv.7716254.v1 | Plasmonic Nanocavities Enable Self-Induced Electrostatic Catalysis | <div>
<div>
<div>
<p>The potential of strong light-matter interactions
remains to be further explored within a chemical context.
Towards this end we here study the electromagnetic
interaction between molecules and plasmonic nanocavities.
By means of electronic structure calculations, we show that
self-induced catalysis emerges without any external driving
due to the interaction of the molecular permanent and
fluctuating dipole moments with the plasmonic cavity modes.
We also exploit this scheme to modify the transition
temperature T<sub>1/2</sub> of spin-crossover complexes as an example
of how one can ultimately control materials response through
strong light-matter interactions.
</p>
</div>
</div>
</div> | Clàudia Climent; Javier Galego; Francisco J. Garcia-Vidal; Johannes Feist | Physical Organic Chemistry; Nanocatalysis - Catalysts & Materials; Plasmonic and Photonic Structures and Devices; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74061469df40a9bf42c29/original/plasmonic-nanocavities-enable-self-induced-electrostatic-catalysis.pdf |
67d946e1fa469535b9a2913e | 10.26434/chemrxiv-2025-b82jd | Optimal cyclic reflux operational policy for ternary mixtures separation | The optimal control of a multicomponent batch distillation campaign with a variable reflux ratio, and, an analysis of the influence of different parameters such as total pressure at the top of the column, initial mixture composition, and tray hold-up, have been presented. This optimal control strategy is applied to the zeotropic ternary mixture case, a mixture of hydrocarbons. In this example, the structure of the optimal control becomes significantly closer and closer to the clear cyclic reflux policy as one considers the influence of the parameters mentioned above, which is important from th aspect of the usage in industry. | Marija Stojkovic | Chemical Engineering and Industrial Chemistry; Process Control | CC BY 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d946e1fa469535b9a2913e/original/optimal-cyclic-reflux-operational-policy-for-ternary-mixtures-separation.pdf |
60c742c6bb8c1a45d83da1bc | 10.26434/chemrxiv.8280761.v2 | Combining Ultra-High Drug Loaded Micelles and Shear Thinning, Injectable Hydrogel Drug Depots for Prolonged Drug Release | Hydrogel based drug depot formulations are of great interest for therapeutic applications. Here, the impact of incorporated drug, neat polymer micelles, and drug-loaded micelles on the viscoelastic properties of a cytocompatible hydrogel was investigated systematically. To challenge the hydrogel with regard to the desired application as injectable drug depot, curcumin (CUR) was chosen as a model compound due to its very low-water solubility and limited stability. CUR was either directly solubilized by the hydrogel or pre-incorporated into polymer micelles. Drug-release from a collagen matrix was studied in a trans-well setup and extended drug release over 10 weeks.<br /> | Michael M Lübtow; Thomas Lorson; Tamara Finger; Florian-Kai Gröber-Becker; Robert Luxenhofer | Aggregates and Assemblies; Biocompatible Materials; Surfactants; Drug delivery systems; Hydrogels; Organic Polymers; Polymer blends; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742c6bb8c1a45d83da1bc/original/combining-ultra-high-drug-loaded-micelles-and-shear-thinning-injectable-hydrogel-drug-depots-for-prolonged-drug-release.pdf |
65cb497866c1381729885338 | 10.26434/chemrxiv-2024-11drs | Working with benchmark datasets in the Cuby framework | The development and benchmarking of computational chemistry methods relies on comparison with benchmark data. More and larger benchmark datasets are becoming available, and working efficiently with them is a necessity. The Cuby framework provides rich functionality for working with datasets, comes with many ready-to-use predefined benchmark sets, and interfaces with a wide range of computational chemistry software. Here we review the tools Cuby provides for working with datasets and provide examples of more advanced workflows, such as handling large numbers of computations on HPC resources and reusing previously computed data. Cuby has also been extended recently to include two important benchmark databases, NCIAtlas and GMTKN55. | Jan Řezáč; Outi Vilhelmiina Kontkanen; Martin Nováček | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cb497866c1381729885338/original/working-with-benchmark-datasets-in-the-cuby-framework.pdf |
