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61cdcd877f367ebdcb64f0a2 | 10.26434/chemrxiv-2021-w1p7q | Shelf-stable electrophilic reagents for the direct incorporation of SCF2CF2H and SCF2CF3 motifs | The introduction of fluoroalkylthioether groups has attracted the attention of the drug discovery community given the special physicochemical and pharmacokinetic features they confer to bioactive compounds. Synthetic advances in the field have been capitalized by methods to incorporate SCF3 and SCF2H motifs, however, longer and synthetically more challenging polyfluoroethyl chains are still underdeveloped. Here, two saccharin-based electrophilic reagents have been disclosed for the efficient incorporation of SCF2CF2H and SCF2CF3 motifs. Their reactivity performance has been thoroughly investigated with a variety of nucleophiles such as thiols, alcohols, amines, alkenes, (hetero)aromatics, and organometallic species, including natural products and pharmaceuticals. Finally, multigram-scale preparation and divergent derivatization has been explored from SCF2CF2H derivatives. | Jordi Mestre; Miguel Bernús; Sergio Castillón; Omar Boutureira | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cdcd877f367ebdcb64f0a2/original/shelf-stable-electrophilic-reagents-for-the-direct-incorporation-of-scf2cf2h-and-scf2cf3-motifs.pdf |
612f62e9d5f08085f7b7e6a7 | 10.26434/chemrxiv-2021-qhl2q | Catalytic Reduction of Dinitrogen to Ammonia and Hydrazine Using Iron–Dinitrogen Complexes Bearing Anionic Benzene-Based PCP-type Pincer Ligands | Among synthetic models of nitrogenases, iron–dinitrogen complexes with a Fe–C bond have attracted increasing attention in recent years. Here we report the synthesis of square-planar iron(I)–dinitrogen complexes supported by anionic benzene-based PCP- and POCOP-type pincer ligands as carbon donors. These complexes catalyze the formation of ammonia and hydrazine from the reaction of dinitrogen (1 atm) with a reductant and a proton source at -78 °C, producing up to 252 equiv of ammonia and 68 equiv of hydrazine (388 equiv of fixed N atom) based on the iron atom of the catalyst. Anionic iron(0)–dinitrogen complexes, considered an essential reactive species in the catalytic reaction, are newly isolated from the reduction of the corresponding iron(I)–dinitrogen complexes. This study examines their reactivity using experiments and DFT calculations. | Shogo Kuriyama; Takeru Kato; Hiromasa Tanaka; Asuka Konomi; Kazunari Yoshizawa; Yoshiaki Nishibayashi | Organometallic Chemistry; Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612f62e9d5f08085f7b7e6a7/original/catalytic-reduction-of-dinitrogen-to-ammonia-and-hydrazine-using-iron-dinitrogen-complexes-bearing-anionic-benzene-based-pcp-type-pincer-ligands.pdf |
6126d25790051e1844e0ef7e | 10.26434/chemrxiv-2021-qc8vv-v2 | A reactivity map for oxidative addition enables quantitative predictions for multiple catalytic reaction classes | Making accurate, quantitative predictions of chemical reactivity based on molecular structure is an unsolved problem in chemical synthesis, particularly for complex molecules. We report a generally applicable, mechanistically based structure-reactivity approach to create a quantitative model for the oxidative addition of (hetero)aryl electrophiles to palladium(0), which is a key step in myriad catalytic processes. This model links simple molecular descriptors to relative rates of oxidative addition for 79 substrates, including chloride, bromide and triflate leaving groups. Because oxidative addition often controls the rate and/or selectivity of palladium-catalyzed reactions, this model can be used to make quantitative predictions about catalytic reaction outcomes. Demonstrated applications include a multivariate linear model for the initial rate of Sonogashira coupling reactions, and successful site-selectivity predictions for a series of multihalogenated substrates relevant to the synthesis of pharmaceuticals and natural products. | Jingru Lu; Sofia Donnecke; Irina Paci; David Leitch | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6126d25790051e1844e0ef7e/original/a-reactivity-map-for-oxidative-addition-enables-quantitative-predictions-for-multiple-catalytic-reaction-classes.pdf |
60c74769f96a000408286f1a | 10.26434/chemrxiv.11653470.v1 | Chemoselective Ring-Opening Polymerization of Bio-Renewable α-Methylene-γ-Butyrolactone via an Organophosphazene/urea Binary Synergistic Catalytic System Toward a Sustainable Polyester | Despite the great potential
of bio-renewable a-methylene-<a></a><a></a><a>g-butyrolactone</a> (MBL) to produce functional recyclable polyester, the
ring-opening polymerization (ROP) of MBL remains as a challenge due to the
competing polymerization of the highly reactive exocyclic double bond and the
low strained five membered ring. In this contribution, we present the first
organocatalytic chemoselective ROP of MBL to exclusively produce recyclable
unsaturated polyester by utilizing a phosphazene base/urea binary catalyst. We
show that delicate chemoselectivity can be realized by controlling the
temperature and using selected urea catalysts. Experimental and theoretical
calculations provide mechanistic insights and indicate that the kinetically
controlled ROP pathway is favored by using urea with stronger acidity at low temperatures. | Yong Shen; Wei Xiong; YongZheng Li; ZhiChao Zhao; Hua Lu; Zhibo Li | Polymerization (Polymers); Polymerization catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74769f96a000408286f1a/original/chemoselective-ring-opening-polymerization-of-bio-renewable-methylene-butyrolactone-via-an-organophosphazene-urea-binary-synergistic-catalytic-system-toward-a-sustainable-polyester.pdf |
60c754c7337d6c5d20e28ab6 | 10.26434/chemrxiv.13721719.v1 | Physical Property Scaling Relationships for Polyelectrolyte Complex Micelles | <p>Polyelectrolyte complex micelles (PCMs) are widely used in the delivery of hydrophilic payloads. Their attractive features include an ability to tune physical attributes, which are strongly dependent on the size and chemical structure of each polymer block. Neutral blocks drive nanoscale phase separation while charged blocks control micelle core size and stability. An understanding of physical property behavior controlled by block size is crucial when designing for use in dynamic or biological environments and provides a greater understanding of the physics of polyelectrolyte assembly. In this work, we use small angle x-ray scattering, and light scattering to determine precise scaling behaviors of physical micelle parameters for commonly used polyelectrolytes. We then compare our results to accumulated published data and theory to show strong agreement, suggesting these laws are universal for PCMs.</p> | Alexander Marras; Trinity Campagna; Jeffrey Vieregg; Matthew Tirrell | Polyelectrolytes - Materials; Biopolymers; Polyelectrolytes - Polymers; Polymers; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754c7337d6c5d20e28ab6/original/physical-property-scaling-relationships-for-polyelectrolyte-complex-micelles.pdf |
6304c7141945adb313e3d431 | 10.26434/chemrxiv-2022-wwxr7 | Viral infection and immunity view of SARS-CoV-2 using RBD-assembled DNA Soccer-ball Framework | Elevated understanding of the viral infection process contributes to development of neutralizing agents and vaccine to combat infectious diseases. Although crystal structure of single SARS-CoV-2 spike/RBD and host receptor ACE2 is known, the viral attachment and immune response initiated by numbers and distribution patterns of natural spikes on SARS-CoV-2 are still obscure. Leveraging a ~74 nm DNA soccer-ball framework (DSF), we developed an aptamer-guided SARS-CoV-2 RBD precisely assembly strategy, thereby exploring the viral infection and immune response in specific numbers and distributions of RBDs. Thirty evenly distributed RBDs on DSF could achieve sufficient binding affinity against host cell (Kd of 122.2 pM), whereas 60 evenly distributed RBDs on DSF could bind to host cell rapidly (Ka of 0.845 min-1). While RBDs in centralized manner compared to evenly distribution facilitated higher and faster binding to host. Moreover, evenly distributed 20 RBDs on DSF achieved up to 88% immunity elicitation of macrophage cells. Overall, this strategy provides a prospective direction for the assembly of virus-like particles based on DNA origami, thereby facilitating understanding of viral infection and efficient vaccine design. | Jialu Zhang; Yunyun Xu; Mingying Chen; Yihao Huang; Ting Song; Chaoyong Yang; Yang Yang; Yanling Song | Analytical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304c7141945adb313e3d431/original/viral-infection-and-immunity-view-of-sars-co-v-2-using-rbd-assembled-dna-soccer-ball-framework.pdf |
67d7b7f7fa469535b97c021a | 10.26434/chemrxiv-2025-n36r6 | Transferable Machine Learning Interatomic Potential for Pd-Catalyzed Cross-Coupling Reactions | Finding efficient substrate-catalyst combinations for palladium-catalyzed cross-coupling reactions remains a critical challenge in synthetic chemistry, with broad implications for pharmaceutical and materials manufacturing. We report AIMNet2-Pd, a machine learned interatomic potential that enables rapid, accurate computational studies of palladium-catalyzed cross-coupling reactions. AIMNet2-Pd replaces computationally expensive electronic structure calculations with a neural network-based model that performs geometry optimization, transition state searches, and energy calculations in seconds while maintaining accuracy within 1-2 kcal mol⁻¹ and ~0.1 Å compared to the reference QM calculations. AIMNet2-Pd makes computational high-throughput catalyst screening and mechanistic studies of realistic systems feasible by providing on-demand thermodynamic and kinetic predictions for each step of a catalytic cycle. Importantly, the applicability of the systems extends beyond the monophosphine ligands in Pd(0)/Pd(II) cycles for which it has been trained on to chemically diverse Pd complexes. This demonstrates AIMNet2-Pd's utility to serve as a general-purpose and high-throughput tool for studying catalytic reactions. | Dylan Anstine; Roman Zubatyuk; Liliana Gallegos; Robert Paton; Olaf Wiest; Benjamin Nebgen; Travis Jones; Gabe Gomes; Sergei Tretiak; Olexandr Isayev | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Machine Learning; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d7b7f7fa469535b97c021a/original/transferable-machine-learning-interatomic-potential-for-pd-catalyzed-cross-coupling-reactions.pdf |
60c756cb702a9b06f318c99c | 10.26434/chemrxiv.14227133.v2 | Enantioselective Total Synthesis of the Archaeal Lipid Parallel GDGT-0 | Archaeal glycerol dibiphytanyl glycerol tetraethers (GDGT) are some of the most unusual membrane lipids identified in nature. These amphiphiles are the major constituents of the membranes of numerous <i>Archaea</i>, some of which are extremophilic organisms. Due to their unique structures, there has been significant interest in studying both the biophysical properties and the biosynthesis of these molecules. However, these studies have thus far been hampered by limited access to chemically pure samples. Herein, we report a concise and stereoselective synthesis of the archaeal tetraether lipid GDGT-0 and the synthesis and self-assembly of derivatives bearing different polar groups. | Isaac D. Falk; Bálint Gál; Ahanjit Bhattacharya; Jeremy H. Wei; Paula V. Welander; Steven Boxer; Noah Burns | Natural Products; Organic Synthesis and Reactions; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756cb702a9b06f318c99c/original/enantioselective-total-synthesis-of-the-archaeal-lipid-parallel-gdgt-0.pdf |
653fcdd248dad23120b54675 | 10.26434/chemrxiv-2023-0n1pq | Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations | Relative binding free energy (RBFE) calculations have emerged as a powerful tool supporting ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, in particular the setup of such calculations. Atom mapping algorithms are an essential component in setting up automatic large-scale hybrid topology RBFE calculation campaigns. Traditional algorithms typically employ a 2D subgraph isomorphism solver (SIS) in order to estimate the maximum common substructure (MCS). SIS-based approaches can be limited by time-intensive operations and issues with capturing geometry-linked chemical properties, leading potentially to suboptimal solutions. To overcome these limitations, we have developed Kartograf, a geometric-graph-based algorithm that uses primarily the 3D coordinates of atoms to find a mapping between two ligands. In free energy approaches, the ligand conformations are usually derived from docking or other previous modeling approaches giving the coordinates a certain importance. By considering the spatial relationships between atoms related to the molecule coordinates, our algorithm bypasses the computationally complex subgraph matching of SIS-based approaches and reduces the problem to a much simpler bipartite graph matching problem. Moreover, Kartograf effectively circumvents typical mapping issues induced by molecule symmetry and stereoisomerism, making it a more robust approach for atom mapping from a geometric perspective. To validate our method, we have calculated mappings with our novel approach using a diverse set of small molecules and used the mappings in relative hydration and binding free energies calculations. The comparison with two SIS-based algorithms showed that Kartograf offers a fast alternative approach. The code for Kartograf is freely available on Github (https://github.com/OpenFreeEnergy/kartograf). While developed for the OpenFE ecosystem, Kartograf can also be utilized as a standalone Python package. | Benjamin Ries; Irfan Alibay; David W H Swenson; Hannah M Baumann; Michael M Henry; James RB Eastwood; Richard J Gowers | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653fcdd248dad23120b54675/original/kartograf-an-accurate-geometry-based-atom-mapper-for-hybrid-topology-relative-free-energy-calculations.pdf |
60c74e86f96a001999287b06 | 10.26434/chemrxiv.12769880.v1 | High Concentrations of Unidentified Extractable Organofluorine observed in Blubber from a Greenland Killer Whale (Orcinus orca) | It is generally accepted that per- and polyfluoroalkyl substances
(PFASs) occur primarily in protein-rich tissues such as blood and liver, but few
studies have examined the occurrence of PFASs (in particular emerging PFASs),
in lipid-rich tissues such as blubber. Here we report the distribution of 24 PFASs,
total fluorine (TF) and extractable organic fluorine (EOF) in eight different
tissues of a killer whale (<i>Orcinus orca</i>)
from East Greenland. The sum of target PFAS concentrations was highest in liver
(352 ng/g ww) and decreased in the order blood > kidney ≈ lung ≈ ovary > skin
≈ muscle ≈ blubber. Most of the EOF was made up of known PFASs in all tissues
except blubber, which displayed the highest concentration of EOF, almost none
of which was attributed to targeted PFASs. Suspect screening using high-resolution
mass spectrometry revealed the presence of additional PFASs but the magnitude
of peak areas could not explain the high concentrations of EOF in blubber. While
the identity of this unknown organofluorine and its pervasiveness in marine
mammals requires further investigation, this work suggests that exposure of
killer whales to organofluorine substances may be underestimated by determination
of legacy PFASs exclusively in liver tissues. | Lara Schultes; Carmen van Noordenburg; Kyra Spaan; Merle Plassmann; Malene Simon; Anna Roos; Jonathan Benskin | Environmental Science; Environmental Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e86f96a001999287b06/original/high-concentrations-of-unidentified-extractable-organofluorine-observed-in-blubber-from-a-greenland-killer-whale-orcinus-orca.pdf |
60c744bb702a9b2c3018a8bf | 10.26434/chemrxiv.7898246.v2 | The Trajectory Taken by Dimeric Cu/Zn Superoxide Dismutase Through the Protein Unfolding and Dissociation Landscape Is Modulated by Salt-Bridge Formation | <p>Native mass spectrometry (MS) is a powerful means for studying
macromolecular protein assemblies, including accessing activated states. However,
much remains to be understood about what governs which regions of the protein
(un)folding funnel are explored by activation of protein ions in vacuum. Here
we examine the trajectory that dimeric Cu/Zn superoxide dismutase (SOD1) dimers
take over the unfolding and dissociation free energy landscape in vacuum. We
examined wild-type SOD1 and six disease-related point-mutants by using tandem
MS and ion-mobility MS (MS/MS-IMMS) coupled with increasing collisional activation
potentials. For six of the seven SOD1 variants, increasing activation promoted
dimers to transition through two unfolding events to access three gas-phase
conformers before dissociating symmetrically into monomers with (as near as
possible) equal charges. The exception was G37R, which proceeded only through the
first unfolding transition, and displayed a much higher abundance of asymmetric
products. We localise this effect to the formation of a new salt-bridge in the
first activated conformation. To examine the data quantitatively, we generated
a model of SOD1 gas phase unfolding and dissociation, and applied Arrhenius-type
analysis to estimate the barriers on the corresponding free energy landscape. This
reveals an increase in the barrier height to unfolding in G37R to be >5
kJ/mol<sup>-1</sup> higher than for the other variants, consistent with
expectations for the strength of a salt-bridge. Our work demonstrates the
importance of bond formation during the unfolding of proteins in vacuum, and provides
a framework for comparing quantitatively the free energy landscape they explore
upon activation.</p> | Luke McAlary; Julian Harrison; J. Andrew Aquilina; Steven Fitzgerald; Celine Kelso; Justin L. P. Benesch; Justin J Yerbury | Bioorganic Chemistry; Mass Spectrometry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744bb702a9b2c3018a8bf/original/the-trajectory-taken-by-dimeric-cu-zn-superoxide-dismutase-through-the-protein-unfolding-and-dissociation-landscape-is-modulated-by-salt-bridge-formation.pdf |
60c757dfee301c7593c7b648 | 10.26434/chemrxiv.14477691.v1 | Machine Learning as a Tool to Engineer Microstructures: Morphological Prediction of Tannin-Based Colloids Using Bayesian Surrogate Models | Oxidized tannic acid (OTA) is a useful biomolecule with a strong tendency to form complexes with metals and proteins. In this study we open the possibility to further the application of OTA when assembled as supramolecular systems, which typically exhibit functions that correlate with shape and associated morphological features. We use artificial intelligence (AI) to selectively engineer OTA into particles encompassing 1-dimensional (1D) to 3-dimensional (3D) constructs. We employed Bayesian regression to correlate colloidal suspension conditions (pH and p<i>K</i><sub>a</sub>) with the size and shape of the assembled colloidal particles. Fewer than 20 experiments were found to be sufficient to build surrogate model landscapes of OTA morphology in the experimental design space, which were chemically interpretable and endowed predictive power on data. We produced multiple property landscapes from the experimental data, helping us to infer solutions that would satisfy, simultaneously, multiple design objectives. The balance between data efficiency and the depth of information delivered by AI approaches testify to their potential to engineer particles, opening new prospects in the emerging field of particle morphogenesis, impacting bioactivity, adhesion, interfacial stabilization and other functions inherent to OTA. | Soo-Ah Jin; Tero Kämäräinen; Patrick Rinke; Orlando J. Rojas; Milica Todorovic | Process Control; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757dfee301c7593c7b648/original/machine-learning-as-a-tool-to-engineer-microstructures-morphological-prediction-of-tannin-based-colloids-using-bayesian-surrogate-models.pdf |
661858b1418a5379b0a7a7a8 | 10.26434/chemrxiv-2024-w29b1 | Meta-Analysis of Molecular Design Strategies for Non-Fullerene Acceptor Based Organic Solar Cell Materials | The design of high-performing OSC materials is an active field of research. Many review articles summarize certain subclasses of NFAs, however, no broad overall analysis has been performed on the photovoltaic impact of chemical modifications made. This meta-analysis investigates various molecular design strategies for NFAs and donors and their effects on OSC device performance. Using a new dataset containing 1975 NFA/donor pairs, we performed matched-pair analysis on many design strategies to try to discern whether it has a significant impact on PCE. For the NFA, the class and size of the NFA, heteroatom substitution, types of rings and their sequence in the fused core, side chains, halogenation of terminal groups, and the presence of a pi-bridge are examined. For the donor polymers, the monomer identities, the types of side chains, and the halogenation of the polymer are examined. Some molecular design strategies that were found to significantly improve the PCE include branched instead of linear side chains, fused cores containing 8 rings, fused NFAs containing pyran, pyrrole, and selenophene, fused cores containing an odd number of thiophenes, the presence of pi-bridge units, halogenating the NFA and donor, incorporation of alkylsilyl chains instead of alkyl chains in donor polymers, as well as multiple others. | Brianna Greenstein; Kyler Daas; Geoffrey Hutchison | Polymer Science; Energy; Conducting polymers; Organic Polymers; Photovoltaics; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661858b1418a5379b0a7a7a8/original/meta-analysis-of-molecular-design-strategies-for-non-fullerene-acceptor-based-organic-solar-cell-materials.pdf |
6349a490de2a213e57a5771d | 10.26434/chemrxiv-2022-v838h | Economic Evaluation of Infrastructures for Thermochemical Upcycling of Post-Consumer Plastic Waste | Thermochemical technologies, such as pyrolysis, offer a potentially scalable pathway for upcycling diverse types of plastic waste (PW) into value-added chemicals. However, deploying these technologies in waste management infrastructures is not straightforward because such systems involve a wide range of interdependent stakeholders, processing facilities, and products. In this work, we present a holistic optimization framework that integrates value-chain analysis, techno-economic analysis, and life-cycle analysis for investigating the economic viability and environmental benefits of upcycling infrastructures that collect, sort, clean, and process post-consumer PW for producing virgin polymer resins. The framework is applied to a case study in the upper Midwest region of the US. Our analysis reveals that the infrastructures are economically viable and could activate a regional circular economy that generates over 1 billion USD in annual profit. Moreover, our analysis reveals that this economy can reduce the carbon footprint of PW incineration by half. Our framework also determines the inherent values of post-consumer PW and of derived products such as plastic bales and pyrolysis oil; we find that, in these infrastructures, PW becomes a highly valuable feedstock with a market value of 500 USD/tonne. We discuss how this market value can generate incentives that foster more effective waste pre-sorting practices by consumers that can help bypass material recycling facilities and increase total system profit. | Jiaze Ma; Philip Tominac; Horacio Aguirre-Villegas; Olumide Olafasakin; Mark Mba-Wright; Craig H. Benson; George W. Huber; Victor M. Zavala | Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Natural Resource Recovery; Petrochemicals | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6349a490de2a213e57a5771d/original/economic-evaluation-of-infrastructures-for-thermochemical-upcycling-of-post-consumer-plastic-waste.pdf |
6379bf0255455e583c8bc595 | 10.26434/chemrxiv-2022-lvt66 | Oxygen K-edge spectra of Yb2O 3 polymorphs, Yb2SiO5, and Yb2Si2O7: First-principles simulations and EELS measurements | First-principles calculations, along with a core-hole technique, are adopted to simulate oxygen K-edge spectra for three polymorphs of Yb2O3 and two types of ytterbium silicates (i.e., Yb2SiO5 and Yb2Si2O7). The twe Yb silicates are compared with experimental spectra, which are measured via electron energy-loss spectroscopy for a polycrystalline sample including both phases. The simulated O K-edge spectra of cubic, monoclinic, and hexagonal Yb2O3 exhibit characteristic twin peaks, which resulted from crystal fi eld splitting of unoccupied Yb5 d orbitals in Yb-O polyhedra. Spacing between the two peaks refl ects a degree of distortion of the polyhedra and local coordination environments around O atoms. The simulated and experimental O K-edge spectra of Yb2SiO5 and Yb2Si2O7 also show twin peaks, where lower-energy peaks are signifi cantly reduced compared to those of Yb2O3. A small diff erence in the lower-energy peaks, which refl ect the local environments of O atoms, enables us to identify Yb silicate phases from an O K-edge spectrum. The derived insights could be widely extended to rare-earth oxides.