60c73f19bb8c1a691d3d9a4a | 10.26434/chemrxiv.7215065.v1 | Low Energy Optical Excitations as an Indicator of Structural Changes Initiated at the Termini of Amyloid Proteins | <div>We combine absorption and fluorscence spectroscopy experiments and theoretical modeling to specifically examine the role of termini interactions on the optical properties.</div><div><div>Optical absorption and fluorescence is measured for a six-chain amino acid 2Y3J (AIIGLM) which forms a segment of the full amyloid beta 1-40. In order to explore the sensitivity of the optical properties to the termini interactions, the experiments were repeated by acetylating the N-terminus.</div><div>Although atomic force microscopy experiments indicate the formation of some form of fibrilar or crystal aggregates in both systems, the optical properties are strikingly different - acetylation significantly reduces optical activity between 280-350 nm.</div></div> | KwangHyok Jong; Yavar T. Azar; Luca Grisanti; Amberley
D. Stephens; Saul T.E. Jones; Dan Credgington; Gabi Kaminski; Ali Hassanali | Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f19bb8c1a691d3d9a4a/original/low-energy-optical-excitations-as-an-indicator-of-structural-changes-initiated-at-the-termini-of-amyloid-proteins.pdf |
66b3dfb25101a2ffa87386f2 | 10.26434/chemrxiv-2024-v52q7 | Local and Global Structural Effects of Doping on Ionic Conductivity in Na3SbS4 Solid Electrolyte | Among Na-ion solid electrolytes, Na3SbS4 has achieved high ionic conductivity (s_ion) exceeding 10 mS/cm through aliovalent doping. s_ion enhancement due to aliovalent doping is qualitatively explained by the increase in the concentration of defects that mediate ion diffusion. However, a rigorous atomic-scale mechanistic explanation is needed. Doping also affects s_ion by modifying ion mobility - an effect that is not well understood and often overlooked. We use first-principles defect calculations to mechanistically explain and quantify the increase/decrease in Na vacancy concentration due to aliovalent doping of Na3SbS4. By focusing on isovalent doping, we reveal local and global structural effects of doping on the migration barrier, and therefore, ion mobility. In conjunction with experiments, we demonstrate the interplay between the local and global effects. Doping with heavier anions to achieve more polarizable frameworks is a common approach to enhancing s_ion. Our findings present a unique approach to enhancing s_ion by doping with smaller and lighter cations that form stiffer bonds with anions, which in turn soften the parent framework. | Cheng-Wei Lee; Mayu Maegawa; Hirofumi Akamatsu; Katsuro Hayashi; Saneyuki Ohno; Prashun Gorai | Theoretical and Computational Chemistry; Energy; Theory - Computational; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b3dfb25101a2ffa87386f2/original/local-and-global-structural-effects-of-doping-on-ionic-conductivity-in-na3sb-s4-solid-electrolyte.pdf |
60c74e12469df4dae7f443cc | 10.26434/chemrxiv.12643220.v2 | Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis | <p>The
recently described O-glycoprotease OpeRATOR presents exciting opportunities for
O-glycoproteomics. This bacterial enzyme purified from <i>Akkermansia (Sp). muciniphila</i>
cleaves N-terminally to serine and threonine residues that are modified with (preferably
asialylated) O-glycans. This <a>provides orthogonal
cleavage relative to canonical proteases (e.g., trypsin) for improved
O-glycopeptide characterization with tandem mass spectrometry (MS/MS). O-glycopeptides
with a modified N-terminal residue, such as those generated by OpeRATOR,
present several potential benefits, perhaps the most notable being <i>de facto</i>
O-glycosite localization without the need of glycan-retaining fragments in
MS/MS spectra. Indeed, O-glycopeptides modified exclusively at the N-terminus
would enable O-glycoproteomic methods to rely solely on collision-based
fragmentation rather than electron-driven dissociation because glycan-retaining
peptide fragments would not be required for localization. The caveat is that
modified peptides would need to reliably contain only a single O-glycosite. </a>Here
we use methods that combine collision- and electron-based fragmentation to
characterize the number of <i>O-</i>glycosites
that are present in <i>O-</i>glycopeptides
derived from OpeRATOR digestion of four known <i>O-</i>glycoproteins.
Our data show that over 50% of <i>O-</i>glycopeptides
generated from combined digestion using OpeRATOR and trypsin contain multiple <i>O-</i>glycosites, indicating that collision-based
fragmentation alone is not sufficient. Electron-based dissociation methods are
necessary to capture the <i>O-</i>glycopeptide
diversity present in OpeRATOR digestions. </p> | Nicholas Riley; Stacy Malaker; Carolyn Bertozzi | Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e12469df4dae7f443cc/original/electron-based-dissociation-is-needed-for-o-glycopeptides-derived-from-ope-rator-proteolysis.pdf |
67b6156b6dde43c9089994c5 | 10.26434/chemrxiv-2024-fhzdt-v2 | Predicting Fluorescence Emission Wavelengths and Quantum Yields via Machine Learning | The search for functional fluorescent organic materials can significantly benefit from rapid and accurate predictions of photophysical properties. However, screening large numbers of potential fluorophore molecules in different solvents faces the limitations of quantum mechanical calculations and experimental measurements. In this work, we develop machine learning (ML) algorithms for predicting the fluorescence of a molecule, focusing on two target properties: emission wavelengths (WLs) and quantum yields (QYs). For this purpose, we employ the Deep4Chem database containing optical properties of 20,236 combinations of 7,016 chromophores in 365 different solvents. Several chemical descriptors, or features, were selected as inputs for each model, and each molecule was characterized by its SMILES fingerprint. The Shapley Additive explanations (SHAP) technique was used to rationalize the results, showing that the most impactful properties are chromophore-related, as expected from chemical intuition. For the best-performing model, the Random Forest, our results for the test set show a root-mean-square error (RMSE) of 28.8 nm (0.15 eV) for WLs and 0.19 for QYs. The developed ML models were used to predict, thus completing, the missing results for the WL and QY target properties in the original Deep4Chem database, resulting in two new databases, one for each property. Testing our ML models for each target property in molecules not included in the original Deep4Chem database presented good results. | Rubens C. Souza; Julio Cesar Duarte; Ronaldo R. Goldschmidt; Itamar Borges Jr | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b6156b6dde43c9089994c5/original/predicting-fluorescence-emission-wavelengths-and-quantum-yields-via-machine-learning.pdf |
6511cfbb60c37f4f76705ace | 10.26434/chemrxiv-2023-362lh | Predicting SARS-CoV-2 Protein Interactions: Insights from Machine Learning | In our research journey, we undertook a comprehensive exploration of protein-protein interaction (PPI) prediction, with a primary focus on unraveling the intricate web of interactions involving the SARS-CoV-2 virus. Our research endeavor encompassed a multi-faceted approach that seamlessly integrated data preprocessing, feature engineering, the application of machine learning models, deep learning techniques, and extensive data visualization to gain profound insights into the complex realm of molecular interactions.The journey commenced with the acquisition of data from the IntAct database, a repository brimming with protein interaction information. However, before diving into analysis, rigorous data preprocessing was imperative. We meticulously scrubbed the data, eliminating undesired identifiers, and harnessed the power of regular expressions to extract and retain only the numeric values crucial for our predictive models. Feature engineering emerged as a pivotal step, allowing us to craft informative data representations conducive to effective model training. Our transformation of the "Confidence Value" variable, extracted from IntAct, into a structured and insightful feature set, was enhanced through one-hot encoding, facilitating our predictive endeavors. Our quest for predictive excellence took two distinct paths: traditional machine learning and deep learning. Utilizing a Random Forest Classifier, we explored classical machine learning methods, achieving commendable accuracy in predicting protein interactions. The introduction of Support Vector Machine (SVM) classifiers further underscored the robustness of our approach, reinforcing its potential in this critical domain. However, the allure of deep learning beckoned, and we ventured into the realm of neural networks. Leveraging TensorFlow and Keras, we meticulously crafted a neural architecture that exhibited remarkable prowess in discerning protein interactions. Our deep learning model unveiled intricate patterns, allowing us to delve deeper into the enigmatic world of PPIs.
The culmination of our efforts was showcased through a captivating array of visualizations, each offering unique insights into the realm of protein interactions. Heatmaps artfully painted the picture of confusion matrices, elucidating the strengths and nuances of our predictive models. ROC curves, precision-recall curves, and bar plots masterfully illustrated the intricate interplay between true positives, false positives, and other critical metrics. Our research transcended the realms of technical prowess. It delved into the ethical dimensions of data integration, underscoring the importance of adhering to the highest standards of scientific ethics. We acknowledged the vital need for data privacy and the responsible handling of biological data, anchoring our research in a strong commitment to ethical conduct. In conclusion, our research stands as a testament to the transformative power of computational approaches in deciphering the complex tapestry of protein interactions. It not only provides predictive models but also serves as a blueprint for ethical data management and interpretation. As we bring this journey to a close, we invite fellow researchers to embark on this captivating voyage of discovery, shedding light on the molecular intricacies of SARS-CoV-2 and paving the way for a deeper understanding of host-virus interactions. | Nihal Dadheech | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6511cfbb60c37f4f76705ace/original/predicting-sars-co-v-2-protein-interactions-insights-from-machine-learning.pdf |