| Takafumi Ogawa; Bin Miao; Jiake Wei; Bin Feng; Naoya Shibata; Tsuneaki Matsudaira; Satoshi Kitaoka | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6379bf0255455e583c8bc595/original/oxygen-k-edge-spectra-of-yb2o-3-polymorphs-yb2si-o5-and-yb2si2o7-first-principles-simulations-and-eels-measurements.pdf |
60c748984c891918ccad2f58 | 10.26434/chemrxiv.11936292.v1 | Targeted Oxidation Strategy (TOS) for Potential Inhibition of Coronaviruses by Disulfiram — a 70-Year Old Anti-Alcoholism Drug | <p>In the new
millennium, the outbreak of new coronavirus has happened three times: SARS-CoV,
MERS-CoV, and 2019-nCoV. Unfortunately, we still have no pharmaceutical weapons
against the diseases caused by these viruses. The pandemic of 2019-nCoV reminds
us of the urgency to search new drugs with totally different mechanism that may
target the weaknesses specific to coronaviruses. Herein, we disclose a new targeted
oxidation strategy (TOS II) leveraging non-covalent interactions potentially to
oxidize and inhibit the activities of cytosolic thiol proteins via
thiol/thiolate oxidation to disulfide (TOD). Quantum mechanical calculations
show encouraging results supporting the feasibility to selectively oxidize
thiol of targeted proteins via TOS II even in relatively reducing cytosolic
microenvironments. Molecular docking against the two thiol proteases M<sup>pro</sup>
and PL<sup>pro</sup> of 2019-nCoV provide evidence to support a TOS II
mechanism for two experimentally identified anti-2019-nCoV disulfide oxidants: disulfiram
and PX-12. Remarkably, disulfiram is an anti-alcoholism drug approved by FDA 70
years ago, thus it can be immediately used in phase III clinical trial for
anti-2019-nCoV treatment. Finally, a preliminary list of promising TOS II drug
candidates targeting the two thiol proteases of 2019-nCoV are proposed upon
virtual screening of 32143 disulfides.</p> | Luyan Xu; Jiahui Tong; Yiran Wu; Suwen Zhao; Bo-Lin Lin | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748984c891918ccad2f58/original/targeted-oxidation-strategy-tos-for-potential-inhibition-of-coronaviruses-by-disulfiram-a-70-year-old-anti-alcoholism-drug.pdf |
61e999c27110e6a8646b273a | 10.26434/chemrxiv-2022-78t5s | Degradable Polystyrene via the Cleavable Comonomer Approach | Polystyrene (PS) is a major commodity polymer, widely used in various applications ranging from packaging to insulation thanks to its low cost, high stiffness and transparency as well as its relatively high softening temper-ature. Similarly to all polymers prepared by radical polymerization, PS is constituted of a C-C backbone and thus is not degradable. To confer degradability to such materials, the copolymerization of vinyl monomers with cyclic monomer that could undergo radical ring-opening is an efficient methodology to introduce pur-posely cleavable bonds into the polymer backbone. Dibenzo[c,e]-oxepane-5-thione (DOT) is a cyclic thionolac-tone monomer known for its efficient copolymerization with acrylate derivatives but so far could not be incor-porated into PS backbones. From a theoretical study combining DFT and kinetic models using the PREDICI software, we showed that modifying experimental conditions could overcome these limitations and that high molar mass degradable polystyrene (Mw close to 150,000 g.mol-1) could be prepared via statistical insertion of thioester groups into the polymer backbone. Thanks to favorable reactivity ratios allowing only a few mol% of thioester units to be randomly incorporated, there was no major modification of the thermal and mechanical properties of the PS. The degradation of such PS could be performed in THF at RT in one hour using 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) as a base, leading to oligomers with Mn close to 1,000 g.mol-1. We success-fully demonstrate further applicability of these copolymerization systems for the photo-triggered decomposi-tion of PS in solution as well as the synthesis of cross-linked PS networks degradable into soluble side-products | Noémie Gil; Baptiste Caron; Didier Siri; Julien Roche; Slim Hadiouch; Douriya Khedaioui; Stephane Ranque; Carole Cassagne; Damien Montarnal; Didier Gigmes; Catherine Lefay; Yohann Guillaneuf | Materials Science; Polymer Science; Biodegradable Materials; Oligomers; Organic Polymers; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e999c27110e6a8646b273a/original/degradable-polystyrene-via-the-cleavable-comonomer-approach.pdf |
60c752f60f50db86a0397aa8 | 10.26434/chemrxiv.13369763.v1 | Integrated Docking and Enhanced Sampling Based Selection of Repurposing Drugs for SARS-CoV-2 by Targeting Host Dependent Factors | Since the onset of global pandemic, the most focused research currently in progress is the development of vaccine candidates and clinical trials of existing FDA approved drugs for other relevant diseases, in order to repurpose them for the COVID-19. Here, we investigate the drug repurposing strategies to counteract the coronavirus infection which involves several potential targetable host proteins involved in viral replication and disease progression. We report the high throughput analysis of literature-derived repurposing drug candidates that can be used to target the genetic regulators known to interact with viral proteins based on experimental and interactome studies. In this work we have performed integrated molecular docking followed by molecular dynamics (MD) simulations and free energy calculations through an expedite insilico process where the number of screened candidates reduces sequentially at every step based on physicochemical information. We elucidate that in addition to the pre-clinical and FDA approved drugs that targets specific regulatory proteins, a range of chemical compounds (Nafamostat, Chloramphenicol, Ponatinib) binds to the other gene transcription and translation regulatory protein with higher affinity and may harbour potential for therapeutic uses.<br /> | Amit Kumawat; Sadanandam Namsani; Debabrata Pramanik; Sudip Roy; Jayant K. Singh | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752f60f50db86a0397aa8/original/integrated-docking-and-enhanced-sampling-based-selection-of-repurposing-drugs-for-sars-co-v-2-by-targeting-host-dependent-factors.pdf |
613a734427d906078483159b | 10.26434/chemrxiv-2021-t1db1 | First d0 Metal-Catalyzed Alkyl–Alkyl Cross Coupling Enabled by a Redox-Active Ligand | Alkyl–alkyl cross coupling through well-defined mechanisms that allow for controlled oxidative addition, prevent beta-hydride elimination, and tolerate hindered electrophiles are still challenging. We describe the first report of a redox-active ligand-enabled alkyl–alkyl cross coupling using a d0 metal. This (tris)amido ScIII complex as well as the oxidized variant are thor-oughly characterized (NMR, X-ray, EPR, CV, UV-Vis, DFT). Insight into the likely radical nature of the mechanism is dis-closed. Additionally, a substrate scope that includes functional groups incompatible with late transition metal catalysis, and both coupling partners bearing beta-hydrogens is reported. | Roman Belli; Victoria Tafuri; Matthew Joannou; Courtney Roberts | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Redox Catalysis; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613a734427d906078483159b/original/first-d0-metal-catalyzed-alkyl-alkyl-cross-coupling-enabled-by-a-redox-active-ligand.pdf |
667e9c45c9c6a5c07aac08b7 | 10.26434/chemrxiv-2024-8z1pm | Recycling of Bulk Polyamide 6 by Dissolution- Precipitation in CaCl2-EtOH-H2O Mixtures | Given the problems of virgin plastic production from fossil resources and the growing amount of plastic waste, a rapid transition towards a circular economy is pursued. For recycling, the separation of mixed plastics into pure fractions is of paramount importance to prevent downcycling. Here, experimental parameters for selective bulk dissolution of polyamide 6 (PA 6) filaments (1.75 mm diameter, 1 cm long) using CaCl2-EtOH-H2O mixtures (CEW) at 75 ◦C are investigated. They include the energy supply mode, dissolution time, CEW composition and the CEW:PA mass ratio. Energy supply with ultrasound instead of microwaves improved the yield of dissolved and recovered PA 6 after 5 hours from 31 to 52%. In total, the PA 6 yield after 3 hours of bulk dissolution could be increased from 18 to 69% by changing the energy supply mode from microwave to ultrasound and the H2O:EtOH molar ratio of CEW from 0.40 to 1.33 whilst maintaining an optimal CEW:PA mass ratio of 8.5. Additionally, master plot analysis suggests that dissolution by microwave energy supply follows a contracting cylinder model, while ultrasonic energy supply aligns with a 2D diffusion or third-order kinetic model. Microscopic observations suggest that, in the case of ultrasonic energy supply, oscillating bubbles on the particle surface enhance the dissolution rate of PA 6 filaments in CEW. | Ruben Goldhahn; Ann-Joelle Minor; Liisa Rihko-Struckmann; Siew-Wan Ohl; Patricia Pfeiffer; Claus-Dieter Ohl; Kai Sundmacher | Polymer Science; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667e9c45c9c6a5c07aac08b7/original/recycling-of-bulk-polyamide-6-by-dissolution-precipitation-in-ca-cl2-et-oh-h2o-mixtures.pdf |
629494016209e0e5eb56f4f1 | 10.26434/chemrxiv-2022-jdg2f | Comment on “Following molecular mobility during chemical reactions: no evidence for active propulsion” and “Molecular diffusivity of click
reaction components: the diffusion enhancement question” | We provide arguments why we consider as inaccurate two recent JACS Communications which disagree with this laboratory’s report of boosted diffusion during the copper-catalyzed azide-alkyne cycloaddition click reaction (CuAAC).
Fillbrook et al. claim that their diffusion NMR experiments offer no evidence for boosted diffusion, but their use of Gd3+-chelates
to speed up NMR relaxations times is flawed conceptually, the authors interpreting Gd3+-chelates as inert. Actually, the same features that make gadolinium ions useful as contrast agents in magnetic resonance imaging render them unsuitable for diffusion NMR. Nonetheless, by correctly adjusting technical aspects of measurement, we confirm boosted diffusion even
in the presence of this MRI contrast agent. The second skeptical Communication, by Rezaei-Ghaleh et al., compares to a reference
state that is not meaningful physically. | Tian Huang; Steve Granick | Physical Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629494016209e0e5eb56f4f1/original/comment-on-following-molecular-mobility-during-chemical-reactions-no-evidence-for-active-propulsion-and-molecular-diffusivity-of-click-reaction-components-the-diffusion-enhancement-question.pdf |
66578cf1418a5379b0941b29 | 10.26434/chemrxiv-2024-mctcl | Isolation and Crystallographic Characterization of an Octavalent Co2O2 Diamond Core | High-valent cobalt-oxides play a pivotal role in alternative energy technology as catalysts for water splitting and as cath-odes in lithium-ion batteries. Despite this importance, the properties governing the stability of high-valent cobalt-oxides, and specifically possible oxygen evolution pathways, are not clear. One root of this limited understanding is the scarcity of high-valent, Co(IV)-containing model complexes; there are no reports of stable, well-defined complexes with multiple Co(IV) centers. Here, an oxidatively robust fluorinated ligand scaffold enables the isolation and crystallographic charac-terization of a Co(IV)2-bis-μ-oxo complex. This complex is remarkably stable, in stark contrast with previously reported Co(IV)2 species which are highly reactive, which demonstrates that oxy-Co(IV)2 species are not necessarily unstable with respect to oxygen evolution. This example underscores a new design strategy for highly oxidizing transition metal frag-ments and provides detailed data on a previously inaccessible chemical unit of relevance to O–O bond formation and oxygen evolution. | Joseph Schneider; Shilin Zeng; Sophie Anferov; Alexander Filatov; John Anderson | Inorganic Chemistry; Coordination Chemistry (Inorg.); Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66578cf1418a5379b0941b29/original/isolation-and-crystallographic-characterization-of-an-octavalent-co2o2-diamond-core.pdf |
667a90f15101a2ffa8758487 | 10.26434/chemrxiv-2024-gzzlg-v2 | Simulation-guided engineering enables a functional switch in selinadiene synthase towards hydroxylation | Engineering sesquiterpene synthases to form predefined alternative products is a major challenge due to their diversity in cyclisation mechanisms and our limited understanding of how amino acid changes affect the steering of these mechanisms. Here, we use a combination of atomistic simulation and site-directed mutagenesis to engineer a selina-4(15),7(11)-diene synthase (SdS) such that its final reactive carbocation is quenched by a trapped active site water, resulting in the formation of a complex hydroxylated sesquiterpene (selina-4-ol). Initially, the SdS G305E variant produced 20% selina-4-ol. As suggested by modelling of the enzyme-carbocation complex, selina-4-ol production could be further improved by varying the pH, resulting in selina-4-ol becoming the major product (48%) at pH 6.0. We incorporated the SdS G305E variant along with genes from the mevalonate pathway into bacterial BL21(DE3) cells and demonstrated production of selina-4-ol at a scale of 10 mg/L in batch fermentation. These results highlight opportunities for simulation-guided engineering of terpene synthases to produce predefined complex hydroxylated sesquiterpenes. | Prabhakar L. Srivastava; Sam T. Johns; Angus Voice; Katharine Morley; Andrés M. Escorcia; David J. Miller; Rudolf K. Allemann; Marc W. Van der Kamp | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667a90f15101a2ffa8758487/original/simulation-guided-engineering-enables-a-functional-switch-in-selinadiene-synthase-towards-hydroxylation.pdf |
60c754d9337d6c22b0e28aec | 10.26434/chemrxiv.13749199.v1 | Introduction to Machine Learning for Chemists: An Undergraduate Course Using Python Notebooks for Visualization, Data Processing, Data Analysis, and Data Modeling | Machine Learning, a subdomain of Artificial intelligence, is a pervasive technology that would mold how chemists interact with data. Therefore, it is a relevant skill to incorporate into the toolbox of any chemistry student. This work presents a course that introduces machine learning for chemistry students based on a set of Python Notebooks and assignments. Python language, one of the most popular programming languages, allows for free software and resources, which ensures availability. The course is constructed for students without previous experience in programming, leading to an incremental progression in depth and complexity that covers both programming and machine learning concepts. The examples used are related to real data from physicochemical characterizations of wines, producing an attractive material that captures the interest of students. Topics included are Introduction to Python, Basic Statistics, Data Visualization and Dimension Reduction, Classification, and Regression. | Deborah Lafuente; Brenda Cohen; Guillermo Fiorini; Agustín García; Mauro Bringas; Ezequiel Morzan; Diego Onna | Chemical Education - General; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754d9337d6c22b0e28aec/original/introduction-to-machine-learning-for-chemists-an-undergraduate-course-using-python-notebooks-for-visualization-data-processing-data-analysis-and-data-modeling.pdf |
60c7477d702a9b6ed318adb6 | 10.26434/chemrxiv.11671806.v1 | Phosphonate Metal-Organic Frameworks: A Novel Family of Semiconductors | <p>Herein is reported the first semiconducting and magnetic phosphonate metal-organic framework (MOF), TUB75, which contains a one-dimensional inorganic building unit composed of a zig-zag chain of corner-sharing copper dimers. The solid-state UV-Vis spectrum of TUB75 reveals the existence of a narrow band gap of 1.4 eV, which agrees well with the 1.77 eV one obtained from DFT calculations. Magnetization measurements show that TUB75 is composed of antiferromagnetically coupled copper dimer chains. Due to their rich structural chemistry and exceptionally high thermal/chemical stabilities, phosphonate MOFs like TUB75 may open new vistas in engineerable electrodes for supercapacitors. </p> | Konrad Siemensmeyer; Craig A. Peeples; Patrik Tholen; Bünyemin Çoşut; Gabriel Hanna; Gündoğ Yücesan | Hybrid Organic-Inorganic Materials; Magnetic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7477d702a9b6ed318adb6/original/phosphonate-metal-organic-frameworks-a-novel-family-of-semiconductors.pdf |
60c7447c842e65b592db2478 | 10.26434/chemrxiv.9159872.v2 | Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative | <div><div><div><p>Designing ligands that bind their target biomolecules with high affinity and specificity is a key step in small- molecule drug discovery, but accurately predicting protein-ligand binding free energies remains challenging. Key sources of errors in the calculations include inadequate sampling of conformational space, ambiguous protonation states, and errors in force fields. Noncovalent complexes between a host molecule with a binding cavity and a drug-like guest molecules have emerged as powerful model systems. As model systems, host-guest complexes reduce many of the errors in more complex protein-ligand binding systems, as their small size greatly facilitates conformational sampling, and one can choose systems that avoid ambiguities in protonation states. These features, combined with their ease of experimental characterization, make host-guest systems ideal model systems to test and ultimately optimize force fields in the context of binding thermodynamics calculations.</p><p><br /></p><p>The Open Force Field Initiative aims to create a modern, open software infrastructure for automatically generating and assessing force fields using data sets. The first force field to arise out of this effort, named SMIRNOFF99Frosst, has approximately one tenth the number of parameters, in version 1.0.5, compared to typical general small molecule force fields, such as GAFF. Here, we evaluate the accuracy of this initial force field, using free energy calculations of 43 α and β-cyclodextrin host-guest pairs for which experimental thermodynamic data are available, and compare with matched calculations using two versions of GAFF. For all three force fields, we used TIP3P water and AM1-BCC charges. The calculations are performed using the attach-pull-release (APR) method as implemented in the open source package, pAPRika. For binding free energies, the root mean square error of the SMIRNOFF99Frosst calculations relative to experiment is 0.9 [0.7, 1.1] kcal/mol, while the corresponding results for GAFF 1.7 and GAFF 2.1 are 0.9 [0.7, 1.1] kcal/mol and 1.7 [1.5, 1.9] kcal/mol, respectively, with 95% confidence ranges in brackets. These results suggest that SMIRNOFF99Frosst performs competitively with existing small molecule force fields and is a parsimonious starting point for optimization.</p></div></div></div> | David Slochower; Niel Henriksen; Lee-Ping Wang; John Chodera; David Mobley; Michael Gilson | Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2019-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7447c842e65b592db2478/original/binding-thermodynamics-of-host-guest-systems-with-smirnoff99frosst-1-0-5-from-the-open-force-field-initiative.pdf |