64b59b4cb053dad33a6c179e | 10.26434/chemrxiv-2023-rxmz4 | Cine Substitution of N-Sulfonylindoles | Nucleophilic substitution at the 2-position of indoles bearing 3-position electron-withdrawing groups follows multiple pathways. Conventional nucleophilic aromatic substitution ensues when there is a 2-position leaving group, but in a cine substitution, the leaving group is on the adjacent nitrogen. Indoles bearing N-methoxy groups are excellent reactants for cine substitution, but are not very synthetically accessible. This study was predicated on finding a replacement in a sulfinate leaving group, which is well precedented in many organic transformations, and which enables easy preparation of the cine substitution reactants. With primary alkoxide nucleophiles, cine substitution proceeds well to generate 2-alkoxy-3-substituted indoles. | Alon Agua; Michael Pirrung | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b59b4cb053dad33a6c179e/original/cine-substitution-of-n-sulfonylindoles.pdf |
61c674bf7f367e15405f50ae | 10.26434/chemrxiv-2021-67sx5 | A General Strategy for the Synthesis of Rare Sugars via Ru(II)-catalyzed and Boron-mediated Selective Epimerization of 1,2-trans-diols to 1,2-cis-diols | Human glycans are primarily composed of nine common sugar building blocks. On the other hand, several hundred monosaccharides have been discovered in bacteria and most of them are not readily available. The ability to access these rare sugars and the corresponding glycocon-jugates can facilitate the studies of various fundamentally important biological processes in bacteria, including interactions between microbiota and the human host. Many rare sugars also exist in a variety of natural products and pharmaceutical reagents with significant biological activi-ties. Although methods have been developed for the synthesis of rare monosaccharides, most of them involve lengthy steps. Herein we report an efficient and general strategy that can provide access to rare sugars from commercially available common monosaccharides via a one-step Ru(II)-catalyzed and boron-mediated selective epimerization of 1,2-trans-diols to 1,2-cis-diols. The formation of boronate esters drives the equilibrium towards 1,2-cis-diol products, which can be immediately used for further selective functionalization and glycosylation. The utility of this strategy was demonstrated by the efficient construction of glycoside skeletons in natural products or bioactive compounds. | Xiaolei Li; Jicheng Wu; Weiping Tang | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c674bf7f367e15405f50ae/original/a-general-strategy-for-the-synthesis-of-rare-sugars-via-ru-ii-catalyzed-and-boron-mediated-selective-epimerization-of-1-2-trans-diols-to-1-2-cis-diols.pdf |
631f2f615351a33257f787bd | 10.26434/chemrxiv-2022-z7qlt | Modifying Poly(caprolactone) Degradation through C–H Functionalization | There is a growing need for degradable polymers for applications in sustainable plastics and medical implants. To enhance the utility of degradable polymers, both better understanding of the factors that influence their degradation and new tools to modulate degradation are needed. We report the C–H xanthylation of poly(caprolactone), a biodegradable polyester, which results in changes in materials properties even at small incorporations. Despite the functionalized materials exhibiting a decrease in crystallinity and hydrophobicity, xanthylated poly(caprolactone) degrades more slowly than its unfunctionalized counterpart. To understand this rate difference, kinetic studies with a small molecule surrogate were performed and demonstrated functionalization adjacent to the hydrolysable ester functional group led to slower degradation. This study illustrates how the interplay between molecular and material characteristics can impact degradation. | Victoria Barber; Meredith Borden; Jill Alty; Ly Tran; Hilmar Koerner; Luke Baldwin; Erik Alexanian; Frank Leibfarth | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631f2f615351a33257f787bd/original/modifying-poly-caprolactone-degradation-through-c-h-functionalization.pdf |