63725294e70b0af9849c1e8e | 10.26434/chemrxiv-2022-qqfbf | Which molecular properties determine the impact sensitivity of an explosive? A machine learning quantitative investigation of nitroaromatic explosives | We decomposed density functional theory charge densities of 53 nitroaromatic molecules into atom-centered electric multipoles using the distributed multipole analysis that provides a detailed picture of the molecular electronic structure. Three electric multipoles, ∑▒〖Q_0 (NO_2)〗 (the charge of the nitro groups), ∑▒〖Q_1 (NO_2)〗 (the total dipole, i.e., polarization, of the nitro groups), ∑▒〖Q_2 (C) 〗 (the total electron delocalization of the C ring atoms), and the number of explosophore groups (#NO_2) were selected as features for a comprehensive machine learning (ML) investigation. The target property was the impact sensitivity h_50 (cm) values quantified by drop-weight measurements. After a preliminary screening of 42 ML algorithms, four were selected based on the lowest root mean square errors: Extra Trees, Random Forests, Gradient Boosting, and AdaBoost. The predicted h_50 values of molecules having very different sensitivities for the four algorithms are in the range 19% - 28% compared to experimental data. The most important properties for predicting h_50 are the electron delocalization in the ring atoms and the polarization of the nitro groups with averaged weights of 39% and 35%, followed by the charge (16%) and number (10%) of nitro groups. A significant result is how the contribution of these properties to h_50 depends on its sensitivities: for the most sensitive explosives (h_50 up to ~ 50 cm), the four properties contribute to reducing h_50, and for intermediate ones (~ 50 cm ≲ h_50 ≲ 100 cm) #NO_2 and ∑▒〖Q_1 (NO_2)〗 contribute to increasing it and the other two properties to reducing it. For highly insensitive explosives (h_50≳ 200 cm), all four properties essentially contribute to increasing it. These results furnish a consistent molecular basis of the sensitivities of known explosives that also can be used for developing safer new ones. | Itamar Borges Jr; Júlio César Duarte; Romulo Dias da Rocha | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63725294e70b0af9849c1e8e/original/which-molecular-properties-determine-the-impact-sensitivity-of-an-explosive-a-machine-learning-quantitative-investigation-of-nitroaromatic-explosives.pdf |
67ca60106dde43c908d7f316 | 10.26434/chemrxiv-2025-k8t91 | Facile preparation of transparent, structurally robust, fire-resistant NaBH4-modified alkaline lignin/CNF film for active packaging | The intrinsic characteristic of UV resistance, antibacterial properties, and thermal stability enabled its extensive application in the functionalized preparation of biodegradable bioplastics. However, the inherent dark color of lignin restricted its broad applications. In this study, a facile and novel reduction method with sodium borohydride for de-coloring of lignin and constructing more hydroxyl groups was proposed. Not only the physicochemical properties of the modified lignin were detected, but also the comprehensive performance of the lignin and nanocellulose composite films were investigated. Results showed that the maximum hydroxyl group content could achieve 8.74 mmol/g, representing a 314.39% increase compared to crude alkaline lignin, which also led the tensile strength of the light-colored composited films to 152.33 MPa with the lignin addition ratio at 23.1%. Besides, excellent ultra-violet shielding efficiency and visible light transmittance were also exhibited, and the limited oxygen index could achieve about 50%. Antimicrobial tests demonstrated 99.99% inhibition rates against both Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), and the biodegradability test also proved its environment compatibility, which was expected to provide a feasible basis for the wide application of transparent lignin composited films. | LIU XIAOGANG; Zeng ShiYi; Li Jing; Gao WenHua; Tong Xin; Guo DaLiang; Chen XiaoHong; Yuan TianZhong; Sha LiZheng | Materials Science; Nanoscience; Biodegradable Materials; Fire-Resistant Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca60106dde43c908d7f316/original/facile-preparation-of-transparent-structurally-robust-fire-resistant-na-bh4-modified-alkaline-lignin-cnf-film-for-active-packaging.pdf |
60c73dd5567dfe8740ec3729 | 10.26434/chemrxiv.6203297.v1 | A Benchmarking Approach for Routine Determination of Flow Battery Kinetics | This work focusses on improved precision and reproducibility in the study of redox flow battery (RFB) kinetics. We measured the electron-transfer reaction rates of the Fe(III/II) redox couple at polycrystalline Pt and Au electrodes in aqueous HCl supporting electrolyte using rotating disk electrode voltammetry. We made considerable effort to implement a systematic electrode preparation protocol, which was necessary for reproducibility. We found the reaction to be quasi-reversible at both electrodes and Pt to be a slightly more effective catalyst than Au. We further discuss some of the benefits and challenges of applying classical electroanalysis to RFB device design. | Tejal Sawant; James McKone | Electrochemical Analysis; Electrochemistry; Electrocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd5567dfe8740ec3729/original/a-benchmarking-approach-for-routine-determination-of-flow-battery-kinetics.pdf |
60c75939ee301c6923c7b875 | 10.26434/chemrxiv.14052293.v3 | Mixed Chirality α-Helix in a Stapled Bicyclic and a Linear Antimicrobial Peptide Revealed by X-Ray Crystallography | <p></p><p>The
peptide α-helix is right-handed when containing amino acids with L-chirality,
and left-handed with D-chirality, however mixed chirality peptides generally do
not form α-helices unless the non-natural residue amino-isobutyric acid is used
as helix inducer. Herein we report the first X-ray crystal structures of mixed
chirality α-helices in short peptides comprising only natural residues at the
example of a stapled bicyclic and a linear membrane disruptive amphiphilic antimicrobial
peptide (AMP) containing seven L- and four D-residues, as complexes of
fucosylated analogs with the bacterial lectin LecB. The mixed chirality α-helices are superimposable to their parent homochiral
α-helices and form under similar conditions as shown by CD spectra and MD
simulations but are resistant to proteolysis. The observation of mixed
chirality α-helix with only natural residues in the protein environment of LecB
suggests a vast unexplored territory of α-helical mixed chirality sequences and
their possible use for optimizing bioactive α-helical peptides.</p><br /><p></p> | stéphane Baeriswyl; Hippolyte Personne; Ivan Di Bonaventura; Thilo Köhler; Christian van Delden; Achim Stocker; Sacha Javor; Jean-Louis Reymond | Bioorganic Chemistry; Stereochemistry; Biopolymers; Biochemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75939ee301c6923c7b875/original/mixed-chirality-helix-in-a-stapled-bicyclic-and-a-linear-antimicrobial-peptide-revealed-by-x-ray-crystallography.pdf |
65eef7739138d2316134ed91 | 10.26434/chemrxiv-2024-bk36r | Efficient and Selective Electrochemical CO2 to Formic Acid Conversion: A First-Principles Study of Single-Atom and Dual-Atom Catalysts on Tin Disulfide Monolayers | Electrochemical CO2 reduction reaction (CO2RR), is a sustainable approach to recycle CO2 and address climate issues, but needs selective catalysts that can operate at low electrode potentials. Single-atom catalysts (SACs) and dual-atom catalysts (DACs) have become increasingly popular, due to their versatility, unique properties and outstanding performances in electrocatalytic reactions. In this paper, we used Density Functional Theory in combination with the computational hydrogen electrode methodology, to study the stability and activity of SACs and DACs by adsorbing metal atoms on SnS2 monolayers. With a focus on optimising the selective conversion of CO2 to formic acid, our analysis of the thermodynamics of CO2RR reveals that the Sn-SAC and Sn-DAC catalysts can efficiently and selectively catalyse formic acid production, being characterised by the low theoretical limiting potentials of approximately -0.25 V and an upper limit for the initial thermodynamic barrier for CO2 adsorption in gas phase of 0.5 eV. Investigation of the catalysts' stability suggests that structures with low metal coverage, with isolated metal centres, may be synthesised. Bader analysis of charge redistribution during CO2RR demonstrates that the SnS2 substrate primarily provides the electronic charges for the reduction of CO2, highlighting the substrate's essential role in the catalysis, which is also confirmed by further electronic structure calculations. | Guanming Chen; Margherita Buraschi; Rashid Al-Heidous; Satyanarayana Bonakala; Fedwa El-Mellouhi; Clotilde S. Cucinotta | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eef7739138d2316134ed91/original/efficient-and-selective-electrochemical-co2-to-formic-acid-conversion-a-first-principles-study-of-single-atom-and-dual-atom-catalysts-on-tin-disulfide-monolayers.pdf |
60c7490fbdbb891f16a390c0 | 10.26434/chemrxiv.12022767.v1 | The Radical Ring-Opening Polymerization of Cyclic Ketene Acetals Revisited: An Experimental and Theoretical Study | Radical Ring-Opening polymerization (rROP) of Cyclic Ketene Acetals (CKAs) combines the advantages of both ring-opening and radical polymerization thereby allowing the robust production of polyesters. In this article we investigate in detail the radical ring-opening polymerization of model CKA monomers and demonstrate by the combination of DFT calculations and kinetic modeling using PREDICI software that we are now able to predict <i>in silico</i> the ring-opening ability of CKA monomers<br /> | Antoine Tardy; Noémie Gil; Christopher M. Plummer; Didier Siri; Didier Gigmes; Catherine Lefay; Yohann Guillaneuf | Organic Polymers; Polymer chains; Polymerization (Polymers); Polymerization kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7490fbdbb891f16a390c0/original/the-radical-ring-opening-polymerization-of-cyclic-ketene-acetals-revisited-an-experimental-and-theoretical-study.pdf |
62bef0d32530217c3a860863 | 10.26434/chemrxiv-2022-m03tb-v2 | Expedient Synthesis of a Library of Heparan Sulfate Like “Head to Tail” Linked Multimers for Structure and Activity Relationship Studies | Heparan sulfate (HS) plays significant roles in various biological processes such as inflammation, cell proliferation, and bacterial and viral infection. The inherent complexity of naturally existing HS has severely hindered the thorough understanding of the relationship between their diverse structures and biological functions. While HS syntheses have advanced significantly in recent years, preparation of HS libraries remains a tremendous challenge due to the difficulties in achieving high yields in glycosylation and sulfation reactions especially with longer glycans and the need to prepare multiple compounds. A new strategy to synthesize a library of HS-like pseudo-hexasaccharides has been developed to expedite library preparation. HS disaccharides were linked in a “head-to-tail” fashion from the reducing end of a module to the non-reducing end of a neighboring module to mimic native HS. Three differentially sulfated HS disaccharides were designed and prepared from a common intermediate. Conjugation of these modules using amide chemistry bypassed the need for challenging glycosylation reactions to extend the HS backbone. Combinatorial syntheses of 27 HS-like pseudo-hexasaccharides were achieved using these three HS modules. This new class of compounds mimicked well the native HS with their binding to fibroblast growth factor 2 (FGF-2) exhibiting similar structure-activity relationship trends as HS hexasaccharides. The ease of synthesis and the ability to mimic natural HS suggest the new head-to-tail linked pseudo-hexasaccharides could be an exciting tool to facilitate the understanding of HS biology. | Jicheng Zhang; Li Liang; Weizhun Yang; Sherif Ramadan; Kedar Baryal; Chang-xin Huo; Jamie Bernard; Jian Liu; Linda Hsieh-wilson; Fuming Zhang; Robert Linhardt; Xuefei Huang | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bef0d32530217c3a860863/original/expedient-synthesis-of-a-library-of-heparan-sulfate-like-head-to-tail-linked-multimers-for-structure-and-activity-relationship-studies.pdf |
6484b6874f8b1884b71bcf3f | 10.26434/chemrxiv-2023-j902p | Electrified Solar Zero Liquid Discharge: Exploring the Potential of PV-ZLD in the US | Current brine management strategies are based on the disposal of brine in nearby aquifers, representing a loss in potential water and mineral resources. Zero liquid discharge (ZLD) is a possible strategy to reduce brine rejection while increasing resource recovery from desalination plants. However, treatment of high-salinity brine through ZLD substantially increases the energy consumption and carbon footprint of a desalination plant. The predominant strategy to reduce the energy consumption and carbon footprint of ZLD is through the use of a hybrid desalination technology that integrates with renewable energy. Here, we built a thermodynamic model of the most mature electrified hybrid technology for ZLD powered by photovoltaics (PV). The PV-ZLD system is comprised of a reverse osmosis system coupled with mechanical vapor compression and crystallization. By coupling the thermodynamic model with a computational model, we are able to examine the potential size and geographic distribution of ZLD plants in Arizona, California, Florida, and Texas (e.g., the top four states that produce desalination brine). A multi-objective optimization framework determines the potential plant size considering the location and a number of operational variables. The objective function aims to maximize the thermodynamic performance of the ZLD system and minimize the cost of water and environmental impacts. Texas has the lowest levelized cost of water (1.2 to 1.7 $/m3 ) which is largely attributed to the state having available backup power. California is the most effective at using solar energy to power ZLD plants (above 90%), but the state also has the largest projected land area requirements. The massive adoption of large-scale PV-ZLD systems depends on the inclusion of efficient preconcentration subsystems that decrease the energy requirements of the brine concentration process, the reduction in CAPEX for PV systems, and the development of a low-cost and low-carbon intensity electric grid. Treating all brine produced in Arizona, California, Florida, and Texas could allow the production of an additional 963 million gallons of freshwater per day. | Rodrigo Caceres Gonzalez ; Marta Hatzell | Energy; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Water Purification; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6484b6874f8b1884b71bcf3f/original/electrified-solar-zero-liquid-discharge-exploring-the-potential-of-pv-zld-in-the-us.pdf |
62510d97ebac3a87bccfb357 | 10.26434/chemrxiv-2022-gmj61 | Thermodynamic modeling of adsorption at the liquid-solid interface | Adsorption-based separation techniques are significantly energy efficient in comparison to the conventional thermal separation techniques such as distillation. Despite the extensive research and development activities undertaken for mixed gas adsorption, the use of adsorption techniques for the separation of multicomponent liquid mixtures is still limited. This is due to the lack of accurate adsorption thermodynamic models, which form the scientific foundation of process simulation of such systems, making the translation to the industrial scale challenging. In this work, we have rigorously computed the surface excess of adsorption for six binary liquid mixtures on silica gel at 303 K using the frameworks of the adsorbed solution theory and the generalized Langmuir isotherm model. The six binary liquid mixtures studied in this work were formed by the pair-wise combinations of four components: benzene, 1,2-dichloroethane, cyclohexane, and n-heptane. We have based our calculations by considering simultaneous equilibria of three phases: saturated binary vapor phase, binary liquid phase, and the adsorbed phase. The composition of the corresponding saturated vapor phase was determined by correlating the experimental vapor-liquid equilibria data using the Non-Random Two-Liquid activity coefficient model. The activity coefficients of the adsorbed phase were calculated using the adsorption Non-Random Two-Liquid activity coefficient model. Devoid of simplifying assumptions, our methodology for computing the surface excess of binary liquid adsorption should be applicable for the adsorption from a wide variety of liquid mixtures. | Rajasi Shukre; Shikha Bhaiya; Usman Hamid; Hla Tun; Chau-Chyun Chen | Energy; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62510d97ebac3a87bccfb357/original/thermodynamic-modeling-of-adsorption-at-the-liquid-solid-interface.pdf |
61150b283b558fa49cfbff6b | 10.26434/chemrxiv-2021-3qs25-v2 | Chain-Growth SuFEx Polycondensation: Molecular Weight Control and Synthesis of Degradable Polysulfates | Sulfur (Ⅵ) fluoride exchange (SuFEx) click chemistry has offered a facile and reliable approach to produce polysulfates and polysulfonates. However, the current SuFEx polymerization methods lack precise control of target molecular weight and dispersity. Herein, we report the first chain-growth SuFEx polycondensation process by exploiting unique reactivity and selectivity of S-F bonds under SuFEx catalysis. Given the higher reactivity of iminosulfur oxydifluoride versus fluorosulfate, the chain-growth SuFEx polycondensation is realized by using an iminosulfur oxydifluoride-containing compound as the reactive chain initiator and deactivated AB-type aryl silyl ether-fluorosulfates bearing an electron-withdrawing group as monomers. When DBU was utilized as the polymerization catalyst, precise control over polymer molecular weight and polydispersity are achieved. The resulting polymers possess great thermal stability but are easily degradable under mild acidic and basic conditions. | Hyunseok Kim; Jiayu Zhao; Jinhye Bae; Liana M. Klivansky; Eric Dailing; Yi Liu; John R. Cappiello; K. Barry Sharpless; Peng Wu | Polymer Science; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61150b283b558fa49cfbff6b/original/chain-growth-su-f-ex-polycondensation-molecular-weight-control-and-synthesis-of-degradable-polysulfates.pdf |
65faecbee9ebbb4db91b4ac1 | 10.26434/chemrxiv-2024-vb20g-v3 | Return of the Ritonavir: A Study on the Stability of Pharmaceuticals Processed in Orbit and Returned to Earth | Despite notable progress in realizing the benefits of microgravity, the physical stability of therapeutics processed in space has not been sufficiently investigated. Environmental factors including vibration, acceleration, radiation, and temperature, if not addressed could impact the feasibility of in-space drug processing. The presented work demonstrates the successful recovery of the metastable Form III of ritonavir generated in orbit. The test samples and passive controls containing each of the anhydrous forms of ritonavir; Form I, Form II, Form III, and amorphous exhibit excellent stability. By providing a detailed experimental dataset centered on survivability, we pave the way for the future of in-space processing of medicines that enable the development of novel drug products on Earth and benefit long-duration human exploration initiatives. | Haley C. Bauser; Pamela A. Smith; Stephan D. Parent; Larry R. Chan; Ami S. Bhavsar; Kenneth H. Condon; Andrew McCalip; Jordan M. Croom; Dale K. Purcell; Susan J. Bogdanowich-Knipp; Daniel T. Smith; Brett A. Cowans; Ruba Alajlouni; Stephen R. Byrn; Adrian Radocea | Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Drug Discovery and Drug Delivery Systems; Pharmaceutical Industry; Process Control | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65faecbee9ebbb4db91b4ac1/original/return-of-the-ritonavir-a-study-on-the-stability-of-pharmaceuticals-processed-in-orbit-and-returned-to-earth.pdf |
66102b09418a5379b02aaab5 | 10.26434/chemrxiv-2024-q511z | HPLC Training for All: Integration of Multi-Language Artificial Intelligence (AI) Avatars in Virtual Reality (VR) Digital Twin Laboratories | The integration of High-Performance Liquid Chromatography (HPLC) training into academic curricula remains a challenge, due to the complexities of its theoretical concepts and the cost-prohibitive nature of HPLC instrumentation. This challenge in training is further compounded for students who are taught in the English language and for whom English is a Foreign Language (EFL), and who may struggle to understand traditional learning materials. This paper introduces a pioneering Virtual Reality (VR) platform for immersive HPLC training that is coupled with a conversationally intelligent Artificial Intelligence (AI) avatar capable of multilingual support. This approach provides students with an on-hand tutor for adaptive, immersive learning practices in whatever language they feel comfortable speaking in. The effectiveness of the AI models were evaluated via a survey of postgraduate Chemistry students at UCL, and the responses were analysed computationally using a series of evaluation metrics. Evaluation from TF-IDF, BLEU and BERT statistical analysis demonstrated that the AI avatar had superior linguistic and instructional performance across English, Spanish, and German, particularly in complex concept explanations, validating the potential for multilingual AI support in education. Survey feedback revealed that the AI Avatars with a knowledge bank significantly improved HPLC learning outcomes, with participants rating their engagement and the quality of learning above traditional methods. | Ayah Al-Dargazelli; Amy Locks; Mae Taylor; Mireia Montaner; Stephen Hilton | Organic Chemistry; Analytical Chemistry; Chemical Education; Chemical Education - General; Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66102b09418a5379b02aaab5/original/hplc-training-for-all-integration-of-multi-language-artificial-intelligence-ai-avatars-in-virtual-reality-vr-digital-twin-laboratories.pdf |
60c754c7ee301c65fdc7b005 | 10.26434/chemrxiv.13655864.v2 | Controlling Exchange Pathways in Dynamic Supramolecular Polymers by Controlling Defects | Supramolecular fibers, composed of monomers that self-assemble directionally <i>via</i> non-covalent interactions, are ubiquitous in nature and of great interest in chemistry. In these structures, the constitutive monomers continuously exchange in-and-out the assembly according to a well-defined supramolecular equilibrium. However, unraveling the exchange pathways and their molecular determinants constitutes a non-trivial challenge. Here we combine coarse-grained modeling, enhanced sampling, and machine learning to investigate the key factors controlling the monomer exchange pathways in synthetic supramolecular polymers having an intrinsic dynamic behavior. We demonstrate how the competition of directional <i>vs. </i>non-directional interactions between the monomers controls the creation/annihilation of defects in the supramolecular polymers, from where monomers exchange proceeds. This competition determines the exchange pathway, dictating whether a fiber statistically swaps monomers from the tips or all along its length. Finally, thanks to their generality, our models allow the investigation of molecular approaches to control the exchange pathways in these dynamic assemblies.<br /> | Anna Lucia de Marco; Davide Bochicchio; Andrea Gardin; Giovanni Doni; Giovanni M. Pavan | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Theory - Computational; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754c7ee301c65fdc7b005/original/controlling-exchange-pathways-in-dynamic-supramolecular-polymers-by-controlling-defects.pdf |
60c751d1bdbb895ad6a3a153 | 10.26434/chemrxiv.13213916.v1 | Synthetic Pathway Determines the Non-equilibrium Crystallography of Li- and Mn-rich Layered Oxides | Li- and Mn-rich layered oxides show significant promise as electrode materials for future Li-ion batteries. However, accurate descriptions of its crystallography remain elusive, with both single-phase solid solution and multi-phase structures being proposed for high performing materials such as Li<sub>1.2</sub>Mn<sub>0.54</sub>Ni<sub>0.13</sub>Co<sub>0.13</sub>O<sub>2</sub>. Herein, we report the synthesis of single- and multi-phase variants of this material through sol-gel and solid-state methods, respectively, and conclusively demonstrate that its crystallography is a direct consequence of the synthetic route and not an inherent property of the composition, as previously argued. This was accomplished via complementary techniques that probe the bulk and local structure followed by in situ methods to map the synthetic progression. As the electrochemical performance and anionic redox behaviour is often rationalised on the basis of the presumed crystal structure, clarifying the structural ambiguities is an important step towards harnessing its potential as an electrode material. | Ashok S. Menon; Seda Ulusoy; Dickson Ojwang; Lars Riekehr; Christophe Didier; Vanessa K. Peterson; Germán Salazar-Alvarez; Peter Svedlindh; Kristina Edström; Cesar Pay Gomez; William Brant | Energy Storage; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751d1bdbb895ad6a3a153/original/synthetic-pathway-determines-the-non-equilibrium-crystallography-of-li-and-mn-rich-layered-oxides.pdf |
60c74460567dfe0f5bec426d | 10.26434/chemrxiv.9784406.v1 | Gold and Silver Dichroic Nanocomposite in the Quest for 3D Printing the Lycurgus Cup | <div>The Lycurgus cup is worldwide admired in
particular because of its fascinating dichroic property. The cup presents a
green colour when the observer and the light source are on the same side
(reflection), and a deep red colour when the observer and the light source are
at opposite sides (transmission). This peculiar effect, which has perplexed scientists for centuries, was
discovered to be due to the presence of nanoparticles in the glass. In
particular, to two different metallic nanoparticles: silver nanoparticles
(AgNP) and gold nanoparticles (AuNP). Here we show how dichroic silver nanoparticles and gold nanoparticles can be embedded in a 3D printable material in order to reproduce the same dichroic effect of the original Lycurgus cup. <br /></div> | Lars Kool; Floris Dekker; Anton Bunschoten; Glen-Jacob Smales; Brian R. Pauw; Aldrik Velders; Vittorio Saggiomo | Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74460567dfe0f5bec426d/original/gold-and-silver-dichroic-nanocomposite-in-the-quest-for-3d-printing-the-lycurgus-cup.pdf |
62e10043a8e4dcaa571ecb69 | 10.26434/chemrxiv-2022-mcm52 | Structure-based computational approaches for characterization and functional elucidation of the fusion protein from Nipah henipavirus | Many epidemics of varying severity have triggered panic and devastation in the past. The Nipah virus has one of the world's highest fatality rates. The encephalitis resulting from acute respiratory distress has been fatal in some instances. Many factors influence the virus's genesis and spread. Developing new methods has improved personal hygiene awareness and surveillance over the contaminated area. An unidentified protein from Nipah henipavirus was the focus of this investigation. The secondary structure of the protein consists of a helix, a sheet, a turn, and a coil. Furthermore, the Ramachandran plot and the Z-score-based and local model quality assessment processes revealed the quality of the modeled protein structure. The protein can be used as a target for developing prospective antiviral medication and vaccine candidates. | Abu Saim Mohammad Saikat | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e10043a8e4dcaa571ecb69/original/structure-based-computational-approaches-for-characterization-and-functional-elucidation-of-the-fusion-protein-from-nipah-henipavirus.pdf |
64d11c8f4a3f7d0c0dc47d57 | 10.26434/chemrxiv-2023-qzkc2 | “Activated Borane” – A Porous Borane Cluster Polymer as an Efficient Lewis Acid-based Catalyst | Borane cluster based porous covalent networks, named activated borane (ActB), were prepared by co-thermolysis of decaborane(14) (nido-B10H14) and selected hydrocarbons (toluene – ActB-Tol, cyclohexane – ActB-cyHx, and n-hexane – ActB-nHx) under anaerobic conditions. These amorphous solid powders exhibit different textural and Lewis acid (LA) properties that vary depending on the nature of the constituent organic linker. For ActB-Tol, its LA strength even approaches that of the commonly-used molecular LA, B(C6F5)3. Most notably, ActBs can act as heterogeneous LA catalysts in hydrosilylation/deoxygenation reactions with various carbonyl substrates, as well as in the gas-phase dehydration of ethanol. These studies reveal the excellent potential of ActBs in catalytic applications, showing a) the possibility for tuning catalytic reaction outcomes (selectivity) in hydrosilylation/deoxygenation reactions by changing the material’s composition, and b) the very high activity toward ethanol dehydration that exceeds commonly used γ-Al2O3 by achieving a stable conversion of ~93 % with a selectivity for ethylene production of ~78 % during a 17 h continuous period on stream at 240°C. | Martin Lamač; Béla Urbán; Michal Horáček; Daniel Bůžek; Lucie Leonová; Aleš Stýskalík; Anna Vykydalová; Karel Škoch; Matouš Kloda; Andrii Mahun; Libor Kobera; Michael Londesborough; Kamil Lang; Jan Demel | Catalysis; Acid Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d11c8f4a3f7d0c0dc47d57/original/activated-borane-a-porous-borane-cluster-polymer-as-an-efficient-lewis-acid-based-catalyst.pdf |
60c74c654c89193ca9ad362f | 10.26434/chemrxiv.12471557.v1 | Photodynamic Controls of Harmful Algal Blooms by an Ultra-efficient and Degradable AIEgen-based Photosensitizer | Harmful <a></a><a>algal blooms</a>
(HAB) have severe impacts on human health, aquatic ecosystems, and economy. There
is still a lack of effective means to control the algal blooms. Herein, a
positively charged photosensitizer with aggregation induced emission (AIE)
characteristics, namely TVP-A, is reported for its super-efficient,
cost-effective, and eco-friendly governance of HAB. TVP-A possesses a
characteristically high quantum yield of harvesting white light into reactive
oxygen species (ROS). Attributed to its positive charges, TVP-A has good
water solubility and can quickly adsorb onto algal cells floating on the water
surface. It effectively triggers cell
death through oxidative destruction of the nuclei and chloroplasts of algae. The extremely low effective concentration of TVP-A and
the short irradiation time by natural light in removing algal blooms ensure its
application at large scales under most weather conditions, without affecting
other existing organisms. The slow but consistent self-degradation of TVP-A
during the photodynamic controls of algal blooms avoids generating any
environmental residues or secondary pollution to environmental systems. TVP-A
thereby serves as an excellent candidate for the green governance of HAB, and
this work represents a new paradigm for the
development of efficient and degradable AIEgens for future environmental
applications. | Qiang Yue; Xuewen He; Neng Yan; sidan tian; Chenchen LIU; Wen-Xiong Wang; Liang Luo; Ben Zhong Tang | Biocompatible Materials; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c654c89193ca9ad362f/original/photodynamic-controls-of-harmful-algal-blooms-by-an-ultra-efficient-and-degradable-ai-egen-based-photosensitizer.pdf |
65e1a4729138d2316168b1d7 | 10.26434/chemrxiv-2024-n2k0r | Atroposelective Synthesis of N-Aryl Phthalimides and Maleimides via NHC-Catalyzed Activation of Carboxylic Acids | Traditionally, N-aryl phthalimides are synthesized by the condensation of phthalic anhydride and aniline derivatives, usually proceeding under harsh conditions. The alternative mild and organocatalytic strategies for their synthesis are underdeveloped. Herein, we demonstrate the first organocatalytic atroposelective synthesis of N-aryl phthalimides via the traditional N-CC=O disconnection under mild conditions. The in-situ acid activation of phthalamic acid and subsequent N-heterocyclic carbene (NHC)-catalyzed atroposelective amidation allowed the synthesis of well-decorated N-aryl phthalimides in excellent yields and enantioselectivities. Mechanistic studies reveal the addition of NHC to the in situ generated isoimides, thus introducing a new mode of generating acylazoliums. Interestingly, both enantiomers of the product can be accessed from the same phthalic anhydride and aniline using the same NHC pre-catalyst. Moreover, this strategy has been extended to the atroposelective synthesis of N-aryl maleimides. | Soumen Barik; Sowmya Shree Ranganathappa; A T Biju | Organic Chemistry; Catalysis; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e1a4729138d2316168b1d7/original/atroposelective-synthesis-of-n-aryl-phthalimides-and-maleimides-via-nhc-catalyzed-activation-of-carboxylic-acids.pdf |
60c74af1567dfec4feec4e7a | 10.26434/chemrxiv.12275165.v1 | Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach | <p>Accurate and efficient computational predictions of ligand binding kinetics can be useful to inform drug discovery campaigns, particularly in the screening and lead optimization phases. Simulation Enabled Estimation of Kinetic Rates, SEEKR, is a multiscale molecular dynamics, Brownian dynamics, and milestoning simulation approach for calculating receptor-ligand association and dissociation rates. Here we present the implementation of a Markovian milestoning with Voronoi tessellations approach that significantly reduces the simulation cost of calculations as well as further improving their parallelizability. The new approach is applied to a host-guest system to assess its effectiveness for rank-ordering compounds by kinetic rates and to the model protein system, trypsin, with the noncovalent inhibitor benzamidine. For both applications, we demonstrate that the new approach requires up to a factor of 10 less simulation time to achieve results with comparable or increased accuracy.</p> | Benjamin Jagger; Anupam Anand Ojha; Rommie Amaro | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74af1567dfec4feec4e7a/original/predicting-ligand-binding-kinetics-using-a-markovian-milestoning-with-voronoi-tessellations-multiscale-approach.pdf |
665a336321291e5d1dc40212 | 10.26434/chemrxiv-2024-rhm2t | Cross-scale catalyst modeling framework: A case
study of H2 storage and release via formic acid | We propose a novel Systems-to-Atoms (S2A) modeling framework that integrates the kinetics of reaction chemistry and structural configurations across various length scales with the aim to establish a versatile template for multiscale modeling of reactive flow problems and to predict the operando activity of catalyst materials. The approach encompasses a microkinetic model to forecast surface reactions on individual facets of catalyst nanoparticles, coupled with the computation of average surface reaction rates for catalyst nanoparticles of specific size distributions. Macro-homogeneous surface reaction kinetics are derived as a function of catalyst loading, and used as input parameter for the continuum-scale reactor model. The cross-scale framework enables the optimization of catalyst utilization through reactor design and operating strategy. To demonstrate the S2A framework, we study the storage and release of hydrogen from formic acid using Pd, Pt, and Cu catalysts. Formic acid is a promising liquid organic hydrogen carrier (LOHC), given its high volumetric capacity and low toxicity and flammability under ambient conditions. The framework predicts observed trends in formic acid dehydrogenation activity for catalysts with comparable weight loading and metal particle diameters, demonstrating satisfactory quantitative alignment. Finally, the seamless transmission of parameter uncertainties between scales is also discussed. | Shyam Deo; Wenyu Sun; Tanusree Chatterjee; Thomas Moore; Mengyao Yuan; Sneha Akhade; Matthew Mcnenly; Giovanna Bucci | Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Reaction Engineering; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665a336321291e5d1dc40212/original/cross-scale-catalyst-modeling-framework-a-case-study-of-h2-storage-and-release-via-formic-acid.pdf |
60c74299702a9b480d18a4a6 | 10.26434/chemrxiv.7699358.v4 | Design Principles for 2-Dimensional Molecular Aggregates using Kasha’s Model: Tunable Photophysics in Near and Shortwave Infrared | Technologies
which utilize near-infrared (700 – 1000 nm) and short-wave infrared (1000 –
2000 nm) electromagnetic radiation have applications in deep-tissue imaging,
telecommunications and satellite telemetry due to low scattering and decreased
background signal in this spectral region. It is therefore necessary to develop
materials that absorb light efficiently beyond 1000 nm. Transition dipole
moment coupling (e.g. J-aggregation) allows for redshifted excitonic states and
provides a pathway to highly absorptive electronic states in the infrared. We present aggregates of two cyanine dyes whose
absorption peaks redshift dramatically upon aggregation in water from ~800
nm to 1000 nm and 1050 nm respectively with sheet-like morphologies and high
molar absorptivities (e ~ 10<sup>5 </sup>M<sup>-1</sup>cm<sup>-1</sup>). We use Frenkel exciton theory to extend
Kasha’s model for J and H aggregation and describe the excitonic states of
2-dimensional aggregates whose slip is controlled by steric hindrance in the
assembled structure. A consequence of the increased dimensionality is the
phenomenon of an intermediate “I-aggregate”, one which redshifts yet displays
spectral signatures of band-edge dark states akin to an H-aggregate. We
distinguish between H-, I- and J-aggregates by showing the relative position of
the bright (absorptive) state within the density of states using temperature
dependent spectroscopy. I-aggregates hold potential for applications as charge
injection moieties for semiconductors and donors for energy transfer in NIR and
SWIR. Our results can be used to better design chromophores with predictable
and tunable aggregation with new photophysical properties. | Arundhati Deshmukh; Danielle Koppel; Chern Chuang; Danielle Cadena; Jianshu Cao; Justin Caram | Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Quantum Mechanics; Quasiparticles and Excitations; Self-Assembly; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74299702a9b480d18a4a6/original/design-principles-for-2-dimensional-molecular-aggregates-using-kasha-s-model-tunable-photophysics-in-near-and-shortwave-infrared.pdf |
64d8feda4a3f7d0c0d1b415b | 10.26434/chemrxiv-2023-1gqxv | Understanding the effect of moderate concentration SDS on CO2 hydrates
growth in the presence of THF | Additives like Tetrahydrofuran (THF) and Sodium Dodecyl Sulfate (SDS) improve
CO2 hydrates thermal stability and growth rate when used separately. It has been
hypothesised that combining them could improve the kinetics of growth and the
thermodynamic stability of CO2 hydrates.