640769430e6a36fabae54173 | 10.26434/chemrxiv-2023-d17rn | Visible Light-Induced Palladium-Carbon Bond Weakening in Catalytically Relevant T-Shaped Complexes | Triggering one-electron redox processes during palladium catalysis holds the potential to unlock new reaction mechanisms and synthetic methods not previously accessible in the typical two-electron reaction manifolds that dominate palladium catalysis. We report that T-shaped organopalladium(II) complexes coordinated by a bulky monophosphine, a class of organometallic intermediate featured in a range of contemporary catalytic reactions, undergo blue light-promoted bond weakening leading to mild and efficient homolytic cleavage of strong Pd(II)–C(sp3) bonds under ambient conditions. The origin of light-triggered radical formation in these systems, which lack an obvious ligand-based chromophore (i.e., π- systems), was investigated using a combination of DFT calculations, photoactinometry, and transient absorption spectroscopy. The available data suggest T-shaped organopalladium(II) complexes manifest unusual blue light-accessible Pd- to-C(sp3) metal-to-ligand charge transfer (MLCT). The quantum efficiency and excited state lifetime of this process were unexpectedly superior compared to a prototypical (α-diimine)Pd(II) complex featuring a low-lying, ligand-centered LUMO (π*). These results suggest coordinatively-unsaturated organopalladium(II) compounds, catalysts in myriad catalytic processes, have untapped potential for one-electron reactivity under visible light excitation. | Peter Waddell; Lei Tian; Anthony Scavuzzo; Gregory Scholes; Brad Carrow | Organic Chemistry; Catalysis; Organometallic Chemistry; Photochemistry (Org.); Photocatalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY 4.0 | CHEMRXIV | 2023-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640769430e6a36fabae54173/original/visible-light-induced-palladium-carbon-bond-weakening-in-catalytically-relevant-t-shaped-complexes.pdf |
630f25d811986c9d234cf3cf | 10.26434/chemrxiv-2022-mm6pw | Evaluating Multi-Resonant Thermally Activated Delayed (MR-TADF) Fluorescent Compounds as Photocatalysts | Donor-acceptor (D-A) thermally activated delayed fluorescent (TADF) compounds, such as 4CzIPN, have become a widely used sub-class of organic photocatalysts for a plethora of photocatalytic reactions. Multi-resonant TADF (MR-TADF) compounds, a subclass of TADF emitters that are rigid nanographene derivatives, such as DiKTa and Mes3DiKTa, have to date not been explored as photocatalysts. In this study both DiKTa and Mes3DiKTa were found to give comparable or better product yield than 4CzIPN in a range of photocatalytic processes that rely upon reductive quenching, oxidative quenching, energy transfer and dual photocatalytic processes. In a model oxidative quench process, DiKTa and Mes3DiKTa gave increased reaction rates in comparison to 4CzIPN, with DiKTa being of particular interest due to the lower material cost (£0.94/mmol) compared to that of 4CzIPN (£3.26/mmol). These results suggest that DiKTa and Mes3DiKTa would be excellent additions to any chemist’s collection of photocatalysts. | Callum Prentice; James Morrison; Andrew Smith; Eli Zysman-Colman | Organic Chemistry; Catalysis; Photochemistry (Org.); Physical Organic Chemistry; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630f25d811986c9d234cf3cf/original/evaluating-multi-resonant-thermally-activated-delayed-mr-tadf-fluorescent-compounds-as-photocatalysts.pdf |
64f1f95d79853bbd78dfa892 | 10.26434/chemrxiv-2023-kmd91 | Accelerated Exploration of Heterogeneous CO2 Hydrogenation Catalysts by Bayesian Optimized High-throughput and Automated Experimentation. | Automated high-throughput platforms and Artificial Intelligence (AI) are already accelerating discovery and optimization in various fields of chemistry and chemical engineering. However, despite some promising solutions, little to no attempts have targeted the full heterogeneous catalyst discovery workflow, with most chemistry laboratories continuing to perform research with a traditional one-at-a-time experiment approach and limited digitization. In this work, we present a closed-loop data-driven approach targeting the optimization of catalysts’ composition for the direct transformation of carbon dioxide (CO2) into methanol, by combining Bayesian Optimization (BO) algorithm, automated synthesis by incipient wetness impregnation and high-throughput catalytic performance evaluation in fixed bed mode. The BO algorithm optimized a four-objective function simultaneously (high CO2 conversion, high methanol selectivity, low methane selectivity, and low metal cost) with a total of 11 parameters (4 supports, 6 metals salts, and one promoter). In 6 weeks, 144 catalysts were synthesized and tested, with limited manual laboratory activity. The results show a significant improvement in the objectives at the end of each iteration. Between the first and fifth catalyst generation, the average CO2 conversion and methanol formation rates have been multiplied by 5.7 and 12.6 respectively, while simultaneously reducing the methane production rate by 3.2 and dividing the metal cost by 6.3 times. Notably, through the exploration process, the BO algorithm rapidly focuses on copper-based catalysts supported on zirconia doped with Zinc and/or Cerium, with the best catalysts, according to the model, showing an optimized composition of 1.85wt% Cu, 0.69wt% Zn, and 0.05wt% Ce supported on ZrO2. When changing the objective, i.e. removing the metal cost as a constrain, the BO algorithm suggests compositions centered on Indium-based catalysts, highlighting an alternative family of catalysts, testifying of the algorithm adaptability and the reusability of the data when targeting different objectives. In only 30 days, the BO, coupled with automated synthesis and high-throughput testing, has been able to replicate the major development stages in the field of heterogeneous catalysts research for CO2 conversion to methanol, made over of the last 100 years with a conventional experimental approach. This data-driven approach proves to be very efficient in exploring and optimizing catalyst composition from the vast multi-parameter space towards multiple performance objectives simultaneously and could be easily extrapolated to different parameter spaces, objectives, and be transposed to other applications. | Adrian Ramirez; Erwin Lam; Daniel Pacheco; Yuhui Hou; Hermann Tribukait; Loic Roch; Christophe Copéret; Paco Laveille | Inorganic Chemistry; Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f1f95d79853bbd78dfa892/original/accelerated-exploration-of-heterogeneous-co2-hydrogenation-catalysts-by-bayesian-optimized-high-throughput-and-automated-experimentation.pdf |