We exploit atomistic molecular dynamics simulation to investigate the combined impact of THF and SDS under different temperatures and concentrations. The simulation insights are verified experimentally using pendant drop tensiometry conducted
at ambient pressures and high-pressure differential scanning calorimetry.
Our simulations revealed that the combination of both additives is synergistic at low
temperatures but antagonistic at temperatures above 274.1 K due to the aggregation
SDS molecules induced by THF molecules. These aggregates effectively remove THF
and CO2 from the hydrate-liquid interface, thereby reducing the driving force for
hydrates growth. Experiments revealed that the critical micelle concentration of SDS
in water decreases by 20% upon the addition of THF. Further experiments showed
that only small amounts of SDS with THF is sufficient to increase the CO2 storage
efficiency by over 40% compared to results obtained without promoters. These results
provide microscopic insights into the mechanisms of THF and SDS promoters on CO2
hydrates, which allow for determining the optimal condition for hydrate growth.
| Xinrui Cai; Joshua Worley; Anh Phan; Matteo Salvalaglio; Carolyn Koh; Alberto Striolo | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Surfactants; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d8feda4a3f7d0c0d1b415b/original/understanding-the-effect-of-moderate-concentration-sds-on-co2-hydrates-growth-in-the-presence-of-thf.pdf |
65ddf95a9138d23161273efe | 10.26434/chemrxiv-2024-21063 | A Practical Synthesis and X-Ray Crystal Structure of (E)-4-(1-naphthylvinyl)pyridine and Related Compounds | The synthesis, structure, and photoreactivity of (E)-4-(1-naphthylvinyl)pyridine ((E)-4-1-nvp; 1) and its coordination compounds has been investigated. Synthesis of (1) via Wittig olefination resulted in a challenging isomer separation and purification process. By synthesizing (1) via a Horner-Wadsworth-Emmons reaction, high stereoselectivity and purity was achieved. The crystal structure of (1) revealed significant intramolecular rotation facilitated by CH···pi interactions, ultimately preventing olefin stacking in both the solid-state structure of (1) and a cocrystal with a structural isomer. Novel Ag(I) and Zn(II) coordination complexes that utilize (1) as a ligand were also synthesized and fully characterized, facilitating the examination of the relationship between molecular planarity and secondary bonding contributions via Hirshfeld surface analyses. These findings deepen our understanding of intermolecular interactions involving (E)-4-1-nvp and offer insights for designing novel photoresponsive materials capable of solid-state [2+2] cycloaddition. | James G. D. Moffat; Victoria N. P. Pham-Tran; Katherine M. Marczenko | Organic Chemistry; Organometallic Chemistry; Photochemistry (Org.); Transition Metal Complexes (Organomet.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ddf95a9138d23161273efe/original/a-practical-synthesis-and-x-ray-crystal-structure-of-e-4-1-naphthylvinyl-pyridine-and-related-compounds.pdf |
66017e439138d231614043a6 | 10.26434/chemrxiv-2024-qkw53 | Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations | The majority of drug-like molecules contain at least one ionizable group, and many common drug scaffolds are subject to tautomeric equilibria. Thus, these compounds are found in a mixture of protonation and/or tautomeric states at physiological pH. Intrinsically, standard classical molecular dynamics (MD) simulations cannot describe such equilibria between states, which negatively impacts the prediction of key molecular properties in silico. Following the formalism described by de Oliveira and co-workers (J. Chem. Theory Comput. 2019, 15, 424–435) to consider the influence of all states on the binding process based on alchemical free energy calculations, we demonstrate in this work that the multistate method replica-exchange enveloping distribution sampling (RE-EDS) is well suited to describe molecules with multiple protonation and/or tautomeric states in a single simulation. We apply our methodology to a series of eight inhibitors of factor Xa with two protonation states and a series of eight inhibitors of glycogen synthase kinase 3β (GSK3β) with two tautomeric states. In particular, we show that given a sufficient phase-space overlap between the states, RE-EDS is computationally more efficient than standard pairwise free-energy methods. | Candide Champion; Philippe H. Hünenberger; Sereina Riniker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66017e439138d231614043a6/original/multistate-method-to-efficiently-account-for-tautomerism-and-protonation-in-alchemical-free-energy-calculations.pdf |
60c7418fbdbb892f24a3837f | 10.26434/chemrxiv.8064458.v1 | General Framework for Calculating Spin–orbit Couplings Using Spinless One-Particle Density Matrices: Theory and Application to the Equation-of-Motion Coupled-Cluster Wave Functions | Standard implementations of non-relativistic excited-state calculations compute only one component of spin multiplets (i.e., Ms =0 triplets), however, matrix elements for all components are necessary for calculations of experimentally relevant spin-dependent quantities. To circumvent explicit calculations of all multiplet components, we employ Wigner–Eckart’s theorem. Applied to a reduced one-particle transition density matrix computed for a single multiplet component, Wigner–Eckart’s theorem generates all other spin–orbit matrix elements. In addition to computational efficiency, this approach also resolves the phase issue arising within Born–Oppenheimer’s separation of nuclear and electronic degrees of freedom. A general formalism and its application to the calculations of spin–orbit couplings using equation-of-motion coupled-cluster wave functions is presented. The two-electron contributions are included via the mean-field spin–orbit treatment. Intrinsic issues of constructing spin–orbit mean-field operators for open-shell references are discussed and a resolution is proposed. The method is benchmarked by using several radicals and diradicals. The merits of the approach are illustrated by a calculation of the barrier for spin inversion in a high-spin tris(pyrrolylmethyl)amine Fe(II) complex. | Pavel Pokhilko; Evgeny Epifanovsky; Anna I. Krylov | Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7418fbdbb892f24a3837f/original/general-framework-for-calculating-spin-orbit-couplings-using-spinless-one-particle-density-matrices-theory-and-application-to-the-equation-of-motion-coupled-cluster-wave-functions.pdf |
60c74602337d6c4b6be270aa | 10.26434/chemrxiv.10743344.v1 | A Bioorthogonal Click Chemistry Toolbox for Targeted Synthesis of Branched and Well-Defined Protein-Protein Conjugates | A highly efficient technology for protein
functionalization with commonly used bioorthogonal motifs for Diels-Alder
cycloaddition with inverse electron demand (DA<sub>inv</sub>). With the aim of
precisely generating branched protein chimeras, we systematically assessed the
reactivity, stability and side product formation of various bioorthogonal
chemistries directly at the protein level. We demonstrate the efficiency and
versatility of our conjugation platform using different functional proteins and
the therapeutic antibody trastuzumab. This technology enables fast and routine
access to tailored and hitherto inaccessible protein chimeras useful for a
variety of scientific disciplines. | Mathis Baalmann; Laura Neises; Sebastian Bitsch; Hendrik Schneider; Lukas Deweid; Nadja Ilkenhans; Martin Wolfring; Michael J. Ziegler; Philipp Werther; Jonas Wilhelm; Harald Kolmar; Richard Wombacher | Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74602337d6c4b6be270aa/original/a-bioorthogonal-click-chemistry-toolbox-for-targeted-synthesis-of-branched-and-well-defined-protein-protein-conjugates.pdf |
6356e4381db0bd2a0c37dedb | 10.26434/chemrxiv-2022-m4ffd | A Simple Approach for Beginners to Drawing Lewis Structures, Resonance Forms, and Isomers | Lewis structures, resonance forms, and isomers are difficult for beginners to draw in a general chemistry class. Though various methods and their improved procedures have appeared in the literature and general chemistry textbooks, most of them are too complicated to understand or can only be applied to a small number of molecules. A simplified approach with the rationale behind it for drawing Lewis structures, resonance forms, and isomers is introduced in this paper. In addition, the adjusted procedures that deal with odd-electron molecules or ions are also proposed. | Qi Cui; Jordan Harshman | Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6356e4381db0bd2a0c37dedb/original/a-simple-approach-for-beginners-to-drawing-lewis-structures-resonance-forms-and-isomers.pdf |
60c744d4702a9b1e1318a8df | 10.26434/chemrxiv.9759314.v2 | Chemical Synthesis of Shiga Toxin Subunit B Using a Next-Generation Traceless “Helping Hand” Solubilizing Tag | This manuscript describes the development and characterization of a second-generation "helping hand" solubilizing tag. This semipermanent tag aids solubility of peptides during purification and handling steps and is compatible with common native chemical ligation conditions. The utility of this tag is demonstrated by the synthesis of the Shiga toxin B subunit. | James Fulcher; Mark Petersen; riley giesler; Zachary Cruz; debra eckert; J. Nicholas Francis; eric kawamoto; Michael Jacobsen; Michael Kay | Bioorganic Chemistry; Organic Compounds and Functional Groups; Biochemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744d4702a9b1e1318a8df/original/chemical-synthesis-of-shiga-toxin-subunit-b-using-a-next-generation-traceless-helping-hand-solubilizing-tag.pdf |
6346f433fb0fd8e457363872 | 10.26434/chemrxiv-2022-bs6ds | A comparison of photodeposited RuOx for
alkaline water electrolysis | The storage of renewable energy is a pressing challenge to overcome in the transition towards a power grid based on plentiful, yet intermittent energy supplies. The renewables-driven electrolysis ofwater to formhydrogen fuel is an attractive avenue, but requires better oxygen-evolution reaction (OER) catalysts to be feasible at scale. RuO2 is touted as one of the superior OER catalysts, but only under acidic conditions – RuO2 electrocatalysts suffer
from poor stability under alkaline conditions. In this work, we evaluate three photodeposited RuO2 OER electrocatalysts, all prepared via a scalable photodeposition method. Based on electrochemical and spectroscopic studies (x-ray photoelectron spectroscopy and
X-ray absorption spectroscopy) our main findings are that nanocrystalline RuO2 catalysts outperform their amorphous counterpart, and are stable under alkaline (0.1 M KOH) conditions. This works thus lifts a major hurdle towards the use of RuO2 for alkaline water
electrolysis. | Katelynn Daly; Santiago Jimenez-Villegas; Benjamin Godwin; Martin Schoen; Oliver Calderon; Ning Chen; Simon Trudel | Catalysis; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6346f433fb0fd8e457363872/original/a-comparison-of-photodeposited-ru-ox-for-alkaline-water-electrolysis.pdf |
60c75330842e65d8fddb3ef1 | 10.26434/chemrxiv.13424102.v1 | Cobalt- and Iron-Catalyzed Regiodivergent Alkene Hydrosilylations | A complementary set of base metal catalysts has been developed for regiodivergent alkene hydrosilylations: iron complexes of amine-iminopyridine ligands are selective for Markovnikov hydrosilylations (branched/linear up to >99:1), while the cobalt complexes bearing the same type of ligands provide excellent levels of anti-Markovnikov selectivity (linear/branched up to >99:1). Both systems exhibit high efficiency and wide functional group tolerance. | Sheng Zhang; Jia-Shiang Liao; Daniel Unruh; Guigen Li; Michael Findlater | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75330842e65d8fddb3ef1/original/cobalt-and-iron-catalyzed-regiodivergent-alkene-hydrosilylations.pdf |
62df0ae48e16073088cdc64b | 10.26434/chemrxiv-2022-fnfck | Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin | One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer non-parabolic as described by the Q-model of electron transfer. We analyze the medium dynamical effect on protein electron transfer produced by coupled Stokes-shift dynamics and the dynamics of the donor-acceptor distance modulating electron tunneling. The equilibrium donor-acceptor distance falls in the plateau region of the rate constant, when it is determined by the protein-water dynamics and the probability of electron tunneling does not affect the rate. The crossover distance found here puts most intraprotein electron-transfer reactions under the umbrella of dynamical control. The crossover between the medium-controlled and tunneling-controlled kinetics is combined with the effect of the protein-water medium on the activation barrier to formulate principles of tunability of protein-based charge-transfer chains. The main principle in optimizing the activation barrier is the departure from the Gaussian-Gibbsian statistics of fluctuations promoting activated transitions. This is achieved either by incomplete (nonergodic) sampling, breaking the link between the Stokes-shift and variance reorganization energies, or through wetting-induced structural changes of the enzyme's active site. | Setare Sarhangi; Dmitry Matyushov | Theoretical and Computational Chemistry; Physical Chemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62df0ae48e16073088cdc64b/original/theory-of-protein-charge-transfer-electron-transfer-between-tryptophan-residue-and-active-site-of-azurin.pdf |
66c38abff3f4b052905cfdb3 | 10.26434/chemrxiv-2024-605fc | Exploration of One-Pot, Tandem Sulfamoylation and Aza-Michael Cyclization Reactions for the Syntheses of Oxathiazinane Heterocycles | We show the first examples of one-pot, tandem sulfamoylation/aza-Michael reactions for the preparation of oxathiazinane heterocycles from linear alkenyl alcohol precursors. Our optimized protocols are tolerant of a variety of functional groups and provide products which are amenable for further transformations. The reactions scale well, and no special precautions are required to exclude air or ambient moisture. | Shyam Sathyamoorthi; Appasaheb Nirpal; Harshit Joshi; Steven Kelley | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c38abff3f4b052905cfdb3/original/exploration-of-one-pot-tandem-sulfamoylation-and-aza-michael-cyclization-reactions-for-the-syntheses-of-oxathiazinane-heterocycles.pdf |
637942967d5220395f698db1 | 10.26434/chemrxiv-2022-2npj5-v2 | Cyclic Voltammetry Quantification of Iron in Ferrous Sulfate Supplements: A Method of Successive Addition to One Solution | There is a growing interest in the introduction of cyclic voltammetry to upper-level undergraduate chemistry students. This work presents a simple buffer-free cyclic voltammetry experiment for the quantification of elemental iron in ferrous sulfate supplements using standard addition to a single solution. The various student learning outcomes highlighted in this work include the introduction to the basic principles of cyclic voltammetry, the construction of a calibration curve based on the Randles−Sevcik equation, obtaining a linear regression equation using Microsoft excel, acid digestion of drug supplements, and quality assurance through a statistical evaluation of experimental data. This laboratory experiment also emphasizes the advantages of using the method of a standard addition to a single solution. | Isaac Agyekum; James Casey | Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637942967d5220395f698db1/original/cyclic-voltammetry-quantification-of-iron-in-ferrous-sulfate-supplements-a-method-of-successive-addition-to-one-solution.pdf |
677c9cc26dde43c908904196 | 10.26434/chemrxiv-2024-xpv5b-v2 | Localized Surface Plasmon Resonance in CuGaS2 Nanoparticles Dictated by Crystal Phase | Localized surface plasmon resonance (LSPR) is widely applied in photo-functional technologies such as photocatalysis and solar cells. Research into LSPR materials has recently extended to semiconductor nanoparticles (NPs) because their composition and structure flexibility allow for tuning of optical properties. However, many of the crystallographic factors governing the LSPR of semiconductor NPs are not understood due to the difficulty of controlling the crystal structure of NPs. Here we report for the first time on the crystal structure and size-controlled synthesis of CuGaS2 (CGS) NPs which are typical I-III-VI semiconductors. Moreover, we investigate their LSPR properties to reveal the crystal structure dependence of LSPR extinction. Chalcopyrite and wurtzite CGS (c-CGS and w-CGS, respectively) dictate LSPR in the NIR region. The extinction coefficient of c-CGS was approximately 3 times larger than that of w-CGS because of the larger polarizability of c-CGS. Semiconductors with larger polarizability are better candidates as NIR light-harvesting materials for plasmon-based photocatalysis and solar cells. These results should significantly deepen our understanding of semiconductor plasmonics and serve as a foundation for developing highly efficient energy conversion systems. | Keito Sano; Daniel Packwood; Masanori Sakamoto | Theoretical and Computational Chemistry; Nanoscience; Nanofabrication; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677c9cc26dde43c908904196/original/localized-surface-plasmon-resonance-in-cu-ga-s2-nanoparticles-dictated-by-crystal-phase.pdf |
60cbb47ffca4902445c7ac4b | 10.26434/chemrxiv-2021-5tvrv | Unsupervised Machine Learning for Unbiased Chemical Classification in X-ray Absorption Spectroscopy and X-ray Emission Spectroscopy | We report a comprehensive computational study of unsupervised machine learning for extraction of chemically relevant information in X-ray absorption near edge structure (XANES) and in valence-to-core X-ray emission spectra (VtC-XES) for classification of a broad ensemble of sulforganic molecules. By progressively decreasing the constraining assumptions of the unsupervised machine learning algorithm, moving from principal component analysis to a variational autoencoder to t-distributed stochastic neighbor embedding (t-SNE), we find improved sensitivity to steadily more refined chemical information. Surprisingly, even in merely two dimensions, t-SNE distinguishes not just oxidation state and general sulfur bonding environment but the aromaticity of the bonding radical group with 87% accuracy as well as identifying even finer details in electronic structure within aromatic or aliphatic sub-classes. We find that the chemical information in XANES and VtC-XES is very similar, although they exhibit an unexpected tendency to have different sensitivity within a given molecular class. | Samantha Tetef; Niranjan Govind; Gerald Seidler | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Artificial Intelligence; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cbb47ffca4902445c7ac4b/original/unsupervised-machine-learning-for-unbiased-chemical-classification-in-x-ray-absorption-spectroscopy-and-x-ray-emission-spectroscopy.pdf |
641438badab08ad68f437fbb | 10.26434/chemrxiv-2023-zms7p | On the use of Soft X-ray STXM for Organic-Inorganic Halide Perovskite Photovoltaic Materials | Perovskite solar cells (PSCs) research is an intense field that could benefit from every available research tool. Synchrotron tools have played an important role in fundamental and applied research for decades. Many synchrotron-based hard X-ray tools are already providing effective feedback to the PSC research community. With several fourth-generation light sources up and running or under development, this contribution will continue to impact every aspect of scientific advancement including PSC research. Arguably, the contribution of soft X-rays in PSC research is relatively limited. In view of the developments in the synchrotron world and the fact that a multimethod approach, combining laboratory-based techniques as well as synchrotron-based techniques, is necessary to provide constructive feedback to the PSC community we present here a collection of arguments and procedures with the aim of highlighting the use of soft X-ray scanning transmission X-ray microscopy (STXM). Some aspects of these arguments are elaborated with STXM investigation of perovskite material formamidinium-methylammonium lead iodide (FA1-xMAxPbI3).
| Sufal Swaraj; Haeyeon Jun; Chloé Dindault; Denis Tondelier; Bernard Geoffroy; Ileana Florea; Jean-Eric Bouree; Philip Schulz; Yvan Bonnassieux | Materials Science; Nanoscience; Energy; Hybrid Organic-Inorganic Materials; Photovoltaics | CC BY 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641438badab08ad68f437fbb/original/on-the-use-of-soft-x-ray-stxm-for-organic-inorganic-halide-perovskite-photovoltaic-materials.pdf |
60c753fdbb8c1ac9c73dc160 | 10.26434/chemrxiv.13578299.v1 | Efficient and Selective N-Dimethylation of Amines with Functional Aldehydes Catalysed by Ru Nanoparticles Heterogeneous Catalyst | <p>N-methylated amines are essential bioactive compounds and have been widely used in the fine and bulk chemical industries, as well as in pharmaceuticals, agrochemicals, and dyes. Developing green, efficient, and low-cost catalysts for methylation of amines by using efficient and easily accessible methylating reagents is highly desired yet remains a significant challenge. Herein, we report the selective N-dimethylation of different functional amines with different functional aldehydes under easily handle-able and industrially applicable conditions using carbon-supported Ru nanoparticles (Ru/C) as a heterogeneous catalyst. A broad spectrum of amines could be efficiently converted to their corresponding N, N-dimethyl amines with good compatibility of various functional groups. This method is widely applicable to N-dimethylation of primary amines including aromatic, aliphatic amines with formaldehyde, and synthesis of tertiary amines from primary, secondary amines with different functional aldehydes. The advantage of this newly described method includes operational simplicity, high turnover number, the ready availability of the catalyst, and good functional group compatibility. This Ru/C catalyzed N-dimethylation reaction possibly proceed through a twice N-methylation reaction process.</p> | Jianguo Liu; Yanpei Song; Xiang Wu; Longlong Ma | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753fdbb8c1ac9c73dc160/original/efficient-and-selective-n-dimethylation-of-amines-with-functional-aldehydes-catalysed-by-ru-nanoparticles-heterogeneous-catalyst.pdf |
60c753f3702a9b6b5f18c46c | 10.26434/chemrxiv.13586393.v1 | Stereoselectivity Predictions for the Pd-Catalyzed 1,4-Conjugate Addition Using Q2MM | The parameterization of a transition state force field for the title reaction is described. Validation for 82 literature examples leads to a MUE of 1.8 kJ/mol and an R2 of 0.877 between computed and experimental stereoselectivities. The use if the TSFF is demonstrated for a virtual library of 27 ligands and 59 enones. <br /> | Jessica Wahlers; Michael Maloney; Farbod Salahi; Anthony Rosales; Paul Helquist; Per-Ola Norrby; Olaf Wiest | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753f3702a9b6b5f18c46c/original/stereoselectivity-predictions-for-the-pd-catalyzed-1-4-conjugate-addition-using-q2mm.pdf |
6724a65a7be152b1d0a8bea8 | 10.26434/chemrxiv-2024-7c8l0 | Monitoring Radical Intermediates in Photoactivated Palladium-Catalysed Coupling of Aryl Halides to Arenes by an Aryl Radical Assay | An aryl radical assay is used to provide information about the formation of aryl radicals from aryl halides in coupling reactions to arenes in the presence of palladium sources and under LED irradiation (lambda = 456 nm). The assay uses 2-haloxylenes as substrates. Aryl radical formation is indicated both by a defined product composition and by signature deuterium isotope effects. Comparison with recently published results for corresponding ground state palladium-catalysed reactions shows three principal differences: (i) in the photoactivated reactions, evidence supports the formation of aryl radical intermediates with all the phosphine ligands tested, in contrast to thermal ground-state chemistry where only specific ligands had encouraged this pathway, while others had promoted a non-radical coupling mechanism; (ii) oxidative addition complexes that are formed from reaction of Pd(0) sources with aryl halides reacted under photoactivation to form biaryl coupled products through radical intermediates, in contrast to their behaviour under thermal activation;. (iii) the photoreactions work well with mild bases like Cs2CO3, while the thermal reactions required KOtBu as base due to the different roles for base under the thermal versus photochemical mechanisms. | Seb Tyerman; Donald MacKay; Kenneth Clark; Alan Kennedy; Craig Robertson; Laura Evans; Robert Edkins; John Murphy | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6724a65a7be152b1d0a8bea8/original/monitoring-radical-intermediates-in-photoactivated-palladium-catalysed-coupling-of-aryl-halides-to-arenes-by-an-aryl-radical-assay.pdf |
60dcda6ee0330eba1512bd6a | 10.26434/chemrxiv-2021-stxtb | Catalytic synthesis of 1H-2-benzoxocins; Cobalt(III)-carbene radical approach to 8-membered heterocyclic enol ethers | The metallo-radical activation of ortho-allylcarbonyl-aryl N-arylsulfonylhydrazones with the paramagnetic cobalt(II) porphyrin catalyst [Co^II(TPP)] (TPP = tetraphenylporphyrin) provides an efficient and powerful method for the synthesis of novel 8-membered heterocyclic enol ethers. The synthetic protocol is versatile, practical and enables the synthesis of a wide range of unique 1H-2-benzoxocins in high yields. The catalytic cyclization reactions proceed with excellent chemoselectivities, have a high functional group tolerance, and provide several opportunities for the synthesis of new bioactive compounds. The reactions are shown to proceed via cobalt(III)-carbene radical intermediates, which are in-volved in intramolecular hydrogen transfer (HAT) from the allylic position to the carbene radical, followed by a near barrierless radical rebound step in the coordination sphere of cobalt. The proposed mechanism is supported by experi-mental observations, density functional theory (DFT) calculations and spin trapping experiments. | Minghui Zhou; Lukas A. Wolzak; Zirui Li; Felix J. de Zwart; Simon Mathew; Bas de Bruin | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dcda6ee0330eba1512bd6a/original/catalytic-synthesis-of-1h-2-benzoxocins-cobalt-iii-carbene-radical-approach-to-8-membered-heterocyclic-enol-ethers.pdf |
60c73efe0f50db9dfc395715 | 10.26434/chemrxiv.7195898.v1 | H/D Isotope Effects on Redox-Switching of DNA Self-Assembled Monolayers Observed by EQCM and Cyclic Voltammetry | An electrochemical quartz crystal microbalance (EQCM) was employed to study the interactions of hexammine ruthenium(III) (RuHex) and hexammine cobalt(III) (CoHex) with a mixed self-assembled monolayer of single-stranded DNA and 6-mercapto-1-hexanol (ssDNA/MCH SAM) immobilized on gold electrodes. When the buffer medium was switched to deuterium oxide (D<sub>2</sub>O) from normal water (H<sub>2</sub>O), we observed a pronounced H/D kinetic isotope effect where a consistent shift of up to 400 mV was seen for the reduction peak potential of CoHex but not with RuHex. This was attributed to a 2400-fold change of the apparent reaction rate constant. Though there was a dramatic increase in the EQCM frequency response at a millisecond time scale in the presence of both redox indicators, compared to the signal observed in a low ionic strength buffer (10 mM tris(hydroxymethyl)aminomethane (Tris)/H<sub>2</sub>SO<sub>4 </sub>at pH 7.5), a 10 Hz decrease in the frequency shift was observed upon switching from H<sub>2</sub>O to D<sub>2</sub>O-based buffer medium. The hydrogen bond network within the ssDNA layer seems to amplify the H/D isotope effect with CoHex. Amplified isotope effects may play a role in living systems. The mechanisms of recently reported H/D isotope effects in medicinal and biochemistry are still widely unclear. Voltammetric and EQCM studies of H/D isotope effects can provide a platform to investigate amplified isotope effects not only with DNA layers, but probably also with proteins and small organic molecules and may be useful for studies of cell proliferation, as well as drug testing. | Sarasi K. K. Galagedera; Gerd-Uwe Flechsig | Analytical Chemistry - General; Biochemical Analysis; Electrochemical Analysis; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73efe0f50db9dfc395715/original/h-d-isotope-effects-on-redox-switching-of-dna-self-assembled-monolayers-observed-by-eqcm-and-cyclic-voltammetry.pdf |
60c74009469df4c31cf42bb9 | 10.26434/chemrxiv.7591190.v1 | Automatically Full Glycan Structural Determination with Logically Derived Sequence Tandem Mass Spectrometry | Here we show the full structures of glycans, including
diastereomers and anomericity of each monosaccharide and linkage position of
each glycosidic bond, can be determined using tandem mass spectrometry guided
by a logically derived sequence (LODES). This new method provides de novo
oligosaccharide structural identifications with high sensitivity and was
applied to automatically in situ structural determination of the oligosaccharides eluted by high performance liquid chromatography. We showed
that the structure of a given trisaccharide from trisaccharide mixture and
bovine milk were determined from
near three
thousand isomers by using six to seven logically selected CID spectra.
The entire procedure of mass spectrum measurement guided by LODES can be
programmed in computer for automatically full glycan structural identification,
a goal that remains a great challenge in glycan analysis. | Shang-Ting Tsai; Chia Yen Liew; Hsu Chen Hsu; Shih-Pei Huang; Wei-Chien Weng; Yu-Hsiang Kuo; Chi-Kung Ni | Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74009469df4c31cf42bb9/original/automatically-full-glycan-structural-determination-with-logically-derived-sequence-tandem-mass-spectrometry.pdf |
623f1bbf13d478a8fe9cdd87 | 10.26434/chemrxiv-2022-tfhx6 | Site Specific NMR Characterization of Abeta-40 Oligomers Cross Seeded by Abeta-42 Oligomers | Extracellular accumulation of β amyloid peptides of 40 (Aβ40) and 42 residues (Aβ42) has been considered as one of the hallmarks in the pathology of Alzheimer’s disease. In this work, we are able to prepare oligomeric aggregates of Aβ with uniform size and high structural homogeneity. Our experimental design is to incubate Aβ peptides in reverse micelles (RMs) so that the peptides could aggregate only through a single nucleation process and the size of the oligomers is confined by the physical dimension of the reverse micelles. The hence obtained Aβ oligomers (AβOs) are 23 nm in diameter and they belong to the category of high molecular-weight (MW) oligomers. The solid-state NMR data revealed that Aβ40Os adopt the structural motif of β-loop-β but the chemical shifts manifested that they are structurally different from low-MW AβOs and mature fibrils. From the thioflavin-T results, we found that high-MW Aβ42Os can seed the fibrillization of Aβ40 monomers. Our protocol allows performing cross-seeding experiments among oligomeric species. By comparing the chemical shifts of Aβ40Os cross seeded by Aβ42Os and those of Aβ40Os prepared in the absence of Aβ42Os, we observed that the structures of E11, K16, and E22 were altered, whereas the backbone conformation of the β-sheet region near the C-terminus is structurally invariant. The use of reverse micelles allows hitherto the most detailed characterization of the structural variability of Aβ40Os. | Han-Wen Chang; Ho-I Ma; Yi-Shan Wu; Ming-Che Lee; Eric Chung-Yueh Yuan; Shing-Jong Huang; Yu-Sheng Cheng; Meng-Hsin Wu; Ling-Hsien Tu; Jerry Chun Chung Chan | Physical Chemistry; Biophysical Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623f1bbf13d478a8fe9cdd87/original/site-specific-nmr-characterization-of-abeta-40-oligomers-cross-seeded-by-abeta-42-oligomers.pdf |
60c744b8bdbb89d23ca388ad | 10.26434/chemrxiv.9891341.v1 | Four-Step Access to the Sesquiterpene Natural Product Presilphiperfolan-1β-ol and Unnatural Derivatives via Supramolecular Catalysis | Herein we report the shortest synthesis of the tricyclic sesquiterpene presilphiperfolan-1β-ol to date, utilizing the supramolecular resorcinarene capsule as catalyst for the key step. This synthetic approach also allows access to unnatural derivatives of the natural product, which would not be accessible through the biosynthetic machinery. Additionally, this study provides useful insight into the biosynthesis of the presilphiperfolanol natural products, including the first direct experimental evidence for the proposed biosynthetic connection between caryophyllene and the presilphiperfolanols. | Leonidas-Dimitrios Syntrivanis; Shani Levi; Alessandro Prescimone; Dan Thomas Major; Konrad Tiefenbacher | Natural Products; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b8bdbb89d23ca388ad/original/four-step-access-to-the-sesquiterpene-natural-product-presilphiperfolan-1-ol-and-unnatural-derivatives-via-supramolecular-catalysis.pdf |
65fb3196e9ebbb4db920b599 | 10.26434/chemrxiv-2021-3kmnc-v2 | Microcanonical Statistical Mechanics of a Nonideal Fluid: A Pedagogical Approach to Obtain the Combined First and Second Law of Thermodynamics | Thermodynamics forms an important part of the chemistry and chemical engineering curriculum at the undergraduate and graduate levels. Over the years, the importance of statistical mechanics and molecular simulations in the curriculum has increased, especially at the graduate level. Given this shift, in this work, we utilize the microcanonical ensemble, which is typically considered to be intractable, and show that it is helpful to employ it as a pedagogical tool that demonstrates the consistency of microcanonical statistical mechanics with the combined first and second law of thermodynamics. We start with Boltzmann's entropy formula and use differential calculus to establish that dE=TdS - PdV for an isolated, nonideal fluid in an arbitrary number of dimensions, with a constant number of particles (N), volume (V), and energy (E), and with temperature T, pressure P, and entropy S. To this end, we write the partition function for an isolated monoatomic fluid. Further, we derive the average of the inverse kinetic energy, which appears in the formulation of the combined first and second law, and show that it is equal to the inverse of the average kinetic energy, thus introducing the system's temperature (T). Subsequently, we obtain an expression for the pressure (P) of a system involving many-body interactions and introduce the system pressure in the combined first and second law via Clausius's virial theorem. We discuss how intermolecular interactions affect the entropy and pressure of a thermodynamic system. Overall, we inform the derivation of the fundamental thermodynamic relationship dE=TdS-PdV using an isolated (microcanonical) system, thereby providing deeper insight into equilibrium statistical thermodynamics. Indeed, we demonstrated that this material resulted in favorable learning outcomes when taught as a 1.5-hour lecture. Accordingly, the material presented here may be incorporated into graduate-level courses on statistical mechanics and/or molecular simulations in various disciplines, including chemistry and physics, as well as chemical, materials, and mechanical engineering. | Ananth Govind Rajan | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Chemical Education - General; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fb3196e9ebbb4db920b599/original/microcanonical-statistical-mechanics-of-a-nonideal-fluid-a-pedagogical-approach-to-obtain-the-combined-first-and-second-law-of-thermodynamics.pdf |
60c74aec702a9b942518b36b | 10.26434/chemrxiv.12275636.v1 | Fractionation of Block Copolymers for Pore Size Control and Reduced Dispersity in Mesoporous Inorganic Thin Films | Mesoporous inorganic thin films are promising materials architectures for a variety of applications, including sensing, catalysis, protective coatings, energy generation and storage. In many cases, precise control over a bicontinuous porous network on the 10-nm length scale is crucial for their operation. A particularly promising route for structure formation utilizes block copolymer (BCP) micelles in solution as sacrificial structure-directing agents for the co-assembly of inorganic precursors. This method offers pore size control via the molecular weight of the pore forming block and is compatible with broad materials library. On the other hand, the molecular weight dependence impedes continuous pore tuning and the intrinsic polymer dispersity presents challenges to the pore size homogeneity. To this end, we demonstrate how chromatographic fractionation of BCPs provides a powerful method to control the pore size and dispersity of the resulting mesoporous thin films. We apply a semi-preparative size exclusion chromatographic fractionation to a polydisperse poly(isobutylene)-block-poly(ethylene oxide) (PIB-b-PEO) BCP obtained from scaled-up synthesis. The isolation of BCP fractions with distinct molecular weight and narrowed dispersity allowed us to not only tune the characteristic pore size from 9.1±1.5 to 14.1±2.1 nm with the identical BCP source material, but also significantly reduce the pore size dispersity compared to the non-fractionated BCP. Our findings offer a route to obtain a library of monodisperse BCPs from a polydisperse feedstock and provide important insights on the direct relationship between macromolecular characteristics and the resulting structure-directed mesopores, in particular related to dispersity. | Alberto Alvarez Fernandez; Barry Reid; Jugal Suthar; Swan Choy; Maximiliano Jesus Jara Fornerod; Niamh Mac Fhionnlaoich; Lixu Yang; Benjamin Schmidt-Hansberg; Stefan Guldin | Coating Materials; Materials Processing; Nanostructured Materials - Materials; Thin Films; Nanofabrication; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aec702a9b942518b36b/original/fractionation-of-block-copolymers-for-pore-size-control-and-reduced-dispersity-in-mesoporous-inorganic-thin-films.pdf |
676b1fbf6dde43c908368eb8 | 10.26434/chemrxiv-2024-kz6h6 | Stackable 3D-Printed Core-Shell Nozzle System for Multi-shell Fiber and Microdroplet Generation | Microfluidics is increasingly utilized in biofabrication to create more complex fiber and droplet structures, including those that involve multiple materials. Layered and core-multiple shell structures are of particular interest as templates for biofabrication and cell growth. Traditional fabrication methods often rely on fixed coaxial, triaxial or quadaxial needles, which are costly and prone to clogging, particularly for smaller inner diameters. Here, we introduce a versatile system based on a 3D printed nozzle which combines two flows: an inner core- and an outer shell-flow. The outlet is fitted with a glass capillary, allowing control of the fiber diameter by adjusting the capillary. The design facilitates the modular “LEGO-Brick” stacking of multiple nozzles, enabling the efficient fabrication of complex fibers. We demonstrate the production of alginate (Alg)/methyl cellulose (MC) composite fibers with variable diameters. Additionally, when the shell was filled with an oil phase and the core with a water phase, microdroplets with controlled diameters were effectively generated. The two-flow system also enables the extrusion of graphene oxide (GO)-based fibers and microbeads, which are widely-used structures in various applications. To demonstrate the capability of the designed nozzle for biofabrication, C2C12 cell-laden GO-based fibers and microbeads were fabricated, exhibiting excellent post-fabrication cell viability. | Jianfeng Li; Peer Fischer | Materials Science; Polymer Science; Carbon-based Materials; Composites; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676b1fbf6dde43c908368eb8/original/stackable-3d-printed-core-shell-nozzle-system-for-multi-shell-fiber-and-microdroplet-generation.pdf |
62bb90b0f5193952db778b6a | 10.26434/chemrxiv-2022-5v0tt | Together, not separately, OH and O3 oxidize Hg(0) to Hg(II) in the atmosphere | Mercury, a highly toxic metal, is emitted to the atmosphere mostly as gaseous Hg(0). Atmospheric Hg(0) enters ecosystems largely through via uptake by vegetation, while Hg(II) largely enters ecosystems in oceans and via rainfall. Consequently, the redox chemistry of atmospheric mercury strongly influences its fate and its global biogeochemical cycling. Here we report on the oxidation and reduction of Hg(I) (BrHg and HOHg radicals) in reactions with ozone, and how the electronic structure of these Hg(I) species affects the kinetics of these reactions. The oxidation reactions lead to XHgO• + O2 (X=Br and OH), while the reduction reaction produces Hg(0), HOX, and O2. According to our calculations with CCSD(T), NEVPT2, and CAM-B3LYP-D3BJ, the kinetics of both oxidation reactions are very similar. These two oxidation reactions are much faster than their reduction counterparts, and this effect is remarkably stronger for the oxidation of HOHg(I) by ozone. Modeling of field data supports the idea that OH and/or O3 (rather than Br) dominates Hg(II) production in the continental boundary layer. Almost all models invoking OH- and ozone-initiated oxidation of Hg(0) assume that these reactions directly produces Hg(II), despite the lack of plausible mechanism for these oxidation reactions. The present work helps reconcile modeling results with mechanistic insights. | Pedro Castro; Vladimir Kellö ; Ivan Cernušák ; Theodore Dibble | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Computational Chemistry and Modeling; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2022-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bb90b0f5193952db778b6a/original/together-not-separately-oh-and-o3-oxidize-hg-0-to-hg-ii-in-the-atmosphere.pdf |
668920c55101a2ffa88cf7a0 | 10.26434/chemrxiv-2023-ktscq-v2 | Modeling Chemical Processes in Explicit Solvents with Machine Learning Potentials | Solvent effects influence all stages of the chemical processes, modulating the stability of intermediates and transition states, as well as altering reaction rates and product ratios. However, accurately modelling these effects remains challenging. Here, we present a general strategy for generating reactive machine learning potentials to model chemical processes in solution. Our approach combines active learning with descriptor-based selectors and automation, enabling the construction of data-efficient training sets that span the relevant chemical and conformational space. We apply this strategy to investigate a Diels-Alder reaction in water and methanol. The generated machine learning potentials enable us to obtain reaction rates that are in agreement with experimental data and analyse the influence of these solvents on the reaction mechanism. Our strategy offers an efficient approach to the routine modelling of chemical reactions in solution, opening up avenues for studying complex chemical processes in an efficient manner. | Hanwen Zhang; Veronika Juraskova; Fernanda Duarte | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668920c55101a2ffa88cf7a0/original/modeling-chemical-processes-in-explicit-solvents-with-machine-learning-potentials.pdf |