60c7467e0f50db21a8396466 | 10.26434/chemrxiv.10541075.v1 | Deoxyfluorination Using CuF2 | <div>Deoxyfluorination is a primary method for the formation of C–F bonds. Bespoke reagents are commonly used due to issues associated with the low reactivity of metal fluorides. Here, we report the development of a simple strategy for deoxyfluorination using first-row transition metal fluorides that overcomes these limitations. Using CuF2 as an exemplar, activation of an O-alkylisourea adduct formed in situ allows effective nucleophilic fluoride transfer to a range of primary and secondary alcohols. Spectroscopic investigations have been used to probe the origin of the enhanced reactivity of CuF2. The utility of the process towards enabling 18F-radiolabeling is also presented.</div> | D. Eilidh Sood; Sue Champion; Daniel M. Dawson; sonia chabbra; Bela E. Bode; Andrew Sutherland; Allan Watson | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7467e0f50db21a8396466/original/deoxyfluorination-using-cu-f2.pdf |
60c753d4bdbb8907d4a3a51d | 10.26434/chemrxiv.13559750.v1 | Dataset of Noncovalent Intermolecular Interaction Energy Curves for 24 Small High-Spin Open-Shell Dimers | <div>We introduce a dataset of 24 interaction energy curves of open-shell noncovalent dimers, referred to as the O24x5 dataset. The dataset consists of high-spin dimers up to eleven atoms selected to assure diversity with respect to interactions types: dispersion, electrostatics and induction. The benchmark interaction energies are obtained at the restricted open-shell CCSD(T) level of theory with complete basis set extrapolation aug-cc-pVQZ--> aug-cc-pV5Z.</div> | Katarzyna Madajczyk; Piotr Zuchowski; Filip Brzęk; Łukasz Rajchel; Dariusz Kędziera; Marcin Modrzejewski; Michał Hapka | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753d4bdbb8907d4a3a51d/original/dataset-of-noncovalent-intermolecular-interaction-energy-curves-for-24-small-high-spin-open-shell-dimers.pdf |
60c743714c89197e7cad263b | 10.26434/chemrxiv.9164786.v1 | Highly Mixed ZrO2/SiO2 Hybrid Aerogel Deriving from Freely Tangled Weakly Branched Primary Clusters Enables Improved Thermal Stability and Excellent Thermal Insulating Performance. | In compared with single component aerogel, hybrid
aerogel with multi-components possessing enhanced properties, especially high thermal
stabilities which are our concerns in this paper, are the promised materials in
various applications. However, how the mixing between variable components
within hybrid aerogel affects their properties still not very clear and needs
more research efforts. In the present research, we chose a ZrO<sub>2</sub>/SiO<sub>2</sub>
hybrid aerogel as represent to study their mixing and the resulted thermal
stabilities. We designed a series of ZrO<sub>2</sub>/SiO<sub>2</sub>
hybrid aerogels with variable ZrO<sub>2</sub>/SiO<sub>2</sub> ratio deriving
from tailored sol-gel parameters, and then studied their shrinkages, nanopore
collapses and crystallization behaviors upon
heat-treatment. | Benxue Liu; Min Gao | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743714c89197e7cad263b/original/highly-mixed-zr-o2-si-o2-hybrid-aerogel-deriving-from-freely-tangled-weakly-branched-primary-clusters-enables-improved-thermal-stability-and-excellent-thermal-insulating-performance.pdf |
66852f3b01103d79c5e5076e | 10.26434/chemrxiv-2024-w3twb | Transition-path times of molecular shuttles under mechanical equilibrium show symmetry | Determining microscopic reversibility during the operation of synthetic devices is crucial for a fundamental understanding of the thermodynamic and kinetic aspects that rule their operation. Here, we used optical tweezers to measure transition paths of individual molecular shuttles oscillating between two different equilibrating co-conformations under the application of mechanical force. We experimentally confirm that the transition-path times of individual molecular shuttles under mechanical equilibrium show symmetry, as derived from the principle of microscopic reversibility. Furthermore, we show that the relation proposed by Bier, Astumian, and colleagues (Bier-Astumian relation), which is a corollary of microscopic reversibility, can be used to extract thermodynamic variables from the analysis of the transition-path times. These measurements provide a first look at the principle of microscopic reversibility in molecular shuttles at the single-molecule level and pave the way for a detailed and quantitative understanding of the dynamics of synthetic molecular machines. | Tomás Nicolás-García; Natalia Martín Sabanés; Rebeca Bocanegra; R. Dean Astumian; Emilio Perez; Borja Ibarra | Physical Chemistry; Organic Chemistry; Nanoscience; Supramolecular Chemistry (Org.); Physical and Chemical Processes; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66852f3b01103d79c5e5076e/original/transition-path-times-of-molecular-shuttles-under-mechanical-equilibrium-show-symmetry.pdf |