60c75315702a9b413418c2f0 | 10.26434/chemrxiv.13385387.v1 | Protein Footprinting, Conformational Dynamics and Interface-Adjacent Neutralization ‘Hotspots’ in the SARS-CoV-2 Spike Protein Receptor Binding Domain / Human ACE2 Interaction | This study provides an HDX-MS based analysis of the interaction between the SARS-CoV-2 spike protein and the human Angiotensin Converting Enzyme 2. <div><br /></div><div>- The data agree exactly with the X-ray co-crystal structure of this complex, but provide additional information based on shifts in dynamics that are observed just outside the interface. </div><div><br /></div><div>- These dynamic changes occur specifically in regions that are the primary targets of neutralizing antibodies that target spike protein, suggesting that the neutralization mechanism may result from suppression of dynamic shifts in the spike Receptor Binding Domain (RBD) that are necessary for favorable binding thermodynamics in the spike / ACE2 interaction.</div> | Dominic Narang; Matthew Balmer; D. Andrew James; Derek Wilson | Biochemistry; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75315702a9b413418c2f0/original/protein-footprinting-conformational-dynamics-and-interface-adjacent-neutralization-hotspots-in-the-sars-co-v-2-spike-protein-receptor-binding-domain-human-ace2-interaction.pdf |
66458adc91aefa6ce11f489c | 10.26434/chemrxiv-2024-5vkbp | MISTER-T: An Open-Source Software Package for Quantum Optimal Control of Multi-Electron Systems on Arbitrary Geometries | We present an open-source software package, MISTER-T (Manipulating an Interacting System of Total Electrons in Real-Time), for the quantum optimal control of interacting electrons within a time-dependent Kohn-Sham formalism. In contrast to other implementations restricted to simple models on rectangular domains, our method enables quantum optimal control calculations for multi-electron systems (in the effective mass formulation) on nonuniform meshes with arbitrary two-dimensional cross-sectional geometries. Our approach is enabled by forward and backward propagator integration methods to evolve the Kohn-Sham equations with a pseudoskeleton decomposition algorithm for enhanced computational efficiency. We provide several examples of the versatility and efficiency of the MISTER-T code in handling complex geometries and quantum control mechanisms. The capabilities of the MISTER-T code provide insight into the implications of varying propagation times and local control mechanisms to understand a variety of strategies for manipulating electron dynamics in these complex systems. | Yuan Chen; Mahmut Okyay; Bryan Wong | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66458adc91aefa6ce11f489c/original/mister-t-an-open-source-software-package-for-quantum-optimal-control-of-multi-electron-systems-on-arbitrary-geometries.pdf |
60c740a04c8919d685ad2179 | 10.26434/chemrxiv.7770758.v1 | High-Throughput Assessment of Hypothetical Zeolite Materials for Their Synthesizability and Industrial Deployability | <div>Zeolites are important microporous framework materials, where 200+ structures are known to exist and many millions so-called hypothetical materials can be computationally created. Here, we screen the “Deem” database of hypothetical zeolite structures to find experimentally feasible and industrially relevant materials. We use established and existing criteria and structure descriptors (lattice energy, local interatomic distances, TTT angles), and we develop new criteria which are based on 5-th neighbor distances to T-atoms, tetrahedral order parameters (or, tetrahedrality), and porosity and channel dimensionality. Our filter funnel for screening the most attractive zeolite materials that we construct consists of 9 different types of criteria and a total of 53 subcriteria. The funnel reduces the pool of candidate materials from initially >300,000 to 24 and 11, respectively, depending on the channel dimensionality constraint applied (2- and 3-dimensional vs only 3-dimensional channels). </div><div>We find that it is critically important to define longer range and more stringent criteria such as the new 5-th neighbor distances to T-atoms and the tetrahedrality descriptor in order to succeed in reducing the huge pool of candidates to a manageable number. Apart from one experimentally achieved structure (SSF), all other candidates are hypothetical frameworks, thus, representing most valuable targets for synthesis and application. Detailed analysis of the screening data allowed us to also propose an exciting future direction how such screening studies as ours could be improved and how framework generating algorithms could be competitively optimized.</div> | Nils Zimmermann; Jose Luis Salcedo Perez; Maciej Haranczyk | Catalysts; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Minerals; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a04c8919d685ad2179/original/high-throughput-assessment-of-hypothetical-zeolite-materials-for-their-synthesizability-and-industrial-deployability.pdf |
60c74328bb8c1a30d43da271 | 10.26434/chemrxiv.8943560.v1 | Rethinking Basic Concepts - Hydrogenation of Alkenes Catalyzed by Bench-Stable Alkyl Mn(I) Complexes | An efficient additive-free manganese-catalyzed hydrogenation of alkenes to alkanes with molecular hydrogen is described. This reaction is environmentally benign and atom economic, implementing an inexpensive, earth abundant non-precious metal catalyst. The most efficient pre-catalyst is the bench-stable alkyl bisphosphine Mn(I) complex fac-[Mn(dippe)(CO)3(CH2CH2CH3)]. The catalytic process is initiated by migratory insertion of a CO ligand into the Mn-alkyl bond to yield an acyl intermediate which undergoes rapid hydrogenolysis to form the active 16e Mn(I) hydride catalyst [Mn(dippe)(CO)2(H)]. A range of mono- and disubstituted alkenes were efficiently converted into alkanes in good to excellent yields. The hydrogenation of 1-alkenes and 1,1-disubstituted alkenes proceeds at 25 oC, while 1,2-disubstituted alkenes require a reaction temperature of 60oC. In all cases, a catalyst loading of 2 mol % and a hydrogen pressure of 50 bar was applied. A mechanism based on DFT calculations is presented.<br /> | Stefan Weber; Berthold Stöger; Luis F. Veiros; Karl Kirchner | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74328bb8c1a30d43da271/original/rethinking-basic-concepts-hydrogenation-of-alkenes-catalyzed-by-bench-stable-alkyl-mn-i-complexes.pdf |
60c73eb7bdbb894b4ba37e97 | 10.26434/chemrxiv.7081151.v1 | MOF Decomposition and Introduction of Repairable Defects Using a Photodegradable Strut | Utilizing a photolabile ligand as MOF strut can make a
framework undergo full or partial decomposition upon irradiation. For the first
time, a nitrophenylacetate derivative has been incorporated into MOF as a
backbone linker via PLSE method. The photo-induced decarboxylation of the NPDAC-MOF
represents a novel way of degrading a MOF, which provides an innovative approach
to formulating photoresponsive porous materials with potential applications in
molecular release and drug delivery. When photoactive linker is mixed with non-photolabile
linker via partial PLSE, the MOF structure can be retained after irradiation,
but with the introduction of multiple defects, offering a new method to create vacancies
in MOFs. Defect repair can be achieved by treatment with replacement ligands,
the scope of which is an interesting area for developing customizable MOF
contents.<br /> | Jingjing Yan; John MacDonald; Shawn Burdette | Photochemistry (Org.); Hybrid Organic-Inorganic Materials; Coordination polymers | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eb7bdbb894b4ba37e97/original/mof-decomposition-and-introduction-of-repairable-defects-using-a-photodegradable-strut.pdf |
60c7574c337d6c3ccae28ffa | 10.26434/chemrxiv.14390516.v1 | Water-Dispersible and Ferroelectric PEGylated Barium Titanate Nanoparticles | <div>Dispersions of ferroelectric nanoparticles in aqueous medium can find promising applications in electro-optical, medical, and smart fluid technologies. In this report, we show the development of highly dispersed nano-sized ferroelectric barium titanate (BaTiO3) powders with high dielectric constant prepared using a simple, one-step low temperature solution method. The surface of these tetragonal-structured nanoparticles were modified with polyethylene glycol as a stabilizer and dispersant. The crystal structure, morphology and dielectric constant of samples are discussed in detail. The colloidal stability and surface behavior of these PEGylated barium titanate nanoparticles are studied by means of z -potential and dynamic light scattering measurements. We show changing the reaction conditions allows to tune the nanoparticle size. This research promotes a pathway to develop advanced ferroelectric nanomaterials with engineered properties in a simple way.</div> | Maryam Taheri; Bryan Zance; Michelle Dolgos; Steven L. Bryant; Simon Trudel | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7574c337d6c3ccae28ffa/original/water-dispersible-and-ferroelectric-pe-gylated-barium-titanate-nanoparticles.pdf |
66dacb31cec5d6c1424d5344 | 10.26434/chemrxiv-2024-cch7s | Deoxygenative Z-selective olefination of aliphatic alcohols | Alcohols are one of the most abundant functional groups in commercially available materials and biologically active compounds. Herein, we report a mild photocatalytic method for the unprecedent deoxygenative Z-selective olefination of aliphatic alcohols. Key to this methodology is the dual role of a phenothiazine photocatalyst, which enables the desired cross-coupling and promotes in-situ E to Z isomerization of the cross-coupled olefin product. This protocol is distin-guished by its wide substrate scope and broad applicability, even in the context of pharmaceuticals and saccharides. Given the mild and water-compatible conditions, our chemistry can also be utilized to functionalize DNA headpieces with saccharides for DELs applications. | Sai Rohini Narayanan Kolusu; Irene Sánchez-Sordo; Carla Aira-Rodríguez; Emanuele Azzi; Manuel Nappi | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dacb31cec5d6c1424d5344/original/deoxygenative-z-selective-olefination-of-aliphatic-alcohols.pdf |
6439159373c6563f14d63612 | 10.26434/chemrxiv-2023-f9p7h | Visible-Light-Driven C−H Imidation of Arenes and Heteroarenes by a Phosphonium Ylide Organophotoredox Catalyst: Application to C−H Functionalization of Alkenes | Phosphonium ylide catalysis through an oxidative quenching cycle has been developed for visible-light-driven C−H imidation of arenes and heteroarenes. The present protocol could be applied not only to trihalomethylative lactonization reactions involving trifluoromethyl, trichloromethyl, and tribromomethyl radicals but also to the first example of an organophotoredox-catalyzed imidative lactonization reaction involving a nitrogen-centered electrophilic radical species. | Yasunori Toda; Toya Kobayashi; Fumiya Hirai; Takamichi Yano; Makoto Oikawa; Kimiya Sukegawa; Masahiro Shimizu; Fuyuki Ito; Hiroyuki Suga | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6439159373c6563f14d63612/original/visible-light-driven-c-h-imidation-of-arenes-and-heteroarenes-by-a-phosphonium-ylide-organophotoredox-catalyst-application-to-c-h-functionalization-of-alkenes.pdf |
60c74c730f50dbf9af396e64 | 10.26434/chemrxiv.12480974.v1 | The ORR in Ca2+ Containing DMSO: Reaction Mechanism, Electrode Surface Characterization and Redox Mediation | In this study we strengthen our fundamental understanding of the underlying reactions of a possible Ca-O<sub>2</sub> battery using a DMSO based electrolyte. Employing the rotating ring disc electrode, we find a transition from a mixed process of O<sub>2</sub><sup>-</sup> and O<sub>2</sub><sup>2-</sup> formation to an exclusive O<sub>2</sub><sup>-</sup> formation at gold electrodes. We will show that in this system Ca-superoxide and Ca-peroxide are formed as soluble species. However, there is a strongly adsorbed layer of ORR products on the electrode surface which is blocking the electrode. Surprisingly the blockade is a partial blockade because the formation of superoxide can be maintained. During an anodic sweep the ORR product layer is stripped from the electrode surface. With X-ray photoelectron spectroscopy the deposited ORR products are shown to be Ca(O<sub>2</sub>)<sub>2</sub>, CaO<sub>2</sub> and CaO as well as side reaction products such as CO<sub>3</sub><sup>2-</sup> and other oxygen containing carbon species. We will give evidences that the strongly attached layer on the electrocatalyst that is partially blocking the electrode could be adsorbed CaO. The disproportionation reaction of O<sub>2</sub><sup>-</sup> in presence of Ca<sup>2+</sup> was demonstrated via mass spectrometry. Finally the ORR mediated by 2,5-Di-tert-1,4-benzoquinone (DBBQ) is investigated by differential electrochemical mass spectrometry (DEMS) and XPS. Similar products as without DBBQ are deposited on the electrode surface. The analysis of the DEMS experiments shows that DBBQ<sup>-</sup> is reducing O2 to O<sub>2</sub><sup>-</sup> and O<sub>2</sub><sup>2-</sup> whereas in the presence of DBBQ<sup>2-</sup> O<sub>2</sub><sup>2-</sup> is formed. The mechanism of the ORR with and without DBBQ will be discussed. | Pawel Peter Bawol; Philip Heinrich Reinsberg; Andreas Koellisch-Mirbach; Christoph Johannes Bondue; Helmut Baltruschat | Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c730f50dbf9af396e64/original/the-orr-in-ca2-containing-dmso-reaction-mechanism-electrode-surface-characterization-and-redox-mediation.pdf |
64230da2647e3dca99a8096c | 10.26434/chemrxiv-2023-xr63l | Production of Magnetic Arsenic-Phosphorus Alloy Nanoribbons with Small Band Gaps and High Hole Conductivities | Quasi-1D nanoribbons provide a unique route to diversifying the properties of their parent 2D nanomaterial, introducing lateral quantum confinement and an abundance of edge sites. Here, a new family of nanomaterials is opened with the creation of arsenic-phosphorus alloy nanoribbons (AsPNRs). By ionically scissoring the layered crystal black arsenic-phosphorus using lithium electride followed by dissolution in amidic solvents, solutions of AsPNRs are formed. The ribbons are typically few-layered, several microns long with widths tens of nanometers across, and both highly flexible and crystalline. The AsPNRs are highly electrically conducting above 130 K due to their small band gap (ca. 0.035 eV), paramagnetic, and have high hole mobilities, as measured with the first generation of AsP devices, directly highlighting their properties and utility in electronic devices | Fengfei Zhang; Eva Aw; Alexander Eaton; Rebecca Shutt; Juhwan Lim; Jung Ho Kim; Thomas Macdonald; Cesar De Leon Reyes; Arjun Ashoka; Raj Pandya; Oliver Payton; Loren Picco; Caroline Knapp; Akshay Rao; Christopher Howard; Adam Clancy | Inorganic Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64230da2647e3dca99a8096c/original/production-of-magnetic-arsenic-phosphorus-alloy-nanoribbons-with-small-band-gaps-and-high-hole-conductivities.pdf |
67a8d97b81d2151a02c4d52c | 10.26434/chemrxiv-2025-4n2nb-v2 | Design of Partial Agonists of ADAMTS Metalloproteinases as Therapeutics for Neurodegenerative Diseases | Neurodegenerative diseases (NDDs) are characterized by progressive neuronal dysfunction and structural instability, precipitated by aberrations in extracellular matrix (ECM) remodeling and chronic neuroinflammation. The ADAMTS family of metalloproteinases plays a key role in regulating ECM dynamics and neuroinflammatory responses, with dysregulation of specific isoforms contributing to the pathology of NDDs such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. This article proposes the development of partial agonists targeting ADAMTS enzymes as a novel therapeutic approach for managing NDDs. By selectively modulating enzymatic activity, partial agonists could mitigate pathological ECM degradation while preserving essential protease functions. Structural scaffolds for partial agonist development are discussed, leveraging insights from bioisosteric design and computational methodologies. Additionally, advanced drug delivery platforms and preclinical validation paradigms are explored to address translational challenges. The integration of emerging technologies and modeling strategies with generative technologies, is highlighted as a means to overcome current limitations and enhance the precision of ADAMTS-targeting therapies. | David Ferguson, MRSB MRSC | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Education; Bioengineering and Biotechnology; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a8d97b81d2151a02c4d52c/original/design-of-partial-agonists-of-adamts-metalloproteinases-as-therapeutics-for-neurodegenerative-diseases.pdf |
6255c85088636c532b0f151d | 10.26434/chemrxiv-2022-pmrc4 | Site-Selective Synthesis of 2,4,6-Collidinium Salts via Electrooxidative C–H Functionalization | 2,4,6-Trisubstituted pyridinium salts have emerged as versatile pseudohalides for SET-mediated radical cross couplings. However, the widely utilized 2,4,6-triphenylpyridinium Katrtizky salt is plagued by poor atom econ-omy and high cost of synthesis. Thus, there is a growing need for developing more practical scaffolds, along with novel strategies for pyridinium salt formation that will support both diverse heterocyclic motifs and sub-strates. A recent report demonstrated 2,4,6-collidinium salts as more atom-economical and cost-effective electron-acceptors, however their steric hinderance limits their synthesis via traditional nucleophilic substitu-tion. Herein, we report the synthesis of benzylic 2,4,6-collidinium salts via the electrooxidative C–H functional-ization of electron-rich arenes. The method proceeds under mild conditions, has broad functional group tol-erance, is applicable to the synthesis of both primary and secondary collidinium salts, and uses an inexpen-sive, recoverable collidine-based electrolyte system. The resulting salts can be isolated via trituration and di-rectly used in subsequent coupling reactions. This method represents the first synthesis of alkyl pyridinium salts via a net C¬¬–H functionalization, providing a complementary approach to traditional substitution and condensation reactions of pre-functionalized substrates. | Bill Motsch; Sarah Wengryniuk | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6255c85088636c532b0f151d/original/site-selective-synthesis-of-2-4-6-collidinium-salts-via-electrooxidative-c-h-functionalization.pdf |
62b469a70bbbc1bdcc72c7af | 10.26434/chemrxiv-2022-hx3fm | High inorganic content with percolated structure in pore-filling membrane: Platform for functional membranes based on zirconium phosphate
| Organic-inorganic composite membranes are used in various applications, such as proton-conducting electrolyte membranes for PEMFCs. In this study, we filled a polyethylene porous substrate with only but plenty of inorganics (around 48 wt.%), zirconium acetylacetonate, the precursor of zirconium phosphate (ZrP)-based inorganics (AcAc-Zr). It was confirmed that the AcAc-Zr in the substrate was converted into ZrP derivatives in situ, keeping the high contents. TEM-EDS analysis revealed that the pores were continuously filled with ZrP, indicating that ZrP was percolated due to the high contents and the original structure of the porous substrate. The conductivities of these ZrP, ZrHEDP, and ZrATMP films were sufficiently high: on the order of 1 mS cm–1 (80°C and 95% relative humidity condition). | Taiyo Taniuchi; Takaya Ogawa; Masaki Yoshida; Toshiki Nakazono; Keiichi Ishihara N. | Inorganic Chemistry; Polymer Science | CC BY 4.0 | CHEMRXIV | 2022-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b469a70bbbc1bdcc72c7af/original/high-inorganic-content-with-percolated-structure-in-pore-filling-membrane-platform-for-functional-membranes-based-on-zirconium-phosphate.pdf |
650ed59760c37f4f764dfae7 | 10.26434/chemrxiv-2023-wzn14 | Computational Tools for Handling Molecular Clusters: Configurational Sampling, Storage, Analysis, and Machine Learning | Computational modeling of atmospheric molecular clusters requires a comprehensive understanding of their complex configurational spaces, interaction patterns, stabilities against fragmentation, and even dynamic behaviors. To address these needs, we introduce the Jammy Key framework, a collection of automated scripts that facilitate and streamline molecular cluster modeling workflows. Jammy Key handles file manipulations between a variety of integrated 3rd party programs. The framework is divided into three main functionalities: (1) Jammy Key for Configurational Sampling (JKCS) to perform systematic configurational sampling of molecular clusters, (2) Jammy Key for Quantum Chemistry (JKQC) to analyze commonly used quantum chemistry output files and facilitate database construction, handling, and analysis, and (3) Jammy Key for Machine Learning (JKML) to manage machine learning methods in optimizing molecular cluster modeling. This automation and machine learning utilization significantly reduces manual labor, greatly speeds up the search for molecular cluster configurations, and thus increases the number of systems that can be studied. Following the example of the Atmospheric Cluster Database (ACDB) of Elm [ACS Omega, 4, 10965–10984, 2019], the molecular clusters modeled in our group using the Jammy Key framework have been stored in an improved online GitHub repository named ACDB 2.0. In this work, we present the Jammy Key package alongside its assorted applications, which underline its versatility. Using several illustrative examples, we discuss how to choose appropriate combinations of methodologies for treating particular cluster types, including reactive, multi-component, charged, or radical clusters, as well as clusters containing flexible or multi-conformer monomers or heavy atoms. Finally, we present a detailed example of using the tools for atmospheric acid–base clusters. | Jakub Kubečka; Vitus Besel; Ivo Neefjes; Yosef Knattrup; Theo Kurtén; Hanna Vehkamäki; Jonas Elm | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Machine Learning; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650ed59760c37f4f764dfae7/original/computational-tools-for-handling-molecular-clusters-configurational-sampling-storage-analysis-and-machine-learning.pdf |
634e5fc02a70912b1460cae3 | 10.26434/chemrxiv-2022-fd190-v6 | Can the CO2 Reduction Reaction be Improved on Cu: Selectivity and Intrinsic Activity of Functionalized Cu Surfaces | Cu is currently the most effective monometallic catalyst for producing valuable multi-carbon-based products, such as ethylene and ethanol, from the CO2 reduction reaction (CO2RR). One approach to optimize the activity and selectivity of the metal Cu catalyst is to functionalize the Cu electrode with a molecular modifier.
We investigate from a data standpoint whether any reported functionalized Cu catalyst improves the intrinsic activity and/or multi-carbon product selectivity compared to the performance of bare Cu foil and the best single crystal Cu facets. Our analysis shows that the reported increases in activity are due to increased surface roughness and disappear once normalizing with respect to electrochemical surface area. The intrinsic activity generally falls below that of bare Cu foil, both for total and product-specific current, which we attribute to non-selective blocking of active sites by the modifier on the surface. Instead, we show that the modifier allows for easier diffusion of CO2 compared to H2O to the surface, leading to greater selectivity for CO2RR and C2+ products. As such, our analysis finds no catalyst for CO2RR that intrinsically outperforms bare Cu. | Oliver Christensen; Siqi Zhao; Zhaozong Sun; Alexander Bagger; Jeppe Vang Lauritsen; Steen Uttrup Pedersen; Kim Daasbjerg; Jan Rossmeisl | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634e5fc02a70912b1460cae3/original/can-the-co2-reduction-reaction-be-improved-on-cu-selectivity-and-intrinsic-activity-of-functionalized-cu-surfaces.pdf |
66a164c85101a2ffa8e789cd | 10.26434/chemrxiv-2024-5q319 | Cooling-Induced Order-Disorder Phase Transition in CsPbBr3 Nanocrystal Superlattices | Perovskite nanocrystal superlattices are being actively studied after reports have emerged on collective excitonic properties at cryogenic temperatures, where energetic disorder is minimized due to the frozen lattice vibrations. However, an important issue related to structural disorder of superlattices at low temperatures has received little attention to date. In this work, we show that CsPbBr3 nanocrystal superlattices undergo a reversible order-disorder transition upon cooling to 90 K. The transition consists of the loss of structural coherence, i.e. increased nanocrystal misalignment, and contraction of the superlattices, as revealed by temperature-dependent X-ray diffraction, and is ascribed to the solidification of ligands (on the basis of Raman spectroscopy). Introducing shorter amines on the nanocrystal surface allows to mitigate these changes, improve order, and shorten interparticle distance. We demonstrate that the low temperature phase of the short ligand-capped nanocrystal superlattices is characterized by a strong exciton migration observable in the photoluminescence decay, which is due to the shrinkage of the inter-nanocrystal distance. | Umberto Filippi; Stefano Toso; Matteo Zaffalon; Andrea Pianetti; Sergio Marras; Luca Goldoni; Francesco Meinardi; Sergio Brovelli; Dmitry Baranov; Liberato Manna | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Self-Assembly; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a164c85101a2ffa8e789cd/original/cooling-induced-order-disorder-phase-transition-in-cs-pb-br3-nanocrystal-superlattices.pdf |
60c751ce4c89193c42ad401f | 10.26434/chemrxiv.12998645.v2 | Ab Initio Metadynamics Calculations of Dimethylamine for Probing pKb Variations in Bulk vs. Surface Environments | The basicity constant, or pK<sub>b</sub>, is an intrinsic physical property of bases that gives a measure of its proton affinity in macroscopic environments. While the pKb is typically defined in reference to the bulk aqueous phase, several studies have suggested that this value can differ significantly at the air-water interface (which can have significant ramifications for particle surface chemistry and aerosol growth modeling). To provide mechanistic insight into surface proton affinity, we carried out <i>ab initio</i> metadynamics calculations to (1) explore the free-energy profile of dimethylamine and (2) provide reasonable estimates of the pKb value in different solvent environments. We find that the free-energy profiles obtained with our metadynamics calculations show a dramatic variation, with interfacial aqueous dimethylamine pK<sub>b</sub> values being significantly lower than in the bulk aqueous environment. Furthermore, our metadynamics calculations indicate that these variations are due to reduced hydrogen bonding at the air-water surface. Taken together, our quantum mechanical metadynamics calculations show that the reactivity of dimethylamine is surprisingly complex, leading to pK<sub>b</sub> variations that critically depend on the different atomic interactions occurring at the microscopic molecular level. | Sohag Biswas; Hyuna Kwon; Kelley Barsanti; Nanna Myllys; James N. Smith; Bryan Wong | Computational Chemistry and Modeling; Theory - Computational; Chemical Kinetics; Interfaces; Physical and Chemical Processes; Quantum Mechanics; Solution Chemistry; Statistical Mechanics; Structure; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751ce4c89193c42ad401f/original/ab-initio-metadynamics-calculations-of-dimethylamine-for-probing-p-kb-variations-in-bulk-vs-surface-environments.pdf |
63bf8672cac31869439dab61 | 10.26434/chemrxiv-2023-dfxjg | Optimization of Pd in Au-Pd nanoparticles for the hydrogenation of alkynes | Supported Au-Pd nanoparticles are an excellent catalyst for the hydrogenation of alkynes, a crucial step for olefin polymerization. They have better selectivity at a high conversion rate for the hydrogenation of 1-hexyne compared to pure Pd. The size, shape, and composition of the supported catalyst ultimately determine their properties. In this work, a combined scanning transmission electron microscopy (STEM) and density functional theory (DFT) study is used to determine how Pd concentration affects the activity and selectivity of Au-Pd particles for the hydrogenation of acetylene. Atomic resolution microscopy shows the increased probability of Pd-rich islands within particles with increasing Pd concentration. DFT models of the surface concentrations of Pd as monomers, dimers, and trimers allowed insight into the origin of the high activity for ethylene production. Specifically, monomers of Pd were found to be more active than dimers and trimers. This provides insight into why Au1-xPdx particles with low Pd concentration have higher production rates, as Pd monomers are more statistically likely. These combined STEM and DFT results explain the existence of an optimum for Au:Pd ratio, where conversion per gram of Pd is maximized at a concentration of 4 % Pd. | Alexandre Foucher; Hio Tong Ngan; Tanya Shirman; Amanda Filie; Kaining Duanmu; Michael Aizenberg; Robert J. Madix; Cynthia M. Friend; Joanna Aizenberg; Philippe Sautet; Eric A. Stach | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bf8672cac31869439dab61/original/optimization-of-pd-in-au-pd-nanoparticles-for-the-hydrogenation-of-alkynes.pdf |
66cfe3e120ac769e5f29dd4b | 10.26434/chemrxiv-2024-7wsd1 | Heterotelechelic Organometallic PEG Reagents Enable Modular Access to Complex Bioconjugates | Organometallic oxidative addition complexes (OACs) have recently emerged as a powerful class of reagents for the rapid and chemoselective modification of biomolecules. Notably, the steric and electronic properties of the ligand and aryl group can be modified to tune the kinetic profile of the reaction and permit regioselective S-arylation. Using the recently developed dicyclohexylphosphine-based bidentate P,N-ligated Au(III) OACs, we computationally and experimentally examined the effects of sterically bulky and electron deficient aryl substrates to achieve selective S-arylation. With this mechanistic insight, aryl substrates based on 4-iodoanisole and 3,5-dimethyl-4-iodoanisole were incorporated as end groups to generate a heterotelechelic bis-Au(III) poly(ethylene glycol) (PEG). This reagent performed rapid and regioselective S-arylation with a model biomolecule, designed ankyrin repeat protein (DARPin), to form a protein-polymer OAC in situ. This OAC mediated a second S-arylation with biologically relevant thiolated small molecules (metal chelator, saccharide, and fluorophore) and macromolecules (polymer and therapeutic peptide). It is envisioned that this approach could be utilized for the rapid construction of biomacromolecular heteroconjugates with S-aryl linkages. | Grace Kunkel; Joseph Treacy; Magdalena Polite; Hayden Montgomery; Evan Doud; Kendall Houk; Alexander Spokoyny; Heather Maynard | Organic Chemistry; Organometallic Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cfe3e120ac769e5f29dd4b/original/heterotelechelic-organometallic-peg-reagents-enable-modular-access-to-complex-bioconjugates.pdf |
60c752a9f96a009d042882c8 | 10.26434/chemrxiv.13332530.v1 | Analysis of the Bath Motion in the MM-SQC Dynamics Using Unsupervised Machine Learning Dimensionality Reduction Approaches: Principal Component Analysis | The system-plus-bath model is an important tool to understand nonadiabatic dynamics for large molecular systems. The understanding of the collective motion of a huge number of bath modes is essential to reveal their key roles in the overall dynamics. We apply the principal component analysis (PCA) to investigate the bath motion based on the massive data generated from the MM-SQC (symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian) nonadiabatic dynamics of the excited-state energy transfer dynamics of Frenkel-exciton model. The PCA method clearly clarifies that two types of bath modes, which either display the strong vibronic couplings or have the frequencies close to electronic transition, are very important to the nonadiabatic dynamics. These observations are fully consistent with the physical insights. This conclusion is obtained purely based on the PCA understanding of the trajectory data, without the large involvement of pre-defined physical knowledge. The results show that the PCA approach, one of the simplest unsupervised machine learning methods, is very powerful to analyze the complicated nonadiabatic dynamics in condensed phase involving many degrees of freedom. | Jiawei Peng; Yu Xie; Deping Hu; Zhenggang Lan | Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752a9f96a009d042882c8/original/analysis-of-the-bath-motion-in-the-mm-sqc-dynamics-using-unsupervised-machine-learning-dimensionality-reduction-approaches-principal-component-analysis.pdf |
62d935014689335108636b04 | 10.26434/chemrxiv-2022-g4p77 | Switchable reactivity of 2-Azetines: Ionic versus radical pathway for accessing β-aminocarbonyls and 2,3-disubstituted azetidines | Abstract. Two unprecedented transformations of 2-azetines are reported. Varied C2-functionalized 2-azetines, prepared under continuous flow conditions, acted as linchpin for the preparation of either -aminocarbonyls or C3-thiolated azetidines. Interestingly, the two transformations occurred following an ionic or radical pathway depending on the reaction conditions. The ionic pathway is triggered under acidic conditions in the presence of water, while the radical process is initiated using white light irradiation following a thiol-ene reactive scheme. These two methods have been applied to the synthesis of several products including bioactive fragments. Mechanistic evidence for the two pathways is provided.
| Renzo Luisi; Leonardo Degennaro; Marco Colella; Pantaleo Musci; Michael Andresini; Debora Cannillo; Elena Graziano; Andrea Aramini | Organic Chemistry; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d935014689335108636b04/original/switchable-reactivity-of-2-azetines-ionic-versus-radical-pathway-for-accessing-aminocarbonyls-and-2-3-disubstituted-azetidines.pdf |
6419c181dab08ad68f786120 | 10.26434/chemrxiv-2023-1rqz1 | Reversing the Regioselectivity of Asymmetric C ̶ H and N ̶ H Bond Annulation with Bromoalkynes Under Cobalt(III)-Catalysis | Metal-catalyzed C-H bond annulation strategy offers a versatile platform, allowing the construction of complex p-chiral molecules through atom- and step-economical fashion. However, regioselective insertion of -coupling partner between M-C bond and high enantio-induction remain elusive. Using commercially available Co(II) salt and chiral-salox ligands, we demonstrate an unorthodox protocol for the regio-reversal, enantioselective C-H bond annulation of phosphanamide with bromoalkyne through asymmetric desymmetrization. This method was accomplished by sequentical C-H bond activation, regioselective migratory insertion, reductive elimination, and ligand exchange with carboxylate, which resulted in the formation of novel P-stereogeneic compounds with good substrate scope and high ee (up to 99% ee). The isolation of reactive intermediates involved in the catalytic cycle and the outcomes of control experiments provide support for a plausible mechanism. | Abir Das; Rajib Mandal; Harihara Subramanian; Subramani Kumaran ; basker sundararaju | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6419c181dab08ad68f786120/original/reversing-the-regioselectivity-of-asymmetric-c-h-and-n-h-bond-annulation-with-bromoalkynes-under-cobalt-iii-catalysis.pdf |
6352d75daa2784f9f746e899 | 10.26434/chemrxiv-2022-z1trp | Accurate Spin-Orbit Coupling and Intersystem Crossing by Relativistic Mixed-Reference Spin-Flip (MRSF)-TDDFT | Relativistic MRSF-TDDFT is developed considering the spin-orbit coupling (SOC) within the mean-field approximation. The resulting SOC-MRSF faithfully reproduces the experiments with very high accuracy, which is also consistent with the values by four-component (4c) relativistic CASSCF and 4c-CASPT2 in the spin-orbit-energy splitting calculations of the C, Si and Ge atoms. Even for the fifth-row element Sn, the SOC-MRSF yielded accurate splittings (~3% error). In the SOC calculations of the molecular 4-thiothymine with a third-row element, SOC-MRSF values are in excellent agreement with those of SO-GMC-QDPT2 level, regardless of geometries and exchange-correlation functionals. The same SOC-MRSF predicted the anticipated chance of S1 (n pi*) -> T1 (pi pi*) intersystem crossing, even in thymine with only second-row elements. With its accuracy and practicality, thus, SOC-MRSF is a promising electronic structure protocol in challenging situations such as nonadiabatic molecular dynamics (NAMD) incorporating both internal conversions and intersystem crossings in large systems. | Konstantin Komarov; Woojin Park; Seunghoon Lee; Tao Zeng; Cheol-Ho Choi | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6352d75daa2784f9f746e899/original/accurate-spin-orbit-coupling-and-intersystem-crossing-by-relativistic-mixed-reference-spin-flip-mrsf-tddft.pdf |
65f0746b9138d23161510400 | 10.26434/chemrxiv-2024-j7ntq | Integrating Genetic Algorithms and Language Models for Enhanced Enzyme Design | Enzymes are molecular machines optimized by nature to allow otherwise impossible chemical processes to occur. Their design is a challenging task due to the complexity of the protein space and the intricate relationships between sequence, structure, and function. Recently, large language models (LLMs) have emerged as powerful tools for modeling and analyzing biological sequences, but their application to protein design is limited by the high cardinality of the protein space. This study introduces a framework that combines LLMs with genetic algorithms (GAs) to optimize enzymes. LLMs are trained on a large dataset of protein sequences to learn relationships between amino acid residues linked to structure and function. This knowledge is then leveraged by GAs to efficiently search for sequences with improved catalytic performance. We focused on two optmization tasks: improving the feasibility of biochemical reactions and increasing their turnover rate. Systematic evaluations on 105 biocatalytic reactions demonstrated that the LLM-GA framework generated mutants outperforming the wild-type enzymes in terms of feasibility in 90% of the instances. Further in-depth evaluation of seven reactions reveals the power of this methodology to make `the best of both worlds' and create mutants with structural features and flexibility comparable to the wild types. Our approach advances the state-of-the-art computational design of biocatalysts, ultimately opening opportunities for more sustainable chemical processes. | Yves Gaetan Nana Teukam; Federico Zipoli; Teodoro Laino; Emanuele Criscuolo; Francesca Grisoni; Matteo Manica | Materials Science; Catalysis; Catalysts; Biocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f0746b9138d23161510400/original/integrating-genetic-algorithms-and-language-models-for-enhanced-enzyme-design.pdf |
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