65773a35bec7913d276052f2 | 10.26434/chemrxiv-2023-03c1m-v2 | Recent Advancements and Trends in 3D Printing for Biomedical Applications | 3D printing has been applied to multiple areas since 1980. Biomedical applications have grown significantly and become the mainstream of 3D printing applications. In this review, we elucidated the publication distribution of biomedical 3D printing using the CAS Content Collection. From 2010 to 2021, journal and patent publications grew steadily, except for the decline in patent publications in 2021. In general, journal publications are higher than patents. There are approximately 90 countries participating in the 3D printing application in this field. We are reporting the publication distributions related to the following categories: (1) four major techniques: powder bed fusion, extrusion, jetting, and photopolymerization; (2) substances: polymers and inorganic substances; (3) biomedical fields: tissue/organs, orthopedic/prosthetic, pharmaceutical, and others. We investigated the correlation between these search terms and revealed the co-occurrence of the concepts appearing in publications related to 3D printing in biomedical applications. This review provides an overview of the current advancement and trends of 3D printing applications in the biomedical area. | Chia-Wei Hsu; Magesh Ganesan; Terra Masumoto; Xiang Yu | Materials Science | CC BY 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65773a35bec7913d276052f2/original/recent-advancements-and-trends-in-3d-printing-for-biomedical-applications.pdf |
61816de57a0021c36343ce26 | 10.26434/chemrxiv-2021-qnhrx-v2 | Surfactant-free syntheses and pair distribution function analysis of osmium nanoparticles
| A surfactant-free synthesis of precious metal nanoparticles performed in low boiling point solvents and in alkaline conditions has been reported recently. This strategy presents several advantages over alternative colloidal syntheses. The resulting nanoparticles are readily relevant for applications like catalysis and the synthetic process is compatible with large scale production. Alkaline mono-alcohols are here investigated as solvent and reducing agents to obtain colloidal Os nanoparticles by this low temperature (< 100 °C) surfactant-free synthesis. The effect of precursor (OsCl3 or H2OsCl6), precursor concentration (up to 100 mM), solvent (methanol or ethanol), presence or absence of base (NaOH) and addition of water (0 to 100 v.%) on the resulting nanomaterials is discussed. It is fond that no base is required to obtain Os nanoparticles as opposed to the case of Pt NPs for instance. The robustness of the synthesis for concentration of precursor up to 100 mM allows to perform X-ray total scattering with pair distribution function (PDF) analysis that shows that the 1-2 nm hcp NPs forms from chain-like [OsOxCly]-complexes. | Mikkel Juelsholt; Jonathan Quinson; Emil Kjær; Baiyu Wang; Rebecca Pittkowski; Susan Cooper; Tiffany Kinnibrugh; Søren Simonsen; Luise Theil Kuhn; Maria Escudero-Escribano; Kirsten Jensen | Materials Science; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61816de57a0021c36343ce26/original/surfactant-free-syntheses-and-pair-distribution-function-analysis-of-osmium-nanoparticles.pdf |
6557a7146e0ec7777f271f23 | 10.26434/chemrxiv-2023-qzj4t-v2 | δ-bonding and spin-orbit coupling make SrAg4Sb2 a topological insulator | Bonding interactions and spin-orbit coupling in the topological insulator SrAg4Sb2 are investigated using DFT with orbital projection analysis. Ag-Ag delta bonding is a key ingredient in the topological insulating state because the 4dxy + 4dx2−y2 delta antibonding band forms a band inversion with the 5s sigma bonding band. Spin-orbit coupling is required to lift d orbital degeneracies and lower the antibonding band enough to create the band inversion. These bonding effects are enabled by a longer-than-covalent Ag-Ag distance in the crystal lattice, which might be a structural characteristic of other transition metal based topological insulators. A simplified model of the topological bands is constructed to capture the essence of the topological insulating state in a way that may be engineered in other materials. | Harry Morgan; William Laderer; Anastassia Alexandrova | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Solid State Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6557a7146e0ec7777f271f23/original/bonding-and-spin-orbit-coupling-make-sr-ag4sb2-a-topological-insulator.pdf |
62acd963f70c21d12c32279f | 10.26434/chemrxiv-2022-7n0n5-v2 | Evolution of Aqueous Electron with Varying Temperature | The temperature-dependent properties of the aqueous electron have been extensively studied using mixed quantum-classical simulations in a wide range of thermodynamic conditions based on one-electron pseudopotentials. While the cavity model appears to explain most of the physical properties of the aqueous electron, only a non-cavity model has so far been successful in accounting for the temperature dependence of the absorption spectrum. Here, we present an accurate and efficient description of the aqueous electron under various thermodynamic conditions by combining hybrid functional-based molecular dynamics, machine learning techniques, and multiple time-step methods.
Our advanced simulations accurately describe the temperature dependence of the absorption maximum in the presence of cavity formation. Specifically, our work
reveals that the red shift of the absorption maximum results from an increasing gyration radius with temperature, rather than from global density variations as
previously suggested. | Jinggang Lan; Vladimir V. Rybkin; Alfredo Pasquarello | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62acd963f70c21d12c32279f/original/evolution-of-aqueous-electron-with-varying-temperature.pdf |
6491f0fca2c387fa9aa64364 | 10.26434/chemrxiv-2023-8lhrq-v2 | Validation of In-field Calibration for Low-Cost Sensors
Measuring Ambient Particulate Matter in Kolkata, India | Low-cost sensors (LCS) provide opportunities for neighborhood-level air pollution data collection, yet significant knowledge gaps remain regarding the accurate application and interpretation of LCS. In this study, we present an in-field calibration of a network of 20 low-cost ambient particulate matter sensors (LCS) in greater Kolkata, India, operating between October 2018-April 2019. In order to understand LCS performance in relation to local reference-grade PM2.5 monitors (RGMs), three of these LCS were co-located with RGMs operated by the West Bengal Pollution Control Board at Rabindra Bharati University (RBU), Victoria Memorial (VICTORIA), and Padmapukur (Howrah, PDM). Data from the co-locations were used to calibrate the LCS network using random forest regression and multiple linear regression approaches. Measured relative humidity and temperature were significant model features. Agreement between the LCS and RGM for 24-h averaged PM2.5 measurements was strongest at RBU, with an uncalibrated root mean squared error (RMSE) of 27.1 μg m-3, followed by PDM (32.6 μg m-3) and VICTORIA (50.7 μg m-3). Multiple linear regression was used to derive calibration models. Cross-calibration between co-located LCS-RGM pairs was tested. The LCS data after cross-calibration correctly identified days as being in or out of attainment with the 24h National Ambient Air Quality Standard of 60 μg m-3 91% of the time. The corrected data accurately identifies days with an India scale Air Quality Index of “poor” or worse 94% of the time. This suggests that LCS can be a useful supplement to RGM networks for air quality management. Diurnal trends and a high level of correlation across the hybrid LCS-RGM network suggest regional and secondary sources of PM2.5 are important in Kolkata. | Siddharth Nobell; Arnab Majumdar; Shovon Mukherjee; Sukumar Chakraborty; Sanjoy Chatterjee; Soumitra Bose; Anindita Dutta; Sandhya Sethuraman; Daniel Westervelt; Shairik Sengupta; Rakhi Basu; V. Faye McNeill | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6491f0fca2c387fa9aa64364/original/validation-of-in-field-calibration-for-low-cost-sensors-measuring-ambient-particulate-matter-in-kolkata-india.pdf |
60c7582e469df4929cf455a8 | 10.26434/chemrxiv.14519073.v1 | A Unified Hamiltonian Formalism of Jahn-Teller and Pseudo-Jahn-Teller Problems in Axial Symmetries | A formalism for expansions of all Jahn-Teller and pseudo-Jahn-Teller Hamiltonian
operators in all axial symmetries is presented. The formalism provides Hamiltonian
expansions up to arbitrarily high order and including an arbitrary number of vibra?tional modes, which are of arbitrary types. It consists of three equations and two
tables. The formalism is user-friendly since it can be used without understanding its
derivation. An example of E00
3 ⊗ e
0
1
Jahn-Teller interaction of cycloheptatrienyl cation
is used to demonstrate the correctness of the formalism. A Python program is devel?oped to automate the generation of Hamiltonian expansions for all axial Jahn-Teller
and pseodo-Jahn-Teller problems, , and interface the expansions to quantum dynamics
simulation program. This is the first unified Hamiltonian formalism for axial Jahn?Teller and pseudo-Jahn-Teller problems. And it is the only one. | James Brown; Robert Lang; Tao Zeng | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7582e469df4929cf455a8/original/a-unified-hamiltonian-formalism-of-jahn-teller-and-pseudo-jahn-teller-problems-in-axial-symmetries.pdf |
6346e084bb6d8b5c9e5623f0 | 10.26434/chemrxiv-2022-v1zwx | Metal-Free S-Arylation of Phosphorothioate Diesters and Re-lated Compounds with Diaryliodonium Salts | We developed a direct metal-free S-arylation of phosphorothioate diesters using diaryliodonium salts. The meth-od allows for the preparation under simple conditions of a broad range of S-aryl phosphorothioates, including complex molecules (e.g., dinucleotide- or TADDOL-derivatives), as well as other related organophosphorus compounds arylated at chalcogen. The reaction proceeds with a full retention of the stereogenic center at phos-phorus atom, opening convenient access to P-chiral products. The mechanism of the reaction was established using DFT calculations. | Sudeep Sarkar; Marcin Kalek | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6346e084bb6d8b5c9e5623f0/original/metal-free-s-arylation-of-phosphorothioate-diesters-and-re-lated-compounds-with-diaryliodonium-salts.pdf |
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